292 calls to tripal_report_error()
- chado_add_admin_form_set_title in legacy/
tripal_core/ api/ tripal_core.chado_nodes.title_and_path.inc - Generic "Set Node Title" sub-form for setting the title of any chado node
- chado_add_admin_form_set_url in legacy/
tripal_core/ api/ tripal_core.chado_nodes.title_and_path.inc - Generic "Set Node URL" sub-form for setting the url of any chado node
- chado_add_mview in tripal_chado/
api/ tripal_chado.mviews.api.inc - Add a materialized view to the chado database to help speed data access. This function supports the older style where postgres column specifications are provided using the $mv_table, $mv_specs and $indexed variables. It also supports the newer…
- chado_add_node_form_properties in legacy/
tripal_core/ api/ tripal_core.chado_nodes.properties.api.inc - chado_add_node_form_relationships in legacy/
tripal_core/ api/ tripal_core.chado_nodes.relationships.api.inc - Provides a form for adding to BASE_relationship and relationship tables
- chado_analysis_insert in legacy/
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_update in legacy/
tripal_analysis/ includes/ tripal_analysis.chado_node.inc - Implements hook_update(). Update analyses
- chado_associate_cvterm in tripal_chado/
api/ modules/ tripal_chado.cv.api.inc - Add a record to a cvterm linking table (ie: feature_cvterm).
- chado_associate_dbxref in tripal_chado/
api/ modules/ tripal_chado.db.api.inc - Add a record to a database reference linking table (ie: feature_dbxref).
- chado_contact_insert in legacy/
tripal_contact/ includes/ tripal_contact.chado_node.inc - Implements of hook_insert().
- chado_contact_update in legacy/
tripal_contact/ includes/ tripal_contact.chado_node.inc - Implements hook_update
- chado_delete_custom_table in tripal_chado/
api/ tripal_chado.custom_tables.api.inc - Deletes the specified custom table.
- chado_delete_phylotree in tripal_chado/
api/ modules/ tripal_chado.phylotree.api.inc - Deletes a phylotree record from Chado.
- chado_delete_property in tripal_chado/
api/ tripal_chado.property.api.inc - Deletes a property for a given base table record using the property name.
- chado_delete_record in tripal_chado/
api/ tripal_chado.query.api.inc - Provides a generic function for deleting a record(s) from any chado table.
- chado_does_pub_exist in legacy/
tripal_pub/ api/ tripal_pub.DEPRECATED.inc - chado_edit_custom_table in tripal_chado/
api/ tripal_chado.custom_tables.api.inc - Edits a custom table in the chado database. It supports using the Drupal Schema API array.
- chado_expand_var in tripal_chado/
api/ tripal_chado.variables.api.inc - Retrieves fields, or tables that were excluded by default from a variable.
- chado_featuremap_insert in legacy/
tripal_featuremap/ includes/ tripal_featuremap.chado_node.inc - Implements hook_insert().
- chado_featuremap_update in legacy/
tripal_featuremap/ includes/ tripal_featuremap.chado_node.inc - Implements hook_update(). Update nodes
- chado_feature_add_synonyms in legacy/
tripal_feature/ includes/ tripal_feature.chado_node.inc - Add synonyms to a feature
- chado_feature_insert in legacy/
tripal_feature/ includes/ tripal_feature.chado_node.inc - Implements hook_insert().
- chado_feature_update in legacy/
tripal_feature/ includes/ tripal_feature.chado_node.inc - Implements hook_update().
- chado_generate_var in tripal_chado/
api/ tripal_chado.variables.api.inc - Generates an object containing the full details of a record(s) in Chado.
- chado_get_analysis in tripal_chado/
api/ modules/ tripal_chado.analysis.api.inc - Retrieves a chado analysis variable.
- chado_get_cv in tripal_chado/
api/ modules/ tripal_chado.cv.api.inc - Retrieves a chado controlled vocabulary variable
- chado_get_cvterm in tripal_chado/
api/ modules/ tripal_chado.cv.api.inc - Retrieves a chado controlled vocabulary term variable.
- chado_get_db in tripal_chado/
api/ modules/ tripal_chado.db.api.inc - Retrieves a chado db variable.
- chado_get_dbxref in tripal_chado/
api/ modules/ tripal_chado.db.api.inc - Retrieves a chado database reference variable.
