Tripal Core Module

  1. 2.x tripal_core/tripal_core.module tripal_core
  2. 1.x tripal_core/tripal_core.module tripal_core

Parent topics

Tripal Modules
All documented functions for the various Tripal Modules excluding API functions and Views Integration functions.

File

tripal_core/tripal_core.module, line 34
The Tripal Core module

Functions

Namesort descending Location Description
print_usage tripal_core/tripal_launch_jobs.php Print out the usage instructions if they are not followed correctly
runjob tripal_core/tripal_launch_jobs_multi.php Runs tripal_launch_jobs() as the specified user
tripal_core_chado_install_done tripal_core/includes/chado_install.inc Finish the Chado Schema Installation
tripal_core_chado_load_form tripal_core/includes/chado_install.inc Load Chado Schema Form
tripal_core_chado_load_form_submit tripal_core/includes/chado_install.inc Submit Load Chado Schema 1.11 Form
tripal_core_custom_tables_schema tripal_core/tripal_core.install Describes the Tripal Custom Tables (tripal_custom_tables) table This keeps track of tables created by Tripal and stored in chado that may or may not also be materialized views.
tripal_core_get_schemas tripal_core/tripal_core.install 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_core_init tripal_core/tripal_core.module Implements hook_init(). Used to set the search_path, create default content and set default variables.
tripal_core_install tripal_core/tripal_core.install Implementation of hook_install().
tripal_core_install_chado tripal_core/includes/chado_install.inc Install Chado Schema
tripal_core_install_sql tripal_core/includes/chado_install.inc Execute the provided SQL
tripal_core_jobs_schema tripal_core/tripal_core.install Describes the Tripal Jobs (tripal_jobs) table This table keeps track of all tripal jobs including their current status and is used by tripal_launch_jobs to determine which jobs need to be run
tripal_core_job_describe_args tripal_core/tripal_core.module Implements hook_job_describe_args(). Describes the arguements for the tripal_update_mview job to allow for greater readability in the jobs details pages.
tripal_core_menu tripal_core/tripal_core.module Implements hook_menu(). Defines all menu items needed by Tripal Core
tripal_core_mviews_schema tripal_core/tripal_core.install Describes the Tripal Materialized View (tripal_mviews) table This table keeps track of all materialized views created by Tripal and stored in chado
tripal_core_perm tripal_core/tripal_core.module Set the permission types that the chado module uses. Essentially we want permissionis that protect creation, editing and deleting of chado data objects
tripal_core_preprocess_tripal_core_job_view tripal_core/includes/jobs.inc Registers variables for the tripal_core_job_view themeing function
tripal_core_reset_chado_schema tripal_core/includes/chado_install.inc Reset the Chado Schema This drops the current chado and chado-related schema and re-creates it
tripal_core_schema tripal_core/tripal_core.install Implementation of hook_schema().
tripal_core_theme tripal_core/tripal_core.module Implements hook_theme(). Registers template files/functions used by this module.
tripal_core_uninstall tripal_core/tripal_core.install Implementation of hook_uninstall().
tripal_core_update_6000 tripal_core/tripal_core.install Update for Drupal 6.x, Tripal 1.0 This update
tripal_custom_tables_action tripal_core/includes/custom_tables.inc Does the specified action for the specified custom table
tripal_custom_tables_form tripal_core/includes/custom_tables.inc A Form to Create/Edit a Custom table
tripal_custom_tables_form_submit tripal_core/includes/custom_tables.inc Submit the Create/Edit Custom table form Implements hook_form_submit().
tripal_custom_tables_form_validate tripal_core/includes/custom_tables.inc Validate the Create/Edit custom table form Implements hook_form_validate().
tripal_custom_tables_list tripal_core/includes/custom_tables.inc A template function to render a listing of all Custom tables
tripal_custom_table_view tripal_core/includes/custom_tables.inc A template function which returns markup to display details for the custom table
tripal_jobs_report tripal_core/includes/jobs.inc Returns the Tripal Job Report
tripal_jobs_report_form tripal_core/includes/jobs.inc
tripal_jobs_report_form_submit tripal_core/includes/jobs.inc
tripal_jobs_view tripal_core/includes/jobs.inc Returns the HTML code to display a given job
tripal_job_set_progress tripal_core/api/tripal_core_jobs.api.inc An internal function for setting the progress for a current job
tripal_mviews_action tripal_core/api/tripal_core_mviews.api.inc Does the specified action for the specified Materialized View
tripal_mviews_form tripal_core/includes/mviews.inc A Form to Create/Edit a Materialized View
tripal_mviews_form_submit tripal_core/includes/mviews.inc Submit the Create/Edit Materialized View Form Implements hook_form_submit().
tripal_mviews_form_validate tripal_core/includes/mviews.inc Validate the Create/Edit Materialized View Form Implements hook_form_validate().
tripal_mviews_report tripal_core/includes/mviews.inc A template function to render a listing of all Materialized Views
tripal_mview_report tripal_core/includes/mviews.inc A template function which returns markup to display details for the current materialized view

