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Tripal 0.3b
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Tripal 0.3b
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Provides functions for managing chado libraries including creating details pages for each library
| chado_library_access | ( | $ | op, |
| $ | node, | ||
| $ | account | ||
| ) |
Set the permission types that the module uses.
Definition at line 75 of file tripal_library.module.
| chado_library_delete | ( | &$ | node | ) |
Delete data from drupal and chado databases when a node is deleted
Definition at line 1450 of file tripal_library.module.
References tripal_db_set_active().
| chado_library_form | ( | $ | node | ) |
When editing or creating a new node of type 'chado_library' we need a form. This function creates the form that will be used for this.
Definition at line 1028 of file tripal_library.module.
References tripal_db_set_active(), and tripal_library_get_property().
| chado_library_insert | ( | $ | node | ) |
When a new chado_library node is created we also need to add information to our chado_library table. This function is called on insert of a new node of type 'chado_library' and inserts the necessary information.
Definition at line 894 of file tripal_library.module.
References chado_get_id_for_node(), tripal_core_chado_insert(), tripal_core_chado_select(), and tripal_library_insert_property().
| chado_library_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 1196 of file tripal_library.module.
References chado_get_id_for_node(), and tripal_core_generate_chado_var().
| chado_library_update | ( | $ | node | ) |
Update nodes
Definition at line 939 of file tripal_library.module.
References chado_get_id_for_node(), tripal_core_chado_select(), tripal_core_chado_update(), and tripal_library_update_property().
| chado_library_validate | ( | $ | node | ) |
validates submission of form when adding or updating a library node
Definition at line 860 of file tripal_library.module.
References tripal_db_set_active().
| chado_library_view | ( | $ | node, |
| $ | teaser = FALSE, |
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| $ | page = FALSE |
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| ) |
This function customizes the view of the chado_library node. It allows us to generate the markup. This function is required for node [Preview]
Definition at line 1213 of file tripal_library.module.
References tripal_db_set_active().
| get_tripal_library_admin_form_cleanup_set | ( | &$ | form | ) |
Definition at line 533 of file tripal_library.module.
Referenced by tripal_library_admin().
| get_tripal_library_admin_form_menu_set | ( | &$ | form | ) |
Definition at line 499 of file tripal_library.module.
Referenced by tripal_library_admin().
| get_tripal_library_admin_form_reindex_set | ( | &$ | form | ) |
Definition at line 604 of file tripal_library.module.
References tripal_db_set_active().
Referenced by tripal_library_admin().
| get_tripal_library_admin_form_sync_set | ( | &$ | form | ) |
Definition at line 648 of file tripal_library.module.
References tripal_db_set_active().
Referenced by tripal_library_admin().
| get_tripal_library_admin_form_taxonomy_set | ( | &$ | form | ) |
Definition at line 558 of file tripal_library.module.
References tripal_db_set_active().
Referenced by tripal_library_admin().
| theme_tripal_library_library_table | ( | $ | libraries | ) |
This function creates the html markup for the library table. It can be overridden in the theme for the site by adding a php method in the template.php file named [theme_name]_tripal_library_library_table(&$libraries)
Definition at line 1244 of file tripal_library.module.
| theme_tripal_library_node_libraries | ( | $ | node | ) |
This function shows library information on an organism/feature node
Definition at line 449 of file tripal_library.module.
References tripal_db_set_active().
| theme_tripal_library_search_index | ( | $ | node | ) |
This function is an extension of the chado_feature_view and chado_organism_view by providing the markup for the library object THAT WILL BE INDEXED.
Definition at line 393 of file tripal_library.module.
References tripal_db_set_active().
| tripal_library_add_taxonomy | ( | $ | node, |
| $ | library_id | ||
| ) |
Add the library as a taxonomy term for associating with library_features
Definition at line 976 of file tripal_library.module.
| tripal_library_admin | ( | ) |
Administrative settings form
Definition at line 266 of file tripal_library.module.
