110 calls to chado_select_record()
- chado_add_node_form_dbxrefs in legacy/
tripal_core/ api/ tripal_core.chado_nodes.dbxrefs.api.inc - Provides a form for adding to BASE_dbxref and dbxref tables
- chado_add_node_form_dbxrefs_add_button_validate in legacy/
tripal_core/ api/ tripal_core.chado_nodes.dbxrefs.api.inc - Validate the user input for creating a new dbxref Called by the add button in chado_add_node_form_dbxrefs
- chado_add_node_form_properties in legacy/
tripal_core/ api/ tripal_core.chado_nodes.properties.api.inc - chado_add_node_form_properties_add_button_validate in legacy/
tripal_core/ api/ tripal_core.chado_nodes.properties.api.inc - Validate the user input for creating a new property Called by the add button in chado_add_node_form_properties
- 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_add_node_form_relationships_add_button_validate in legacy/
tripal_core/ api/ tripal_core.chado_nodes.relationships.api.inc - Validate the user input for creating a new relationship. Called by the add button in chado_add_node_form_relationships.
- 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_validate in legacy/
tripal_contact/ includes/ tripal_contact.chado_node.inc - Implements hook_validate(). Validates submission of form when adding or updating a contact node.
- 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_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_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_cvterm in tripal_chado/
api/ modules/ tripal_chado.cv.api.inc - Retrieves a chado controlled vocabulary term variable.
- chado_get_cvterm_select_options in tripal_chado/
api/ modules/ tripal_chado.cv.api.inc - Create an options array to be used in a form element which provides a list of all chado cvterms.
- chado_get_cv_select_options in tripal_chado/
api/ modules/ tripal_chado.cv.api.inc - Create an options array to be used in a form element which provides a list of all chado cvs.
- 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_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_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_library_form in legacy/
tripal_library/ includes/ tripal_library.chado_node.inc - Implements hook_form().
- chado_linker__prop::load in tripal_chado/
includes/ TripalFields/ chado_linker__prop/ chado_linker__prop.inc - chado_node_sync_records in legacy/
tripal_core/ api/ tripal_core.chado_nodes.api.inc - Generic function for syncing records in Chado with Drupal nodes.
- chado_organism_validate in legacy/
tripal_organism/ includes/ tripal_organism.chado_node.inc - Implementation of hook_validate().
- chado_phylogeny_import_tree in tripal_chado/
api/ modules/ tripal_chado.phylotree.api.inc - Iterates through the tree array and creates phylonodes in Chado.
- chado_project_form in legacy/
tripal_project/ includes/ tripal_project.chado_node.inc - Implementation of hook_form().
- 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_pub_form in legacy/
tripal_pub/ includes/ tripal_pub.chado_node.inc - Implements hook_form().
- chado_pub_validate in legacy/
tripal_pub/ includes/ tripal_pub.chado_node.inc - Implements hook_validate().
- chado_schema_get_foreign_key in tripal_chado/
api/ tripal_chado.query.api.inc - Gets the value of a foreign key relationship.
- 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_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.
- drush_tripal_phylogeny_trp_delete_phylotree in legacy/
tripal_phylogeny/ tripal_phylogeny.drush.inc - Deletes a phylotree record.
- drush_tripal_phylogeny_trp_update_phylotree in legacy/
tripal_phylogeny/ tripal_phylogeny.drush.inc - FASTAImporter::form in tripal_chado/
includes/ TripalImporter/ FASTAImporter.inc - FASTAImporter::loadFastaFeature in tripal_chado/
includes/ TripalImporter/ FASTAImporter.inc - A helper function for loadFasta() to load a single feature
- GFF3Importer::loadAlias in tripal_chado/
includes/ TripalImporter/ GFF3Importer.inc - Load any aliases for a feature
- GFF3Importer::loadDbxref in tripal_chado/
includes/ TripalImporter/ GFF3Importer.inc - Load the dbxref attribute for a feature
- GFF3Importer::loadDerivesFrom in tripal_chado/
includes/ TripalImporter/ GFF3Importer.inc - Load the derives from attribute for a gff3 feature
- GFF3Importer::loadFasta in tripal_chado/
includes/ TripalImporter/ GFF3Importer.inc - Load the FASTA sequences at the bottom of a GFF3 file
- GFF3Importer::loadFeature in tripal_chado/
includes/ TripalImporter/ GFF3Importer.inc - Create the feature record & link it to it's analysis
- GFF3Importer::loadFeatureLoc in tripal_chado/
includes/ TripalImporter/ GFF3Importer.inc - Insert the location of the feature
- GFF3Importer::loadGFF3 in tripal_chado/
includes/ TripalImporter/ GFF3Importer.inc - Actually load a GFF3 file. This is the function called by tripal jobs
- GFF3Importer::loadOntology in tripal_chado/
includes/ TripalImporter/ GFF3Importer.inc - Load the cvterms for a feature.
