120 calls to chado_query()

chado_add_index in tripal_core/api/tripal_core.chado_schema.api.inc
A Chado-aware wrapper for the db_add_index() function.
chado_add_node_form_dbxrefs in 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 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_delete in tripal_analysis/includes/tripal_analysis.chado_node.inc
Implements hook_delete(). Removes analysis from the chado database.
chado_cleanup_orphaned_nodes_part in 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 tripal_contact/includes/tripal_contact.chado_node.inc
Implements hook_delete().
chado_contact_form in tripal_contact/includes/tripal_contact.chado_node.inc
Implementation of hook_form().
chado_create_custom_table in tripal_core/api/tripal_core.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_core/api/tripal_core.custom_tables.api.inc
Deletes the specified custom table
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_example_delete in tripal_example/includes/tripal_example.chado_node.inc
Implementation of hook_delete(). This function runs after the node has been deleted from the Drupal schema and allows us to delete the corresponding record in Chado.
chado_featuremap_delete in tripal_featuremap/includes/tripal_featuremap.chado_node.inc
Implements hook_delete().
chado_featuremap_validate in tripal_featuremap/includes/tripal_featuremap.chado_node.inc
Validates submission of form when adding or updating a map node
chado_feature_add_synonyms in tripal_feature/includes/tripal_feature.chado_node.inc
Add synonyms to a feature
chado_feature_delete in tripal_feature/includes/tripal_feature.chado_node.inc
Implements hook_delete().
chado_feature_form in tripal_feature/includes/tripal_feature.chado_node.inc
Implementation of hook_form().
chado_feature_validate in tripal_feature/includes/tripal_feature.chado_node.inc
Implementation of hook_validate().
chado_get_table_max_rank in tripal_core/api/tripal_core.chado_general.api.inc
Get max rank for a given set of criteria This function was developed with the many property tables in chado in mind but will work for any table with a rank
chado_get_version in tripal_core/api/tripal_core.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_core module which then sets the…
chado_insert_record in tripal_core/api/tripal_core.chado_query.api.inc
Provides a generic routine for inserting into any Chado table
chado_library_delete in tripal_library/includes/tripal_library.chado_node.inc
Implements hook_delete().
chado_library_form in tripal_library/includes/tripal_library.chado_node.inc
Implements hook_form().
chado_library_validate in tripal_library/includes/tripal_library.chado_node.inc
Implements hook_validate().
chado_node_sync_form in 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 tripal_core/api/tripal_core.chado_nodes.api.inc
Generic function for syncing records in Chado with Drupal nodes.
chado_organism_delete in tripal_organism/includes/tripal_organism.chado_node.inc
Implements hook_delete().
chado_organism_validate in tripal_organism/includes/tripal_organism.chado_node.inc
Implementation of hook_validate().
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_phylotree_delete in tripal_phylogeny/includes/tripal_phylogeny.chado_node.inc
Implements hook_delete().
chado_phylotree_form in tripal_phylogeny/includes/tripal_phylogeny.chado_node.inc
Implementation of hook_form().
chado_project_delete in tripal_project/includes/tripal_project.chado_node.inc
Implementation of hook_delete().
chado_project_validate in tripal_project/includes/tripal_project.chado_node.inc
Implements hook_validate(). Validates submission of form when adding or updating a project node
chado_pub_delete in tripal_pub/includes/tripal_pub.chado_node.inc
Implements hook_delete().
chado_pub_form in tripal_pub/includes/tripal_pub.chado_node.inc
Implements hook_form().
chado_pub_insert in tripal_pub/includes/tripal_pub.chado_node.inc
Implements hook_insert().
chado_pub_update in tripal_pub/includes/tripal_pub.chado_node.inc
Implements hook_update().
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_delete in tripal_stock/includes/tripal_stock.chado_node.inc
Implements hook_delete(). Handles deleting of chado_stocks
chado_stock_form in 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 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_core/api/tripal_core.chado_query.api.inc
Provides a generic routine for updating into any Chado table
phylotree_feature_summary in tripal_phylogeny/includes/tripal_phylogeny.chado_node.inc
Phylotree feature summary.
