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+<?php
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+/**
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+ * @file
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+ * Describes the chado tables in version 1.3
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+ */
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+
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+/**
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+ * @defgroup tripal_schema_v1_3_api Chado v1.3 Schema API
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+ * @ingroup tripal_chado_schema_api
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+ * @{
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+ * Provides an application programming interface (API) for describing Chado
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+ * tables. This API consists of a set of functions, one for each table in Chado.
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+ * Each function simply returns a Drupal style array that defines the table.
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+ *
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+ * Because Drupal does not handle foreign key (FK) relationships, which are
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+ * needed to for Tripal Views, they have been added to the schema defintitions
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+ * below.
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+ *
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+ * The functions provided in this documentation should not be called as is,
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+ * but if you need the Drupal-style array definition for any table, use the
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+ * following function call:
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+ *
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+ * $table_desc = chado_get_schema($table)
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+ *
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+ * where the variable $table contains the name of the table you want to
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+ * retireve. The chado_get_schema function determines the appropriate version
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+ * of Chado and uses the Drupal hook infrastructure to call the appropriate
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+ * hook function to retrieve the table schema.
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+ *
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+ * If you need to augment these schema definitions within your own module,
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+ * you need to implement the hook_chado_schema_v1_3_[table name]() hook where
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+ * [table name] is the name of the chado table whose schema definition you
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+ * want to augment.
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+ * @}
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+ */
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+
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+/**
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+ * Implements hook_chado_schema_v1_3_acquisition()
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+ *
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+ * Purpose: To describe the structure of 'acquisition' to tripal
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+ * @see chado_insert_record()
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+ * @see chado_update_record()
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+ * @see chado_select_record()
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+ * @see chado_generate_var()
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+ * @see chado_expan_var()
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+ *
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+ * @return
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+ * An array describing the 'acquisition' table
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+ *
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+ * @ingroup tripal_chado_v1.3_schema_api
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+ *
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+ */
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+function tripal_core_chado_schema_v1_3_acquisition() {
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+ $description = array(
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+ 'description' => '',
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+ 'table' => 'acquisition',
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+ 'fields' => array(
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+ 'acquisition_id' => array(
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+ 'size' => 'big',
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+ 'type' => 'serial',
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+ 'not null' => TRUE,
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+ ),
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+ 'assay_id' => array(
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+ 'size' => 'big',
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+ 'type' => 'int',
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+ 'not null' => TRUE,
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+ ),
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+ 'protocol_id' => array(
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+ 'size' => 'big',
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+ 'type' => 'int',
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+ 'not null' => FALSE,
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+ ),
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+ 'channel_id' => array(
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+ 'size' => 'big',
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+ 'type' => 'int',
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+ 'not null' => FALSE,
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+ ),
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+ 'acquisitiondate' => array(
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+ 'size' => 'normal',
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+ 'type' => 'datetime',
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+ 'not null' => FALSE,
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+ 'default' => 'now()',
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+ ),
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+ 'name' => array(
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+ 'size' => 'normal',
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+ 'type' => 'text',
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+ 'not null' => FALSE,
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+ ),
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+ 'uri' => array(
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+ 'size' => 'normal',
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+ 'type' => 'text',
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+ 'not null' => FALSE,
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+ ),
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+ ),
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+ 'unique keys' => array(
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+ 'acquisition_c1' => array(
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+ 0 => 'name',
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+ ),
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+ ),
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+ 'indexes' => array(
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+ 'acquisition_idx1' => array(
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+ 0 => 'assay_id',
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+ ),
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+ 'acquisition_idx2' => array(
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+ 0 => 'protocol_id',
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+ ),
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+ 'acquisition_idx3' => array(
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+ 0 => 'channel_id',
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+ ),
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+ ),
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+ 'primary key' => array(
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+ 0 => 'acquisition_id',
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+ ),
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+ 'foreign keys' => array(
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+ 'assay' => array(
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+ 'table' => 'assay',
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+ 'columns' => array(
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+ 'assay_id' => 'assay_id',
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+ ),
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+ ),
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+ 'protocol' => array(
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+ 'table' => 'protocol',
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+ 'columns' => array(
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+ 'protocol_id' => 'protocol_id',
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+ ),
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+ ),
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+ 'channel' => array(
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+ 'table' => 'channel',
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+ 'columns' => array(
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+ 'channel_id' => 'channel_id',
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+ ),
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+ ),
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+ ),
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+ 'referring_tables' => array(
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+ 0 => 'acquisitionprop',
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+ 1 => 'acquisition_relationship',
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+ 3 => 'quantification',
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+ ),
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+ );
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+ return $description;
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+}
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+/**
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+ * Implements hook_chado_schema_v1_3_acquisitionprop()
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+ *
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+ * Purpose: To describe the structure of 'acquisitionprop' to tripal
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+ * @see chado_insert_record()
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+ * @see chado_update_record()
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+ * @see chado_select_record()
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+ * @see chado_generate_var()
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+ * @see chado_expan_var()
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+ *
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+ * @return
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+ * An array describing the 'acquisitionprop' table
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+ *
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+ * @ingroup tripal_chado_v1.3_schema_api
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+ *
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+ */
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+function tripal_core_chado_schema_v1_3_acquisitionprop() {
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+ $description = array(
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+ 'description' => '',
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+ 'table' => 'acquisitionprop',
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+ 'fields' => array(
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+ 'acquisitionprop_id' => array(
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+ 'size' => 'big',
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+ 'type' => 'serial',
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+ 'not null' => TRUE,
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+ ),
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+ 'acquisition_id' => array(
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+ 'size' => 'big',
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+ 'type' => 'int',
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+ 'not null' => TRUE,
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+ ),
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+ 'type_id' => array(
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+ 'size' => 'big',
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+ 'type' => 'int',
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+ 'not null' => TRUE,
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+ ),
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+ 'value' => array(
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+ 'size' => 'normal',
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+ 'type' => 'text',
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+ 'not null' => FALSE,
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+ ),
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+ 'rank' => array(
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+ 'size' => 'normal',
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+ 'type' => 'int',
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+ 'not null' => TRUE,
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+ 'default' => 0,
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+ ),
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+ ),
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+ 'unique keys' => array(
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+ 'acquisitionprop_c1' => array(
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+ 0 => 'acquisition_id',
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+ 1 => 'type_id',
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+ 2 => 'rank',
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+ ),
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+ ),
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+ 'indexes' => array(
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+ 'acquisitionprop_idx1' => array(
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+ 0 => 'acquisition_id',
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+ ),
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+ 'acquisitionprop_idx2' => array(
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+ 0 => 'type_id',
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+ ),
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+ ),
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+ 'primary key' => array(
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+ 0 => 'acquisitionprop_id',
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+ ),
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+ 'foreign keys' => array(
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+ 'acquisition' => array(
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+ 'table' => 'acquisition',
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+ 'columns' => array(
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+ 'acquisition_id' => 'acquisition_id',
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+ ),
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+ ),
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+ 'cvterm' => array(
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+ 'table' => 'cvterm',
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+ 'columns' => array(
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+ 'type_id' => 'cvterm_id',
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+ ),
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+ ),
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+ ),
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+ 'referring_tables' => array(
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+ ),
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+ );
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+ return $description;
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+}
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+/**
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+ * Implements hook_chado_schema_v1_3_acquisition_relationship()
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+ *
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+ * Purpose: To describe the structure of 'acquisition_relationship' to tripal
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+ * @see chado_insert_record()
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+ * @see chado_update_record()
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+ * @see chado_select_record()
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+ * @see chado_generate_var()
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+ * @see chado_expan_var()
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+ *
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+ * @return
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+ * An array describing the 'acquisition_relationship' table
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+ *
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+ * @ingroup tripal_chado_v1.3_schema_api
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+ *
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+ */
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+function tripal_core_chado_schema_v1_3_acquisition_relationship() {
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+ $description = array(
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+ 'description' => '',
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+ 'table' => 'acquisition_relationship',
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+ 'fields' => array(
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+ 'acquisition_relationship_id' => array(
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+ 'size' => 'big',
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+ 'type' => 'serial',
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+ 'not null' => TRUE,
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+ ),
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+ 'subject_id' => array(
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+ 'size' => 'big',
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+ 'type' => 'int',
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+ 'not null' => TRUE,
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+ ),
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+ 'type_id' => array(
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+ 'size' => 'big',
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+ 'type' => 'int',
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+ 'not null' => TRUE,
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+ ),
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+ 'object_id' => array(
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+ 'size' => 'big',
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+ 'type' => 'int',
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+ 'not null' => TRUE,
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+ ),
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+ 'value' => array(
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+ 'size' => 'normal',
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+ 'type' => 'text',
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+ 'not null' => FALSE,
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+ ),
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+ 'rank' => array(
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+ 'size' => 'normal',
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+ 'type' => 'int',
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+ 'not null' => TRUE,
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+ 'default' => 0,
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+ ),
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+ ),
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+ 'unique keys' => array(
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+ 'acquisition_relationship_c1' => array(
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+ 0 => 'subject_id',
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+ 1 => 'object_id',
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+ 2 => 'type_id',
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+ 3 => 'rank',
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+ ),
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+ ),
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+ 'indexes' => array(
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+ 'acquisition_relationship_idx1' => array(
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+ 0 => 'subject_id',
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+ ),
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+ 'acquisition_relationship_idx2' => array(
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+ 0 => 'type_id',
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+ ),
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+ 'acquisition_relationship_idx3' => array(
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+ 0 => 'object_id',
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+ ),
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+ ),
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+ 'primary key' => array(
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+ 0 => 'acquisition_relationship_id',
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+ ),
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+ 'foreign keys' => array(
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+ 'acquisition' => array(
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+ 'table' => 'acquisition',
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+ 'columns' => array(
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+ 'subject_id' => 'acquisition_id',
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+ 'object_id' => 'acquisition_id',
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+ ),
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+ ),
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+ 'cvterm' => array(
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+ 'table' => 'cvterm',
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+ 'columns' => array(
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+ 'type_id' => 'cvterm_id',
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+ ),
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+ ),
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+ ),
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+ 'referring_tables' => array(
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+ ),
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+ );
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+ return $description;
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+}
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+/**
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+ * Implements hook_chado_schema_v1_3_analysis()
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+ *
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+ * Purpose: To describe the structure of 'analysis' to tripal
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+ * @see chado_insert_record()
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+ * @see chado_update_record()
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+ * @see chado_select_record()
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+ * @see chado_generate_var()
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+ * @see chado_expan_var()
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+ *
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+ * @return
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+ * An array describing the 'analysis' table
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+ *
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+ * @ingroup tripal_chado_v1.3_schema_api
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+ *
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+ */
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+function tripal_core_chado_schema_v1_3_analysis() {
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+ $description = array(
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+ 'description' => '',
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+ 'table' => 'analysis',
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+ 'fields' => array(
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+ 'analysis_id' => array(
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+ 'size' => 'big',
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+ 'type' => 'serial',
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+ 'not null' => TRUE,
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+ ),
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+ 'name' => array(
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+ 'size' => 'normal',
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+ 'type' => 'varchar',
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+ 'length' => '255',
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+ 'not null' => FALSE,
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+ ),
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+ 'description' => array(
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+ 'size' => 'normal',
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+ 'type' => 'text',
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+ 'not null' => FALSE,
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+ ),
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+ 'program' => array(
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+ 'size' => 'normal',
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+ 'type' => 'varchar',
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+ 'length' => '255',
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+ 'not null' => TRUE,
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+ ),
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+ 'programversion' => array(
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+ 'size' => 'normal',
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+ 'type' => 'varchar',
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+ 'length' => '255',
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+ 'not null' => TRUE,
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+ ),
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+ 'algorithm' => array(
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+ 'size' => 'normal',
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+ 'type' => 'varchar',
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+ 'length' => '255',
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+ 'not null' => FALSE,
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+ ),
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+ 'sourcename' => array(
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+ 'size' => 'normal',
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+ 'type' => 'varchar',
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+ 'length' => '255',
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+ 'not null' => FALSE,
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+ ),
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+ 'sourceversion' => array(
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+ 'size' => 'normal',
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+ 'type' => 'varchar',
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+ 'length' => '255',
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+ 'not null' => FALSE,
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+ ),
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+ 'sourceuri' => array(
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+ 'size' => 'normal',
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+ 'type' => 'text',
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+ 'not null' => FALSE,
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+ ),
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+ 'timeexecuted' => array(
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+ 'size' => 'normal',
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+ 'type' => 'datetime',
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+ 'not null' => TRUE,
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+ 'default' => 'now()',
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+ ),
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+ ),
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+ 'unique keys' => array(
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+ 'analysis_c1' => array(
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+ 0 => 'program',
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+ 1 => 'programversion',
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+ 2 => 'sourcename',
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+ ),
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+ ),
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+ 'primary key' => array(
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+ 0 => 'analysis_id',
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+ ),
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+ 'foreign keys' => array(
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+ ),
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+ 'referring_tables' => array(
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+ 0 => 'analysis_cvterm',
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+ 1 => 'analysis_dbxref',
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+ 2 => 'analysisfeature',
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+ 3 => 'analysis_organism',
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+ 4 => 'analysisprop',
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+ 5 => 'analysis_pub',
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+ 6 => 'analysis_relationship',
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+ 8 => 'nd_experiment_analysis',
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+ 9 => 'phylotree',
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+ 10 => 'project_analysis',
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+ 11 => 'quantification',
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+ ),
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+ );
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+ return $description;
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+}
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+/**
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+ * Implements hook_chado_schema_v1_3_analysis_cvterm()
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+ *
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+ * Purpose: To describe the structure of 'analysis_cvterm' to tripal
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+ * @see chado_insert_record()
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+ * @see chado_update_record()
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+ * @see chado_select_record()
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+ * @see chado_generate_var()
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+ * @see chado_expan_var()
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+ *
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+ * @return
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+ * An array describing the 'analysis_cvterm' table
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+ *
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+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_analysis_cvterm() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'analysis_cvterm',
|
|
|
+ 'fields' => array(
|
|
|
+ 'analysis_cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'analysis_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'is_not' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'analysis_cvterm_c1' => array(
|
|
|
+ 0 => 'analysis_id',
|
|
|
+ 1 => 'cvterm_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'analysis_cvterm_idx1' => array(
|
|
|
+ 0 => 'analysis_id',
|
|
|
+ ),
|
|
|
+ 'analysis_cvterm_idx2' => array(
|
|
|
+ 0 => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'analysis_cvterm_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'analysis' => array(
|
|
|
+ 'table' => 'analysis',
|
|
|
+ 'columns' => array(
|
|
|
+ 'analysis_id' => 'analysis_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cvterm_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_analysis_dbxref()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'analysis_dbxref' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'analysis_dbxref' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_analysis_dbxref() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'analysis_dbxref',
|
|
|
+ 'fields' => array(
|
|
|
+ 'analysis_dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'analysis_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'is_current' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 'ru',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'analysis_dbxref_c1' => array(
|
|
|
+ 0 => 'analysis_id',
|
|
|
+ 1 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'analysis_dbxref_idx1' => array(
|
|
|
+ 0 => 'analysis_id',
|
|
|
+ ),
|
|
|
+ 'analysis_dbxref_idx2' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'analysis_dbxref_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'analysis' => array(
|
|
|
+ 'table' => 'analysis',
|
|
|
+ 'columns' => array(
|
|
|
+ 'analysis_id' => 'analysis_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_analysisfeature()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'analysisfeature' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'analysisfeature' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_analysisfeature() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'analysisfeature',
