Organism Module
- 2.x tripal_organism/tripal_organism.module tripal_organism
- 1.x tripal_organism/tripal_organism.module tripal_organism
@file
Parent topics
File
- tripal_organism/
tripal_organism.module, line 6 - tripal_organism Organism Module
Functions
Name |
Location | Description |
|---|---|---|
| chado_organism_access |
tripal_organism/ |
Implement hook_access(). |
| chado_organism_add_image |
tripal_organism/ |
|
| chado_organism_delete |
tripal_organism/ |
Delete organism from both drupal and chado databases. Check dependency before deleting from chado. |
| chado_organism_form |
tripal_organism/ |
When editing or creating a new node of type 'chado_organism' we need a form. This function creates the form that will be used for this. |
| chado_organism_insert |
tripal_organism/ |
When a new chado_organism node is created we also need to add information to our chado_organism table. This function is called on insert of a new node of type 'chado_organism' and inserts the necessary information. |
| chado_organism_load |
tripal_organism/ |
When a node is requested by the user this function is called to allow us to add auxiliary data to the node object. |
| chado_organism_update |
tripal_organism/ |
Update organisms |
| chado_organism_validate |
tripal_organism/ |
|
| chado_organism_view |
tripal_organism/ |
This function customizes the view of the chado_organism node. It allows us to generate the markup. |
| get_chado_organisms |
tripal_organism/ |
This function uses organism_id's of all drupal organism nodes as input and pull the organism information (genus, species, common_name, comment) from chado database. The return type is an object array that stores $organism objects sorted by… |
| get_tripal_organism_admin_form_cleanup_set |
tripal_organism/ |
|
| get_tripal_organism_admin_form_reindex_set |
tripal_organism/ |
|
| get_tripal_organism_admin_form_sync_set |
tripal_organism/ |
|
| get_tripal_organism_admin_form_taxonomy_set |
tripal_organism/ |
|
| tripal_organism_admin |
tripal_organism/ |
Administrative settings for chado_orgnism |
| tripal_organism_admin_validate |
tripal_organism/ |
|
| tripal_organism_block |
tripal_organism/ |
Display block with organisms |
| tripal_organism_cleanup |
tripal_organism/ |
Remove orphaned drupal nodes |
| tripal_organism_cron |
tripal_organism/ |
|
| tripal_organism_get_schemas |
tripal_organism/ |
This function simply defines all tables needed for the module to work correctly. By putting the table definitions in a separate function we can easily provide the entire list for hook_install or individual tables for an update. |
| tripal_organism_help |
tripal_organism/ |
Display help and module information |
| tripal_organism_init |
tripal_organism/ |
|
| tripal_organism_install |
tripal_organism/ |
Implementation of hook_install(). |
| tripal_organism_job_describe_args |
tripal_organism/ |
|
| tripal_organism_menu |
tripal_organism/ |
Menu items are automatically added for the new node types created by this module to the 'Create Content' Navigation menu item. This function adds more menu items needed for this module. |
| tripal_organism_nodeapi |
tripal_organism/ |
|
| tripal_organism_node_info |
tripal_organism/ |
Provide information to drupal about the node types that we're creating in this module |
| tripal_organism_perm |
tripal_organism/ |
Set the permission types that the chado module uses. Essentially we want permissionis that protect creation, editing and deleting of chado data objects |
| tripal_organism_reindex_features |
tripal_organism/ |
|
| tripal_organism_schema |
tripal_organism/ |
Implementation of hook_schema(). |
| tripal_organism_sync_organisms |
tripal_organism/ |
Synchronize organisms from chado to drupal |
| tripal_organism_taxonify_features |
tripal_organism/ |
|
| tripal_organism_theme |
tripal_organism/ |
We need to let drupal know about our theme functions and their arguments. We create theme functions to allow users of the module to customize the look and feel of the output generated in this module |
| tripal_organism_uninstall |
tripal_organism/ |
Implementation of hook_uninstall(). |
| tripal_organism_views_api |
tripal_organism/ |
Implements hook_views_api() Purpose: Essentially this hook tells drupal that there is views support for for this module which then includes tripal_db.views.inc where all the views integration code is |