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@@ -1,1129 +0,0 @@
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-<?php
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-/**
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- * @file
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- * Functions to install chado schema through Drupal
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- */
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-
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-/**
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- * Prepares Chado for Tripal use
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- */
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-function tripal_chado_prepare_form($form, $form_state) {
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- $form = array();
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-
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- if (variable_get('tripal_chado_is_prepared') == TRUE) {
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- drupal_set_message('Your site is prepared.');
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- }
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- $form['instructions'] = array(
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- '#type' => 'item',
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- '#title' => 'Prepare Drupal for Chado.',
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- '#description' => t("Before a Drupal site can use Chado (via Tripal), both
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- Chado and Drupal must be prepared a bit more. Tripal will add some new
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- materialized views, custom tables and controlled vocabularies to Chado.
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- It will also add some management tables to Drupal. You only are
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- required to prepare your Drupal site if this is a brand-new Drupal
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- installation or if Chado was installed outside of Tripal. If you
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- installed Chado using Tripal then you do not need to run this step.
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- If you are upgrading from a previous version of Tripal, you do not
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- need to prepare your site, and you can click the 'Skip' button."),
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- );
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-
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- $form['prepare-button'] = array(
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- '#type' => 'submit',
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- '#value' => t('Prepare this site'),
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- '#name' => 'prepare-chado',
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- );
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- $form['skip-button'] = array(
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- '#type' => 'submit',
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- '#value' => t('Skip'),
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- '#name' => 'prepare-skip',
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- );
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- return $form;
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-}
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-
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-/**
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- * Submit function for the tripal_chado_prepare_form().
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- *
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- * @param $form
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- * @param $form_state
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- */
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-function tripal_chado_prepare_form_submit($form, $form_state) {
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- if ($form_state['clicked_button']['#name'] == "prepare-chado") {
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- global $user;
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- $args = array();
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- $includes = array(
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- module_load_include('inc', 'tripal_chado', 'includes/tripal_chado.setup'),
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- module_load_include('inc', 'tripal_chado', 'includes/loaders/tripal_chado.obo_loader'),
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- );
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- tripal_add_job('Prepare Chado', 'tripal_chado',
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- 'tripal_chado_prepare_chado', $args,
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- $user->uid, 10, $includes);
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- }
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- if ($form_state['clicked_button']['#name'] == "prepare-skip") {
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- variable_set('tripal_chado_is_prepared', TRUE);
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- }
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-}
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-
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-/**
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- *
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- */
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-function tripal_chado_load_ontologies() {
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-
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- // Insert commonly used ontologies into the tables.
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- $ontologies = array(
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- array(
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- 'name' => 'Relationship Ontology (legacy)',
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- 'path' => '{tripal_chado}/files/legacy_ro.obo',
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- 'auto_load' => FALSE,
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- 'cv_name' => 'ro'
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- ),
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- array(
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- 'name' => 'Gene Ontology',
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- 'path' => 'http://purl.obolibrary.org/obo/go.obo',
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- 'auto_load' => FALSE,
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- 'cv_name' => 'cellualar_component'
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- ),
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- array(
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- 'name' => 'Taxonomic Rank',
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- 'path' => 'http://purl.obolibrary.org/obo/taxrank.obo',
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- 'auto_load' => TRUE,
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- 'cv_name' => 'taxonomic_rank'
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- ),
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- array(
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- 'name' => 'Tripal Contact',
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- 'path' => '{tripal_chado}/files/tcontact.obo',
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- 'auto_load' => TRUE,
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- 'cv_name' => 'tripal_contact'
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- ),
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- array(
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- 'name' => 'Tripal Publication',
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- 'path' => '{tripal_chado}/files/tpub.obo',
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- 'auto_load' => TRUE,
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- 'cv_name' => 'tripal_pub'
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- ),
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- array(
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- 'name' => 'Sequence Ontology',
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- 'path' => 'http://purl.obolibrary.org/obo/so.obo',
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- 'auto_load' => TRUE,
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- 'cv_name' => 'sequence'
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- ),
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-
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- );
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- for ($i = 0; $i < count($ontologies); $i++) {
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- $obo_id = tripal_insert_obo($ontologies[$i]['name'], $ontologies[$i]['path']);
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- if ($ontologies[$i]['auto_load'] == TRUE) {
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- // Only load ontologies that are not already in the cv table.
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- $cv = tripal_get_cv(array('name' => $ontologies[$i]['cv_name']));
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- if (!$cv) {
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- tripal_chado_load_obo_v1_2_id($obo_id);
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- }
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- }
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- }
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-}
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-/**
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- * Prepares Chado for use by Tripal.
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- */
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-function tripal_chado_prepare_chado() {
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-
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- try {
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-
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- // We want to provide a set of commonly used entity types by default. This
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- // way when a user first installs Tripal there are some commonly used
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- // formats.
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- module_load_include('inc', 'tripal', 'api/tripal.api');
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- module_load_include('inc', 'tripal', 'includes/tripal.admin');
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- module_load_include('inc', 'tripal_chado', 'includes/tripal_chado.semweb');
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-
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- // Get the effective version. Pass true as second argument
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- // to warn the user if the current version is not compatible.
