def search(country, level1='', level2='', level3='', level4='', auto=False, dbsession=None):
assert dbsession
country_id = EK._id(country.strip(), dbsession, '@REGION', auto)
level1_id = EK._id(level1.strip(), dbsession, '@REGION', auto)
level2_id = EK._id(level2.strip(), dbsession, '@REGION', auto)
level3_id = EK._id(level3.strip(), dbsession, '@REGION', auto)
level4_id = EK._id(level4.strip(), dbsession, '@REGION', auto)
q = Location.query(dbsession).filter(
and_(Location.country_id == country_id,
Location.level1_id == level1_id,
Location.level2_id == level2_id,
Location.level3_id == level3_id,
Location.level4_id == level4_id) )
r = q.all()
if len(r) == 0 and auto:
location = Location( country_id = country_id,
level1_id = level1_id,
level2_id = level2_id,
level3_id = level3_id,
level4_id = level4_id )
dbsession.add( location )
dbsession.flush([location])
return location
return r[0]
def search(code, session):
""" provide case-insensitive search for marker code """
if '/' in code:
species, code = code.split('/')
if callable(session):
session = session()
species_id = EK._id(species, dbsession=session)
q = Marker.query(session).filter( func.lower(Marker.code) == func.lower(code),
Marker.species_id == species_id)
else:
q = Marker.query(session).filter( func.lower(Marker.code) == func.lower(code) )
return q.one()
def update(self, obj):
if type(obj) == dict:
if obj.get('storage') is not None:
self.storage = obj.get('storage') # blood storage
if obj.get('method') is not None:
self.method = obj.get('method') # blood withdrawal method
if obj.get('pcr_method') is not None:
self.pcr_method_id = EK._id(obj.get('pcr_method'), grp = '@PCR_METHOD',
dbsession = object_session(self), auto=True)
if obj.get('pcr') is not None:
self.pcr = obj.get('pcr')
if obj.get('microscopy') is not None:
self.microscopy = obj.get('microscopy')
if obj.get('type') is not None:
self.type = obj.get('type')
if obj.get('day') is not None:
self.day = int(obj.get('day'))
if self.day == 0 and self.type == '':
self.type = 'P'
if obj.get('case_detection') is not None:
self.passive_case_detection = obj.get('case_detection').lower().startswith('y')
if obj.get('symptomatic_status') is not None:
self.symptomatic_status = obj.get('symptomatic_status').lower().startswith('y')
if obj.get('nationality_status') is not None:
self.nationality_status = obj.get('nationality_status').lower().startswith('y')
if obj.get('imported_case') is not None:
self.imported_case = obj.get('imported_case').lower().startswith('y')
if obj.get('parasite_density') is not None:
self.parasitemia = int(obj.get('parasite_density', -1))
# deals with subject
subject_code = obj.get('subject_code', None)
related_sample = obj.get('related_sample', None)
session = object_session(self)
if subject_code:
# find subject
subject = Subject.search(code=subject_code, dbsession = session)
self.subject_id = subject.id
elif related_sample:
# find sample
sample = self.batch.search_sample(related_sample)
if sample is None:
raise RuntimeError('ERROR for sample code %s: related sample code %s does not exist' % (self.code, related_sample))
self.subject_id = sample.subject_id
elif not self.subject:
# create new subject
while True:
code = '#' + random_string(8)
# we need to check subject code first !
if Subject.query(session).filter(Subject.code == code).count() == 0:
break
subject = Subject( code = code, gender = obj['gender'],
yearofbirth = obj['yearofbirth'] )
session.add(subject)
subject.update( obj )
session.flush([subject])
cerr('subject %s nationality_id %d' % (subject.code, subject.nationality_id))
self.subject = subject
#self.subject_id = 0
# now if subject_code &
else:
raise NotImplementedError('PROG/ERR - not implemented yet')
super().update( obj )
return
def update(self, obj):
if type(obj) == dict:
if obj.get('storage') is not None:
self.storage = obj.get('storage') # blood storage
if obj.get('method') is not None:
self.method = obj.get('method') # blood withdrawal method
if obj.get('pcr_method') is not None:
self.pcr_method_id = EK._id(obj.get('pcr_method'), grp = '@PCR_METHOD',
dbsession = object_session(self), auto=True)
if obj.get('pcr') is not None:
self.pcr = obj.get('pcr')
if obj.get('microscopy') is not None:
self.microscopy = obj.get('microscopy')
if obj.get('type') is not None:
self.type = obj.get('type')
if obj.get('day') is not None:
self.day = int(obj.get('day'))
if self.day == 0 and self.type == '':
self.type = 'P'
if obj.get('case_detection') is not None:
self.passive_case_detection = obj.get('case_detection').lower().startswith('y')
if obj.get('symptomatic_status') is not None:
self.symptomatic_status = obj.get('symptomatic_status').lower().startswith('y')
if obj.get('nationality_status') is not None:
self.nationality_status = obj.get('nationality_status').lower().startswith('y')
if obj.get('imported_case') is not None:
self.imported_case = obj.get('imported_case').lower().startswith('y')
if obj.get('parasite_density') is not None:
self.parasitemia = int(obj.get('parasite_density', -1))
# deals with subject
subject_code = obj.get('subject_code', None)
related_sample = obj.get('related_sample', None)
session = object_session(self)
if subject_code:
# find subject
subject = Subject.search(code=subject_code, dbsession = session)
self.subject_id = subject.id
elif related_sample:
# find sample
sample = self.batch.search_sample(related_sample)
if sample is None:
raise RuntimeError('ERROR for sample code %s: related sample code %s does not exist' % (self.code, related_sample))
self.subject_id = sample.subject_id
elif not self.subject:
# create new subject
while True:
code = '#' + random_string(8)
# we need to check subject code first !
if Subject.query(session).filter(Subject.code == code).count() == 0:
break
subject = Subject( code = code, gender = obj['gender'],
yearofbirth = obj['yearofbirth'] )
session.add(subject)
subject.update( obj )
session.flush([subject])
cerr('subject %s nationality_id %d' % (subject.code, subject.nationality_id))
self.subject = subject
#self.subject_id = 0
# now if subject_code &
else:
raise NotImplementedError('PROG/ERR - not implemented yet')
super().update( obj )
return
if obj.passive_case_detection is not None:
self.passive_case_detection = obj.passive_case_detection
if obj.storage_id is not None:
self.storage_id = 0 #obj.storage_id
if obj.method_id is not None:
self.method_id = 0 #obj.method_id
if obj.pcr_method_id is not None:
self.pcr_method_id = 0 #obj.pcr_method_id
if obj.pcr_id is not None:
self.pcr_id = 0 #obj.pcr_id
if obj.microscopy_id is not None:
self.microscopy_id = 0 #obj.microscopy_id
if obj.recurent is not None:
self.recurrent = obj.recurrent
if obj.subject_is:
self.subject_id = obj.subject_id