- chado_get_feature_sequences in tripal_chado/
api/ modules/ tripal_chado.feature.api.inc - Retrieves the sequences for a given feature.
- chado_get_id_for_node in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - chado_get_multiple_stocks in tripal_chado/
api/ modules/ tripal_chado.stock.api.inc - Retrieves a chado stock variable.
- chado_get_node_id in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - chado_get_node_url in legacy/
tripal_core/ api/ tripal_core.chado_nodes.title_and_path.inc - Get the url of a node based on the url Format set in the admin section of the module. If the format has not yet been set than the the unique constrain and name fields will be used to generate a default format
- chado_get_organism in tripal_chado/
api/ modules/ tripal_chado.organism.api.inc - Retrieves a chado organism variable.
- chado_get_property in tripal_chado/
api/ tripal_chado.property.api.inc - Retrieve a property for a given base table record.
- chado_get_publication in tripal_chado/
api/ modules/ tripal_chado.pub.api.inc - Retrieves a chado publication array.
- chado_get_record_with_property in tripal_chado/
api/ tripal_chado.property.api.inc - Get all records in the base table assigned one or more properties.
- chado_get_stock in tripal_chado/
api/ modules/ tripal_chado.stock.api.inc - Retrieves a chado stock variable
- chado_get_token_value in legacy/
tripal_core/ api/ tripal_core.chado_nodes.title_and_path.inc - Retrieve the value of the token from the node based on the $token_info['location']
- chado_insert_contact in tripal_chado/
api/ modules/ tripal_chado.contact.api.inc - Adds a contact to the Chado contact table.
- chado_insert_cv in tripal_chado/
api/ modules/ tripal_chado.cv.api.inc - Adds a controlled vocabulary to the CV table of Chado.
- chado_insert_cvterm in tripal_chado/
api/ modules/ tripal_chado.cv.api.inc - Add's a controlled vocabulary term to Chado.
- chado_insert_db in tripal_chado/
api/ modules/ tripal_chado.db.api.inc - Adds a new database to the Chado DB table and returns the DB object.
- chado_insert_dbxref in tripal_chado/
api/ modules/ tripal_chado.db.api.inc - Add a database reference.
- chado_insert_phylotree in tripal_chado/
api/ modules/ tripal_chado.phylotree.api.inc - Inserts a phylotree record into Chado.
- chado_insert_property in tripal_chado/
api/ tripal_chado.property.api.inc - Insert a property for a given base table.
- chado_insert_record in tripal_chado/
api/ tripal_chado.query.api.inc - Provides a generic routine for inserting into any Chado table
- chado_node_additional_dbxrefs_form in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - chado_node_additional_dbxrefs_form_retreive in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - chado_node_additional_dbxrefs_form_update_dbxrefs in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - chado_node_get_unique_constraint_format in legacy/
tripal_core/ api/ tripal_core.chado_nodes.title_and_path.inc - Generate the unique constraint for a given base table using the Chado Schema API definition
- chado_node_properties_form in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - chado_node_properties_form_retreive in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - chado_node_properties_form_update_properties in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - chado_node_relationships_form in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - chado_node_relationships_form_retreive in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - chado_node_relationships_form_update_relationships in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - chado_organism_insert in legacy/
tripal_organism/ includes/ tripal_organism.chado_node.inc - Implements hook_insert().
- chado_organism_validate in legacy/
tripal_organism/ includes/ tripal_organism.chado_node.inc - Implementation of hook_validate().
- chado_pager_query in tripal_chado/
api/ tripal_chado.query.api.inc - Use this function instead of pager_query() when selecting a subset of records from a Chado table.
- chado_phylogeny_get_node_types_vocab in tripal_chado/
api/ modules/ tripal_chado.phylotree.api.inc - Get the vocabulary terms used to describe nodes in the tree.
- chado_phylogeny_import_tree_file in tripal_chado/
api/ modules/ tripal_chado.phylotree.api.inc - Imports a tree file.
- chado_phylotree_insert in legacy/
tripal_phylogeny/ includes/ tripal_phylogeny.chado_node.inc - Implements hook_insert().
- chado_phylotree_update in legacy/
tripal_phylogeny/ includes/ tripal_phylogeny.chado_node.inc - Implements hook_update().