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- $version = chado_get_version(FALSE, FALSE);
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-
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- // We want to force the version of Chado to be set properly.
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- $real_version = chado_get_version(TRUE);
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-
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- // Create the temp table we will use for loading OBO files.
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- tripal_chado_add_tripal_obo_temp_table();
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-
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- // Import commonly used ontologies if needed.
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- tripal_chado_load_ontologies();
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-
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- // Populate the semantic web associations for Chado tables/fields.
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- tripal_chado_populate_chado_semweb_table();
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-
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- // Initialize the population of the chado_cvterm_mapping table. This will
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- // map existing data types already in Chado so that when users want to
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- // add new content types it simplifies the form for them.
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- tripal_chado_map_cvterms();
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-
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- // Create the 'Organism' entity type. This uses the obi:organism term.
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- $error = '';
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- $args = array(
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- 'vocabulary' => 'OBI',
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- 'accession' => '0100026',
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- 'term_name' => 'organism',
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- 'storage_args' => array(
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- 'data_table' => 'organism',
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- )
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- );
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- $term = tripal_load_term_entity(array('vocabulary' => 'OBI', 'accession' => '0100026'));
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- $bundle = tripal_load_bundle_entity(array('term_id' => $term->id));
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- if (!$term or !$bundle) {
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- if (!tripal_create_bundle($args, $error)) {
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- throw new Exception($error['!message']);
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- }
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- }
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-
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- // Create the 'Analysis' entity type. This uses the local:analysis term.
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- $error = '';
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- $args = array(
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- 'vocabulary' => 'local',
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- 'accession' => 'analysis',
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- 'term_name' => 'analysis',
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- 'storage_args' => array(
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- 'data_table' => 'analysis',
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- )
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- );
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- $term = tripal_load_term_entity(array('vocabulary' => 'local', 'accession' => 'analysis'));
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- $bundle = tripal_load_bundle_entity(array('term_id' => $term->id));
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- if (!$term or !$bundle) {
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- if (!tripal_create_bundle($args, $error)) {
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- throw new Exception($error['!message']);
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- }
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- }
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-
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- // Create the 'Project' entity type. This uses the local:project term.
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- $error = '';
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- $args = array(
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- 'vocabulary' => 'local',
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- 'accession' => 'project',
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- 'term_name' => 'project',
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- 'storage_args' => array(
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- 'data_table' => 'project',
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- )
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- );
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- $term = tripal_load_term_entity(array('vocabulary' => 'local', 'accession' => 'project'));
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- $bundle = tripal_load_bundle_entity(array('term_id' => $term->id));
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- if (!$term or !$bundle) {
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- if (!tripal_create_bundle($args, $error)) {
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- throw new Exception($error['!message']);
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- }
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- }
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-
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- // Create the 'Map' entity type. This uses the local:project term.
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- $error = '';
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- $args = array(
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- 'vocabulary' => 'data',
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- 'accession' => '1274',
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- 'term_name' => 'Map',
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- 'storage_args' => array(
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- 'data_table' => 'featuremap',
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- )
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- );
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- $term = tripal_load_term_entity(array('vocabulary' => 'data', 'accession' => '1274'));
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- $bundle = tripal_load_bundle_entity(array('term_id' => $term->id));
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- if (!$term or !$bundle) {
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- if (!tripal_create_bundle($args, $error)) {
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- throw new Exception($error['!message']);
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- }
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- }
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-
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- // Import a publication so we get all of the properties before
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- // creating the content type.
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- tripal_import_pub_by_dbxref('PMID:24163125');
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-
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- // Create the 'Publication' entity type.
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- $error = '';
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- $args = array(
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- 'vocabulary' => 'TPUB',
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- 'accession' => '0000002',
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- 'term_name' => 'Publication',
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- 'storage_args' => array(
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- 'data_table' => 'pub',
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- )
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- );
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- $term = tripal_load_term_entity(array('vocabulary' => 'TPUB', 'accession' => '0000002'));
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- $bundle = tripal_load_bundle_entity(array('term_id' => $term->id));
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- if (!$term or !$bundle) {
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- if (!tripal_create_bundle($args, $error)) {
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- throw new Exception($error['!message']);
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- }
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- }
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-
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- // Now remove the publication that was added above.
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- $values = array(
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- 'dbxref_id' => array(
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- 'accession' => '24163125',
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- 'db_id' => array(
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- 'name' => 'PMID',
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- ),
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- ),
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- );
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- $result = chado_select_record('pub_dbxref', array('pub_id'), $values);
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- chado_delete_record('pub', array('pub_id' => $result[0]->pub_id));
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-
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- // Create the 'Gene' entity type.
