Legacy Chado Nodes
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:
- chado_add_node_form_properties() and chado_update_node_form_properties() to provide an interface for adding/removing properties
- chado_add_node_form_dbxrefs() and chado_update_node_form_dbxrefs() to provide an interface for adding/removing additional database references
- chado_add_node_form_relationships() and chado_update_node_form_relationships() to provide an interface for adding/removing relationships between chado records from your base table
Parent topics
File
- legacy/
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
Name |
Location | Description |
|---|---|---|
| chado_add_admin_form_set_title |
legacy/ |
Generic "Set Node Title" sub-form for setting the title of any chado node |
| chado_add_admin_form_set_url |
legacy/ |
Generic "Set Node URL" sub-form for setting the url of any chado node |
| chado_add_node_form_dbxrefs |
legacy/ |
Provides a form for adding to BASE_dbxref and dbxref tables |
| chado_add_node_form_relationships |
legacy/ |
Provides a form for adding to BASE_relationship and relationship tables |
| chado_cleanup_orphaned_nodes |
legacy/ |
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 |
legacy/ |
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 |
legacy/ |
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 |
legacy/ |
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 |
legacy/ |
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 |
legacy/ |
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_get_token_value |
legacy/ |
Retrieve the value of the token from the node based on the $token_info['location'] |
| chado_node_add_token_format |
legacy/ |
Save a format to be used by chado_get_node_title() or chado_get_node_url() |
| chado_node_generate_tokens |
legacy/ |
Generate tokens for a particular base table |
| chado_node_get_base_table |
legacy/ |
Determine the chado base table for a given content type |
| chado_node_get_legacy_title_default |
legacy/ |
Handles legacy title options |
| chado_node_get_legacy_url_default |
legacy/ |
Handles legacy URL options |
| chado_node_get_title_format |
legacy/ |
Get the title format for a specific content type |
| chado_node_get_token_format |
legacy/ |
Get the format for the given application of a given content type (ie: the feature title) |
| chado_node_get_unique_constraint_format |
legacy/ |
Generate the unique constraint for a given base table using the Chado Schema API definition |
| chado_node_get_url_format |
legacy/ |
Get the url format for a specific content type |
| chado_node_sync_form |
legacy/ |
Generic Sync Form to aid in sync'ing (create drupal nodes linking to chado content) any chado node type. |
| chado_node_sync_records |
legacy/ |
Generic function for syncing records in Chado with Drupal nodes. |
| chado_retrieve_node_form_dbxrefs |
legacy/ |
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 |
legacy/ |
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 |
legacy/ |
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_set_node_url |
legacy/ |
Set the URL for a given node. |
| chado_update_existing_node_urls |
legacy/ |
Tripal Job for updating all node URLs for a particular node type. |
| chado_update_node_form_dbxrefs |
legacy/ |
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 |
legacy/ |
This function is used in hook_insert or hook_update and handles inserting of any new properties |
| chado_update_node_form_relationships |
legacy/ |
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 |
legacy/ |
Create New Node |
| hook_chado_node_sync_form |
legacy/ |
Alter the Chado node sync form. |
| hook_chado_node_sync_form_submit |
legacy/ |
Bypass chado node api sync form submit. |
| hook_chado_node_sync_select_query |
legacy/ |
Alter the query that retrieves records to be sync'd (optional) |
Files
|
Name |
Location | Description |
|---|---|---|
| tripal_core.chado_nodes.dbxrefs.api.inc |
legacy/ |
API to manage the Chado dbxref table for various Tripal Node Types |
| tripal_core.chado_nodes.properties.api.inc |
legacy/ |
API to manage the chado prop table for various Tripal Node Types |
| tripal_core.chado_nodes.relationships.api.inc |
legacy/ |
API to manage the chado _relationship table for various Tripal Node Types |