def createSample(sample_name, sample_type, **kwargs):
"""
sample_name: string, name for the new sample, required
sample_type: required, either:
- string, name for existing type in Types collection, or
- mongo type object for existing type in Types collection
kwargs: passed to constructor
"""
kwargs['sampleName'] = sample_name
kwargs['requestList'] = []
kwargs['resultList'] = []
# initialize request count to zero
if not kwargs.has_key('request_count'):
kwargs['request_count'] = 0
if isinstance(sample_type, unicode) or isinstance(sample_type, str):
kwargs['sample_type'] = type_from_name(sample_type, as_mongo_obj=True)
# try:
# kwargs['sample_type'] = Types.objects(__raw__={'name': type_name})[0]
# except IndexError:
# raise ValueError('no sample type found matching "{0}"'.format(type_name))
s = Sample(**kwargs)
s.save()
return s.sample_id
def getSampleNamebyID(sample_id):
"""
sample_id: required, integer
"""
s = Sample.objects(__raw__={'sample_id': sample_id})
return _try0_dict_key(s, 'sample', 'sample_id', sample_id, -99,
dict_key='sampleName')
def getSampleByID(sample_id, as_mongo_obj=False):
"""
sample_id: required, integer
"""
s = Sample.objects(__raw__={'sample_id': sample_id})
return _try0_maybe_mongo(s, 'sample', 'sample_id', sample_id, None,
as_mongo_obj=as_mongo_obj)
def getSampleRequestCount(sample_id):
"""
get the 'request_count' attribute of the specified sample
"""
s = Sample.objects(__raw__={'sample_id': sample_id})
return _try0_dict_key(s, 'sample', 'sample_id', sample_id, None,
dict_key='request_count')
def find_sample_request():
req_list = []
for samp in Sample.objects():
for req in samp.requestList:
req_list.append(req.to_mongo())
return req_list
def getResultsforSample(sample_id):
"""
Takes a sample_id and returns it's resultsList or [].
"""
sample = Sample.objects(__raw__={'sample_id': sample_id}
).only('resultList')
return [r.to_mongo() for r in
_try0_maybe_mongo(sample, 'sample', 'sample_id', sample_id, None,
as_mongo_obj=True).resultList]
def incrementSampleRequestCount(sample_id):
"""
increment the 'request_count' attribute of the specified sample by 1
"""
# potential for race here?
s = Sample.objects(__raw__={'sample_id': sample_id})[0]
s.update(inc__request_count=1)
s.reload()
return s.request_count
def find_sample():
ret_list = []
headers = ['sample_name', 'sample_type']
#return [s.to_mongo() for s in Sample.objects()]
for samp in Sample.objects():
s = samp.to_mongo()
s['sample_type'] = samp.sample_type.name
ret_list.append(s)
return (headers, ret_list)
def addResulttoSample(result_type, sample_id, result_obj=None, timestamp=None,
as_mongo_obj=False, **kwargs):
"""
like addResulttoRequest, but without a request
"""
r = createResult(result_type, sample_id=sample_id, result_obj=result_obj, timestamp=timestamp,
as_mongo_obj=True, **kwargs)
try:
sample = Sample.objects(sample_id=sample_id)[0]
except IndexError:
return None
sample.resultList.append(r)
sample.save()
return r.to_mongo()
def deleteResult(result_id, get_result=False):
"""
Takes a result_id, deletes, and optionally returns the matching result or None.
When should we ever be doing this?
result_id: required, int
"""
result_id = int(result_id)
# delete it from any samples first
sample_qs = Sample.objects(__raw__={'resultList.result_id': result_id})
sample = _try0_maybe_mongo(sample_qs, 'result', 'result_id', result_id, None,
as_mongo_obj=True)
for res in sample.resultList:
if res.result_id == result_id:
tmp = res
sample.resultList.remove(res)
sample.save()
# then directly in Results
r = getResult(result_id, as_mongo_obj=True)
r.delete()
def addResultforRequest(result_type, request_id, result_obj=None, timestamp=None,
as_mongo_obj=False, **kwargs):
"""
like createResult, but also adds it to the resultList of result['sample_id']
"""
r = createResult(result_type, request_id, result_obj=result_obj, timestamp=timestamp,
as_mongo_obj=True, **kwargs)
request = r.request_id
#sample_qs = Sample.objects(__raw__={'requestList.request_id': request_id})
#sample = _try0_maybe_mongo(sample_qs, 'request', 'request_id', request_id, None,
# as_mongo_obj=True)
try:
sample = Sample.objects(requestList__in=[request])[0]
except IndexError:
return None
sample.resultList.append(r)
sample.save()
return r.to_mongo()
def getSampleIDbyName(sample_name):
s = Sample.objects(__raw__={'sampleName': sample_name})
return _try0_dict_key(s, 'sample', 'sampleName', sample_name, -99,
dict_key='sample_id')