|
|
|
+ 'fields' => array(
|
|
|
+ 'analysisfeature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'analysis_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'rawscore' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'float',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'normscore' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'float',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'significance' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'float',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'identity' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'float',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'analysisfeature_c1' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ 1 => 'analysis_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'analysisfeature_idx1' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ ),
|
|
|
+ 'analysisfeature_idx2' => array(
|
|
|
+ 0 => 'analysis_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'analysisfeature_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'feature' => array(
|
|
|
+ 'table' => 'feature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_id' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'analysis' => array(
|
|
|
+ 'table' => 'analysis',
|
|
|
+ 'columns' => array(
|
|
|
+ 'analysis_id' => 'analysis_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'analysisfeatureprop',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_analysisfeatureprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'analysisfeatureprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'analysisfeatureprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_analysisfeatureprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'analysisfeatureprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'analysisfeatureprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'analysisfeature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'analysisfeature_id_type_id_rank' => array(
|
|
|
+ 0 => 'analysisfeature_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'analysisfeatureprop_idx1' => array(
|
|
|
+ 0 => 'analysisfeature_id',
|
|
|
+ ),
|
|
|
+ 'analysisfeatureprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'analysisfeatureprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'analysisfeature' => array(
|
|
|
+ 'table' => 'analysisfeature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'analysisfeature_id' => 'analysisfeature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_analysis_organism()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'analysis_organism' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'analysis_organism' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_analysis_organism() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'analysis_organism',
|
|
|
+ 'fields' => array(
|
|
|
+ 'analysis_id' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'networkmod_qtl_indx0' => array(
|
|
|
+ 0 => 'analysis_id',
|
|
|
+ ),
|
|
|
+ 'networkmod_qtl_indx1' => array(
|
|
|
+ 0 => 'organism_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'analysis' => array(
|
|
|
+ 'table' => 'analysis',
|
|
|
+ 'columns' => array(
|
|
|
+ 'analysis_id' => 'analysis_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'organism' => array(
|
|
|
+ 'table' => 'organism',
|
|
|
+ 'columns' => array(
|
|
|
+ 'organism_id' => 'organism_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_analysisprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'analysisprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'analysisprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_analysisprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'analysisprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'analysisprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'analysis_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'analysisprop_c1' => array(
|
|
|
+ 0 => 'analysis_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'analysisprop_idx1' => array(
|
|
|
+ 0 => 'analysis_id',
|
|
|
+ ),
|
|
|
+ 'analysisprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'analysisprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'analysis' => array(
|
|
|
+ 'table' => 'analysis',
|
|
|
+ 'columns' => array(
|
|
|
+ 'analysis_id' => 'analysis_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_analysis_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'analysis_pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'analysis_pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_analysis_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'analysis_pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'analysis_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'analysis_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'analysis_pub_c1' => array(
|
|
|
+ 0 => 'analysis_id',
|
|
|
+ 1 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'analysis_pub_idx1' => array(
|
|
|
+ 0 => 'analysis_id',
|
|
|
+ ),
|
|
|
+ 'analysis_pub_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'analysis_pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'analysis' => array(
|
|
|
+ 'table' => 'analysis',
|
|
|
+ 'columns' => array(
|
|
|
+ 'analysis_id' => 'analysis_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_analysis_relationship()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'analysis_relationship' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'analysis_relationship' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_analysis_relationship() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'analysis_relationship',
|
|
|
+ 'fields' => array(
|
|
|
+ 'analysis_relationship_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'analysis_relationship_c1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ 1 => 'object_id',
|
|
|
+ 2 => 'type_id',
|
|
|
+ 3 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'analysis_relationship_idx1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ ),
|
|
|
+ 'analysis_relationship_idx2' => array(
|
|
|
+ 0 => 'object_id',
|
|
|
+ ),
|
|
|
+ 'analysis_relationship_idx3' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'analysis_relationship_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'analysis' => array(
|
|
|
+ 'table' => 'analysis',
|
|
|
+ 'columns' => array(
|
|
|
+ 'subject_id' => 'analysis_id',
|
|
|
+ 'object_id' => 'analysis_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_arraydesign()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'arraydesign' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'arraydesign' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_arraydesign() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'arraydesign',
|
|
|
+ 'fields' => array(
|
|
|
+ 'arraydesign_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'manufacturer_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'platformtype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'substratetype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'protocol_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'version' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'array_dimensions' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'element_dimensions' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'num_of_elements' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'num_array_columns' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'num_array_rows' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'num_grid_columns' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'num_grid_rows' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'num_sub_columns' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'num_sub_rows' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'arraydesign_c1' => array(
|
|
|
+ 0 => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'arraydesign_idx1' => array(
|
|
|
+ 0 => 'manufacturer_id',
|
|
|
+ ),
|
|
|
+ 'arraydesign_idx2' => array(
|
|
|
+ 0 => 'platformtype_id',
|
|
|
+ ),
|
|
|
+ 'arraydesign_idx3' => array(
|
|
|
+ 0 => 'substratetype_id',
|
|
|
+ ),
|
|
|
+ 'arraydesign_idx4' => array(
|
|
|
+ 0 => 'protocol_id',
|
|
|
+ ),
|
|
|
+ 'arraydesign_idx5' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'arraydesign_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'contact' => array(
|
|
|
+ 'table' => 'contact',
|
|
|
+ 'columns' => array(
|
|
|
+ 'manufacturer_id' => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'platformtype_id' => 'cvterm_id',
|
|
|
+ 'substratetype_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'protocol' => array(
|
|
|
+ 'table' => 'protocol',
|
|
|
+ 'columns' => array(
|
|
|
+ 'protocol_id' => 'protocol_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'arraydesignprop',
|
|
|
+ 1 => 'assay',
|
|
|
+ 2 => 'element',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_arraydesignprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'arraydesignprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'arraydesignprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_arraydesignprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'arraydesignprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'arraydesignprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'arraydesign_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'arraydesignprop_c1' => array(
|
|
|
+ 0 => 'arraydesign_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'arraydesignprop_idx1' => array(
|
|
|
+ 0 => 'arraydesign_id',
|
|
|
+ ),
|
|
|
+ 'arraydesignprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'arraydesignprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'arraydesign' => array(
|
|
|
+ 'table' => 'arraydesign',
|
|
|
+ 'columns' => array(
|
|
|
+ 'arraydesign_id' => 'arraydesign_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_assay()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'assay' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'assay' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_assay() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'assay',
|
|
|
+ 'fields' => array(
|
|
|
+ 'assay_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'arraydesign_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'protocol_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'assaydate' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ 'default' => 'now()',
|
|
|
+ ),
|
|
|
+ 'arrayidentifier' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'arraybatchidentifier' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'operator_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'assay_c1' => array(
|
|
|
+ 0 => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'assay_idx1' => array(
|
|
|
+ 0 => 'arraydesign_id',
|
|
|
+ ),
|
|
|
+ 'assay_idx2' => array(
|
|
|
+ 0 => 'protocol_id',
|
|
|
+ ),
|
|
|
+ 'assay_idx3' => array(
|
|
|
+ 0 => 'operator_id',
|
|
|
+ ),
|
|
|
+ 'assay_idx4' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'assay_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'arraydesign' => array(
|
|
|
+ 'table' => 'arraydesign',
|
|
|
+ 'columns' => array(
|
|
|
+ 'arraydesign_id' => 'arraydesign_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'protocol' => array(
|
|
|
+ 'table' => 'protocol',
|
|
|
+ 'columns' => array(
|
|
|
+ 'protocol_id' => 'protocol_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'contact' => array(
|
|
|
+ 'table' => 'contact',
|
|
|
+ 'columns' => array(
|
|
|
+ 'operator_id' => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'acquisition',
|
|
|
+ 1 => 'assay_biomaterial',
|
|
|
+ 2 => 'assay_project',
|
|
|
+ 3 => 'assayprop',
|
|
|
+ 4 => 'control',
|
|
|
+ 5 => 'study_assay',
|
|
|
+ 6 => 'studyfactorvalue',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_assay_biomaterial()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'assay_biomaterial' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'assay_biomaterial' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_assay_biomaterial() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'assay_biomaterial',
|
|
|
+ 'fields' => array(
|
|
|
+ 'assay_biomaterial_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'assay_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'biomaterial_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'channel_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'assay_biomaterial_c1' => array(
|
|
|
+ 0 => 'assay_id',
|
|
|
+ 1 => 'biomaterial_id',
|
|
|
+ 2 => 'channel_id',
|
|
|
+ 3 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'assay_biomaterial_idx1' => array(
|
|
|
+ 0 => 'assay_id',
|
|
|
+ ),
|
|
|
+ 'assay_biomaterial_idx2' => array(
|
|
|
+ 0 => 'biomaterial_id',
|
|
|
+ ),
|
|
|
+ 'assay_biomaterial_idx3' => array(
|
|
|
+ 0 => 'channel_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'assay_biomaterial_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'assay' => array(
|
|
|
+ 'table' => 'assay',
|
|
|
+ 'columns' => array(
|
|
|
+ 'assay_id' => 'assay_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'biomaterial' => array(
|
|
|
+ 'table' => 'biomaterial',
|
|
|
+ 'columns' => array(
|
|
|
+ 'biomaterial_id' => 'biomaterial_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'channel' => array(
|
|
|
+ 'table' => 'channel',
|
|
|
+ 'columns' => array(
|
|
|
+ 'channel_id' => 'channel_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_assay_project()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'assay_project' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'assay_project' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_assay_project() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'assay_project',
|
|
|
+ 'fields' => array(
|
|
|
+ 'assay_project_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'assay_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'project_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'assay_project_c1' => array(
|
|
|
+ 0 => 'assay_id',
|
|
|
+ 1 => 'project_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'assay_project_idx1' => array(
|
|
|
+ 0 => 'assay_id',
|
|
|
+ ),
|
|
|
+ 'assay_project_idx2' => array(
|
|
|
+ 0 => 'project_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'assay_project_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'assay' => array(
|
|
|
+ 'table' => 'assay',
|
|
|
+ 'columns' => array(
|
|
|
+ 'assay_id' => 'assay_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'project' => array(
|
|
|
+ 'table' => 'project',
|
|
|
+ 'columns' => array(
|
|
|
+ 'project_id' => 'project_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_assayprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'assayprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'assayprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_assayprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'assayprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'assayprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'assay_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'assayprop_c1' => array(
|
|
|
+ 0 => 'assay_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'assayprop_idx1' => array(
|
|
|
+ 0 => 'assay_id',
|
|
|
+ ),
|
|
|
+ 'assayprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'assayprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'assay' => array(
|
|
|
+ 'table' => 'assay',
|
|
|
+ 'columns' => array(
|
|
|
+ 'assay_id' => 'assay_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_biomaterial()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'biomaterial' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'biomaterial' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_biomaterial() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'biomaterial',
|
|
|
+ 'fields' => array(
|
|
|
+ 'biomaterial_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'taxon_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'biosourceprovider_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'biomaterial_c1' => array(
|
|
|
+ 0 => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'biomaterial_idx1' => array(
|
|
|
+ 0 => 'taxon_id',
|
|
|
+ ),
|
|
|
+ 'biomaterial_idx2' => array(
|
|
|
+ 0 => 'biosourceprovider_id',
|
|
|
+ ),
|
|
|
+ 'biomaterial_idx3' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'biomaterial_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'organism' => array(
|
|
|
+ 'table' => 'organism',
|
|
|
+ 'columns' => array(
|
|
|
+ 'taxon_id' => 'organism_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'contact' => array(
|
|
|
+ 'table' => 'contact',
|
|
|
+ 'columns' => array(
|
|
|
+ 'biosourceprovider_id' => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'assay_biomaterial',
|
|
|
+ 1 => 'biomaterial_dbxref',
|
|
|
+ 2 => 'biomaterialprop',
|
|
|
+ 3 => 'biomaterial_relationship',
|
|
|
+ 5 => 'biomaterial_treatment',
|
|
|
+ 6 => 'treatment',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_biomaterial_dbxref()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'biomaterial_dbxref' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'biomaterial_dbxref' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_biomaterial_dbxref() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'biomaterial_dbxref',
|
|
|
+ 'fields' => array(
|
|
|
+ 'biomaterial_dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'biomaterial_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'biomaterial_dbxref_c1' => array(
|
|
|
+ 0 => 'biomaterial_id',
|
|
|
+ 1 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'biomaterial_dbxref_idx1' => array(
|
|
|
+ 0 => 'biomaterial_id',
|
|
|
+ ),
|
|
|
+ 'biomaterial_dbxref_idx2' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'biomaterial_dbxref_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'biomaterial' => array(
|
|
|
+ 'table' => 'biomaterial',
|
|
|
+ 'columns' => array(
|
|
|
+ 'biomaterial_id' => 'biomaterial_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_biomaterialprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'biomaterialprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'biomaterialprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_biomaterialprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'biomaterialprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'biomaterialprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'biomaterial_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'biomaterialprop_c1' => array(
|
|
|
+ 0 => 'biomaterial_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'biomaterialprop_idx1' => array(
|
|
|
+ 0 => 'biomaterial_id',
|
|
|
+ ),
|
|
|
+ 'biomaterialprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'biomaterialprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'biomaterial' => array(
|
|
|
+ 'table' => 'biomaterial',
|
|
|
+ 'columns' => array(
|
|
|
+ 'biomaterial_id' => 'biomaterial_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_biomaterial_relationship()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'biomaterial_relationship' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'biomaterial_relationship' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_biomaterial_relationship() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'biomaterial_relationship',
|
|
|
+ 'fields' => array(
|
|
|
+ 'biomaterial_relationship_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'biomaterial_relationship_c1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ 1 => 'object_id',
|
|
|
+ 2 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'biomaterial_relationship_idx1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ ),
|
|
|
+ 'biomaterial_relationship_idx2' => array(
|
|
|
+ 0 => 'object_id',
|
|
|
+ ),
|
|
|
+ 'biomaterial_relationship_idx3' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'biomaterial_relationship_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'biomaterial' => array(
|
|
|
+ 'table' => 'biomaterial',
|
|
|
+ 'columns' => array(
|
|
|
+ 'subject_id' => 'biomaterial_id',
|
|
|
+ 'object_id' => 'biomaterial_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_biomaterial_treatment()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'biomaterial_treatment' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'biomaterial_treatment' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_biomaterial_treatment() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'biomaterial_treatment',
|
|
|
+ 'fields' => array(
|
|
|
+ 'biomaterial_treatment_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'biomaterial_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'treatment_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'unittype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'float',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'biomaterial_treatment_c1' => array(
|
|
|
+ 0 => 'biomaterial_id',
|
|
|
+ 1 => 'treatment_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'biomaterial_treatment_idx1' => array(
|
|
|
+ 0 => 'biomaterial_id',
|
|
|
+ ),
|
|
|
+ 'biomaterial_treatment_idx2' => array(
|
|
|
+ 0 => 'treatment_id',
|
|
|
+ ),
|
|
|
+ 'biomaterial_treatment_idx3' => array(
|
|
|
+ 0 => 'unittype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'biomaterial_treatment_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'biomaterial' => array(
|
|
|
+ 'table' => 'biomaterial',
|
|
|
+ 'columns' => array(
|
|
|
+ 'biomaterial_id' => 'biomaterial_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'treatment' => array(
|
|
|
+ 'table' => 'treatment',
|
|
|
+ 'columns' => array(
|
|
|
+ 'treatment_id' => 'treatment_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'unittype_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_cell_line()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'cell_line' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'cell_line' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_cell_line() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'cell_line',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cell_line_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'uniquename' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'timeaccessioned' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 'now()',
|
|
|
+ ),
|
|
|
+ 'timelastmodified' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 'now()',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cell_line_c1' => array(
|
|
|
+ 0 => 'uniquename',
|
|
|
+ 1 => 'organism_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'cell_line_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'organism' => array(
|
|
|
+ 'table' => 'organism',
|
|
|
+ 'columns' => array(
|
|
|
+ 'organism_id' => 'organism_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'cell_line_cvterm',
|
|
|
+ 1 => 'cell_line_dbxref',
|
|
|
+ 2 => 'cell_line_feature',
|
|
|
+ 3 => 'cell_line_library',
|
|
|
+ 4 => 'cell_lineprop',
|
|
|
+ 5 => 'cell_line_pub',
|
|
|
+ 6 => 'cell_line_relationship',
|
|
|
+ 8 => 'cell_line_synonym',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_cell_line_cvterm()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'cell_line_cvterm' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'cell_line_cvterm' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_cell_line_cvterm() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'cell_line_cvterm',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cell_line_cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cell_line_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cell_line_cvterm_c1' => array(
|
|
|
+ 0 => 'cell_line_id',
|
|
|
+ 1 => 'cvterm_id',
|
|
|
+ 2 => 'pub_id',
|
|
|
+ 3 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'cell_line_cvterm_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cell_line' => array(
|
|
|
+ 'table' => 'cell_line',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cell_line_id' => 'cell_line_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cvterm_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'cell_line_cvtermprop',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_cell_line_cvtermprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'cell_line_cvtermprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'cell_line_cvtermprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_cell_line_cvtermprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'cell_line_cvtermprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cell_line_cvtermprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cell_line_cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cell_line_cvtermprop_c1' => array(
|
|
|
+ 0 => 'cell_line_cvterm_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'cell_line_cvtermprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cell_line_cvterm' => array(
|
|
|
+ 'table' => 'cell_line_cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cell_line_cvterm_id' => 'cell_line_cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_cell_line_dbxref()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'cell_line_dbxref' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'cell_line_dbxref' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_cell_line_dbxref() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'cell_line_dbxref',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cell_line_dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cell_line_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'is_current' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 'ru',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cell_line_dbxref_c1' => array(
|
|
|
+ 0 => 'cell_line_id',
|
|
|
+ 1 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'cell_line_dbxref_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cell_line' => array(
|
|
|
+ 'table' => 'cell_line',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cell_line_id' => 'cell_line_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_cell_line_feature()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'cell_line_feature' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'cell_line_feature' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_cell_line_feature() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'cell_line_feature',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cell_line_feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cell_line_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cell_line_feature_c1' => array(
|
|
|
+ 0 => 'cell_line_id',
|
|
|
+ 1 => 'feature_id',
|
|
|
+ 2 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'cell_line_feature_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cell_line' => array(
|
|
|
+ 'table' => 'cell_line',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cell_line_id' => 'cell_line_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'feature' => array(
|
|
|
+ 'table' => 'feature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_id' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_cell_line_library()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'cell_line_library' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'cell_line_library' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_cell_line_library() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'cell_line_library',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cell_line_library_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cell_line_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'library_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cell_line_library_c1' => array(
|
|
|
+ 0 => 'cell_line_id',
|
|
|
+ 1 => 'library_id',
|
|
|
+ 2 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'cell_line_library_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cell_line' => array(
|
|
|
+ 'table' => 'cell_line',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cell_line_id' => 'cell_line_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'library' => array(
|
|
|
+ 'table' => 'library',
|
|
|
+ 'columns' => array(
|
|
|
+ 'library_id' => 'library_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_cell_lineprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'cell_lineprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'cell_lineprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_cell_lineprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'cell_lineprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cell_lineprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cell_line_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cell_lineprop_c1' => array(
|
|
|
+ 0 => 'cell_line_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'cell_lineprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cell_line' => array(
|
|
|
+ 'table' => 'cell_line',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cell_line_id' => 'cell_line_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'cell_lineprop_pub',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_cell_lineprop_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'cell_lineprop_pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'cell_lineprop_pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_cell_lineprop_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'cell_lineprop_pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cell_lineprop_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cell_lineprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cell_lineprop_pub_c1' => array(
|
|
|
+ 0 => 'cell_lineprop_id',
|
|
|
+ 1 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'cell_lineprop_pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cell_lineprop' => array(
|
|
|
+ 'table' => 'cell_lineprop',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cell_lineprop_id' => 'cell_lineprop_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_cell_line_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'cell_line_pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'cell_line_pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_cell_line_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'cell_line_pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cell_line_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cell_line_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cell_line_pub_c1' => array(
|
|
|
+ 0 => 'cell_line_id',
|
|
|
+ 1 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'cell_line_pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cell_line' => array(
|
|
|
+ 'table' => 'cell_line',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cell_line_id' => 'cell_line_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_cell_line_relationship()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'cell_line_relationship' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'cell_line_relationship' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_cell_line_relationship() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'cell_line_relationship',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cell_line_relationship_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cell_line_relationship_c1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ 1 => 'object_id',
|
|
|
+ 2 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'cell_line_relationship_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cell_line' => array(
|
|
|
+ 'table' => 'cell_line',
|
|
|
+ 'columns' => array(
|
|
|
+ 'subject_id' => 'cell_line_id',
|
|
|
+ 'object_id' => 'cell_line_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_cell_line_synonym()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'cell_line_synonym' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'cell_line_synonym' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_cell_line_synonym() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'cell_line_synonym',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cell_line_synonym_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cell_line_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'synonym_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'is_current' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => FALSE,
|
|
|
+ ),
|
|
|
+ 'is_internal' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cell_line_synonym_c1' => array(
|
|
|
+ 0 => 'synonym_id',
|
|
|
+ 1 => 'cell_line_id',
|
|
|
+ 2 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'cell_line_synonym_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cell_line' => array(
|
|
|
+ 'table' => 'cell_line',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cell_line_id' => 'cell_line_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'synonym' => array(
|
|
|
+ 'table' => 'synonym',
|
|
|
+ 'columns' => array(
|
|
|
+ 'synonym_id' => 'synonym_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_chadoprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'chadoprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'chadoprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_chadoprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'chadoprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'chadoprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'chadoprop_c1' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ 1 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'chadoprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_channel()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'channel' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'channel' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_channel() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'channel',
|
|
|
+ 'fields' => array(
|
|
|
+ 'channel_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'definition' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'channel_c1' => array(
|
|
|
+ 0 => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'channel_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'acquisition',
|
|
|
+ 1 => 'assay_biomaterial',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_contact()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'contact' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'contact' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_contact() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'contact',
|
|
|
+ 'fields' => array(
|
|
|
+ 'contact_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'contact_c1' => array(
|
|
|
+ 0 => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'contact_id',
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'library_contact_idx2' => array(
|
|
|
+ 0 => 'contact_id',
|
|
|
+ ),
|
|
|
+ 'pubauthor_contact_idx2' => array(
|
|
|
+ 0 => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'arraydesign',
|
|
|
+ 1 => 'assay',
|
|
|
+ 2 => 'biomaterial',
|
|
|
+ 3 => 'contactprop',
|
|
|
+ 4 => 'contact_relationship',
|
|
|
+ 6 => 'feature_contact',
|
|
|
+ 7 => 'featuremap_contact',
|
|
|
+ 8 => 'library_contact',
|
|
|
+ 9 => 'nd_experiment_contact',
|
|
|
+ 10 => 'project_contact',
|