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- $error = '';
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- $args = array(
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- 'vocabulary' => 'SO',
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- 'accession' => '0000704',
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- 'term_name' => 'gene',
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- 'storage_args' => array(
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- 'data_table' => 'feature',
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- 'type_column' => 'type_id',
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- )
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- );
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- $term = tripal_load_term_entity(array('vocabulary' => 'SO', 'accession' => '0000704'));
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- $bundle = tripal_load_bundle_entity(array('term_id' => $term->id));
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- if (!$term or !$bundle) {
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- if (!tripal_create_bundle($args, $error)) {
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- throw new Exception($error['!message']);
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- }
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- }
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-
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- // Create the 'mRNA' entity type.
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- $error = '';
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- $args = array(
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- 'vocabulary' => 'SO',
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- 'accession' => '0000234',
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- 'term_name' => 'mRNA',
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- 'storage_args' => array(
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- 'data_table' => 'feature',
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- 'type_column' => 'type_id',
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- )
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- );
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- $term = tripal_load_term_entity(array('vocabulary' => 'SO', 'accession' => '0000234'));
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- $bundle = tripal_load_bundle_entity(array('term_id' => $term->id));
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- if (!$term or !$bundle) {
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- if (!tripal_create_bundle($args, $error)) {
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- throw new Exception($error['!message']);
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- }
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- }
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-
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- // Add the cv_root_mview.
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- tripal_chado_add_cv_root_mview_mview();
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-
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- // Support for Analyses
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- // we may need the analysisfeatureprop table if it doesn't already exist
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- tripal_chado_add_analysisfeatureprop_table();
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-
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- // add materialized views
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- tripal_chado_add_analysis_organism_mview();
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-
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- // Support for Contacts
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- // Add the contactprop table to Chado.
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- tripal_chado_add_contactprop_table();
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-
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- // Support for Features
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- // Add the materialized view.
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- tripal_chado_add_organism_feature_count_mview();
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-
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- // Add the custom tables for the GFF loader.
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- tripal_chado_add_tripal_gff_temp_table();
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- tripal_chado_add_tripal_gffcds_temp_table();
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- tripal_chado_add_tripal_gffprotein_temp_table();
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-
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- // Support for FeatureMaps.
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- // add the featuremapprop table to Chado
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- tripal_chado_add_featuremap_dbxref_table();
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- tripal_chado_add_featuremapprop_table();
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- //tripal_chado_add_featuremappos_table();
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-
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- // Support for Libraries.
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- // add the materialized view
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- tripal_chado_add_library_feature_count_mview();
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-
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- // Support for Pubs.
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- // add the custom tables
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- tripal_chado_add_pubauthor_contact_table();
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- // Add the supported loaders
