chado package

Submodules

chado.client module

Base chado client

class chado.client.Client(engine, metadata, session, ci)

Bases: object

Base client class implementing methods to make queries to the server

chado.exceptions module

exception chado.exceptions.RecordNotFoundError

Bases: Exception

Raised when a db select failed.

chado.util module

class chado.util.UtilClient(engine, metadata, session, ci)

Bases: chado.client.Client

Some chado utilities

dbshell()

Open a psql session to the database

Return type:None
Returns:None
launch_docker_image(background=False, no_yeast=False)

Launch a chado docker image.

Parameters:
  • background (bool) – Launch the image in the background
  • no_yeast (bool) – Disable loading of example yeast data
Return type:

None
Returns:

None

Module contents

class chado.ChadoInstance(dbhost='localhost', dbname='chado', dbuser='chado', dbpass='chado', dbschema='public', dbport=5432, dburl=None, offline=False, no_reflect=False, reflect_tripal_tables=False, pool_connections=True, **kwargs)

Bases: object

create_cvterm(term, cv_name, db_name, term_definition='', cv_definition='', db_definition='', accession='')
get_cvterm_id(name, cv, allow_synonyms=False)

get_cvterm_id allows lookup of CV terms by their name. This method caches the result in order to not hit the DB for every query. Maybe should investigate pre-loading popular terms? (E.g. gene, mRNA, etc)

get_cvterm_name(cv_id)

get_cvterm_name allows lookup of CV terms by their ID. This method caches the result in order to not hit the DB for every query. Maybe should investigate pre-loading popular terms? (E.g. gene, mRNA, etc)

get_pub_id(name)

Allows lookup of publication by their uniquename. This method caches the result in order to not hit the DB for every query.

class chado.ChadoModel

Bases: object