|
|
+ 11 => 'pubauthor_contact',
|
|
|
+ 12 => 'quantification',
|
|
|
+ 13 => 'stockcollection',
|
|
|
+ 14 => 'study',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_contactprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'contactprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'contactprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_contactprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'contactprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'contactprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'contact_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'contactprop_c1' => array(
|
|
|
+ 0 => 'contact_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'contactprop_idx1' => array(
|
|
|
+ 0 => 'contact_id',
|
|
|
+ ),
|
|
|
+ 'contactprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'contactprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'contact' => array(
|
|
|
+ 'table' => 'contact',
|
|
|
+ 'columns' => array(
|
|
|
+ 'contact_id' => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_contact_relationship()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'contact_relationship' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'contact_relationship' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_contact_relationship() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'contact_relationship',
|
|
|
+ 'fields' => array(
|
|
|
+ 'contact_relationship_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'contact_relationship_c1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ 1 => 'object_id',
|
|
|
+ 2 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'contact_relationship_idx1' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ 'contact_relationship_idx2' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ ),
|
|
|
+ 'contact_relationship_idx3' => array(
|
|
|
+ 0 => 'object_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'contact_relationship_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'contact' => array(
|
|
|
+ 'table' => 'contact',
|
|
|
+ 'columns' => array(
|
|
|
+ 'subject_id' => 'contact_id',
|
|
|
+ 'object_id' => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_control()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'control' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'control' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_control() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'control',
|
|
|
+ 'fields' => array(
|
|
|
+ 'control_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'assay_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'tableinfo_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'row_id' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'control_idx1' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ 'control_idx2' => array(
|
|
|
+ 0 => 'assay_id',
|
|
|
+ ),
|
|
|
+ 'control_idx3' => array(
|
|
|
+ 0 => 'tableinfo_id',
|
|
|
+ ),
|
|
|
+ 'control_idx4' => array(
|
|
|
+ 0 => 'row_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'control_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'assay' => array(
|
|
|
+ 'table' => 'assay',
|
|
|
+ 'columns' => array(
|
|
|
+ 'assay_id' => 'assay_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'tableinfo' => array(
|
|
|
+ 'table' => 'tableinfo',
|
|
|
+ 'columns' => array(
|
|
|
+ 'tableinfo_id' => 'tableinfo_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_cv()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'cv' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'cv' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_cv() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'cv',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cv_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'definition' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cv_c1' => array(
|
|
|
+ 0 => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'cv_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'cvprop',
|
|
|
+ 1 => 'cvterm',
|
|
|
+ 2 => 'cvtermpath',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_cvprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'cvprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'cvprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_cvprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'cvprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cvprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cv_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cvprop_c1' => array(
|
|
|
+ 0 => 'cv_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'cvprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cv' => array(
|
|
|
+ 'table' => 'cv',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cv_id' => 'cv_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_cv_root_mview()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'cv_root_mview' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'cv_root_mview' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_cv_root_mview() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'cv_root_mview',
|
|
|
+ 'fields' => array(
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cv_id' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cv_name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'cv_root_mview_indx1' => array(
|
|
|
+ 0 => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ 'cv_root_mview_indx2' => array(
|
|
|
+ 0 => 'cv_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_cvterm()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'cvterm' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'cvterm' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_cvterm() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cv_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '1024',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'definition' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'is_obsolete' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ 'is_relationshiptype' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cvterm_c1' => array(
|
|
|
+ 0 => 'name',
|
|
|
+ 1 => 'cv_id',
|
|
|
+ 2 => 'is_obsolete',
|
|
|
+ ),
|
|
|
+ 'cvterm_c2' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'cvterm_idx1' => array(
|
|
|
+ 0 => 'cv_id',
|
|
|
+ ),
|
|
|
+ 'cvterm_idx2' => array(
|
|
|
+ 0 => 'name',
|
|
|
+ ),
|
|
|
+ 'cvterm_idx3' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cv' => array(
|
|
|
+ 'table' => 'cv',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cv_id' => 'cv_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'acquisitionprop',
|
|
|
+ 1 => 'acquisition_relationship',
|
|
|
+ 2 => 'analysis_cvterm',
|
|
|
+ 3 => 'analysisfeatureprop',
|
|
|
+ 4 => 'analysisprop',
|
|
|
+ 5 => 'analysis_relationship',
|
|
|
+ 6 => 'arraydesign',
|
|
|
+ 8 => 'arraydesignprop',
|
|
|
+ 9 => 'assayprop',
|
|
|
+ 10 => 'biomaterialprop',
|
|
|
+ 11 => 'biomaterial_relationship',
|
|
|
+ 12 => 'biomaterial_treatment',
|
|
|
+ 13 => 'cell_line_cvterm',
|
|
|
+ 14 => 'cell_line_cvtermprop',
|
|
|
+ 15 => 'cell_lineprop',
|
|
|
+ 16 => 'cell_line_relationship',
|
|
|
+ 17 => 'chadoprop',
|
|
|
+ 18 => 'contact',
|
|
|
+ 19 => 'contactprop',
|
|
|
+ 20 => 'contact_relationship',
|
|
|
+ 21 => 'control',
|
|
|
+ 22 => 'cvprop',
|
|
|
+ 23 => 'cvterm_dbxref',
|
|
|
+ 24 => 'cvtermpath',
|
|
|
+ 27 => 'cvtermprop',
|
|
|
+ 29 => 'cvterm_relationship',
|
|
|
+ 32 => 'cvtermsynonym',
|
|
|
+ 34 => 'dbprop',
|
|
|
+ 35 => 'dbxrefprop',
|
|
|
+ 36 => 'element',
|
|
|
+ 37 => 'element_relationship',
|
|
|
+ 38 => 'elementresult_relationship',
|
|
|
+ 39 => 'environment_cvterm',
|
|
|
+ 40 => 'expression_cvterm',
|
|
|
+ 42 => 'expression_cvtermprop',
|
|
|
+ 43 => 'expressionprop',
|
|
|
+ 44 => 'feature',
|
|
|
+ 45 => 'feature_cvterm',
|
|
|
+ 46 => 'feature_cvtermprop',
|
|
|
+ 47 => 'feature_expressionprop',
|
|
|
+ 48 => 'feature_genotype',
|
|
|
+ 49 => 'featuremap',
|
|
|
+ 50 => 'featuremapprop',
|
|
|
+ 51 => 'featureposprop',
|
|
|
+ 52 => 'featureprop',
|
|
|
+ 53 => 'feature_pubprop',
|
|
|
+ 54 => 'feature_relationship',
|
|
|
+ 55 => 'feature_relationshipprop',
|
|
|
+ 56 => 'genotype',
|
|
|
+ 57 => 'genotypeprop',
|
|
|
+ 58 => 'library',
|
|
|
+ 59 => 'library_cvterm',
|
|
|
+ 60 => 'library_expressionprop',
|
|
|
+ 61 => 'library_featureprop',
|
|
|
+ 62 => 'libraryprop',
|
|
|
+ 63 => 'library_relationship',
|
|
|
+ 64 => 'nd_experiment',
|
|
|
+ 65 => 'nd_experiment_analysis',
|
|
|
+ 66 => 'nd_experimentprop',
|
|
|
+ 67 => 'nd_experiment_stock',
|
|
|
+ 68 => 'nd_experiment_stockprop',
|
|
|
+ 69 => 'nd_geolocationprop',
|
|
|
+ 70 => 'nd_protocol',
|
|
|
+ 71 => 'nd_protocolprop',
|
|
|
+ 72 => 'nd_protocol_reagent',
|
|
|
+ 73 => 'nd_reagent',
|
|
|
+ 74 => 'nd_reagentprop',
|
|
|
+ 75 => 'nd_reagent_relationship',
|
|
|
+ 76 => 'organism',
|
|
|
+ 77 => 'organism_cvterm',
|
|
|
+ 78 => 'organism_cvtermprop',
|
|
|
+ 79 => 'organismprop',
|
|
|
+ 80 => 'organism_relationship',
|
|
|
+ 81 => 'phendesc',
|
|
|
+ 82 => 'phenotype',
|
|
|
+ 86 => 'phenotype_comparison_cvterm',
|
|
|
+ 87 => 'phenotype_cvterm',
|
|
|
+ 88 => 'phenotypeprop',
|
|
|
+ 89 => 'phenstatement',
|
|
|
+ 90 => 'phylonode',
|
|
|
+ 91 => 'phylonodeprop',
|
|
|
+ 92 => 'phylonode_relationship',
|
|
|
+ 93 => 'phylotree',
|
|
|
+ 94 => 'phylotreeprop',
|
|
|
+ 95 => 'projectprop',
|
|
|
+ 96 => 'project_relationship',
|
|
|
+ 97 => 'protocol',
|
|
|
+ 98 => 'protocolparam',
|
|
|
+ 100 => 'pub',
|
|
|
+ 101 => 'pubprop',
|
|
|
+ 102 => 'pub_relationship',
|
|
|
+ 103 => 'quantificationprop',
|
|
|
+ 104 => 'quantification_relationship',
|
|
|
+ 105 => 'stock',
|
|
|
+ 106 => 'stockcollection',
|
|
|
+ 107 => 'stockcollectionprop',
|
|
|
+ 108 => 'stock_cvterm',
|
|
|
+ 109 => 'stock_cvtermprop',
|
|
|
+ 110 => 'stock_dbxrefprop',
|
|
|
+ 111 => 'stock_feature',
|
|
|
+ 112 => 'stock_featuremap',
|
|
|
+ 113 => 'stockprop',
|
|
|
+ 114 => 'stock_relationship',
|
|
|
+ 115 => 'stock_relationship_cvterm',
|
|
|
+ 116 => 'studydesignprop',
|
|
|
+ 117 => 'studyfactor',
|
|
|
+ 118 => 'studyprop',
|
|
|
+ 119 => 'studyprop_feature',
|
|
|
+ 120 => 'synonym',
|
|
|
+ 121 => 'treatment',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_cvterm_dbxref()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'cvterm_dbxref' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'cvterm_dbxref' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_cvterm_dbxref() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'cvterm_dbxref',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cvterm_dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'is_for_definition' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cvterm_dbxref_c1' => array(
|
|
|
+ 0 => 'cvterm_id',
|
|
|
+ 1 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'cvterm_dbxref_idx1' => array(
|
|
|
+ 0 => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ 'cvterm_dbxref_idx2' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'cvterm_dbxref_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cvterm_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_cvtermpath()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'cvtermpath' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'cvtermpath' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_cvtermpath() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'cvtermpath',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cvtermpath_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cv_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pathdistance' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cvtermpath_c1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ 1 => 'object_id',
|
|
|
+ 2 => 'type_id',
|
|
|
+ 3 => 'pathdistance',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'cvtermpath_idx1' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ 'cvtermpath_idx2' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ ),
|
|
|
+ 'cvtermpath_idx3' => array(
|
|
|
+ 0 => 'object_id',
|
|
|
+ ),
|
|
|
+ 'cvtermpath_idx4' => array(
|
|
|
+ 0 => 'cv_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'cvtermpath_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ 'subject_id' => 'cvterm_id',
|
|
|
+ 'object_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cv' => array(
|
|
|
+ 'table' => 'cv',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cv_id' => 'cv_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_cvtermprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'cvtermprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'cvtermprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_cvtermprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'cvtermprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cvtermprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cvterm_id_type_id_value_rank' => array(
|
|
|
+ 0 => 'cvterm_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'value',
|
|
|
+ 3 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'cvtermprop_idx1' => array(
|
|
|
+ 0 => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ 'cvtermprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'cvtermprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cvterm_id' => 'cvterm_id',
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_cvterm_relationship()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'cvterm_relationship' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'cvterm_relationship' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_cvterm_relationship() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'cvterm_relationship',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cvterm_relationship_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cvterm_relationship_c1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ 1 => 'object_id',
|
|
|
+ 2 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'cvterm_relationship_idx1' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ 'cvterm_relationship_idx2' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ ),
|
|
|
+ 'cvterm_relationship_idx3' => array(
|
|
|
+ 0 => 'object_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'cvterm_relationship_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ 'subject_id' => 'cvterm_id',
|
|
|
+ 'object_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_cvtermsynonym()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'cvtermsynonym' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'cvtermsynonym' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_cvtermsynonym() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'cvtermsynonym',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cvtermsynonym_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'synonym' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '1024',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cvtermsynonym_c1' => array(
|
|
|
+ 0 => 'cvterm_id',
|
|
|
+ 1 => 'synonym',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'cvtermsynonym_idx1' => array(
|
|
|
+ 0 => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'cvtermsynonym_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cvterm_id' => 'cvterm_id',
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_db()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'db' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'db' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_db() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'db',
|
|
|
+ 'fields' => array(
|
|
|
+ 'db_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'urlprefix' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'url' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'db_c1' => array(
|
|
|
+ 0 => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'db_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'dbprop',
|
|
|
+ 1 => 'dbxref',
|
|
|
+ 2 => 'stockcollection_db',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_dbprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'dbprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'dbprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_dbprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'dbprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'dbprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'db_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'dbprop_c1' => array(
|
|
|
+ 0 => 'db_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'dbprop_idx1' => array(
|
|
|
+ 0 => 'db_id',
|
|
|
+ ),
|
|
|
+ 'dbprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'dbprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'db' => array(
|
|
|
+ 'table' => 'db',
|
|
|
+ 'columns' => array(
|
|
|
+ 'db_id' => 'db_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_dbxref()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'dbxref' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'dbxref' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_dbxref() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'fields' => array(
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'db_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'accession' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '1024',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'version' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => '',
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'dbxref_c1' => array(
|
|
|
+ 0 => 'db_id',
|
|
|
+ 1 => 'accession',
|
|
|
+ 2 => 'version',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'dbxref_idx1' => array(
|
|
|
+ 0 => 'db_id',
|
|
|
+ ),
|
|
|
+ 'dbxref_idx2' => array(
|
|
|
+ 0 => 'accession',
|
|
|
+ ),
|
|
|
+ 'dbxref_idx3' => array(
|
|
|
+ 0 => 'version',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'db' => array(
|
|
|
+ 'table' => 'db',
|
|
|
+ 'columns' => array(
|
|
|
+ 'db_id' => 'db_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'analysis_dbxref',
|
|
|
+ 1 => 'arraydesign',
|
|
|
+ 2 => 'assay',
|
|
|
+ 3 => 'biomaterial',
|
|
|
+ 4 => 'biomaterial_dbxref',
|
|
|
+ 5 => 'cell_line_dbxref',
|
|
|
+ 6 => 'cvterm',
|
|
|
+ 7 => 'cvterm_dbxref',
|
|
|
+ 8 => 'dbxrefprop',
|
|
|
+ 9 => 'element',
|
|
|
+ 10 => 'feature',
|
|
|
+ 11 => 'feature_cvterm_dbxref',
|
|
|
+ 12 => 'feature_dbxref',
|
|
|
+ 13 => 'featuremap_dbxref',
|
|
|
+ 14 => 'library_dbxref',
|
|
|
+ 15 => 'nd_experiment_dbxref',
|
|
|
+ 16 => 'nd_experiment_stock_dbxref',
|
|
|
+ 17 => 'organism_dbxref',
|
|
|
+ 18 => 'phylonode_dbxref',
|
|
|
+ 19 => 'phylotree',
|
|
|
+ 20 => 'project_dbxref',
|
|
|
+ 21 => 'protocol',
|
|
|
+ 22 => 'pub_dbxref',
|
|
|
+ 23 => 'stock',
|
|
|
+ 24 => 'stock_dbxref',
|
|
|
+ 25 => 'study',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_dbxrefprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'dbxrefprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'dbxrefprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_dbxrefprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'dbxrefprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'dbxrefprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'dbxrefprop_c1' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'dbxrefprop_idx1' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ 'dbxrefprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'dbxrefprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_eimage()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'eimage' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'eimage' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_eimage() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'eimage',
|
|
|
+ 'fields' => array(
|
|
|
+ 'eimage_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'eimage_data' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'eimage_type' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'image_uri' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'eimage_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'expression_image',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_element()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'element' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'element' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_element() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'element',
|
|
|
+ 'fields' => array(
|
|
|
+ 'element_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'arraydesign_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'element_c1' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ 1 => 'arraydesign_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'element_idx1' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ ),
|
|
|
+ 'element_idx2' => array(
|
|
|
+ 0 => 'arraydesign_id',
|
|
|
+ ),
|
|
|
+ 'element_idx3' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ 'element_idx4' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'element_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'feature' => array(
|
|
|
+ 'table' => 'feature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_id' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'arraydesign' => array(
|
|
|
+ 'table' => 'arraydesign',
|
|
|
+ 'columns' => array(
|
|
|
+ 'arraydesign_id' => 'arraydesign_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'element_relationship',
|
|
|
+ 2 => 'elementresult',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_element_relationship()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'element_relationship' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'element_relationship' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_element_relationship() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'element_relationship',
|
|
|
+ 'fields' => array(
|
|
|
+ 'element_relationship_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'element_relationship_c1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ 1 => 'object_id',
|
|
|
+ 2 => 'type_id',
|
|
|
+ 3 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'element_relationship_idx1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ ),
|
|
|
+ 'element_relationship_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ 'element_relationship_idx3' => array(
|
|
|
+ 0 => 'object_id',
|
|
|
+ ),
|
|
|
+ 'element_relationship_idx4' => array(
|
|
|
+ 0 => 'value',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'element_relationship_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'element' => array(
|
|
|
+ 'table' => 'element',
|
|
|
+ 'columns' => array(
|
|
|
+ 'subject_id' => 'element_id',
|
|
|
+ 'object_id' => 'element_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_elementresult()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'elementresult' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'elementresult' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_elementresult() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'elementresult',
|
|
|
+ 'fields' => array(
|
|
|
+ 'elementresult_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'element_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'quantification_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'signal' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'float',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'elementresult_c1' => array(
|
|
|
+ 0 => 'element_id',
|
|
|
+ 1 => 'quantification_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'elementresult_idx1' => array(
|
|
|
+ 0 => 'element_id',
|
|
|
+ ),
|
|
|
+ 'elementresult_idx2' => array(
|
|
|
+ 0 => 'quantification_id',
|
|
|
+ ),
|
|
|
+ 'elementresult_idx3' => array(
|
|
|
+ 0 => 'signal',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'elementresult_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'element' => array(
|
|
|
+ 'table' => 'element',
|
|
|
+ 'columns' => array(
|
|
|
+ 'element_id' => 'element_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'quantification' => array(
|
|
|
+ 'table' => 'quantification',
|
|
|
+ 'columns' => array(
|
|
|
+ 'quantification_id' => 'quantification_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'elementresult_relationship',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_elementresult_relationship()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'elementresult_relationship' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'elementresult_relationship' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_elementresult_relationship() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'elementresult_relationship',
|
|
|
+ 'fields' => array(
|
|
|
+ 'elementresult_relationship_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'elementresult_relationship_c1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ 1 => 'object_id',
|
|
|
+ 2 => 'type_id',
|
|
|
+ 3 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'elementresult_relationship_idx1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ ),
|
|
|
+ 'elementresult_relationship_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ 'elementresult_relationship_idx3' => array(
|
|
|
+ 0 => 'object_id',
|
|
|
+ ),
|
|
|
+ 'elementresult_relationship_idx4' => array(
|
|
|
+ 0 => 'value',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'elementresult_relationship_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'elementresult' => array(
|
|
|
+ 'table' => 'elementresult',
|
|
|
+ 'columns' => array(
|
|
|
+ 'subject_id' => 'elementresult_id',
|
|
|
+ 'object_id' => 'elementresult_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_environment()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'environment' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'environment' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_environment() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'environment',
|
|
|
+ 'fields' => array(
|
|
|
+ 'environment_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'uniquename' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'environment_c1' => array(
|
|
|
+ 0 => 'uniquename',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'environment_idx1' => array(
|
|
|
+ 0 => 'uniquename',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'environment_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'environment_cvterm',
|
|
|
+ 1 => 'phendesc',
|
|
|
+ 2 => 'phenotype_comparison',
|
|
|
+ 4 => 'phenstatement',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_environment_cvterm()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'environment_cvterm' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'environment_cvterm' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_environment_cvterm() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'environment_cvterm',
|
|
|
+ 'fields' => array(
|
|
|
+ 'environment_cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'environment_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'environment_cvterm_c1' => array(
|
|
|
+ 0 => 'environment_id',
|
|
|
+ 1 => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'environment_cvterm_idx1' => array(
|
|
|
+ 0 => 'environment_id',
|
|
|
+ ),
|
|
|
+ 'environment_cvterm_idx2' => array(
|
|
|
+ 0 => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'environment_cvterm_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'environment' => array(
|
|
|
+ 'table' => 'environment',
|
|
|
+ 'columns' => array(
|
|
|
+ 'environment_id' => 'environment_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cvterm_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_expression()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'expression' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'expression' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_expression() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'expression',
|
|
|
+ 'fields' => array(
|
|
|
+ 'expression_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'uniquename' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'md5checksum' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'char',
|
|
|
+ 'length' => '32',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'expression_c1' => array(
|
|
|
+ 0 => 'uniquename',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'expression_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'expression_cvterm',
|
|
|
+ 1 => 'expression_image',
|
|
|
+ 2 => 'expressionprop',
|
|
|
+ 3 => 'expression_pub',
|
|
|
+ 4 => 'feature_expression',
|
|
|
+ 5 => 'library_expression',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_expression_cvterm()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'expression_cvterm' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'expression_cvterm' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_expression_cvterm() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'expression_cvterm',
|
|
|
+ 'fields' => array(
|
|
|
+ 'expression_cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'expression_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ 'cvterm_type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'expression_cvterm_c1' => array(
|
|
|
+ 0 => 'expression_id',
|
|
|
+ 1 => 'cvterm_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ 3 => 'cvterm_type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'expression_cvterm_idx1' => array(
|
|
|
+ 0 => 'expression_id',
|
|
|
+ ),
|
|
|
+ 'expression_cvterm_idx2' => array(
|
|
|
+ 0 => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ 'expression_cvterm_idx3' => array(
|
|
|
+ 0 => 'cvterm_type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'expression_cvterm_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'expression' => array(
|
|
|
+ 'table' => 'expression',
|
|
|
+ 'columns' => array(
|
|
|
+ 'expression_id' => 'expression_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cvterm_id' => 'cvterm_id',
|
|
|
+ 'cvterm_type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'expression_cvtermprop',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_expression_cvtermprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'expression_cvtermprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'expression_cvtermprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_expression_cvtermprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'expression_cvtermprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'expression_cvtermprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'expression_cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'expression_cvtermprop_c1' => array(
|
|
|
+ 0 => 'expression_cvterm_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'expression_cvtermprop_idx1' => array(
|
|
|
+ 0 => 'expression_cvterm_id',
|
|
|
+ ),
|
|
|
+ 'expression_cvtermprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'expression_cvtermprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'expression_cvterm' => array(
|
|
|
+ 'table' => 'expression_cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'expression_cvterm_id' => 'expression_cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_expression_image()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'expression_image' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'expression_image' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_expression_image() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'expression_image',
|
|
|
+ 'fields' => array(
|
|
|
+ 'expression_image_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'expression_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'eimage_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'expression_image_c1' => array(
|
|
|
+ 0 => 'expression_id',
|
|
|
+ 1 => 'eimage_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'expression_image_idx1' => array(
|
|
|
+ 0 => 'expression_id',
|
|
|
+ ),
|
|
|
+ 'expression_image_idx2' => array(
|
|
|
+ 0 => 'eimage_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'expression_image_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'expression' => array(
|
|
|
+ 'table' => 'expression',
|
|
|
+ 'columns' => array(
|
|
|
+ 'expression_id' => 'expression_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'eimage' => array(
|
|
|
+ 'table' => 'eimage',
|
|
|
+ 'columns' => array(
|
|
|
+ 'eimage_id' => 'eimage_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_expressionprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'expressionprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'expressionprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_expressionprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'expressionprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'expressionprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'expression_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'expressionprop_c1' => array(
|
|
|
+ 0 => 'expression_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'expressionprop_idx1' => array(
|
|
|
+ 0 => 'expression_id',
|
|
|
+ ),
|
|
|
+ 'expressionprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'expressionprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'expression' => array(
|
|
|
+ 'table' => 'expression',
|
|
|
+ 'columns' => array(
|
|
|
+ 'expression_id' => 'expression_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_expression_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'expression_pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'expression_pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_expression_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'expression_pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'expression_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'expression_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'expression_pub_c1' => array(
|
|
|
+ 0 => 'expression_id',
|
|
|
+ 1 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'expression_pub_idx1' => array(
|
|
|
+ 0 => 'expression_id',
|
|
|
+ ),
|
|
|
+ 'expression_pub_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'expression_pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'expression' => array(
|
|
|
+ 'table' => 'expression',
|
|
|
+ 'columns' => array(
|
|
|
+ 'expression_id' => 'expression_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_feature()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'feature' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'feature' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_feature() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'feature',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'uniquename' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'residues' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'seqlen' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'md5checksum' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'char',
|
|
|
+ 'length' => '32',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'is_analysis' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => FALSE,
|
|
|
+ ),
|
|
|
+ 'is_obsolete' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => FALSE,
|
|
|
+ ),
|
|
|
+ 'timeaccessioned' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 'now()',
|
|
|
+ ),
|
|
|
+ 'timelastmodified' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 'now()',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'feature_c1' => array(
