90 uses of TRIPAL_ERROR

chado_add_admin_form_set_title in tripal_core/api/tripal_core.chado_nodes.title_and_path.api.inc
Generic "Set Node Title" sub-form for setting the title of any chado node
chado_add_admin_form_set_url in tripal_core/api/tripal_core.chado_nodes.title_and_path.api.inc
Generic "Set Node URL" sub-form for setting the url of any chado node
chado_add_node_form_properties in tripal_core/api/tripal_core.chado_nodes.properties.api.inc
chado_add_node_form_relationships in 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 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 tripal_analysis/includes/tripal_analysis.chado_node.inc
Implements hook_update(). Update analyses
chado_contact_insert in tripal_contact/includes/tripal_contact.chado_node.inc
Implements of hook_insert().
chado_contact_update in tripal_contact/includes/tripal_contact.chado_node.inc
Implements hook_update
chado_delete_custom_table in tripal_core/api/tripal_core.custom_tables.api.inc
Deletes the specified custom table
chado_delete_property in tripal_core/api/tripal_core.chado_general.api.inc
Deletes a property for a given base table record using the property name
chado_delete_record in tripal_core/api/tripal_core.chado_query.api.inc
Provides a generic function for deleting a record(s) from any chado table
chado_edit_custom_table in tripal_core/api/tripal_core.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_core/api/tripal_core.chado_variables.api.inc
Retrieves fields, or tables that were excluded by default from a variable.
chado_featuremap_insert in tripal_featuremap/includes/tripal_featuremap.chado_node.inc
Implements hook_insert().
chado_featuremap_update in tripal_featuremap/includes/tripal_featuremap.chado_node.inc
Implements hook_update(). Update nodes
chado_feature_add_synonyms in tripal_feature/includes/tripal_feature.chado_node.inc
Add synonyms to a feature
chado_generate_var in tripal_core/api/tripal_core.chado_variables.api.inc
Generates an object containing the full details of a record(s) in Chado.
chado_get_node_url in tripal_core/api/tripal_core.chado_nodes.title_and_path.api.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_property in tripal_core/api/tripal_core.chado_general.api.inc
Retrieve a property for a given base table record.
chado_get_record_with_property in tripal_core/api/tripal_core.chado_general.api.inc
Get all records in the base table assigned one or more properties.
chado_insert_property in tripal_core/api/tripal_core.chado_general.api.inc
Insert a property for a given base table.
chado_insert_record in tripal_core/api/tripal_core.chado_query.api.inc
Provides a generic routine for inserting into any Chado table
chado_node_get_unique_constraint_format in tripal_core/api/tripal_core.chado_nodes.title_and_path.api.inc
Generate the unique constraint for a given base table using the Chado Schema API definition
chado_organism_insert in tripal_organism/includes/tripal_organism.chado_node.inc
Implements hook_insert().
chado_pager_query in tripal_core/api/tripal_core.chado_query.api.inc
Use this function instead of pager_query() when selecting a subset of records from a Chado table.
chado_query in tripal_core/api/tripal_core.chado_query.api.inc
Use this function instead of db_query() to avoid switching databases when making query to the chado database.
chado_select_record in tripal_core/api/tripal_core.chado_query.api.inc
Provides a generic routine for selecting data from a Chado table
chado_stock_update in tripal_stock/includes/tripal_stock.chado_node.inc
Implements hook_update(). Handles Editing/Updating of main stock info
chado_update_node_form_properties in 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_property in tripal_core/api/tripal_core.chado_general.api.inc
Update a property for a given base table record and property name.
chado_update_record in tripal_core/api/tripal_core.chado_query.api.inc
Provides a generic routine for updating into any Chado table
process_data_array_for_line in tripal_bulk_loader/includes/tripal_bulk_loader.loader.inc
Process the data array for a given line
tripal_add_legacy_mview in tripal_core/api/tripal_core.DEPRECATED.api.inc
tripal_add_mview in tripal_core/api/tripal_core.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…
tripal_add_node_variable in tripal_core/api/tripal_core.tripal_variables.api.inc
Associates a variable and it's value to a node.
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_clone_views_integration in tripal_views/api/tripal_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_install_chado in tripal_core/includes/tripal_core.chado_install.inc
Install Chado Schema
tripal_core_is_tripal_node_type in tripal_core/api/tripal_core.DEPRECATED.api.inc
tripal_create_files_dir in tripal_core/api/tripal_core.files.api.inc
Creates a directory for a module in the Drupal's public files directory.
tripal_cv_obo_quiterror in tripal_cv/includes/tripal_cv.obo_loader.inc
Immediately terminates loading of the OBO file.
tripal_delete_phylotree in tripal_phylogeny/api/tripal_phylogeny.api.inc
Deletes a phylotree record from Chado.
