Chado Node API

Many Tripal modules implement Drupal node types as a means of displaying chado records individually through Drupal as a single web page. In order to do this, many of the same drupal hooks are implemented and the code between modules is actually quite similar. This API aims to abstract much of the common functionality in order to make it easier for new Tripal modules to implement drupal node types and to centralize the maintenance effort as much as possible.

A generic sync form has been created. See chado_node_sync_form() for instructions on how to implement this form in your module.

Many of the base chado tables also have associated prop, _dbxref and _relationship tables. Generic mini-forms have been created to help you handle these forms. To implement this functionality you call the mini-form from your module node form and then call the associated update functions from both your hook_insert and hook_update. The functions of interest are as follows:

Parent topics

File

tripal_core/api/tripal_core.chado_nodes.api.inc, line 7
API to handle much of the common functionality implemented when creating a drupal node type.

Functions

Namesort descending Location Description
chado_add_admin_form_set_title tripal_core/api/tripal_core.chado_nodes.title_and_path.inc Generic "Set Node Title" sub-form for setting the title of any chado node
chado_add_admin_form_set_url tripal_core/api/tripal_core.chado_nodes.title_and_path.inc Generic "Set Node URL" sub-form for setting the url of any chado node
chado_add_node_form_dbxrefs 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_relationships tripal_core/api/tripal_core.chado_nodes.relationships.api.inc Provides a form for adding to BASE_relationship and relationship tables
chado_cleanup_orphaned_nodes tripal_core/api/tripal_core.chado_nodes.api.inc This function is a wrapper for the chado_cleanup_orphaned_nodes function. It breaks up the work of chado_cleanup_orphaned_nodes into smaller pieces that are more managable for servers that may have low php memory settings.
chado_cleanup_orphaned_nodes_part 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_get_id_from_nid tripal_core/api/tripal_core.chado_nodes.api.inc Get chado id for a node. E.g, if you want to get 'analysis_id' from the 'analysis' table for a synced 'chado_analysis' node, (the same for organisms and features): $analysis_id = chado_get_id_from_nid…
chado_get_nid_from_id tripal_core/api/tripal_core.chado_nodes.api.inc Get node id for a chado feature/organism/analysis. E.g, if you want to get the node id for an analysis, use: $nid = chado_get_nid_from_id ('analysis', $analysis_id) Likewise, $nid = chado_get_nid_from_id ('organism',…
chado_get_node_title tripal_core/api/tripal_core.chado_nodes.title_and_path.inc Get the title of a node based on the Title Format set in the admin section of the module. If the format has not yet been set than the the unique constrain and name fields will be used to generate a default format
chado_get_node_url tripal_core/api/tripal_core.chado_nodes.title_and_path.inc Get the url of a node based on the url Format set in the admin section of the module. If the format has not yet been set than the the unique constrain and name fields will be used to generate a default format
chado_node_get_base_table tripal_core/api/tripal_core.chado_nodes.api.inc Determine the chado base table for a given content type
chado_node_sync_form 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 tripal_core/api/tripal_core.chado_nodes.api.inc Generic function for syncing records in Chado with Drupal nodes.
chado_retrieve_node_form_dbxrefs tripal_core/api/tripal_core.chado_nodes.dbxrefs.api.inc This function is used in a hook_insert, hook_update for a node form when the additional_dbxrefs form has been added to the form. It retrieves all of the dbxrefs and returns them in an array of the format:
chado_retrieve_node_form_properties tripal_core/api/tripal_core.chado_nodes.properties.api.inc This function is used in a hook_insert, hook_update for a node form when the chado node properties form has been added to the form. It retrieves all of the properties and returns them in an array of the format:
chado_retrieve_node_form_relationships tripal_core/api/tripal_core.chado_nodes.relationships.api.inc This function is used in a hook_insert, hook_update for a node form when the relationships form has been added to the form. It retrieves all of the relationships and returns them in an array of the format:
chado_update_node_form_dbxrefs tripal_core/api/tripal_core.chado_nodes.dbxrefs.api.inc This function is used in hook_insert or hook_update and handles inserting of any new dbxrefs and creation of links between those dbxrefs and node content
chado_update_node_form_properties tripal_core/api/tripal_core.chado_nodes.properties.api.inc This function is used in hook_insert or hook_update and handles inserting of any new properties
chado_update_node_form_relationships tripal_core/api/tripal_core.chado_nodes.relationships.api.inc This function is used in hook_insert or hook_update and handles inserting of relationships between the current nodetype and other memebers of the same nodetype
hook_chado_node_sync_create_new_node tripal_core/api/tripal_core.chado_nodes.api.inc Create New Node
hook_chado_node_sync_form tripal_core/api/tripal_core.chado_nodes.api.inc Alter the Chado node sync form.
hook_chado_node_sync_form_submit tripal_core/api/tripal_core.chado_nodes.api.inc Bypass chado node api sync form submit.
hook_chado_node_sync_select_query tripal_core/api/tripal_core.chado_nodes.api.inc Alter the query that retrieves records to be sync'd (optional)
theme_chado_add_node_form_dbxrefs_table tripal_core/api/tripal_core.chado_nodes.dbxrefs.api.inc Function to theme the add/remove dbxrefs form into a table
theme_chado_add_node_form_properties tripal_core/api/tripal_core.chado_nodes.properties.api.inc Function to theme the add/remove properties form into a table
theme_chado_add_node_form_relationships_table tripal_core/api/tripal_core.chado_nodes.relationships.api.inc Function to theme the add/remove relationships form into a table

Files

Namesort descending Location Description
tripal_core.chado_nodes.dbxrefs.api.inc tripal_core/api/tripal_core.chado_nodes.dbxrefs.api.inc API to manage the chado _dbxref table for various Tripal Node Types
tripal_core.chado_nodes.properties.api.inc tripal_core/api/tripal_core.chado_nodes.properties.api.inc API to manage the chado prop table for various Tripal Node Types
tripal_core.chado_nodes.relationships.api.inc tripal_core/api/tripal_core.chado_nodes.relationships.api.inc API to manage the chado _relationship table for various Tripal Node Types