|
|
|
+ 0 => 'organism_id',
|
|
|
+ 1 => 'uniquename',
|
|
|
+ 2 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'feature_idx1' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ 'feature_idx2' => array(
|
|
|
+ 0 => 'organism_id',
|
|
|
+ ),
|
|
|
+ 'feature_idx3' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ 'feature_idx4' => array(
|
|
|
+ 0 => 'uniquename',
|
|
|
+ ),
|
|
|
+ 'feature_name_ind1' => array(
|
|
|
+ 0 => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'organism' => array(
|
|
|
+ 'table' => 'organism',
|
|
|
+ 'columns' => array(
|
|
|
+ 'organism_id' => 'organism_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'analysisfeature',
|
|
|
+ 1 => 'cell_line_feature',
|
|
|
+ 2 => 'element',
|
|
|
+ 3 => 'feature_contact',
|
|
|
+ 4 => 'feature_cvterm',
|
|
|
+ 5 => 'feature_dbxref',
|
|
|
+ 6 => 'feature_expression',
|
|
|
+ 7 => 'feature_genotype',
|
|
|
+ 9 => 'featureloc',
|
|
|
+ 11 => 'feature_phenotype',
|
|
|
+ 12 => 'featurepos',
|
|
|
+ 14 => 'featureprop',
|
|
|
+ 15 => 'feature_pub',
|
|
|
+ 16 => 'featurerange',
|
|
|
+ 21 => 'feature_relationship',
|
|
|
+ 23 => 'feature_synonym',
|
|
|
+ 24 => 'library_feature',
|
|
|
+ 25 => 'nd_reagent',
|
|
|
+ 26 => 'phylonode',
|
|
|
+ 27 => 'project_feature',
|
|
|
+ 28 => 'stock_feature',
|
|
|
+ 29 => 'studyprop_feature',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_feature_contact()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'feature_contact' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'feature_contact' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_feature_contact() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'feature_contact',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_contact_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'contact_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'feature_contact_c1' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ 1 => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'feature_contact_idx1' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ ),
|
|
|
+ 'feature_contact_idx2' => array(
|
|
|
+ 0 => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'feature_contact_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'contact' => array(
|
|
|
+ 'table' => 'contact',
|
|
|
+ 'columns' => array(
|
|
|
+ 'contact_id' => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'feature' => array(
|
|
|
+ 'table' => 'feature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_id' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_feature_cvterm()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'feature_cvterm' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'feature_cvterm' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_feature_cvterm() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'feature_cvterm',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'is_not' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'feature_cvterm_c1' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ 1 => 'cvterm_id',
|
|
|
+ 2 => 'pub_id',
|
|
|
+ 3 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'feature_cvterm_idx1' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ ),
|
|
|
+ 'feature_cvterm_idx2' => array(
|
|
|
+ 0 => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ 'feature_cvterm_idx3' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'feature_cvterm_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'feature' => array(
|
|
|
+ 'table' => 'feature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_id' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cvterm_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'feature_cvterm_dbxref',
|
|
|
+ 1 => 'feature_cvtermprop',
|
|
|
+ 2 => 'feature_cvterm_pub',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_feature_cvterm_dbxref()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'feature_cvterm_dbxref' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'feature_cvterm_dbxref' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_feature_cvterm_dbxref() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'feature_cvterm_dbxref',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_cvterm_dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'feature_cvterm_dbxref_c1' => array(
|
|
|
+ 0 => 'feature_cvterm_id',
|
|
|
+ 1 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'feature_cvterm_dbxref_idx1' => array(
|
|
|
+ 0 => 'feature_cvterm_id',
|
|
|
+ ),
|
|
|
+ 'feature_cvterm_dbxref_idx2' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'feature_cvterm_dbxref_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'feature_cvterm' => array(
|
|
|
+ 'table' => 'feature_cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_cvterm_id' => 'feature_cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_feature_cvtermprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'feature_cvtermprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'feature_cvtermprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_feature_cvtermprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'feature_cvtermprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_cvtermprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'feature_cvtermprop_c1' => array(
|
|
|
+ 0 => 'feature_cvterm_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'feature_cvtermprop_idx1' => array(
|
|
|
+ 0 => 'feature_cvterm_id',
|
|
|
+ ),
|
|
|
+ 'feature_cvtermprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'feature_cvtermprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'feature_cvterm' => array(
|
|
|
+ 'table' => 'feature_cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_cvterm_id' => 'feature_cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_feature_cvterm_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'feature_cvterm_pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'feature_cvterm_pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_feature_cvterm_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'feature_cvterm_pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_cvterm_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'feature_cvterm_pub_c1' => array(
|
|
|
+ 0 => 'feature_cvterm_id',
|
|
|
+ 1 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'feature_cvterm_pub_idx1' => array(
|
|
|
+ 0 => 'feature_cvterm_id',
|
|
|
+ ),
|
|
|
+ 'feature_cvterm_pub_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'feature_cvterm_pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'feature_cvterm' => array(
|
|
|
+ 'table' => 'feature_cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_cvterm_id' => 'feature_cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_feature_dbxref()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'feature_dbxref' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'feature_dbxref' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_feature_dbxref() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'feature_dbxref',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'is_current' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 'ru',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'feature_dbxref_c1' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ 1 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'feature_dbxref_idx1' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ ),
|
|
|
+ 'feature_dbxref_idx2' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'feature_dbxref_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'feature' => array(
|
|
|
+ 'table' => 'feature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_id' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_feature_expression()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'feature_expression' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'feature_expression' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_feature_expression() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'feature_expression',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_expression_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'expression_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'feature_expression_c1' => array(
|
|
|
+ 0 => 'expression_id',
|
|
|
+ 1 => 'feature_id',
|
|
|
+ 2 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'feature_expression_idx1' => array(
|
|
|
+ 0 => 'expression_id',
|
|
|
+ ),
|
|
|
+ 'feature_expression_idx2' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ ),
|
|
|
+ 'feature_expression_idx3' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'feature_expression_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'expression' => array(
|
|
|
+ 'table' => 'expression',
|
|
|
+ 'columns' => array(
|
|
|
+ 'expression_id' => 'expression_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'feature' => array(
|
|
|
+ 'table' => 'feature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_id' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'feature_expressionprop',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_feature_expressionprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'feature_expressionprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'feature_expressionprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_feature_expressionprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'feature_expressionprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_expressionprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_expression_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'feature_expressionprop_c1' => array(
|
|
|
+ 0 => 'feature_expression_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'feature_expressionprop_idx1' => array(
|
|
|
+ 0 => 'feature_expression_id',
|
|
|
+ ),
|
|
|
+ 'feature_expressionprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'feature_expressionprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'feature_expression' => array(
|
|
|
+ 'table' => 'feature_expression',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_expression_id' => 'feature_expression_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_feature_genotype()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'feature_genotype' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'feature_genotype' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_feature_genotype() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'feature_genotype',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_genotype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'genotype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'chromosome_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cgroup' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'feature_genotype_c1' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ 1 => 'genotype_id',
|
|
|
+ 2 => 'cvterm_id',
|
|
|
+ 3 => 'chromosome_id',
|
|
|
+ 4 => 'rank',
|
|
|
+ 5 => 'cgroup',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'feature_genotype_idx1' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ ),
|
|
|
+ 'feature_genotype_idx2' => array(
|
|
|
+ 0 => 'genotype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'feature_genotype_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'feature' => array(
|
|
|
+ 'table' => 'feature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_id' => 'feature_id',
|
|
|
+ 'chromosome_id' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'genotype' => array(
|
|
|
+ 'table' => 'genotype',
|
|
|
+ 'columns' => array(
|
|
|
+ 'genotype_id' => 'genotype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cvterm_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_featureloc()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'featureloc' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'featureloc' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_featureloc() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'featureloc',
|
|
|
+ 'fields' => array(
|
|
|
+ 'featureloc_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'srcfeature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'fmin' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'is_fmin_partial' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => FALSE,
|
|
|
+ ),
|
|
|
+ 'fmax' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'is_fmax_partial' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => FALSE,
|
|
|
+ ),
|
|
|
+ 'strand' => array(
|
|
|
+ 'size' => 'small',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'phase' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'residue_info' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'locgroup' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'binloc_boxrange' => array(
|
|
|
+ 0 => 'fmin',
|
|
|
+ ),
|
|
|
+ 'binloc_boxrange_src' => array(
|
|
|
+ 0 => 'srcfeature_id',
|
|
|
+ 1 => 'fmin',
|
|
|
+ ),
|
|
|
+ 'featureloc_idx1' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ ),
|
|
|
+ 'featureloc_idx1b' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ 1 => 'fmin',
|
|
|
+ 2 => 'fmax',
|
|
|
+ ),
|
|
|
+ 'featureloc_idx2' => array(
|
|
|
+ 0 => 'srcfeature_id',
|
|
|
+ ),
|
|
|
+ 'featureloc_idx3' => array(
|
|
|
+ 0 => 'srcfeature_id',
|
|
|
+ 1 => 'fmin',
|
|
|
+ 2 => 'fmax',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'featureloc_c1' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ 1 => 'locgroup',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'featureloc_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'feature' => array(
|
|
|
+ 'table' => 'feature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_id' => 'feature_id',
|
|
|
+ 'srcfeature_id' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'featureloc_pub',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_featureloc_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'featureloc_pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'featureloc_pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_featureloc_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'featureloc_pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'featureloc_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'featureloc_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'featureloc_pub_c1' => array(
|
|
|
+ 0 => 'featureloc_id',
|
|
|
+ 1 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'featureloc_pub_idx1' => array(
|
|
|
+ 0 => 'featureloc_id',
|
|
|
+ ),
|
|
|
+ 'featureloc_pub_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'featureloc_pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'featureloc' => array(
|
|
|
+ 'table' => 'featureloc',
|
|
|
+ 'columns' => array(
|
|
|
+ 'featureloc_id' => 'featureloc_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_featuremap()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'featuremap' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'featuremap' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_featuremap() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'featuremap',
|
|
|
+ 'fields' => array(
|
|
|
+ 'featuremap_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'unittype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'featuremap_c1' => array(
|
|
|
+ 0 => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'featuremap_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'unittype_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'featuremap_contact',
|
|
|
+ 1 => 'featuremap_dbxref',
|
|
|
+ 2 => 'featuremap_organism',
|
|
|
+ 3 => 'featuremapprop',
|
|
|
+ 4 => 'featuremap_pub',
|
|
|
+ 5 => 'featurepos',
|
|
|
+ 6 => 'featurerange',
|
|
|
+ 7 => 'stock_featuremap',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_featuremap_contact()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'featuremap_contact' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'featuremap_contact' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_featuremap_contact() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'featuremap_contact',
|
|
|
+ 'fields' => array(
|
|
|
+ 'featuremap_contact_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'featuremap_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'contact_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'featuremap_contact_c1' => array(
|
|
|
+ 0 => 'featuremap_id',
|
|
|
+ 1 => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'featuremap_contact_idx1' => array(
|
|
|
+ 0 => 'featuremap_id',
|
|
|
+ ),
|
|
|
+ 'featuremap_contact_idx2' => array(
|
|
|
+ 0 => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'featuremap_contact_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'contact' => array(
|
|
|
+ 'table' => 'contact',
|
|
|
+ 'columns' => array(
|
|
|
+ 'contact_id' => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'featuremap' => array(
|
|
|
+ 'table' => 'featuremap',
|
|
|
+ 'columns' => array(
|
|
|
+ 'featuremap_id' => 'featuremap_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_featuremap_dbxref()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'featuremap_dbxref' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'featuremap_dbxref' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_featuremap_dbxref() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'featuremap_dbxref',
|
|
|
+ 'fields' => array(
|
|
|
+ 'featuremap_dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'featuremap_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'is_current' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 'ru',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'featuremap_dbxref_idx1' => array(
|
|
|
+ 0 => 'featuremap_id',
|
|
|
+ ),
|
|
|
+ 'featuremap_dbxref_idx2' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'featuremap_dbxref_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'featuremap' => array(
|
|
|
+ 'table' => 'featuremap',
|
|
|
+ 'columns' => array(
|
|
|
+ 'featuremap_id' => 'featuremap_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_featuremap_organism()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'featuremap_organism' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'featuremap_organism' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_featuremap_organism() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'featuremap_organism',
|
|
|
+ 'fields' => array(
|
|
|
+ 'featuremap_organism_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'featuremap_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'featuremap_organism_c1' => array(
|
|
|
+ 0 => 'featuremap_id',
|
|
|
+ 1 => 'organism_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'featuremap_organism_idx1' => array(
|
|
|
+ 0 => 'featuremap_id',
|
|
|
+ ),
|
|
|
+ 'featuremap_organism_idx2' => array(
|
|
|
+ 0 => 'organism_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'featuremap_organism_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'featuremap' => array(
|
|
|
+ 'table' => 'featuremap',
|
|
|
+ 'columns' => array(
|
|
|
+ 'featuremap_id' => 'featuremap_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'organism' => array(
|
|
|
+ 'table' => 'organism',
|
|
|
+ 'columns' => array(
|
|
|
+ 'organism_id' => 'organism_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_featuremapprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'featuremapprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'featuremapprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_featuremapprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'featuremapprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'featuremapprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'featuremap_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'featuremapprop_c1' => array(
|
|
|
+ 0 => 'featuremap_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'featuremapprop_idx1' => array(
|
|
|
+ 0 => 'featuremap_id',
|
|
|
+ ),
|
|
|
+ 'featuremapprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'featuremapprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'featuremap' => array(
|
|
|
+ 'table' => 'featuremap',
|
|
|
+ 'columns' => array(
|
|
|
+ 'featuremap_id' => 'featuremap_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_featuremap_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'featuremap_pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'featuremap_pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_featuremap_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'featuremap_pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'featuremap_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'featuremap_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'featuremap_pub_idx1' => array(
|
|
|
+ 0 => 'featuremap_id',
|
|
|
+ ),
|
|
|
+ 'featuremap_pub_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'featuremap_pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'featuremap' => array(
|
|
|
+ 'table' => 'featuremap',
|
|
|
+ 'columns' => array(
|
|
|
+ 'featuremap_id' => 'featuremap_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_feature_phenotype()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'feature_phenotype' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'feature_phenotype' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_feature_phenotype() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'feature_phenotype',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_phenotype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'phenotype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'feature_phenotype_c1' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ 1 => 'phenotype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'feature_phenotype_idx1' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ ),
|
|
|
+ 'feature_phenotype_idx2' => array(
|
|
|
+ 0 => 'phenotype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'feature_phenotype_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'feature' => array(
|
|
|
+ 'table' => 'feature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_id' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'phenotype' => array(
|
|
|
+ 'table' => 'phenotype',
|
|
|
+ 'columns' => array(
|
|
|
+ 'phenotype_id' => 'phenotype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_featurepos()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'featurepos' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'featurepos' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_featurepos() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'featurepos',
|
|
|
+ 'fields' => array(
|
|
|
+ 'featurepos_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'featuremap_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'map_feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'mappos' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'float',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'featurepos_idx1' => array(
|
|
|
+ 0 => 'featuremap_id',
|
|
|
+ ),
|
|
|
+ 'featurepos_idx2' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ ),
|
|
|
+ 'featurepos_idx3' => array(
|
|
|
+ 0 => 'map_feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'featurepos_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'featuremap' => array(
|
|
|
+ 'table' => 'featuremap',
|
|
|
+ 'columns' => array(
|
|
|
+ 'featuremap_id' => 'featuremap_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'feature' => array(
|
|
|
+ 'table' => 'feature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_id' => 'feature_id',
|
|
|
+ 'map_feature_id' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'featureposprop',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_featureposprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'featureposprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'featureposprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_featureposprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'featureposprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'featureposprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'featurepos_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'featureposprop_c1' => array(
|
|
|
+ 0 => 'featurepos_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'featureposprop_idx1' => array(
|
|
|
+ 0 => 'featurepos_id',
|
|
|
+ ),
|
|
|
+ 'featureposprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'featureposprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'featurepos' => array(
|
|
|
+ 'table' => 'featurepos',
|
|
|
+ 'columns' => array(
|
|
|
+ 'featurepos_id' => 'featurepos_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_featureprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'featureprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'featureprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_featureprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'featureprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'featureprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'featureprop_c1' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'featureprop_idx1' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ ),
|
|
|
+ 'featureprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'featureprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'feature' => array(
|
|
|
+ 'table' => 'feature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_id' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'featureprop_pub',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_featureprop_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'featureprop_pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'featureprop_pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_featureprop_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'featureprop_pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'featureprop_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'featureprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'featureprop_pub_c1' => array(
|
|
|
+ 0 => 'featureprop_id',
|
|
|
+ 1 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'featureprop_pub_idx1' => array(
|
|
|
+ 0 => 'featureprop_id',
|
|
|
+ ),
|
|
|
+ 'featureprop_pub_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'featureprop_pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'featureprop' => array(
|
|
|
+ 'table' => 'featureprop',
|
|
|
+ 'columns' => array(
|
|
|
+ 'featureprop_id' => 'featureprop_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_feature_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'feature_pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'feature_pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_feature_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'feature_pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'feature_pub_c1' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ 1 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'feature_pub_idx1' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ ),
|
|
|
+ 'feature_pub_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'feature_pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'feature' => array(
|
|
|
+ 'table' => 'feature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_id' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'feature_pubprop',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_feature_pubprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'feature_pubprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'feature_pubprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_feature_pubprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'feature_pubprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_pubprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'feature_pubprop_c1' => array(
|
|
|
+ 0 => 'feature_pub_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'feature_pubprop_idx1' => array(
|
|
|
+ 0 => 'feature_pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'feature_pubprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'feature_pub' => array(
|
|
|
+ 'table' => 'feature_pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_pub_id' => 'feature_pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_featurerange()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'featurerange' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'featurerange' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_featurerange() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'featurerange',
|
|
|
+ 'fields' => array(
|
|
|
+ 'featurerange_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'featuremap_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'leftstartf_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'leftendf_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rightstartf_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rightendf_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'rangestr' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'featurerange_idx1' => array(
|
|
|
+ 0 => 'featuremap_id',
|
|
|
+ ),
|
|
|
+ 'featurerange_idx2' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ ),
|
|
|
+ 'featurerange_idx3' => array(
|
|
|
+ 0 => 'leftstartf_id',
|
|
|
+ ),
|
|
|
+ 'featurerange_idx4' => array(
|
|
|
+ 0 => 'leftendf_id',
|
|
|
+ ),
|
|
|
+ 'featurerange_idx5' => array(
|
|
|
+ 0 => 'rightstartf_id',
|
|
|
+ ),
|
|
|
+ 'featurerange_idx6' => array(
|
|
|
+ 0 => 'rightendf_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'featurerange_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'featuremap' => array(
|
|
|
+ 'table' => 'featuremap',
|
|
|
+ 'columns' => array(
|
|
|
+ 'featuremap_id' => 'featuremap_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'feature' => array(
|
|
|
+ 'table' => 'feature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_id' => 'feature_id',
|
|
|
+ 'leftstartf_id' => 'feature_id',
|
|
|
+ 'leftendf_id' => 'feature_id',
|
|
|
+ 'rightstartf_id' => 'feature_id',
|
|
|
+ 'rightendf_id' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_feature_relationship()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'feature_relationship' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'feature_relationship' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_feature_relationship() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'feature_relationship',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_relationship_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'feature_relationship_c1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ 1 => 'object_id',
|
|
|
+ 2 => 'type_id',
|
|
|
+ 3 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'feature_relationship_idx1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ ),
|
|
|
+ 'feature_relationship_idx1b' => array(
|
|
|
+ 0 => 'object_id',
|
|
|
+ 1 => 'subject_id',
|
|
|
+ 2 => 'type_id',
|
|
|
+ ),
|
|
|
+ 'feature_relationship_idx2' => array(
|
|
|
+ 0 => 'object_id',
|
|
|
+ ),
|
|
|
+ 'feature_relationship_idx3' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'feature_relationship_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'feature' => array(
|
|
|
+ 'table' => 'feature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'subject_id' => 'feature_id',
|
|
|
+ 'object_id' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'feature_relationshipprop',
|
|
|
+ 1 => 'feature_relationship_pub',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_feature_relationshipprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'feature_relationshipprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'feature_relationshipprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_feature_relationshipprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'feature_relationshipprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_relationshipprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_relationship_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'feature_relationshipprop_c1' => array(
|
|
|
+ 0 => 'feature_relationship_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'feature_relationshipprop_idx1' => array(
|
|
|
+ 0 => 'feature_relationship_id',
|
|
|
+ ),
|
|
|
+ 'feature_relationshipprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'feature_relationshipprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'feature_relationship' => array(
|
|
|
+ 'table' => 'feature_relationship',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_relationship_id' => 'feature_relationship_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'feature_relationshipprop_pub',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_feature_relationshipprop_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'feature_relationshipprop_pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'feature_relationshipprop_pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_feature_relationshipprop_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'feature_relationshipprop_pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_relationshipprop_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_relationshipprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'feature_relationshipprop_pub_c1' => array(
|
|
|
+ 0 => 'feature_relationshipprop_id',
|
|
|
+ 1 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'feature_relationshipprop_pub_idx1' => array(
|
|
|
+ 0 => 'feature_relationshipprop_id',
|
|
|
+ ),
|
|
|
+ 'feature_relationshipprop_pub_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'feature_relationshipprop_pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'feature_relationshipprop' => array(
|
|
|
+ 'table' => 'feature_relationshipprop',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_relationshipprop_id' => 'feature_relationshipprop_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_feature_relationship_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'feature_relationship_pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'feature_relationship_pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_feature_relationship_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'feature_relationship_pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_relationship_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_relationship_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'feature_relationship_pub_c1' => array(
|
|
|
+ 0 => 'feature_relationship_id',
|
|
|
+ 1 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'feature_relationship_pub_idx1' => array(
|
|
|
+ 0 => 'feature_relationship_id',
|
|
|
+ ),
|
|
|
+ 'feature_relationship_pub_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'feature_relationship_pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'feature_relationship' => array(
|
|
|
+ 'table' => 'feature_relationship',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_relationship_id' => 'feature_relationship_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_feature_synonym()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'feature_synonym' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'feature_synonym' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_feature_synonym() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'feature_synonym',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_synonym_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'synonym_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'is_current' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => FALSE,
