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@@ -0,0 +1,12125 @@
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+<?php
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+
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+/* @file: This file contains default schema definitions for all chado tables
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+ * to be used with tripal_core chado insert/update/select functions.
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+ * These schema definitions can be augmented by the various modules
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+ * (specifically to add missing foreign key definitions) by implementing
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+ * hook_chado_<table name>_schema().
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+ */
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+
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+/****************************************************************************
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+ * Implements hook_organism_dbxref_schema()
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+ * Purpose: To describe the structure of organism_dbxref to tripal
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+ * @see tripal_core.api.inc: tripal_core_chado_insert()
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+ * @see tripal_core.api.inc: tripal_core_chado_update()
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+ * @see tripal_core.api.inc: tripal_core_chado_select()
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+ *
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+ * @return
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+ * An array describing the current table
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+ */
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+function tripal_core_chado_organism_dbxref_schema () {
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+ $description = array();
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+
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+ $description = array(
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+ 'table' => 'organism_dbxref',
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+// 'description' => 'TODO: please describe this table!',
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+ 'fields' => array(
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+ 'organism_dbxref_id' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'serial',
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+ 'not null' => '1',
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+ ),
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+ 'organism_id' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'int',
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+ 'not null' => '1',
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+ ),
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+ 'dbxref_id' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'int',
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+ 'not null' => '1',
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+ ),
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+ ),
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+ 'primary key' => array(
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+ '0' => 'organism_dbxref_id',
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+ ),
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+ 'unique keys' => array(
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+ 'organism_dbxref_c1' => array(
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+ '0' => 'organism_id',
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+ '1' => 'dbxref_id',
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+ ),
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+ ),
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+ 'indexes' => array(
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+ 'organism_dbxref_idx1' => array(
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+ '0' => 'organism_id',
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+ ),
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+ 'organism_dbxref_idx2' => array(
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+ '0' => 'dbxref_id',
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+ ),
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+ ),
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+ 'foreign keys' => array(
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+ ),
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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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+/****************************************************************************
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+ * Implements hook_organismprop_schema()
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+ * Purpose: To describe the structure of organismprop to tripal
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+ * @see tripal_core.api.inc: tripal_core_chado_insert()
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+ * @see tripal_core.api.inc: tripal_core_chado_update()
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+ * @see tripal_core.api.inc: tripal_core_chado_select()
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+ *
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+ * @return
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+ * An array describing the current table
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+ */
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+function tripal_core_chado_organismprop_schema () {
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+ $description = array();
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+
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+ $description = array(
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+ 'table' => 'organismprop',
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+// 'description' => 'TODO: please describe this table!',
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+ 'fields' => array(
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+ 'organismprop_id' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'serial',
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+ 'not null' => '1',
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+ ),
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+ 'organism_id' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'int',
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+ 'not null' => '1',
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+ ),
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+ 'type_id' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'int',
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+ 'not null' => '1',
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+ ),
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+ 'value' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'text',
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+ 'not null' => '',
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+ ),
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+ 'rank' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'int',
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+ 'not null' => '1',
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+ 'default' => '0',
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+ ),
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+ ),
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+ 'primary key' => array(
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+ '0' => 'organismprop_id',
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+ ),
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+ 'unique keys' => array(
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+ 'organismprop_c1' => array(
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+ '0' => 'organism_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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+ 'organismprop_idx1' => array(
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+ '0' => 'organism_id',
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+ ),
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+ 'organismprop_idx2' => array(
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+ '0' => 'type_id',
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+ ),
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+ ),
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+ 'foreign keys' => array(
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+ ),
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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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+/****************************************************************************
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+ * Implements hook_phendesc_schema()
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+ * Purpose: To describe the structure of phendesc to tripal
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+ * @see tripal_core.api.inc: tripal_core_chado_insert()
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+ * @see tripal_core.api.inc: tripal_core_chado_update()
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+ * @see tripal_core.api.inc: tripal_core_chado_select()
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+ *
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+ * @return
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+ * An array describing the current table
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+ */
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+function tripal_core_chado_phendesc_schema () {
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+ $description = array();
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+
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+ $description = array(
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+ 'table' => 'phendesc',
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+// 'description' => 'TODO: please describe this table!',
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+ 'fields' => array(
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+ 'phendesc_id' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'serial',
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+ 'not null' => '1',
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+ ),
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+ 'genotype_id' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'int',
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+ 'not null' => '1',
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+ ),
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+ 'environment_id' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'int',
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+ 'not null' => '1',
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+ ),
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+ 'description' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'text',
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+ 'not null' => '1',
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+ ),
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+ 'type_id' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'int',
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+ 'not null' => '1',
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+ ),
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+ 'pub_id' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'int',
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+ 'not null' => '1',
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+ ),
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+ ),
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+ 'primary key' => array(
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+ '0' => 'phendesc_id',
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+ ),
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+ 'unique keys' => array(
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+ 'phendesc_c1' => array(
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+ '0' => 'genotype_id',
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+ '1' => 'environment_id',
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+ '2' => 'type_id',
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+ '3' => 'pub_id',
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+ ),
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+ ),
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+ 'indexes' => array(
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+ 'phendesc_idx1' => array(
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+ '0' => 'genotype_id',
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+ ),
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+ 'phendesc_idx2' => array(
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+ '0' => 'environment_id',
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+ ),
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+ 'phendesc_idx3' => array(
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+ '0' => 'pub_id',
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+ ),
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+ ),
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+ 'foreign keys' => array(
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+ ),
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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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+/****************************************************************************
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+ * Implements hook_phenotype_schema()
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+ * Purpose: To describe the structure of phenotype to tripal
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+ * @see tripal_core.api.inc: tripal_core_chado_insert()
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+ * @see tripal_core.api.inc: tripal_core_chado_update()
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+ * @see tripal_core.api.inc: tripal_core_chado_select()
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+ *
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+ * @return
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+ * An array describing the current table
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+ */
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+function tripal_core_chado_phenotype_schema () {
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+ $description = array();
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+
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+ $description = array(
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+ 'table' => 'phenotype',
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+// 'description' => 'TODO: please describe this table!',
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+ 'fields' => array(
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+ 'phenotype_id' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'serial',
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+ 'not null' => '1',
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+ ),
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+ 'uniquename' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'text',
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+ 'not null' => '1',
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+ ),
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+ 'observable_id' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'int',
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+ 'not null' => '',
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+ ),
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+ 'attr_id' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'int',
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+ 'not null' => '',
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+ ),
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+ 'value' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'text',
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+ 'not null' => '',
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+ ),
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+ 'cvalue_id' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'int',
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+ 'not null' => '',
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+ ),
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+ 'assay_id' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'int',
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+ 'not null' => '',
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+ ),
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+ ),
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+ 'primary key' => array(
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+ '0' => 'phenotype_id',
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+ ),
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+ 'unique keys' => array(
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+ 'phenotype_c1' => array(