- chado_publication_exists in tripal_chado/
api/ modules/ tripal_chado.pub.api.inc - The publication table of Chado only has a unique constraint for the uniquename of the publiation, but in reality a publication can be considered unique by a combination of the title, publication type, published year and series name (e.g. journal name…
- chado_publish_records in tripal_chado/
api/ tripal_chado.api.inc - Publishes content in Chado as a new TripalEntity entity.
- chado_query in tripal_chado/
api/ tripal_chado.query.api.inc - A substitute for db_query() when querying from Chado.
- chado_replace_tokens in tripal_chado/
api/ tripal_chado.api.inc - Replace all Chado Tokens in a given string.
- chado_schema_get_foreign_key in tripal_chado/
api/ tripal_chado.query.api.inc - Gets the value of a foreign key relationship.
- chado_select_record in tripal_chado/
api/ tripal_chado.query.api.inc - Provides a generic routine for selecting data from a Chado table.
- chado_set_node_url in legacy/
tripal_core/ api/ tripal_core.chado_nodes.title_and_path.inc - Set the URL for a given node.
- chado_stock_insert in legacy/
tripal_stock/ includes/ tripal_stock.chado_node.inc - Implements hook_insert(). Inserts data from chado_stock_form() into drupal and chado
- chado_stock_update in legacy/
tripal_stock/ includes/ tripal_stock.chado_node.inc - Implements hook_update(). Handles Editing/Updating of main stock info
- chado_update_existing_node_urls in legacy/
tripal_core/ api/ tripal_core.chado_nodes.title_and_path.inc - Tripal Job for updating all node URLs for a particular node type.
- chado_update_node_form_properties in legacy/
tripal_core/ api/ tripal_core.chado_nodes.properties.api.inc - This function is used in hook_insert or hook_update and handles inserting of any new properties
- chado_update_phylotree in tripal_chado/
api/ modules/ tripal_chado.phylotree.api.inc - Updates a phylotree record into Chado.
- chado_update_property in tripal_chado/
api/ tripal_chado.property.api.inc - Update a property for a given base table record and property name.
- chado_update_record in tripal_chado/
api/ tripal_chado.query.api.inc - Provides a generic routine for updating into any Chado table.
- chado_validate_phylotree in tripal_chado/
api/ modules/ tripal_chado.phylotree.api.inc - Validates an $options array for insert or update of a phylotree record.
- FASTAImporter::loadFasta in tripal_chado/
includes/ TripalImporter/ FASTAImporter.inc - Load a fasta file.
- get_max_chado_rank in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - pub_search in legacy/
tripal_pub/ api/ tripal_pub.DEPRECATED.inc - sio__vocabulary_widget::form in tripal_chado/
includes/ TripalFields/ sio__vocabulary/ sio__vocabulary_widget.inc - TripalEntityController::setAlias in tripal/
includes/ TripalEntityController.inc - Sets the URL alias for an entity.
- TripalField::__construct in tripal/
includes/ TripalFields/ TripalField.inc - Instantiates a new TripalField object.
- TripalJob::logMessage in tripal/
includes/ TripalJob.inc - Logs a message for the job.
- tripal_add_job in tripal/
api/ tripal.jobs.api.inc - Adds a job to the Tripal Job queue
- tripal_add_legacy_mview in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_add_node_variable in legacy/
tripal_core/ api/ tripal_core.tripal_variables.api.inc - Associates a variable and it's value to a node.
- tripal_add_views_integration in tripal_chado_views/
api/ tripal_chado_views.api.inc - Add views integration records into the tripal_views* tables.
- tripal_admin_notification_import_field in tripal/
includes/ tripal.admin_blocks.inc - Import the field from the admin notification table on the dashboard.