|
|
|
+ ),
|
|
|
+ 'is_internal' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'feature_synonym_c1' => array(
|
|
|
+ 0 => 'synonym_id',
|
|
|
+ 1 => 'feature_id',
|
|
|
+ 2 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'feature_synonym_idx1' => array(
|
|
|
+ 0 => 'synonym_id',
|
|
|
+ ),
|
|
|
+ 'feature_synonym_idx2' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ ),
|
|
|
+ 'feature_synonym_idx3' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'feature_synonym_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'synonym' => array(
|
|
|
+ 'table' => 'synonym',
|
|
|
+ 'columns' => array(
|
|
|
+ 'synonym_id' => 'synonym_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'feature' => array(
|
|
|
+ 'table' => 'feature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_id' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_genotype()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'genotype' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'genotype' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_genotype() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'genotype',
|
|
|
+ 'fields' => array(
|
|
|
+ 'genotype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'uniquename' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'genotype_c1' => array(
|
|
|
+ 0 => 'uniquename',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'genotype_idx1' => array(
|
|
|
+ 0 => 'uniquename',
|
|
|
+ ),
|
|
|
+ 'genotype_idx2' => array(
|
|
|
+ 0 => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'genotype_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'feature_genotype',
|
|
|
+ 1 => 'genotypeprop',
|
|
|
+ 2 => 'nd_experiment_genotype',
|
|
|
+ 3 => 'phendesc',
|
|
|
+ 4 => 'phenotype_comparison',
|
|
|
+ 6 => 'phenstatement',
|
|
|
+ 7 => 'stock_genotype',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_genotypeprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'genotypeprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'genotypeprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_genotypeprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'genotypeprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'genotypeprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'genotype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'genotypeprop_c1' => array(
|
|
|
+ 0 => 'genotype_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'genotypeprop_idx1' => array(
|
|
|
+ 0 => 'genotype_id',
|
|
|
+ ),
|
|
|
+ 'genotypeprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'genotypeprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'genotype' => array(
|
|
|
+ 'table' => 'genotype',
|
|
|
+ 'columns' => array(
|
|
|
+ 'genotype_id' => 'genotype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_library()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'library' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'library' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_library() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'library',
|
|
|
+ 'fields' => array(
|
|
|
+ 'library_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'uniquename' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'is_obsolete' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ 'timeaccessioned' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 'now()',
|
|
|
+ ),
|
|
|
+ 'timelastmodified' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 'now()',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'library_c1' => array(
|
|
|
+ 0 => 'organism_id',
|
|
|
+ 1 => 'uniquename',
|
|
|
+ 2 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'library_contact_idx1' => array(
|
|
|
+ 0 => 'library_id',
|
|
|
+ ),
|
|
|
+ 'library_idx1' => array(
|
|
|
+ 0 => 'organism_id',
|
|
|
+ ),
|
|
|
+ 'library_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ 'library_idx3' => array(
|
|
|
+ 0 => 'uniquename',
|
|
|
+ ),
|
|
|
+ 'library_name_ind1' => array(
|
|
|
+ 0 => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'library_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'organism' => array(
|
|
|
+ 'table' => 'organism',
|
|
|
+ 'columns' => array(
|
|
|
+ 'organism_id' => 'organism_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'cell_line_library',
|
|
|
+ 1 => 'library_contact',
|
|
|
+ 2 => 'library_cvterm',
|
|
|
+ 3 => 'library_dbxref',
|
|
|
+ 4 => 'library_expression',
|
|
|
+ 5 => 'library_feature',
|
|
|
+ 6 => 'libraryprop',
|
|
|
+ 7 => 'library_pub',
|
|
|
+ 8 => 'library_relationship',
|
|
|
+ 10 => 'library_synonym',
|
|
|
+ 11 => 'stock_library',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_library_contact()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'library_contact' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'library_contact' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_library_contact() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'library_contact',
|
|
|
+ 'fields' => array(
|
|
|
+ 'library_contact_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'library_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'contact_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'library_contact_c1' => array(
|
|
|
+ 0 => 'library_id',
|
|
|
+ 1 => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'library_contact_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'library' => array(
|
|
|
+ 'table' => 'library',
|
|
|
+ 'columns' => array(
|
|
|
+ 'library_id' => 'library_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'contact' => array(
|
|
|
+ 'table' => 'contact',
|
|
|
+ 'columns' => array(
|
|
|
+ 'contact_id' => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_library_cvterm()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'library_cvterm' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'library_cvterm' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_library_cvterm() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'library_cvterm',
|
|
|
+ 'fields' => array(
|
|
|
+ 'library_cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'library_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'library_cvterm_c1' => array(
|
|
|
+ 0 => 'library_id',
|
|
|
+ 1 => 'cvterm_id',
|
|
|
+ 2 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'library_cvterm_idx1' => array(
|
|
|
+ 0 => 'library_id',
|
|
|
+ ),
|
|
|
+ 'library_cvterm_idx2' => array(
|
|
|
+ 0 => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ 'library_cvterm_idx3' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'library_cvterm_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'library' => array(
|
|
|
+ 'table' => 'library',
|
|
|
+ 'columns' => array(
|
|
|
+ 'library_id' => 'library_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cvterm_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_library_dbxref()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'library_dbxref' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'library_dbxref' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_library_dbxref() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'library_dbxref',
|
|
|
+ 'fields' => array(
|
|
|
+ 'library_dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'library_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'is_current' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 'ru',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'library_dbxref_c1' => array(
|
|
|
+ 0 => 'library_id',
|
|
|
+ 1 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'library_dbxref_idx1' => array(
|
|
|
+ 0 => 'library_id',
|
|
|
+ ),
|
|
|
+ 'library_dbxref_idx2' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'library_dbxref_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'library' => array(
|
|
|
+ 'table' => 'library',
|
|
|
+ 'columns' => array(
|
|
|
+ 'library_id' => 'library_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_library_expression()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'library_expression' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'library_expression' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_library_expression() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'library_expression',
|
|
|
+ 'fields' => array(
|
|
|
+ 'library_expression_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'library_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'expression_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'library_expression_c1' => array(
|
|
|
+ 0 => 'library_id',
|
|
|
+ 1 => 'expression_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'library_expression_idx1' => array(
|
|
|
+ 0 => 'library_id',
|
|
|
+ ),
|
|
|
+ 'library_expression_idx2' => array(
|
|
|
+ 0 => 'expression_id',
|
|
|
+ ),
|
|
|
+ 'library_expression_idx3' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'library_expression_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'library' => array(
|
|
|
+ 'table' => 'library',
|
|
|
+ 'columns' => array(
|
|
|
+ 'library_id' => 'library_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'expression' => array(
|
|
|
+ 'table' => 'expression',
|
|
|
+ 'columns' => array(
|
|
|
+ 'expression_id' => 'expression_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'library_expressionprop',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_library_expressionprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'library_expressionprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'library_expressionprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_library_expressionprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'library_expressionprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'library_expressionprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'library_expression_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'library_expressionprop_c1' => array(
|
|
|
+ 0 => 'library_expression_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'library_expressionprop_idx1' => array(
|
|
|
+ 0 => 'library_expression_id',
|
|
|
+ ),
|
|
|
+ 'library_expressionprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'library_expressionprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'library_expression' => array(
|
|
|
+ 'table' => 'library_expression',
|
|
|
+ 'columns' => array(
|
|
|
+ 'library_expression_id' => 'library_expression_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_library_feature()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'library_feature' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'library_feature' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_library_feature() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'library_feature',
|
|
|
+ 'fields' => array(
|
|
|
+ 'library_feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'library_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'library_feature_c1' => array(
|
|
|
+ 0 => 'library_id',
|
|
|
+ 1 => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'library_feature_idx1' => array(
|
|
|
+ 0 => 'library_id',
|
|
|
+ ),
|
|
|
+ 'library_feature_idx2' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'library_feature_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'library' => array(
|
|
|
+ 'table' => 'library',
|
|
|
+ 'columns' => array(
|
|
|
+ 'library_id' => 'library_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'feature' => array(
|
|
|
+ 'table' => 'feature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_id' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'library_featureprop',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_library_featureprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'library_featureprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'library_featureprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_library_featureprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'library_featureprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'library_featureprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'library_feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'library_featureprop_c1' => array(
|
|
|
+ 0 => 'library_feature_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'library_featureprop_idx1' => array(
|
|
|
+ 0 => 'library_feature_id',
|
|
|
+ ),
|
|
|
+ 'library_featureprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'library_featureprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'library_feature' => array(
|
|
|
+ 'table' => 'library_feature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'library_feature_id' => 'library_feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_libraryprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'libraryprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'libraryprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_libraryprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'libraryprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'libraryprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'library_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'libraryprop_c1' => array(
|
|
|
+ 0 => 'library_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'libraryprop_idx1' => array(
|
|
|
+ 0 => 'library_id',
|
|
|
+ ),
|
|
|
+ 'libraryprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'libraryprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'library' => array(
|
|
|
+ 'table' => 'library',
|
|
|
+ 'columns' => array(
|
|
|
+ 'library_id' => 'library_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'libraryprop_pub',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_libraryprop_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'libraryprop_pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'libraryprop_pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_libraryprop_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'libraryprop_pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'libraryprop_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'libraryprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'libraryprop_pub_c1' => array(
|
|
|
+ 0 => 'libraryprop_id',
|
|
|
+ 1 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'libraryprop_pub_idx1' => array(
|
|
|
+ 0 => 'libraryprop_id',
|
|
|
+ ),
|
|
|
+ 'libraryprop_pub_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'libraryprop_pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'libraryprop' => array(
|
|
|
+ 'table' => 'libraryprop',
|
|
|
+ 'columns' => array(
|
|
|
+ 'libraryprop_id' => 'libraryprop_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_library_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'library_pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'library_pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_library_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'library_pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'library_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'library_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'library_pub_c1' => array(
|
|
|
+ 0 => 'library_id',
|
|
|
+ 1 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'library_pub_idx1' => array(
|
|
|
+ 0 => 'library_id',
|
|
|
+ ),
|
|
|
+ 'library_pub_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'library_pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'library' => array(
|
|
|
+ 'table' => 'library',
|
|
|
+ 'columns' => array(
|
|
|
+ 'library_id' => 'library_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_library_relationship()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'library_relationship' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'library_relationship' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_library_relationship() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'library_relationship',
|
|
|
+ 'fields' => array(
|
|
|
+ 'library_relationship_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'library_relationship_c1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ 1 => 'object_id',
|
|
|
+ 2 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'library_relationship_idx1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ ),
|
|
|
+ 'library_relationship_idx2' => array(
|
|
|
+ 0 => 'object_id',
|
|
|
+ ),
|
|
|
+ 'library_relationship_idx3' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'library_relationship_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'library' => array(
|
|
|
+ 'table' => 'library',
|
|
|
+ 'columns' => array(
|
|
|
+ 'subject_id' => 'library_id',
|
|
|
+ 'object_id' => 'library_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'library_relationship_pub',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_library_relationship_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'library_relationship_pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'library_relationship_pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_library_relationship_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'library_relationship_pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'library_relationship_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'library_relationship_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'library_relationship_pub_c1' => array(
|
|
|
+ 0 => 'library_relationship_id',
|
|
|
+ 1 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'library_relationship_pub_idx1' => array(
|
|
|
+ 0 => 'library_relationship_id',
|
|
|
+ ),
|
|
|
+ 'library_relationship_pub_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'library_relationship_pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'library_relationship' => array(
|
|
|
+ 'table' => 'library_relationship',
|
|
|
+ 'columns' => array(
|
|
|
+ 'library_relationship_id' => 'library_relationship_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_library_synonym()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'library_synonym' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'library_synonym' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_library_synonym() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'library_synonym',
|
|
|
+ 'fields' => array(
|
|
|
+ 'library_synonym_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'synonym_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'library_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'is_current' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 'ru',
|
|
|
+ ),
|
|
|
+ 'is_internal' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'library_synonym_c1' => array(
|
|
|
+ 0 => 'synonym_id',
|
|
|
+ 1 => 'library_id',
|
|
|
+ 2 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'library_synonym_idx1' => array(
|
|
|
+ 0 => 'synonym_id',
|
|
|
+ ),
|
|
|
+ 'library_synonym_idx2' => array(
|
|
|
+ 0 => 'library_id',
|
|
|
+ ),
|
|
|
+ 'library_synonym_idx3' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'library_synonym_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'synonym' => array(
|
|
|
+ 'table' => 'synonym',
|
|
|
+ 'columns' => array(
|
|
|
+ 'synonym_id' => 'synonym_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'library' => array(
|
|
|
+ 'table' => 'library',
|
|
|
+ 'columns' => array(
|
|
|
+ 'library_id' => 'library_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_magedocumentation()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'magedocumentation' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'magedocumentation' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_magedocumentation() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'magedocumentation',
|
|
|
+ 'fields' => array(
|
|
|
+ 'magedocumentation_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'mageml_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'tableinfo_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'row_id' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'mageidentifier' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'magedocumentation_idx1' => array(
|
|
|
+ 0 => 'mageml_id',
|
|
|
+ ),
|
|
|
+ 'magedocumentation_idx2' => array(
|
|
|
+ 0 => 'tableinfo_id',
|
|
|
+ ),
|
|
|
+ 'magedocumentation_idx3' => array(
|
|
|
+ 0 => 'row_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'magedocumentation_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'mageml' => array(
|
|
|
+ 'table' => 'mageml',
|
|
|
+ 'columns' => array(
|
|
|
+ 'mageml_id' => 'mageml_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'tableinfo' => array(
|
|
|
+ 'table' => 'tableinfo',
|
|
|
+ 'columns' => array(
|
|
|
+ 'tableinfo_id' => 'tableinfo_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_mageml()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'mageml' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'mageml' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_mageml() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'mageml',
|
|
|
+ 'fields' => array(
|
|
|
+ 'mageml_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'mage_package' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'mage_ml' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'mageml_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'magedocumentation',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_materialized_view()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'materialized_view' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'materialized_view' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_materialized_view() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'materialized_view',
|
|
|
+ 'fields' => array(
|
|
|
+ 'materialized_view_id' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'last_update' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'refresh_time' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '64',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'mv_schema' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '64',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'mv_table' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '128',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'mv_specs' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'indexed' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'query' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'special_index' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'name' => array(
|
|
|
+ 0 => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_nd_experiment()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'nd_experiment' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'nd_experiment' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_nd_experiment() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'nd_experiment',
|
|
|
+ 'fields' => array(
|
|
|
+ 'nd_experiment_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'nd_geolocation_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'nd_experiment_idx1' => array(
|
|
|
+ 0 => 'nd_geolocation_id',
|
|
|
+ ),
|
|
|
+ 'nd_experiment_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'nd_experiment_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'nd_geolocation' => array(
|
|
|
+ 'table' => 'nd_geolocation',
|
|
|
+ 'columns' => array(
|
|
|
+ 'nd_geolocation_id' => 'nd_geolocation_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'nd_experiment_analysis',
|
|
|
+ 1 => 'nd_experiment_contact',
|
|
|
+ 2 => 'nd_experiment_dbxref',
|
|
|
+ 3 => 'nd_experiment_genotype',
|
|
|
+ 4 => 'nd_experiment_phenotype',
|
|
|
+ 5 => 'nd_experiment_project',
|
|
|
+ 6 => 'nd_experimentprop',
|
|
|
+ 7 => 'nd_experiment_protocol',
|
|
|
+ 8 => 'nd_experiment_pub',
|
|
|
+ 9 => 'nd_experiment_stock',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_nd_experiment_analysis()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'nd_experiment_analysis' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'nd_experiment_analysis' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_nd_experiment_analysis() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'nd_experiment_analysis',
|
|
|
+ 'fields' => array(
|
|
|
+ 'nd_experiment_analysis_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'nd_experiment_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'analysis_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'nd_experiment_analysis_idx1' => array(
|
|
|
+ 0 => 'nd_experiment_id',
|
|
|
+ ),
|
|
|
+ 'nd_experiment_analysis_idx2' => array(
|
|
|
+ 0 => 'analysis_id',
|
|
|
+ ),
|
|
|
+ 'nd_experiment_analysis_idx3' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'nd_experiment_analysis_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'nd_experiment' => array(
|
|
|
+ 'table' => 'nd_experiment',
|
|
|
+ 'columns' => array(
|
|
|
+ 'nd_experiment_id' => 'nd_experiment_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'analysis' => array(
|
|
|
+ 'table' => 'analysis',
|
|
|
+ 'columns' => array(
|
|
|
+ 'analysis_id' => 'analysis_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_nd_experiment_contact()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'nd_experiment_contact' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'nd_experiment_contact' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_nd_experiment_contact() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'nd_experiment_contact',
|
|
|
+ 'fields' => array(
|
|
|
+ 'nd_experiment_contact_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'nd_experiment_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'contact_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'nd_experiment_contact_idx1' => array(
|
|
|
+ 0 => 'nd_experiment_id',
|
|
|
+ ),
|
|
|
+ 'nd_experiment_contact_idx2' => array(
|
|
|
+ 0 => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'nd_experiment_contact_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'nd_experiment' => array(
|
|
|
+ 'table' => 'nd_experiment',
|
|
|
+ 'columns' => array(
|
|
|
+ 'nd_experiment_id' => 'nd_experiment_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'contact' => array(
|
|
|
+ 'table' => 'contact',
|
|
|
+ 'columns' => array(
|
|
|
+ 'contact_id' => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_nd_experiment_dbxref()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'nd_experiment_dbxref' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'nd_experiment_dbxref' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_nd_experiment_dbxref() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'nd_experiment_dbxref',
|
|
|
+ 'fields' => array(
|
|
|
+ 'nd_experiment_dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'nd_experiment_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'nd_experiment_dbxref_idx1' => array(
|
|
|
+ 0 => 'nd_experiment_id',
|
|
|
+ ),
|
|
|
+ 'nd_experiment_dbxref_idx2' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'nd_experiment_dbxref_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'nd_experiment' => array(
|
|
|
+ 'table' => 'nd_experiment',
|
|
|
+ 'columns' => array(
|
|
|
+ 'nd_experiment_id' => 'nd_experiment_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_nd_experiment_genotype()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'nd_experiment_genotype' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'nd_experiment_genotype' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_nd_experiment_genotype() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'nd_experiment_genotype',
|
|
|
+ 'fields' => array(
|
|
|
+ 'nd_experiment_genotype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'nd_experiment_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'genotype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'nd_experiment_genotype_c1' => array(
|
|
|
+ 0 => 'nd_experiment_id',
|
|
|
+ 1 => 'genotype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'nd_experiment_genotype_idx1' => array(
|
|
|
+ 0 => 'nd_experiment_id',
|
|
|
+ ),
|
|
|
+ 'nd_experiment_genotype_idx2' => array(
|
|
|
+ 0 => 'genotype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'nd_experiment_genotype_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'nd_experiment' => array(
|
|
|
+ 'table' => 'nd_experiment',
|
|
|
+ 'columns' => array(
|
|
|
+ 'nd_experiment_id' => 'nd_experiment_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'genotype' => array(
|
|
|
+ 'table' => 'genotype',
|
|
|
+ 'columns' => array(
|
|
|
+ 'genotype_id' => 'genotype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_nd_experiment_phenotype()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'nd_experiment_phenotype' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'nd_experiment_phenotype' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_nd_experiment_phenotype() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'nd_experiment_phenotype',
|
|
|
+ 'fields' => array(
|
|
|
+ 'nd_experiment_phenotype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'nd_experiment_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'phenotype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'nd_experiment_phenotype_c1' => array(
|
|
|
+ 0 => 'nd_experiment_id',
|
|
|
+ 1 => 'phenotype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'nd_experiment_phenotype_idx1' => array(
|
|
|
+ 0 => 'nd_experiment_id',
|
|
|
+ ),
|
|
|
+ 'nd_experiment_phenotype_idx2' => array(
|
|
|
+ 0 => 'phenotype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'nd_experiment_phenotype_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'nd_experiment' => array(
|
|
|
+ 'table' => 'nd_experiment',
|
|
|
+ 'columns' => array(
|
|
|
+ 'nd_experiment_id' => 'nd_experiment_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'phenotype' => array(
|
|
|
+ 'table' => 'phenotype',
|
|
|
+ 'columns' => array(
|
|
|
+ 'phenotype_id' => 'phenotype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_nd_experiment_project()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'nd_experiment_project' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'nd_experiment_project' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_nd_experiment_project() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'nd_experiment_project',
|
|
|
+ 'fields' => array(
|
|
|
+ 'nd_experiment_project_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'project_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'nd_experiment_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'nd_experiment_project_c1' => array(
|
|
|
+ 0 => 'project_id',
|
|
|
+ 1 => 'nd_experiment_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'nd_experiment_project_idx1' => array(
|
|
|
+ 0 => 'project_id',
|
|
|
+ ),
|
|
|
+ 'nd_experiment_project_idx2' => array(
|
|
|
+ 0 => 'nd_experiment_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'nd_experiment_project_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'project' => array(
|
|
|
+ 'table' => 'project',
|
|
|
+ 'columns' => array(
|
|
|
+ 'project_id' => 'project_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'nd_experiment' => array(
|
|
|
+ 'table' => 'nd_experiment',
|
|
|
+ 'columns' => array(
|
|
|
+ 'nd_experiment_id' => 'nd_experiment_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_nd_experimentprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'nd_experimentprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'nd_experimentprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_nd_experimentprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'nd_experimentprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'nd_experimentprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'nd_experiment_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'nd_experimentprop_c1' => array(
|
|
|
+ 0 => 'nd_experiment_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'nd_experimentprop_idx1' => array(
|
|
|
+ 0 => 'nd_experiment_id',
|
|
|
+ ),
|
|
|
+ 'nd_experimentprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'nd_experimentprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'nd_experiment' => array(
|
|
|
+ 'table' => 'nd_experiment',
|
|
|
+ 'columns' => array(
|
|
|
+ 'nd_experiment_id' => 'nd_experiment_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_nd_experiment_protocol()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'nd_experiment_protocol' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'nd_experiment_protocol' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_nd_experiment_protocol() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'nd_experiment_protocol',
|
|
|
+ 'fields' => array(
|
|
|
+ 'nd_experiment_protocol_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'nd_experiment_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'nd_protocol_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'nd_experiment_protocol_idx1' => array(
|
|
|
+ 0 => 'nd_experiment_id',
|
|
|
+ ),
|
|
|
+ 'nd_experiment_protocol_idx2' => array(
|
|
|
+ 0 => 'nd_protocol_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'nd_experiment_protocol_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'nd_experiment' => array(
|
|
|
+ 'table' => 'nd_experiment',
|
|
|
+ 'columns' => array(
|
|
|
+ 'nd_experiment_id' => 'nd_experiment_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'nd_protocol' => array(
|
|
|
+ 'table' => 'nd_protocol',
|
|
|
+ 'columns' => array(
|
|
|
+ 'nd_protocol_id' => 'nd_protocol_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_nd_experiment_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'nd_experiment_pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'nd_experiment_pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_nd_experiment_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'nd_experiment_pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'nd_experiment_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'nd_experiment_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'nd_experiment_pub_c1' => array(
|
|
|
+ 0 => 'nd_experiment_id',
|
|
|
+ 1 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'nd_experiment_pub_idx1' => array(
|
|
|
+ 0 => 'nd_experiment_id',
|
|
|
+ ),
|
|
|
+ 'nd_experiment_pub_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'nd_experiment_pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'nd_experiment' => array(
|
|
|
+ 'table' => 'nd_experiment',
|
|
|
+ 'columns' => array(
|
|
|
+ 'nd_experiment_id' => 'nd_experiment_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_nd_experiment_stock()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'nd_experiment_stock' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'nd_experiment_stock' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_nd_experiment_stock() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'nd_experiment_stock',
|
|
|
+ 'fields' => array(
|
|
|
+ 'nd_experiment_stock_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'nd_experiment_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'stock_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'nd_experiment_stock_idx1' => array(