tripal_featuremap_add_featuremap_dbxref in tripal_featuremap/api/tripal_featuremap.DEPRECATED.inc
tripal_feature_gff3_exporter in tripal_feature/includes/tripal_feature.gff_exporter.inc
tripal_feature_load_fasta in tripal_feature/includes/tripal_feature.fasta_loader.inc
Actually load a fasta file. This is the function called by tripal jobs
tripal_feature_load_fasta_feature in tripal_feature/includes/tripal_feature.fasta_loader.inc
A helper function for tripal_feature_load_fasta() to load a single feature
tripal_feature_load_gff3 in tripal_feature/includes/tripal_feature.gff_loader.inc
Actually load a GFF3 file. This is the function called by tripal jobs
tripal_feature_load_gff3_derives_from in tripal_feature/includes/tripal_feature.gff_loader.inc
Load the derives from attribute for a gff3 feature
tripal_feature_load_gff3_parents in tripal_feature/includes/tripal_feature.gff_loader.inc
Load the parents for a gff3 feature
tripal_feature_load_gff3_target in tripal_feature/includes/tripal_feature.gff_loader.inc
Load the target attribute of a gff3 record
tripal_get_analysis in tripal_analysis/api/tripal_analysis.api.inc
Retrieves an chado analysis variable
tripal_get_cv in tripal_cv/api/tripal_cv.api.inc
Retrieves a chado controlled vocabulary variable
tripal_get_cvterm in tripal_cv/api/tripal_cv.api.inc
Retrieves a chado controlled vocabulary term variable
tripal_get_db in tripal_db/api/tripal_db.api.inc
Retrieves a chado db variable
tripal_get_dbxref in tripal_db/api/tripal_db.api.inc
Retrieves a chado database reference variable
tripal_get_feature_sequences in tripal_feature/api/tripal_feature.api.inc
Retrieves the sequences for a given feature.
tripal_get_multiple_stocks in tripal_stock/api/tripal_stock.api.inc
Retrieves a chado stock variable
tripal_get_organism in tripal_organism/api/tripal_organism.api.inc
Retrieves a chado organism variable
tripal_get_publication in tripal_pub/api/tripal_pub.api.inc
Retrieves a chado publication array
tripal_get_stock in tripal_stock/api/tripal_stock.api.inc
Retrieves a chado stock variable
tripal_insert_bulk_loader_template in tripal_bulk_loader/api/tripal_bulk_loader.api.templates.inc
Inserts a bulk loader template record.
tripal_insert_contact in tripal_contact/api/tripal_contact.api.inc
Adds a contact to the Chado contact table
tripal_insert_cvterm in tripal_cv/api/tripal_cv.api.inc
Add's a controlled vocabulary term to Chado.
tripal_insert_phylotree in tripal_phylogeny/api/tripal_phylogeny.api.inc
Inserts a phylotree record into Chado.
tripal_insert_variable in tripal_core/api/tripal_core.tripal_variables.api.inc
Adds a new variable name.
tripal_phylogeny_get_node_types_vocab in tripal_phylogeny/includes/tripal_phylogeny.import_tree.inc
tripal_phylogeny_import_tree_file in tripal_phylogeny/includes/tripal_phylogeny.import_tree.inc
Imports a tree file.
tripal_publication_exists in tripal_pub/api/tripal_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…
tripal_pub_add_authors in tripal_pub/includes/tripal_pub.pub_importers.inc
Add one or more authors to a publication
tripal_pub_add_publication in tripal_pub/includes/tripal_pub.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_pub/includes/tripal_pub.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_pub/includes/tripal_pub.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_pub/includes/importers/tripal_pub.PMID.inc
Retreives from PubMed a set of publications from the previously initiated query.
tripal_pub_PMID_parse_publication_type in tripal_pub/includes/importers/tripal_pub.PMID.inc
Parses the section from the XML returned from PubMed that contains information about a publication
tripal_pub_PMID_parse_pubxml in tripal_pub/includes/importers/tripal_pub.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_pub/includes/importers/tripal_pub.PMID.inc
Initailizes a PubMed Search using a given search string
tripal_report_error in tripal_core/api/tripal_core.tripal.api.inc
Provide better error notice for Tripal. If the environment variable 'TRIPAL_DEBUG' is set to 1 then this function will add backtrace information to the message.
tripal_search_chado_token_across_nodetypes_getter_callback in 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 tripal_core/includes/tripal_core.search.inc
Implements a getter callback for chado token formats.
tripal_set_message in tripal_core/api/tripal_core.tripal.api.inc
Display messages to tripal administrators.
tripal_update_cvtermpath in tripal_cv/api/tripal_cv.api.inc
Updates the cvtermpath table of Chado for the specified CV.
tripal_update_phylotree in tripal_phylogeny/api/tripal_phylogeny.api.inc
Updates a phylotree record into Chado.
tripal_validate_phylotree in tripal_phylogeny/api/tripal_phylogeny.api.inc
Validates an $options array for insert or update of a phylotree record.
tripal_views_integration_ajax_join_field in tripal_views/includes/tripal_views_integration_UI.inc