- tripal_analysis_delete_property in legacy/
tripal_analysis/ api/ tripal_analysis.DEPRECATED.inc - tripal_analysis_get_node in legacy/
tripal_analysis/ api/ tripal_analysis.DEPRECATED.inc - tripal_analysis_get_property in legacy/
tripal_analysis/ api/ tripal_analysis.DEPRECATED.inc - tripal_analysis_insert_property in legacy/
tripal_analysis/ api/ tripal_analysis.DEPRECATED.inc - tripal_analysis_register_child in legacy/
tripal_analysis/ api/ tripal_analysis.DEPRECATED.inc - tripal_analysis_unregister_child in legacy/
tripal_analysis/ api/ tripal_analysis.DEPRECATED.inc - tripal_analysis_update_property in legacy/
tripal_analysis/ api/ tripal_analysis.DEPRECATED.inc - tripal_bulk_loader_delete_field in tripal_bulk_loader/
api/ tripal_bulk_loader.DEPRECATED.inc - tripal_bulk_loader_delete_record in tripal_bulk_loader/
api/ tripal_bulk_loader.DEPRECATED.inc - tripal_bulk_loader_edit_template_record_form_submit in tripal_bulk_loader/
includes/ tripal_bulk_loader.admin.templates.inc - Edit Record Form Submit
- tripal_bulk_loader_is_record_name_unique in tripal_bulk_loader/
api/ tripal_bulk_loader.DEPRECATED.inc - tripal_bulk_loader_template_field_form_submit in tripal_bulk_loader/
includes/ tripal_bulk_loader.admin.templates.inc - Add Field Submit
- tripal_bulk_loader_throw_error in tripal_bulk_loader/
includes/ tripal_bulk_loader.loader.inc - Used to throw a hopefully human-readable error.
- tripal_cancel_job in tripal/
api/ tripal.jobs.api.inc - Cancel a Tripal Job currently waiting in the job queue.
- tripal_chado_bundle_fields_info_base in tripal_chado/
includes/ tripal_chado.fields.inc - tripal_chado_gff3_exporter in tripal_chado/
includes/ exporters/ tripal_chado.gff_exporter.inc - tripal_chado_install_chado in tripal_chado/
includes/ tripal_chado.install.inc - Install Chado Schema
- tripal_chado_views_add_field_to_integration in tripal_chado_views/
api/ tripal_chado_views.DEPRECATED.inc - tripal_chado_views_admin_disable_view in tripal_chado_views/
api/ tripal_chado_views.DEPRECATED.inc - tripal_chado_views_admin_enable_view in tripal_chado_views/
api/ tripal_chado_views.DEPRECATED.inc - tripal_chado_views_clone_integration in tripal_chado_views/
api/ tripal_chado_views.DEPRECATED.inc - tripal_chado_views_get_integration_array_for_chado_table in tripal_chado_views/
includes/ tripal_chado_views_integration.inc - Returns the array needed to integrate a given chado table with views
- tripal_chado_views_get_lightest_priority_setup in tripal_chado_views/
api/ tripal_chado_views.DEPRECATED.inc - tripal_chado_views_get_setup_id in tripal_chado_views/
api/ tripal_chado_views.DEPRECATED.inc - tripal_chado_views_get_table_lightest_priority in tripal_chado_views/
api/ tripal_chado_views.DEPRECATED.inc - tripal_chado_views_integration_add_entry in tripal_chado_views/
api/ tripal_chado_views.DEPRECATED.inc - tripal_chado_views_integration_ajax_join_field in tripal_chado_views/
includes/ tripal_chado_views_integration_UI.inc - tripal_chado_views_integration_export_entry in tripal_chado_views/
api/ tripal_chado_views.DEPRECATED.inc - tripal_chado_views_integration_remove_entry_by_setup_id in tripal_chado_views/
api/ tripal_chado_views.DEPRECATED.inc - tripal_chado_views_integration_remove_entry_by_table_name in tripal_chado_views/
api/ tripal_chado_views.DEPRECATED.inc - tripal_chado_views_integration_update_entry in tripal_chado_views/
api/ tripal_chado_views.DEPRECATED.inc - tripal_chado_views_is_integrated in tripal_chado_views/
api/ tripal_chado_views.DEPRECATED.inc - tripal_chado_views_is_lightest_priority_setup in tripal_chado_views/
api/ tripal_chado_views.DEPRECATED.inc - tripal_chado_views_make_view_compatible_with_external in tripal_chado_views/
api/ tripal_chado_views.DEPRECATED.inc - tripal_chado_views_rebuild_views_integrations in tripal_chado_views/
api/ tripal_chado_views.DEPRECATED.inc - tripal_chado_views_remove_join_from_integration in tripal_chado_views/
api/ tripal_chado_views.DEPRECATED.inc - tripal_chado_views_views_data in tripal_chado_views/
tripal_chado_views.views.inc - Implements hook_views_data().
