def gen_report(request):
try:
params = json.loads(request.body)
specimenid = params['specimenid']
specimen = Specimen.objects.get(specimenid=specimenid)
if specimen is None:
return em.create_fail_response('object not exist', em.FAIL)
specimengates = SpecimenGate.objects.filter(specimenid=specimenid)
render = PdfReportRender(specimen, specimengates)
filename = render.render_report()
createtime = datetime.datetime.now()
try:
hisreport = SpecimenReport.objects.get(specimenid=specimenid)
hisreport.delete()
except Exception as e:
logger.exception(e)
report = SpecimenReport(specimenid=specimenid,
specimenreportpath=filename,
createtime=createtime)
report.save()
logger.info('report file:' + filename)
return em.create_sucess_response(report.to_json())
except Exception as e:
logger.exception(e)
return em.create_fail_response(e, em.FAIL)
def delete_gate(request):
try:
params = json.loads(request.body)
gates = SpecimenGate.objects.filter(specimenid=params['specimenid'],
fcsfilename=params['fcsfilename'],
gatetype=params['gatetype'])
if gates is not None:
gates.delete()
return em.create_success_null()
except Exception as e:
logger.exception(e)
return em.create_fail_response(e, em.FAIL)
def query_gate(request):
try:
params = json.loads(request.body)
specimenid = params['specimenid']
gates = SpecimenGate.objects.get(specimenid=specimenid)
result = []
for gate in gates:
result.append(gate.to_json())
return em.create_sucess_response(result)
except Exception as e:
logger.exception(e)
return em.create_fail_response(e, em.FAIL)
def upload_specimen_fcsfiles(request):
try:
file = request.FILES.get("file", None)
filemeta = file.name
specimenid = int(request.POST['specimenid'])
specimen = Specimen.objects.get(specimenid=specimenid)
if specimen is None:
return em.create_fail_response('specimen is not exist', em.FAIL)
storgedir = specimen.specimendir
specimenfilepath = get_fcsfilepath(storgedir, file.name)
if not file:
return em.create_fail_response('no files for upload', em.FAIL)
destination = open(specimenfilepath, 'wb+')
for chunk in file.chunks():
destination.write(chunk)
destination.close()
return em.create_success_null()
except Exception as e:
logger.exception(e)
return em.create_fail_response(e, em.FAIL)
def query_report(request):
try:
params = json.loads(request.body)
specimenid = params['specimenid']
report = SpecimenReport.objects.filter(
specimenid=specimenid).order_by('createtime')[0]
return em.create_sucess_response({
'filename': report.specimenreportpath,
'token': datetime.datetime.now()
})
except Exception as e:
logger.exception(e)
return em.create_fail_response(e, em.FAIL)
def query_specimen_fcsfiles(request):
try:
params = json.loads(request.body)
specimenid = params['specimenid']
specimen = Specimen.objects.get(specimenid=specimenid)
querysubdir = specimen.specimendir
response = {}
fcsfilenames = [
filename for filename in os.listdir(get_fcsfiledir(querysubdir))
if re.search('.fcs$', filename)
]
return em.create_sucess_response({'fcsfilenames': fcsfilenames})
except Exception as e:
logger.exception(e)
return em.create_fail_response(e, em.FAIL)
def query_specimen_fcsfile_data(request):
try:
params = json.loads(request.body)
filename = params['filename']
specimenid = params['specimenid']
specimen = Specimen.objects.get(specimenid=specimenid)
if specimen is None:
logger.error('param vaild')
querysubdir = specimen.specimendir
cols = {}
meta, df = fcsparser.parse(get_fcsfilepath(querysubdir, filename))
for col in numpy.array(df.columns).tolist():
cols[col] = df[col].tolist()
cols['filename'] = filename
cols['specimenid'] = specimenid
return em.create_sucess_response(cols)
except Exception as e:
logger.exception(e)
return em.create_fail_response(e, em.FAIL)
def cell_stat(request):
try:
params = json.loads(request.body)
filename = params['fcsfilename']
specimenid = params['specimenid']
polygons = params['polygongate']
specimen = Specimen.objects.get(specimenid=specimenid)
meta, df = fcsparser.parse(
get_fcsfilepath(specimen.specimendir, filename))
actual_x = df[SSC_A]
actual_y = df[PerCP_A]
gate = Gate()
gate.load(polygons)
x = actual_x.values.reshape(actual_x.values.size, 1)
y = actual_y.values.reshape(actual_y.values.size, 1)
points = numpy.concatenate((x, y), axis=1)
result = gate.stat(points)
result['detail'] = {}
return em.create_sucess_response(result)
except Exception as e:
logger.exception(e)
return em.create_fail_response(e, em.FAIL)
def save_spceiment_fcsfile_gate(request):
try:
params = json.loads(request.body)
# delete history gate
hisgates = SpecimenGate.objects.filter(
specimenid=params['specimenid'],
fcsfilename=params['fcsfilename'],
gatetype=params['gatetype'])
if hisgates is not None:
hisgates.delete()
logger.info("delete history gate success")
now_time = datetime.datetime.now()
gate = SpecimenGate(specimenid=params['specimenid'],
fcsfilename=params['fcsfilename'],
gates=json.dumps(params['gates']),
gatetype=params['gatetype'],
createtime=now_time,
modifytime=now_time)
gate.save()
return em.create_sucess_response(gate.to_json())
except Exception as e:
logger.exception(e)
return em.create_fail_response(e, em.FAIL)