comparison chado.py @ 14:86589f36dfad draft

"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"

13:313a27d7d64a

        os.environ['GALAXY_CHADO_DBNAME'],
        os.environ['GALAXY_CHADO_DBUSER'],
        os.environ['GALAXY_CHADO_DBPASS'],
        os.environ['GALAXY_CHADO_DBSCHEMA'],
        os.environ['GALAXY_CHADO_DBPORT'],
        no_reflect=True
    )


def list_organisms(*args, **kwargs):

def _list_analyses(ci, *args, **kwargs):
    ans_data = []
    for an in ci.analysis.get_analyses():
        ans_data.append((an['name'], str(an['analysis_id']), False))
    return ans_data

14:86589f36dfad

        os.environ['GALAXY_CHADO_DBNAME'],
        os.environ['GALAXY_CHADO_DBUSER'],
        os.environ['GALAXY_CHADO_DBPASS'],
        os.environ['GALAXY_CHADO_DBSCHEMA'],
        os.environ['GALAXY_CHADO_DBPORT'],
        no_reflect=True,
        pool_connections=False
    )


def list_organisms(*args, **kwargs):

def _list_analyses(ci, *args, **kwargs):
    ans_data = []
    for an in ci.analysis.get_analyses():
        ans_data.append((an['name'], str(an['analysis_id']), False))
    return ans_data


def list_dbs(*args, **kwargs):

    ci = _get_instance()

    # Key for cached data
    cacheKey = 'dbs'
    # We don't want to trust "if key in cache" because between asking and fetch
    # it might through key error.
    if cacheKey not in cache:
        # However if it ISN'T there, we know we're safe to fetch + put in
        # there.<?xml version="1.0"?>

        data = _list_dbs(ci, *args, **kwargs)
        cache[cacheKey] = data
        ci.session.close()
        return data
    try:
        # The cache key may or may not be in the cache at this point, it
        # /likely/ is. However we take no chances that it wasn't evicted between
        # when we checked above and now, so we reference the object from the
        # cache in preparation to return.
        data = cache[cacheKey]
        ci.session.close()
        return data
    except KeyError:
        # If access fails due to eviction, we will fail over and can ensure that
        # data is inserted.
        data = _list_dbs(ci, *args, **kwargs)
        cache[cacheKey] = data
        ci.session.close()
        return data


def _list_dbs(ci, *args, **kwargs):
    dbs_data = []
    for db in ci.load._get_dbs():
        dbs_data.append((db['name'], str(db['db_id']), False))
    return dbs_data