def save_uploaded_plans_for_template(request):
"""add plans, with CSV validation"""
logger.info(request)
if request.method != 'POST':
logger.exception(format_exc())
transaction.rollback()
return HttpResponse(json.dumps({
"error":
"Error, unsupported HTTP Request method (%s) for saving plan upload."
% request.method
}),
mimetype="application/json")
postedfile = request.FILES['postedfile']
destination = tempfile.NamedTemporaryFile(delete=False)
for chunk in postedfile.chunks():
destination.write(chunk)
postedfile.close()
destination.close()
#check to ensure it is not empty
headerCheck = open(destination.name, "rU")
firstCSV = []
for firstRow in csv.reader(headerCheck):
firstCSV.append(firstRow)
#logger.info("views.save_uploaded_plans_for_template() firstRow=%s;" %(firstRow))
headerCheck.close()
if not firstRow:
os.unlink(destination.name)
transaction.rollback()
return HttpResponse(json.dumps(
{"status": "Error: batch planning file is empty"}),
mimetype="text/html")
index = 0
plans = []
rawPlanDataList = []
failed = {}
file = open(destination.name, "rU")
reader = csv.DictReader(file)
for index, row in enumerate(reader, start=1):
errorMsg, aPlanDict, rawPlanDict, isToSkipRow = validate_csv_plan(row)
logger.info(
"views.save_uploaded_plans_for_template() index=%d; errorMsg=%s; planDict=%s"
% (index, errorMsg, rawPlanDict))
if errorMsg:
logger.info(
"views.save_uploaded_plans_for_template() ERROR MESSAGE index=%d; errorMsg=%s; planDict=%s"
% (index, errorMsg, rawPlanDict))
failed[index] = errorMsg
continue
elif isToSkipRow:
logger.info(
"views.save_uploaded_plans_for_template() SKIPPED ROW index=%d; row=%s"
% (index, row))
continue
else:
plans.append(aPlanDict)
rawPlanDataList.append(rawPlanDict)
destination.close() # now close and remove the temp file
os.unlink(destination.name)
if index == 0:
transaction.rollback()
return HttpResponse(json.dumps({
"status":
"Error: There must be at least one plan! Please reload the page and try again with more plans."
}),
mimetype="text/html")
if failed:
r = {
"status": "Plan validation failed. The plans have not been saved.",
"failed": failed
}
logger.info("views.save_uploaded_plans_for_template() failed=%s" % (r))
transaction.rollback()
return HttpResponse(json.dumps(r), mimetype="text/html")
#saving to db needs to be the last thing to happen
try:
index = 0
for planFamily in plans:
plan = planFamily['plan']
plan.save()
expObj = planFamily['exp']
expObj.plan = plan
expObj.expName = plan.planGUID
expObj.unique = plan.planGUID
expObj.displayname = plan.planGUID
expObj.save()
easObj = planFamily['eas']
easObj.experiment = expObj
easObj.isEditable = True
easObj.save()
#saving/associating samples
sampleDisplayedNames = planFamily['samples']
sampleNames = [
name.replace(' ', '_') for name in sampleDisplayedNames
]
externalId = None
for name, displayedName in zip(sampleNames, sampleDisplayedNames):
sample_kwargs = {
'name': name,
'displayedName': displayedName,
'date': plan.date,
'status': plan.planStatus,
'externalId': externalId
}
sample = Sample.objects.get_or_create(
name=name, externalId=externalId,
defaults=sample_kwargs)[0]
sample.experiments.add(expObj)
sample.save()
planDict = rawPlanDataList[index]
# add QCtype thresholds
qcTypes = QCType.objects.all()
for qcType in qcTypes:
qc_threshold = planDict.get(qcType.qcName, '')
if qc_threshold:
# get existing PlannedExperimentQC if any
plannedExpQcs = PlannedExperimentQC.objects.filter(
plannedExperiment=plan.id, qcType=qcType.id)
if len(plannedExpQcs) > 0:
for plannedExpQc in plannedExpQcs:
plannedExpQc.threshold = qc_threshold
plannedExpQc.save()
else:
kwargs = {
'plannedExperiment': plan,
'qcType': qcType,
'threshold': qc_threshold
}
plannedExpQc = PlannedExperimentQC(**kwargs)
plannedExpQc.save()
# add projects
projectObjList = get_projects(request.user, planDict)
for project in projectObjList:
if project:
plan.projects.add(project)
index += 1
except:
logger.exception(format_exc())
transaction.rollback()
return HttpResponse(json.dumps(
{"status": "Error saving plans to database!"}),
mimetype="text/html")
##return HttpResponse(json.dumps({"error": "Internal error while trying to save the plan."}), mimetype="application/json")
else:
transaction.commit()
r = {
"status":
"Plans Uploaded! The plans will be listed on the planned run page.",
"failed": failed
}
return HttpResponse(json.dumps(r), mimetype="text/html")
