192 calls to chado_query()
- chado_analysis_delete in tripal_analysis/tripal_analysis.module
- Removes analysis from the chado database
- chado_analysis_form in tripal_analysis/includes/tripal_analysis.form.inc
- When editing or creating a new node of type 'chado_analysis' we need
a form. This function creates the form that will be used for this.
- chado_analysis_insert in tripal_analysis/tripal_analysis.module
- 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_node_form_add_analysisprop_table_props in tripal_analysis/includes/tripal_analysis.form.inc
- chado_analysis_update in tripal_analysis/tripal_analysis.module
- Update analyses
- chado_contact_delete in tripal_contact/tripal_contact.module
- Implementation of tripal_contact_delete().
- chado_contact_form in tripal_contact/includes/tripal_contact.form.inc
- Implementation of tripal_contact_form().
- chado_contact_insert in tripal_contact/tripal_contact.module
- Implementation of tripal_contact_insert().
- chado_contact_node_form_add_contactprop_table_props in tripal_contact/includes/tripal_contact.form.inc
- chado_contact_update in tripal_contact/tripal_contact.module
- chado_contact_validate in tripal_contact/includes/tripal_contact.form.inc
- validates submission of form when adding or updating a contact node
- chado_featuremap_delete in tripal_featuremap/tripal_featuremap.module
- Delete data from drupal and chado databases when a node is deleted
- chado_featuremap_form in tripal_featuremap/includes/tripal_featuremap.form.inc
- When editing or creating a new node of type 'chado_featuremap' we need
a form. This function creates the form that will be used for this.
- chado_featuremap_insert in tripal_featuremap/tripal_featuremap.module
- When a new chado_featuremap node is created we also need to add information
to our chado_featuremap table. This function is called on insert of a new node
of type 'chado_featuremap' and inserts the necessary information.
- chado_featuremap_node_form_add_featuremapprop_table_props in tripal_featuremap/includes/tripal_featuremap.form.inc
- chado_featuremap_update in tripal_featuremap/tripal_featuremap.module
- Update nodes
- chado_featuremap_validate in tripal_featuremap/includes/tripal_featuremap.form.inc
- validates submission of form when adding or updating a map node
- chado_feature_add_gbaccession in tripal_feature/tripal_feature.module
- chado_feature_add_synonyms in tripal_feature/tripal_feature.module
- chado_feature_delete in tripal_feature/tripal_feature.module
- chado_feature_form in tripal_feature/tripal_feature.module
- chado_feature_validate in tripal_feature/tripal_feature.module
- chado_library_delete in tripal_library/tripal_library.module
- Delete data from drupal and chado databases when a node is deleted
- chado_library_form in tripal_library/tripal_library.module
- When editing or creating a new node of type 'chado_library' we need
a form. This function creates the form that will be used for this.
- chado_library_validate in tripal_library/tripal_library.module
- validates submission of form when adding or updating a library node
- chado_library_view in tripal_library/tripal_library.module
- This function customizes the view of the chado_library node. It allows
us to generate the markup. This function is required for node [Preview]
- chado_organism_delete in tripal_organism/tripal_organism.module
- Delete organism from both drupal and chado databases. Check dependency before
deleting from chado.
- chado_organism_validate in tripal_organism/tripal_organism.module
- chado_pager_query in tripal_core/api/tripal_core_chado.api.inc
- Use this function instead of pager_query() when selecting a
subset of records from a Chado table.
- chado_project_delete in tripal_project/tripal_project.module
- Implementation of hook_delete().
- chado_project_validate in tripal_project/tripal_project.module
- validates submission of form when adding or updating a project node
- chado_pub_delete in tripal_pub/tripal_pub.module
- Implementation of tripal_pub_delete().
- chado_pub_form in tripal_pub/includes/pub_form.inc
- chado_pub_insert in tripal_pub/tripal_pub.module
- Implementation of tripal_pub_insert().
- chado_pub_node_form_add_pubprop_table_props in tripal_pub/includes/pub_form.inc
- chado_pub_update in tripal_pub/tripal_pub.module
- chado_query_range in tripal_core/api/tripal_core_chado.api.inc
- Use this function instead of db_query_range().