- tripal_clone_views_integration in tripal_chado_views/
api/ tripal_chado_views.api.inc - Clone an integration. This is often a great way to create your own module-specific integration while still benifiting from an existing (or even the lightest priority) integration.
- tripal_contact_add_contact in legacy/
tripal_contact/ api/ tripal_contact.DEPRECATED.inc - tripal_contact_delete_property in legacy/
tripal_contact/ api/ tripal_contact.DEPRECATED.inc - tripal_contact_get_property in legacy/
tripal_contact/ api/ tripal_contact.DEPRECATED.inc - tripal_contact_insert_property in legacy/
tripal_contact/ api/ tripal_contact.DEPRECATED.inc - tripal_contact_update_property in legacy/
tripal_contact/ api/ tripal_contact.DEPRECATED.inc - tripal_core_chado_delete in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_chado_get_foreign_key in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_chado_insert in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_chado_node_cleanup_orphaned in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_chado_node_sync_form in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_chado_node_sync_records in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_chado_schema_exists in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_chado_select in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_chado_update in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_create_custom_table in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_delete_property in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_delete_property_by_id in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_edit_custom_table in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_expand_chado_vars in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_generate_chado_var in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_get_chado_tables in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_get_chado_table_schema in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_get_chado_version in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_get_property in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_get_token_value_for_property in legacy/
tripal_core/ includes/ tripal_core.search.inc - Retrieve values for all tokens for an entity property getter function.
- tripal_core_insert_property in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_is_chado_installed in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_is_chado_local in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_is_tripal_node_type in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_report_error in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - @todo Remove. This was not in Tripal 1.x.
- tripal_core_schema_exists in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_update_property in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_core_update_property_by_id in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_create_files_dir in tripal/
api/ tripal.files.api.inc - Creates a directory for a module in the Drupal's public files directory.
- tripal_create_moddir in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_create_mod_subdir in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_custom_tables_get_table_id in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_cv_add_cv in legacy/
tripal_cv/ api/ tripal_cv.DEPRECATED.inc - tripal_cv_add_cvterm in legacy/
tripal_cv/ api/ tripal_cv.DEPRECATED.inc - tripal_cv_add_obo_ref in legacy/
tripal_cv/ api/ tripal_cv.DEPRECATED.inc - tripal_cv_cvterm_name_autocomplete in legacy/
tripal_cv/ api/ tripal_cv.DEPRECATED.inc - tripal_cv_get_cv in legacy/
tripal_cv/ api/ tripal_cv.DEPRECATED.inc - tripal_cv_get_cvterm_by_id in legacy/
tripal_cv/ api/ tripal_cv.DEPRECATED.inc - tripal_cv_get_cvterm_by_name in legacy/
tripal_cv/ api/ tripal_cv.DEPRECATED.inc - tripal_cv_get_cvterm_by_synonym in legacy/
tripal_cv/ api/ tripal_cv.DEPRECATED.inc - tripal_cv_get_cvterm_options in legacy/
tripal_cv/ api/ tripal_cv.DEPRECATED.inc - tripal_cv_get_cv_by_id in legacy/
tripal_cv/ api/ tripal_cv.DEPRECATED.inc - tripal_cv_get_cv_by_name in legacy/
