def get_ampliseq_designs(user, password, pipeline, ctx):
response, designs = _get_all_ampliseq_designs(user, password)
if designs:
ctx['unordered_solutions'] = []
ctx['ordered_solutions'] = []
unordered_tmpList = []
ordered_tmpList = []
for design in designs:
for template in design.get('DesignSolutions', []):
ampliSeq = AmpliSeqPanelImport(data=template)
solution, meta = ampliSeq.handle_versioned_plans()
solution_id = solution['id']
configurationChoices = solution['configuration_choices']
if match(solution, pipeline):
if solution.get('ordered', False):
ctx['ordered_solutions'].append((design, solution))
ordered_tmpList.append({
'configuration_choices': configurationChoices,
'id': solution_id
})
else:
ctx['unordered_solutions'].append((design, solution))
unordered_tmpList.append({
'configuration_choices': configurationChoices,
'id': solution_id
})
unordered_tmpList = convert(unordered_tmpList)
ordered_tmpList = convert(ordered_tmpList)
ctx['unordered_solution'] = json.dumps(unordered_tmpList)
ctx['ordered_solution'] = json.dumps(ordered_tmpList)
return response, ctx
else:
return response, {}
def get_ampliseq_designs(user, password, pipeline, ctx):
http = httplib2.Http(disable_ssl_certificate_validation=settings.DEBUG)
http.add_credentials(user, password)
url = urlparse.urljoin(settings.AMPLISEQ_URL, "ws/design/list")
response, content = http.request(url)
if response['status'] == '200':
design_data = json.loads(content)
designs = design_data.get('AssayDesigns', [])
ctx['unordered_solutions'] = []
ctx['ordered_solutions'] = []
unordered_tmpList = []
ordered_tmpList = []
for design in designs:
for template in design.get('DesignSolutions', []):
ampliSeq = AmpliSeqPanelImport(data=template)
solution, meta = ampliSeq.handle_versioned_plans()
solution_id = solution['id']
configurationChoices = solution['configuration_choices']
if match(solution, pipeline):
if solution.get('ordered', False):
ctx['ordered_solutions'].append((design, solution))
ordered_tmpList.append({'configuration_choices': configurationChoices, 'id': solution_id})
else:
ctx['unordered_solutions'].append((design, solution))
unordered_tmpList.append({'configuration_choices': configurationChoices, 'id': solution_id})
unordered_tmpList = convert(unordered_tmpList)
ordered_tmpList = convert(ordered_tmpList)
ctx['unordered_solution'] = json.dumps(unordered_tmpList)
ctx['ordered_solution'] = json.dumps(ordered_tmpList)
return response, ctx
else:
return response, {}
def get_ampliseq_designs(user, password, pipeline, ctx):
response, designs = _get_all_ampliseq_designs(user, password)
if designs:
ctx['unordered_solutions'] = []
ctx['ordered_solutions'] = []
unordered_tmpList = []
ordered_tmpList = []
for design in designs:
for template in design.get('DesignSolutions', []):
ampliSeq = AmpliSeqPanelImport(data=template)
solution, meta = ampliSeq.handle_versioned_plans()
solution_id = solution['id']
configurationChoices = solution['configuration_choices']
if match(solution, pipeline):
if solution.get('ordered', False):
ctx['ordered_solutions'].append((design, solution))
ordered_tmpList.append({'configuration_choices': configurationChoices, 'id': solution_id})
else:
ctx['unordered_solutions'].append((design, solution))
unordered_tmpList.append({'configuration_choices': configurationChoices, 'id': solution_id})
unordered_tmpList = convert(unordered_tmpList)
ordered_tmpList = convert(ordered_tmpList)
ctx['unordered_solution'] = json.dumps(unordered_tmpList)
ctx['ordered_solution'] = json.dumps(ordered_tmpList)
return response, ctx
else:
return response, {}
def validateStep(self):
self.validationErrors.pop(SavePlanFieldNames.NO_BARCODE, None)
self.validationErrors.pop(SavePlanFieldNames.BAD_BARCODES, None)
samplesTable = json.loads(
self.savedFields[SavePlanFieldNames.SAMPLES_TABLE])
barcodeSet = self.savedFields[SavePlanFieldNames.BARCODE_SET]
selectedBarcodes = []
endBarcodeSet = self.savedFields[SavePlanFieldNames.END_BARCODE_SET]
selectedEndBarcodes = []
for row in samplesTable:
sample_name = row.get(SavePlanFieldNames.SAMPLE_NAME, '').strip()
if sample_name:
if barcodeSet:
selectedBarcodes.append(
row.get(SavePlanFieldNames.
BARCODE_SAMPLE_BARCODE_ID_UI_KEY))
if endBarcodeSet:
endBarcode_id_value = row.get(
SavePlanFieldNames.