Classes

Namesort descending Location Description
tripal_views_handler_filter_select_cvterm tripal_views/views/handlers/tripal_views_handler_filter_select_cvterm.inc @file Purpose: This Handler provides a select list for the type field
tripal_views_handler_filter_select_string tripal_views/views/handlers/tripal_views_handler_filter_select_string.inc @file Purpose: This Handler provides a generic select list for any chado field that is a string The select list includes all distinct values for that field.
views_handler_field_chado_count tripal_views/views/handlers/deprecated/views_handler_field_chado_count.inc @file Purpose: Provide a field that counts the number of records in the current table are connected to the base table. For example, this field could be used to count the number of features connected to a given organism -base table=organism, current…
views_handler_field_dbxref_accession_link tripal_views/views/handlers/deprecated/views_handler_field_dbxref_accession_link.inc @file Used for a custom field so that field can render the database reference link
views_handler_field_node_optional tripal_views/views/handlers/deprecated/views_handler_field_node_optional.inc @file Field handler to provide simple renderer that allows linking to a node.
views_handler_field_readable_date tripal_views/views/handlers/deprecated/views_handler_field_readable_date.inc @file A handler to provide proper displays for dates.
views_handler_filter_chado_boolean tripal_views/views/handlers/deprecated/views_handler_filter_chado_boolean.inc @file Purpose: This handler provides a TRUE/FALSE or YES/NO select for chado fields of type boolean (includes both 0/1 and t/f booleans)
views_handler_filter_chado_select_cvterm_name tripal_views/views/handlers/deprecated/views_handler_filter_chado_select_cvterm_name.inc @file Purpose: This Handler provides a select list for the type field
views_handler_filter_chado_select_string tripal_views/views/handlers/deprecated/views_handler_filter_chado_select_string.inc @file Purpose: This Handler provides a generic select list for any chado field that is a string The select list includes all distinct values for that field.

Files

Namesort descending Location Description
custom_tables.inc tripal_core/includes/custom_tables.inc Contains functions for creating, editing and deleting custom tables on the Tripal website.
tripal_views_handler_filter_select_cvterm.inc tripal_views/views/handlers/tripal_views_handler_filter_select_cvterm.inc Purpose: This Handler provides a select list for the type field
tripal_views_handler_filter_select_string.inc tripal_views/views/handlers/tripal_views_handler_filter_select_string.inc Purpose: This Handler provides a generic select list for any chado field that is a string The select list includes all distinct values for that field.
views_handler_field_chado_count.inc tripal_views/views/handlers/deprecated/views_handler_field_chado_count.inc Purpose: Provide a field that counts the number of records in the current table are connected to the base table. For example, this field could be used to count the number of features connected to a given organism -base table=organism, current…
views_handler_field_dbxref_accession_link.inc tripal_views/views/handlers/deprecated/views_handler_field_dbxref_accession_link.inc Used for a custom field so that field can render the database reference link
views_handler_field_node_optional.inc tripal_views/views/handlers/deprecated/views_handler_field_node_optional.inc Field handler to provide simple renderer that allows linking to a node.
views_handler_field_readable_date.inc tripal_views/views/handlers/deprecated/views_handler_field_readable_date.inc A handler to provide proper displays for dates.
views_handler_filter_chado_boolean.inc tripal_views/views/handlers/deprecated/views_handler_filter_chado_boolean.inc Purpose: This handler provides a TRUE/FALSE or YES/NO select for chado fields of type boolean (includes both 0/1 and t/f booleans)
views_handler_filter_chado_select_cvterm_name.inc tripal_views/views/handlers/deprecated/views_handler_filter_chado_select_cvterm_name.inc Purpose: This Handler provides a select list for the type field
views_handler_filter_chado_select_string.inc tripal_views/views/handlers/deprecated/views_handler_filter_chado_select_string.inc Purpose: This Handler provides a generic select list for any chado field that is a string The select list includes all distinct values for that field.