146 calls to chado_query()

chado_add_index in tripal_chado/api/tripal_chado.schema.api.inc: A Chado-aware wrapper for the db_add_index() function.
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_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_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_delete in legacy/tripal_analysis/includes/tripal_analysis.chado_node.inc: Implements hook_delete(). Removes analysis from the chado database.
chado_autocomplete_contact in tripal_chado/api/modules/tripal_chado.contact.api.inc: This function is intended to be used in autocomplete forms for contacts.
chado_autocomplete_cv in tripal_chado/api/modules/tripal_chado.cv.api.inc: This function is intended to be used in autocomplete forms.
chado_autocomplete_cvterm in tripal_chado/api/modules/tripal_chado.cv.api.inc: This function is intended to be used in autocomplete forms for searching for CV terms that begin with the provided string.
chado_autocomplete_dbxref in tripal_chado/api/modules/tripal_chado.db.api.inc: This function is intended to be used in autocomplete forms for searching for accession that begin with the provided string.
chado_autocomplete_feature in tripal_chado/api/modules/tripal_chado.feature.api.inc: Used for autocomplete in forms for identifying for publications.
chado_autocomplete_organism in tripal_chado/api/modules/tripal_chado.organism.api.inc: This function is intended to be used in autocomplete forms for searching for organisms that begin with the provided string.
chado_autocomplete_pub in tripal_chado/api/modules/tripal_chado.pub.api.inc: Used for autocomplete in forms for identifying for publications.
chado_cleanup_orphaned_nodes_part in legacy/tripal_core/api/tripal_core.chado_nodes.api.inc: This function will delete Drupal nodes for any sync'ed table (e.g. feature, organism, analysis, stock, library) if the chado record has been deleted or the entry in the chado_[table] table has been removed.
chado_contact_delete in legacy/tripal_contact/includes/tripal_contact.chado_node.inc: Implements hook_delete().
chado_contact_form in legacy/tripal_contact/includes/tripal_contact.chado_node.inc: Implementation of hook_form().
chado_create_custom_table in tripal_chado/api/tripal_chado.custom_tables.api.inc: Add a new table to the Chado schema. This function is simply a wrapper for the db_create_table() function of Drupal, but ensures the table is created inside the Chado schema rather than the Drupal schema. If the table already exists then it will be…
chado_delete_custom_table in tripal_chado/api/tripal_chado.custom_tables.api.inc: Deletes the specified custom table.
chado_delete_mview in tripal_chado/api/tripal_chado.mviews.api.inc: Does the specified action for the specified Materialized View.
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_featuremap_delete in legacy/tripal_featuremap/includes/tripal_featuremap.chado_node.inc: Implements hook_delete().
chado_featuremap_validate in legacy/tripal_featuremap/includes/tripal_featuremap.chado_node.inc: Validates submission of form when adding or updating a map node
chado_feature_add_synonyms in legacy/tripal_feature/includes/tripal_feature.chado_node.inc: Add synonyms to a feature
chado_feature_delete in legacy/tripal_feature/includes/tripal_feature.chado_node.inc: Implements hook_delete().
chado_feature_form in legacy/tripal_feature/includes/tripal_feature.chado_node.inc: Implementation of hook_form().
chado_feature_validate in legacy/tripal_feature/includes/tripal_feature.chado_node.inc: Implementation of hook_validate().
chado_get_analysis_select_options in tripal_chado/api/modules/tripal_chado.analysis.api.inc: Returns a list of analyses that are currently synced with Drupal to use in select lists.
chado_get_bulk_feature_sequences in tripal_chado/api/modules/tripal_chado.feature.api.inc: Retrieves the bulk sequences for a given feature.
chado_get_db_select_options in tripal_chado/api/modules/tripal_chado.db.api.inc: Create an options array to be used in a form element which provides a list of all chado dbs.
chado_get_feature_sequences in tripal_chado/api/modules/tripal_chado.feature.api.inc: Retrieves the sequences for a given feature.