BARCODE_SAMPLE_END_BARCODE_ID_UI_KEY)
if endBarcode_id_value:
selectedEndBarcodes.append(endBarcode_id_value)
if barcodeSet:
errors = validate_barcode_sample_association(
selectedBarcodes, barcodeSet)
myErrors = convert(errors)
if myErrors.get("MISSING_BARCODE", ""):
self.validationErrors[
SavePlanFieldNames.NO_BARCODE] = myErrors.get(
"MISSING_BARCODE", "")
if myErrors.get("DUPLICATE_BARCODE", ""):
self.validationErrors[
SavePlanFieldNames.BAD_BARCODES] = myErrors.get(
"DUPLICATE_BARCODE", "")
if selectedEndBarcodes:
applProduct = self.savedObjects[SavePlanFieldNames.APPL_PRODUCT]
if applProduct and applProduct.dualBarcodingRule == "no_reuse":
errors = validate_barcode_sample_association(
selectedEndBarcodes,
endBarcodeSet,
isEndBarcodeExists=True)
myErrors = convert(errors)
if myErrors.get("DUPLICATE_BARCODE", ""):
self.validationErrors[
SavePlanFieldNames.BAD_BARCODES] = myErrors.get(
"DUPLICATE_BARCODE", "")
self.prepopulatedFields[SavePlanFieldNames.FIRE_VALIDATION] = "0"
def validateStep(self):
self.validationErrors.pop(SavePlanFieldNames.NO_BARCODE,None)
self.validationErrors.pop(SavePlanFieldNames.BAD_BARCODES,None)
samplesTable = json.loads(self.savedFields[SavePlanFieldNames.SAMPLES_TABLE])
barcodeSet = self.savedFields[SavePlanFieldNames.BARCODE_SET]
selectedBarcodes = []
for row in samplesTable:
sample_name = row.get(SavePlanFieldNames.SAMPLE_NAME,'').strip()
if sample_name:
if barcodeSet:
selectedBarcodes.append(row.get('barcodeId'))
if barcodeSet:
errors = validate_barcode_sample_association(selectedBarcodes, barcodeSet)
myErrors = convert(errors)
if myErrors.get("MISSING_BARCODE", ""):
self.validationErrors[SavePlanFieldNames.NO_BARCODE] = myErrors.get("MISSING_BARCODE", "")
if myErrors.get("DUPLICATE_BARCODE", ""):
self.validationErrors[SavePlanFieldNames.BAD_BARCODES] = myErrors.get("DUPLICATE_BARCODE", "")
self.prepopulatedFields[SavePlanFieldNames.FIRE_VALIDATION] = "0"
def validateStep(self):
self.validationErrors.pop(SavePlanFieldNames.NO_BARCODE, None)
self.validationErrors.pop(SavePlanFieldNames.BAD_BARCODES, None)
samplesTable = json.loads(self.savedFields[SavePlanFieldNames.SAMPLES_TABLE])
barcodeSet = self.savedFields[SavePlanFieldNames.BARCODE_SET]
selectedBarcodes = []
for row in samplesTable:
sample_name = row.get(SavePlanFieldNames.SAMPLE_NAME, '').strip()
if sample_name:
if barcodeSet:
selectedBarcodes.append(row.get('barcodeId'))
if barcodeSet:
errors = validate_barcode_sample_association(selectedBarcodes, barcodeSet)
myErrors = convert(errors)
if myErrors.get("MISSING_BARCODE", ""):
self.validationErrors[SavePlanFieldNames.NO_BARCODE] = myErrors.get("MISSING_BARCODE", "")
if myErrors.get("DUPLICATE_BARCODE", ""):
self.validationErrors[SavePlanFieldNames.BAD_BARCODES] = myErrors.get("DUPLICATE_BARCODE", "")
self.prepopulatedFields[SavePlanFieldNames.FIRE_VALIDATION] = "0"
def validateStep(self):
self.validationErrors.pop(SavePlanFieldNames.NO_BARCODE, None)
self.validationErrors.pop(SavePlanFieldNames.BAD_BARCODES, None)
samplesTable = json.loads(self.savedFields[SavePlanFieldNames.SAMPLES_TABLE])
barcodeSet = self.savedFields[SavePlanFieldNames.BARCODE_SET]
selectedBarcodes = []
endBarcodeSet = self.savedFields[SavePlanFieldNames.END_BARCODE_SET]
selectedEndBarcodes = []
for row in samplesTable:
sample_name = row.get(SavePlanFieldNames.SAMPLE_NAME, '').strip()
if sample_name:
if barcodeSet:
selectedBarcodes.append(row.get(SavePlanFieldNames.BARCODE_SAMPLE_BARCODE_ID_UI_KEY))
if endBarcodeSet:
endBarcode_id_value = row.get(SavePlanFieldNames.BARCODE_SAMPLE_END_BARCODE_ID_UI_KEY)
if endBarcode_id_value:
selectedEndBarcodes.append(endBarcode_id_value)
if barcodeSet:
errors = validate_barcode_sample_association(selectedBarcodes, barcodeSet)
myErrors = convert(errors)
if myErrors.get("MISSING_BARCODE", ""):
self.validationErrors[SavePlanFieldNames.NO_BARCODE] = myErrors.get("MISSING_BARCODE", "")
if myErrors.get("DUPLICATE_BARCODE", ""):
self.validationErrors[SavePlanFieldNames.BAD_BARCODES] = myErrors.get("DUPLICATE_BARCODE", "")
if selectedEndBarcodes:
applProduct = self.savedObjects[SavePlanFieldNames.APPL_PRODUCT]
if applProduct and applProduct.dualBarcodingRule == "no_reuse":
errors = validate_barcode_sample_association(selectedEndBarcodes, endBarcodeSet, isEndBarcodeExists = True)
myErrors = convert(errors)
if myErrors.get("DUPLICATE_BARCODE", ""):
self.validationErrors[SavePlanFieldNames.BAD_BARCODES] = myErrors.get("DUPLICATE_BARCODE", "")
self.prepopulatedFields[SavePlanFieldNames.FIRE_VALIDATION] = "0"
def get_ampliseq_designs(user, password, pipeline, ctx):
http = httplib2.Http(disable_ssl_certificate_validation=settings.DEBUG)
http.add_credentials(user, password)
url = urlparse.urljoin(settings.AMPLISEQ_URL, "ws/design/list")
response, content = http.request(url)
if response['status'] == '200':
design_data = json.loads(content)
designs = design_data.get('AssayDesigns', [])
ctx['unordered_solutions'] = []
ctx['ordered_solutions'] = []
unordered_tmpList = []
ordered_tmpList = []
for design in designs:
for template in design.get('DesignSolutions', []):
ampliSeq = AmpliSeqPanelImport(data=template)
solution, meta = ampliSeq.handle_versioned_plans()
solution_id = solution['id']
configurationChoices = solution['configuration_choices']
if match(solution, pipeline):
if solution.get('ordered', False):
ctx['ordered_solutions'].append((design, solution))
ordered_tmpList.append({
'configuration_choices': configurationChoices,
'id': solution_id
})
else:
ctx['unordered_solutions'].append((design, solution))
unordered_tmpList.append({
'configuration_choices': configurationChoices,
'id': solution_id
})
unordered_tmpList = convert(unordered_tmpList)
ordered_tmpList = convert(ordered_tmpList)
ctx['unordered_solution'] = json.dumps(unordered_tmpList)
ctx['ordered_solution'] = json.dumps(ordered_tmpList)
return response, ctx
else:
return response, {}
def get_fixed_designs_list(fixed_design_data, pipeline):
