def build_institute(internal_id, display_name, sanger_recipients=None,
coverage_cutoff=None, frequency_cutoff=None):
"""Build a institute object
Args:
internal_id(str)
display_name(str)
sanger_recipients(list(str)): List with email addresses
Returns:
institute_obj(scout.models.Institute)
"""
LOG.info("Building institute %s with display name %s", internal_id,display_name)
institute_obj = Institute(
internal_id=internal_id,
display_name=display_name,
sanger_recipients=sanger_recipients,
coverage_cutoff = coverage_cutoff,
frequency_cutoff = frequency_cutoff
)
for key in list(institute_obj):
if institute_obj[key] is None:
institute_obj.pop(key)
return institute_obj
def build_institute(internal_id,
display_name,
sanger_recipients=None,
coverage_cutoff=None,
frequency_cutoff=None):
"""Build a institute object
Args:
internal_id(str)
display_name(str)
sanger_recipients(list(str)): List with email addresses
Returns:
institute_obj(scout.models.Institute)
"""
LOG.info("Building institute %s with display name %s", internal_id,
display_name)
institute_obj = Institute(internal_id=internal_id,
display_name=display_name,
sanger_recipients=sanger_recipients,
coverage_cutoff=coverage_cutoff,
frequency_cutoff=frequency_cutoff)
for key in list(institute_obj):
if institute_obj[key] is None:
institute_obj.pop(key)
return institute_obj
def add_institute(self, internal_id, display_name):
"""Add a institute to the database
Args:
internal_id(str): The internal id (like cust003)
display_name(str): The display name for a institute (like CMMS)
"""
logger.info("Creating institute with internal_id: {0} and"\
" display_name: {1}".format(internal_id, display_name))
institute = Institute(
internal_id=internal_id,
display_name=display_name
)
institute.save()
def get_institute(request):
print('')
logger.info("setup a institute")
institute = Institute(
internal_id='cust000',
display_name='clinical'
)
logger.info("Adding institute to database")
institute.save()
def teardown():
print('\n')
logger.info('Removing institute')
institute.delete()
logger.info('Institute removed')
request.addfinalizer(teardown)
return institute
def build_institute(
internal_id,
display_name,
loqusdb_id=None,
sanger_recipients=None,
collaborators=None,
phenotype_groups=None,
cohorts=None,
coverage_cutoff=None,
frequency_cutoff=None,
):
"""Build a institute object
Args:
internal_id(str)
display_name(str)
sanger_recipients(list(str)): List with email addresses
collaborators(list(str)): List of institute _id to enable sharing with
phenotype_groups(list(phenotype)): List of phenotype groups
cohorts(list(str)): List of cohorts
Returns:
institute_obj(scout.models.Institute)
"""
LOG.info("Building institute %s with display name %s", internal_id,
display_name)
institute_obj = Institute(
internal_id=internal_id,
display_name=display_name,
sanger_recipients=sanger_recipients,
loqusdb_id=loqusdb_id,
collaborators=collaborators,
phenotype_groups=phenotype_groups,
cohorts=cohorts,
coverage_cutoff=coverage_cutoff,
frequency_cutoff=frequency_cutoff,
)
for key in list(institute_obj):
if institute_obj[key] is None:
institute_obj.pop(key)
return institute_obj
def get_institute(institute_name):
"""
Take a institute name and return a institute object.
Args:
institute_name: A string that represents the name of an institute
Returns:
A mongoengine Institute object described in scout.models.institute.py
"""
return Institute(internal_id=institute_name, display_name=institute_name)