def create_event(self, institute, case, user, link, category, verb,
subject, level='specific', variant_id="", content=""):
"""Create an Event with the parameters given.
Arguments:
institute (Institute): A Institute object
case (Case): A Case object
user (User): A User object
link (str): The url to be used in the event
category (str): Case or Variant
verb (str): What type of event
subject (str): What is operated on
level (str): 'specific' or 'global'. Default is 'specific'
variant (Variant): A variant object
content (str): The content of the comment
"""
event = Event(
institute=institute,
case=case,
author=user.to_dbref(),
link=link,
category=category,
verb=verb,
subject=subject,
level=level,
variant_id=variant_id,
content=content
)
logger.debug("Saving Event")
event.save()
logger.debug("Event Saved")
def delete_event(self, event_id):
"""Delete a event
Arguments:
event_id (str): The database key for the event
"""
logger.info("Deleting event{0}".format(event_id))
Event.objects(id=event_id).delete()
logger.debug("Event {0} deleted".format(event_id))
def delete_event(self, event_id):
"""
Delete a event
Arguments:
event_id (str): The database key for the event
"""
self.logger.info("Deleting event{0}".format(
event_id
))
Event.objects(id=event_id).delete()
self.logger.debug("Event {0} deleted".format(
event_id
))
def has_comments(self):
"""
Return True is there are any comments for this variant in the database
"""
if Event.objects(verb='comment', variant_id=self.variant_id,
institute=self.institute):
return True
return False
def has_comments(self):
"""
Return True is there are any comments for this variant in the database
"""
if Event.objects(verb='comment',
variant_id=self.variant_id,
institute=self.institute):
return True
return False
def test_add_mim(setup_database, get_institute, get_user, get_case):
logger.info("Add OMIM term for a case")
# Non existing mim phenotype
mim_term = "MIM:614300"
setup_database.add_phenotype(
institute=get_institute, case=get_case, user=get_user, link="mimlink", omim_term=mim_term
)
# Assert that the synopsis has been added to the case
updated_case = Case.objects.get(case_id="acase")
assert len(updated_case.phenotype_terms) != 0
# Check that the event not exists
for event in Event.objects(verb="add_phenotype"):
assert event.link == "mimlink"
event.delete()
Arguments:
institute (Institute): A Institute object
case (Case): A Case object
user (User): A User object
link (str): The url to be used in the event
category (str): Case or Variant
verb (str): What type of event
subject (str): What is operated on
level (str): 'specific' or 'global'. Default is 'specific'
variant (Variant): A variant object
content (str): The content of the comment
"""
event = Event(
institute=institute,
case=case,
author=user.to_dbref(),
link=link,
category=category,
verb=verb,
subject=subject,
level=level,
variant_id=variant_id,
content=content
)
self.logger.debug("Saving Event")
event.save()
self.logger.debug("Event Saved")