# creates fixed_solutions: a list of dictionaries with :
# Design id : Ready-to-Use ampliseq panel ID
# configuration_choices : the instrument/chip types supported by the corresponding panel.
# Type : Community or Fixed Panel - used to to link to Ampliseq website
# Genome : Supported genome by the specific panel.
# final_fixed_soln_data : #Lists all the design panels available for the specific pipeline
# fixed_ids_choices : This is used to compare the parametized files available and show the warnings
fixed = []
fixedDesigns = fixed_design_data.get('TemplateDesigns', [])
for template in fixedDesigns:
ampliSeq = AmpliSeqPanelImport(data=template)
data, meta = ampliSeq.handle_versioned_plans()
fixed.append(data)
if fixed:
ordered_solutions = []
tmpList = []
tmpFixedsolLists = []
fixed_solutions = filter(
lambda x: x['status'] == "ORDERABLE" and match(x, pipeline), fixed)
for design in fixed_solutions:
designID = design['id']
configurationChoices = design['configuration_choices']
tmpDict = {
'id': designID,
'configuration_choices': configurationChoices
}
tmpFixedSolDict = {
'id': designID,
'genome': design['genome'],
"name": design["name"],
"type": design["type"],
}
tmpList.append(tmpDict)
tmpFixedsolLists.append(tmpFixedSolDict)
#This is used to compare the parametized files available and show the warnings
fixed_ids_choices = json.dumps(convert(tmpList))
#Lists all the design panels available for the specific pipeline
final_fixed_soln_data = tmpFixedsolLists
return final_fixed_soln_data, ordered_solutions, fixed_ids_choices
def get_fixed_designs_list(fixed_design_data, pipeline):
# creates fixed_solutions: a list of dictionaries with :
# Design id : Ready-to-Use ampliseq panel ID
# configuration_choices : the instrument/chip types supported by the corresponding panel.
# Type : Community or Fixed Panel - used to to link to Ampliseq website
# Genome : Supported genome by the specific panel.
# final_fixed_soln_data : #Lists all the design panels available for the specific pipeline
# fixed_ids_choices : This is used to compare the parametized files available and show the warnings
fixed = []
fixedDesigns = fixed_design_data.get('TemplateDesigns', [])
for template in fixedDesigns:
ampliSeq = AmpliSeqPanelImport(data=template)
data, meta = ampliSeq.handle_versioned_plans()
fixed.append(data)
if fixed:
ordered_solutions = []
tmpList = []
tmpFixedsolLists = []
fixed_solutions = filter(lambda x: x['status'] == "ORDERABLE" and match(x, pipeline), fixed)
for design in fixed_solutions:
designID = design['id']
configurationChoices = design['configuration_choices']
tmpDict = {'id': designID,
'configuration_choices': configurationChoices}
tmpFixedSolDict = {'id': designID,
'genome': design['genome'],
"name" : design["name"],
"type" : design["type"],
}
tmpList.append(tmpDict)
tmpFixedsolLists.append(tmpFixedSolDict)
#This is used to compare the parametized files available and show the warnings
fixed_ids_choices = json.dumps(convert(tmpList))
#Lists all the design panels available for the specific pipeline
final_fixed_soln_data = tmpFixedsolLists
return final_fixed_soln_data, ordered_solutions, fixed_ids_choices
def updateSavedFieldsForSamples_retired(self):
#logger.debug("ENTER barcode_by_sample_step_data.updateSavedFieldsForSamples() self.savedFields[SavePlanFieldNames.BARCODE_SET]=%s" %(self.savedFields[SavePlanFieldNames.BARCODE_SET]))
#convert tuple to string
planReference = str(self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE])
planHotSpotRegionBedFile = str(self.prepopulatedFields[SavePlanFieldNames.PLAN_HOTSPOT_REGION_BED_FILE])
planTargetRegionBedFile = str(self.prepopulatedFields[SavePlanFieldNames.PLAN_TARGET_REGION_BED_FILE])
#logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() type(self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE])=%s; self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE]=%s" %(type(self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE]), self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE]))
hasAnyChanges = False
myTable = json.loads(self.savedFields[SavePlanFieldNames.SAMPLES_TABLE])
#convert unicode to str
myTable = convert(myTable)
for index, row in enumerate(myTable):
#logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() B4 CHANGES... BARCODE_SET LOOP row=%s" %(row))
sample_name = row.get(SavePlanFieldNames.SAMPLE_NAME,'').strip()
if sample_name:
sample_nucleotideType = row.get(SavePlanFieldNames.BARCODE_SAMPLE_NUCLEOTIDE_TYPE, "")
sampleReference = row.get(SavePlanFieldNames.BARCODE_SAMPLE_REFERENCE, "")
sampleHotSpotRegionBedFile = row.get(SavePlanFieldNames.BARCODE_SAMPLE_HOTSPOT_REGION_BED_FILE, "")
sampleTargetRegionBedFile = row.get(SavePlanFieldNames.BARCODE_SAMPLE_TARGET_REGION_BED_FILE, "")
runType = self.prepopulatedFields[SavePlanFieldNames.RUN_TYPE]
if runType == "AMPS_DNA_RNA" and sample_nucleotideType == "RNA":
newSampleReference = sampleReference
newSampleHotSpotRegionBedFile = sampleHotSpotRegionBedFile
newSampleTargetRegionBedFile = sampleTargetRegionBedFile
else:
newSampleReference = planReference
newSampleHotSpotRegionBedFile = planHotSpotRegionBedFile
newSampleTargetRegionBedFile = planTargetRegionBedFile
#logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() BARCODE_SET LOOP planReference=%s; type(newSampleReference)=%s; newSampleReference=%s;" %(planReference, type(newSampleReference), newSampleReference))