def save_uploaded_plans_for_template(request):
"""add plans, with CSV validation"""
logger.info(request)
if request.method != 'POST':
logger.exception(format_exc())
transaction.rollback()
return HttpResponse(json.dumps({"error": "Error, unsupported HTTP Request method (%s) for saving plan upload." % request.method}), mimetype="application/json")
postedfile = request.FILES['postedfile']
destination = tempfile.NamedTemporaryFile(delete=False)
for chunk in postedfile.chunks():
destination.write(chunk)
postedfile.close()
destination.close()
#check to ensure it is not empty
headerCheck = open(destination.name, "rU")
firstCSV = []
for firstRow in csv.reader(headerCheck):
firstCSV.append(firstRow)
#logger.info("views.save_uploaded_plans_for_template() firstRow=%s;" %(firstRow))
headerCheck.close()
if not firstRow:
os.unlink(destination.name)
transaction.rollback()
return HttpResponse(json.dumps({"status": "Error: batch planning file is empty"}), mimetype="text/html")
index = 0
plans = []
rawPlanDataList = []
failed = {}
file = open(destination.name, "rU")
reader = csv.DictReader(file)
for index, row in enumerate(reader, start=1):
errorMsg, aPlanDict, rawPlanDict, isToSkipRow = validate_csv_plan(row)
logger.info("views.save_uploaded_plans_for_template() index=%d; errorMsg=%s; planDict=%s" %(index, errorMsg, rawPlanDict))
if errorMsg:
logger.info("views.save_uploaded_plans_for_template() ERROR MESSAGE index=%d; errorMsg=%s; planDict=%s" %(index, errorMsg, rawPlanDict))
failed[index] = errorMsg
continue
elif isToSkipRow:
logger.info("views.save_uploaded_plans_for_template() SKIPPED ROW index=%d; row=%s" %(index, row))
continue
else:
plans.append(aPlanDict)
rawPlanDataList.append(rawPlanDict)
destination.close() # now close and remove the temp file
os.unlink(destination.name)
if index == 0:
transaction.rollback()
return HttpResponse(json.dumps({"status": "Error: There must be at least one plan! Please reload the page and try again with more plans."}), mimetype="text/html")
if failed:
r = {"status": "Plan validation failed. The plans have not been saved.", "failed": failed}
logger.info("views.save_uploaded_plans_for_template() failed=%s" %(r))
transaction.rollback()
return HttpResponse(json.dumps(r), mimetype="text/html")
#saving to db needs to be the last thing to happen
try:
index = 0
for planFamily in plans:
plan = planFamily['plan']
plan.save()
expObj = planFamily['exp']
expObj.plan = plan
expObj.expName = plan.planGUID
expObj.unique = plan.planGUID
expObj.displayname = plan.planGUID
expObj.save()
easObj = planFamily['eas']
easObj.experiment = expObj
easObj.isEditable = True
easObj.save()
#saving/associating samples
sampleDisplayedNames = planFamily['samples']
sampleNames = [name.replace(' ', '_') for name in sampleDisplayedNames]
externalId = None
for name, displayedName in zip(sampleNames, sampleDisplayedNames):
sample_kwargs = {
'name' : name,
'displayedName' : displayedName,
'date' : plan.date,
'status' : plan.planStatus,
'externalId': externalId
}
sample = Sample.objects.get_or_create(name=name, externalId=externalId, defaults=sample_kwargs)[0]
sample.experiments.add(expObj)
sample.save()
planDict = rawPlanDataList[index]
# add QCtype thresholds
qcTypes = QCType.objects.all()
for qcType in qcTypes:
qc_threshold = planDict.get(qcType.qcName, '')
if qc_threshold:
# get existing PlannedExperimentQC if any
plannedExpQcs = PlannedExperimentQC.objects.filter(plannedExperiment=plan.id, qcType=qcType.id)
if len(plannedExpQcs) > 0:
for plannedExpQc in plannedExpQcs:
plannedExpQc.threshold = qc_threshold
plannedExpQc.save()
else:
kwargs = {
'plannedExperiment': plan,
'qcType': qcType,
'threshold': qc_threshold
}
plannedExpQc = PlannedExperimentQC(**kwargs)
plannedExpQc.save()
# add projects
projectObjList = get_projects(request.user, planDict)
for project in projectObjList:
if project:
plan.projects.add(project)
index += 1
except:
logger.exception(format_exc())
transaction.rollback()
return HttpResponse(json.dumps({"status": "Error saving plans to database!"}), mimetype="text/html")
##return HttpResponse(json.dumps({"error": "Internal error while trying to save the plan."}), mimetype="application/json")
else:
transaction.commit()
r = {"status": "Plans Uploaded! The plans will be listed on the planned run page.", "failed": failed}
return HttpResponse(json.dumps(r), mimetype="text/html")
