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Tripal 0.3b
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Tripal 0.3b
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| chado_organism_access | ( | $ | op, |
| $ | node, | ||
| $ | account | ||
| ) |
The following function proves access control for users trying to perform actions on data managed by this module
Definition at line 132 of file tripal_organism.module.
| chado_organism_add_image | ( | $ | node | ) |
Definition at line 807 of file tripal_organism.module.
Referenced by chado_organism_insert(), and chado_organism_update().
| chado_organism_delete | ( | $ | node | ) |
Delete organism from both drupal and chado databases. Check dependency before deleting from chado.
Definition at line 767 of file tripal_organism.module.
References chado_get_id_for_node(), tripal_core_chado_delete(), and tripal_db_set_active().
| chado_organism_form | ( | $ | node, |
| $ | param | ||
| ) |
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.
Definition at line 832 of file tripal_organism.module.
References tripal_core_expand_chado_vars().
| chado_organism_insert | ( | $ | node | ) |
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.
Definition at line 688 of file tripal_organism.module.
References chado_get_id_for_node(), chado_organism_add_image(), chado_query(), and tripal_core_chado_insert().
| chado_organism_load | ( | $ | node | ) |
When a node is requested by the user this function is called to allow us to add auxiliary data to the node object.
Definition at line 916 of file tripal_organism.module.
References chado_get_id_for_node(), tripal_core_expand_chado_vars(), and tripal_core_generate_chado_var().
| chado_organism_update | ( | $ | node | ) |
Update organisms
Definition at line 733 of file tripal_organism.module.
References chado_get_id_for_node(), chado_organism_add_image(), and tripal_core_chado_update().
| chado_organism_validate | ( | $ | node, |
| &$ | form | ||
| ) |
Definition at line 667 of file tripal_organism.module.
References tripal_core_chado_select().
| chado_organism_view | ( | $ | node, |
| $ | teaser = FALSE, |
||
| $ | page = FALSE |
||
| ) |
This function customizes the view of the chado_organism node. It allows us to generate the markup.
Definition at line 935 of file tripal_organism.module.
| get_chado_organisms | ( | ) |
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 $organism objects sorted by common_name
Definition at line 1079 of file tripal_organism.module.
References tripal_db_set_active().
Referenced by tripal_organism_show_organisms().
| get_tripal_organism_admin_form_cleanup_set | ( | &$ | form | ) |
Definition at line 337 of file tripal_organism.module.
Referenced by tripal_organism_admin().
| get_tripal_organism_admin_form_reindex_set | ( | &$ | form | ) |
Definition at line 408 of file tripal_organism.module.
References tripal_db_set_active().
Referenced by tripal_organism_admin().
| get_tripal_organism_admin_form_sync_set | ( | &$ | form | ) |
Definition at line 452 of file tripal_organism.module.
References tripal_db_set_active(), and tripal_get_module_active_jobs().
Referenced by tripal_organism_admin().
| get_tripal_organism_admin_form_taxonomy_set | ( | &$ | form | ) |
Definition at line 362 of file tripal_organism.module.
References tripal_db_set_active().
Referenced by tripal_organism_admin().
| theme_tripal_organism_organism_page | ( | $ | organisms | ) |
Definition at line 1036 of file tripal_organism.module.
| tripal_organism_admin | ( | ) |
Administrative settings for chado_orgnism
Definition at line 302 of file tripal_organism.module.
References get_tripal_organism_admin_form_cleanup_set(), get_tripal_organism_admin_form_reindex_set(), get_tripal_organism_admin_form_sync_set(), get_tripal_organism_admin_form_taxonomy_set(), and tripal_get_module_active_jobs().
| tripal_organism_admin_validate | ( | $ | form, |
| &$ | form_state | ||
| ) |
Definition at line 528 of file tripal_organism.module.