|
|
|
+ 0 => 'nd_experiment_id',
|
|
|
+ ),
|
|
|
+ 'nd_experiment_stock_idx2' => array(
|
|
|
+ 0 => 'stock_id',
|
|
|
+ ),
|
|
|
+ 'nd_experiment_stock_idx3' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'nd_experiment_stock_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'nd_experiment' => array(
|
|
|
+ 'table' => 'nd_experiment',
|
|
|
+ 'columns' => array(
|
|
|
+ 'nd_experiment_id' => 'nd_experiment_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'stock' => array(
|
|
|
+ 'table' => 'stock',
|
|
|
+ 'columns' => array(
|
|
|
+ 'stock_id' => 'stock_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'nd_experiment_stock_dbxref',
|
|
|
+ 1 => 'nd_experiment_stockprop',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_nd_experiment_stock_dbxref()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'nd_experiment_stock_dbxref' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'nd_experiment_stock_dbxref' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_nd_experiment_stock_dbxref() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'nd_experiment_stock_dbxref',
|
|
|
+ 'fields' => array(
|
|
|
+ 'nd_experiment_stock_dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'nd_experiment_stock_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'nd_experiment_stock_dbxref_idx1' => array(
|
|
|
+ 0 => 'nd_experiment_stock_id',
|
|
|
+ ),
|
|
|
+ 'nd_experiment_stock_dbxref_idx2' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'nd_experiment_stock_dbxref_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'nd_experiment_stock' => array(
|
|
|
+ 'table' => 'nd_experiment_stock',
|
|
|
+ 'columns' => array(
|
|
|
+ 'nd_experiment_stock_id' => 'nd_experiment_stock_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_nd_experiment_stockprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'nd_experiment_stockprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'nd_experiment_stockprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_nd_experiment_stockprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'nd_experiment_stockprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'nd_experiment_stockprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'nd_experiment_stock_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'nd_experiment_stockprop_c1' => array(
|
|
|
+ 0 => 'nd_experiment_stock_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'nd_experiment_stockprop_idx1' => array(
|
|
|
+ 0 => 'nd_experiment_stock_id',
|
|
|
+ ),
|
|
|
+ 'nd_experiment_stockprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'nd_experiment_stockprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'nd_experiment_stock' => array(
|
|
|
+ 'table' => 'nd_experiment_stock',
|
|
|
+ 'columns' => array(
|
|
|
+ 'nd_experiment_stock_id' => 'nd_experiment_stock_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_nd_geolocation()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'nd_geolocation' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'nd_geolocation' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_nd_geolocation() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'nd_geolocation',
|
|
|
+ 'fields' => array(
|
|
|
+ 'nd_geolocation_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'latitude' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'float',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'longitude' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'float',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'geodetic_datum' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '32',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'altitude' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'float',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'nd_geolocation_idx1' => array(
|
|
|
+ 0 => 'latitude',
|
|
|
+ ),
|
|
|
+ 'nd_geolocation_idx2' => array(
|
|
|
+ 0 => 'longitude',
|
|
|
+ ),
|
|
|
+ 'nd_geolocation_idx3' => array(
|
|
|
+ 0 => 'altitude',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'nd_geolocation_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'nd_experiment',
|
|
|
+ 1 => 'nd_geolocationprop',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_nd_geolocationprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'nd_geolocationprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'nd_geolocationprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_nd_geolocationprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'nd_geolocationprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'nd_geolocationprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'nd_geolocation_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'nd_geolocationprop_c1' => array(
|
|
|
+ 0 => 'nd_geolocation_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'nd_geolocationprop_idx1' => array(
|
|
|
+ 0 => 'nd_geolocation_id',
|
|
|
+ ),
|
|
|
+ 'nd_geolocationprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'nd_geolocationprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'nd_geolocation' => array(
|
|
|
+ 'table' => 'nd_geolocation',
|
|
|
+ 'columns' => array(
|
|
|
+ 'nd_geolocation_id' => 'nd_geolocation_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_nd_protocol()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'nd_protocol' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'nd_protocol' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_nd_protocol() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'nd_protocol',
|
|
|
+ 'fields' => array(
|
|
|
+ 'nd_protocol_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'nd_protocol_idx1' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'name' => array(
|
|
|
+ 0 => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'nd_protocol_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'nd_experiment_protocol',
|
|
|
+ 1 => 'nd_protocolprop',
|
|
|
+ 2 => 'nd_protocol_reagent',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_nd_protocolprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'nd_protocolprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'nd_protocolprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_nd_protocolprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'nd_protocolprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'nd_protocolprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'nd_protocol_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'nd_protocolprop_c1' => array(
|
|
|
+ 0 => 'nd_protocol_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'nd_protocolprop_idx1' => array(
|
|
|
+ 0 => 'nd_protocol_id',
|
|
|
+ ),
|
|
|
+ 'nd_protocolprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'nd_protocolprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'nd_protocol' => array(
|
|
|
+ 'table' => 'nd_protocol',
|
|
|
+ 'columns' => array(
|
|
|
+ 'nd_protocol_id' => 'nd_protocol_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_nd_protocol_reagent()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'nd_protocol_reagent' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'nd_protocol_reagent' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_nd_protocol_reagent() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'nd_protocol_reagent',
|
|
|
+ 'fields' => array(
|
|
|
+ 'nd_protocol_reagent_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'nd_protocol_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'reagent_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'nd_protocol_reagent_idx1' => array(
|
|
|
+ 0 => 'nd_protocol_id',
|
|
|
+ ),
|
|
|
+ 'nd_protocol_reagent_idx2' => array(
|
|
|
+ 0 => 'reagent_id',
|
|
|
+ ),
|
|
|
+ 'nd_protocol_reagent_idx3' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'nd_protocol_reagent_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'nd_protocol' => array(
|
|
|
+ 'table' => 'nd_protocol',
|
|
|
+ 'columns' => array(
|
|
|
+ 'nd_protocol_id' => 'nd_protocol_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'nd_reagent' => array(
|
|
|
+ 'table' => 'nd_reagent',
|
|
|
+ 'columns' => array(
|
|
|
+ 'reagent_id' => 'nd_reagent_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_nd_reagent()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'nd_reagent' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'nd_reagent' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_nd_reagent() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'nd_reagent',
|
|
|
+ 'fields' => array(
|
|
|
+ 'nd_reagent_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '80',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'nd_reagent_idx1' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ 'nd_reagent_idx2' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'nd_reagent_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'feature' => array(
|
|
|
+ 'table' => 'feature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_id' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'nd_protocol_reagent',
|
|
|
+ 1 => 'nd_reagentprop',
|
|
|
+ 2 => 'nd_reagent_relationship',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_nd_reagentprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'nd_reagentprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'nd_reagentprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_nd_reagentprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'nd_reagentprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'nd_reagentprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'nd_reagent_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'nd_reagentprop_c1' => array(
|
|
|
+ 0 => 'nd_reagent_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'nd_reagentprop_idx1' => array(
|
|
|
+ 0 => 'nd_reagent_id',
|
|
|
+ ),
|
|
|
+ 'nd_reagentprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'nd_reagentprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'nd_reagent' => array(
|
|
|
+ 'table' => 'nd_reagent',
|
|
|
+ 'columns' => array(
|
|
|
+ 'nd_reagent_id' => 'nd_reagent_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_nd_reagent_relationship()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'nd_reagent_relationship' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'nd_reagent_relationship' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_nd_reagent_relationship() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'nd_reagent_relationship',
|
|
|
+ 'fields' => array(
|
|
|
+ 'nd_reagent_relationship_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'subject_reagent_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'object_reagent_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'nd_reagent_relationship_idx1' => array(
|
|
|
+ 0 => 'subject_reagent_id',
|
|
|
+ ),
|
|
|
+ 'nd_reagent_relationship_idx2' => array(
|
|
|
+ 0 => 'object_reagent_id',
|
|
|
+ ),
|
|
|
+ 'nd_reagent_relationship_idx3' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'nd_reagent_relationship_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'nd_reagent' => array(
|
|
|
+ 'table' => 'nd_reagent',
|
|
|
+ 'columns' => array(
|
|
|
+ 'subject_reagent_id' => 'nd_reagent_id',
|
|
|
+ 'object_reagent_id' => 'nd_reagent_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_organism()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'organism' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'organism' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_organism() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'organism',
|
|
|
+ 'fields' => array(
|
|
|
+ 'organism_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'abbreviation' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'genus' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'species' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'common_name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'infraspecific_name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '1024',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'comment' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'organism_c1' => array(
|
|
|
+ 0 => 'genus',
|
|
|
+ 1 => 'species',
|
|
|
+ 2 => 'type_id',
|
|
|
+ 3 => 'infraspecific_name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'organism_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'analysis_organism',
|
|
|
+ 1 => 'biomaterial',
|
|
|
+ 2 => 'cell_line',
|
|
|
+ 3 => 'feature',
|
|
|
+ 4 => 'featuremap_organism',
|
|
|
+ 5 => 'library',
|
|
|
+ 6 => 'organism_cvterm',
|
|
|
+ 7 => 'organism_dbxref',
|
|
|
+ 8 => 'organismprop',
|
|
|
+ 9 => 'organism_pub',
|
|
|
+ 10 => 'organism_relationship',
|
|
|
+ 12 => 'phenotype_comparison',
|
|
|
+ 13 => 'phylonode_organism',
|
|
|
+ 14 => 'stock',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_organism_cvterm()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'organism_cvterm' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'organism_cvterm' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_organism_cvterm() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'organism_cvterm',
|
|
|
+ 'fields' => array(
|
|
|
+ 'organism_cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'organism_cvterm_c1' => array(
|
|
|
+ 0 => 'organism_id',
|
|
|
+ 1 => 'cvterm_id',
|
|
|
+ 2 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'organism_cvterm_idx1' => array(
|
|
|
+ 0 => 'organism_id',
|
|
|
+ ),
|
|
|
+ 'organism_cvterm_idx2' => array(
|
|
|
+ 0 => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'organism_cvterm_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'organism' => array(
|
|
|
+ 'table' => 'organism',
|
|
|
+ 'columns' => array(
|
|
|
+ 'organism_id' => 'organism_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cvterm_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'organism_cvtermprop',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_organism_cvtermprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'organism_cvtermprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'organism_cvtermprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_organism_cvtermprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'organism_cvtermprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'organism_cvtermprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'organism_cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'organism_cvtermprop_c1' => array(
|
|
|
+ 0 => 'organism_cvterm_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'organism_cvtermprop_idx1' => array(
|
|
|
+ 0 => 'organism_cvterm_id',
|
|
|
+ ),
|
|
|
+ 'organism_cvtermprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'organism_cvtermprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'organism_cvterm' => array(
|
|
|
+ 'table' => 'organism_cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'organism_cvterm_id' => 'organism_cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_organism_dbxref()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'organism_dbxref' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'organism_dbxref' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_organism_dbxref() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'organism_dbxref',
|
|
|
+ 'fields' => array(
|
|
|
+ 'organism_dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'organism_dbxref_c1' => array(
|
|
|
+ 0 => 'organism_id',
|
|
|
+ 1 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'organism_dbxref_idx1' => array(
|
|
|
+ 0 => 'organism_id',
|
|
|
+ ),
|
|
|
+ 'organism_dbxref_idx2' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'organism_dbxref_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'organism' => array(
|
|
|
+ 'table' => 'organism',
|
|
|
+ 'columns' => array(
|
|
|
+ 'organism_id' => 'organism_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_organism_feature_count()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'organism_feature_count' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'organism_feature_count' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_organism_feature_count() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'organism_feature_count',
|
|
|
+ 'fields' => array(
|
|
|
+ 'organism_id' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'genus' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'species' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'common_name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'num_features' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_type' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'organism_feature_count_idx1' => array(
|
|
|
+ 0 => 'organism_id',
|
|
|
+ ),
|
|
|
+ 'organism_feature_count_idx2' => array(
|
|
|
+ 0 => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ 'organism_feature_count_idx3' => array(
|
|
|
+ 0 => 'feature_type',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_organismprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'organismprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'organismprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_organismprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'organismprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'organismprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'organismprop_c1' => array(
|
|
|
+ 0 => 'organism_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'organismprop_idx1' => array(
|
|
|
+ 0 => 'organism_id',
|
|
|
+ ),
|
|
|
+ 'organismprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'organismprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'organism' => array(
|
|
|
+ 'table' => 'organism',
|
|
|
+ 'columns' => array(
|
|
|
+ 'organism_id' => 'organism_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'organismprop_pub',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_organismprop_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'organismprop_pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'organismprop_pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_organismprop_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'organismprop_pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'organismprop_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'organismprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'organismprop_pub_c1' => array(
|
|
|
+ 0 => 'organismprop_id',
|
|
|
+ 1 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'organismprop_pub_idx1' => array(
|
|
|
+ 0 => 'organismprop_id',
|
|
|
+ ),
|
|
|
+ 'organismprop_pub_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'organismprop_pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'organismprop' => array(
|
|
|
+ 'table' => 'organismprop',
|
|
|
+ 'columns' => array(
|
|
|
+ 'organismprop_id' => 'organismprop_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_organism_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'organism_pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'organism_pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_organism_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'organism_pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'organism_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'organism_pub_c1' => array(
|
|
|
+ 0 => 'organism_id',
|
|
|
+ 1 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'organism_pub_idx1' => array(
|
|
|
+ 0 => 'organism_id',
|
|
|
+ ),
|
|
|
+ 'organism_pub_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'organism_pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'organism' => array(
|
|
|
+ 'table' => 'organism',
|
|
|
+ 'columns' => array(
|
|
|
+ 'organism_id' => 'organism_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_organism_relationship()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'organism_relationship' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'organism_relationship' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_organism_relationship() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'organism_relationship',
|
|
|
+ 'fields' => array(
|
|
|
+ 'organism_relationship_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'organism_relationship_c1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ 1 => 'object_id',
|
|
|
+ 2 => 'type_id',
|
|
|
+ 3 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'organism_relationship_idx1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ ),
|
|
|
+ 'organism_relationship_idx2' => array(
|
|
|
+ 0 => 'object_id',
|
|
|
+ ),
|
|
|
+ 'organism_relationship_idx3' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'organism_relationship_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'organism' => array(
|
|
|
+ 'table' => 'organism',
|
|
|
+ 'columns' => array(
|
|
|
+ 'object_id' => 'organism_id',
|
|
|
+ 'subject_id' => 'organism_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_phendesc()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'phendesc' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'phendesc' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_phendesc() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'phendesc',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phendesc_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'genotype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'environment_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'phendesc_c1' => array(
|
|
|
+ 0 => 'genotype_id',
|
|
|
+ 1 => 'environment_id',
|
|
|
+ 2 => 'type_id',
|
|
|
+ 3 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'phendesc_idx1' => array(
|
|
|
+ 0 => 'genotype_id',
|
|
|
+ ),
|
|
|
+ 'phendesc_idx2' => array(
|
|
|
+ 0 => 'environment_id',
|
|
|
+ ),
|
|
|
+ 'phendesc_idx3' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'phendesc_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'genotype' => array(
|
|
|
+ 'table' => 'genotype',
|
|
|
+ 'columns' => array(
|
|
|
+ 'genotype_id' => 'genotype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'environment' => array(
|
|
|
+ 'table' => 'environment',
|
|
|
+ 'columns' => array(
|
|
|
+ 'environment_id' => 'environment_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_phenotype()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'phenotype' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'phenotype' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_phenotype() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'phenotype',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phenotype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'uniquename' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'observable_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'attr_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'cvalue_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'assay_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'phenotype_c1' => array(
|
|
|
+ 0 => 'uniquename',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'phenotype_idx1' => array(
|
|
|
+ 0 => 'cvalue_id',
|
|
|
+ ),
|
|
|
+ 'phenotype_idx2' => array(
|
|
|
+ 0 => 'observable_id',
|
|
|
+ ),
|
|
|
+ 'phenotype_idx3' => array(
|
|
|
+ 0 => 'attr_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'phenotype_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'observable_id' => 'cvterm_id',
|
|
|
+ 'attr_id' => 'cvterm_id',
|
|
|
+ 'cvalue_id' => 'cvterm_id',
|
|
|
+ 'assay_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'feature_phenotype',
|
|
|
+ 1 => 'nd_experiment_phenotype',
|
|
|
+ 2 => 'phenotype_comparison',
|
|
|
+ 4 => 'phenotype_cvterm',
|
|
|
+ 5 => 'phenotypeprop',
|
|
|
+ 6 => 'phenstatement',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_phenotype_comparison()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'phenotype_comparison' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'phenotype_comparison' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_phenotype_comparison() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'phenotype_comparison',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phenotype_comparison_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'genotype1_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'environment1_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'genotype2_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'environment2_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'phenotype1_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'phenotype2_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'phenotype_comparison_c1' => array(
|
|
|
+ 0 => 'genotype1_id',
|
|
|
+ 1 => 'environment1_id',
|
|
|
+ 2 => 'genotype2_id',
|
|
|
+ 3 => 'environment2_id',
|
|
|
+ 4 => 'phenotype1_id',
|
|
|
+ 5 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'phenotype_comparison_idx1' => array(
|
|
|
+ 0 => 'genotype1_id',
|
|
|
+ ),
|
|
|
+ 'phenotype_comparison_idx2' => array(
|
|
|
+ 0 => 'genotype2_id',
|
|
|
+ ),
|
|
|
+ 'phenotype_comparison_idx4' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'phenotype_comparison_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'genotype' => array(
|
|
|
+ 'table' => 'genotype',
|
|
|
+ 'columns' => array(
|
|
|
+ 'genotype1_id' => 'genotype_id',
|
|
|
+ 'genotype2_id' => 'genotype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'environment' => array(
|
|
|
+ 'table' => 'environment',
|
|
|
+ 'columns' => array(
|
|
|
+ 'environment1_id' => 'environment_id',
|
|
|
+ 'environment2_id' => 'environment_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'phenotype' => array(
|
|
|
+ 'table' => 'phenotype',
|
|
|
+ 'columns' => array(
|
|
|
+ 'phenotype1_id' => 'phenotype_id',
|
|
|
+ 'phenotype2_id' => 'phenotype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'organism' => array(
|
|
|
+ 'table' => 'organism',
|
|
|
+ 'columns' => array(
|
|
|
+ 'organism_id' => 'organism_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'phenotype_comparison_cvterm',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_phenotype_comparison_cvterm()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'phenotype_comparison_cvterm' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'phenotype_comparison_cvterm' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_phenotype_comparison_cvterm() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'phenotype_comparison_cvterm',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phenotype_comparison_cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'phenotype_comparison_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'phenotype_comparison_cvterm_c1' => array(
|
|
|
+ 0 => 'phenotype_comparison_id',
|
|
|
+ 1 => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'phenotype_comparison_cvterm_idx1' => array(
|
|
|
+ 0 => 'phenotype_comparison_id',
|
|
|
+ ),
|
|
|
+ 'phenotype_comparison_cvterm_idx2' => array(
|
|
|
+ 0 => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'phenotype_comparison_cvterm_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'phenotype_comparison' => array(
|
|
|
+ 'table' => 'phenotype_comparison',
|
|
|
+ 'columns' => array(
|
|
|
+ 'phenotype_comparison_id' => 'phenotype_comparison_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cvterm_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_phenotype_cvterm()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'phenotype_cvterm' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'phenotype_cvterm' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_phenotype_cvterm() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'phenotype_cvterm',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phenotype_cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'phenotype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'phenotype_cvterm_c1' => array(
|
|
|
+ 0 => 'phenotype_id',
|
|
|
+ 1 => 'cvterm_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'phenotype_cvterm_idx1' => array(
|
|
|
+ 0 => 'phenotype_id',
|
|
|
+ ),
|
|
|
+ 'phenotype_cvterm_idx2' => array(
|
|
|
+ 0 => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'phenotype_cvterm_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'phenotype' => array(
|
|
|
+ 'table' => 'phenotype',
|
|
|
+ 'columns' => array(
|
|
|
+ 'phenotype_id' => 'phenotype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cvterm_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_phenotypeprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'phenotypeprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'phenotypeprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_phenotypeprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'phenotypeprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phenotypeprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'phenotype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'phenotypeprop_c1' => array(
|
|
|
+ 0 => 'phenotype_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'phenotypeprop_idx1' => array(
|
|
|
+ 0 => 'phenotype_id',
|
|
|
+ ),
|
|
|
+ 'phenotypeprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'phenotypeprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'phenotype' => array(
|
|
|
+ 'table' => 'phenotype',
|
|
|
+ 'columns' => array(
|
|
|
+ 'phenotype_id' => 'phenotype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_phenstatement()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'phenstatement' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'phenstatement' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_phenstatement() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'phenstatement',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phenstatement_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'genotype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'environment_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'phenotype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'phenstatement_c1' => array(
|
|
|
+ 0 => 'genotype_id',
|
|
|
+ 1 => 'phenotype_id',
|
|
|
+ 2 => 'environment_id',
|
|
|
+ 3 => 'type_id',
|
|
|
+ 4 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'phenstatement_idx1' => array(
|
|
|
+ 0 => 'genotype_id',
|
|
|
+ ),
|
|
|
+ 'phenstatement_idx2' => array(
|
|
|
+ 0 => 'phenotype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'phenstatement_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'genotype' => array(
|
|
|
+ 'table' => 'genotype',
|
|
|
+ 'columns' => array(
|
|
|
+ 'genotype_id' => 'genotype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'environment' => array(
|
|
|
+ 'table' => 'environment',
|
|
|
+ 'columns' => array(
|
|
|
+ 'environment_id' => 'environment_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'phenotype' => array(
|
|
|
+ 'table' => 'phenotype',
|
|
|
+ 'columns' => array(
|
|
|
+ 'phenotype_id' => 'phenotype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_phylonode()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'phylonode' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'phylonode' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_phylonode() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'phylonode',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phylonode_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'phylotree_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'parent_phylonode_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'left_idx' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'right_idx' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'label' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'distance' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'float',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'parent_phylonode_id' => array(
|
|
|
+ 0 => 'parent_phylonode_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'phylotree_id_left_idx' => array(
|
|
|
+ 0 => 'phylotree_id',
|
|
|
+ 1 => 'left_idx',
|
|
|
+ ),
|
|
|
+ 'phylotree_id_right_idx' => array(
|
|
|
+ 0 => 'phylotree_id',
|
|
|
+ 1 => 'right_idx',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'phylonode_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'phylotree' => array(
|
|
|
+ 'table' => 'phylotree',
|
|
|
+ 'columns' => array(
|
|
|
+ 'phylotree_id' => 'phylotree_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'phylonode' => array(
|
|
|
+ 'table' => 'phylonode',
|
|
|
+ 'columns' => array(
|
|
|
+ 'parent_phylonode_id' => 'phylonode_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'feature' => array(
|
|
|
+ 'table' => 'feature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_id' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'phylonode',
|
|
|
+ 1 => 'phylonode_dbxref',
|
|
|
+ 2 => 'phylonode_organism',
|
|
|
+ 3 => 'phylonodeprop',
|
|
|
+ 4 => 'phylonode_pub',
|
|
|
+ 5 => 'phylonode_relationship',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_phylonode_dbxref()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'phylonode_dbxref' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'phylonode_dbxref' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_phylonode_dbxref() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'phylonode_dbxref',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phylonode_dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'phylonode_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'phylonode_dbxref_idx1' => array(
|
|
|
+ 0 => 'phylonode_id',
|
|
|
+ ),
|
|
|
+ 'phylonode_dbxref_idx2' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'phylonode_id_dbxref_id' => array(
|
|
|
+ 0 => 'phylonode_id',
|
|
|
+ 1 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'phylonode_dbxref_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'phylonode' => array(
|
|
|
+ 'table' => 'phylonode',
|
|
|
+ 'columns' => array(
|
|
|
+ 'phylonode_id' => 'phylonode_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_phylonode_organism()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'phylonode_organism' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'phylonode_organism' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_phylonode_organism() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'phylonode_organism',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phylonode_organism_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'phylonode_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'phylonode_organism_idx1' => array(
|
|
|
+ 0 => 'phylonode_id',
|
|
|
+ ),
|
|
|
+ 'phylonode_organism_idx2' => array(
|
|
|
+ 0 => 'organism_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'phylonode_id' => array(
|
|
|
+ 0 => 'phylonode_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'phylonode_organism_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'phylonode' => array(
|
|
|
+ 'table' => 'phylonode',
|
|
|
+ 'columns' => array(
|
|
|
+ 'phylonode_id' => 'phylonode_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'organism' => array(
|
|
|
+ 'table' => 'organism',
|
|
|
+ 'columns' => array(
|
|
|
