Chado Buddy Documentation

[dsenalik]

This is a place for notes and about Chado Buddies for use in developing documentation from PR tripal/tripal#1844

Branch: 89-chado-buddy

One of the simplest cases is working with the chado db table. The db and dbxref tables are handled by the ChadoDbxrefBuddy class

To use it, you will first get a connection to the Buddy service

$buddy_service = \Drupal::service('tripal_chado.chado_buddy');

Then you create an instance of whatever buddy you want to use, for example:

$buddy_instance = $buddy_service->createInstance('chado_dbxref_buddy', []);

Each buddy instance will have various functions to get, set, or update values.
This table summarizes the functions available

chado table:	db	dbxref	cv	cvterm	# arrays
lookup	getDb()	getDbxref()	getCv()	getCvterm()	1
insert	insertDb()	insertDbxref()	insertCv()	insertCvterm()	1
update	updateDb()	updateDbxref()	updateCv()	updateCvterm()	2
upsert	upsertDb()	upsertDbxref()	upsertCv()	upsertCvterm()	1
associate	-	associateDbxref()	-	associateCvterm()	na

For update functions, there are two arrays, the first contains the new values, the second contains the query values (conditions)

The array values for the db functions can contain the following keys. These directly correspond to columns in the chado.db table.
db_name must be used as an alias for name to prevent ambiguity for cv functions.

table	table column	required for insert
db	db_id	no
db	name (db_name)*	yes
db	description (db_description)*	no
db	urlprefix	no
db	url	no

The array values for the dbxref functions can contain the following keys. These directly correspond to columns in either the chado.dbxref or chado.db tables. Asterisk notes when key differs from column name to prevent ambiguity.
db_name must be used as an alias for name to prevent ambiguity for cv functions.

table	table column	required for insert
dbxref	dbxref_id	only used for query
dbxref	accession	yes
dbxref	version	no
dbxref	description (dbxref_description)*	no
db	db_id	yes, but either db_id or name or db_name required
db	name (db_name)*	see above
db	description (db_description)*	no
db	urlprefix	no
db	url	no

The array values for the cv functions can contain the following keys. These directly correspond to columns in the chado.cv table. Asterisk notes when key differs from column name to prevent ambiguity.
cv_name must be used as an alias for name to prevent ambiguity for db functions.

table	table column	required for insert
cv	cv_id	no
cv	name (cv_name)*	yes
cv	urlprefix	no
cv	url	no

The array values for the cvterm functions can contain the following keys. These directly correspond to columns in either the chado.cvterm, chado.cv, chado.dbxref, or chado.db tables. Asterisk notes when key differs from column name to prevent ambiguity.
db_name must be used as an alias for name to prevent ambiguity for db functions.

table	table column	required for insert
cvterm	cvterm_id	only used for query
cvterm	cv_id	yes but can instead use cv_name
cvterm	dbxref_id	yes but can instead use accession + (db_id or db_name)
cvterm	name (cvterm_name)*	yes
cvterm	definition (cvterm_definition)*	no
cvterm	is_obsolete	no
cvterm	is_relationshiptype	no
cv	cv_id	no
cv	name (cv_name)*	yes
cv	definition (cv_definition)*	no
dbxref	dbxref_id	only if using an existing dbxref
dbxref	accession	yes but can instead use existing dbxref_id
dbxref	version	no
dbxref	description (dbxref_description)*	no
db	db_id	yes, but either db_id or name or db_name required, and only if adding a new dbxref
db	name (db_name)*	see above
db	description (db_description)*	no
db	urlprefix	no
db	url	no