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- variable_set('tripal_pub_supported_dbs', array('PMID', 'AGL'));
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-
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- // Support for Stocks.
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- // add the materialized view
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- tripal_chado_add_organism_stock_count_mview();
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-
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- // Set a variable to indicate the site is prepared.
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- variable_set('tripal_chado_is_prepared', TRUE);
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- }
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- catch (Exception $e) {
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- throw new Exception($e);
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- }
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-}
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-
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-/**
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- * Creates a materialized view that stores the type & number of stocks per organism
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- *
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- * @ingroup tripal_stock
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- */
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-function tripal_chado_add_organism_stock_count_mview() {
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- $view_name = 'organism_stock_count';
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- $comment = 'Stores the type and number of stocks per organism';
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-
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- $schema = array(
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- 'description' => $comment,
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- 'table' => $view_name,
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- 'fields' => array(
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- 'organism_id' => array(
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- 'size' => 'big',
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- 'type' => 'int',
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- 'not null' => TRUE,
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- ),
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- 'genus' => array(
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- 'type' => 'varchar',
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- 'length' => '255',
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- 'not null' => TRUE,
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- ),
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- 'species' => array(
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- 'type' => 'varchar',
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- 'length' => '255',
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- 'not null' => TRUE,
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- ),
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- 'common_name' => array(
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- 'type' => 'varchar',
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- 'length' => '255',
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- 'not null' => FALSE,
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- ),
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- 'num_stocks' => array(
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- 'type' => 'int',
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- 'not null' => TRUE,
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- ),
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- 'cvterm_id' => array(
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- 'size' => 'big',
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- 'type' => 'int',
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- 'not null' => TRUE,
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- ),
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- 'stock_type' => array(
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- 'type' => 'varchar',
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- 'length' => '255',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'indexes' => array(
|
|
|
- 'organism_stock_count_idx1' => array('organism_id'),
|
|
|
- 'organism_stock_count_idx2' => array('cvterm_id'),
|
|
|
- 'organism_stock_count_idx3' => array('stock_type'),
|
|
|
- ),
|
|
|
- );
|
|
|
-
|
|
|
- $sql = "
|
|
|
- SELECT
|
|
|
- O.organism_id, O.genus, O.species, O.common_name,
|
|
|
- count(S.stock_id) as num_stocks,
|
|
|
- CVT.cvterm_id, CVT.name as stock_type
|
|
|
- FROM organism O
|
|
|
- INNER JOIN stock S ON O.Organism_id = S.organism_id
|
|
|
- INNER JOIN cvterm CVT ON S.type_id = CVT.cvterm_id
|
|
|
- GROUP BY
|
|
|
- O.Organism_id, O.genus, O.species, O.common_name, CVT.cvterm_id, CVT.name
|
|
|
- ";
|
|
|
-
|
|
|
- tripal_add_mview($view_name, 'tripal_stock', $schema, $sql, $comment);
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Add custom table related to publications
|
|
|
- * - pubauthor_contact
|
|
|
- *
|
|
|
- * @ingroup tripal_pub
|
|
|
- */
|
|
|
-function tripal_chado_add_pubauthor_contact_table() {
|
|
|
- $schema = array (
|
|
|
- 'table' => 'pubauthor_contact',
|
|
|
- 'fields' => array (
|
|
|
- 'pubauthor_contact_id' => array (
|
|
|
- 'type' => 'serial',
|
|
|
- 'not null' => true,
|
|
|
- ),
|
|
|
- 'contact_id' => array (
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => true,
|
|
|
- ),
|
|
|
- 'pubauthor_id' => array (
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => true,
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'primary key' => array (
|
|
|
- 0 => 'pubauthor_contact_id',
|
|
|
- ),
|
|
|
- 'unique keys' => array (
|
|
|
- 'pubauthor_contact_c1' => array (
|
|
|
- 0 => 'contact_id',
|
|
|
- 1 => 'pubauthor_id',
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'foreign keys' => array (