#cascade the reference and BED file info to sample if none specified at the sample level
if runType != "AMPS_DNA_RNA":
if not sampleReference:
newSampleReference = planReference
newSampleHotSpotRegionBedFile = planHotSpotRegionBedFile
newSampleTargetRegionBedFile = planTargetRegionBedFile
hasChanged = False
if newSampleReference != sampleReference:
row[SavePlanFieldNames.BARCODE_SAMPLE_REFERENCE] = newSampleReference
hasChanged = True
if newSampleHotSpotRegionBedFile != sampleHotSpotRegionBedFile:
row[SavePlanFieldNames.BARCODE_SAMPLE_HOTSPOT_REGION_BED_FILE] = newSampleHotSpotRegionBedFile
hasChanged = True
if newSampleTargetRegionBedFile != sampleTargetRegionBedFile:
row[SavePlanFieldNames.BARCODE_SAMPLE_TARGET_REGION_BED_FILE] = newSampleTargetRegionBedFile
hasChanged = True
#logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() hasChanged=%s; row=%s" %(hasChanged, row))
if hasChanged:
myTable[index] = row
#logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() AFTER CHANGES BARCODE_SET LOOP myTable[index]=%s" %(myTable[index]))
hasAnyChanges = True
if hasAnyChanges:
#logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() hasAnyChanges AFTER CHANGES... type=%s; myTable=%s" %(type(myTable), myTable))
#convert list with single quotes to str with double quotes. Then convert it to be unicode
self.savedFields[SavePlanFieldNames.SAMPLES_TABLE] = unicode(json.dumps(myTable))
#logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() hasAnyChanges AFTER unicode(json.dumps)... type=%s; self.savedFields[samplesTable]=%s" %(type(self.savedFields[SavePlanFieldNames.SAMPLES_TABLE]), self.savedFields[SavePlanFieldNames.SAMPLES_TABLE]))
self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST] = json.loads(self.savedFields[SavePlanFieldNames.SAMPLES_TABLE])
self.updateSavedObjectsFromSavedFields()
def updateSavedFieldsForSamples_retired(self):
# logger.debug("ENTER barcode_by_sample_step_data.updateSavedFieldsForSamples() self.savedFields[SavePlanFieldNames.BARCODE_SET]=%s" %(self.savedFields[SavePlanFieldNames.BARCODE_SET]))
# convert tuple to string
planReference = str(self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE])
planHotSpotRegionBedFile = str(self.prepopulatedFields[SavePlanFieldNames.PLAN_HOTSPOT_REGION_BED_FILE])
planTargetRegionBedFile = str(self.prepopulatedFields[SavePlanFieldNames.PLAN_TARGET_REGION_BED_FILE])
# logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() type(self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE])=%s; self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE]=%s" %(type(self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE]), self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE]))
hasAnyChanges = False
myTable = json.loads(self.savedFields[SavePlanFieldNames.SAMPLES_TABLE])
# convert unicode to str
myTable = convert(myTable)
for index, row in enumerate(myTable):
# logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() B4 CHANGES... BARCODE_SET LOOP row=%s" %(row))
sample_name = row.get(SavePlanFieldNames.SAMPLE_NAME, '').strip()
if sample_name:
sample_nucleotideType = row.get(SavePlanFieldNames.BARCODE_SAMPLE_NUCLEOTIDE_TYPE, "")
sampleReference = row.get(SavePlanFieldNames.BARCODE_SAMPLE_REFERENCE, "")
sampleHotSpotRegionBedFile = row.get(SavePlanFieldNames.BARCODE_SAMPLE_HOTSPOT_REGION_BED_FILE, "")
sampleTargetRegionBedFile = row.get(SavePlanFieldNames.BARCODE_SAMPLE_TARGET_REGION_BED_FILE, "")
runType = self.prepopulatedFields[SavePlanFieldNames.RUN_TYPE]
if runType == "AMPS_DNA_RNA" and sample_nucleotideType == "RNA":
newSampleReference = sampleReference
newSampleHotSpotRegionBedFile = sampleHotSpotRegionBedFile
newSampleTargetRegionBedFile = sampleTargetRegionBedFile
else:
newSampleReference = planReference
newSampleHotSpotRegionBedFile = planHotSpotRegionBedFile
newSampleTargetRegionBedFile = planTargetRegionBedFile
# logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() BARCODE_SET LOOP planReference=%s; type(newSampleReference)=%s; newSampleReference=%s;" %(planReference, type(newSampleReference), newSampleReference))
# cascade the reference and BED file info to sample if none specified at the sample level
if runType != "AMPS_DNA_RNA":
if not sampleReference:
newSampleReference = planReference
newSampleHotSpotRegionBedFile = planHotSpotRegionBedFile
newSampleTargetRegionBedFile = planTargetRegionBedFile
hasChanged = False
if newSampleReference != sampleReference:
row[SavePlanFieldNames.BARCODE_SAMPLE_REFERENCE] = newSampleReference
hasChanged = True
if newSampleHotSpotRegionBedFile != sampleHotSpotRegionBedFile:
row[SavePlanFieldNames.BARCODE_SAMPLE_HOTSPOT_REGION_BED_FILE] = newSampleHotSpotRegionBedFile
hasChanged = True
if newSampleTargetRegionBedFile != sampleTargetRegionBedFile:
row[SavePlanFieldNames.BARCODE_SAMPLE_TARGET_REGION_BED_FILE] = newSampleTargetRegionBedFile
hasChanged = True
# logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() hasChanged=%s; row=%s" %(hasChanged, row))
if hasChanged:
myTable[index] = row
# logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() AFTER CHANGES BARCODE_SET LOOP myTable[index]=%s" %(myTable[index]))
hasAnyChanges = True
if hasAnyChanges:
# logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() hasAnyChanges AFTER CHANGES... type=%s; myTable=%s" %(type(myTable), myTable))
# convert list with single quotes to str with double quotes. Then convert it to be unicode
self.savedFields[SavePlanFieldNames.SAMPLES_TABLE] = unicode(json.dumps(myTable))
# logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() hasAnyChanges AFTER unicode(json.dumps)... type=%s; self.savedFields[samplesTable]=%s" %(type(self.savedFields[SavePlanFieldNames.SAMPLES_TABLE]), self.savedFields[SavePlanFieldNames.SAMPLES_TABLE]))
self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST] = json.loads(self.savedFields[SavePlanFieldNames.SAMPLES_TABLE])
self.updateSavedObjectsFromSavedFields()
def updateSavedFieldsForSamples_may_no_longer_needed(self):
# logger.debug("ENTER save_plan_step_data.updateSavedFieldsForSamples() B4 type=%s; self.savedFields[samplesTable]=%s" %(type(self.savedFields[SavePlanFieldNames.SAMPLES_TABLE]), self.savedFields[SavePlanFieldNames.SAMPLES_TABLE]))
# logger.debug("ENTER save_plan_step_data.updateSavedFieldsForSamples() B4 type=%s; self.savedObjects[samplesTableList]=%s" %(type(self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST]), self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST]))
# convert tuple to string
planReference = str(self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE])
planHotSptRegionBedFile = str(self.prepopulatedFields[SavePlanFieldNames.PLAN_HOTSPOT_REGION_BED_FILE])
planTargetRegionBedFile = str(self.prepopulatedFields[SavePlanFieldNames.PLAN_TARGET_REGION_BED_FILE])
# logger.debug("save_plan_step_data.updateSavedFieldsForSamples() type(planReference)=%s; planReference=%s" %(type(planReference), planReference))
# logger.debug("save_plan_step_data.updateSavedFieldsForSamples() type(self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE])=%s; self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE]=%s" %(type(self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE]), self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE]))
hasAnyChanges = False
myTable = json.loads(self.savedFields[SavePlanFieldNames.SAMPLES_TABLE])
# convert unicode to str
myTable = convert(myTable)
isCreate = self.sh_type in [StepHelperType.CREATE_NEW_PLAN, StepHelperType.CREATE_NEW_TEMPLATE]
# logger.debug("save_plan_step_data.updateSavedFieldsForSamples() isCreate()=%s" %(isCreate))
for index, row in enumerate(myTable):
# logger.debug("save_plan_step_data.updateSavedFieldsForSamples() B4 CHANGES... BARCODE_SET LOOP row=%s" %(row))
sample_name = row.get(SavePlanFieldNames.SAMPLE_NAME, '').strip()
if sample_name:
sample_nucleotideType = row.get(SavePlanFieldNames.BARCODE_SAMPLE_NUCLEOTIDE_TYPE, "")
sampleReference = row.get(SavePlanFieldNames.BARCODE_SAMPLE_REFERENCE, "")
sampleHotSpotRegionBedFile = row.get(SavePlanFieldNames.BARCODE_SAMPLE_HOTSPOT_REGION_BED_FILE, "")
sampleTargetRegionBedFile = row.get(SavePlanFieldNames.BARCODE_SAMPLE_TARGET_REGION_BED_FILE, "")
runType = self.prepopulatedFields[SavePlanFieldNames.RUN_TYPE]
if runType == "AMPS_DNA_RNA" and sample_nucleotideType == "RNA":
newSampleReference = sampleReference
newSampleHotspotRegionBedFile = sampleHotSpotRegionBedFile
newSampleTargetRegionBedFile = sampleTargetRegionBedFile
else:
if not sampleReference and self.savedObjects[SavePlanFieldNames.APPL_PRODUCT] and not self.savedObjects[SavePlanFieldNames.APPL_PRODUCT].isReferenceBySampleSupported and isCreate:
logger.debug("save_plan_step_data.updateSavedFieldsForSamples() GOING to set sampleReference to planReference... planReference=%s" % (planReference))
sampleReference = planReference
sampleHotSpotRegionBedFile = planHotSptRegionBedFile
sampleTargetRegionBedFile = planTargetRegionBedFile
# else:
# logger.debug("save_plan_step_data.updateSavedFieldsForSamples() SKIP SETTING sampleReference to planReference... isCreate=%s" %(isCreate))
newSampleReference = planReference
newSampleHotspotRegionBedFile = planHotSptRegionBedFile
newSampleTargetRegionBedFile = planTargetRegionBedFile
hasChanged = False
if newSampleReference != sampleReference:
row[SavePlanFieldNames.BARCODE_SAMPLE_REFERENCE] = newSampleReference
hasChanged = True
if newSampleHotspotRegionBedFile != sampleHotSpotRegionBedFile:
row[SavePlanFieldNames.BARCODE_SAMPLE_HOTSPOT_REGION_BED_FILE] = newSampleHotspotRegionBedFile
hasChanged = True
if newSampleTargetRegionBedFile != sampleTargetRegionBedFile:
row[SavePlanFieldNames.BARCODE_SAMPLE_TARGET_REGION_BED_FILE] = newSampleTargetRegionBedFile
hasChanged = True
if hasChanged:
myTable[index] = row
# logger.debug("save_plan_step_data.updateSavedFieldsForSamples() AFTER CHANGES BARCODE_SET LOOP myTable[index]=%s" %(myTable[index]))
hasAnyChanges = True
if hasAnyChanges:
logger.debug("save_plan_step_data.updateSavedFieldsForSamples() hasAnyChanges AFTER CHANGES... type=%s; myTable=%s" % (type(myTable), myTable))
# convert list with single quotes to str with double quotes. Then convert it to be unicode
self.savedFields[SavePlanFieldNames.SAMPLES_TABLE] = unicode(json.dumps(myTable))
# logger.debug("save_plan_step_data.updateSavedFieldsForSamples() hasAnyChanges AFTER unicode(json.dumps)... type=%s; self.savedFields[samplesTable]=%s" %(type(self.savedFields[SavePlanFieldNames.SAMPLES_TABLE]), self.savedFields[SavePlanFieldNames.SAMPLES_TABLE]))
self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST] = json.loads(self.savedFields[SavePlanFieldNames.SAMPLES_TABLE])