- chado_stock_delete in tripal_stock/tripal_stock.module
- Implements hook_delete(): Handles deleting of chado_stocks
- chado_stock_form in tripal_stock/tripal_stock.module
- Implements hook_form(): Creates the main Add/Edit/Delete Form for chado stocks
- chado_stock_validate in tripal_stock/tripal_stock.module
- Implements hook_validate(): Validate the input from the chado_stock node form
- get_chado_organisms in tripal_organism/tripal_organism.module
- This function uses organism_id's of all drupal organism nodes as input and
pull the organism information (genus, species, common_name, comment) from
chado database. The return type is an object array that stores $organism
objects sorted by…
- get_max_chado_rank in tripal_stock/includes/other_module_api_functions.inc
- get_tripal_analysis_admin_form_reindex_set in tripal_analysis/includes/tripal_analysis.admin.inc
- The "Reindex Analysis Nodes" form
- get_tripal_analysis_admin_form_sync_set in tripal_analysis/includes/tripal_analysis.admin.inc
- The "sync Analysis in chado with drupal" form
- get_tripal_analysis_admin_form_taxonomy_set in tripal_analysis/includes/tripal_analysis.admin.inc
- Displays the Set Drupal Taxonomy for Analysis Features From
- get_tripal_contact_admin_form_reindex_set in tripal_contact/includes/tripal_contact.admin.inc
- get_tripal_featuremap_admin_form_reindex_set in tripal_featuremap/includes/tripal_featuremap.admin.inc
- get_tripal_featuremap_admin_form_sync_set in tripal_featuremap/includes/tripal_featuremap.admin.inc
- get_tripal_featuremap_admin_form_taxonomy_set in tripal_featuremap/includes/tripal_featuremap.admin.inc
- get_tripal_library_admin_form_reindex_set in tripal_library/includes/tripal_library.admin.inc
- get_tripal_library_admin_form_sync_set in tripal_library/includes/tripal_library.admin.inc
- get_tripal_library_admin_form_taxonomy_set in tripal_library/includes/tripal_library.admin.inc
- get_tripal_organism_admin_form_reindex_set in tripal_organism/includes/tripal_organism.admin.inc
- get_tripal_organism_admin_form_sync_set in tripal_organism/includes/tripal_organism.admin.inc
- get_tripal_organism_admin_form_taxonomy_set in tripal_organism/includes/tripal_organism.admin.inc
- get_tripal_project_admin_form_sync_set in tripal_project/includes/tripal_project.admin.inc
- get_tripal_pub_admin_form_default_type in tripal_pub/includes/tripal_pub.admin.inc
- get_tripal_pub_admin_form_select_search_list in tripal_pub/includes/tripal_pub.admin.inc
- get_tripal_stock_admin_form_vocabulary_set in tripal_stock/includes/tripal_stock.admin.inc
- theme_tripal_library_node_libraries in tripal_library/tripal_library.module
- This function shows library information on an organism/feature node
- theme_tripal_library_search_index in tripal_library/tripal_library.module
- This function is an extension of the chado_feature_view and
chado_organism_view by providing the markup for the library object
THAT WILL BE INDEXED.
- tripal_analysis_admin_validate in tripal_analysis/includes/tripal_analysis.admin.inc
- Validate the administrative form
@todo Stephen: Why is validate used rather then submit?
- tripal_analysis_create_analysisfeatureprop in tripal_analysis/tripal_analysis.install
- 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_analysis_sync_analyses in tripal_analysis/includes/tripal_analysis.admin.inc
- Synchronize analyses from chado to drupal
- tripal_analysis_update_6100 in tripal_analysis/tripal_analysis.install
- Update for Drupal 6.x, Tripal 1.1, Analysis Module 1.1
This update adds a new analysis_organism materialized view
- 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_admin_validate in tripal_contact/includes/tripal_contact.admin.inc
- tripal_contact_preprocess_tripal_contact_relationships in tripal_contact/tripal_contact.module
- tripal_core_chado_clear_prepared in tripal_core/api/tripal_core_chado.api.inc
- Clears prepared statements to avoid conflicts
- tripal_core_chado_delete in tripal_core/api/tripal_core_chado.api.inc
- Provides a generic function for deleting a record(s) from any chado table
- tripal_core_chado_execute_prepared in tripal_core/api/tripal_core_chado.api.inc
- Execute a prepared statement with the supplied values
- tripal_core_chado_insert in tripal_core/api/tripal_core_chado.api.inc
- Provides a generic routine for inserting into any Chado table
- tripal_core_chado_prepare in tripal_core/api/tripal_core_chado.api.inc
- Prepare a chado query
- tripal_core_chado_select in tripal_core/api/tripal_core_chado.api.inc
- Provides a generic routine for selecting data from a Chado table
- tripal_core_chado_update in tripal_core/api/tripal_core_chado.api.inc
- Provides a generic routine for updating into any Chado table
- tripal_core_clean_orphaned_nodes in tripal_core/api/tripal_core_chado.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.
