tripal_library.install
- 2.x tripal_library/tripal_library.install
- 3.x legacy/tripal_library/tripal_library.install
- 1.x tripal_library/tripal_library.install
Installation of the library module
File
legacy/tripal_library/tripal_library.installView source
- <?php
- /**
- * @file
- * Installation of the library module
- */
-
- /**
- * Implements hook_disable().
- * Disable default views when module is disabled
- *
- * @ingroup tripal_legacy_library
- */
- function tripal_library_disable() {
-
- // Disable all default views provided by this module
- require_once("tripal_library.views_default.inc");
- $views = tripal_library_views_default_views();
- foreach (array_keys($views) as $view_name) {
- tripal_disable_view($view_name,FALSE,array('suppress_error' => TRUE));
- }
-
- }
-
- /**
- * Implementation of hook_requirements().
- *
- * @ingroup tripal_legacy_library
- */
- function tripal_library_requirements($phase) {
- $requirements = array();
- if ($phase == 'install') {
- // make sure chado is installed
- if (!$GLOBALS["chado_is_installed"]) {
- $requirements ['tripal_library'] = array(
- 'title' => "tripal_library",
- 'value' => "ERROR: Chado must be installed before this module can be enabled",
- 'severity' => REQUIREMENT_ERROR,
- );
- }
- }
- return $requirements;
- }
-
- /**
- * Implementation of hook_install().
- *
- * @ingroup tripal_legacy_library
- */
- function tripal_library_install() {
-
- // add cvterms
- tripal_library_add_cvs();
- tripal_library_add_cvterms();
-
- // set the default vocabularies
- tripal_set_default_cv('libraryprop', 'type_id', 'library_property');
- tripal_set_default_cv('library', 'type_id', 'library_type');
- }
-
- /**
- * Implementation of hook_uninstall().
- *
- * @ingroup tripal_legacy_library
- */
- function tripal_library_uninstall() {
-
- }
-
- /**
- * Implementation of hook_schema().
- *
- * @ingroup tripal_legacy_library
- */
- function tripal_library_schema() {
- $schema['chado_library'] = 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
- ),
- 'library_id' => array(
- 'type' => 'int',
- 'not null' => TRUE,
- 'default' => 0
- )
- ),
- 'indexes' => array(
- 'chado_library_idx1' => array('library_id')
- ),
- 'unique keys' => array(
- 'chado_library_uq1' => array('nid', 'vid'),
- 'chado_library_uq2' => array('vid')
- ),
- 'primary key' => array('nid'),
- );
- return $schema;
- }
-
- /**
- * Adds new CV's used by this module
- *
- * @ingroup tripal_legacy_library
- */
- function tripal_library_add_cvs(){
- tripal_insert_cv(
- 'library_property',
- 'Contains properties for libraries.'
- );
- tripal_insert_cv(
- 'library_type',
- 'Contains terms for types of libraries (e.g. BAC, cDNA, FOSMID, etc).'
- );
- }
-
- /**
- * Adds cvterms needed for the library module
- *
- * @ingroup tripal_legacy_library
- */
- function tripal_library_add_cvterms() {
-
- // Insert cvterm 'library_description' into cvterm table of chado
- // database. This CV term is used to keep track of the library
- // description in the libraryprop table.
- tripal_insert_cvterm(
- array(
- 'name' => 'Library Description',
- 'definition' => 'Description of a library',
- 'cv_name' => 'library_property',
- 'is_relationship' => 0,
- 'db_name' => 'tripal'
- ),
- array('update_existing' => TRUE)
- );
-
- // add cvterms for the map unit types
- tripal_insert_cvterm(
- array(
- 'name' => 'cdna_library',
- 'definition' => 'cDNA library',
- 'cv_name' => 'library_type',
- 'is_relationship' => 0,
- 'db_name' => 'tripal'
- ),
- array('update_existing' => TRUE)
- );
- tripal_insert_cvterm(
- array(
- 'name' => 'bac_library',
- 'definition' => 'Bacterial Artifical Chromsome (BAC) library',
- 'cv_name' => 'library_type',
- 'is_relationship' => 0,
- 'db_name' => 'tripal'
- ),
- array('update_existing' => TRUE)
- );
- tripal_insert_cvterm(
- array(
- 'name' => 'fosmid_library',
- 'definition' => 'Fosmid library',
- 'cv_name' => 'library_type',
- 'is_relationship' => 0,
- 'db_name' => 'tripal'
- ),
- array('update_existing' => TRUE)
- );
- tripal_insert_cvterm(
- array(
- 'name' => 'cosmid_library',
- 'definition' => 'Cosmid library',
- 'cv_name' => 'library_type',
- 'is_relationship' => 0,
- 'db_name' => 'tripal'
- ),
- array('update_existing' => TRUE)
- );
- tripal_insert_cvterm(
- array(
- 'name' => 'yac_library',
- 'definition' => 'Yeast Artificial Chromosome (YAC) library',
- 'cv_name' => 'library_type',
- 'is_relationship' => 0,
- 'db_name' => 'tripal'
- ),
- array('update_existing' => TRUE)
- );
- tripal_insert_cvterm(
- array(
- 'name' => 'genomic_library',
- 'definition' => 'Genomic Library',
- 'cv_name' => 'library_type',
- 'is_relationship' => 0,
- 'db_name' => 'tripal'
- ),
- array('update_existing' => TRUE)
- );
- }