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+ '0' => 'uniquename',
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+ ),
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+ ),
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+ 'indexes' => array(
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+ 'phenotype_idx1' => array(
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+ '0' => 'cvalue_id',
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+ ),
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+ 'phenotype_idx2' => array(
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+ '0' => 'observable_id',
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+ ),
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+ 'phenotype_idx3' => array(
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+ '0' => 'attr_id',
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+ ),
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+ ),
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+ 'foreign keys' => array(
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+ ),
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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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+/****************************************************************************
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+ * Implements hook_organism_schema()
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+ * Purpose: To describe the structure of organism to tripal
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+ * @see tripal_core.api.inc: tripal_core_chado_insert()
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+ * @see tripal_core.api.inc: tripal_core_chado_update()
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+ * @see tripal_core.api.inc: tripal_core_chado_select()
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+ *
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+ * @return
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+ * An array describing the current table
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+ */
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+function tripal_core_chado_organism_schema () {
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+ $description = array();
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+
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+ $description = array(
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+ 'table' => 'organism',
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+// 'description' => 'TODO: please describe this table!',
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+ 'fields' => array(
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+ 'organism_id' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'serial',
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+ 'not null' => '1',
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+ ),
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+ 'abbreviation' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'varchar',
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+ 'length' => '255',
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+ 'not null' => '',
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+ ),
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+ 'genus' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'varchar',
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+ 'length' => '255',
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+ 'not null' => '1',
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+ ),
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+ 'species' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'varchar',
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+ 'length' => '255',
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+ 'not null' => '1',
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+ ),
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+ 'common_name' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'varchar',
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+ 'length' => '255',
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+ 'not null' => '',
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+ ),
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+ 'comment' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'text',
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+ 'not null' => '',
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+ ),
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+ ),
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+ 'primary key' => array(
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+ '0' => 'organism_id',
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+ ),
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+ 'unique keys' => array(
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+ 'organism_c1' => array(
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+ '0' => 'genus',
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+ '1' => 'species',
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+ ),
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+ ),
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+ 'indexes' => array(
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+ ),
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+ 'foreign keys' => array(
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+ ),
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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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+/****************************************************************************
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+ * Implements hook_materialized_view_schema()
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+ * Purpose: To describe the structure of materialized_view to tripal
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+ * @see tripal_core.api.inc: tripal_core_chado_insert()
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+ * @see tripal_core.api.inc: tripal_core_chado_update()
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+ * @see tripal_core.api.inc: tripal_core_chado_select()
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+ *
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+ * @return
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+ * An array describing the current table
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+ */
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+function tripal_core_chado_materialized_view_schema () {
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+ $description = array();
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+
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+ $description = array(
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+ 'table' => 'materialized_view',
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+// 'description' => 'TODO: please describe this table!',
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+ 'fields' => array(
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+ 'materialized_view_id' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'serial',
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+ 'not null' => '1',
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+ ),
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+ 'last_update' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'datetime',
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+ 'not null' => '',
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+ ),
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+ 'refresh_time' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'int',
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+ 'not null' => '',
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+ ),
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+ 'name' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'varchar',
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+ 'length' => '64',
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+ 'not null' => '',
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+ ),
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+ 'mv_schema' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'varchar',
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+ 'length' => '64',
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+ 'not null' => '',
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+ ),
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+ 'mv_table' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'varchar',
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+ 'length' => '128',
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+ 'not null' => '',
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+ ),
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+ 'mv_specs' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'text',
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+ 'not null' => '',
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+ ),
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+ 'indexed' => array(
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+// 'description' => 'TODO: please describe this field!',
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+ 'type' => 'text',
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+ 'not null' => '',
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+ ),
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+ 'query' => array(
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+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'special_index' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'name' => array(
|
|
|
+ '0' => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_libraryprop_schema()
|
|
|
+ * Purpose: To describe the structure of libraryprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_libraryprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'libraryprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'libraryprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'library_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'libraryprop_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_libraryprop_pub_schema()
|
|
|
+ * Purpose: To describe the structure of libraryprop_pub to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_libraryprop_pub_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'libraryprop_pub',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'libraryprop_pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'libraryprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'libraryprop_pub_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_magedocumentation_schema()
|
|
|
+ * Purpose: To describe the structure of magedocumentation to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_magedocumentation_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'magedocumentation',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'magedocumentation_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'mageml_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'tableinfo_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'row_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'mageidentifier' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'magedocumentation_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'magedocumentation_idx1' => array(
|
|
|
+ '0' => 'mageml_id',
|
|
|
+ ),
|
|
|
+ 'magedocumentation_idx2' => array(
|
|
|
+ '0' => 'tableinfo_id',
|
|
|
+ ),
|
|
|
+ 'magedocumentation_idx3' => array(
|
|
|
+ '0' => 'row_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_mageml_schema()
|
|
|
+ * Purpose: To describe the structure of mageml to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_mageml_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'mageml',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'mageml_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'mage_package' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'mage_ml' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'mageml_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_phenotype_comparison_schema()
|
|
|
+ * Purpose: To describe the structure of phenotype_comparison to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_phenotype_comparison_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'phenotype_comparison',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phenotype_comparison_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'genotype1_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'environment1_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'genotype2_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'environment2_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'phenotype1_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'phenotype2_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'phenotype_comparison_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_phenotype_comparison_cvterm_schema()
|
|
|
+ * Purpose: To describe the structure of phenotype_comparison_cvterm to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_phenotype_comparison_cvterm_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'phenotype_comparison_cvterm',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phenotype_comparison_cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'phenotype_comparison_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'phenotype_comparison_cvterm_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_phylonode_relationship_schema()
|
|
|
+ * Purpose: To describe the structure of phylonode_relationship to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_phylonode_relationship_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'phylonode_relationship',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phylonode_relationship_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'phylotree_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'phylonode_relationship_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'subject_id' => array(
|
|
|
+ '0' => 'subject_id',
|
|
|
+ '1' => 'object_id',
|
|
|
+ '2' => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'phylonode_relationship_idx1' => array(
|
|
|
+ '0' => 'subject_id',
|
|
|
+ ),
|
|
|
+ 'phylonode_relationship_idx2' => array(
|
|
|
+ '0' => 'object_id',
|
|
|
+ ),
|
|
|
+ 'phylonode_relationship_idx3' => array(
|
|
|
+ '0' => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_phylonodeprop_schema()
|
|
|
+ * Purpose: To describe the structure of phylonodeprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_phylonodeprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'phylonodeprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phylonodeprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'phylonode_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'phylonodeprop_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'phylonode_id' => array(
|
|
|
+ '0' => 'phylonode_id',
|
|
|
+ '1' => 'type_id',
|
|
|
+ '2' => 'value',
|
|
|
+ '3' => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'phylonodeprop_idx1' => array(
|
|
|
+ '0' => 'phylonode_id',
|
|
|
+ ),
|
|
|
+ 'phylonodeprop_idx2' => array(
|
|
|
+ '0' => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_phylotree_schema()
|
|
|
+ * Purpose: To describe the structure of phylotree to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_phylotree_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'phylotree',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phylotree_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'analysis_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'comment' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'phylotree_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'phylotree_idx1' => array(
|
|
|
+ '0' => 'phylotree_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_phylotree_pub_schema()
|
|
|
+ * Purpose: To describe the structure of phylotree_pub to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_phylotree_pub_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'phylotree_pub',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phylotree_pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'phylotree_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'phylotree_pub_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'phylotree_id' => array(
|
|
|
+ '0' => 'phylotree_id',
|
|
|
+ '1' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'phylotree_pub_idx1' => array(
|
|
|
+ '0' => 'phylotree_id',
|
|
|
+ ),
|
|
|
+ 'phylotree_pub_idx2' => array(
|
|
|
+ '0' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_phylonode_pub_schema()
|
|
|
+ * Purpose: To describe the structure of phylonode_pub to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_phylonode_pub_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'phylonode_pub',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phylonode_pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'phylonode_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'phylonode_pub_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'phylonode_id' => array(
|
|
|
+ '0' => 'phylonode_id',
|
|
|
+ '1' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'phylonode_pub_idx1' => array(
|
|
|
+ '0' => 'phylonode_id',