tripal_cv/ api/ tripal_cv.DEPRECATED.inc - tripal_cv_get_cv_id in legacy/
tripal_cv/ api/ tripal_cv.DEPRECATED.inc - tripal_cv_get_cv_options in legacy/
tripal_cv/ api/ tripal_cv.DEPRECATED.inc - tripal_cv_submit_obo_job in legacy/
tripal_cv/ api/ tripal_cv.DEPRECATED.inc - tripal_cv_update_cvtermpath in legacy/
tripal_cv/ api/ tripal_cv.DEPRECATED.inc - tripal_db_add_db in legacy/
tripal_db/ api/ tripal_db.DEPRECATED.inc - tripal_db_add_dbxref in legacy/
tripal_db/ api/ tripal_db.DEPRECATED.inc - tripal_db_add_dbxref_link in legacy/
tripal_db/ api/ tripal_db.DEPRECATED.inc - tripal_db_get_db in legacy/
tripal_db/ api/ tripal_db.DEPRECATED.inc - tripal_db_get_dbxref in legacy/
tripal_db/ api/ tripal_db.DEPRECATED.inc - tripal_db_get_dbxref_by_accession in legacy/
tripal_db/ api/ tripal_db.DEPRECATED.inc - tripal_db_get_db_by_db_id in legacy/
tripal_db/ api/ tripal_db.DEPRECATED.inc - tripal_db_get_db_by_name in legacy/
tripal_db/ api/ tripal_db.DEPRECATED.inc - tripal_db_get_db_options in legacy/
tripal_db/ api/ tripal_db.DEPRECATED.inc - tripal_db_set_active in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_featuremap_add_featuremap_dbxref in legacy/
tripal_featuremap/ api/ tripal_featuremap.DEPRECATED.inc - tripal_featuremap_delete_property in legacy/
tripal_featuremap/ api/ tripal_featuremap.DEPRECATED.inc - tripal_featuremap_get_property in legacy/
tripal_featuremap/ api/ tripal_featuremap.DEPRECATED.inc - tripal_featuremap_insert_property in legacy/
tripal_featuremap/ api/ tripal_featuremap.DEPRECATED.inc - tripal_featuremap_update_property in legacy/
tripal_featuremap/ api/ tripal_featuremap.DEPRECATED.inc - tripal_feature_add_cvterm in legacy/
tripal_feature/ api/ tripal_feature.DEPRECATED.inc - tripal_feature_add_dbxref in legacy/
tripal_feature/ api/ tripal_feature.DEPRECATED.inc - tripal_feature_analysis_delete_property in legacy/
tripal_feature/ api/ tripal_feature.DEPRECATED.inc - tripal_feature_analysis_delete_property_by_id in legacy/
tripal_feature/ api/ tripal_feature.DEPRECATED.inc - tripal_feature_analysis_get_property in legacy/
tripal_feature/ api/ tripal_feature.DEPRECATED.inc - tripal_feature_analysis_insert_property in legacy/
tripal_feature/ api/ tripal_feature.DEPRECATED.inc - tripal_feature_analysis_update_property in legacy/
tripal_feature/ api/ tripal_feature.DEPRECATED.inc - tripal_feature_analysis_update_property_by_id in legacy/
tripal_feature/ api/ tripal_feature.DEPRECATED.inc - tripal_feature_delete_property in legacy/
tripal_feature/ api/ tripal_feature.DEPRECATED.inc - tripal_feature_delete_property_by_id in legacy/
tripal_feature/ api/ tripal_feature.DEPRECATED.inc - tripal_feature_get_property in legacy/
tripal_feature/ api/ tripal_feature.DEPRECATED.inc - tripal_feature_insert_property in legacy/
tripal_feature/ api/ tripal_feature.DEPRECATED.inc - tripal_feature_reverse_complement in legacy/
tripal_feature/ api/ tripal_feature.DEPRECATED.inc - tripal_feature_update_property in legacy/
tripal_feature/ api/ tripal_feature.DEPRECATED.inc - tripal_feature_update_property_by_id in legacy/
tripal_feature/ api/ tripal_feature.DEPRECATED.inc - tripal_file_directory_path in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - @todo Remove. This was not in Tripal 1.x.
- tripal_get_chado_custom_schema in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_get_job in tripal/
api/ tripal.jobs.api.inc - Retrieve information regarding a tripal job
- tripal_get_job_end in tripal/
api/ tripal.DEPRECATED.api.inc - DEPRECATED
- tripal_get_job_progress in tripal/
api/ tripal.jobs.api.inc - Retrieves the current proress of a job.
- tripal_get_job_start in tripal/
api/ tripal.DEPRECATED.api.inc - DEPRECATED
- tripal_get_job_submit_date in tripal/
api/ tripal.DEPRECATED.api.inc - DEPRECATED
- tripal_get_max_chado_rank in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_get_moddir in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_get_module_active_jobs in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_get_remote_API_doc in tripal_ws/
api/ tripal_ws.api.inc - Retrieves the API documentation for a remote Tripal web service.