+ 'organism_id' => 'organism_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_phylonodeprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'phylonodeprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'phylonodeprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_phylonodeprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'phylonodeprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phylonodeprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'phylonode_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'phylonodeprop_idx1' => array(
|
|
|
+ 0 => 'phylonode_id',
|
|
|
+ ),
|
|
|
+ 'phylonodeprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'phylonode_id_type_id_value_rank' => array(
|
|
|
+ 0 => 'phylonode_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'value',
|
|
|
+ 3 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'phylonodeprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'phylonode' => array(
|
|
|
+ 'table' => 'phylonode',
|
|
|
+ 'columns' => array(
|
|
|
+ 'phylonode_id' => 'phylonode_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_phylonode_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'phylonode_pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'phylonode_pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_phylonode_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'phylonode_pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phylonode_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'phylonode_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'phylonode_pub_idx1' => array(
|
|
|
+ 0 => 'phylonode_id',
|
|
|
+ ),
|
|
|
+ 'phylonode_pub_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'phylonode_id_pub_id' => array(
|
|
|
+ 0 => 'phylonode_id',
|
|
|
+ 1 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'phylonode_pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'phylonode' => array(
|
|
|
+ 'table' => 'phylonode',
|
|
|
+ 'columns' => array(
|
|
|
+ 'phylonode_id' => 'phylonode_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_phylonode_relationship()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'phylonode_relationship' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'phylonode_relationship' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_phylonode_relationship() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'phylonode_relationship',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phylonode_relationship_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'phylotree_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'phylonode_relationship_idx1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ ),
|
|
|
+ 'phylonode_relationship_idx2' => array(
|
|
|
+ 0 => 'object_id',
|
|
|
+ ),
|
|
|
+ 'phylonode_relationship_idx3' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'phylonode_relationship_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'subject_id_object_id_type_id' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ 1 => 'object_id',
|
|
|
+ 2 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'phylonode' => array(
|
|
|
+ 'table' => 'phylonode',
|
|
|
+ 'columns' => array(
|
|
|
+ 'subject_id' => 'phylonode_id',
|
|
|
+ 'object_id' => 'phylonode_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'phylotree' => array(
|
|
|
+ 'table' => 'phylotree',
|
|
|
+ 'columns' => array(
|
|
|
+ 'phylotree_id' => 'phylotree_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_phylotree()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'phylotree' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'phylotree' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_phylotree() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'phylotree',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phylotree_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'analysis_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'comment' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'phylotree_idx1' => array(
|
|
|
+ 0 => 'phylotree_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'phylotree_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'analysis' => array(
|
|
|
+ 'table' => 'analysis',
|
|
|
+ 'columns' => array(
|
|
|
+ 'analysis_id' => 'analysis_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'phylonode',
|
|
|
+ 1 => 'phylonode_relationship',
|
|
|
+ 2 => 'phylotreeprop',
|
|
|
+ 3 => 'phylotree_pub',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_phylotreeprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'phylotreeprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'phylotreeprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_phylotreeprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'phylotreeprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phylotreeprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'phylotree_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'phylotreeprop_c1' => array(
|
|
|
+ 0 => 'phylotree_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'phylotreeprop_idx1' => array(
|
|
|
+ 0 => 'phylotree_id',
|
|
|
+ ),
|
|
|
+ 'phylotreeprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'phylotreeprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'phylotree' => array(
|
|
|
+ 'table' => 'phylotree',
|
|
|
+ 'columns' => array(
|
|
|
+ 'phylotree_id' => 'phylotree_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_phylotree_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'phylotree_pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'phylotree_pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_phylotree_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'phylotree_pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phylotree_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'phylotree_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'phylotree_pub_idx1' => array(
|
|
|
+ 0 => 'phylotree_id',
|
|
|
+ ),
|
|
|
+ 'phylotree_pub_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'phylotree_id_pub_id' => array(
|
|
|
+ 0 => 'phylotree_id',
|
|
|
+ 1 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'phylotree_pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'phylotree' => array(
|
|
|
+ 'table' => 'phylotree',
|
|
|
+ 'columns' => array(
|
|
|
+ 'phylotree_id' => 'phylotree_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_project()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'project' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'project' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_project() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'project',
|
|
|
+ 'fields' => array(
|
|
|
+ 'project_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'project_c1' => array(
|
|
|
+ 0 => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'project_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'assay_project',
|
|
|
+ 1 => 'nd_experiment_project',
|
|
|
+ 2 => 'project_analysis',
|
|
|
+ 3 => 'project_contact',
|
|
|
+ 4 => 'project_dbxref',
|
|
|
+ 5 => 'project_feature',
|
|
|
+ 6 => 'projectprop',
|
|
|
+ 7 => 'project_pub',
|
|
|
+ 8 => 'project_relationship',
|
|
|
+ 10 => 'project_stock',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_project_analysis()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'project_analysis' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'project_analysis' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_project_analysis() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'project_analysis',
|
|
|
+ 'fields' => array(
|
|
|
+ 'project_analysis_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'project_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'analysis_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'project_analysis_c1' => array(
|
|
|
+ 0 => 'project_id',
|
|
|
+ 1 => 'analysis_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'project_analysis_idx1' => array(
|
|
|
+ 0 => 'project_id',
|
|
|
+ ),
|
|
|
+ 'project_analysis_idx2' => array(
|
|
|
+ 0 => 'analysis_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'project_analysis_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'project' => array(
|
|
|
+ 'table' => 'project',
|
|
|
+ 'columns' => array(
|
|
|
+ 'project_id' => 'project_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'analysis' => array(
|
|
|
+ 'table' => 'analysis',
|
|
|
+ 'columns' => array(
|
|
|
+ 'analysis_id' => 'analysis_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_project_contact()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'project_contact' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'project_contact' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_project_contact() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'project_contact',
|
|
|
+ 'fields' => array(
|
|
|
+ 'project_contact_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'project_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'contact_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'project_contact_c1' => array(
|
|
|
+ 0 => 'project_id',
|
|
|
+ 1 => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'project_contact_idx1' => array(
|
|
|
+ 0 => 'project_id',
|
|
|
+ ),
|
|
|
+ 'project_contact_idx2' => array(
|
|
|
+ 0 => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'project_contact_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'project' => array(
|
|
|
+ 'table' => 'project',
|
|
|
+ 'columns' => array(
|
|
|
+ 'project_id' => 'project_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'contact' => array(
|
|
|
+ 'table' => 'contact',
|
|
|
+ 'columns' => array(
|
|
|
+ 'contact_id' => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_project_dbxref()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'project_dbxref' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'project_dbxref' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_project_dbxref() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'project_dbxref',
|
|
|
+ 'fields' => array(
|
|
|
+ 'project_dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'project_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'is_current' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 'ru',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'project_dbxref_c1' => array(
|
|
|
+ 0 => 'project_id',
|
|
|
+ 1 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'project_dbxref_idx1' => array(
|
|
|
+ 0 => 'project_id',
|
|
|
+ ),
|
|
|
+ 'project_dbxref_idx2' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'project_dbxref_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'project' => array(
|
|
|
+ 'table' => 'project',
|
|
|
+ 'columns' => array(
|
|
|
+ 'project_id' => 'project_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_project_feature()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'project_feature' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'project_feature' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_project_feature() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'project_feature',
|
|
|
+ 'fields' => array(
|
|
|
+ 'project_feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'project_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'project_feature_c1' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ 1 => 'project_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'project_feature_idx1' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ ),
|
|
|
+ 'project_feature_idx2' => array(
|
|
|
+ 0 => 'project_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'project_feature_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'feature' => array(
|
|
|
+ 'table' => 'feature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_id' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'project' => array(
|
|
|
+ 'table' => 'project',
|
|
|
+ 'columns' => array(
|
|
|
+ 'project_id' => 'project_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_projectprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'projectprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'projectprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_projectprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'projectprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'projectprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'project_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'projectprop_c1' => array(
|
|
|
+ 0 => 'project_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'projectprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'project' => array(
|
|
|
+ 'table' => 'project',
|
|
|
+ 'columns' => array(
|
|
|
+ 'project_id' => 'project_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_project_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'project_pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'project_pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_project_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'project_pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'project_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'project_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'project_pub_c1' => array(
|
|
|
+ 0 => 'project_id',
|
|
|
+ 1 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'project_pub_idx1' => array(
|
|
|
+ 0 => 'project_id',
|
|
|
+ ),
|
|
|
+ 'project_pub_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'project_pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'project' => array(
|
|
|
+ 'table' => 'project',
|
|
|
+ 'columns' => array(
|
|
|
+ 'project_id' => 'project_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_project_relationship()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'project_relationship' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'project_relationship' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_project_relationship() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'project_relationship',
|
|
|
+ 'fields' => array(
|
|
|
+ 'project_relationship_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'subject_project_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'object_project_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'project_relationship_c1' => array(
|
|
|
+ 0 => 'subject_project_id',
|
|
|
+ 1 => 'object_project_id',
|
|
|
+ 2 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'project_relationship_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'project' => array(
|
|
|
+ 'table' => 'project',
|
|
|
+ 'columns' => array(
|
|
|
+ 'subject_project_id' => 'project_id',
|
|
|
+ 'object_project_id' => 'project_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_project_stock()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'project_stock' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'project_stock' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_project_stock() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'project_stock',
|
|
|
+ 'fields' => array(
|
|
|
+ 'project_stock_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'stock_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'project_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'project_stock_c1' => array(
|
|
|
+ 0 => 'stock_id',
|
|
|
+ 1 => 'project_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'project_stock_idx1' => array(
|
|
|
+ 0 => 'stock_id',
|
|
|
+ ),
|
|
|
+ 'project_stock_idx2' => array(
|
|
|
+ 0 => 'project_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'project_stock_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'stock' => array(
|
|
|
+ 'table' => 'stock',
|
|
|
+ 'columns' => array(
|
|
|
+ 'stock_id' => 'stock_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'project' => array(
|
|
|
+ 'table' => 'project',
|
|
|
+ 'columns' => array(
|
|
|
+ 'project_id' => 'project_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_protocol()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'protocol' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'protocol' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_protocol() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'protocol',
|
|
|
+ 'fields' => array(
|
|
|
+ 'protocol_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'uri' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'protocoldescription' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'hardwaredescription' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'softwaredescription' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'protocol_c1' => array(
|
|
|
+ 0 => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'protocol_idx1' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ 'protocol_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ 'protocol_idx3' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'protocol_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'acquisition',
|
|
|
+ 1 => 'arraydesign',
|
|
|
+ 2 => 'assay',
|
|
|
+ 3 => 'protocolparam',
|
|
|
+ 4 => 'quantification',
|
|
|
+ 5 => 'treatment',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_protocolparam()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'protocolparam' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'protocolparam' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_protocolparam() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'protocolparam',
|
|
|
+ 'fields' => array(
|
|
|
+ 'protocolparam_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'protocol_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'datatype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'unittype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'protocolparam_idx1' => array(
|
|
|
+ 0 => 'protocol_id',
|
|
|
+ ),
|
|
|
+ 'protocolparam_idx2' => array(
|
|
|
+ 0 => 'datatype_id',
|
|
|
+ ),
|
|
|
+ 'protocolparam_idx3' => array(
|
|
|
+ 0 => 'unittype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'protocolparam_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'protocol' => array(
|
|
|
+ 'table' => 'protocol',
|
|
|
+ 'columns' => array(
|
|
|
+ 'protocol_id' => 'protocol_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'datatype_id' => 'cvterm_id',
|
|
|
+ 'unittype_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'title' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'volumetitle' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'volume' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'series_name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'issue' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'pyear' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'pages' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'miniref' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'uniquename' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'is_obsolete' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ 'default' => FALSE,
|
|
|
+ ),
|
|
|
+ 'publisher' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'pubplace' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'pub_c1' => array(
|
|
|
+ 0 => 'uniquename',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'pub_idx1' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'analysis_pub',
|
|
|
+ 1 => 'cell_line_cvterm',
|
|
|
+ 2 => 'cell_line_feature',
|
|
|
+ 3 => 'cell_line_library',
|
|
|
+ 4 => 'cell_lineprop_pub',
|
|
|
+ 5 => 'cell_line_pub',
|
|
|
+ 6 => 'cell_line_synonym',
|
|
|
+ 7 => 'expression_pub',
|
|
|
+ 8 => 'feature_cvterm',
|
|
|
+ 9 => 'feature_cvterm_pub',
|
|
|
+ 10 => 'feature_expression',
|
|
|
+ 11 => 'featureloc_pub',
|
|
|
+ 12 => 'featuremap_pub',
|
|
|
+ 13 => 'featureprop_pub',
|
|
|
+ 14 => 'feature_pub',
|
|
|
+ 15 => 'feature_relationshipprop_pub',
|
|
|
+ 16 => 'feature_relationship_pub',
|
|
|
+ 17 => 'feature_synonym',
|
|
|
+ 18 => 'library_cvterm',
|
|
|
+ 19 => 'library_expression',
|
|
|
+ 20 => 'libraryprop_pub',
|
|
|
+ 21 => 'library_pub',
|
|
|
+ 22 => 'library_relationship_pub',
|
|
|
+ 23 => 'library_synonym',
|
|
|
+ 24 => 'nd_experiment_pub',
|
|
|
+ 25 => 'organism_cvterm',
|
|
|
+ 26 => 'organismprop_pub',
|
|
|
+ 27 => 'organism_pub',
|
|
|
+ 28 => 'phendesc',
|
|
|
+ 29 => 'phenotype_comparison',
|
|
|
+ 30 => 'phenotype_comparison_cvterm',
|
|
|
+ 31 => 'phenstatement',
|
|
|
+ 32 => 'phylonode_pub',
|
|
|
+ 33 => 'phylotree_pub',
|
|
|
+ 34 => 'project_pub',
|
|
|
+ 35 => 'protocol',
|
|
|
+ 36 => 'pubauthor',
|
|
|
+ 37 => 'pub_dbxref',
|
|
|
+ 38 => 'pubprop',
|
|
|
+ 39 => 'pub_relationship',
|
|
|
+ 41 => 'stock_cvterm',
|
|
|
+ 42 => 'stockprop_pub',
|
|
|
+ 43 => 'stock_pub',
|
|
|
+ 44 => 'stock_relationship_cvterm',
|
|
|
+ 45 => 'stock_relationship_pub',
|
|
|
+ 46 => 'study',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_pubauthor()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'pubauthor' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'pubauthor' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_pubauthor() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'pubauthor',
|
|
|
+ 'fields' => array(
|
|
|
+ 'pubauthor_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'editor' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ 'default' => FALSE,
|
|
|
+ ),
|
|
|
+ 'surname' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '100',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'givennames' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '100',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'suffix' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '100',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'pubauthor_c1' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ 1 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'pubauthor_contact_idx1' => array(
|
|
|
+ 0 => 'pubauthor_id',
|
|
|
+ ),
|
|
|
+ 'pubauthor_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'pubauthor_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'pubauthor_contact',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_pubauthor_contact()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'pubauthor_contact' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'pubauthor_contact' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_pubauthor_contact() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'pubauthor_contact',
|
|
|
+ 'fields' => array(
|
|
|
+ 'pubauthor_contact_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'contact_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pubauthor_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'pubauthor_contact_c1' => array(
|
|
|
+ 0 => 'contact_id',
|
|
|
+ 1 => 'pubauthor_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'pubauthor_contact_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'pubauthor' => array(
|
|
|
+ 'table' => 'pubauthor',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pubauthor_id' => 'pubauthor_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'contact' => array(
|
|
|
+ 'table' => 'contact',
|
|
|
+ 'columns' => array(
|
|
|
+ 'contact_id' => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_pub_dbxref()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'pub_dbxref' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'pub_dbxref' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_pub_dbxref() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'pub_dbxref',
|
|
|
+ 'fields' => array(
|
|
|
+ 'pub_dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'is_current' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 'ru',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'pub_dbxref_c1' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ 1 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'pub_dbxref_idx1' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ 'pub_dbxref_idx2' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'pub_dbxref_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_pubprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'pubprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'pubprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_pubprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'pubprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'pubprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'pubprop_c1' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'pubprop_idx1' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ 'pubprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'pubprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_pub_relationship()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'pub_relationship' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'pub_relationship' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_pub_relationship() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'pub_relationship',
|
|
|
+ 'fields' => array(
|
|
|
+ 'pub_relationship_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'pub_relationship_c1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ 1 => 'object_id',
|
|
|
+ 2 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'pub_relationship_idx1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ ),
|
|
|
+ 'pub_relationship_idx2' => array(
|
|
|
+ 0 => 'object_id',
|
|
|
+ ),
|
|
|
+ 'pub_relationship_idx3' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'pub_relationship_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'subject_id' => 'pub_id',
|
|
|
+ 'object_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_quantification()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'quantification' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'quantification' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_quantification() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'quantification',
|
|
|
+ 'fields' => array(
|
|
|
+ 'quantification_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'acquisition_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'operator_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'protocol_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'analysis_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'quantificationdate' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ 'default' => 'now()',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'uri' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'quantification_c1' => array(
|
|
|
+ 0 => 'name',
|
|
|
+ 1 => 'analysis_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'quantification_idx1' => array(
|
|
|
+ 0 => 'acquisition_id',
|
|
|
+ ),
|
|
|
+ 'quantification_idx2' => array(
|
|
|
+ 0 => 'operator_id',
|
|
|
+ ),
|
|
|
+ 'quantification_idx3' => array(
|
|
|
+ 0 => 'protocol_id',
|
|
|
+ ),
|
|
|
+ 'quantification_idx4' => array(
|
|
|
+ 0 => 'analysis_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'quantification_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'acquisition' => array(
|
|
|
+ 'table' => 'acquisition',
|
|
|
+ 'columns' => array(
|
|
|
+ 'acquisition_id' => 'acquisition_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'contact' => array(
|
|
|
+ 'table' => 'contact',
|
|
|
+ 'columns' => array(
|
|
|
+ 'operator_id' => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'protocol' => array(
|
|
|
+ 'table' => 'protocol',
|
|
|
+ 'columns' => array(
|
|
|
+ 'protocol_id' => 'protocol_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'analysis' => array(
|
|
|
+ 'table' => 'analysis',
|
|
|
+ 'columns' => array(
|
|
|
+ 'analysis_id' => 'analysis_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'elementresult',
|
|
|
+ 1 => 'quantificationprop',
|
|
|
+ 2 => 'quantification_relationship',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_quantificationprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'quantificationprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'quantificationprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_quantificationprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'quantificationprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'quantificationprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'quantification_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'quantificationprop_c1' => array(
|
|
|
+ 0 => 'quantification_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'quantificationprop_idx1' => array(
|
|
|
+ 0 => 'quantification_id',
|
|
|
+ ),
|
|
|
+ 'quantificationprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'quantificationprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'quantification' => array(
|
|
|
+ 'table' => 'quantification',
|
|
|
+ 'columns' => array(
|
|
|
+ 'quantification_id' => 'quantification_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_quantification_relationship()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'quantification_relationship' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'quantification_relationship' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_quantification_relationship() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'quantification_relationship',
|
|
|
+ 'fields' => array(
|
|
|
+ 'quantification_relationship_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'quantification_relationship_c1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ 1 => 'object_id',
|
|
|
+ 2 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'quantification_relationship_idx1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ ),
|
|
|
+ 'quantification_relationship_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ 'quantification_relationship_idx3' => array(
|
|
|
+ 0 => 'object_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'quantification_relationship_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'quantification' => array(
|
|
|
+ 'table' => 'quantification',
|
|
|
+ 'columns' => array(
|
|
|
+ 'subject_id' => 'quantification_id',
|
|
|
+ 'object_id' => 'quantification_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_stock()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'stock' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'stock' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_stock() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'stock',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stock_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'uniquename' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'is_obsolete' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'stock_c1' => array(
|
|
|
+ 0 => 'organism_id',
|
|
|
+ 1 => 'uniquename',
|
|
|
+ 2 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'stock_idx1' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ 'stock_idx2' => array(
|
|
|
+ 0 => 'organism_id',
|
|
|
+ ),
|
|
|
+ 'stock_idx3' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ 'stock_idx4' => array(
|
|
|
+ 0 => 'uniquename',
|
|
|
+ ),
|
|
|
+ 'stock_name_ind1' => array(
|
|
|
+ 0 => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'stock_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'organism' => array(
|
|
|
+ 'table' => 'organism',
|
|
|
+ 'columns' => array(
|
|
|
+ 'organism_id' => 'organism_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'nd_experiment_stock',
|
|
|
+ 1 => 'project_stock',
|
|
|
+ 2 => 'stockcollection_stock',
|
|
|
+ 3 => 'stock_cvterm',
|
|
|
+ 4 => 'stock_dbxref',
|
|
|
+ 5 => 'stock_feature',
|
|
|
+ 6 => 'stock_featuremap',
|
|
|
+ 7 => 'stock_genotype',
|
|
|
+ 8 => 'stock_library',
|
|
|
+ 9 => 'stockprop',
|
|
|
+ 10 => 'stock_pub',
|
|
|
+ 11 => 'stock_relationship',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_stockcollection()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'stockcollection' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'stockcollection' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_stockcollection() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'stockcollection',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stockcollection_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'contact_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'uniquename' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'stockcollection_c1' => array(
|
|
|
+ 0 => 'uniquename',
|
|
|
+ 1 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'stockcollection_idx1' => array(
|
|
|
+ 0 => 'contact_id',
|
|
|
+ ),
|
|
|
+ 'stockcollection_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ 'stockcollection_idx3' => array(
|
|
|
+ 0 => 'uniquename',
|
|
|
+ ),
|
|
|
+ 'stockcollection_name_ind1' => array(
|
|
|
+ 0 => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'stockcollection_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'contact' => array(
|
|
|
+ 'table' => 'contact',
|
|
|
+ 'columns' => array(
|
|
|
+ 'contact_id' => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'stockcollection_db',
|
|
|
+ 1 => 'stockcollectionprop',
|
|
|
+ 2 => 'stockcollection_stock',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_stockcollection_db()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'stockcollection_db' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'stockcollection_db' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_stockcollection_db() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'stockcollection_db',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stockcollection_db_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'stockcollection_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'db_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'stockcollection_db_c1' => array(
|
|
|
+ 0 => 'stockcollection_id',
|
|
|
+ 1 => 'db_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'stockcollection_db_idx1' => array(
|
|
|
+ 0 => 'stockcollection_id',
|
|
|
+ ),
|
|
|
+ 'stockcollection_db_idx2' => array(
|
|
|
+ 0 => 'db_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'stockcollection_db_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'db' => array(
|
|
|
+ 'table' => 'db',
|
|
|
+ 'columns' => array(
|
|
|
+ 'db_id' => 'db_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'stockcollection' => array(
|
|
|
+ 'table' => 'stockcollection',
|
|
|
+ 'columns' => array(
|
|
|
+ 'stockcollection_id' => 'stockcollection_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_stockcollectionprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'stockcollectionprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'stockcollectionprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_stockcollectionprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'stockcollectionprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stockcollectionprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'stockcollection_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'stockcollectionprop_c1' => array(
|
|
|
+ 0 => 'stockcollection_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'stockcollectionprop_idx1' => array(
|
|
|
+ 0 => 'stockcollection_id',
|
|
|
+ ),
|
|
|
+ 'stockcollectionprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'stockcollectionprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'stockcollection' => array(
|
|
|
+ 'table' => 'stockcollection',
|
|
|
+ 'columns' => array(
|
|
|
+ 'stockcollection_id' => 'stockcollection_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_stockcollection_stock()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'stockcollection_stock' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'stockcollection_stock' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_stockcollection_stock() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'stockcollection_stock',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stockcollection_stock_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'stockcollection_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'stock_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'stockcollection_stock_c1' => array(