|
|
|
+ ),
|
|
|
+ 'phylonode_pub_idx2' => array(
|
|
|
+ '0' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_phylonode_organism_schema()
|
|
|
+ * Purpose: To describe the structure of phylonode_organism to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_phylonode_organism_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'phylonode_organism',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phylonode_organism_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'phylonode_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'phylonode_organism_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'phylonode_id' => array(
|
|
|
+ '0' => 'phylonode_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'phylonode_organism_idx1' => array(
|
|
|
+ '0' => 'phylonode_id',
|
|
|
+ ),
|
|
|
+ 'phylonode_organism_idx2' => array(
|
|
|
+ '0' => 'organism_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_phenotype_cvterm_schema()
|
|
|
+ * Purpose: To describe the structure of phenotype_cvterm to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_phenotype_cvterm_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'phenotype_cvterm',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phenotype_cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'phenotype_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'phenotype_cvterm_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_phenstatement_schema()
|
|
|
+ * Purpose: To describe the structure of phenstatement to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_phenstatement_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'phenstatement',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phenstatement_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'genotype_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'environment_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'phenotype_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'phenstatement_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_phylonode_schema()
|
|
|
+ * Purpose: To describe the structure of phylonode to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_phylonode_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'phylonode',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phylonode_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'phylotree_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'parent_phylonode_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'left_idx' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'right_idx' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'label' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'distance' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'float',
|
|
|
+ 'size' => 'big',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'phylonode_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'phylotree_id' => array(
|
|
|
+ '0' => 'phylotree_id',
|
|
|
+ '1' => 'left_idx',
|
|
|
+ ),
|
|
|
+ 'phylonode_phylotree_id_key1' => array(
|
|
|
+ '0' => 'phylotree_id',
|
|
|
+ '1' => 'right_idx',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_phylonode_dbxref_schema()
|
|
|
+ * Purpose: To describe the structure of phylonode_dbxref to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_phylonode_dbxref_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'phylonode_dbxref',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'phylonode_dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'phylonode_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'phylonode_dbxref_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'phylonode_id' => array(
|
|
|
+ '0' => 'phylonode_id',
|
|
|
+ '1' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'phylonode_dbxref_idx1' => array(
|
|
|
+ '0' => 'phylonode_id',
|
|
|
+ ),
|
|
|
+ 'phylonode_dbxref_idx2' => array(
|
|
|
+ '0' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_library_synonym_schema()
|
|
|
+ * Purpose: To describe the structure of library_synonym to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_library_synonym_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'library_synonym',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'library_synonym_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'synonym_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'library_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'is_current' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'ru',
|
|
|
+ ),
|
|
|
+ 'is_internal' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'als',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'library_synonym_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_library_pub_schema()
|
|
|
+ * Purpose: To describe the structure of library_pub to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_library_pub_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'library_pub',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'library_pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'library_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'library_pub_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_featureprop_pub_schema()
|
|
|
+ * Purpose: To describe the structure of featureprop_pub to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_featureprop_pub_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'featureprop_pub',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'featureprop_pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'featureprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'featureprop_pub_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_featureprop_schema()
|
|
|
+ * Purpose: To describe the structure of featureprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_featureprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'featureprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'featureprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'featureprop_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_featurerange_schema()
|
|
|
+ * Purpose: To describe the structure of featurerange to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_featurerange_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'featurerange',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'featurerange_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'featuremap_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'leftstartf_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'leftendf_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rightstartf_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rightendf_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'rangestr' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'featurerange_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_featureset_meets_schema()
|
|
|
+ * Purpose: To describe the structure of featureset_meets to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_featureset_meets_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'featureset_meets',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'subject_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_fnr_type_schema()
|
|
|
+ * Purpose: To describe the structure of fnr_type to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_fnr_type_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'fnr_type',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'type' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '1024',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'residues' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'seqlen' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'md5checksum' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'char',
|
|
|
+ 'length' => '32',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'timeaccessioned' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'timelastmodified' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_featurepos_schema()
|
|
|
+ * Purpose: To describe the structure of featurepos to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_featurepos_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'featurepos',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'featurepos_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'featuremap_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'map_feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'mappos' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'float',
|
|
|
+ 'size' => 'big',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'featurepos_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'featurepos_idx1' => array(
|
|
|
+ '0' => 'featuremap_id',
|
|
|
+ ),
|
|
|
+ 'featurepos_idx2' => array(
|
|
|
+ '0' => 'feature_id',
|
|
|
+ ),
|
|
|
+ 'featurepos_idx3' => array(
|
|
|
+ '0' => 'map_feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_featuremap_pub_schema()
|
|
|
+ * Purpose: To describe the structure of featuremap_pub to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_featuremap_pub_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'featuremap_pub',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'featuremap_pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'featuremap_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'featuremap_pub_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'featuremap_pub_idx1' => array(
|
|
|
+ '0' => 'featuremap_id',
|
|
|
+ ),
|
|
|
+ 'featuremap_pub_idx2' => array(
|
|
|
+ '0' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_union_schema()
|
|
|
+ * Purpose: To describe the structure of feature_union to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_union_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_union',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'subject_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'srcfeature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'subject_strand' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'size' => 'small',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'object_strand' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'size' => 'small',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'fmin' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'fmax' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_featureloc_schema()
|
|
|
+ * Purpose: To describe the structure of featureloc to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_featureloc_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'featureloc',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'featureloc_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'srcfeature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'fmin' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'is_fmin_partial' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'als',
|
|
|
+ ),
|
|
|
+ 'fmax' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'is_fmax_partial' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'als',
|
|
|
+ ),
|
|
|
+ 'strand' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'size' => 'small',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'phase' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'residue_info' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'locgroup' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'featureloc_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'featureloc_c1' => array(
|
|
|
+ '0' => 'feature_id',
|
|
|
+ '1' => 'locgroup',
|
|
|
+ '2' => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'binloc_boxrange' => array(
|
|
|
+ '0' => 'fmin',
|
|
|
+ ),
|
|
|
+ 'binloc_boxrange_src' => array(
|
|
|
+ '0' => 'srcfeature_id',
|
|
|
+ '1' => 'fmin',
|
|
|
+ ),
|
|
|
+ 'featureloc_idx1' => array(
|
|
|
+ '0' => 'feature_id',
|
|
|
+ ),
|
|
|
+ 'featureloc_idx2' => array(
|
|
|
+ '0' => 'srcfeature_id',
|
|
|
+ ),
|
|
|
+ 'featureloc_idx3' => array(
|
|
|
+ '0' => 'srcfeature_id',
|
|
|
+ '1' => 'fmin',
|
|
|
+ '2' => 'fmax',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_featureloc_pub_schema()
|
|
|
+ * Purpose: To describe the structure of featureloc_pub to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_featureloc_pub_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'featureloc_pub',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'featureloc_pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'featureloc_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'featureloc_pub_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_featuremap_schema()
|
|
|
+ * Purpose: To describe the structure of featuremap to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_featuremap_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'featuremap',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'featuremap_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'unittype_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'featuremap_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'featuremap_c1' => array(
|
|
|
+ '0' => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_fp_key_schema()
|
|
|
+ * Purpose: To describe the structure of fp_key to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_fp_key_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'fp_key',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'pkey' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '1024',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_genotype_schema()
|
|
|
+ * Purpose: To describe the structure of genotype to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_genotype_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'genotype',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'genotype_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'uniquename' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'genotype_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'genotype_c1' => array(
|
|
|
+ '0' => 'uniquename',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'genotype_idx1' => array(
|
|
|
+ '0' => 'uniquename',
|
|
|
+ ),
|
|
|
+ 'genotype_idx2' => array(
|
|
|
+ '0' => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_library_cvterm_schema()
|
|
|
+ * Purpose: To describe the structure of library_cvterm to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_library_cvterm_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'library_cvterm',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'library_cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'library_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'library_cvterm_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_library_dbxref_schema()
|
|
|
+ * Purpose: To describe the structure of library_dbxref to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_library_dbxref_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'library_dbxref',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'library_dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'library_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'is_current' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'ru',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'library_dbxref_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_library_feature_schema()
|
|
|
+ * Purpose: To describe the structure of library_feature to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_library_feature_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'library_feature',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'library_feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'library_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'library_feature_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_library_feature_count_schema()
|
|
|
+ * Purpose: To describe the structure of library_feature_count to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_library_feature_count_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'library_feature_count',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'library_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'num_features' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'feature_type' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'library_feature_count_index' => array(
|
|
|
+ '0' => 'library_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_library_schema()
|
|
|
+ * Purpose: To describe the structure of library to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_library_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'library',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'library_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'uniquename' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'is_obsolete' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ 'timeaccessioned' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'ow(',
|
|
|
+ ),
|
|
|
+ 'timelastmodified' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'ow(',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'library_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'library_c1' => array(
|
|
|
+ '0' => 'organism_id',
|
|
|
+ '1' => 'uniquename',
|
|
|
+ '2' => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'library_idx1' => array(
|
|
|
+ '0' => 'organism_id',
|
|
|
+ ),
|
|
|
+ 'library_idx2' => array(
|
|
|
+ '0' => 'type_id',
|
|
|
+ ),
|
|
|
+ 'library_idx3' => array(
|
|
|
+ '0' => 'uniquename',
|
|
|
+ ),
|
|
|
+ 'library_name_ind1' => array(
|
|
|
+ '0' => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_intronloc_view_schema()
|
|
|
