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.