def set_and_verify_project_id_on(data):
project_name = data.get('project_name')
if project_name:
project_id = get_id_where('projects', db, name=project_name)
data['project_id'] = project_id
del data['project_name']
if project_id is None:
raise voluptuous.Invalid('no project with name {}'.format(project_name))
else:
project_id = data['project_id']
if get_id_where('projects', db, id=project_id) is None:
raise voluptuous.Invalid('no project with id {}'.format(project_id))
def _set_or_verify_bam_id_on(run, bam_type):
"""After calling this, run['(bam_type)_bam_id'] will be set to a valid BAM ID.
If there is not a matching BAM, it will raise voluptuous.Invalid.
"""
id_key = bam_type + '_bam_id'
uri_key = bam_type + '_bam_uri'
bam_id = run.get(id_key)
if bam_id:
if get_where('bams', db, id=bam_id) is None:
raise voluptuous.Invalid(
'bam with id "{}" does not exist'.format(bam_id))
elif run.get(uri_key):
bam_id = get_id_where('bams', db, uri=run[uri_key])
if bam_id is None:
raise voluptuous.Invalid(
'bam with uri "{}" does not exist'.format(run[uri_key]))
run[id_key] = bam_id
del run[uri_key]