- GFF3Importer::loadParents in tripal_chado/
includes/ TripalImporter/ GFF3Importer.inc - Load the parents for a gff3 feature
- GFF3Importer::loadProperty in tripal_chado/
includes/ TripalImporter/ GFF3Importer.inc - Load a preoprty (featurepop) for the feature
- GFF3Importer::loadTarget in tripal_chado/
includes/ TripalImporter/ GFF3Importer.inc - Load the target attribute of a gff3 record
- OBOImporter::addCvtermDbxref in tripal_chado/
includes/ TripalImporter/ OBOImporter.inc - Adds a database reference to a cvterm
- OBOImporter::addCvtermProp in tripal_chado/
includes/ TripalImporter/ OBOImporter.inc - Adds a property to a cvterm
- OBOImporter::addDbxref in tripal_chado/
includes/ TripalImporter/ OBOImporter.inc - Adds a database cross reference to a cvterm
- OBOImporter::addRelationship in tripal_chado/
includes/ TripalImporter/ OBOImporter.inc - Adds a cvterm relationship
- OBOImporter::addSynonym in tripal_chado/
includes/ TripalImporter/ OBOImporter.inc - Adds the synonyms to a term
- OBOImporter::getTerm in tripal_chado/
includes/ TripalImporter/ OBOImporter.inc - Retrieves the term array from the temp loading table for a given term id.
- process_data_array_for_line in tripal_bulk_loader/
includes/ tripal_bulk_loader.loader.inc - Process the data array for a given line
- sbo__relationship::validate in tripal_chado/
includes/ TripalFields/ sbo__relationship/ sbo__relationship.inc - sbo__relationship_widget::validate in tripal_chado/
includes/ TripalFields/ sbo__relationship/ sbo__relationship_widget.inc - schema__additional_type::settingsFormValidate in tripal_chado/
includes/ TripalFields/ schema__additional_type/ schema__additional_type.inc - sio__annotation::load in tripal_chado/
includes/ TripalFields/ sio__annotation/ sio__annotation.inc - TaxonomyImporter::findOrganism in tripal_chado/
includes/ TripalImporter/ TaxonomyImporter.inc - Checks the Chado database to see if the organism already exists.
- TaxonomyImporter::initTree in tripal_chado/
includes/ TripalImporter/ TaxonomyImporter.inc - Create the taxonomic tree in Chado.
- TaxonomyImporter::rebuildTree in tripal_chado/
includes/ TripalImporter/ TaxonomyImporter.inc - Iterates through all existing organisms and rebuilds the taxonomy tree.
- tripal_analysis_delete_analyses in legacy/
tripal_analysis/ includes/ tripal_analysis.delete.inc - Function to actually delete the features indicated
- tripal_analysis_validate in legacy/
tripal_analysis/ includes/ tripal_analysis.chado_node.inc - This validation is being used for three activities: CASE A: Update a node that exists in both drupal and chado CASE B: Synchronizing a node from chado to drupal CASE C: Inserting a new node that exists in niether drupal nor chado
- tripal_bulk_loader_add_foreignkey_to_values in tripal_bulk_loader/
includes/ tripal_bulk_loader.loader.inc - Handles foreign keys in the values array.
- tripal_chado_add_db_form_fields in tripal_chado/
includes/ tripal_chado.db.inc - Fields commmon between the add/edit forms
- tripal_chado_db_form_fields_validate in tripal_chado/
includes/ tripal_chado.db.inc - Generic form validation for shared fields of both the edit and add forms
- tripal_chado_field_storage_write_table in tripal_chado/
includes/ tripal_chado.field_storage.inc - Write (inserts/updates/deletes) values for a Chado table.