+ * Purpose: To describe the structure of intronloc_view to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_intronloc_view_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'intronloc_view',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'exon1_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'exon2_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'fmin' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'fmax' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'strand' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'size' => 'small',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'srcfeature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_gff3atts_schema()
|
|
|
+ * Purpose: To describe the structure of gff3atts to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_gff3atts_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'gff3atts',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'type' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'attribute' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_gff3view_schema()
|
|
|
+ * Purpose: To describe the structure of gff3view to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_gff3view_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'gff3view',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'ref' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'source' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'type' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '1024',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'fstart' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'fend' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'score' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'float',
|
|
|
+ 'size' => 'big',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'strand' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'size' => 'small',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'phase' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'seqlen' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_gffatts_schema()
|
|
|
+ * Purpose: To describe the structure of gffatts to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_gffatts_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'gffatts',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'type' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'attribute' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_intron_combined_view_schema()
|
|
|
+ * Purpose: To describe the structure of intron_combined_view to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_intron_combined_view_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'intron_combined_view',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'exon1_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'exon2_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'fmin' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'fmax' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'strand' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'size' => 'small',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'srcfeature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'intron_rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'transcript_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_project_schema()
|
|
|
+ * Purpose: To describe the structure of project to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_project_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'project',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'project_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'project_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'project_c1' => array(
|
|
|
+ '0' => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_protein_coding_gene_schema()
|
|
|
+ * Purpose: To describe the structure of protein_coding_gene to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_protein_coding_gene_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'protein_coding_gene',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'uniquename' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'residues' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'seqlen' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'md5checksum' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'char',
|
|
|
+ 'length' => '32',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'is_analysis' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'is_obsolete' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'timeaccessioned' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'timelastmodified' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_studyfactorvalue_schema()
|
|
|
+ * Purpose: To describe the structure of studyfactorvalue to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_studyfactorvalue_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'studyfactorvalue',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'studyfactorvalue_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'studyfactor_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'assay_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'factorvalue' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'studyfactorvalue_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'studyfactorvalue_idx1' => array(
|
|
|
+ '0' => 'studyfactor_id',
|
|
|
+ ),
|
|
|
+ 'studyfactorvalue_idx2' => array(
|
|
|
+ '0' => 'assay_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_studyfactor_schema()
|
|
|
+ * Purpose: To describe the structure of studyfactor to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_studyfactor_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'studyfactor',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'studyfactor_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'studydesign_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'studyfactor_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'studyfactor_idx1' => array(
|
|
|
+ '0' => 'studydesign_id',
|
|
|
+ ),
|
|
|
+ 'studyfactor_idx2' => array(
|
|
|
+ '0' => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_studyprop_schema()
|
|
|
+ * Purpose: To describe the structure of studyprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_studyprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'studyprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'studyprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'study_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'studyprop_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'study_id' => array(
|
|
|
+ '0' => 'study_id',
|
|
|
+ '1' => 'type_id',
|
|
|
+ '2' => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'studyprop_idx1' => array(
|
|
|
+ '0' => 'study_id',
|
|
|
+ ),
|
|
|
+ 'studyprop_idx2' => array(
|
|
|
+ '0' => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_studyprop_feature_schema()
|
|
|
+ * Purpose: To describe the structure of studyprop_feature to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_studyprop_feature_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'studyprop_feature',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'studyprop_feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'studyprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'studyprop_feature_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'studyprop_id' => array(
|
|
|
+ '0' => 'studyprop_id',
|
|
|
+ '1' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'studyprop_feature_idx1' => array(
|
|
|
+ '0' => 'studyprop_id',
|
|
|
+ ),
|
|
|
+ 'studyprop_feature_idx2' => array(
|
|
|
+ '0' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_synonym_schema()
|
|
|
+ * Purpose: To describe the structure of synonym to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_synonym_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'synonym',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'synonym_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'synonym_sgml' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'synonym_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'synonym_c1' => array(
|
|
|
+ '0' => 'name',
|
|
|
+ '1' => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'synonym_idx1' => array(
|
|
|
+ '0' => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_studydesignprop_schema()
|
|
|
+ * Purpose: To describe the structure of studydesignprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_studydesignprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'studydesignprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'studydesignprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'studydesign_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'studydesignprop_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_studydesign_schema()
|
|
|
+ * Purpose: To describe the structure of studydesign to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_studydesign_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'studydesign',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'studydesign_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'study_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'studydesign_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'studydesign_idx1' => array(
|
|
|
+ '0' => 'study_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_stockprop_schema()
|
|
|
+ * Purpose: To describe the structure of stockprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_stockprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'stockprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stockprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'stock_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'stockprop_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_stockprop_pub_schema()
|
|
|
+ * Purpose: To describe the structure of stockprop_pub to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_stockprop_pub_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'stockprop_pub',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stockprop_pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'stockprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'stockprop_pub_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_study_schema()
|
|
|
+ * Purpose: To describe the structure of study to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_study_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'study',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'study_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'contact_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'study_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_study_assay_schema()
|
|
|
+ * Purpose: To describe the structure of study_assay to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_study_assay_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'study_assay',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'study_assay_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'study_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'assay_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'study_assay_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_tableinfo_schema()
|
|
|
+ * Purpose: To describe the structure of tableinfo to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_tableinfo_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'tableinfo',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'tableinfo_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '30',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'primary_key_column' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '30',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'is_view' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ 'view_on_table_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'superclass_table_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'is_updateable' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '1',
|
|
|
+ ),
|
|
|
+ 'modification_date' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'date',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'ow(',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'tableinfo_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'tableinfo_c1' => array(
|
|
|
+ '0' => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_treatment_schema()
|
|
|
+ * Purpose: To describe the structure of treatment to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_treatment_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'treatment',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'treatment_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ 'biomaterial_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'protocol_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'treatment_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'treatment_idx1' => array(
|
|
|
+ '0' => 'biomaterial_id',
|
|
|
+ ),
|
|
|
+ 'treatment_idx2' => array(
|
|
|
+ '0' => 'type_id',
|
|
|
+ ),
|
|
|
+ 'treatment_idx3' => array(
|
|
|
+ '0' => 'protocol_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_tripal_obo_schema()
|
|
|
+ * Purpose: To describe the structure of tripal_obo to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_tripal_obo_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'tripal_obo',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cv_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'unsigned' => '1',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ 'file' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '1024',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'url' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '1024',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'cv_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'cv_id' => array(
|
|
|
+ '0' => 'cv_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_tripal_organism_views_common_name_schema()
|
|
|
+ * Purpose: To describe the structure of tripal_organism_views_common_name to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_tripal_organism_views_common_name_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'tripal_organism_views_common_name',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'nid' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'unsigned' => '1',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ 'common_name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'NA',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_type_feature_count_schema()
|
|
|
+ * Purpose: To describe the structure of type_feature_count to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_type_feature_count_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'type_feature_count',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'type' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '1024',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'num_features' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'size' => 'big',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_stockcollectionprop_schema()
|
|
|
+ * Purpose: To describe the structure of stockcollectionprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_stockcollectionprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'stockcollectionprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stockcollectionprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'stockcollection_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'stockcollectionprop_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_stockcollection_stock_schema()
|
|
|
+ * Purpose: To describe the structure of stockcollection_stock to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_stockcollection_stock_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'stockcollection_stock',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stockcollection_stock_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'stockcollection_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'stock_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'stockcollection_stock_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_public_feature_schema()
|
|
|
+ * Purpose: To describe the structure of public_feature to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_public_feature_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'public_feature',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'vid' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'unsigned' => '1',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ 'nid' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'unsigned' => '1',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ 'sync_date' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'nid',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'nid_vid' => array(
|
|
|
+ '0' => 'nid',
|
|
|
+ '1' => 'vid',
|
|
|
+ ),
|
|
|
+ 'vid' => array(
|
|
|
+ '0' => 'vid',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'feature_id' => array(
|
|
|
+ '0' => 'feature_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_public_library_schema()
|
|
|
+ * Purpose: To describe the structure of public_library to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_public_library_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'public_library',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'vid' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'unsigned' => '1',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ 'nid' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'unsigned' => '1',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ 'library_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'nid',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'nid_vid' => array(