chado_get_organism_select_options in tripal_chado/api/modules/tripal_chado.organism.api.inc: Returns a list of organisms that are currently synced with Drupal to use in select lists.
chado_get_table_max_rank in tripal_chado/api/tripal_chado.query.api.inc: Get max rank for a given set of criteria.
chado_get_table_property_types in tripal_chado/api/tripal_chado.property.api.inc: Retrieves all of the property types currently availalbe in a prop table.
chado_get_version in tripal_chado/api/tripal_chado.schema.api.inc: Returns the version number of the currently installed Chado instance. It can return the real or effective version. Note, this function is executed in the hook_init() of the tripal_chado module which then sets the…
chado_insert_cvterm in tripal_chado/api/modules/tripal_chado.cv.api.inc: Add's a controlled vocabulary term to Chado.
chado_insert_record in tripal_chado/api/tripal_chado.query.api.inc: Provides a generic routine for inserting into any Chado table
chado_library_delete in legacy/tripal_library/includes/tripal_library.chado_node.inc: Implements hook_delete().
chado_library_form in legacy/tripal_library/includes/tripal_library.chado_node.inc: Implements hook_form().
chado_library_validate in legacy/tripal_library/includes/tripal_library.chado_node.inc: Implements hook_validate().
chado_node_sync_form in legacy/tripal_core/api/tripal_core.chado_nodes.api.inc: Generic Sync Form to aid in sync'ing (create drupal nodes linking to chado content) any chado node type.
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_delete in legacy/tripal_organism/includes/tripal_organism.chado_node.inc: Implements hook_delete().
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_phylotree_delete in legacy/tripal_phylogeny/includes/tripal_phylogeny.chado_node.inc: Implements hook_delete().
chado_phylotree_form in legacy/tripal_phylogeny/includes/tripal_phylogeny.chado_node.inc: Implementation of hook_form().
chado_populate_mview in tripal_chado/api/tripal_chado.mviews.api.inc: Update a Materialized View.
chado_project_delete in legacy/tripal_project/includes/tripal_project.chado_node.inc: Implementation of hook_delete().
chado_project_validate in legacy/tripal_project/includes/tripal_project.chado_node.inc: Implements hook_validate(). Validates submission of form when adding or updating a project node
chado_publish_records in tripal_chado/api/tripal_chado.api.inc: Publishes content in Chado as a new TripalEntity entity.
chado_pub_create_citations in tripal_chado/api/modules/tripal_chado.pub.api.inc: Launch the Tripal job to generate citations.
chado_pub_delete in legacy/tripal_pub/includes/tripal_pub.chado_node.inc: Implements hook_delete().
chado_pub_form in legacy/tripal_pub/includes/tripal_pub.chado_node.inc: Implements hook_form().
chado_pub_insert in legacy/tripal_pub/includes/tripal_pub.chado_node.inc: Implements hook_insert().
chado_pub_update in legacy/tripal_pub/includes/tripal_pub.chado_node.inc: Implements hook_update().
chado_reimport_publications in tripal_chado/api/modules/tripal_chado.pub.api.inc: Updates publication records.
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_delete in legacy/tripal_stock/includes/tripal_stock.chado_node.inc: Implements hook_delete(). Handles deleting of chado_stocks
chado_stock_form in legacy/tripal_stock/includes/tripal_stock.chado_node.inc: Implements hook_form(). Creates the main Add/Edit/Delete Form for chado stocks
chado_stock_validate in legacy/tripal_stock/includes/tripal_stock.chado_node.inc: Implements hook_validate(). Validate the input from the chado_stock node form
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.
chado_views_handler_filter_fk::get_select_options in tripal_chado/views_handlers/chado_views_handler_filter.inc
data__protein_sequence::load in tripal_chado/includes/TripalFields/data__protein_sequence/data__protein_sequence.inc
FASTAImporter::form in tripal_chado/includes/TripalImporter/FASTAImporter.inc
FASTAImporter::formValidate in tripal_chado/includes/TripalImporter/FASTAImporter.inc
FASTAImporter::loadFasta in tripal_chado/includes/TripalImporter/FASTAImporter.inc: Load a fasta file.