- tripal_core_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…
- tripal_core_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.
- 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/chado_install.inc
- Install Chado Schema
- tripal_custom_tables_action in tripal_core/includes/custom_tables.inc
- Does the specified action for the specified custom table
- tripal_cv_add_cvterm in tripal_cv/api/tripal_cv.api.inc
- Add's a CV term to the cvterm table. If the parent CV does not exist then
that too is added to the CV table. If the cvterm is a relationship term
then the $is_relationship argument should be set. The function will try
to first find the…
- tripal_cv_add_form_submit in tripal_cv/includes/tripal_cv_admin.inc
- Purpose: The submit function for the add controlled vocabulary form
- tripal_cv_count_chart in tripal_cv/includes/charts.inc
- This function generates an array with fields compatible with Google charts used
for generating pie charts of counts associated with terms in
a controlled vocabulary. An example would be counts of features assigned
to terms in the Sequence Ontology.
- tripal_cv_cvtermpath_form in tripal_cv/includes/obo_loader.inc
- Form for re-doing the cvterm path
- tripal_cv_cvtermpath_form_submit in tripal_cv/includes/tripal_cv_admin.inc
- Cvterm path form submit
- tripal_cv_cvterm_info in tripal_cv/includes/trees.inc
- Describe a cvterm (Rendered)
- tripal_cv_cvterm_name_autocomplete 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_cv_edit_form in tripal_cv/includes/tripal_cv_admin.inc
- Purpose: Provides a form to allow updating/deleteing of controlled vocabularies
- tripal_cv_edit_form_submit in tripal_cv/includes/tripal_cv_admin.inc
- Purpose: The submit function of the update/delete controlled vocabulary form
- tripal_cv_get_cv_id in tripal_cv/api/tripal_cv.api.inc
- Retrieve the cv id for the specified CV by name
- tripal_cv_get_term_children in tripal_cv/includes/trees.inc
- Generates SON needed for jsTree -expanding a term to view children
- tripal_cv_init_tree in tripal_cv/includes/trees.inc
- Generates JSON needed for jsTree Root-level Branches
- tripal_cv_list_form in tripal_cv/includes/trees.inc
- Form listing CVs
- tripal_cv_load_obo_v1_2 in tripal_cv/includes/obo_loader.inc
- tripal_cv_obo_load_typedefs in tripal_cv/includes/obo_loader.inc
- tripal_cv_obo_process_terms in tripal_cv/includes/obo_loader.inc
- tripal_cv_select_form in tripal_cv/includes/tripal_cv_admin.inc
- Purpose: 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_update_cvtermpath in tripal_cv/api/tripal_cv.api.inc
- Updates the cvtermpath table of Chado for the specified CV.
- tripal_db_commit_transaction in tripal_core/api/tripal_core_chado.api.inc
- A simple function to commit a database transaction
- tripal_db_form in tripal_db/includes/tripal_db.admin.inc
- tripal_db_get_dbxref_by_accession in tripal_db/api/tripal_db.api.inc
- Purpose: To retrieve a chado dbxref object with a given accession
- tripal_db_get_db_by_db_id in tripal_db/api/tripal_db.api.inc
- Purpose: To retrieve a chado db object
- tripal_db_get_db_options in tripal_db/api/tripal_db.api.inc
- Purpose: Create an options array to be used in a form element
which provides a list of all chado dbs
- tripal_db_rollback_transaction in tripal_core/api/tripal_core_chado.api.inc
- Rollback changes.