|
|
|
+ '0' => 'nid',
|
|
|
+ '1' => 'vid',
|
|
|
+ ),
|
|
|
+ 'vid' => array(
|
|
|
+ '0' => 'vid',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'library_id' => array(
|
|
|
+ '0' => 'library_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_public_organism_schema()
|
|
|
+ * Purpose: To describe the structure of public_organism to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_public_organism_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'public_organism',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'vid' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'unsigned' => '1',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ 'nid' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'unsigned' => '1',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'nid',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'nid_vid' => array(
|
|
|
+ '0' => 'nid',
|
|
|
+ '1' => 'vid',
|
|
|
+ ),
|
|
|
+ 'vid' => array(
|
|
|
+ '0' => 'vid',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'organism_id' => array(
|
|
|
+ '0' => 'organism_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_pubprop_schema()
|
|
|
+ * Purpose: To describe the structure of pubprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_pubprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'pubprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'pubprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'pubprop_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_pubauthor_schema()
|
|
|
+ * Purpose: To describe the structure of pubauthor to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_pubauthor_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'pubauthor',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'pubauthor_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'editor' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => '',
|
|
|
+ 'default' => 'als',
|
|
|
+ ),
|
|
|
+ 'surname' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '100',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'givennames' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '100',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'suffix' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '100',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'pubauthor_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'pubauthor_c1' => array(
|
|
|
+ '0' => 'pub_id',
|
|
|
+ '1' => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'pubauthor_idx2' => array(
|
|
|
+ '0' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_pub_relationship_schema()
|
|
|
+ * Purpose: To describe the structure of pub_relationship to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_pub_relationship_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'pub_relationship',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'pub_relationship_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'pub_relationship_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_protocol_schema()
|
|
|
+ * Purpose: To describe the structure of protocol to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_protocol_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'protocol',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'protocol_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'uri' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'protocoldescription' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'hardwaredescription' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'softwaredescription' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'protocol_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_protocolparam_schema()
|
|
|
+ * Purpose: To describe the structure of protocolparam to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_protocolparam_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'protocolparam',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'protocolparam_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'protocol_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'datatype_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'unittype_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'protocolparam_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'protocolparam_idx1' => array(
|
|
|
+ '0' => 'protocol_id',
|
|
|
+ ),
|
|
|
+ 'protocolparam_idx2' => array(
|
|
|
+ '0' => 'datatype_id',
|
|
|
+ ),
|
|
|
+ 'protocolparam_idx3' => array(
|
|
|
+ '0' => 'unittype_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_pub_schema()
|
|
|
+ * Purpose: To describe the structure of pub to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_pub_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'pub',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'title' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'volumetitle' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'volume' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'series_name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'issue' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'pyear' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'pages' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'miniref' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'uniquename' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'is_obsolete' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => '',
|
|
|
+ 'default' => 'als',
|
|
|
+ ),
|
|
|
+ 'publisher' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'pubplace' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'pub_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'pub_c1' => array(
|
|
|
+ '0' => 'uniquename',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'pub_idx1' => array(
|
|
|
+ '0' => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_pub_dbxref_schema()
|
|
|
+ * Purpose: To describe the structure of pub_dbxref to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_pub_dbxref_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'pub_dbxref',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'pub_dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'is_current' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'ru',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'pub_dbxref_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_quantification_schema()
|
|
|
+ * Purpose: To describe the structure of quantification to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_quantification_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'quantification',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'quantification_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'acquisition_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'operator_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'protocol_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'analysis_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'quantificationdate' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => '',
|
|
|
+ 'default' => 'ow(',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'uri' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'quantification_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_quantification_relationship_schema()
|
|
|
+ * Purpose: To describe the structure of quantification_relationship to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_quantification_relationship_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'quantification_relationship',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'quantification_relationship_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'quantification_relationship_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_stock_pub_schema()
|
|
|
+ * Purpose: To describe the structure of stock_pub to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_stock_pub_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'stock_pub',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stock_pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'stock_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'stock_pub_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_stock_relationship_schema()
|
|
|
+ * Purpose: To describe the structure of stock_relationship to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_stock_relationship_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'stock_relationship',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stock_relationship_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'stock_relationship_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_stock_relationship_pub_schema()
|
|
|
+ * Purpose: To describe the structure of stock_relationship_pub to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_stock_relationship_pub_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'stock_relationship_pub',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stock_relationship_pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'stock_relationship_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'stock_relationship_pub_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_stockcollection_schema()
|
|
|
+ * Purpose: To describe the structure of stockcollection to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_stockcollection_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'stockcollection',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stockcollection_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'contact_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'uniquename' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'stockcollection_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_stock_genotype_schema()
|
|
|
+ * Purpose: To describe the structure of stock_genotype to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_stock_genotype_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'stock_genotype',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stock_genotype_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'stock_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'genotype_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'stock_genotype_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_stock_dbxref_schema()
|
|
|
+ * Purpose: To describe the structure of stock_dbxref to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_stock_dbxref_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'stock_dbxref',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stock_dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'stock_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'is_current' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'ru',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'stock_dbxref_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_quantificationprop_schema()
|
|
|
+ * Purpose: To describe the structure of quantificationprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_quantificationprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'quantificationprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'quantificationprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'quantification_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'quantificationprop_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_stats_paths_to_root_schema()
|
|
|
+ * Purpose: To describe the structure of stats_paths_to_root to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_stats_paths_to_root_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'stats_paths_to_root',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'total_paths' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'size' => 'big',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'avg_distance' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'numeric',
|
|
|
+ 'not null' => '',
|
|
|
+ 'precision' => '0',
|
|
|
+ 'scale' => '0',
|
|
|
+ ),
|
|
|
+ 'min_distance' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'max_distance' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_stock_schema()
|
|
|
+ * Purpose: To describe the structure of stock to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_stock_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'stock',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stock_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'uniquename' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'is_obsolete' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'als',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'stock_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_stock_cvterm_schema()
|
|
|
+ * Purpose: To describe the structure of stock_cvterm to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_stock_cvterm_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'stock_cvterm',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'stock_cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'stock_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'stock_cvterm_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'stock_cvterm_c1' => array(
|
|
|
+ '0' => 'stock_id',
|
|
|
+ '1' => 'cvterm_id',
|
|
|
+ '2' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'stock_cvterm_idx1' => array(
|
|
|
+ '0' => 'stock_id',
|
|
|
+ ),
|
|
|
+ 'stock_cvterm_idx2' => array(
|
|
|
+ '0' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ 'stock_cvterm_idx3' => array(
|
|
|
+ '0' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_synonym_schema()
|
|
|
+ * Purpose: To describe the structure of feature_synonym to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_synonym_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_synonym',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_synonym_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'synonym_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'is_current' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'als',
|
|
|
+ ),
|
|
|
+ 'is_internal' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'als',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'feature_synonym_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_relationshipprop_pub_schema()
|
|
|
+ * Purpose: To describe the structure of feature_relationshipprop_pub to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_relationshipprop_pub_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_relationshipprop_pub',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_relationshipprop_pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_relationshipprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'feature_relationshipprop_pub_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cell_line_relationship_schema()
|
|
|
+ * Purpose: To describe the structure of cell_line_relationship to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cell_line_relationship_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cell_line_relationship',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cell_line_relationship_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'cell_line_relationship_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cell_line_relationship_c1' => array(
|
|
|
+ '0' => 'subject_id',
|
|
|
+ '1' => 'object_id',
|
|
|
+ '2' => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cell_line_pub_schema()
|
|
|
+ * Purpose: To describe the structure of cell_line_pub to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cell_line_pub_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cell_line_pub',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cell_line_pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cell_line_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'cell_line_pub_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cell_line_pub_c1' => array(
|
|
|
+ '0' => 'cell_line_id',
|
|
|
+ '1' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cell_line_synonym_schema()
|
|
|
+ * Purpose: To describe the structure of cell_line_synonym to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cell_line_synonym_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cell_line_synonym',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cell_line_synonym_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cell_line_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'synonym_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'is_current' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'als',
|
|
|
+ ),
|
|
|
+ 'is_internal' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'als',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'cell_line_synonym_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cell_line_synonym_c1' => array(
|
|
|
+ '0' => 'synonym_id',
|
|
|
+ '1' => 'cell_line_id',
|
|
|
+ '2' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cell_lineprop_schema()
|
|
|
+ * Purpose: To describe the structure of cell_lineprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cell_lineprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cell_lineprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cell_lineprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cell_line_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'cell_lineprop_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cell_lineprop_c1' => array(
|
|
|
+ '0' => 'cell_line_id',
|
|
|
+ '1' => 'type_id',
|
|
|
+ '2' => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cell_lineprop_pub_schema()