logger.debug("save_plan_step_data.updateSavedFieldsForSamples() hasAnyChanges AFTER json.loads... type=%s; self.savedObjects[samplesTableList]=%s" % (type(self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST]), self.savedObjects[SavePlanFieldNames.SAMPLES_TABLE_LIST]))
def validateStep(self):
any_samples = False
self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_NAME] = []
self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_EXTERNAL_ID] = []
self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_DESCRIPTION] = []
self.validationErrors[SavePlanFieldNames.BAD_TUBE_LABEL] = []
self.validationErrors[SavePlanFieldNames.BAD_CHIP_BARCODE] = []
self.validationErrors[SavePlanFieldNames.BAD_IR_SET_ID] = []
self.validationErrors.pop(SavePlanFieldNames.NO_BARCODE, None)
self.validationErrors.pop(SavePlanFieldNames.BAD_BARCODES, None)
barcodeSet = self.savedFields[SavePlanFieldNames.BARCODE_SET]
selectedBarcodes = []
endBarcodeSet = self.savedFields[SavePlanFieldNames.END_BARCODE_SET]
selectedEndBarcodes = []
samplesTable = json.loads(self.savedFields[SavePlanFieldNames.SAMPLES_TABLE])
# logger.debug("save_plan_step_data - anySamples? samplesTable=%s" %(samplesTable))
for row in samplesTable:
sample_name = row.get(SavePlanFieldNames.SAMPLE_NAME, '').strip()
# logger.debug("save_plan_step_data - anySamples? sampleName=%s" %(sample_name))
if sample_name:
any_samples = True
if validate_sample_name(sample_name):
self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_NAME].append(sample_name)
external_id = row.get(SavePlanFieldNames.SAMPLE_EXTERNAL_ID, '')
if external_id:
self.validate_field(external_id, self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_EXTERNAL_ID])
description = row.get(SavePlanFieldNames.SAMPLE_DESCRIPTION, '')
if description:
self.validate_field(description, self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_DESCRIPTION], False,
MAX_LENGTH_SAMPLE_DESCRIPTION)
ir_set_id = row.get('irSetId', '')
if ir_set_id and not (str(ir_set_id).isdigit()):
self.validationErrors[SavePlanFieldNames.BAD_IR_SET_ID].append(ir_set_id)
tube_label = row.get('tubeLabel', '')
if validate_sample_tube_label(tube_label):
self.validationErrors[SavePlanFieldNames.BAD_TUBE_LABEL].append(tube_label)
chip_barcode = row.get('chipBarcode', '')
if validate_chipBarcode(chip_barcode):
self.validationErrors[SavePlanFieldNames.BAD_CHIP_BARCODE].append(chip_barcode)
if barcodeSet:
selectedBarcodes.append(row.get(SavePlanFieldNames.BARCODE_SAMPLE_BARCODE_ID_UI_KEY))
if endBarcodeSet:
endBarcode_id_value = row.get(SavePlanFieldNames.BARCODE_SAMPLE_END_BARCODE_ID_UI_KEY)
if endBarcode_id_value:
selectedEndBarcodes.append(endBarcode_id_value)
if any_samples:
self.validationErrors.pop(SavePlanFieldNames.NO_SAMPLES, None)
else:
self.validationErrors[SavePlanFieldNames.NO_SAMPLES] = "You must enter at least one sample"
if not self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_NAME]:
self.validationErrors.pop(SavePlanFieldNames.BAD_SAMPLE_NAME, None)
if not self.validationErrors[SavePlanFieldNames.BAD_TUBE_LABEL]:
self.validationErrors.pop(SavePlanFieldNames.BAD_TUBE_LABEL, None)
if not self.validationErrors[SavePlanFieldNames.BAD_CHIP_BARCODE]:
self.validationErrors.pop(SavePlanFieldNames.BAD_CHIP_BARCODE, None)
if not self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_EXTERNAL_ID]:
self.validationErrors.pop(SavePlanFieldNames.BAD_SAMPLE_EXTERNAL_ID, None)
if not self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_DESCRIPTION]:
self.validationErrors.pop(SavePlanFieldNames.BAD_SAMPLE_DESCRIPTION, None)
if not self.validationErrors[SavePlanFieldNames.BAD_IR_SET_ID]:
self.validationErrors.pop(SavePlanFieldNames.BAD_IR_SET_ID, None)
#20170928-TODO-WIP
if barcodeSet:
errors = validate_barcode_sample_association(selectedBarcodes, barcodeSet)
myErrors = convert(errors)
if myErrors.get("MISSING_BARCODE", ""):
self.validationErrors[SavePlanFieldNames.NO_BARCODE] = myErrors.get("MISSING_BARCODE", "")
if myErrors.get("DUPLICATE_BARCODE", ""):
self.validationErrors[SavePlanFieldNames.BAD_BARCODES] = myErrors.get("DUPLICATE_BARCODE", "")
if selectedEndBarcodes:
applProduct = self.savedObjects[SavePlanFieldNames.APPL_PRODUCT]
if applProduct and applProduct.dualBarcodingRule == "no_reuse":
errors = validate_barcode_sample_association(selectedEndBarcodes, endBarcodeSet, isEndBarcodeExists = True)
myErrors = convert(errors)
if myErrors.get("DUPLICATE_BARCODE", ""):
self.validationErrors[SavePlanFieldNames.BAD_BARCODES] = myErrors.get("DUPLICATE_BARCODE", "")
def validateStep(self):
any_samples = False
self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_NAME] = []
self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_EXTERNAL_ID] = []
self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_DESCRIPTION] = []
self.validationErrors[SavePlanFieldNames.BAD_TUBE_LABEL] = []
self.validationErrors[SavePlanFieldNames.BAD_IR_SET_ID] = []
self.validationErrors.pop(SavePlanFieldNames.NO_BARCODE, None)
self.validationErrors.pop(SavePlanFieldNames.BAD_BARCODES, None)
barcodeSet = self.savedFields[SavePlanFieldNames.BARCODE_SET]
selectedBarcodes = []