|
|
|
- 'contact' => array (
|
|
|
- 'table' => 'contact',
|
|
|
- 'columns' => array (
|
|
|
- 'contact_id' => 'contact_id',
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'pubauthor' => array (
|
|
|
- 'table' => 'pubauthor',
|
|
|
- 'columns' => array (
|
|
|
- 'pubauthor_id' => 'pubauthor_id',
|
|
|
- ),
|
|
|
- ),
|
|
|
- ),
|
|
|
- );
|
|
|
- chado_create_custom_table('pubauthor_contact', $schema, TRUE);
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
- * Adds a materialized view keeping track of the type of features associated with each library
|
|
|
- *
|
|
|
- * @ingroup tripal_library
|
|
|
- */
|
|
|
-function tripal_chado_add_library_feature_count_mview(){
|
|
|
- $view_name = 'library_feature_count';
|
|
|
- $comment = 'Provides count of feature by type that are associated with all libraries';
|
|
|
-
|
|
|
- $schema = array(
|
|
|
- 'table' => $view_name,
|
|
|
- 'description' => $comment,
|
|
|
- 'fields' => array(
|
|
|
- 'library_id' => array(
|
|
|
- 'size' => 'big',
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- 'name' => array(
|
|
|
- 'type' => 'varchar',
|
|
|
- 'length' => 255,
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- 'num_features' => array(
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- 'feature_type' => array(
|
|
|
- 'type' => 'varchar',
|
|
|
- 'length' => 255,
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'indexes' => array(
|
|
|
- 'library_feature_count_idx1' => array('library_id'),
|
|
|
- ),
|
|
|
- );
|
|
|
-
|
|
|
- $sql = "
|
|
|
- SELECT
|
|
|
- L.library_id, L.name,
|
|
|
- count(F.feature_id) as num_features,
|
|
|
- CVT.name as feature_type
|
|
|
- FROM library L
|
|
|
- INNER JOIN library_feature LF ON LF.library_id = L.library_id
|
|
|
- INNER JOIN feature F ON LF.feature_id = F.feature_id
|
|
|
- INNER JOIN cvterm CVT ON F.type_id = CVT.cvterm_id
|
|
|
- GROUP BY L.library_id, L.name, CVT.name
|
|
|
- ";
|
|
|
-
|
|
|
- tripal_add_mview($view_name, 'tripal_library', $schema, $sql, $comment);
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Add custom tables needed by the feature map module
|
|
|
- * - featuremapprop
|
|
|
- * - featuremap_dbxref
|
|
|
- * - featureposprop
|
|
|
- *
|
|
|
- * @ingroup tripal_featuremap
|
|
|
- */
|
|
|
-function tripal_chado_add_featuremapprop_table(){
|
|
|
- // add the featuremaprop table to Chado
|
|
|
- $schema = array (
|
|
|
- 'table' => 'featuremapprop',
|
|
|
- 'fields' => array (
|
|
|
- 'featuremapprop_id' => array (
|
|
|
- 'type' => 'serial',
|
|
|
- 'not null' => true,
|
|
|
- ),
|
|
|
- 'featuremap_id' => array (
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => true,
|
|
|
- ),
|
|
|
- 'type_id' => array (
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => true,
|
|
|
- ),
|
|
|
- 'value' => array (
|
|
|
- 'type' => 'text',
|
|
|
- 'not null' => false,
|
|
|
- ),
|
|
|
- 'rank' => array (
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => true,
|
|
|
- 'default' => 0,
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'primary key' => array (
|
|
|
- 0 => 'featuremapprop_id',
|
|
|
- ),
|
|
|
- 'unique keys' => array (
|
|
|
- 'featuremapprop_c1' => array (
|
|
|
- 0 => 'featuremap_id',
|
|
|
- 1 => 'type_id',
|
|
|
- 2 => 'rank',
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'indexes' => array (
|
|
|
- 'featuremapprop_idx1' => array (
|
|
|
- 0 => 'featuremap_id',
|
|
|
- ),
|
|
|
- 'featuremapprop_idx2' => array (
|
|
|
- 0 => 'type_id',
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'foreign keys' => array (
|
|
|
- 'cvterm' => array (
|
|
|
- 'table' => 'cvterm',
|
|
|
- 'columns' => array (
|
|
|
- 'type_id' => 'cvterm_id',
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'featuremap' => array (
|
|
|
- 'table' => 'featuremap',
|
|
|
- 'columns' => array (
|
|
|
- 'featuremap_id' => 'featuremap_id',
|
|
|
- ),
|
|
|
- ),
|
|
|
- ),
|
|
|
- );
|
|
|
- chado_create_custom_table('featuremapprop', $schema, TRUE);
|
|
|
-}
|
|
|
-/**
|
|
|
- *
|
|
|
- */
|
|
|
-function tripal_chado_add_featuremap_dbxref_table(){
|
|
|
- // add the featuremap_dbxref table to Chado
|
|
|
- $schema = array (
|
|
|
- 'table' => 'featuremap_dbxref',
|
|
|
- 'fields' => array (
|
|
|
- 'featuremap_dbxref_id' => array (
|
|
|
- 'type' => 'serial',
|
|
|
- 'not null' => true,
|
|
|
- ),
|
|
|
- 'featuremap_id' => array (
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => true,
|
|
|
- ),
|
|
|
- 'dbxref_id' => array (
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => true,
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'primary key' => array (
|
|
|
- 0 => 'featuremap_dbxref_id',
|
|
|
- ),
|
|
|
- 'unique keys' => array (
|
|
|
- 'featuremap_dbxref_c1' => array (
|
|
|
- 0 => 'featuremap_id',
|
|
|
- 1 => 'dbxref_id',
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'indexes' => array (
|
|
|
- 'featuremap_dbxref_idx1' => array (
|
|
|
- 0 => 'featuremap_dbxref_id',
|
|
|
- ),
|
|
|
- 'featuremap_dbxref_idx2' => array (
|
|
|
- 0 => 'dbxref_id',
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'foreign keys' => array (
|
|
|
- 'dbxref' => array (
|
|
|
- 'table' => 'dbxref',
|
|
|
- 'columns' => array (
|
|
|
- 'dbxref_id' => 'dbxref_id',
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'featuremap' => array (
|
|
|
- 'table' => 'featuremap',
|
|
|
- 'columns' => array (
|
|
|
- 'featuremap_id' => 'featuremap_id',
|
|
|
- ),
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'referring_tables' => NULL,
|
|
|
- );
|
|
|
- chado_create_custom_table('featuremap_dbxref', $schema, TRUE);
|
|
|
-}
|
|
|
-/**
|
|
|
- *
|
|
|
- */
|
|
|
-function tripal_chado_add_featureposprop_table(){
|
|
|
- $schema = array (
|
|
|
- 'table' => 'featureposprop',
|
|
|
- 'fields' => array (
|
|
|
- 'featureposprop_id' => array (
|
|
|
- 'type' => 'serial',
|
|
|
- 'not null' => true,
|
|
|
- ),
|
|
|
- 'featurepos_id' => array (
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => true,
|
|
|
- ),
|
|
|
- 'type_id' => array (
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => true,
|
|
|
- ),
|
|
|
- 'value' => array (
|
|
|
- 'type' => 'text',
|
