Analysis Module

  1. 2.x tripal_analysis/tripal_analysis.module tripal_analysis
  2. 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

Namesort descending Location Description
chado_analysis_delete tripal_analysis/includes/tripal_analysis.chado_node.inc Implements hook_delete(). Removes analysis from the chado database.
chado_analysis_form tripal_analysis/includes/tripal_analysis.chado_node.inc 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/includes/tripal_analysis.chado_node.inc 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/includes/tripal_analysis.chado_node.inc 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/includes/tripal_analysis.chado_node.inc Implements hook_update(). Update analyses
chado_analysis_validate tripal_analysis/includes/tripal_analysis.chado_node.inc Implements hook_validate(). Validates the user input before creating an analysis node
tripal_analysis_add_cvs tripal_analysis/tripal_analysis.install Add cvs related to analyses
tripal_analysis_add_cvterms tripal_analysis/tripal_analysis.install Adds controlled vocabulary terms needed by this module.
tripal_analysis_add_mview_analysis_organism tripal_analysis/tripal_analysis.install Creates a view showing the link between an organism & it's analysis through associated features.
tripal_analysis_admin tripal_analysis/includes/tripal_analysis.admin.inc Administration page callbacks for the Tripal Analysis module
tripal_analysis_admin_analysis_view tripal_analysis/includes/tripal_analysis.admin.inc Landing page for administration. Ensures Views are enabled & if not provides links to do so.
tripal_analysis_admin_validate tripal_analysis/includes/tripal_analysis.admin.inc Validate the administrative form @todo Stephen: Why is validate used rather then submit?
tripal_analysis_check_permission tripal_analysis/includes/tripal_analysis_privacy.inc Perform permission check by analysis_id only if 'node_privacy_byrole' module is enabled
tripal_analysis_create_analysisfeatureprop tripal_analysis/tripal_analysis.install Create a legacy custom chado table (analysisfeatureprop) to store properties of analysisfeature links.
tripal_analysis_defaultvalue_admin_analysis tripal_analysis/tripal_analysis.views_default.inc Defines the analysis admin default view.
tripal_analysis_defaultvalue_user_analysis tripal_analysis/tripal_analysis.views_default.inc Defines the analysis user search default view.
tripal_analysis_delete_analyses tripal_analysis/includes/tripal_analysis.delete.inc Function to actually delete the features indicated
tripal_analysis_delete_form tripal_analysis/includes/tripal_analysis.delete.inc A form for indicating the analyses to delete *
tripal_analysis_delete_form_submit tripal_analysis/includes/tripal_analysis.delete.inc Submit for the delete features form
tripal_analysis_disable tripal_analysis/tripal_analysis.install Implements hook_disable(). Disable default views when module is disabled
tripal_analysis_form_alter tripal_analysis/tripal_analysis.module Implementation of hook_form_alter().
tripal_analysis_help tripal_analysis/tripal_analysis.module Implements hook_help(). Purpose: Adds a help page to the module list
tripal_analysis_init tripal_analysis/tripal_analysis.module Implements hook_init(). Add tripal javascript to page headers
tripal_analysis_install tripal_analysis/tripal_analysis.install Implementation of hook_install().
tripal_analysis_menu tripal_analysis/tripal_analysis.module Implementation of hook_menu(). Entry points and paths of the module
tripal_analysis_node_access tripal_analysis/includes/tripal_analysis.chado_node.inc Implements hook_access().
tripal_analysis_node_info tripal_analysis/includes/tripal_analysis.chado_node.inc Implements hook_node_info().
tripal_analysis_node_insert tripal_analysis/includes/tripal_analysis.chado_node.inc Implements hook_node_insert(). Acts on all content types.
tripal_analysis_node_presave tripal_analysis/includes/tripal_analysis.chado_node.inc Implements hook_node_presave(). Called for all node types.
tripal_analysis_node_update tripal_analysis/includes/tripal_analysis.chado_node.inc Implements hook_node_update(). Acts on all content types.
tripal_analysis_node_view tripal_analysis/includes/tripal_analysis.chado_node.inc Implements hook_node_view(). Called for all node types.
tripal_analysis_permission tripal_analysis/tripal_analysis.module Implements hook_permission().
tripal_analysis_requirements tripal_analysis/tripal_analysis.install Implementation of hook_requirements().
tripal_analysis_schema tripal_analysis/tripal_analysis.install Implementation of hook_schema().
tripal_analysis_set_feature_permission tripal_analysis/includes/tripal_analysis_privacy.inc Set permissions for features associated with an analysis @todo Stephen: ensure the $nid param is defined correctly
tripal_analysis_theme tripal_analysis/tripal_analysis.module 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/tripal_analysis.install Implementation of hook_uninstall().
tripal_analysis_validate tripal_analysis/includes/tripal_analysis.chado_node.inc 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/tripal_analysis.module 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/tripal_analysis.views_default.inc Implements hook_views_default_views().

Files

Namesort descending Location Description
tripal_analysis.admin.inc tripal_analysis/includes/tripal_analysis.admin.inc Contains functions displaying administrative pages and forms.
tripal_analysis.api.inc tripal_analysis/api/tripal_analysis.api.inc Provides functions for managing analysis'.
tripal_analysis.chado_node.inc tripal_analysis/includes/tripal_analysis.chado_node.inc Implements Drupal Node hooks to create the chado_analysis node content type.
tripal_analysis.install tripal_analysis/tripal_analysis.install Implements hooks from the Schema API.
tripal_analysis.module tripal_analysis/tripal_analysis.module Contains basic functionality for the analysis module.
tripal_analysis.views_default.inc tripal_analysis/tripal_analysis.views_default.inc Contains the default views for the analysis module.
tripal_analysis_privacy.inc tripal_analysis/includes/tripal_analysis_privacy.inc Perform permission check (required node_privacy_byrole module).