|
|
|
+ * Purpose: To describe the structure of cell_lineprop_pub to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cell_lineprop_pub_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cell_lineprop_pub',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cell_lineprop_pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cell_lineprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'cell_lineprop_pub_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cell_lineprop_pub_c1' => array(
|
|
|
+ '0' => 'cell_lineprop_id',
|
|
|
+ '1' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cell_line_library_schema()
|
|
|
+ * Purpose: To describe the structure of cell_line_library to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cell_line_library_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cell_line_library',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cell_line_library_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cell_line_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'library_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'cell_line_library_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cell_line_library_c1' => array(
|
|
|
+ '0' => 'cell_line_id',
|
|
|
+ '1' => 'library_id',
|
|
|
+ '2' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cell_line_feature_schema()
|
|
|
+ * Purpose: To describe the structure of cell_line_feature to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cell_line_feature_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cell_line_feature',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cell_line_feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cell_line_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'cell_line_feature_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cell_line_feature_c1' => array(
|
|
|
+ '0' => 'cell_line_id',
|
|
|
+ '1' => 'feature_id',
|
|
|
+ '2' => 'pub_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cell_line_schema()
|
|
|
+ * Purpose: To describe the structure of cell_line to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cell_line_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cell_line',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cell_line_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'uniquename' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'timeaccessioned' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'ow(',
|
|
|
+ ),
|
|
|
+ 'timelastmodified' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'ow(',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'cell_line_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cell_line_c1' => array(
|
|
|
+ '0' => 'uniquename',
|
|
|
+ '1' => 'organism_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cell_line_cvterm_schema()
|
|
|
+ * Purpose: To describe the structure of cell_line_cvterm to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cell_line_cvterm_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cell_line_cvterm',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cell_line_cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cell_line_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'cell_line_cvterm_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cell_line_cvterm_c1' => array(
|
|
|
+ '0' => 'cell_line_id',
|
|
|
+ '1' => 'cvterm_id',
|
|
|
+ '2' => 'pub_id',
|
|
|
+ '3' => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cell_line_cvtermprop_schema()
|
|
|
+ * Purpose: To describe the structure of cell_line_cvtermprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cell_line_cvtermprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cell_line_cvtermprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cell_line_cvtermprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cell_line_cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'cell_line_cvtermprop_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cell_line_cvtermprop_c1' => array(
|
|
|
+ '0' => 'cell_line_cvterm_id',
|
|
|
+ '1' => 'type_id',
|
|
|
+ '2' => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cell_line_dbxref_schema()
|
|
|
+ * Purpose: To describe the structure of cell_line_dbxref to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cell_line_dbxref_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cell_line_dbxref',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cell_line_dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cell_line_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'is_current' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'ru',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'cell_line_dbxref_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cell_line_dbxref_c1' => array(
|
|
|
+ '0' => 'cell_line_id',
|
|
|
+ '1' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_channel_schema()
|
|
|
+ * Purpose: To describe the structure of channel to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_channel_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'channel',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'channel_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'definition' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'channel_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'channel_c1' => array(
|
|
|
+ '0' => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_common_ancestor_cvterm_schema()
|
|
|
+ * Purpose: To describe the structure of common_ancestor_cvterm to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_common_ancestor_cvterm_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'common_ancestor_cvterm',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cvterm1_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'cvterm2_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'ancestor_cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'pathdistance1' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'pathdistance2' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'total_pathdistance' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cv_cvterm_count_with_obs_schema()
|
|
|
+ * Purpose: To describe the structure of cv_cvterm_count_with_obs to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cv_cvterm_count_with_obs_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cv_cvterm_count_with_obs',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'num_terms_incl_obs' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'size' => 'big',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cv_leaf_schema()
|
|
|
+ * Purpose: To describe the structure of cv_leaf to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cv_leaf_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cv_leaf',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cv_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cv_link_count_schema()
|
|
|
+ * Purpose: To describe the structure of cv_link_count to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cv_link_count_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cv_link_count',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cv_name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'relation_name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '1024',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'relation_cv_name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'num_links' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'size' => 'big',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cv_path_count_schema()
|
|
|
+ * Purpose: To describe the structure of cv_path_count to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cv_path_count_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cv_path_count',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cv_name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'relation_name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '1024',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'relation_cv_name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'num_paths' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'size' => 'big',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cv_cvterm_count_schema()
|
|
|
+ * Purpose: To describe the structure of cv_cvterm_count to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cv_cvterm_count_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cv_cvterm_count',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'num_terms_excl_obs' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'size' => 'big',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cv_schema()
|
|
|
+ * Purpose: To describe the structure of cv to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cv_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cv',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cv_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'definition' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'cv_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cv_c1' => array(
|
|
|
+ '0' => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_common_descendant_cvterm_schema()
|
|
|
+ * Purpose: To describe the structure of common_descendant_cvterm to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_common_descendant_cvterm_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'common_descendant_cvterm',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cvterm1_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'cvterm2_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'ancestor_cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'pathdistance1' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'pathdistance2' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'total_pathdistance' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_contact_schema()
|
|
|
+ * Purpose: To describe the structure of contact to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_contact_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'contact',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'contact_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'contact_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'contact_c1' => array(
|
|
|
+ '0' => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_contact_relationship_schema()
|
|
|
+ * Purpose: To describe the structure of contact_relationship to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_contact_relationship_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'contact_relationship',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'contact_relationship_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'contact_relationship_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_control_schema()
|
|
|
+ * Purpose: To describe the structure of control to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_control_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'control',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'control_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'assay_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'tableinfo_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'row_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'control_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_biomaterialprop_schema()
|
|
|
+ * Purpose: To describe the structure of biomaterialprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_biomaterialprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'biomaterialprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'biomaterialprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'biomaterial_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'biomaterialprop_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_biomaterial_treatment_schema()
|
|
|
+ * Purpose: To describe the structure of biomaterial_treatment to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_biomaterial_treatment_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'biomaterial_treatment',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'biomaterial_treatment_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'biomaterial_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'treatment_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'unittype_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'float',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'biomaterial_treatment_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_acquisition_relationship_schema()
|
|
|
+ * Purpose: To describe the structure of acquisition_relationship to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_acquisition_relationship_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'acquisition_relationship',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'acquisition_relationship_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'acquisition_relationship_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'acquisition_relationship_c1' => array(
|
|
|
+ '0' => 'subject_id',
|
|
|
+ '1' => 'object_id',
|
|
|
+ '2' => 'type_id',
|
|
|
+ '3' => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'acquisition_relationship_idx1' => array(
|
|
|
+ '0' => 'subject_id',
|
|
|
+ ),
|
|
|
+ 'acquisition_relationship_idx2' => array(
|
|
|
+ '0' => 'type_id',
|
|
|
+ ),
|
|
|
+ 'acquisition_relationship_idx3' => array(
|
|
|
+ '0' => 'object_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_acquisition_schema()
|
|
|
+ * Purpose: To describe the structure of acquisition to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_acquisition_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'acquisition',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'acquisition_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'assay_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'protocol_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'channel_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'acquisitiondate' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => '',
|
|
|
+ 'default' => 'ow(',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'uri' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'acquisition_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'acquisition_c1' => array(
|
|
|
+ '0' => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'acquisition_idx1' => array(
|
|
|
+ '0' => 'assay_id',
|
|
|
+ ),
|
|
|
+ 'acquisition_idx2' => array(
|
|
|
+ '0' => 'protocol_id',
|
|
|
+ ),
|
|
|
+ 'acquisition_idx3' => array(
|
|
|
+ '0' => 'channel_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_acquisitionprop_schema()
|
|
|
+ * Purpose: To describe the structure of acquisitionprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_acquisitionprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'acquisitionprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'acquisitionprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'acquisition_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'acquisitionprop_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'acquisitionprop_c1' => array(
|
|
|
+ '0' => 'acquisition_id',
|
|
|
+ '1' => 'type_id',
|
|
|
+ '2' => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'acquisitionprop_idx1' => array(
|
|
|
+ '0' => 'acquisition_id',
|
|
|
+ ),
|
|
|
+ 'acquisitionprop_idx2' => array(
|
|
|
+ '0' => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_all_feature_names_schema()
|
|
|
+ * Purpose: To describe the structure of all_feature_names to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_all_feature_names_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'all_feature_names',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_analysis_schema()
|
|
|
+ * Purpose: To describe the structure of analysis to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_analysis_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'analysis',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'analysis_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'program' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'programversion' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'algorithm' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'sourcename' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'sourceversion' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'sourceuri' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'timeexecuted' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'ow(',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'analysis_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'analysis_c1' => array(
|
|
|
+ '0' => 'program',
|
|
|
+ '1' => 'programversion',
|
|
|
+ '2' => 'sourcename',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_analysisfeature_schema()
|
|
|
+ * Purpose: To describe the structure of analysisfeature to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_analysisfeature_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'analysisfeature',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'analysisfeature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'analysis_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'rawscore' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'float',
|
|
|
+ 'size' => 'big',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'normscore' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'float',
|
|
|
+ 'size' => 'big',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'significance' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'float',
|
|
|