FASTAImporter::loadFastaResidues in tripal_chado/includes/TripalImporter/FASTAImporter.inc: Adds the residues column to the feature.
GFF3Importer::form in tripal_chado/includes/TripalImporter/GFF3Importer.inc
GFF3Importer::loadAlias in tripal_chado/includes/TripalImporter/GFF3Importer.inc: Load any aliases for a feature
GFF3Importer::loadGFF3 in tripal_chado/includes/TripalImporter/GFF3Importer.inc: Actually load a GFF3 file. This is the function called by tripal jobs
GFF3Importer::loadParents in tripal_chado/includes/TripalImporter/GFF3Importer.inc: Load the parents for a gff3 feature
GFF3Importer::loadTarget in tripal_chado/includes/TripalImporter/GFF3Importer.inc: Load the target attribute of a gff3 record
OBOImporter::loadOBO_v1_2 in tripal_chado/includes/TripalImporter/OBOImporter.inc: Imports a given OBO file into Chado. This function is usually called by one of three wrapper functions: loadOBO_v1_2_id, loadOBO_v1_2_file or tirpal_cv_load_obo_v1_2_url. But, it can be called directly if the full path to an OBO file is available on…
OBOImporter::loadTypeDefs in tripal_chado/includes/TripalImporter/OBOImporter.inc: OBO files are divided into a typedefs terms section and vocabulary terms section. This function loads the typedef terms from the OBO.
OBOImporter::processTerm in tripal_chado/includes/TripalImporter/OBOImporter.inc: Uses the provided term array to add/update information to Chado about the term including the term, dbxref, synonyms, properties, and relationships.
OBOImporter::processTerms in tripal_chado/includes/TripalImporter/OBOImporter.inc: OBO files are divided into a typedefs section and a terms section.
phylotree_feature_summary in legacy/tripal_phylogeny/includes/tripal_phylogeny.chado_node.inc: Phylotree feature summary.
sbo__relationship::instanceSettingsFormValidate in tripal_chado/includes/TripalFields/sbo__relationship/sbo__relationship.inc: _state
sbo__relationship_widget::form 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
schema__additional_type_widget::form in tripal_chado/includes/TripalFields/schema__additional_type/schema__additional_type_widget.inc
sep__protocol_widget::form in tripal_chado/includes/TripalFields/sep__protocol/sep__protocol_widget.inc: Provides the form for editing of this field.
so__transcript::load in tripal_chado/includes/TripalFields/so__transcript/so__transcript.inc
TaxonomyImporter::findOrganism in tripal_chado/includes/TripalImporter/TaxonomyImporter.inc: Checks the Chado database to see if the organism already exists.
TaxonomyImporter::rebuildTree in tripal_chado/includes/TripalImporter/TaxonomyImporter.inc: Iterates through all existing organisms and rebuilds the taxonomy tree.
TaxonomyImporter::run in tripal_chado/includes/TripalImporter/TaxonomyImporter.inc: Performs the import.
tripal_analysis_delete_form in legacy/tripal_analysis/includes/tripal_analysis.delete.inc: A form for indicating the analyses to delete *
tripal_analysis_set_feature_permission in legacy/tripal_analysis/includes/tripal_analysis_privacy.inc: Set permissions for features associated with an analysis @todo Stephen: ensure the $nid param is defined correctly
tripal_bulk_loader_load_data in tripal_bulk_loader/includes/tripal_bulk_loader.loader.inc: Tripal Bulk Loader
tripal_bulk_loader_set_constants_form_validate in tripal_bulk_loader/includes/tripal_bulk_loader.constants.inc: Validate that the values entered exist in the database if indicated in hte template array
tripal_chado_add_analysisfeatureprop_table in tripal_chado/includes/setup/tripal_chado.chado_v1_1.inc: Create a legacy custom chado table (analysisfeatureprop) to store properties of analysisfeature links.