- tripal_db_set_savepoint_transaction in tripal_core/api/tripal_core_chado.api.inc
- Set a savepoint to roll the current transaction back to if an error is encountered
- tripal_db_start_transaction in tripal_core/api/tripal_core_chado.api.inc
- Start a transaction block. Ensures the use of a persistent chado connection
- tripal_edit_mview in tripal_core/api/tripal_core_mviews.api.inc
- Edits 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_featuremap_admin_validate in tripal_featuremap/includes/tripal_featuremap.admin.inc
- tripal_featuremap_sync_featuremaps in tripal_featuremap/includes/tripal_featuremap.admin.inc
- tripal_feature_add_ONE_dbreference_form_submit in tripal_feature/includes/tripal_feature-db_references.inc
- tripal_feature_add_ONE_dbreference_form_validate in tripal_feature/includes/tripal_feature-db_references.inc
- tripal_feature_add_ONE_relationship_form_validate in tripal_feature/includes/tripal_feature-relationships.inc
- tripal_feature_delete_db_reference in tripal_feature/includes/tripal_feature-db_references.inc
- tripal_feature_delete_form in tripal_feature/includes/tripal_feature-delete.inc
- tripal_feature_delete_form_validate in tripal_feature/includes/tripal_feature-delete.inc
- tripal_feature_edit_ALL_relationships_form_validate in tripal_feature/includes/tripal_feature-relationships.inc
- tripal_feature_fasta_load_form in tripal_feature/includes/fasta_loader.inc
- tripal_feature_fasta_load_form_validate in tripal_feature/includes/fasta_loader.inc
- tripal_feature_get_feature_relationships in tripal_feature/api/tripal_feature.api.inc
- Using the tripal_core_expand_chado_vars 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…
- tripal_feature_get_formatted_sequence in tripal_feature/api/tripal_feature.api.inc
- Retrieves the sequence for a feature.
- tripal_feature_get_matched_alignments in tripal_feature/tripal_feature.module
- tripal_feature_gff3_load_form in tripal_feature/includes/gff_loader.inc
- tripal_feature_load_fasta in tripal_feature/includes/fasta_loader.inc
- tripal_feature_load_featurelocs in tripal_feature/tripal_feature.module
- tripal_feature_load_featureloc_sequences in tripal_feature/tripal_feature.module
- tripal_feature_load_gff3 in tripal_feature/includes/gff_loader.inc
- tripal_feature_load_gff3_alias in tripal_feature/includes/gff_loader.inc
- tripal_feature_load_gff3_parents in tripal_feature/includes/gff_loader.inc
- tripal_feature_load_organism in tripal_feature/tripal_feature.module
- tripal_feature_load_organism_feature_browser in tripal_feature/tripal_feature.module
- tripal_feature_load_organism_feature_counts in tripal_feature/tripal_feature.module
- tripal_feature_load_properties in tripal_feature/tripal_feature.module
- tripal_feature_load_references in tripal_feature/tripal_feature.module
- tripal_feature_load_relationships in tripal_feature/tripal_feature.module
- tripal_feature_load_synonyms in tripal_feature/tripal_feature.module
- tripal_feature_match_features_page in tripal_feature/tripal_feature.module
- tripal_feature_seq_extract_form in tripal_feature/includes/seq_extract.inc
- *
- tripal_feature_seq_extract_get_features in tripal_feature/includes/seq_extract.inc
- tripal_feature_set_taxonomy in tripal_feature/includes/tripal_feature.admin.inc
- tripal_feature_sync_feature in tripal_feature/includes/tripal_feature.sync_features.inc
- tripal_feature_sync_features in tripal_feature/includes/tripal_feature.sync_features.inc
- tripal_feature_update_db_reference in tripal_feature/includes/tripal_feature-db_references.inc
- tripal_get_max_chado_rank in tripal_core/api/tripal_core_chado.api.inc
- Purpose: Get max rank for a given set of criteria
This function was developed with the many property tables in chado in mind
- tripal_library_admin_validate in tripal_library/includes/tripal_library.admin.inc
- tripal_library_feature_set_taxonomy in tripal_library/includes/tripal_library.admin.inc
- tripal_library_reindex_features in tripal_library/includes/tripal_library.admin.inc
- tripal_library_sync_libraries in tripal_library/includes/tripal_library.admin.inc
- tripal_library_taxonify_features in tripal_library/includes/tripal_library.admin.inc
- tripal_organism_admin_validate in tripal_organism/includes/tripal_organism.admin.inc
- tripal_organism_get_synced in tripal_organism/api/tripal_organism.api.inc
- Returns a list of organisms that are currently synced with Drupal
- tripal_organism_reindex_features in tripal_organism/includes/tripal_organism.admin.inc