|
|
- 'not null' => false,
|
|
|
- ),
|
|
|
- 'rank' => array (
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => true,
|
|
|
- 'default' => 0,
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'primary key' => array (
|
|
|
- 0 => 'featureposprop_id',
|
|
|
- ),
|
|
|
- 'unique keys' => array (
|
|
|
- 'featureposprop_id' => array (
|
|
|
- 0 => 'featurepos_id',
|
|
|
- 1 => 'type_id',
|
|
|
- 2 => 'rank',
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'indexes' => array (
|
|
|
- 'featureposprop_c1' => array (
|
|
|
- 0 => 'featurepos_id',
|
|
|
- ),
|
|
|
- 'featureposprop_idx2' => array (
|
|
|
- 0 => 'type_id',
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'foreign keys' => array (
|
|
|
- 'cvterm' => array (
|
|
|
- 'table' => 'cvterm',
|
|
|
- 'columns' => array (
|
|
|
- 'type_id' => 'cvterm_id',
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'featurepos' => array (
|
|
|
- 'table' => 'featurepos',
|
|
|
- 'columns' => array (
|
|
|
- 'featurepos_id' => 'featurepos_id',
|
|
|
- ),
|
|
|
- ),
|
|
|
- ),
|
|
|
- );
|
|
|
- chado_create_custom_table('featureposprop', $schema, TRUE);
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- *
|
|
|
- */
|
|
|
-function tripal_chado_add_tripal_gff_temp_table() {
|
|
|
- $schema = array(
|
|
|
- 'table' => 'tripal_gff_temp',
|
|
|
- 'fields' => array(
|
|
|
- 'feature_id' => array(
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- 'organism_id' => array(
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- 'uniquename' => array(
|
|
|
- 'type' => 'text',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- 'type_name' => array(
|
|
|
- 'type' => 'varchar',
|
|
|
- 'length' => '1024',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'indexes' => array(
|
|
|
- 'tripal_gff_temp_idx0' => array('feature_id'),
|
|
|
- 'tripal_gff_temp_idx0' => array('organism_id'),
|
|
|
- 'tripal_gff_temp_idx1' => array('uniquename'),
|
|
|
- ),
|
|
|
- 'unique keys' => array(
|
|
|
- 'tripal_gff_temp_uq0' => array('feature_id'),
|
|
|
- 'tripal_gff_temp_uq1' => array('uniquename', 'organism_id', 'type_name'),
|
|
|
- ),
|
|
|
- );
|
|
|
- chado_create_custom_table('tripal_gff_temp', $schema, TRUE);
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- *
|
|
|
- */
|
|
|
-function tripal_chado_add_tripal_gffcds_temp_table($skip_recreate = TRUE) {
|
|
|
- $schema = array(
|
|
|
- 'table' => 'tripal_gffcds_temp',
|
|
|
- 'fields' => array(
|
|
|
- 'feature_id' => array(
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- 'parent_id' => array(
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- 'phase' => array(
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => FALSE,
|
|
|
- ),
|
|
|
- 'strand' => array(
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- 'fmin' => array(
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- 'fmax' => array(
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'indexes' => array(
|
|
|
- 'tripal_gff_temp_idx0' => array('feature_id'),
|
|
|
- 'tripal_gff_temp_idx0' => array('parent_id'),
|
|
|
- ),
|
|
|
- );
|
|
|
- chado_create_custom_table('tripal_gffcds_temp', $schema, $skip_recreate);
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- *
|
|
|
- */
|
|
|
-function tripal_chado_add_tripal_gffprotein_temp_table() {
|
|
|
- $schema = array(
|
|
|
- 'table' => 'tripal_gffprotein_temp',
|
|
|
- 'fields' => array(
|
|
|
- 'feature_id' => array(
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- 'parent_id' => array(
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- 'fmin' => array(
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- 'fmax' => array(
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'indexes' => array(
|
|
|
- 'tripal_gff_temp_idx0' => array('feature_id'),
|
|
|
- 'tripal_gff_temp_idx0' => array('parent_id'),
|
|
|
- ),
|
|
|
- 'unique keys' => array(
|
|
|
- 'tripal_gff_temp_uq0' => array('feature_id'),
|
|
|
- ),
|
|
|
- );
|
|
|
- chado_create_custom_table('tripal_gffprotein_temp', $schema, TRUE);
|
|
|
-}
|
|
|
-/**
|
|
|
- * Creates a materialized view that stores the type & number of features per organism
|
|
|
- *
|
|
|
- * @ingroup tripal_feature
|
|
|
- */
|
|
|
-function tripal_chado_add_organism_feature_count_mview() {
|
|
|
- $view_name = 'organism_feature_count';
|
|
|
- $comment = 'Stores the type and number of features per organism';
|
|
|
-
|
|
|
- $schema = array(
|
|
|
- 'description' => $comment,
|
|
|
- 'table' => $view_name,
|
|
|
- 'fields' => array(
|
|
|
- 'organism_id' => array(
|
|
|
- 'size' => 'big',
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- 'genus' => array(
|
|
|
- 'type' => 'varchar',
|
|
|
- 'length' => '255',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- 'species' => array(
|
|
|
- 'type' => 'varchar',
|
|
|
- 'length' => '255',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- 'common_name' => array(
|
|
|
- 'type' => 'varchar',
|
|
|
- 'length' => '255',
|
|
|
- 'not null' => FALSE,
|
|
|
- ),
|
|
|
- 'num_features' => array(
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- 'cvterm_id' => array(
|
|
|
- 'size' => 'big',
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- 'feature_type' => array(
|
|
|
- 'type' => 'varchar',
|
|
|
- 'length' => '255',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'indexes' => array(
|
|
|
- 'organism_feature_count_idx1' => array('organism_id'),
|
|
|
- 'organism_feature_count_idx2' => array('cvterm_id'),
|
|
|
- 'organism_feature_count_idx3' => array('feature_type'),
|
|
|
- ),
|
|
|
- );
|
|
|
-
|
|
|
- $sql = "
|
|
|
- SELECT
|
|
|
- O.organism_id, O.genus, O.species, O.common_name,
|
|
|
- count(F.feature_id) as num_features,
|
|
|
- CVT.cvterm_id, CVT.name as feature_type
|
|
|
- FROM organism O
|
|
|
- INNER JOIN feature F ON O.Organism_id = F.organism_id
|
|
|
- INNER JOIN cvterm CVT ON F.type_id = CVT.cvterm_id
|
|
|
- GROUP BY
|
|
|
- O.Organism_id, O.genus, O.species, O.common_name, CVT.cvterm_id, CVT.name
|
|
|
- ";
|
|
|
-
|
|
|
- tripal_add_mview($view_name, 'tripal_feature', $schema, $sql, $comment);
|
|
|
-}
|
|
|
-/**
|
|
|
- * Add any custom tables needed by this module.