samplesTable = json.loads(self.savedFields[SavePlanFieldNames.SAMPLES_TABLE])
# logger.debug("save_plan_step_data - anySamples? samplesTable=%s" %(samplesTable))
for row in samplesTable:
sample_name = row.get(SavePlanFieldNames.SAMPLE_NAME, "").strip()
# logger.debug("save_plan_step_data - anySamples? sampleName=%s" %(sample_name))
if sample_name:
any_samples = True
if validate_sample_name(sample_name):
self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_NAME].append(sample_name)
external_id = row.get(SavePlanFieldNames.SAMPLE_EXTERNAL_ID, "")
if external_id:
self.validate_field(external_id, self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_EXTERNAL_ID])
description = row.get(SavePlanFieldNames.SAMPLE_DESCRIPTION, "")
if description:
self.validate_field(
description,
self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_DESCRIPTION],
False,
MAX_LENGTH_SAMPLE_DESCRIPTION,
)
ir_set_id = row.get("irSetId", "")
if ir_set_id and not (str(ir_set_id).isdigit()):
self.validationErrors[SavePlanFieldNames.BAD_IR_SET_ID].append(ir_set_id)
tube_label = row.get("tubeLabel", "")
if validate_sample_tube_label(tube_label):
self.validationErrors[SavePlanFieldNames.BAD_TUBE_LABEL].append(tube_label)
if barcodeSet:
selectedBarcodes.append(row.get("barcodeId"))
if any_samples:
self.validationErrors.pop(SavePlanFieldNames.NO_SAMPLES, None)
else:
self.validationErrors[SavePlanFieldNames.NO_SAMPLES] = "You must enter at least one sample"
if not self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_NAME]:
self.validationErrors.pop(SavePlanFieldNames.BAD_SAMPLE_NAME, None)
if not self.validationErrors[SavePlanFieldNames.BAD_TUBE_LABEL]:
self.validationErrors.pop(SavePlanFieldNames.BAD_TUBE_LABEL, None)
if not self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_EXTERNAL_ID]:
self.validationErrors.pop(SavePlanFieldNames.BAD_SAMPLE_EXTERNAL_ID, None)
if not self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_DESCRIPTION]:
self.validationErrors.pop(SavePlanFieldNames.BAD_SAMPLE_DESCRIPTION, None)
if not self.validationErrors[SavePlanFieldNames.BAD_IR_SET_ID]:
self.validationErrors.pop(SavePlanFieldNames.BAD_IR_SET_ID, None)
if barcodeSet:
errors = validate_barcode_sample_association(selectedBarcodes, barcodeSet)
myErrors = convert(errors)
if myErrors.get("MISSING_BARCODE", ""):
self.validationErrors[SavePlanFieldNames.NO_BARCODE] = myErrors.get("MISSING_BARCODE", "")
if myErrors.get("DUPLICATE_BARCODE", ""):
self.validationErrors[SavePlanFieldNames.BAD_BARCODES] = myErrors.get("DUPLICATE_BARCODE", "")
def get_fixed_designs_list(fixed_design_data):
# creates fixed_solutions: a list of dictionaries with :
# Design id : Ready-to-Use ampliseq panel ID
# Type : Community or Fixed Panel - used to to link to Ampliseq website
# Genome : Supported genome by the specific panel.
# ChemistryType : Ampliseq or AmpliseqHD
# final_fixed_soln_data : #Lists all the design panels available for all the pipeline
# fixed_ids_choices : This is used to compare the parametized files available and show the warnings
fixed = []
chemistryType = "ampliseq"
ampliseq_url = settings.AMPLISEQ_URL
fixedDesigns = fixed_design_data.get("TemplateDesigns", [])
for template in fixedDesigns:
ampliSeq = AmpliSeqPanelImport(data=template)
data, meta = ampliSeq.handle_versioned_plans()
fixed.append(data)
if fixed:
ordered_solutions = []
tmpList = []
tmpFixedsolLists = []
fixed_solutions = filter(lambda x: x["status"] == "ORDERABLE", fixed)
for design in fixed_solutions:
designID = design["id"]
sourceUrl = design["resultsUri"]
configurationChoices = design["configuration_choices"]
uploadHistoryLink = None
status = None
downloadObj = getASPanelImportStatus("fixed", designID, sourceUrl=sourceUrl)
if downloadObj:
uploadHistoryLink = "/rundb/uploadstatus/{0}/".format(downloadObj.id)
status = downloadObj.status
tmpDict = {"id": designID, "configuration_choices": configurationChoices}
description = design["description"]
rec_app = None
if description:
desc = re.sub(r"\r\n", "", description.strip())
pattern = (
"<td>\s+<strong>Recommended Application</strong>\s+(.*?)\s+</td>"
)
rec_app = re.search(pattern, desc)
if rec_app:
rec_app = rec_app.group(1)
else:
description = (
"No description available for this panel from Ampliseq.com"
)
panelType = design.get("panelType") or "ready-to-use"
tmpFixedSolDict = {
"id": designID,
"design_id": designID,
"displayedID": designID,
"solution_id": "",
"genome": design["genome"],
"name": design["name"],
"type": design["type"],
"pipeline": design["pipeline"],
"ampliseq_url": ampliseq_url,
"chemistryType": chemistryType,
"panelType": panelType,
"status": status,
"uploadHistory": uploadHistoryLink,
"description": description,
"recommended_application": rec_app,
}
tmpList.append(tmpDict)
tmpFixedsolLists.append(tmpFixedSolDict)
# This is used to compare the parametized files available and show the warnings
fixed_ids_choices = json.dumps(convert(tmpList))
# Lists all the design panels available for the specific pipeline
final_fixed_soln_data = tmpFixedsolLists
return final_fixed_soln_data, ordered_solutions, fixed_ids_choices
def validateStep(self):
any_samples = False
self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_NAME] = []
self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_EXTERNAL_ID] = []