|
|
|
+ 0 => 'stockcollection_id',
|
|
|
+ 1 => 'stock_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'stockcollection_stock_idx1' => array(
|
|
|
+ 0 => 'stockcollection_id',
|
|
|
+ ),
|
|
|
+ 'stockcollection_stock_idx2' => array(
|
|
|
+ 0 => 'stock_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'stockcollection_stock_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'stockcollection' => array(
|
|
|
+ 'table' => 'stockcollection',
|
|
|
+ 'columns' => array(
|
|
|
+ 'stockcollection_id' => 'stockcollection_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'stock' => array(
|
|
|
+ 'table' => 'stock',
|
|
|
+ 'columns' => array(
|
|
|
+ 'stock_id' => 'stock_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_stock_cvterm()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'stock_cvterm' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'stock_cvterm' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_stock_cvterm() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'stock_cvterm',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stock_cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'stock_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'is_not' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'stock_cvterm_c1' => array(
|
|
|
+ 0 => 'stock_id',
|
|
|
+ 1 => 'cvterm_id',
|
|
|
+ 2 => 'pub_id',
|
|
|
+ 3 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'stock_cvterm_idx1' => array(
|
|
|
+ 0 => 'stock_id',
|
|
|
+ ),
|
|
|
+ 'stock_cvterm_idx2' => array(
|
|
|
+ 0 => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ 'stock_cvterm_idx3' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'stock_cvterm_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'stock' => array(
|
|
|
+ 'table' => 'stock',
|
|
|
+ 'columns' => array(
|
|
|
+ 'stock_id' => 'stock_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cvterm_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'stock_cvtermprop',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_stock_cvtermprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'stock_cvtermprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'stock_cvtermprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_stock_cvtermprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'stock_cvtermprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stock_cvtermprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'stock_cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'stock_cvtermprop_c1' => array(
|
|
|
+ 0 => 'stock_cvterm_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'stock_cvtermprop_idx1' => array(
|
|
|
+ 0 => 'stock_cvterm_id',
|
|
|
+ ),
|
|
|
+ 'stock_cvtermprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'stock_cvtermprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'stock_cvterm' => array(
|
|
|
+ 'table' => 'stock_cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'stock_cvterm_id' => 'stock_cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_stock_dbxref()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'stock_dbxref' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'stock_dbxref' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_stock_dbxref() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'stock_dbxref',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stock_dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'stock_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'is_current' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 'ru',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'stock_dbxref_c1' => array(
|
|
|
+ 0 => 'stock_id',
|
|
|
+ 1 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'stock_dbxref_idx1' => array(
|
|
|
+ 0 => 'stock_id',
|
|
|
+ ),
|
|
|
+ 'stock_dbxref_idx2' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'stock_dbxref_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'stock' => array(
|
|
|
+ 'table' => 'stock',
|
|
|
+ 'columns' => array(
|
|
|
+ 'stock_id' => 'stock_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'stock_dbxrefprop',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_stock_dbxrefprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'stock_dbxrefprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'stock_dbxrefprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_stock_dbxrefprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'stock_dbxrefprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stock_dbxrefprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'stock_dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'stock_dbxrefprop_c1' => array(
|
|
|
+ 0 => 'stock_dbxref_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'stock_dbxrefprop_idx1' => array(
|
|
|
+ 0 => 'stock_dbxref_id',
|
|
|
+ ),
|
|
|
+ 'stock_dbxrefprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'stock_dbxrefprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'stock_dbxref' => array(
|
|
|
+ 'table' => 'stock_dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'stock_dbxref_id' => 'stock_dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_stock_feature()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'stock_feature' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'stock_feature' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_stock_feature() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'stock_feature',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stock_feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'stock_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'stock_feature_c1' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ 1 => 'stock_id',
|
|
|
+ 2 => 'type_id',
|
|
|
+ 3 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'stock_feature_idx1' => array(
|
|
|
+ 0 => 'stock_feature_id',
|
|
|
+ ),
|
|
|
+ 'stock_feature_idx2' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ ),
|
|
|
+ 'stock_feature_idx3' => array(
|
|
|
+ 0 => 'stock_id',
|
|
|
+ ),
|
|
|
+ 'stock_feature_idx4' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'stock_feature_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'feature' => array(
|
|
|
+ 'table' => 'feature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_id' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'stock' => array(
|
|
|
+ 'table' => 'stock',
|
|
|
+ 'columns' => array(
|
|
|
+ 'stock_id' => 'stock_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_stock_featuremap()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'stock_featuremap' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'stock_featuremap' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_stock_featuremap() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'stock_featuremap',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stock_featuremap_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'featuremap_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'stock_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'stock_featuremap_c1' => array(
|
|
|
+ 0 => 'featuremap_id',
|
|
|
+ 1 => 'stock_id',
|
|
|
+ 2 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'stock_featuremap_idx1' => array(
|
|
|
+ 0 => 'featuremap_id',
|
|
|
+ ),
|
|
|
+ 'stock_featuremap_idx2' => array(
|
|
|
+ 0 => 'stock_id',
|
|
|
+ ),
|
|
|
+ 'stock_featuremap_idx3' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'stock_featuremap_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'featuremap' => array(
|
|
|
+ 'table' => 'featuremap',
|
|
|
+ 'columns' => array(
|
|
|
+ 'featuremap_id' => 'featuremap_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'stock' => array(
|
|
|
+ 'table' => 'stock',
|
|
|
+ 'columns' => array(
|
|
|
+ 'stock_id' => 'stock_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_stock_genotype()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'stock_genotype' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'stock_genotype' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_stock_genotype() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'stock_genotype',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stock_genotype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'stock_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'genotype_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'stock_genotype_c1' => array(
|
|
|
+ 0 => 'stock_id',
|
|
|
+ 1 => 'genotype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'stock_genotype_idx1' => array(
|
|
|
+ 0 => 'stock_id',
|
|
|
+ ),
|
|
|
+ 'stock_genotype_idx2' => array(
|
|
|
+ 0 => 'genotype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'stock_genotype_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'stock' => array(
|
|
|
+ 'table' => 'stock',
|
|
|
+ 'columns' => array(
|
|
|
+ 'stock_id' => 'stock_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'genotype' => array(
|
|
|
+ 'table' => 'genotype',
|
|
|
+ 'columns' => array(
|
|
|
+ 'genotype_id' => 'genotype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_stock_library()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'stock_library' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'stock_library' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_stock_library() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'stock_library',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stock_library_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'library_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'stock_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'stock_library_c1' => array(
|
|
|
+ 0 => 'library_id',
|
|
|
+ 1 => 'stock_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'stock_library_idx1' => array(
|
|
|
+ 0 => 'library_id',
|
|
|
+ ),
|
|
|
+ 'stock_library_idx2' => array(
|
|
|
+ 0 => 'stock_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'stock_library_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'library' => array(
|
|
|
+ 'table' => 'library',
|
|
|
+ 'columns' => array(
|
|
|
+ 'library_id' => 'library_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'stock' => array(
|
|
|
+ 'table' => 'stock',
|
|
|
+ 'columns' => array(
|
|
|
+ 'stock_id' => 'stock_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_stockprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'stockprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'stockprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_stockprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'stockprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stockprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'stock_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'stockprop_c1' => array(
|
|
|
+ 0 => 'stock_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'stockprop_idx1' => array(
|
|
|
+ 0 => 'stock_id',
|
|
|
+ ),
|
|
|
+ 'stockprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'stockprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'stock' => array(
|
|
|
+ 'table' => 'stock',
|
|
|
+ 'columns' => array(
|
|
|
+ 'stock_id' => 'stock_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'stockprop_pub',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_stockprop_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'stockprop_pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'stockprop_pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_stockprop_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'stockprop_pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stockprop_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'stockprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'stockprop_pub_c1' => array(
|
|
|
+ 0 => 'stockprop_id',
|
|
|
+ 1 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'stockprop_pub_idx1' => array(
|
|
|
+ 0 => 'stockprop_id',
|
|
|
+ ),
|
|
|
+ 'stockprop_pub_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'stockprop_pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'stockprop' => array(
|
|
|
+ 'table' => 'stockprop',
|
|
|
+ 'columns' => array(
|
|
|
+ 'stockprop_id' => 'stockprop_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_stock_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'stock_pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'stock_pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_stock_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'stock_pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stock_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'stock_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'stock_pub_c1' => array(
|
|
|
+ 0 => 'stock_id',
|
|
|
+ 1 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'stock_pub_idx1' => array(
|
|
|
+ 0 => 'stock_id',
|
|
|
+ ),
|
|
|
+ 'stock_pub_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'stock_pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'stock' => array(
|
|
|
+ 'table' => 'stock',
|
|
|
+ 'columns' => array(
|
|
|
+ 'stock_id' => 'stock_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_stock_relationship()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'stock_relationship' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'stock_relationship' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_stock_relationship() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'stock_relationship',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stock_relationship_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'stock_relationship_c1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ 1 => 'object_id',
|
|
|
+ 2 => 'type_id',
|
|
|
+ 3 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'stock_relationship_idx1' => array(
|
|
|
+ 0 => 'subject_id',
|
|
|
+ ),
|
|
|
+ 'stock_relationship_idx2' => array(
|
|
|
+ 0 => 'object_id',
|
|
|
+ ),
|
|
|
+ 'stock_relationship_idx3' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'stock_relationship_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'stock' => array(
|
|
|
+ 'table' => 'stock',
|
|
|
+ 'columns' => array(
|
|
|
+ 'subject_id' => 'stock_id',
|
|
|
+ 'object_id' => 'stock_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'stock_relationship_cvterm',
|
|
|
+ 1 => 'stock_relationship_pub',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_stock_relationship_cvterm()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'stock_relationship_cvterm' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'stock_relationship_cvterm' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_stock_relationship_cvterm() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'stock_relationship_cvterm',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stock_relationship_cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'stock_relationship_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'stock_relationship_cvterm_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'stock_relationship' => array(
|
|
|
+ 'table' => 'stock_relationship',
|
|
|
+ 'columns' => array(
|
|
|
+ 'stock_relationship_id' => 'stock_relationship_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'cvterm_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_stock_relationship_pub()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'stock_relationship_pub' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'stock_relationship_pub' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_stock_relationship_pub() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'stock_relationship_pub',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stock_relationship_pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'stock_relationship_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'stock_relationship_pub_c1' => array(
|
|
|
+ 0 => 'stock_relationship_id',
|
|
|
+ 1 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'stock_relationship_pub_idx1' => array(
|
|
|
+ 0 => 'stock_relationship_id',
|
|
|
+ ),
|
|
|
+ 'stock_relationship_pub_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'stock_relationship_pub_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'stock_relationship' => array(
|
|
|
+ 'table' => 'stock_relationship',
|
|
|
+ 'columns' => array(
|
|
|
+ 'stock_relationship_id' => 'stock_relationship_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_study()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'study' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'study' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_study() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'study',
|
|
|
+ 'fields' => array(
|
|
|
+ 'study_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'contact_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'study_c1' => array(
|
|
|
+ 0 => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'study_idx1' => array(
|
|
|
+ 0 => 'contact_id',
|
|
|
+ ),
|
|
|
+ 'study_idx2' => array(
|
|
|
+ 0 => 'pub_id',
|
|
|
+ ),
|
|
|
+ 'study_idx3' => array(
|
|
|
+ 0 => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'study_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'contact' => array(
|
|
|
+ 'table' => 'contact',
|
|
|
+ 'columns' => array(
|
|
|
+ 'contact_id' => 'contact_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'pub' => array(
|
|
|
+ 'table' => 'pub',
|
|
|
+ 'columns' => array(
|
|
|
+ 'pub_id' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'dbxref' => array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+ 'columns' => array(
|
|
|
+ 'dbxref_id' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'study_assay',
|
|
|
+ 1 => 'studydesign',
|
|
|
+ 2 => 'studyprop',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_study_assay()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'study_assay' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'study_assay' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_study_assay() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'study_assay',
|
|
|
+ 'fields' => array(
|
|
|
+ 'study_assay_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'study_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'assay_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'study_assay_c1' => array(
|
|
|
+ 0 => 'study_id',
|
|
|
+ 1 => 'assay_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'study_assay_idx1' => array(
|
|
|
+ 0 => 'study_id',
|
|
|
+ ),
|
|
|
+ 'study_assay_idx2' => array(
|
|
|
+ 0 => 'assay_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'study_assay_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'study' => array(
|
|
|
+ 'table' => 'study',
|
|
|
+ 'columns' => array(
|
|
|
+ 'study_id' => 'study_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'assay' => array(
|
|
|
+ 'table' => 'assay',
|
|
|
+ 'columns' => array(
|
|
|
+ 'assay_id' => 'assay_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_studydesign()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'studydesign' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'studydesign' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_studydesign() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'studydesign',
|
|
|
+ 'fields' => array(
|
|
|
+ 'studydesign_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'study_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'studydesign_idx1' => array(
|
|
|
+ 0 => 'study_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'studydesign_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'study' => array(
|
|
|
+ 'table' => 'study',
|
|
|
+ 'columns' => array(
|
|
|
+ 'study_id' => 'study_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'studydesignprop',
|
|
|
+ 1 => 'studyfactor',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_studydesignprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'studydesignprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'studydesignprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_studydesignprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'studydesignprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'studydesignprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'studydesign_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'studydesignprop_c1' => array(
|
|
|
+ 0 => 'studydesign_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'studydesignprop_idx1' => array(
|
|
|
+ 0 => 'studydesign_id',
|
|
|
+ ),
|
|
|
+ 'studydesignprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'studydesignprop_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'studydesign' => array(
|
|
|
+ 'table' => 'studydesign',
|
|
|
+ 'columns' => array(
|
|
|
+ 'studydesign_id' => 'studydesign_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_studyfactor()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'studyfactor' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'studyfactor' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_studyfactor() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'studyfactor',
|
|
|
+ 'fields' => array(
|
|
|
+ 'studyfactor_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'studydesign_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'studyfactor_idx1' => array(
|
|
|
+ 0 => 'studydesign_id',
|
|
|
+ ),
|
|
|
+ 'studyfactor_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'studyfactor_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'studydesign' => array(
|
|
|
+ 'table' => 'studydesign',
|
|
|
+ 'columns' => array(
|
|
|
+ 'studydesign_id' => 'studydesign_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'studyfactorvalue',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_studyfactorvalue()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'studyfactorvalue' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'studyfactorvalue' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_studyfactorvalue() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'studyfactorvalue',
|
|
|
+ 'fields' => array(
|
|
|
+ 'studyfactorvalue_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'studyfactor_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'assay_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'factorvalue' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'studyfactorvalue_idx1' => array(
|
|
|
+ 0 => 'studyfactor_id',
|
|
|
+ ),
|
|
|
+ 'studyfactorvalue_idx2' => array(
|
|
|
+ 0 => 'assay_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'studyfactorvalue_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'studyfactor' => array(
|
|
|
+ 'table' => 'studyfactor',
|
|
|
+ 'columns' => array(
|
|
|
+ 'studyfactor_id' => 'studyfactor_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'assay' => array(
|
|
|
+ 'table' => 'assay',
|
|
|
+ 'columns' => array(
|
|
|
+ 'assay_id' => 'assay_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_studyprop()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'studyprop' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'studyprop' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_studyprop() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'studyprop',
|
|
|
+ 'fields' => array(
|
|
|
+ 'studyprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'study_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'studyprop_idx1' => array(
|
|
|
+ 0 => 'study_id',
|
|
|
+ ),
|
|
|
+ 'studyprop_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'studyprop_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'study_id_type_id_rank' => array(
|
|
|
+ 0 => 'study_id',
|
|
|
+ 1 => 'type_id',
|
|
|
+ 2 => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'study' => array(
|
|
|
+ 'table' => 'study',
|
|
|
+ 'columns' => array(
|
|
|
+ 'study_id' => 'study_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'studyprop_feature',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_studyprop_feature()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'studyprop_feature' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'studyprop_feature' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_studyprop_feature() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'studyprop_feature',
|
|
|
+ 'fields' => array(
|
|
|
+ 'studyprop_feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'studyprop_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'studyprop_feature_idx1' => array(
|
|
|
+ 0 => 'studyprop_id',
|
|
|
+ ),
|
|
|
+ 'studyprop_feature_idx2' => array(
|
|
|
+ 0 => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'studyprop_feature_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'studyprop_id_feature_id' => array(
|
|
|
+ 0 => 'studyprop_id',
|
|
|
+ 1 => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'studyprop' => array(
|
|
|
+ 'table' => 'studyprop',
|
|
|
+ 'columns' => array(
|
|
|
+ 'studyprop_id' => 'studyprop_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'feature' => array(
|
|
|
+ 'table' => 'feature',
|
|
|
+ 'columns' => array(
|
|
|
+ 'feature_id' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_synonym()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'synonym' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'synonym' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_synonym() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'synonym',
|
|
|
+ 'fields' => array(
|
|
|
+ 'synonym_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'synonym_sgml' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'synonym_c1' => array(
|
|
|
+ 0 => 'name',
|
|
|
+ 1 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'synonym_idx1' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'synonym_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'cell_line_synonym',
|
|
|
+ 1 => 'feature_synonym',
|
|
|
+ 2 => 'library_synonym',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_tableinfo()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'tableinfo' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'tableinfo' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_tableinfo() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'tableinfo',
|
|
|
+ 'fields' => array(
|
|
|
+ 'tableinfo_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '30',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'primary_key_column' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '30',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'is_view' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ 'view_on_table_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'superclass_table_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'is_updateable' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 1,
|
|
|
+ ),
|
|
|
+ 'modification_date' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'date',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 'now()',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'tableinfo_c1' => array(
|
|
|
+ 0 => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'tableinfo_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'control',
|
|
|
+ 1 => 'magedocumentation',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Implements hook_chado_schema_v1_3_treatment()
|
|
|
+ *
|
|
|
+ * Purpose: To describe the structure of 'treatment' to tripal
|
|
|
+ * @see chado_insert_record()
|
|
|
+ * @see chado_update_record()
|
|
|
+ * @see chado_select_record()
|
|
|
+ * @see chado_generate_var()
|
|
|
+ * @see chado_expan_var()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the 'treatment' table
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_schema_v1_3_treatment() {
|
|
|
+ $description = array(
|
|
|
+ 'description' => '',
|
|
|
+ 'table' => 'treatment',
|
|
|
+ 'fields' => array(
|
|
|
+ 'treatment_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ 'default' => 0,
|
|
|
+ ),
|
|
|
+ 'biomaterial_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => TRUE,
|
|
|
+ ),
|
|
|
+ 'protocol_id' => array(
|
|
|
+ 'size' => 'big',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+ 'size' => 'normal',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => FALSE,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'treatment_idx1' => array(
|
|
|
+ 0 => 'biomaterial_id',
|
|
|
+ ),
|
|
|
+ 'treatment_idx2' => array(
|
|
|
+ 0 => 'type_id',
|
|
|
+ ),
|
|
|
+ 'treatment_idx3' => array(
|
|
|
+ 0 => 'protocol_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ 0 => 'treatment_id',
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ 'biomaterial' => array(
|
|
|
+ 'table' => 'biomaterial',
|
|
|
+ 'columns' => array(
|
|
|
+ 'biomaterial_id' => 'biomaterial_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'cvterm' => array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+ 'columns' => array(
|
|
|
+ 'type_id' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'protocol' => array(
|
|
|
+ 'table' => 'protocol',
|
|
|
+ 'columns' => array(
|
|
|
+ 'protocol_id' => 'protocol_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'referring_tables' => array(
|
|
|
+ 0 => 'biomaterial_treatment',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Lists the table names in the v1.3 chado schema
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array containing all of the table names
|
|
|
+ *
|
|
|
+ * @ingroup tripal_chado_v1.3_schema_api
|
|
|
+ *
|
|
|
+ */
|
|
|
+function tripal_core_chado_get_v1_3_tables() {
|
|
|
+ $tables = array(
|
|
|
+ 'acquisition',
|
|
|
+ 'acquisitionprop',
|
|
|
+ 'acquisition_relationship',
|
|
|
+ 'analysis',
|
|
|
+ 'analysis_cvterm',
|
|
|
+ 'analysis_dbxref',
|
|
|
+ 'analysisfeature',
|
|
|
+ 'analysisfeatureprop',
|
|
|
+ 'analysis_organism',
|
|
|
+ 'analysisprop',
|
|
|
+ 'analysis_pub',
|
|
|
+ 'analysis_relationship',
|
|
|
+ 'arraydesign',
|
|
|
+ 'arraydesignprop',
|
|
|
+ 'assay',
|
|
|
+ 'assay_biomaterial',
|
|
|
+ 'assay_project',
|
|
|
+ 'assayprop',
|
|
|
+ 'biomaterial',
|
|
|
+ 'biomaterial_dbxref',
|
|
|
+ 'biomaterialprop',
|
|
|
+ 'biomaterial_relationship',
|
|
|
+ 'biomaterial_treatment',
|
|
|
+ 'cell_line',
|
|
|
+ 'cell_line_cvterm',
|
|
|
+ 'cell_line_cvtermprop',
|
|
|
+ 'cell_line_dbxref',
|
|
|
+ 'cell_line_feature',
|
|
|
+ 'cell_line_library',
|
|
|
+ 'cell_lineprop',
|
|
|
+ 'cell_lineprop_pub',
|
|
|
+ 'cell_line_pub',
|
|
|
+ 'cell_line_relationship',
|
|
|
+ 'cell_line_synonym',
|
|
|
+ 'chadoprop',
|
|
|
+ 'channel',
|
|
|
+ 'contact',
|
|
|
+ 'contactprop',
|
|
|
+ 'contact_relationship',
|
|
|
+ 'control',
|
|
|
+ 'cv',
|
|
|
+ 'cvprop',
|
|
|
+ 'cv_root_mview',
|
|
|
+ 'cvterm',
|
|
|
+ 'cvterm_dbxref',
|
|
|
+ 'cvtermpath',
|
|
|
+ 'cvtermprop',
|
|
|
+ 'cvterm_relationship',
|
|
|
+ 'cvtermsynonym',
|
|
|
+ 'db',
|
|
|
+ 'dbprop',
|
|
|
+ 'dbxref',
|
|
|
+ 'dbxrefprop',
|
|
|
+ 'eimage',
|
|
|
+ 'element',
|
|
|
+ 'element_relationship',
|
|
|
+ 'elementresult',
|
|
|
+ 'elementresult_relationship',
|
|
|
+ 'environment',
|
|
|
+ 'environment_cvterm',
|
|
|
+ 'expression',
|
|
|
+ 'expression_cvterm',
|
|
|
+ 'expression_cvtermprop',
|
|
|
+ 'expression_image',
|
|
|
+ 'expressionprop',
|
|
|
+ 'expression_pub',
|
|
|
+ 'feature',
|
|
|
+ 'feature_contact',
|
|
|
+ 'feature_cvterm',
|
|
|
+ 'feature_cvterm_dbxref',
|
|
|
+ 'feature_cvtermprop',
|
|
|
+ 'feature_cvterm_pub',
|
|
|
+ 'feature_dbxref',
|
|
|
+ 'feature_expression',
|
|
|
+ 'feature_expressionprop',
|
|
|
+ 'feature_genotype',
|
|
|
+ 'featureloc',
|
|
|
+ 'featureloc_pub',
|
|
|
+ 'featuremap',
|
|
|
+ 'featuremap_contact',
|
|
|
+ 'featuremap_dbxref',
|
|
|
+ 'featuremap_organism',
|
|
|
+ 'featuremapprop',
|
|
|
+ 'featuremap_pub',
|
|
|
+ 'feature_phenotype',
|
|
|
+ 'featurepos',
|
|
|
+ 'featureposprop',
|
|
|
+ 'featureprop',
|
|
|
+ 'featureprop_pub',
|
|
|
+ 'feature_pub',
|
|
|
+ 'feature_pubprop',
|
|
|
+ 'featurerange',
|
|
|
+ 'feature_relationship',
|
|
|
+ 'feature_relationshipprop',
|
|
|
+ 'feature_relationshipprop_pub',
|
|
|
+ 'feature_relationship_pub',
|
|
|
+ 'feature_synonym',
|
|
|
+ 'genotype',
|
|
|
+ 'genotypeprop',
|
|
|
+ 'library',
|
|
|
+ 'library_contact',
|
|
|
+ 'library_cvterm',
|
|
|
+ 'library_dbxref',
|
|
|
+ 'library_expression',
|
|
|
+ 'library_expressionprop',
|
|
|
+ 'library_feature',
|
|
|
+ 'library_featureprop',
|
|
|
+ 'libraryprop',
|
|
|
+ 'libraryprop_pub',
|
|
|
+ 'library_pub',
|
|
|
+ 'library_relationship',
|
|
|
+ 'library_relationship_pub',
|
|
|
+ 'library_synonym',
|
|
|
+ 'magedocumentation',
|
|
|
+ 'mageml',
|
|
|
+ 'materialized_view',
|
|
|
+ 'nd_experiment',
|
|
|
+ 'nd_experiment_analysis',
|
|
|
+ 'nd_experiment_contact',
|
|
|
+ 'nd_experiment_dbxref',
|
|
|
+ 'nd_experiment_genotype',
|
|
|
+ 'nd_experiment_phenotype',
|
|
|
+ 'nd_experiment_project',
|
|
|
+ 'nd_experimentprop',
|
|
|
+ 'nd_experiment_protocol',
|
|
|
+ 'nd_experiment_pub',
|
|
|
+ 'nd_experiment_stock',
|
|
|
+ 'nd_experiment_stock_dbxref',
|
|
|
+ 'nd_experiment_stockprop',
|
|
|
+ 'nd_geolocation',
|
|
|
+ 'nd_geolocationprop',
|
|
|
+ 'nd_protocol',
|
|
|
+ 'nd_protocolprop',
|
|
|
+ 'nd_protocol_reagent',
|
|
|
+ 'nd_reagent',
|
|
|
+ 'nd_reagentprop',
|
|
|
+ 'nd_reagent_relationship',
|
|
|
+ 'organism',
|
|
|
+ 'organism_cvterm',
|
|
|
+ 'organism_cvtermprop',
|
|
|
+ 'organism_dbxref',
|
|
|
+ 'organism_feature_count',
|
|
|
+ 'organismprop',
|
|
|
+ 'organismprop_pub',
|
|
|
+ 'organism_pub',
|
|
|
+ 'organism_relationship',
|
|
|
+ 'phendesc',
|
|
|
+ 'phenotype',
|
|
|
+ 'phenotype_comparison',
|
|
|
+ 'phenotype_comparison_cvterm',
|
|
|
+ 'phenotype_cvterm',
|
|
|
+ 'phenotypeprop',
|
|
|
+ 'phenstatement',
|
|
|
+ 'phylonode',
|
|
|
+ 'phylonode_dbxref',
|
|
|
+ 'phylonode_organism',
|
|
|
+ 'phylonodeprop',
|
|
|
+ 'phylonode_pub',
|
|
|
+ 'phylonode_relationship',
|
|
|
+ 'phylotree',
|
|
|
+ 'phylotreeprop',
|
|
|
+ 'phylotree_pub',
|
|
|
+ 'project',
|
|
|
+ 'project_analysis',
|
|
|
+ 'project_contact',
|
|
|
+ 'project_dbxref',
|
|
|
+ 'project_feature',
|
|
|
+ 'projectprop',
|
|
|
+ 'project_pub',
|
|
|
+ 'project_relationship',
|
|
|
+ 'project_stock',
|
|
|
+ 'protocol',
|
|
|
+ 'protocolparam',
|
|
|
+ 'pub',
|
|
|
+ 'pubauthor',
|
|
|
+ 'pubauthor_contact',
|
|
|
+ 'pub_dbxref',
|
|
|
+ 'pubprop',
|
|
|
+ 'pub_relationship',
|
|
|
+ 'quantification',
|
|
|
+ 'quantificationprop',
|
|
|
+ 'quantification_relationship',
|
|
|
+ 'stock',
|
|
|
+ 'stockcollection',
|
|
|
+ 'stockcollection_db',
|
|
|
+ 'stockcollectionprop',
|
|
|
+ 'stockcollection_stock',
|
|
|
+ 'stock_cvterm',
|
|
|
+ 'stock_cvtermprop',
|
|
|
+ 'stock_dbxref',
|
|
|
+ 'stock_dbxrefprop',
|
|
|
+ 'stock_feature',
|
|
|
+ 'stock_featuremap',
|
|
|
+ 'stock_genotype',
|
|
|
+ 'stock_library',
|
|
|
+ 'stockprop',
|
|
|
+ 'stockprop_pub',
|
|
|
+ 'stock_pub',
|
|
|
+ 'stock_relationship',
|
|
|
+ 'stock_relationship_cvterm',
|
|
|
+ 'stock_relationship_pub',
|
|
|
+ 'study',
|
|
|
+ 'study_assay',
|
|
|
+ 'studydesign',
|
|
|
+ 'studydesignprop',
|
|
|
+ 'studyfactor',
|
|
|
+ 'studyfactorvalue',
|
|
|
+ 'studyprop',
|
|
|
+ 'studyprop_feature',
|
|
|
+ 'synonym',
|
|
|
+ 'tableinfo',
|
|
|
+ 'treatment',
|
|
|
+ );
|
|
|
+ return $tables;
|
|
|
+}
|