+ 'size' => 'big',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'identity' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'float',
|
|
|
+ 'size' => 'big',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'analysisfeature_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_analysisfeatureprop_schema()
|
|
|
+ * Purpose: To describe the structure of analysisfeatureprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_analysisfeatureprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'analysisfeatureprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'analysisfeatureprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'analysisfeature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'analysisfeatureprop_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'analysisfeature_id_type_id_rank' => array(
|
|
|
+ '0' => 'analysisfeature_id',
|
|
|
+ '1' => 'type_id',
|
|
|
+ '2' => 'rank',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_assayprop_schema()
|
|
|
+ * Purpose: To describe the structure of assayprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_assayprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'assayprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'assayprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'assay_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'assayprop_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_biomaterial_schema()
|
|
|
+ * Purpose: To describe the structure of biomaterial to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_biomaterial_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'biomaterial',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'biomaterial_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'taxon_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'biosourceprovider_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'biomaterial_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_biomaterial_dbxref_schema()
|
|
|
+ * Purpose: To describe the structure of biomaterial_dbxref to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_biomaterial_dbxref_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'biomaterial_dbxref',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'biomaterial_dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'biomaterial_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'biomaterial_dbxref_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_biomaterial_relationship_schema()
|
|
|
+ * Purpose: To describe the structure of biomaterial_relationship to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_biomaterial_relationship_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'biomaterial_relationship',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'biomaterial_relationship_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'biomaterial_relationship_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_assay_project_schema()
|
|
|
+ * Purpose: To describe the structure of assay_project to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_assay_project_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'assay_project',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'assay_project_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'assay_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'project_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'assay_project_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_assay_biomaterial_schema()
|
|
|
+ * Purpose: To describe the structure of assay_biomaterial to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_assay_biomaterial_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'assay_biomaterial',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'assay_biomaterial_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'assay_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'biomaterial_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'channel_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'assay_biomaterial_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_analysisprop_schema()
|
|
|
+ * Purpose: To describe the structure of analysisprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_analysisprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'analysisprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'analysisprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'analysis_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'analysisprop_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_arraydesign_schema()
|
|
|
+ * Purpose: To describe the structure of arraydesign to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_arraydesign_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'arraydesign',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'arraydesign_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'manufacturer_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'platformtype_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'substratetype_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'protocol_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'version' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'array_dimensions' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'element_dimensions' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'num_of_elements' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'num_array_columns' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'num_array_rows' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'num_grid_columns' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'num_grid_rows' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'num_sub_columns' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'num_sub_rows' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'arraydesign_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_arraydesignprop_schema()
|
|
|
+ * Purpose: To describe the structure of arraydesignprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_arraydesignprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'arraydesignprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'arraydesignprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'arraydesign_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'arraydesignprop_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_assay_schema()
|
|
|
+ * Purpose: To describe the structure of assay to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_assay_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'assay',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'assay_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'arraydesign_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'protocol_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'assaydate' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => '',
|
|
|
+ 'default' => 'ow(',
|
|
|
+ ),
|
|
|
+ 'arrayidentifier' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'arraybatchidentifier' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'operator_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'assay_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cv_root_schema()
|
|
|
+ * Purpose: To describe the structure of cv_root to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cv_root_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cv_root',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cv_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'root_cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cvterm_schema()
|
|
|
+ * Purpose: To describe the structure of cvterm to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cvterm_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cvterm',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cv_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '1024',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'definition' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'is_obsolete' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ 'is_relationshiptype' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_dbxref_schema()
|
|
|
+ * Purpose: To describe the structure of feature_dbxref to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_dbxref_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_dbxref',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'is_current' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'ru',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'feature_dbxref_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_cvtermprop_schema()
|
|
|
+ * Purpose: To describe the structure of feature_cvtermprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_cvtermprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_cvtermprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_cvtermprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'feature_cvtermprop_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_difference_schema()
|
|
|
+ * Purpose: To describe the structure of feature_difference to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_difference_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_difference',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'subject_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'srcfeature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'size' => 'small',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'fmin' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'fmax' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'strand' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_disjoint_schema()
|
|
|
+ * Purpose: To describe the structure of feature_disjoint to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_disjoint_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_disjoint',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'subject_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_distance_schema()
|
|
|
+ * Purpose: To describe the structure of feature_distance to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_distance_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_distance',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'subject_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'srcfeature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'subject_strand' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'size' => 'small',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'object_strand' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'size' => 'small',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'distance' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_cvterm_pub_schema()
|
|
|
+ * Purpose: To describe the structure of feature_cvterm_pub to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_cvterm_pub_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_cvterm_pub',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_cvterm_pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'feature_cvterm_pub_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_cvterm_dbxref_schema()
|
|
|
+ * Purpose: To describe the structure of feature_cvterm_dbxref to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_cvterm_dbxref_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_cvterm_dbxref',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_cvterm_dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'feature_cvterm_dbxref_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_f_type_schema()
|
|
|
+ * Purpose: To describe the structure of f_type to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_f_type_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'f_type',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'type' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '1024',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'residues' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'seqlen' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'md5checksum' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'char',
|
|
|
+ 'length' => '32',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'timeaccessioned' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'timelastmodified' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_schema()
|
|
|
+ * Purpose: To describe the structure of feature to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'organism_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'uniquename' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'residues' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'seqlen' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'md5checksum' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'char',
|
|
|
+ 'length' => '32',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'is_analysis' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'als',
|
|
|
+ ),
|
|
|
+ 'is_obsolete' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'als',
|
|
|
+ ),
|
|
|
+ 'timeaccessioned' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'ow(',
|
|
|
+ ),
|
|
|
+ 'timelastmodified' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'datetime',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'ow(',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'feature_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_contains_schema()
|
|
|
+ * Purpose: To describe the structure of feature_contains to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_contains_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_contains',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'subject_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_cvterm_schema()
|
|
|
+ * Purpose: To describe the structure of feature_cvterm to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_cvterm_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_cvterm',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'is_not' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => 'als',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'feature_cvterm_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_expression_schema()
|
|
|
+ * Purpose: To describe the structure of feature_expression to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_expression_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_expression',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_expression_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'expression_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'feature_expression_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_expressionprop_schema()
|
|
|
+ * Purpose: To describe the structure of feature_expressionprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_expressionprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_expressionprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_expressionprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_expression_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'feature_expressionprop_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_pubprop_schema()
|
|
|
+ * Purpose: To describe the structure of feature_pubprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_pubprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_pubprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_pubprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'feature_pubprop_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_relationship_schema()
|
|
|
+ * Purpose: To describe the structure of feature_relationship to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_relationship_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_relationship',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_relationship_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'feature_relationship_id',
|
|
|
+ ),
|
|
|
+ '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_idx2' => array(
|
|
|
+ '0' => 'object_id',
|
|
|
+ ),
|
|
|
+ 'feature_relationship_idx3' => array(
|
|
|
+ '0' => 'type_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_relationship_pub_schema()
|
|
|
+ * Purpose: To describe the structure of feature_relationship_pub to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_relationship_pub_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_relationship_pub',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_relationship_pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_relationship_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'feature_relationship_pub_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_relationshipprop_schema()
|
|
|
+ * Purpose: To describe the structure of feature_relationshipprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_relationshipprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_relationshipprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_relationshipprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_relationship_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'feature_relationshipprop_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_pub_schema()
|
|
|
+ * Purpose: To describe the structure of feature_pub to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_pub_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_pub',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'feature_pub_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_phenotype_schema()
|
|
|