self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_DESCRIPTION] = []
self.validationErrors[SavePlanFieldNames.BAD_TUBE_LABEL] = []
self.validationErrors[SavePlanFieldNames.BAD_IR_SET_ID] = []
self.validationErrors.pop(SavePlanFieldNames.NO_BARCODE, None)
self.validationErrors.pop(SavePlanFieldNames.BAD_BARCODES, None)
barcodeSet = self.savedFields[SavePlanFieldNames.BARCODE_SET]
selectedBarcodes = []
samplesTable = json.loads(
self.savedFields[SavePlanFieldNames.SAMPLES_TABLE])
#logger.debug("save_plan_step_data - anySamples? samplesTable=%s" %(samplesTable))
for row in samplesTable:
sample_name = row.get(SavePlanFieldNames.SAMPLE_NAME, '').strip()
#logger.debug("save_plan_step_data - anySamples? sampleName=%s" %(sample_name))
if sample_name:
any_samples = True
if validate_sample_name(sample_name):
self.validationErrors[
SavePlanFieldNames.BAD_SAMPLE_NAME].append(sample_name)
external_id = row.get(SavePlanFieldNames.SAMPLE_EXTERNAL_ID,
'')
if external_id:
self.validate_field(
external_id, self.validationErrors[
SavePlanFieldNames.BAD_SAMPLE_EXTERNAL_ID])
description = row.get(SavePlanFieldNames.SAMPLE_DESCRIPTION,
'')
if description:
self.validate_field(
description, self.validationErrors[
SavePlanFieldNames.BAD_SAMPLE_DESCRIPTION], False,
MAX_LENGTH_SAMPLE_DESCRIPTION)
ir_set_id = row.get('irSetId', '')
if ir_set_id and not (str(ir_set_id).isdigit()):
self.validationErrors[
SavePlanFieldNames.BAD_IR_SET_ID].append(ir_set_id)
tube_label = row.get('tubeLabel', '')
if validate_sample_tube_label(tube_label):
self.validationErrors[
SavePlanFieldNames.BAD_TUBE_LABEL].append(tube_label)
if barcodeSet:
selectedBarcodes.append(row.get('barcodeId'))
if any_samples:
self.validationErrors.pop(SavePlanFieldNames.NO_SAMPLES, None)
else:
self.validationErrors[
SavePlanFieldNames.
NO_SAMPLES] = "You must enter at least one sample"
if not self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_NAME]:
self.validationErrors.pop(SavePlanFieldNames.BAD_SAMPLE_NAME, None)
if not self.validationErrors[SavePlanFieldNames.BAD_TUBE_LABEL]:
self.validationErrors.pop(SavePlanFieldNames.BAD_TUBE_LABEL, None)
if not self.validationErrors[
SavePlanFieldNames.BAD_SAMPLE_EXTERNAL_ID]:
self.validationErrors.pop(
SavePlanFieldNames.BAD_SAMPLE_EXTERNAL_ID, None)
if not self.validationErrors[
SavePlanFieldNames.BAD_SAMPLE_DESCRIPTION]:
self.validationErrors.pop(
SavePlanFieldNames.BAD_SAMPLE_DESCRIPTION, None)
if not self.validationErrors[SavePlanFieldNames.BAD_IR_SET_ID]:
self.validationErrors.pop(SavePlanFieldNames.BAD_IR_SET_ID, None)
if barcodeSet:
errors = validate_barcode_sample_association(
selectedBarcodes, barcodeSet)
myErrors = convert(errors)
if myErrors.get("MISSING_BARCODE", ""):
self.validationErrors[
SavePlanFieldNames.NO_BARCODE] = myErrors.get(
"MISSING_BARCODE", "")
if myErrors.get("DUPLICATE_BARCODE", ""):
self.validationErrors[
SavePlanFieldNames.BAD_BARCODES] = myErrors.get(
"DUPLICATE_BARCODE", "")
def get_ampliseq_designs(user, password, api_url):
ctx = {}
ampliseq_url = settings.AMPLISEQ_URL
chemistryType = "Ampliseq"
if "hd" in api_url:
chemistryType = "AmpliseqHD"
response, designs = _get_all_ampliseq_designs(api_url, user, password)
if designs:
ctx["unordered_solutions"] = []
ctx["ordered_solutions"] = []
unordered_tmpList = []
ordered_tmpList = []
for design in designs:
for template in design.get("DesignSolutions", []):
ampliSeq = AmpliSeqPanelImport(data=template)
solution, meta = ampliSeq.handle_versioned_plans()
solution_id = solution["id"]
configurationChoices = solution["configuration_choices"]
sourceUrl = solution["resultsUri"]
uploadHistoryLink = None
status = None
downloadObj = getASPanelImportStatus(
"ordered", design["id"], solution_id, sourceUrl
)
if downloadObj:
try:
uploadHistoryLink = "/rundb/uploadstatus/{0}/".format(
downloadObj.id
)
status = downloadObj.status
except Exception as Err:
logger.error(
"Unknown error %s" % Err
) # do not crash if any unknown issue
if solution.get("ordered", False):
panelType = template.get("panelType") or "on-demand"
ordered_tmpList.append(
{
"configuration_choices": configurationChoices,
"id": solution_id,
"solution_id": solution_id,
"displayedID": template.get(
"request_id_and_solution_ordering_id", ""
),
"design_id": design["id"],
"name": template["designName"],
"genome": template["genome"],
"pipeline": template["pipeline"],
"ampliseq_url": ampliseq_url,
"chemistryType": chemistryType,
"panelType": panelType,
"status": status,
"uploadHistory": uploadHistoryLink,
"recommended_application": "",
}
)
else:
panelType = template.get("panelType") or "made-to-order"
unordered_tmpList.append(
{
"configuration_choices": configurationChoices,
"id": solution_id,
"displayedID": template.get(
"request_id_and_solution_ordering_id", ""
),
"solution_id": solution_id,
"design_id": design["id"],
"name": template["designName"],
"genome": template["genome"],
"pipeline": template["pipeline"],
"ampliseq_url": ampliseq_url,
"chemistryType": chemistryType,
"panelType": panelType,
"status": status,
"uploadHistory": uploadHistoryLink,
"recommended_application": "",
}
)
unordered_tmpList = convert(unordered_tmpList)
ordered_tmpList = convert(ordered_tmpList)
ctx["unordered_solutions"] = unordered_tmpList
ctx["ordered_solutions"] = ordered_tmpList
return ctx
else:
return {}