- tripal_chado_prepare_chado in tripal_chado/
includes/ setup/ tripal_chado.setup.inc - Prepares Chado for use by Tripal.
- tripal_core_chado_select in legacy/
tripal_core/ api/ tripal_core.DEPRECATED.inc - tripal_cv_add_cvterm_form_fields in tripal_chado/
includes/ tripal_chado.cv.inc - Form fields in common between add/edit forms
- tripal_cv_add_cv_form_fields in tripal_chado/
includes/ tripal_chado.cv.inc - Form fields in common between the cv add & edit form.
- tripal_cv_cvterm_add_form_submit in tripal_chado/
includes/ tripal_chado.cv.inc - Adds new terms to an existing cv
- tripal_cv_cvterm_add_form_validate in tripal_chado/
includes/ tripal_chado.cv.inc - Validate cv add form
- tripal_cv_cvterm_edit_form_submit in tripal_chado/
includes/ tripal_chado.cv.inc - Edits existing controlled vocabulary terms
- tripal_cv_cvterm_edit_form_validate in tripal_chado/
includes/ tripal_chado.cv.inc - Validate cvterm edit form
- tripal_cv_form_fields_validate in tripal_chado/
includes/ tripal_chado.cv.inc - Generic validation form for shared fields of both the edit and add forms
- tripal_featuremap_add_featuremap_dbxref in legacy/
tripal_featuremap/ api/ tripal_featuremap.DEPRECATED.inc - tripal_feature_analysis_delete_property 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_delete_features in legacy/
tripal_feature/ includes/ tripal_feature.delete.inc - Function to actually delete the features indicated
- tripal_feature_job_describe_args in legacy/
tripal_feature/ tripal_feature.module - Implements hook_job_describe_args() in order to describe the various feature jobs to the tripal jobs interface.
- tripal_feature_node_presave in legacy/
tripal_feature/ includes/ tripal_feature.chado_node.inc - Implements hook_node_presave(). Acts on all content types.
- tripal_feature_preprocess_tripal_feature_bar_chart_type_organism_summary in legacy/
tripal_feature/ theme/ tripal_feature.theme.inc - tripal_library_features.tpl.php in legacy/
tripal_library/ theme/ templates/ tripal_library_features.tpl.php - tripal_organism_delete_organisms in legacy/
tripal_organism/ includes/ tripal_organism.delete.inc - Function to actually delete the features indicated
- tripal_organism_feature_browser.tpl.php in legacy/
tripal_feature/ theme/ templates/ tripal_organism_feature_browser.tpl.php - tripal_organism_job_describe_args in legacy/
tripal_organism/ tripal_organism.module - Implements hook_job_describe_args().
- tripal_owl_check_class_depedencies in tripal_chado/
includes/ loaders/ tripal_cv.owl_loader.php - Checks for required vocabularies that are not loaded into Chado.
- tripal_phylogeny_prepare_tree_viewer in tripal_chado/
includes/ tripal_chado.phylotree.inc - Prepares a phylogenetic tree for viewing.
- tripal_pub_importers_list in tripal_chado/
includes/ loaders/ tripal_chado.pub_importers.inc - A function to generate a table containing the list of publication importers
- tripal_pub_importer_setup_form in tripal_chado/
includes/ loaders/ tripal_chado.pub_importers.inc - The form used for creating publication importers.
- tripal_pub_importer_setup_page in tripal_chado/
includes/ loaders/ tripal_chado.pub_importers.inc - Creates the page that contains the publication importer setup form and test results.
- tripal_search_publications in tripal_chado/
includes/ tripal_chado.pub_search.inc - Builds the SQL statement need to search Chado for the publications that match the user supplied criteria. Tpyically, this function is called by the search form generated by the tripal_chado_pub_search_form() function but this function is included in…
- tripal_stock_get_stock_by_name_identifier in legacy/
tripal_stock/ api/ tripal_stock.DEPRECATED.inc - tripal_stock_node_presave in legacy/
tripal_stock/ includes/ tripal_stock.chado_node.inc - Implements hook_node_presave(). Acts on all content types.
- tripal_views_handler_filter_select_id::get_select_options in tripal_chado_views/
views/ handlers/ tripal_views_handler_filter_select_id.inc - Provide the options used in the select list. Override this function in extended handlers to easily change option list.