References $user, tripal_add_job(), and tripal_db_set_active().
| tripal_organism_block | ( | $ | op = 'list', |
| $ | delta = '0', |
||
| $ | edit = array() |
||
| ) |
Display block with organisms
| op | - parameter to define the phase being called for the block |
| delta | - id of the block to return (ignored when op is list) |
| edit | - when op is save, contains the submitted form data |
Definition at line 49 of file tripal_organism.module.
| tripal_organism_cron | ( | ) |
Definition at line 656 of file tripal_organism.module.
| tripal_organism_get_schemas | ( | ) |
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.
Definition at line 71 of file tripal_organism.install.
Referenced by tripal_organism_schema().
| tripal_organism_get_synced | ( | ) |
Returns a list of organisms that are currently synced with Drupal
Definition at line 1196 of file tripal_organism.module.
References tripal_db_set_active().
Referenced by get_tripal_feature_admin_form_sync_set().
| tripal_organism_help | ( | $ | path, |
| $ | arg | ||
| ) |
Display help and module information
| path | which path of the site we're displaying help |
| arg | array that holds the current path as would be returned from arg() function |
Definition at line 1002 of file tripal_organism.module.
| tripal_organism_init | ( | ) |
Definition at line 14 of file tripal_organism.module.
| tripal_organism_install | ( | ) |
Implementation of hook_install();
Definition at line 8 of file tripal_organism.install.
References tripal_create_moddir().
| tripal_organism_menu | ( | ) |
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.
Definition at line 95 of file tripal_organism.module.
| tripal_organism_module_description_page | ( | ) |
Purpose: Provide Guidance to new Tripal Admin
Definition at line 167 of file tripal_organism.module.
| tripal_organism_node_info | ( | ) |
Provide information to drupal about the node types that we're creating in this module
Definition at line 26 of file tripal_organism.module.
| tripal_organism_nodeapi | ( | &$ | node, |
| $ | op, | ||
| $ | teaser, | ||
| $ | page | ||
| ) |
Definition at line 643 of file tripal_organism.module.
| tripal_organism_perm | ( | ) |
Set the permission types that the chado module uses. Essentially we want permissionis that protect creation, editing and deleting of chado data objects
Definition at line 151 of file tripal_organism.module.
| tripal_organism_reindex_features | ( | $ | organism_id = NULL, |
| $ | job_id = NULL |
||
| ) |
Definition at line 1112 of file tripal_organism.module.
References tripal_db_set_active(), tripal_feature_sync_feature(), and tripal_job_set_progress().
| tripal_organism_requirements | ( | $ | phase | ) |
Implementation of hook_requirements(). Make sure 'Tripal Core' is enabled before installation
Definition at line 112 of file tripal_organism.install.
| tripal_organism_schema | ( | ) |
Implementation of hook_schema().
Definition at line 32 of file tripal_organism.install.
References tripal_organism_get_schemas().
| tripal_organism_show_organisms | ( | ) |
Display the summary view of organisms when click on the 'Organisms' primary-link
Definition at line 1020 of file tripal_organism.module.
References get_chado_organisms().
| tripal_organism_sync_organisms | ( | $ | organism_id = NULL, |
| $ | job_id = NULL |
||
| ) |
Synchronize organisms from chado to drupal
Definition at line 946 of file tripal_organism.module.
References $user, and tripal_db_set_active().
| tripal_organism_taxonify_features | ( | $ | organism_id = NULL, |
| $ | job_id = NULL |
||
| ) |
Definition at line 1149 of file tripal_organism.module.
References tripal_db_set_active(), tripal_feature_set_taxonomy(), tripal_feature_set_vocabulary(), and tripal_job_set_progress().
| tripal_organism_theme | ( | ) |
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
Definition at line 620 of file tripal_organism.module.
| tripal_organism_uninstall | ( | ) |
Implementation of hook_uninstall()
Definition at line 42 of file tripal_organism.install.
| tripal_organism_views_api | ( | ) |
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
Definition at line 1295 of file tripal_organism.module.
| tripal_organisms_cleanup | ( | $ | dummy = NULL, |
| $ | job_id = NULL |
||
| ) |
Definition at line 1221 of file tripal_organism.module.
References tripal_job_set_progress().
1.7.4 
