def validateField(self, field_name, new_field_value):
self.validationErrors.pop(field_name, None)
errors = None
if field_name == SavePlanFieldNames.CHIP_BARCODE_LABEL:
errors = validate_chipBarcode(new_field_value)
if errors:
self.validationErrors[field_name] = '\n'.join(errors)
if field_name == SavePlanFieldNames.BARCODE_SAMPLE_TUBE_LABEL:
errors = validate_sample_tube_label(new_field_value)
if errors:
self.validationErrors[field_name] = '\n'.join(errors)
# if the plan has been sequenced, do not enforce the target bed file to be selected
planStatus = self.getDefaultSectionPrepopulatedFieldDict().get("planStatus", "")
if field_name == SavePlanFieldNames.SAMPLES_TABLE:
sample_table_list = json.loads(new_field_value)
samples_errors = []
applProduct = self.savedObjects[SavePlanFieldNames.APPL_PRODUCT]
# applProduct object is not saved yet
if applProduct:
isTargetRegionSelectionRequired = applProduct.isTargetRegionBEDFileSelectionRequiredForRefSelection
else:
isTargetRegionSelectionRequired = False
applicationGroupName = self.prepopulatedFields[SavePlanFieldNames.APPLICATION_GROUP_NAME]
for row in sample_table_list:
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, "")
sampleTargetRegionBedFile = row.get(SavePlanFieldNames.BARCODE_SAMPLE_TARGET_REGION_BED_FILE, "")
runType = self.prepopulatedFields[SavePlanFieldNames.RUN_TYPE]
logger.debug("barcode_by_sample_step_data.validateField()() runType=%s; sample_nucleotideType=%s; sampleReference=%s; sampleTargetRegionBedFile=%s" % (runType, sample_nucleotideType, sampleReference, sampleTargetRegionBedFile))
errors = []
# if the plan has been sequenced, do not enforce the target bed file to be selected
if planStatus != "run":
errors = validate_targetRegionBedFile_for_runType(sampleTargetRegionBedFile, runType, sampleReference, sample_nucleotideType, applicationGroupName, "Target Regions BED File for " + sample_name)
if errors:
samples_errors.append('\n'.join(errors))
if samples_errors:
logger.debug("barcode_by_sample_step_data.validateField()() samples_errors=%s" % (samples_errors))
self.validationErrors[field_name] = '\n'.join(samples_errors)
def validateField(self, field_name, new_field_value):
self.validationErrors.pop(field_name, None)
errors = None
if field_name == SavePlanFieldNames.CHIP_BARCODE_LABEL:
errors = validate_chipBarcode(new_field_value)
if errors:
self.validationErrors[field_name] = '\n'.join(errors)
if field_name == SavePlanFieldNames.BARCODE_SAMPLE_TUBE_LABEL:
errors = validate_sample_tube_label(new_field_value)
if errors:
self.validationErrors[field_name] = '\n'.join(errors)
# if the plan has been sequenced, do not enforce the target bed file to be selected
planStatus = self.getDefaultSectionPrepopulatedFieldDict().get("planStatus", "")
if field_name == SavePlanFieldNames.SAMPLES_TABLE:
sample_table_list = json.loads(new_field_value)
samples_errors = []
applProduct = self.savedObjects[SavePlanFieldNames.APPL_PRODUCT]
# applProduct object is not saved yet
if applProduct:
isTargetRegionSelectionRequired = applProduct.isTargetRegionBEDFileSelectionRequiredForRefSelection
else:
isTargetRegionSelectionRequired = False
applicationGroupName = self.prepopulatedFields[SavePlanFieldNames.APPLICATION_GROUP_NAME]
for row in sample_table_list:
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, "")
sampleTargetRegionBedFile = row.get(SavePlanFieldNames.BARCODE_SAMPLE_TARGET_REGION_BED_FILE, "")
runType = self.prepopulatedFields[SavePlanFieldNames.RUN_TYPE]
logger.debug("barcode_by_sample_step_data.validateField()() runType=%s; sample_nucleotideType=%s; sampleReference=%s; sampleTargetRegionBedFile=%s" % (runType, sample_nucleotideType, sampleReference, sampleTargetRegionBedFile))
errors = []
# if the plan has been sequenced, do not enforce the target bed file to be selected
if planStatus != "run":
errors = validate_targetRegionBedFile_for_runType(sampleTargetRegionBedFile, runType, sampleReference, sample_nucleotideType, applicationGroupName, "Target Regions BED File for " + sample_name)
if errors:
samples_errors.append('\n'.join(errors))
if samples_errors:
logger.debug("barcode_by_sample_step_data.validateField()() samples_errors=%s" % (samples_errors))
self.validationErrors[field_name] = '\n'.join(samples_errors)
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 validateField(self, field_name, new_field_value):
self.validationErrors.pop(field_name, None)
# if the plan has been sequenced, do not enforce the target bed file to be selected
planStatus = self.getDefaultSectionPrepopulatedFieldDict().get("planStatus", "")
if field_name == SavePlanFieldNames.PLAN_NAME:
errors = validate_plan_name(new_field_value, 'Plan Name')
if errors:
self.validationErrors[field_name] = '\n'.join(errors)
elif field_name == SavePlanFieldNames.NOTE:
errors = validate_notes(new_field_value)
if errors:
self.validationErrors[field_name] = '\n'.join(errors)
elif field_name == SavePlanFieldNames.BARCODE_SAMPLE_TUBE_LABEL:
errors = validate_sample_tube_label(new_field_value)
if errors:
self.validationErrors[field_name] = '\n'.join(errors)
elif field_name == SavePlanFieldNames.CHIP_BARCODE_LABEL:
errors = validate_chipBarcode(new_field_value)
if errors:
self.validationErrors[field_name] = '\n'.join(errors)
elif field_name in self.qcNames:
'''
All qc thresholds must be positive integers
'''
errors = validate_QC(new_field_value, field_name)
if errors:
self.validationErrors[field_name] = errors[0]
else:
self.validationErrors.pop(field_name, None)
elif field_name == SavePlanFieldNames.SAMPLES_TABLE:
sample_table_list = json.loads(new_field_value)
samples_errors = []
applProduct = self.savedObjects[SavePlanFieldNames.APPL_PRODUCT]
# applProduct object is not saved yet
if applProduct:
isTargetRegionSelectionRequired = applProduct.isTargetRegionBEDFileSelectionRequiredForRefSelection
else:
isTargetRegionSelectionRequired = False
applicationGroupName = self.prepopulatedFields[SavePlanFieldNames.APPLICATION_GROUP_NAME]
for row in sample_table_list:
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, "")
sampleTargetRegionBedFile = row.get(SavePlanFieldNames.BARCODE_SAMPLE_TARGET_REGION_BED_FILE, "")
runType = self.prepopulatedFields[SavePlanFieldNames.RUN_TYPE]
errors = []
# if the plan has been sequenced, do not enforce the target bed file to be selected
isMainBEDFileValidated = "default_targetBedFile" in self.validationErrors
if not isMainBEDFileValidated and planStatus != "run" and (self.sh_type not in StepHelperType.TEMPLATE_TYPES):
errors = validate_targetRegionBedFile_for_runType(sampleTargetRegionBedFile, runType, sampleReference, sample_nucleotideType, applicationGroupName, "Target Regions BED File for " + sample_name)
if errors:
samples_errors.append('\n'.join(errors))
if samples_errors:
self.validationErrors[field_name] = '\n'.join(samples_errors)