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_analysis_create_analysisfeatureprop in tripal_analysis/tripal_analysis.install
Create a legacy custom chado table (analysisfeatureprop) to store properties of analysisfeature links.
tripal_analysis_delete_form in tripal_analysis/includes/tripal_analysis.delete.inc
A form for indicating the analyses to delete *
tripal_analysis_set_feature_permission in 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_autocomplete_contact in tripal_contact/api/tripal_contact.api.inc
This function is intended to be used in autocomplete forms for contacts.
tripal_autocomplete_cvterm in tripal_cv/api/tripal_cv.api.inc
This function is intended to be used in autocomplete forms for searching for CV terms that begin with the provided string
tripal_autocomplete_organism in tripal_organism/api/tripal_organism.api.inc
This function is intended to be used in autocomplete forms for searching for organisms that begin with the provided string
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_contact_update_7201 in tripal_contact/tripal_contact.install
Adds missing foreign key constraints
tripal_core_init in tripal_core/tripal_core.module
Implements hook_init(). Used to set the search_path, create default content and set default variables.
tripal_core_install_chado in tripal_core/includes/tripal_core.chado_install.inc
Install Chado Schema
tripal_core_upgrade_chado_1_2_to_1_3_pre_alter in tripal_core/includes/tripal_core.chado_install.inc
Upgrade custom tables that may match the tables now in Chado v1.3.
tripal_cv_create_tripal_obo_temp in tripal_cv/tripal_cv.install
Creates a temporary table to store obo details while loading an obo file
tripal_cv_cvtermpath_form in tripal_cv/includes/tripal_cv.cvtermpath_form.inc
Form for re-doing the cvterm path
tripal_cv_cvtermpath_form_submit in tripal_cv/includes/tripal_cv.cvtermpath_form.inc
Cvterm path form submit
tripal_cv_cvterm_add_form in tripal_cv/includes/tripal_cv.cvterm_form.inc
Form for adding cvterms
tripal_cv_cvterm_edit_form in tripal_cv/includes/tripal_cv.cvterm_form.inc
Form for editing cvterms
tripal_cv_cv_edit_form in tripal_cv/includes/tripal_cv.cv_form.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_cv_load_obo_v1_2 in tripal_cv/includes/tripal_cv.obo_loader.inc
Imports a given OBO file into Chado. This function is usually called by one of three wrapper functions: tripal_cv_load_obo_v1_2_id, tripal_cv_load_obo_v1_2_file or tirpal_cv_load_obo_v1_2_url. But, it can be called directly if the full path to an…
tripal_cv_obo_load_typedefs in tripal_cv/includes/tripal_cv.obo_loader.inc
OBO files are divided into a typedefs terms section and vocabulary terms section. This function loads the typedef terms from the OBO.
tripal_cv_obo_process_terms in tripal_cv/includes/tripal_cv.obo_loader.inc
OBO files are divided into a typedefs section and a terms section. This function loads the typedef terms from the OBO.
tripal_cv_uninstall in tripal_cv/tripal_cv.install
Implementation of hook_uninstall().
tripal_db_db_edit_form in tripal_db/includes/tripal_db.admin.inc
Form to edit existing databases. Implements hook_form().
tripal_delete_mview in tripal_core/api/tripal_core.mviews.api.inc
Does the specified action for the specified Materialized View
tripal_featuremap_update_7201 in tripal_featuremap/tripal_featuremap.install
Adds missing foreign key constraints
tripal_feature_delete_features in tripal_feature/includes/tripal_feature.delete.inc
Function to actually delete the features indicated
tripal_feature_fasta_load_form in tripal_feature/includes/tripal_feature.fasta_loader.inc
The form to submit a fasta loading job
tripal_feature_fasta_load_form_validate in tripal_feature/includes/tripal_feature.fasta_loader.inc
Validate the fasta loader job form
tripal_feature_get_feature_relationships in 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 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_gff3_exporter in tripal_feature/includes/tripal_feature.gff_exporter.inc
tripal_feature_gff3_load_form in tripal_feature/includes/tripal_feature.gff_loader.inc
The form to submit a GFF3 loading job
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_residues in tripal_feature/includes/tripal_feature.fasta_loader.inc
Adds the residues column to the feature.
