Analysis Module
- 2.x tripal_analysis/tripal_analysis.module tripal_analysis
- 3.x legacy/tripal_analysis/tripal_analysis.module tripal_analysis
- 1.x tripal_analysis/tripal_analysis.module tripal_analysis
Integrates the Chado Analysis module with Drupal Nodes & Views
File
- tripal_analysis/
tripal_analysis.module, line 19 - Contains basic functionality for the analysis module.
Functions
Name |
Location | Description |
|---|---|---|
| chado_analysis_delete |
tripal_analysis/ |
Implements hook_delete(). Removes analysis from the chado database. |
| chado_analysis_form |
tripal_analysis/ |
Implements hook_form(). When editing or creating a new node of type 'chado_analysis' we need a form. This function creates the form that will be used for this. |
| chado_analysis_insert |
tripal_analysis/ |
Implements hook_insert(). When a new chado_analysis node is created we also need to add information to our chado_analysis table. This function is called on insert of a new node of type 'chado_analysis' and inserts the necessary information. |
| chado_analysis_load |
tripal_analysis/ |
Implements hook_load(). When a node is requested by the user this function is called to allow us to add auxiliary data to the node object. |
| chado_analysis_update |
tripal_analysis/ |
Implements hook_update(). Update analyses |
| chado_analysis_validate |
tripal_analysis/ |
Implements hook_validate(). Validates the user input before creating an analysis node |
| tripal_analysis_add_cvs |
tripal_analysis/ |
Add cvs related to analyses |
| tripal_analysis_add_cvterms |
tripal_analysis/ |
Adds controlled vocabulary terms needed by this module. |
| tripal_analysis_add_mview_analysis_organism |
tripal_analysis/ |
Creates a view showing the link between an organism & it's analysis through associated features. |
| tripal_analysis_admin |
tripal_analysis/ |
Administration page callbacks for the Tripal Analysis module |
| tripal_analysis_admin_analysis_view |
tripal_analysis/ |
Landing page for administration. Ensures Views are enabled & if not provides links to do so. |
| tripal_analysis_admin_validate |
tripal_analysis/ |
Validate the administrative form @todo Stephen: Why is validate used rather then submit? |
| tripal_analysis_check_permission |
tripal_analysis/ |
Perform permission check by analysis_id only if 'node_privacy_byrole' module is enabled |
| tripal_analysis_create_analysisfeatureprop |
tripal_analysis/ |
Create a legacy custom chado table (analysisfeatureprop) to store properties of analysisfeature links. |
| tripal_analysis_defaultvalue_admin_analysis |
tripal_analysis/ |
Defines the analysis admin default view. |
| tripal_analysis_defaultvalue_user_analysis |
tripal_analysis/ |
Defines the analysis user search default view. |
| tripal_analysis_delete_analyses |
tripal_analysis/ |
Function to actually delete the features indicated |
| tripal_analysis_delete_form |
tripal_analysis/ |
A form for indicating the analyses to delete * |
| tripal_analysis_delete_form_submit |
tripal_analysis/ |
Submit for the delete features form |
| tripal_analysis_disable |
tripal_analysis/ |
Implements hook_disable(). Disable default views when module is disabled |
| tripal_analysis_form_alter |
tripal_analysis/ |
Implementation of hook_form_alter(). |
| tripal_analysis_help |
tripal_analysis/ |
Implements hook_help(). Purpose: Adds a help page to the module list |
| tripal_analysis_init |
tripal_analysis/ |
Implements hook_init(). Add tripal javascript to page headers |
| tripal_analysis_install |
tripal_analysis/ |
Implementation of hook_install(). |
| tripal_analysis_menu |
tripal_analysis/ |
Implementation of hook_menu(). Entry points and paths of the module |
| tripal_analysis_node_access |
tripal_analysis/ |
Implements hook_access(). |
| tripal_analysis_node_info |
tripal_analysis/ |
Implements hook_node_info(). |
| tripal_analysis_node_insert |
tripal_analysis/ |
Implements hook_node_insert(). Acts on all content types. |
| tripal_analysis_node_presave |
tripal_analysis/ |
Implements hook_node_presave(). Called for all node types. |
| tripal_analysis_node_update |
tripal_analysis/ |
Implements hook_node_update(). Acts on all content types. |
| tripal_analysis_node_view |
tripal_analysis/ |
Implements hook_node_view(). Called for all node types. |
| tripal_analysis_permission |
tripal_analysis/ |
Implements hook_permission(). |
| tripal_analysis_requirements |
tripal_analysis/ |
Implementation of hook_requirements(). |
| tripal_analysis_schema |
tripal_analysis/ |
Implementation of hook_schema(). |
| tripal_analysis_set_feature_permission |
tripal_analysis/ |
Set permissions for features associated with an analysis @todo Stephen: ensure the $nid param is defined correctly |
| tripal_analysis_theme |
tripal_analysis/ |
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_analysis_uninstall |
tripal_analysis/ |
Implementation of hook_uninstall(). |
| tripal_analysis_validate |
tripal_analysis/ |
This validation is being used for three activities: CASE A: Update a node that exists in both drupal and chado CASE B: Synchronizing a node from chado to drupal CASE C: Inserting a new node that exists in niether drupal nor chado |
| tripal_analysis_views_api |
tripal_analysis/ |
Implements hook_views_api(). Essentially this hook tells drupal that there is views support for for this module which then includes tripal_analysis.views.inc where all the views integration code is |
| tripal_analysis_views_default_views |
tripal_analysis/ |
Implements hook_views_default_views(). |
Files
|
Name |
Location | Description |
|---|---|---|
| tripal_analysis.admin.inc |
tripal_analysis/ |
Contains functions displaying administrative pages and forms. |
| tripal_analysis.api.inc |
tripal_analysis/ |
Provides functions for managing analysis'. |
| tripal_analysis.chado_node.inc |
tripal_analysis/ |
Implements Drupal Node hooks to create the chado_analysis node content type. |
| tripal_analysis.install |
tripal_analysis/ |
Implements hooks from the Schema API. |
| tripal_analysis.module |
tripal_analysis/ |
Contains basic functionality for the analysis module. |
| tripal_analysis.views_default.inc |
tripal_analysis/ |
Contains the default views for the analysis module. |
| tripal_analysis_privacy.inc |
tripal_analysis/ |
Perform permission check (required node_privacy_byrole module). |