- tripal_get_remote_content in tripal_ws/
api/ tripal_ws.api.inc - Makes a request to the "content" service of a remote Tripal web site.
- tripal_get_remote_context in tripal_ws/
api/ tripal_ws.api.inc - Retrieves the JSON-LD context for any remote Tripal web service.
- tripal_get_term_children in tripal/
api/ tripal.terms.api.inc - Retrieves the immediate children of the given term.
- tripal_get_term_details in tripal/
api/ tripal.terms.api.inc - Retrieves full information about a vocabulary term.
- tripal_get_vocabulary_root_terms in tripal/
api/ tripal.terms.api.inc - Retrieves the immediate children of the given term.
- tripal_insert_bulk_loader_template in tripal_bulk_loader/
api/ tripal_bulk_loader.api.templates.inc - Inserts a bulk loader template record.
- tripal_insert_variable in tripal/
api/ tripal.variables.api.inc - Adds a new variable name.
- tripal_jobs_cancel in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_jobs_check_running in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_jobs_get_end_time in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_jobs_get_start_time in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_jobs_get_submit_date in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_jobs_launch in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_jobs_rerun in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_job_set_progress in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_library_delete_property in legacy/
tripal_library/ api/ tripal_library.DEPRECATED.inc - tripal_library_get_property in legacy/
tripal_library/ api/ tripal_library.DEPRECATED.inc - tripal_library_insert_property in legacy/
tripal_library/ api/ tripal_library.DEPRECATED.inc - tripal_library_update_property in legacy/
tripal_library/ api/ tripal_library.DEPRECATED.inc - tripal_load_remote_entity in tripal_ws/
api/ tripal_ws.api.inc - Queries a remote site for an entity.
- tripal_mviews_action in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_mviews_get_mview_id in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_organism_get_image_url in legacy/
tripal_organism/ api/ tripal_organism.DEPRECATED.inc - tripal_organism_get_organism_by_nid in legacy/
tripal_organism/ api/ tripal_organism.DEPRECATED.inc - tripal_organism_get_organism_by_organism_id in legacy/
tripal_organism/ api/ tripal_organism.DEPRECATED.inc - tripal_organism_get_synced in legacy/
tripal_organism/ api/ tripal_organism.DEPRECATED.inc - tripal_project_delete_property in legacy/
tripal_project/ api/ tripal_project.DEPRECATED.inc - tripal_project_get_property in legacy/
tripal_project/ api/ tripal_project.DEPRECATED.inc - tripal_project_insert_property in legacy/
tripal_project/ api/ tripal_project.DEPRECATED.inc - tripal_project_update_property in legacy/
tripal_project/ api/ tripal_project.DEPRECATED.inc - tripal_pub_add_authors in tripal_chado/
includes/ loaders/ tripal_chado.pub_importers.inc - Add one or more authors to a publication
- tripal_pub_add_publication in tripal_chado/
includes/ loaders/ tripal_chado.pub_importers.inc - Adds a new publication to the Chado, along with all properties and database cross-references. If the publication does not already exist in Chado then it is added. If it does exist nothing is done. If the $update parameter is TRUE then the…
- tripal_pub_add_publications in tripal_chado/
includes/ loaders/ tripal_chado.pub_importers.inc - Adds publications that have been retrieved from a remote database and consolidated into an array of details.
- tripal_pub_add_pub_dbxref in legacy/
tripal_pub/ api/ tripal_pub.DEPRECATED.inc - tripal_pub_delete_property in legacy/
tripal_pub/ api/ tripal_pub.DEPRECATED.inc - tripal_pub_get_property in legacy/
tripal_pub/ api/ tripal_pub.DEPRECATED.inc - tripal_pub_get_publication_array in tripal_chado/
includes/ loaders/ tripal_chado.pub_importers.inc - This function generates an array suitable for use with the tripal_pub_create_citation function for any publication already stored in the Chado tables.