References get_tripal_library_admin_form_cleanup_set(), get_tripal_library_admin_form_menu_set(), get_tripal_library_admin_form_reindex_set(), get_tripal_library_admin_form_sync_set(), get_tripal_library_admin_form_taxonomy_set(), and tripal_get_module_active_jobs().
| tripal_library_admin_validate | ( | $ | form, |
| &$ | form_state | ||
| ) |
Definition at line 717 of file tripal_library.module.
References $user, tripal_add_job(), and tripal_db_set_active().
| tripal_library_block | ( | $ | op = 'list', |
| $ | delta = '0', |
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| $ | edit = array() |
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| ) |
Display block with libraries
| 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 1488 of file tripal_library.module.
| tripal_library_cleanup | ( | $ | dummy = NULL, |
| $ | job_id = NULL |
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| ) |
Definition at line 1606 of file tripal_library.module.
References tripal_job_set_progress().
| tripal_library_cron | ( | ) |
Definition at line 822 of file tripal_library.module.
| tripal_library_feature_set_taxonomy | ( | $ | library_id = NULL | ) |
Definition at line 1290 of file tripal_library.module.
References tripal_db_set_active().
| tripal_library_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 104 of file tripal_library.install.
Referenced by tripal_library_schema().
| tripal_library_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 22 of file tripal_library.module.
| tripal_library_install | ( | ) |
Implementation of hook_install();
Definition at line 8 of file tripal_library.install.
References tripal_add_cvterms(), tripal_add_mview(), tripal_create_moddir(), and tripal_db_set_active().
| tripal_library_library_access | ( | $ | op, |
| $ | node, | ||
| $ | account | ||
| ) |
CHADO_LIBRARY NODE FUNCTIONS
The following function proves access control for users trying to perform actions on data managed by this module
Definition at line 834 of file tripal_library.module.
| tripal_library_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 104 of file tripal_library.module.
| tripal_library_module_description_page | ( | ) |
Purpose: Provide Guidance to new Tripal Admin
Definition at line 164 of file tripal_library.module.
| tripal_library_node_info | ( | ) |
Provide information to drupal about the node types that we're creating in this module
Definition at line 40 of file tripal_library.module.
| tripal_library_nodeapi | ( | &$ | node, |
| $ | op, | ||
| $ | teaser, | ||
| $ | page | ||
| ) |
HOOK: Implementation of hook_nodeapi() Display library information for associated features or organisms This function also provides contents for indexing
Definition at line 304 of file tripal_library.module.
| tripal_library_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 62 of file tripal_library.module.
| tripal_library_reindex_features | ( | $ | library_id = NULL, |
| $ | job_id = NULL |
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| ) |
Definition at line 1344 of file tripal_library.module.
References tripal_db_set_active(), tripal_feature_sync_feature(), and tripal_job_set_progress().
| tripal_library_requirements | ( | $ | phase | ) |
Implementation of hook_requirements(). Make sure 'Tripal Core' is enabled before installation
Definition at line 144 of file tripal_library.install.
| tripal_library_schema | ( | ) |
Implementation of hook_schema().
Definition at line 62 of file tripal_library.install.
References tripal_library_get_schemas().
| tripal_library_show_libraries | ( | ) |
Definition at line 802 of file tripal_library.module.
References get_chado_libraries().
| tripal_library_sync_libraries | ( | $ | library_id = NULL, |
| $ | job_id = NULL |
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| ) |
Definition at line 1138 of file tripal_library.module.
References $user, and tripal_db_set_active().
| tripal_library_taxonify_features | ( | $ | library_id = NULL, |
| $ | job_id = NULL |
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| ) |
Definition at line 1392 of file tripal_library.module.
References tripal_db_set_active(), tripal_feature_set_taxonomy(), tripal_feature_set_vocabulary(), and tripal_job_set_progress().
| tripal_library_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 346 of file tripal_library.module.
| tripal_library_uninstall | ( | ) |
Implementation of hook_uninstall()
Definition at line 72 of file tripal_library.install.
References tripal_mviews_action().
| tripal_library_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 151 of file tripal_library.module.
1.7.4 
