Classes
class	views_handler_field_chado_count
class	views_handler_field_chado_tf_boolean
class	views_handler_field_cvterm_name
class	views_handler_field_dbxref_accession_link
class	views_handler_field_node_optional
class	views_handler_field_readable_date
class	views_handler_field_type_name
class	views_handler_filter_chado_boolean
class	views_handler_filter_chado_select_cvterm_name
class	views_handler_filter_chado_select_string
Functions
	tripal_core_chado_v1_11_load_form ()
	tripal_core_chado_v1_11_load_form_submit ($form, &$form_state)
	tripal_core_install_chado ($dummy=NULL, $job=NULL)
	tripal_core_reset_chado_schema ()
	tripal_core_install_sql ($sql_file)
	tripal_core_chado_install_done ()
	tripal_job_set_progress ($job_id, $percentage)
	tripal_jobs_report ()
	tripal_jobs_view ($job_id)
	tripal_core_preprocess_tripal_core_job_view (&$variables)
	tripal_mviews_action ($op, $mview_id)
	tripal_mviews_form (&$form_state=NULL, $mview_id=NULL)
	tripal_mviews_form_submit ($form, &$form_state)
	tripal_core_init ()
	tripal_core_menu ()
	tripal_core_views_api ()
	tripal_core_theme ()
	tripal_core_job_describe_args ($callback, $args)
	tripal_core_views_handlers ()
	tripal_core_views_pre_render (&$view)
	tripal_core_add_node_ids_to_view (&$view)
	print_usage ($stdout)
	runjob ($sitename, $username)

Function Documentation

print_usage ( $ stdout )

Definition at line 51 of file tripal_launch_jobs.php.

References $stdout.

runjob	(	$	sitename,
		$	username
	)

Definition at line 86 of file tripal_launch_jobs_multi.php.

References $_SERVER, $user, $username, and tripal_jobs_launch().

tripal_core_add_node_ids_to_view ( &$ view )

Adds nid fields to all pertinent view results

Purpose: To add basetable_nid fields to all result arrays of a view only if the basetable_nid field is added. This function will only be called if chado/drupal are not in the same database (ie: only if a join between the base and node table isn't possible.

Note: Supports adding Node IDs to analysis, feature, library, organism, stock

Parameters:

$view the view object passed to hook_views_pre_render

Returns:: the views object with nids added to the result array

Definition at line 122 of file tripal_core.views.inc.

Referenced by tripal_core_views_pre_render().

tripal_core_chado_install_done ( )

Definition at line 234 of file chado_install.php.

Referenced by tripal_core_install_sql().

tripal_core_chado_v1_11_load_form ( )

Definition at line 8 of file chado_install.php.

tripal_core_chado_v1_11_load_form_submit	(	$	form,
		&$	form_state
	)

Definition at line 27 of file chado_install.php.

References $args, $user, and tripal_add_job().

tripal_core_init ( )

Definition at line 27 of file tripal_core.module.

References tripal_core_is_chado_installed(), and tripal_db_set_active().

tripal_core_install_chado	(	$	dummy = `NULL`,
		$	job = `NULL`
	)

Definition at line 41 of file chado_install.php.

References tripal_core_install_sql(), and tripal_core_reset_chado_schema().

tripal_core_install_sql ( $ sql_file )

Definition at line 69 of file chado_install.php.

References tripal_core_chado_install_done().

Referenced by tripal_core_install_chado().

tripal_core_job_describe_args	(	$	callback,
		$	args
	)

Definition at line 262 of file tripal_core.module.

References $args.

tripal_core_menu ( )

Definition at line 69 of file tripal_core.module.

tripal_core_preprocess_tripal_core_job_view ( &$ variables )

Registers variables for the tripal_core_job_view themeing function

Parameters:

$variables An array containing all variables supplied to this template

Definition at line 354 of file jobs.php.

References $args, $job, tripal_jobs_get_end_time(), tripal_jobs_get_start_time(), and tripal_jobs_get_submit_date().

tripal_core_reset_chado_schema ( )

Definition at line 53 of file chado_install.php.

Referenced by tripal_core_install_chado().

tripal_core_theme ( )

Definition at line 250 of file tripal_core.module.

tripal_core_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_core.views.inc where all the views integration code is

Definition at line 239 of file tripal_core.module.

tripal_core_views_handlers ( )

Implements hook_views_handlers()

Purpose: Register all custom handlers with views where a handler describes either "the type of field", "how a field should be filtered", "how a field should be sorted"

Returns:: An array of handler definitions

Definition at line 54 of file tripal_core.views.inc.

tripal_core_views_pre_render ( &$ view )

Implements hook_views_pre_render

Purpose: Intercepts the view after the query has been executed All the results are stored in $view->result Looking up the NID here ensures the query is only executed once for all stocks in the table.

Todo:: add if !<chado/drupal same db> around NID portion

Definition at line 97 of file tripal_core.views.inc.

References tripal_core_add_node_ids_to_view().

tripal_job_set_progress	(	$	job_id,
		$	percentage
	)

An internal function for setting the progress for a current job

Parameters:

$job_id	The job_id to set the progress for
$percentage	The progress to set the job to

Returns:: True on success and False otherwise

Definition at line 86 of file jobs.php.

Referenced by tripal_core_load_gff3(), tripal_cv_obo_process_terms(), tripal_feature_load_fasta(), tripal_feature_sync_features(), tripal_features_cleanup(), tripal_features_reindex(), tripal_features_set_taxonomy(), tripal_library_cleanup(), tripal_library_reindex_features(), tripal_library_taxonify_features(), tripal_organism_reindex_features(), tripal_organism_taxonify_features(), and tripal_organisms_cleanup().

tripal_jobs_report ( )

Returns the Tripal Job Report

Returns:: The HTML to be rendered which describes the job report

Definition at line 124 of file jobs.php.

References $cancel_link, $job, $rerun_link, tripal_jobs_get_end_time(), tripal_jobs_get_start_time(), and tripal_jobs_get_submit_date().

tripal_jobs_view ( $ job_id )

Returns the HTML code to display a given job

Parameters:

$job_id The job_id of the job to display

Returns:: The HTML describing the indicated job

Definition at line 342 of file jobs.php.

tripal_mviews_action	(	$	op,
		$	mview_id
	)

Definition at line 105 of file mviews.php.

References $args, $user, tripal_add_job(), and tripal_db_set_active().

Referenced by tripal_cv_uninstall(), tripal_feature_add_organism_count_mview(), tripal_feature_uninstall(), and tripal_library_uninstall().

tripal_mviews_form	(	&$	form_state = `NULL`,
		$	mview_id = `NULL`
	)

$form['special_index']= array( '#type' => 'textarea', '#title' => t('View Name'), '#description' => t('Please enter the name for this materialized view.'), '#required' => TRUE, '#default_value' => $default_special_index, '#weight' => 7 );

Definition at line 305 of file mviews.php.

tripal_mviews_form_submit	(	$	form,
		&$	form_state
	)

Definition at line 422 of file mviews.php.

References tripal_add_mview().

Classes

Functions

Function Documentation