class Subject(BaseMixIn, Base):
""" subjects """
__tablename__ = 'subjects'
code = Column(types.String(24), unique=True, nullable=False)
yearofbirth = Column(types.Float, nullable=False)
gender = Column(types.String(1), nullable=False)
notes = deferred( Column(types.Text(), nullable=False, server_default='') )
## optional fields, unique personal identity
name = Column(types.String(48), nullable=False, server_default='')
birthday = Column(types.Date)
birthplace = Column(types.String(32), nullable=False, server_default='')
idnumber = Column(types.String(32), nullable=False, server_default='')
nationality_id = Column(types.Integer, ForeignKey('eks.id'), nullable=False)
nationality = EK.proxy('nationality_id', '@REGION')
## custom fields
int1 = Column(types.Integer, nullable=False, server_default='0') # custom usage
int2 = Column(types.Integer, nullable=False, server_default='0') # custom usage
string1 = Column(types.String(16), nullable=False, server_default='') # custom usage
string2 = Column(types.String(16), nullable=False, server_default='') # custom usage
flags = Column(types.Integer, nullable=False, server_default='0')
__table_args__ = ( UniqueConstraint( 'code', 'gender', 'yearofbirth' ), {} )
@staticmethod
def search( code, gender=None, yearofbirth=None, auto=False, dbsession=None ):
assert dbsession
q = Subject.query().filter( and_( Subject.code == code, Subject.gender == gender,
Subject.yearofbirth == yearofbirth ) )
r = q.all()
if len(r) == 0:
if auto:
subject = Subject( code = code, gender = gender, yearofbirth = yearofbirth )
dbsession.add( subject )
#dbsession.flush()
return subject
return None
return r[0]
@staticmethod
def autocode():
return '#%08x' % random.randrange(256**4)
def update(self, d):
if type(d) == dict:
if not self.nationality_id:
self.nationality = ''
if d.get('nationality', None) is not None:
self.nationality = d['nationality']
cerr('set nationality to %s' % d['nationality'])
else:
raise NotImplementedError('can only update from dict')
class SubjectStringData(Base):
__tablename__ = 'subjectstrings'
id = Column(types.Integer, primary_key=True)
subject_id = Column(types.Integer, ForeignKey('subjects.id', ondelete='CASCADE'),
nullable=False)
key_id = Column(types.Integer, ForeignKey('eks.id', ondelete='CASCADE'),
nullable=False)
key = EK.proxy('key_id', '@EXTFIELD')
value = Column(types.String(64), nullable=False)
__table_args__ = ( UniqueConstraint('subject_id', 'key_id'), {} )
class PathoSample(get_dbhandler_class().Sample):
""" PlasmogenSample - Plasmodium Sample
This class contains information about Plasmodium samples
"""
passive_case_detection = Column(types.Boolean, nullable=True)
symptomatic_status = Column(types.Boolean, nullable=True)
imported_case = Column(types.Boolean, nullable=True)
nationality_status = Column(types.Boolean, nullable=True)
storage_id = Column(types.Integer, ForeignKey('eks.id'), nullable=False)
storage = EK.proxy('storage_id', '@BLOOD-STORAGE')
""" sample storage method """
method_id = Column(types.Integer, ForeignKey('eks.id'), nullable=False)
method = EK.proxy('method_id', '@BLOOD-WITHDRAWAL')
""" blood withdrawal method """
pcr_method_id = Column(types.Integer, ForeignKey('eks.id'), nullable=False)
pcr_method = EK.proxy('pcr_method_id', '@PCR-METHOD')
""" PCR method for detection """
pcr_id = Column(types.Integer, ForeignKey('eks.id'), nullable=False)
pcr = EK.proxy('pcr_id', '@SPECIES')
""" species identification based on PCR """
microscopy_id = Column(types.Integer, ForeignKey('eks.id'), nullable=False)
microscopy = EK.proxy('microscopy_id', '@SPECIES')
""" species identification based on microscopy """
parasitemia = Column(types.Float, nullable=False, server_default='-1')
recurrent = Column(types.Boolean, nullable=False, default=False)
""" if this a recurrent case """
subject_id = Column(types.Integer, ForeignKey('subjects.id'), nullable=False)
subject = relationship(Subject, uselist=False,
backref=backref("samples", lazy='dynamic', passive_deletes=True))
""" link to subject/individual """
day = Column(types.Integer, nullable=False, server_default = '0')
""" sampling day for a particular subject/individual """
__mapper_args__ = { 'polymorphic_identity': 2 }
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
@staticmethod
def search( subject_id = None, code=None, collection_date=None, location_id=None,
batch_id = None, auto=False, _q = None ):
if not _q:
_q = PlasmoSample.query()
if code:
_q = _q.filter( PlasmoSample.code == code )
if collection_date:
_q = _q.filter( PlasmoSample.collection_date == collection_date )
if location_id:
_q = _q.filter( PlasmoSample.location_id == location_id )
if batch_id:
_q = _q.filter( PlasmoSample.batch_id == batch_id )
#q = q.filter( and_( *filters ) )
r = _q.all()
if len(r) == 0:
if auto:
if not batch_id:
raise RuntimeError('Sample searching with auto-creation must be supplied '
'with batch_id' )
sample = PlasmoSample( subject_id=subject_id, code=code,
location_id=location_id, collection_date=collection_date,
batch_id = batch_id)
#raise RuntimeError(collection_date)
print('Creating sample with code: %s with batch_id: %d' %
(sample.code, sample.batch_id))
dbsession.add( sample )
return sample
return None
if len(r) == 1:
return r[0]
return r
@staticmethod
def csv2dict( *args, **kwargs ):
return dictfmt.csv2dict( *args, **kwargs )