|
|
|
- * - Contactprop: keep track of properties of contact
|
|
|
- *
|
|
|
- * @ingroup tripal_contact
|
|
|
- */
|
|
|
-function tripal_chado_add_contactprop_table(){
|
|
|
- $schema = array (
|
|
|
- 'table' => 'contactprop',
|
|
|
- 'fields' => array (
|
|
|
- 'contactprop_id' => array (
|
|
|
- 'type' => 'serial',
|
|
|
- 'not null' => true,
|
|
|
- ),
|
|
|
- 'contact_id' => array (
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => true,
|
|
|
- ),
|
|
|
- 'type_id' => array (
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => true,
|
|
|
- ),
|
|
|
- 'value' => array (
|
|
|
- 'type' => 'text',
|
|
|
- 'not null' => false,
|
|
|
- ),
|
|
|
- 'rank' => array (
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => true,
|
|
|
- 'default' => 0,
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'primary key' => array (
|
|
|
- 0 => 'contactprop_id',
|
|
|
- ),
|
|
|
- 'unique keys' => array (
|
|
|
- 'contactprop_c1' => array (
|
|
|
- 0 => 'contact_id',
|
|
|
- 1 => 'type_id',
|
|
|
- 2 => 'rank',
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'indexes' => array (
|
|
|
- 'contactprop_idx1' => array (
|
|
|
- 0 => 'contact_id',
|
|
|
- ),
|
|
|
- 'contactprop_idx2' => array (
|
|
|
- 0 => 'type_id',
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'foreign keys' => array (
|
|
|
- 'cvterm' => array (
|
|
|
- 'table' => 'cvterm',
|
|
|
- 'columns' => array (
|
|
|
- 'type_id' => 'cvterm_id',
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'contact' => array (
|
|
|
- 'table' => 'contact',
|
|
|
- 'columns' => array (
|
|
|
- 'contact_id' => 'contact_id',
|
|
|
- ),
|
|
|
- ),
|
|
|
- ),
|
|
|
- );
|
|
|
- chado_create_custom_table('contactprop', $schema, TRUE);
|
|
|
-}
|
|
|
-/**
|
|
|
- * Create a legacy custom chado table (analysisfeatureprop) to store properties of
|
|
|
- * analysisfeature links.
|
|
|
- *
|
|
|
- * @ingroup tripal_analysis
|
|
|
- */
|
|
|
-function tripal_chado_add_analysisfeatureprop_table() {
|
|
|
-
|
|
|
- // Create analysisfeatureprop table in chado. This is needed for Chado
|
|
|
- // version 1.11, the table exists in Chado 1.2.
|
|
|
- if (!db_table_exists('chado.analysisfeatureprop')) {
|
|
|
- $sql = "
|
|
|
- CREATE TABLE {analysisfeatureprop} (
|
|
|
- analysisfeatureprop_id SERIAL PRIMARY KEY,
|
|
|
- analysisfeature_id INTEGER NOT NULL,
|
|
|
- type_id INTEGER NOT NULL,
|
|
|
- value TEXT,
|
|
|
- rank INTEGER NOT NULL,
|
|
|
- CONSTRAINT analysisfeature_id_type_id_rank UNIQUE (analysisfeature_id, type_id, rank),
|
|
|
- CONSTRAINT analysisfeatureprop_analysisfeature_id_fkey FOREIGN KEY (analysisfeature_id) REFERENCES {analysisfeature}(analysisfeature_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED,
|
|
|
- CONSTRAINT analysisfeatureprop_type_id_fkey FOREIGN KEY (type_id) REFERENCES {cvterm}(cvterm_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
|
|
|
- )
|
|
|
- ";
|
|
|
- chado_query($sql);
|
|
|
- }
|
|
|
-}
|
|
|
-/**
|
|
|
- * Creates a view showing the link between an organism & it's analysis through associated features.