- tripal_organism_sync_organisms in tripal_organism/includes/tripal_organism.admin.inc
- Synchronize organisms from chado to drupal
- tripal_organism_taxonify_features in tripal_organism/includes/tripal_organism.admin.inc
- tripal_project_admin_validate in tripal_project/includes/tripal_project.admin.inc
- tripal_project_preprocess_tripal_project_relationships in tripal_project/tripal_project.module
- tripal_project_sync_all_projects in tripal_project/includes/tripal_project.admin.inc
- tripal_project_sync_projects in tripal_project/includes/tripal_project.admin.inc
- Synchronize projects from chado to drupal
- tripal_pub_add_authors in tripal_pub/api/tripal_pub.api.inc
- tripal_pub_add_publication in tripal_pub/api/tripal_pub.api.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_create_citations in tripal_pub/includes/pub_citation.inc
- tripal_pub_get_publication_array in tripal_pub/api/tripal_pub.api.inc
- tripal_pub_preprocess_tripal_pub_relationships in tripal_pub/tripal_pub.module
- tripal_pub_search_form in tripal_pub/includes/pub_search.inc
- Purpose: Provides the form to search pubmed
- tripal_pub_update_publications in tripal_pub/api/tripal_pub.api.inc
- tripal_stock_add_ONE_dbreference_form_submit in tripal_stock/includes/tripal_stock-db_references.inc
- Implements hoook_form_submit(): Actually adds the db reference to the stock
- tripal_stock_add_ONE_dbreference_form_validate in tripal_stock/includes/tripal_stock-db_references.inc
- Implements hook_form_validate(): Validates the input from tripal_stock_add_ONE_dbreference_form()
- tripal_stock_add_ONE_property_form_submit in tripal_stock/includes/tripal_stock-properties.inc
- tripal_stock_add_ONE_property_form_validate in tripal_stock/includes/tripal_stock-properties.inc
- tripal_stock_add_ONE_relationship_form_submit in tripal_stock/includes/tripal_stock-relationships.inc
- tripal_stock_add_ONE_relationship_form_validate in tripal_stock/includes/tripal_stock-relationships.inc
- tripal_stock_delete_db_reference in tripal_stock/includes/tripal_stock-db_references.inc
- Deletes a given database reference
- tripal_stock_delete_property in tripal_stock/includes/tripal_stock-properties.inc
- tripal_stock_delete_relationship in tripal_stock/includes/tripal_stock-relationships.inc
- tripal_stock_edit_ALL_relationships_form_validate in tripal_stock/includes/tripal_stock-relationships.inc
- tripal_stock_is_obsolete_form_submit in tripal_stock/includes/tripal_stock-secondary_tables.inc
- tripal_stock_match_stocks_page in tripal_stock/tripal_stock.module
- tripal_stock_preprocess_tripal_stock_relationships in tripal_stock/tripal_stock.module
- tripal_stock_sync_stock in tripal_stock/includes/tripal_stock.sync_stocks.inc
- tripal_stock_sync_stocks in tripal_stock/includes/tripal_stock.sync_stocks.inc
- tripal_stock_update_db_reference in tripal_stock/includes/tripal_stock-db_references.inc
- Updates a Database Reference
- tripal_stock_update_property in tripal_stock/includes/tripal_stock-properties.inc
- tripal_stock_update_relationship in tripal_stock/includes/tripal_stock-relationships.inc
- tripal_views_handler_filter_select_cvterm::init in tripal_views/views/handlers/tripal_views_handler_filter_select_cvterm.inc
- Executed when the field is added
Determine which cv to limit the cvterms to
- tripal_views_handler_filter_select_string::value_form in tripal_views/views/handlers/tripal_views_handler_filter_select_string.inc
- Defines the value field in both the views filter options form
and the exposed form
- views_handler_field_chado_count::pre_render in tripal_views/views/handlers/deprecated/views_handler_field_chado_count.inc
- Run before any fields are rendered.
- views_handler_field_dbxref_accession_link::render in tripal_views/views/handlers/deprecated/views_handler_field_dbxref_accession_link.inc
- Render the field.
- views_handler_filter_chado_select_cvterm_name::init in tripal_views/views/handlers/deprecated/views_handler_filter_chado_select_cvterm_name.inc
- Executed when the field is added
Determine which cv to limit the cvterms to
- views_handler_filter_chado_select_string::value_form in tripal_views/views/handlers/deprecated/views_handler_filter_chado_select_string.inc
- Defines the value field in both the views filter options form
and the exposed form
- views_handler_join_chado_aggregator::get_aggregate_sql_for_table_field in tripal_views/views/handlers/views_handler_join_chado_aggregator.inc
- Create the SQL needed to aggregate a table
