118 uses of TRIPAL_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_semweb_term in tripal_chado/api/tripal_chado.semweb.api.inc: Associates a controlled vocabulary term with a field in a Chado table.
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_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_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_multiple_stocks in tripal_chado/api/modules/tripal_chado.stock.api.inc: Retrieves a chado stock variable.
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_insert_contact in tripal_chado/api/modules/tripal_chado.contact.api.inc: Adds a contact to the Chado contact table.
chado_insert_cvterm in tripal_chado/api/modules/tripal_chado.cv.api.inc: Add's a controlled vocabulary term to Chado.
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_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_organism_insert in legacy/tripal_organism/includes/tripal_organism.chado_node.inc: Implements hook_insert().
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_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_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_stock_update in legacy/tripal_stock/includes/tripal_stock.chado_node.inc: Implements hook_update(). Handles Editing/Updating of main stock info
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.
FASTAImporter::loadFastaFeature in tripal_chado/includes/TripalImporter/FASTAImporter.inc: A helper function for loadFasta() to load a single feature
GFF3Importer::loadDerivesFrom in tripal_chado/includes/TripalImporter/GFF3Importer.inc: Load the derives from attribute for a gff3 feature
GFF3Importer::loadGFF3 in tripal_chado/includes/TripalImporter/GFF3Importer.inc: Actually load a GFF3 file. This is the function called by tripal jobs
GFF3Importer::loadTarget in tripal_chado/includes/TripalImporter/GFF3Importer.inc: Load the target attribute of a gff3 record
process_data_array_for_line in tripal_bulk_loader/includes/tripal_bulk_loader.loader.inc: Process the data array for a given line
sio__vocabulary_widget::form in tripal_chado/includes/TripalFields/sio__vocabulary/sio__vocabulary_widget.inc
TripalDaemon::runSequentialTripalJob in tripal_daemon/TripalDaemon.inc: Run Sequential Tripal Job.
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.
TripalImporter::logMessage in tripal/includes/TripalImporter.inc: Logs a message for the importer.
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_admin_notification_import_field in tripal/includes/tripal.admin_blocks.inc: Import the field from the admin notification table on the dashboard.
tripal_bulk_loader_delete_template_field_form in tripal_bulk_loader/includes/tripal_bulk_loader.admin.templates.inc: Delete Field Form
tripal_bulk_loader_delete_template_record_form in tripal_bulk_loader/includes/tripal_bulk_loader.admin.templates.inc: Delete Record Form
tripal_bulk_loader_duplicate_template_record_form in tripal_bulk_loader/includes/tripal_bulk_loader.admin.templates.inc: Duplicate Record Form
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_load_data in tripal_bulk_loader/includes/tripal_bulk_loader.loader.inc: Tripal Bulk Loader
tripal_bulk_loader_modify_template_base_form in tripal_bulk_loader/includes/tripal_bulk_loader.admin.templates.inc: The main form reached at admin/tripal/tripal_bulk_loader/create and /edit
tripal_bulk_loader_template_field_form_submit in tripal_bulk_loader/includes/tripal_bulk_loader.admin.templates.inc: Add Field Submit
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_integration_ajax_join_field in tripal_chado_views/includes/tripal_chado_views_integration_UI.inc
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_core_is_tripal_node_type in legacy/tripal_core/api/tripal_core.DEPRECATED.inc
tripal_create_bundle_fields in tripal/api/tripal.entities.api.inc: Refreshes the bundle such that new fields added by modules will be found.
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_featuremap_add_featuremap_dbxref in legacy/tripal_featuremap/api/tripal_featuremap.DEPRECATED.inc
tripal_get_job in tripal/api/tripal.jobs.api.inc: Retrieve information regarding a tripal job
tripal_get_job_progress in tripal/api/tripal.jobs.api.inc: Retrieves the current proress of a job.
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_launch_job in tripal/api/tripal.jobs.api.inc: A function used to manually launch all queued tripal jobs.
tripal_load_remote_entity in tripal_ws/api/tripal_ws.api.inc: Queries a remote site for an entity.
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_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_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_report_error in tripal/api/tripal.notice.api.inc: Provide better error notice for Tripal.
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_run_importer in tripal/api/tripal.importer.api.inc: Imports data into the database.
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_set_job_progress in tripal/api/tripal.jobs.api.inc: An internal function for setting the progress for a current job.
tripal_set_message in tripal/api/tripal.notice.api.inc: Display messages to tripal administrators.
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.
_chado_update_cvtermpath_loop_increment in tripal_chado/api/modules/tripal_chado.cv.api.inc