123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151 |
- <?php
- /**
- * @file
- * Installation of the feature module
- */
- /**
- * Implements hook_disable().
- *
- * Disable default views when module is disabled
- *
- * @ingroup tripal_legacy_feature
- */
- function tripal_feature_disable() {
- // Disable all default views provided by this module
- require_once("tripal_feature.views_default.inc");
- $views = tripal_feature_views_default_views();
- foreach (array_keys($views) as $view_name) {
- tripal_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
- }
- }
- /**
- * Implements hook_requirements().
- *
- * @ingroup tripal_legacy_feature
- */
- function tripal_feature_requirements($phase) {
- $requirements = array();
- if ($phase == 'install') {
- // make sure chado is installed
- if (!$GLOBALS["chado_is_installed"]) {
- $requirements ['tripal_feature'] = array(
- 'title' => "t ripal_feature",
- 'value' => "ERROR: Chado must be installed before this module can be enabled",
- 'severity' => REQUIREMENT_ERROR,
- );
- }
- }
- return $requirements;
- }
- /**
- * Implements hook_install().
- *
- * @ingroup tripal_legacy_feature
- */
- function tripal_feature_install() {
- // Note: the feature_property OBO that came with Chado v1.2 should not
- // be automatically installed. Some of the terms are duplicates of
- // others in better maintained vocabularies. New Tripal sites should
- // use those.
- // $obo_path = '{tripal_feature}/files/feature_property.obo';
- // $obo_id = tripal_insert_obo('Chado Feature Properties', $obo_path);
- // tripal_submit_obo_job(array('obo_id' => $obo_id));
- // Add the vocabularies used by the feature module.
- tripal_feature_add_cvs();
- // Set the default vocabularies.
- tripal_set_default_cv('feature', 'type_id', 'sequence');
- tripal_set_default_cv('featureprop', 'type_id', 'feature_property');
- tripal_set_default_cv('feature_relationship', 'type_id', 'feature_relationship');
- }
- /**
- * Implements hook_uninstall().
- *
- * @ingroup tripal_legacy_feature
- */
- function tripal_feature_uninstall() {
- }
- /**
- * Implementation of hook_schema().
- *
- * @ingroup tripal_legacy_feature
- */
- function tripal_feature_schema() {
- $schema['chado_feature'] = array(
- 'fields' => array(
- 'vid' => array(
- 'type' => 'int',
- 'unsigned' => TRUE,
- 'not null' => TRUE,
- 'default' => 0
- ),
- 'nid' => array(
- 'type' => 'int',
- 'unsigned' => TRUE,
- 'not null' => TRUE,
- 'default' => 0
- ),
- 'feature_id' => array(
- 'type' => 'int',
- 'not null' => TRUE,
- 'default' => 0
- ),
- 'sync_date' => array(
- 'type' => 'int',
- 'not null' => FALSE,
- 'description' => 'UNIX integer sync date/time'
- ),
- ),
- 'indexes' => array(
- 'chado_feature_idx1' => array('feature_id')
- ),
- 'unique keys' => array(
- 'chado_feature_uq1' => array('nid', 'vid'),
- 'chado_feature_uq2' => array('vid')
- ),
- 'primary key' => array('nid'),
- );
- return $schema;
- };
- /**
- * Add cvs related to publications
- *
- * @ingroup tripal_pub
- */
- function tripal_feature_add_cvs() {
- // Add cv for relationship types
- tripal_insert_cv(
- 'feature_relationship',
- 'Contains types of relationships between features.'
- );
- // The feature_property CV may already exists. It comes with Chado, but
- // we need to add it just in case it doesn't get added before the feature
- // module is installed. But as of Tripal v3.0 the Chado version of this
- // vocabulary is no longer loaded by default.
- tripal_insert_cv(
- 'feature_property',
- 'Stores properties about features'
- );
- // the feature type vocabulary should be the sequence ontology, and even though
- // this ontology should get loaded we will create it here just so that we can
- // set the default vocabulary for the feature.type_id field
- tripal_insert_cv(
- 'sequence',
- 'The Sequence Ontology'
- );
- }
|