- tripal_pub_get_pubs_by_dbxref in legacy/
tripal_pub/ api/ tripal_pub.DEPRECATED.inc - tripal_pub_get_pubs_by_title_type_pyear_series in legacy/
tripal_pub/ api/ tripal_pub.DEPRECATED.inc - tripal_pub_get_pub_by_uniquename in legacy/
tripal_pub/ api/ tripal_pub.DEPRECATED.inc - tripal_pub_get_raw_data in legacy/
tripal_pub/ api/ tripal_pub.DEPRECATED.inc - tripal_pub_get_remote_search_results in legacy/
tripal_pub/ api/ tripal_pub.DEPRECATED.inc - tripal_pub_import_by_dbxref in legacy/
tripal_pub/ api/ tripal_pub.DEPRECATED.inc - tripal_pub_import_publications in legacy/
tripal_pub/ api/ tripal_pub.DEPRECATED.inc - tripal_pub_import_publications_by_import_id in legacy/
tripal_pub/ api/ tripal_pub.DEPRECATED.inc - tripal_pub_insert_property in legacy/
tripal_pub/ api/ tripal_pub.DEPRECATED.inc - tripal_pub_PMID_fetch in tripal_chado/
includes/ loaders/ tripal_chado.pub_importer_PMID.inc - Retrieves from PubMed a set of publications from the previously initiated query.
- tripal_pub_PMID_parse_publication_type in tripal_chado/
includes/ loaders/ tripal_chado.pub_importer_PMID.inc - Parses the section from the XML returned from PubMed that contains information about a publication
- tripal_pub_PMID_parse_pubxml in tripal_chado/
includes/ loaders/ tripal_chado.pub_importer_PMID.inc - This function parses the XML containing details of a publication and converts it into an associative array of where keys are Tripal Pub ontology terms and the values are extracted from the XML. The XML should contain only a single publication record.
- tripal_pub_PMID_search_init in tripal_chado/
includes/ loaders/ tripal_chado.pub_importer_PMID.inc - Initailizes a PubMed Search using a given search string
- tripal_pub_update_property in legacy/
tripal_pub/ api/ tripal_pub.DEPRECATED.inc - tripal_pub_update_publications in legacy/
tripal_pub/ api/ tripal_pub.DEPRECATED.inc - tripal_rerun_job in tripal/
api/ tripal.jobs.api.inc - Set a job to be re-run (ie: add it back into the job queue).
- tripal_reset_file_expiration in tripal/
api/ tripal.quotas.api.inc - Resets the expiration data of a file managed by Tripal.
- tripal_search_chado_token_across_nodetypes_getter_callback in legacy/
tripal_core/ includes/ tripal_core.search.inc - Implements a getter callback for foreign keys collon between content types.
- tripal_search_chado_token_getter_callback in legacy/
tripal_core/ includes/ tripal_core.search.inc - Implements a getter callback for chado token formats.
- tripal_search_update_default_index in legacy/
tripal_core/ includes/ tripal_core.search.inc - The Search API provides a default node index which has a number of node-specific fields enabled by default. We want to ensure our chado fields are also enabled by default thus making for easier enabling of Tripal search.
- tripal_set_default_cv in legacy/
tripal_cv/ api/ tripal_cv.api.inc - This function sets the default vocabulary for a given table and field.
- tripal_set_job_progress in tripal/
api/ tripal.jobs.api.inc - An internal function for setting the progress for a current job.
- tripal_stock_get_all_stocks in legacy/
tripal_stock/ api/ tripal_stock.DEPRECATED.inc - tripal_stock_get_stocks in legacy/
tripal_stock/ api/ tripal_stock.DEPRECATED.inc - tripal_stock_get_stocks_by_stockprop in legacy/
tripal_stock/ api/ tripal_stock.DEPRECATED.inc - tripal_stock_get_stock_by_name_identifier in legacy/
tripal_stock/ api/ tripal_stock.DEPRECATED.inc - tripal_stock_get_stock_by_nid in legacy/
tripal_stock/ api/ tripal_stock.DEPRECATED.inc - tripal_stock_get_stock_by_stock_id in legacy/
tripal_stock/ api/ tripal_stock.DEPRECATED.inc - tripal_tripal_cron_notification in tripal/
api/ tripal.entities.api.inc - Refreshes the bundle such that new fields added by modules will be found during cron.
- tripal_update_cvtermpath_old in tripal_chado/
api/ modules/ tripal_chado.cv.api.inc - Updates the cvtermpath table of Chado for the specified CV.
- tripal_update_mview in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - _chado_update_cvtermpath_loop_increment in tripal_chado/
api/ modules/ tripal_chado.cv.api.inc