+ * Purpose: To describe the structure of feature_phenotype to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_phenotype_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_phenotype',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_phenotype_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'phenotype_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'feature_phenotype_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_genotype_schema()
|
|
|
+ * Purpose: To describe the structure of feature_genotype to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_genotype_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_genotype',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_genotype_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'genotype_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'chromosome_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cgroup' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'feature_genotype_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_intersection_schema()
|
|
|
+ * Purpose: To describe the structure of feature_intersection to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_intersection_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_intersection',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'subject_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'srcfeature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'subject_strand' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'size' => 'small',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'object_strand' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'size' => 'small',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'fmin' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'fmax' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_meets_schema()
|
|
|
+ * Purpose: To describe the structure of feature_meets to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_meets_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_meets',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'subject_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_feature_meets_on_same_strand_schema()
|
|
|
+ * Purpose: To describe the structure of feature_meets_on_same_strand to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_feature_meets_on_same_strand_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'feature_meets_on_same_strand',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'subject_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_f_loc_schema()
|
|
|
+ * Purpose: To describe the structure of f_loc to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_f_loc_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'f_loc',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'nbeg' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'nend' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'strand' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'size' => 'small',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_expressionprop_schema()
|
|
|
+ * Purpose: To describe the structure of expressionprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_expressionprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'expressionprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'expressionprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'expression_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'expressionprop_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_db_dbxref_count_schema()
|
|
|
+ * Purpose: To describe the structure of db_dbxref_count to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_db_dbxref_count_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'db_dbxref_count',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'num_dbxrefs' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'size' => 'big',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_dbxref_schema()
|
|
|
+ * Purpose: To describe the structure of dbxref to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_dbxref_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'dbxref',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'db_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'accession' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'version' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '',
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'dbxref_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_dbxrefprop_schema()
|
|
|
+ * Purpose: To describe the structure of dbxrefprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_dbxrefprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'dbxrefprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'dbxrefprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'dbxrefprop_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_dfeatureloc_schema()
|
|
|
+ * Purpose: To describe the structure of dfeatureloc to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_dfeatureloc_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'dfeatureloc',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'featureloc_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'srcfeature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'nbeg' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'is_nbeg_partial' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'nend' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'is_nend_partial' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'boolean',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'strand' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'size' => 'small',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'phase' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'residue_info' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'locgroup' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_db_schema()
|
|
|
+ * Purpose: To describe the structure of db to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_db_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'db',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'db_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'name' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'urlprefix' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'url' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'db_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'db_c1' => array(
|
|
|
+ '0' => 'name',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cvtermsynonym_schema()
|
|
|
+ * Purpose: To describe the structure of cvtermsynonym to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cvtermsynonym_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cvtermsynonym',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cvtermsynonym_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'synonym' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '1024',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'cvtermsynonym_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cvtermsynonym_c1' => array(
|
|
|
+ '0' => 'cvterm_id',
|
|
|
+ '1' => 'synonym',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'cvtermsynonym_idx1' => array(
|
|
|
+ '0' => 'cvterm_id',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cvterm_dbxref_schema()
|
|
|
+ * Purpose: To describe the structure of cvterm_dbxref to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cvterm_dbxref_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cvterm_dbxref',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cvterm_dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'is_for_definition' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'cvterm_dbxref_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cvterm_relationship_schema()
|
|
|
+ * Purpose: To describe the structure of cvterm_relationship to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cvterm_relationship_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cvterm_relationship',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cvterm_relationship_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'cvterm_relationship_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cvtermpath_schema()
|
|
|
+ * Purpose: To describe the structure of cvtermpath to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cvtermpath_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cvtermpath',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cvtermpath_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cv_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pathdistance' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'cvtermpath_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_cvtermprop_schema()
|
|
|
+ * Purpose: To describe the structure of cvtermprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_cvtermprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'cvtermprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'cvtermprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'cvtermprop_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'cvterm_id' => 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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_eimage_schema()
|
|
|
+ * Purpose: To describe the structure of eimage to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_eimage_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'eimage',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'eimage_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'eimage_data' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'eimage_type' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'image_uri' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'varchar',
|
|
|
+ 'length' => '255',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'eimage_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_element_schema()
|
|
|
+ * Purpose: To describe the structure of element to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_element_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'element',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'element_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'arraydesign_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'dbxref_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'element_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_expression_cvterm_schema()
|
|
|
+ * Purpose: To describe the structure of expression_cvterm to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_expression_cvterm_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'expression_cvterm',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'expression_cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'expression_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ 'cvterm_type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'expression_cvterm_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'expression_cvterm_c1' => array(
|
|
|
+ '0' => 'expression_id',
|
|
|
+ '1' => 'cvterm_id',
|
|
|
+ '2' => '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_expression_cvtermprop_schema()
|
|
|
+ * Purpose: To describe the structure of expression_cvtermprop to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_expression_cvtermprop_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'expression_cvtermprop',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'expression_cvtermprop_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'expression_cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'expression_cvtermprop_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_expression_image_schema()
|
|
|
+ * Purpose: To describe the structure of expression_image to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_expression_image_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'expression_image',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'expression_image_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'expression_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'eimage_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'expression_image_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_expression_pub_schema()
|
|
|
+ * Purpose: To describe the structure of expression_pub to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_expression_pub_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'expression_pub',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'expression_pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'expression_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'pub_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'expression_pub_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_expression_schema()
|
|
|
+ * Purpose: To describe the structure of expression to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_expression_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'expression',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'expression_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'uniquename' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'md5checksum' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'char',
|
|
|
+ 'length' => '32',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'expression_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'expression_c1' => array(
|
|
|
+ '0' => 'uniquename',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_environment_cvterm_schema()
|
|
|
+ * Purpose: To describe the structure of environment_cvterm to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_environment_cvterm_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'environment_cvterm',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'environment_cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'environment_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'cvterm_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'environment_cvterm_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_element_relationship_schema()
|
|
|
+ * Purpose: To describe the structure of element_relationship to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_element_relationship_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'element_relationship',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'element_relationship_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'element_relationship_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_elementresult_schema()
|
|
|
+ * Purpose: To describe the structure of elementresult to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_elementresult_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'elementresult',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'elementresult_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'element_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'quantification_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'signal' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'float',
|
|
|
+ 'size' => 'big',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'elementresult_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_elementresult_relationship_schema()
|
|
|
+ * Purpose: To describe the structure of elementresult_relationship to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_elementresult_relationship_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'elementresult_relationship',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'elementresult_relationship_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'subject_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'type_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'object_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'value' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ 'rank' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'int',
|
|
|
+ 'not null' => '1',
|
|
|
+ 'default' => '0',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'elementresult_relationship_id',
|
|
|
+ ),
|
|
|
+ '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',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|
|
|
+
|
|
|
+/****************************************************************************
|
|
|
+ * Implements hook_environment_schema()
|
|
|
+ * Purpose: To describe the structure of environment to tripal
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_insert()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_update()
|
|
|
+ * @see tripal_core.api.inc: tripal_core_chado_select()
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * An array describing the current table
|
|
|
+ */
|
|
|
+function tripal_core_chado_environment_schema () {
|
|
|
+ $description = array();
|
|
|
+
|
|
|
+ $description = array(
|
|
|
+ 'table' => 'environment',
|
|
|
+// 'description' => 'TODO: please describe this table!',
|
|
|
+ 'fields' => array(
|
|
|
+ 'environment_id' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'serial',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'uniquename' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '1',
|
|
|
+ ),
|
|
|
+ 'description' => array(
|
|
|
+// 'description' => 'TODO: please describe this field!',
|
|
|
+ 'type' => 'text',
|
|
|
+ 'not null' => '',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'primary key' => array(
|
|
|
+ '0' => 'environment_id',
|
|
|
+ ),
|
|
|
+ 'unique keys' => array(
|
|
|
+ 'environment_c1' => array(
|
|
|
+ '0' => 'uniquename',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'indexes' => array(
|
|
|
+ 'environment_idx1' => array(
|
|
|
+ '0' => 'uniquename',
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'foreign keys' => array(
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ return $description;
|
|
|
+}
|