def validate(self):
err = []
## barcodedSamples from eas / barcodeSampleInfo from plan
if self.barcodedSamples is None:
return True
for sample in self.barcodedSamples:
err.extend(plan_validator.validate_sample_name(sample))
if err:
raise ValidationError(err)
return True
def validate(self):
err = []
## barcodedSamples from eas / barcodeSampleInfo from plan
if self.barcodedSamples is None:
return True
for sample in self.barcodedSamples:
err.extend(plan_validator.validate_sample_name(sample))
if err:
raise ValidationError(err)
return True
def _validate_sample(input, selectedTemplate, planObj):
"""
validate sample name with leading/trailing blanks in the input ignored
"""
errorMsg = None
sampleDisplayedName = ""
if not input:
errorMsg = "Required column is empty"
else:
errors = validate_sample_name(input)
if errors:
errorMsg = ' '.join(errors)
else:
sampleDisplayedName = input.strip()
return errorMsg, sampleDisplayedName
def _validate_sample(input, selectedTemplate, planObj):
"""
validate sample name with leading/trailing blanks in the input ignored
"""
errorMsg = None
sampleDisplayedName = ""
if not input:
errorMsg = "Required column is empty"
else:
errors = validate_sample_name(input)
if errors:
errorMsg = ' '.join(errors)
else:
sampleDisplayedName = input.strip()
return errorMsg, sampleDisplayedName
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 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", "")