|
|
|
- *
|
|
|
- * @ingroup tripal_analysis
|
|
|
- */
|
|
|
-function tripal_chado_add_analysis_organism_mview() {
|
|
|
- $view_name = 'analysis_organism';
|
|
|
- $comment = t('This view is for associating an organism (via it\'s associated features) to an analysis.');
|
|
|
-
|
|
|
- // this is the SQL used to identify the organism to which an analsysis
|
|
|
- // has been used. This is obtained though the analysisfeature -> feature -> organism
|
|
|
- // joins
|
|
|
- $sql = "
|
|
|
- SELECT DISTINCT A.analysis_id, O.organism_id
|
|
|
- FROM analysis A
|
|
|
- INNER JOIN analysisfeature AF ON A.analysis_id = AF.analysis_id
|
|
|
- INNER JOIN feature F ON AF.feature_id = F.feature_id
|
|
|
- INNER JOIN organism O ON O.organism_id = F.organism_id
|
|
|
- ";
|
|
|
-
|
|
|
- // the schema array for describing this view
|
|
|
- $schema = array(
|
|
|
- 'table' => $view_name,
|
|
|
- 'description' => $comment,
|
|
|
- 'fields' => array(
|
|
|
- 'analysis_id' => array(
|
|
|
- 'size' => 'big',
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- 'organism_id' => array(
|
|
|
- 'size' => 'big',
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'indexes' => array(
|
|
|
- 'networkmod_qtl_indx0' => array('analysis_id'),
|
|
|
- 'networkmod_qtl_indx1' => array('organism_id'),
|
|
|
- ),
|
|
|
- 'foreign keys' => array(
|
|
|
- 'analysis' => array(
|
|
|
- 'table' => 'analysis',
|
|
|
- 'columns' => array(
|
|
|
- 'analysis_id' => 'analysis_id',
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'organism' => array(
|
|
|
- 'table' => 'organism',
|
|
|
- 'columns' => array(
|
|
|
- 'organism_id' => 'organism_id',
|
|
|
- ),
|
|
|
- ),
|
|
|
- ),
|
|
|
- );
|
|
|
-
|
|
|
- // add the view
|
|
|
- tripal_add_mview($view_name, 'tripal_analysis', $schema, $sql, $comment);
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Add a materialized view of root terms for all chado cvs. This is needed for viewing cv trees
|
|
|
- *
|
|
|
- * @ingroup tripal_cv
|
|
|
- */
|
|
|
-function tripal_chado_add_cv_root_mview_mview() {
|
|
|
- $mv_name = 'cv_root_mview';
|
|
|
- $comment = 'A list of the root terms for all controlled vocabularies. This is needed for viewing CV trees';
|
|
|
- $schema = array(
|
|
|
- 'table' => $mv_name,
|
|
|
- 'description' => $comment,
|
|
|
- 'fields' => array(
|
|
|
- 'name' => array(
|
|
|
- 'type' => 'varchar',
|
|
|
- 'length' => 255,
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- 'cvterm_id' => array(
|
|
|
- 'size' => 'big',
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- 'cv_id' => array(
|
|
|
- 'size' => 'big',
|
|
|
- 'type' => 'int',
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- 'cv_name' => array(
|
|
|
- 'type' => 'varchar',
|
|
|
- 'length' => 255,
|
|
|
- 'not null' => TRUE,
|
|
|
- ),
|
|
|
- ),
|
|
|
- 'indexes' => array(
|
|
|
- 'cv_root_mview_indx1' => array('cvterm_id'),
|
|
|
- 'cv_root_mview_indx2' => array('cv_id'),
|
|
|
- ),
|
|
|
- );
|
|
|
-
|
|
|
- $sql = "
|
|
|
- SELECT DISTINCT CVT.name,CVT.cvterm_id, CV.cv_id, CV.name
|
|
|
- FROM cvterm_relationship CVTR
|
|
|
- INNER JOIN cvterm CVT on CVTR.object_id = CVT.cvterm_id
|
|
|
- INNER JOIN cv CV on CV.cv_id = CVT.cv_id
|
|
|
- WHERE CVTR.object_id not in
|
|
|
- (SELECT subject_id FROM cvterm_relationship)
|
|
|
- ";
|
|
|
-
|
|
|
- // Create the MView
|
|
|
- tripal_add_mview($mv_name, 'tripal_cv', $schema, $sql, $comment);
|
|
|
-}
|
|
|
-/**
|
|
|
- * Creates a temporary table to store obo details while loading an obo file
|
|
|
- *
|
|
|
- * @ingroup tripal_cv
|
|
|
- */
|
|
|
-function tripal_chado_add_tripal_obo_temp_table() {
|
|
|
- // the tripal_obo_temp table is used for temporary housing of records when loading OBO files
|
|
|
- // we create it here using plain SQL because we want it to be in the chado schema but we
|
|
|
- // do not want to use the Tripal Custom Table API because we don't want it to appear in the
|
|
|
- // list of custom tables. It needs to be available for the Tripal Chado API so we create it
|
|
|
- // here and then define it in the tripal_cv/api/tripal_cv.schema.api.inc
|
|
|
- if (!chado_table_exists('tripal_obo_temp')) {
|
|
|
- $sql = "
|
|
|
- CREATE TABLE {tripal_obo_temp} (
|
|
|
- id character varying(255) NOT NULL,
|
|
|
- stanza text NOT NULL,
|
|
|
- type character varying(50) NOT NULL,
|
|
|
- CONSTRAINT tripal_obo_temp_uq0 UNIQUE (id)
|
|
|
- );
|
|
|
- ";
|
|
|
- chado_query($sql);
|
|
|
- $sql = "CREATE INDEX tripal_obo_temp_idx0 ON {tripal_obo_temp} USING btree (id)";
|
|
|
- chado_query($sql);
|
|
|
- $sql = "CREATE INDEX tripal_obo_temp_idx1 ON {tripal_obo_temp} USING btree (type)";
|
|
|
- chado_query($sql);
|
|
|
- }
|
|
|
-}
|
|
|
-
|
Stephen Ficklin