tripal_feature_load_featurelocs in tripal_feature/theme/tripal_feature.theme.inc
Load the locations for a given feature
tripal_feature_load_featureloc_sequences in tripal_feature/theme/tripal_feature.theme.inc
Get the sequence this feature is located on
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_alias in tripal_feature/includes/tripal_feature.gff_loader.inc
Load any aliases for a 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_feature_load_organism_feature_counts in tripal_feature/theme/tripal_feature.theme.inc
Load the arguments for the organism feature counts browser
tripal_feature_load_relationships in tripal_feature/theme/tripal_feature.theme.inc
Get the relationships for a feature.
tripal_feature_match_features_page in tripal_feature/tripal_feature.module
tripal_feature_seq_extract_form in tripal_feature/includes/tripal_feature.seq_extract.inc
Form to choose which features to extract sequence for
tripal_get_analysis_select_options in tripal_analysis/api/tripal_analysis.api.inc
Returns a list of analyses that are currently synced with Drupal to use in select lists
tripal_get_bulk_feature_sequences in tripal_feature/api/tripal_feature.api.inc
tripal_get_db_select_options in tripal_db/api/tripal_db.api.inc
Create an options array to be used in a form element which provides a list of all chado dbs
tripal_get_feature_sequences in tripal_feature/api/tripal_feature.api.inc
Retrieves the sequences for a given feature.
tripal_get_organism_select_options in tripal_organism/api/tripal_organism.api.inc
Returns a list of organisms that are currently synced with Drupal to use in select lists
tripal_insert_cvterm in tripal_cv/api/tripal_cv.api.inc
Add's a controlled vocabulary term to Chado.
tripal_library_update_7200 in tripal_library/tripal_library.install
This is the required update for tripal_library when upgrading from Drupal core API 6.x.
tripal_natural_diversity_preprocess_tripal_stock_nd_genotypes in 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 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 tripal_organism/includes/tripal_organism.delete.inc
A form for indicating the organisms to delete
tripal_phylogeny_ajax_get_tree_json in tripal_phylogeny/tripal_phylogeny.module
Get json representation of a phylotree id.
tripal_phylogeny_ncbi_taxonomy_import in tripal_phylogeny/includes/tripal_phylogeny.taxonomy.inc
tripal_phylogeny_prepare_tree_viewer in tripal_phylogeny/theme/tripal_phylogeny.theme.inc
tripal_populate_mview in tripal_core/api/tripal_core.mviews.api.inc
Update a Materialized View
tripal_project_update_7200 in tripal_project/tripal_project.install
This is the required update for tripal_project when upgrading from Drupal core API 6.x.
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_admin in tripal_pub/includes/tripal_pub.admin.inc
Administrative settings form
tripal_pub_create_citations in tripal_pub/includes/tripal_pub.pub_citation.inc
Launch the Tripal job to generate citations. Called by tripal jobs
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_search_form in tripal_pub/includes/tripal_pub.pub_search.inc
Provides the form to search pubmed
tripal_pub_update_7201 in tripal_pub/tripal_pub.install
Adds missing foreign key constraints
tripal_reimport_publications in tripal_pub/includes/tripal_pub.pub_importers.inc
Updates publication records that currently exist in the Chado pub table with the most recent data in the remote database.
tripal_search_publications in tripal_pub/includes/tripal_pub.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_pub_search_form() function but this function is included in the…
tripal_stock_load_organism_stock_counts in tripal_stock/tripal_stock.module
Load the arguments for the organism stock counts browser
tripal_stock_match_stocks_page in tripal_stock/tripal_stock.module
tripal_update_cvtermpath in tripal_cv/api/tripal_cv.api.inc
Updates the cvtermpath table of Chado for the specified CV.
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_handler_filter_select_cvterm::get_select_options in tripal_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_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_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.