def _get_chiptype_json(request, chipType, plan):
chipResource = ChipResource()
chipResource_serialize_json = None
if chipType:
try:
try:
chip = chipResource.obj_get(name=chipType)
except Chip.DoesNotExist:
chip = chipResource.obj_get(name=chipType[:3])
chipResource_bundle = chipResource.build_bundle(obj=chip,
request=request)
chipResource_serialize_json = chipResource.serialize(
None, chipResource.full_dehydrate(chipResource_bundle),
'application/json')
except Chip.DoesNotExist:
logger.error(
"views._get_chiptype_json() Plan.pk=%d; name=%s has invalid chip type=%s"
% (plan.id, plan.planName, chipType))
chipResource_bundle = None
chipResource_serialize_json = json.dumps("INVALID")
else:
chipResource_bundle = None
chipResource_serialize_json = json.dumps(None)
return chipResource_serialize_json
def _get_chiptype_json(request, chipType):
chipResource = ChipResource()
chipResource_serialize_json = None
if chipType:
chip = chipResource.obj_get(name=chipType)
chipResource_bundle = chipResource.build_bundle(obj=chip,
request=request)
chipResource_serialize_json = chipResource.serialize(
None, chipResource.full_dehydrate(chipResource_bundle),
'application/json')
else:
chipResource_bundle = None
chipResource_serialize_json = json.dumps(None)
return chipResource_serialize_json
def _get_chiptype_json(request, chipType, plan):
chipResource = ChipResource()
chipResource_serialize_json = None
if chipType:
try:
try:
chip = chipResource.obj_get(name = chipType)
except Chip.DoesNotExist:
chip = chipResource.obj_get(name = chipType[:3])
chipResource_bundle = chipResource.build_bundle(obj=chip, request=request)
chipResource_serialize_json = chipResource.serialize(None, chipResource.full_dehydrate(chipResource_bundle), 'application/json')
except Chip.DoesNotExist:
logger.error("views._get_chiptype_json() Plan.pk=%d; name=%s has invalid chip type=%s" %(plan.id, plan.planName, chipType))
chipResource_bundle = None
chipResource_serialize_json = json.dumps("INVALID")
else:
chipResource_bundle = None
chipResource_serialize_json = json.dumps(None)
return chipResource_serialize_json
def _plan_template_helper(request, _id, isForTemplate, intent):
data = _get_allApplProduct_data(isForTemplate)
planTemplate = get_object_or_404(PlannedExperiment, pk=_id)
runType = get_object_or_404(RunType, runType=planTemplate.runType)
# add experiment attributes
experiment = planTemplate.experiment
exp_keys = [
('autoAnalyze', 'autoAnalyze'),
('flows', 'flows'),
('notes', 'notes'),
('sequencekitname', 'sequencekitname'),
]
for plankey, key in exp_keys:
setattr(planTemplate, plankey, getattr(experiment, key, ''))
chipResource = ChipResource()
try:
chip = chipResource.obj_get(name=experiment.chipType)
if chip:
setattr(planTemplate, "chipType", experiment.chipType)
except Chip.DoesNotExist:
try:
chip = chipResource.obj_get(name=experiment.chipType[:3])
if chip:
setattr(planTemplate, "chipType", experiment.chipType[:3])
except Chip.DoesNotExist:
setattr(planTemplate, "chipType", experiment.chipType)
setattr(planTemplate, "sample", experiment.get_sample())
setattr(planTemplate, "sampleDisplayedName",
experiment.get_sampleDisplayedName())
setattr(planTemplate, "isIonChef", planTemplate.is_ionChef())
# add EAS attributes
if experiment:
eas = experiment.get_EAS()
else:
eas = None
eas_keys = [('barcodedSamples', 'barcodedSamples'),
('barcodeId', 'barcodeKitName'),
('bedfile', 'targetRegionBedFile'),
('forward3primeadapter', 'threePrimeAdapter'),
('libraryKey', 'libraryKey'),
('librarykitname', 'libraryKitName'),
('regionfile', 'hotSpotRegionBedFile'),
('selectedPlugins', 'selectedPlugins')]
for plankey, key in eas_keys:
setattr(planTemplate, plankey, getattr(eas, key, ''))
if eas:
setattr(planTemplate, "library",
eas.reference if eas.reference != "none" else '')
else:
setattr(planTemplate, "library", "")
chipTypeDetails = None
if planTemplate.chipType:
chipTypeDetails = get_object_or_404(Chip, name=planTemplate.chipType)
selectedProjectNames = [
selectedProject.name
for selectedProject in list(planTemplate.projects.all())
]
logger.debug("views._plan_template_helper selectedProjectNames=%s" %
selectedProjectNames)
# mark plugins selected if any
for plugin in data['plugins']:
if plugin.name in planTemplate.selectedPlugins.keys():
plugin.selected = True
plugin.userInput = json.dumps(
planTemplate.selectedPlugins[plugin.name].get(
'userInput', None))
else:
plugin.selected = False
# mark uploaders selected if any
for plugin in data['uploaders']:
if plugin.name in planTemplate.selectedPlugins.keys():
plugin.selected = True
##in case we're copying old plans that have dict {} data type for userInput. new format is list of dict [{}]
userInput = planTemplate.selectedPlugins[plugin.name].get(
'userInput', None)
plugin.userInput = json.dumps(userInput)
if (isinstance(userInput, dict)):
plugin.userInput = json.dumps([userInput])
if 'IonReporter' in plugin.name:
data['irConfigSaved'] = plugin.userInput
data[
'irConfigSaved_version'] = 1.0 if plugin.name == 'IonReporterUploader_V1_0' else plugin.version
else:
plugin.selected = False
#planTemplateData contains what are available for selection
#and what each application product's characteristics and default selection
ctxd = {
"intent": intent,
"planTemplateData": data,
"selectedApplProductData": "",
"selectedPlanTemplate": planTemplate,
"selectedRunType": runType,
"selectedProjectNames": selectedProjectNames,
"selectedChipTypeDetails": chipTypeDetails
}
context = RequestContext(request, ctxd)
return context
def _plan_template_helper(request, _id, isForTemplate, intent):
data = _get_allApplProduct_data(isForTemplate)
planTemplate = get_object_or_404(PlannedExperiment, pk=_id)
runType = get_object_or_404(RunType, runType=planTemplate.runType)
# add experiment attributes
experiment = planTemplate.experiment
exp_keys = [
('autoAnalyze', 'autoAnalyze'),
('flows', 'flows'),
('notes', 'notes'),
('sequencekitname', 'sequencekitname'),
]
for plankey, key in exp_keys:
setattr(planTemplate, plankey, getattr(experiment,key,''))
chipResource = ChipResource()
try:
chip = chipResource.obj_get(name = experiment.chipType)
if chip:
setattr(planTemplate, "chipType", experiment.chipType)
except Chip.DoesNotExist:
try:
chip = chipResource.obj_get(name = experiment.chipType[:3])
if chip:
setattr(planTemplate, "chipType", experiment.chipType[:3])
except Chip.DoesNotExist:
setattr(planTemplate, "chipType", experiment.chipType)
setattr(planTemplate, "sample", experiment.get_sample())
setattr(planTemplate, "sampleDisplayedName", experiment.get_sampleDisplayedName())
setattr(planTemplate, "isIonChef", planTemplate.is_ionChef())
# add EAS attributes
if experiment:
eas = experiment.get_EAS()
else:
eas = None
eas_keys = [
('barcodedSamples', 'barcodedSamples'),
('barcodeId', 'barcodeKitName'),
('bedfile', 'targetRegionBedFile'),
('forward3primeadapter', 'threePrimeAdapter'),
('libraryKey', 'libraryKey'),
('librarykitname', 'libraryKitName'),
('regionfile', 'hotSpotRegionBedFile'),
('selectedPlugins', 'selectedPlugins')
]
for plankey, key in eas_keys:
setattr(planTemplate, plankey, getattr(eas,key,''))
if eas:
setattr(planTemplate, "library", eas.reference if eas.reference != "none" else '')
else:
setattr(planTemplate, "library", "")
chipTypeDetails = None
if planTemplate.chipType:
chipTypeDetails = get_object_or_404(Chip, name=planTemplate.chipType)
selectedProjectNames = [selectedProject.name for selectedProject in list(planTemplate.projects.all())]
logger.debug("views._plan_template_helper selectedProjectNames=%s" % selectedProjectNames)
# mark plugins selected if any
for plugin in data['plugins']:
if plugin.name in planTemplate.selectedPlugins.keys():
plugin.selected = True
plugin.userInput = json.dumps(planTemplate.selectedPlugins[plugin.name].get('userInput',None))
else:
plugin.selected = False
# mark uploaders selected if any
for plugin in data['uploaders']:
if plugin.name in planTemplate.selectedPlugins.keys():
plugin.selected = True
##in case we're copying old plans that have dict {} data type for userInput. new format is list of dict [{}]
userInput = planTemplate.selectedPlugins[plugin.name].get('userInput',None)
plugin.userInput = json.dumps(userInput)
if (isinstance(userInput, dict)):
plugin.userInput = json.dumps([userInput])
if 'IonReporter' in plugin.name:
data['irConfigSaved'] = plugin.userInput
data['irConfigSaved_version'] = 1.0 if plugin.name == 'IonReporterUploader_V1_0' else plugin.version
else:
plugin.selected = False
#planTemplateData contains what are available for selection
#and what each application product's characteristics and default selection
ctxd = {
"intent": intent,
"planTemplateData": data,
"selectedApplProductData": "",
"selectedPlanTemplate": planTemplate,
"selectedRunType": runType,
"selectedProjectNames": selectedProjectNames,
"selectedChipTypeDetails": chipTypeDetails
}
context = RequestContext(request, ctxd)
return context