tripal_chado_add_tripal_obo_temp_table in tripal_chado/includes/setup/tripal_chado.chado_vx_x.inc: Creates a temporary table to store obo details while loading an obo file
tripal_chado_bundle_fields_info_linker in tripal_chado/includes/tripal_chado.fields.inc
tripal_chado_bundle_instances_info_linker in tripal_chado/includes/tripal_chado.fields.inc
tripal_chado_db_edit_form in tripal_chado/includes/tripal_chado.db.inc: Form to edit existing databases. Implements hook_form().
tripal_chado_feature_seq_extract_form in tripal_chado/includes/tripal_chado.seq_extract.inc: Form to choose which features to extract sequence for
tripal_chado_fix_v1_3_custom_tables in tripal_chado/includes/setup/tripal_chado.setup.inc: Many of the custom tables created for Chado v1.2 are now in Chado v1.3.
tripal_chado_gff3_exporter in tripal_chado/includes/exporters/tripal_chado.gff_exporter.inc
tripal_chado_install in tripal_chado/tripal_chado.install
tripal_chado_install_chado in tripal_chado/includes/tripal_chado.install.inc: Install Chado Schema
tripal_chado_map_cvterms in tripal_chado/includes/tripal_chado.mapping.inc: This function populates the Tripal entity tables using existing data in the database.
tripal_chado_migrate_form in tripal_chado/includes/tripal_chado.migrate.inc: Implements hook_form()
tripal_chado_migrate_map_types in tripal_chado/includes/tripal_chado.migrate.inc: Map all tv2_content_type to tv3_content_type
tripal_chado_migrate_organism_images in tripal_chado/includes/tripal_chado.migrate.inc: Migrate images for Tripal v2 organism content
tripal_chado_pub_search_admin_form in tripal_chado/includes/tripal_chado.pub_search.inc
tripal_chado_pub_search_form in tripal_chado/includes/tripal_chado.pub_search.inc: Provides the form to search pubmed
tripal_chado_seq_extract_form in tripal_chado/includes/exporters/tripal_chado.seq_extract.inc: Form to choose which features to extract sequence for
tripal_chado_update_7300 in tripal_chado/tripal_chado.install: Fixes the phase on the tripal_gffcds_temp table used for importing GFF files, and fixes the db.name term mapping.
tripal_chado_upgrade_chado_1_2_to_1_3_pre_alter in tripal_chado/includes/tripal_chado.install.inc: Upgrade custom tables that may match the tables now in Chado v1.3.
tripal_chado_vocab_get_root_terms in tripal_chado/includes/tripal_chado.vocab_storage.inc: Implements hook_vocab_get_root_terms().
tripal_chado_vocab_get_term_children in tripal_chado/includes/tripal_chado.vocab_storage.inc: Implements hook_vocab_get_term_children().
tripal_chado_vocab_get_vocabularies in tripal_chado/includes/tripal_chado.vocab_storage.inc: Implements hook_vocab_get_vocabularies().
tripal_chado_vocab_get_vocabulary in tripal_chado/includes/tripal_chado.vocab_storage.inc: Implements hook_vocab_get_vocabulary().
tripal_cv_cvtermpath_form in tripal_chado/includes/tripal_chado.cv.inc: Form for re-doing the cvterm path
tripal_cv_cvtermpath_form_submit in tripal_chado/includes/tripal_chado.cv.inc: Cvterm path form submit
tripal_cv_cvterm_add_form in tripal_chado/includes/tripal_chado.cv.inc: Form for adding cvterms
tripal_cv_cvterm_edit_form in tripal_chado/includes/tripal_chado.cv.inc: Form for editing cvterms
tripal_cv_cv_edit_form in tripal_chado/includes/tripal_chado.cv.inc: Provides the actual "Select CV" form on the Update/Delete Controlled Vocabulary page. This form also triggers the edit javascript @todo Modify this form to use Drupal AJAX
tripal_db_dbxref_accession_autocomplete in legacy/tripal_db/tripal_db.module: This function is intended to be used in autocomplete forms for searching for accession that begin with the provided string
tripal_feature_delete_features in legacy/tripal_feature/includes/tripal_feature.delete.inc: Function to actually delete the features indicated
tripal_feature_get_feature_relationships in legacy/tripal_feature/theme/tripal_feature.theme.inc: Using the chado_expand_var function to retrieve a set of relationships can be very slow, especialy if there are many relationships This function is intended to help speed up the retrieval of relationships by only retrieving the base information for…
tripal_feature_get_matched_alignments in legacy/tripal_feature/theme/tripal_feature.theme.inc: This function is for features that align through an intermediate such as 'EST_match' or 'match'. This occurs in the case where two sequences align but where one does not align perfectly. Some ESTs may be in a contig but not all…
tripal_feature_load_featurelocs in legacy/tripal_feature/theme/tripal_feature.theme.inc: Load the locations for a given feature
tripal_feature_load_featureloc_sequences in legacy/tripal_feature/theme/tripal_feature.theme.inc: Get the sequence this feature is located on
tripal_feature_load_organism_feature_counts in legacy/tripal_feature/theme/tripal_feature.theme.inc: Load the arguments for the organism feature counts browser
tripal_feature_load_relationships in legacy/tripal_feature/theme/tripal_feature.theme.inc: Get the relationships for a feature.
tripal_feature_match_features_page in tripal_chado/tripal_chado.module: Uses the value provided in the $id argument to find all features that match that ID by name, featurename or synonym. If it matches uniquenly to a single feature it will redirect to that feature page, otherwise, a list of matching features is shown.
tripal_get_importer_form in tripal/includes/tripal.importer.inc: Build the form for a TripalImporter implementation.
tripal_natural_diversity_preprocess_tripal_stock_nd_genotypes in legacy/tripal_natural_diversity/theme/tripal_natural_diversity.theme.inc: Because the nd_experiment_id can be associated with projects, phenotypes, stocks, genotypes, etc. it becomes slow to allow the template to use the chado_expand_var function to traverse the FK relationships. Ideally we would use the chado_expand_var…
tripal_natural_diversity_preprocess_tripal_stock_nd_phenotypes in legacy/tripal_natural_diversity/theme/tripal_natural_diversity.theme.inc: Because the nd_experiment_id can be associated with projects, phenotypes, stocks, genotypes, etc. it becomes slow to allow the template to use the chado_expand_var function to traverse the FK relationships. Ideally we would use the chado_expand_var…
tripal_organism_delete_form in legacy/tripal_organism/includes/tripal_organism.delete.inc: A form for indicating the organisms to delete
tripal_phylogeny_ajax_get_tree_json in tripal_chado/includes/tripal_chado.phylotree.inc: Get json representation of a phylotree id.
tripal_phylogeny_prepare_tree_viewer in tripal_chado/includes/tripal_chado.phylotree.inc: Prepares a phylogenetic tree for viewing.
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_admin in legacy/tripal_pub/includes/tripal_pub.admin.inc: Administrative settings form
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_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_load_organism_stock_counts in legacy/tripal_stock/tripal_stock.module: Load the arguments for the organism stock counts browser
tripal_stock_match_stocks_page in legacy/tripal_stock/tripal_stock.module
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_views_handler_filter_select_cvterm::get_select_options in tripal_chado_views/views/handlers/tripal_views_handler_filter_select_cvterm.inc: Provide the options used in the select list. Override this function in extended handlers to easily change option list.
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.
tripal_views_handler_filter_select_string::get_select_options in tripal_chado_views/views/handlers/tripal_views_handler_filter_select_string.inc: Provide the options used in the select list. Override this function in extended handlers to easily change option list.