def validateField_in_section(self, field_name, new_field_value):
"""
field validation for a step that acts as a section to another step
"""
# logger.debug("at validateField_in_section field_name=%s; new_field_value=%s" %(field_name, new_field_value))
if field_name == ReferenceFieldNames.REFERENCE:
if new_field_value and new_field_value not in [ref.short_name for ref in self.prepopulatedFields[ReferenceFieldNames.REFERENCES]]:
self.prepopulatedFields[ReferenceFieldNames.REFERENCE_MISSING] = True
self.validationErrors[field_name] = "Reference Library not found: %s" % new_field_value
else:
self.prepopulatedFields[ReferenceFieldNames.REFERENCE_MISSING] = False
self.validationErrors.pop(field_name, None)
# if the plan has been sequenced, do not enforce the target bed file to be selected
if self.prepopulatedFields[ReferenceFieldNames.PLAN_STATUS] != "run":
if field_name == ReferenceFieldNames.TARGET_BED_FILE:
reference = self.savedFields[ReferenceFieldNames.REFERENCE]
targetRegionBedFile = new_field_value
runType = self.prepopulatedFields[ReferenceFieldNames.RUN_TYPE] if self.prepopulatedFields[ReferenceFieldNames.RUN_TYPE] else ""
applicationGroupName = self.prepopulatedFields[ReferenceFieldNames.APPLICATION_GROUP_NAME]
logger.debug(" validateField_in_section reference=%s; targetBed=%s; runType=%s; applicationGroupName=%s" % (reference, new_field_value, runType, applicationGroupName))
errors = []
errors = validate_targetRegionBedFile_for_runType(targetRegionBedFile, runType, reference, "", applicationGroupName, "Target Regions BED File")
if errors:
self.validationErrors[field_name] = ''.join(errors)
else:
self.validationErrors.pop(field_name, None)
def validateField_in_section(self, field_name, new_field_value):
"""
field validation for a step that acts as a section to another step
"""
#logger.debug("at validateField_in_section field_name=%s; new_field_value=%s" %(field_name, new_field_value))
if field_name == ReferenceFieldNames.REFERENCE:
if new_field_value in [ref.short_name for ref in self.prepopulatedFields[ReferenceFieldNames.REFERENCES]]:
self.prepopulatedFields[ReferenceFieldNames.REFERENCE_MISSING] = False
#if the plan has been sequenced, do not enforce the target bed file to be selected
if self.prepopulatedFields[ReferenceFieldNames.PLAN_STATUS] != "run":
if field_name == ReferenceFieldNames.TARGET_BED_FILE:
reference = self.savedFields[ReferenceFieldNames.REFERENCE]
targetRegionBedFile = new_field_value
runType = self.prepopulatedFields[ReferenceFieldNames.RUN_TYPE] if self.prepopulatedFields[ReferenceFieldNames.RUN_TYPE] else ""
applicationGroupName = self.prepopulatedFields[ReferenceFieldNames.APPLICATION_GROUP_NAME]
logger.debug(" validateField_in_section reference=%s; targetBed=%s; runType=%s; applicationGroupName=%s" %(reference, new_field_value, runType, applicationGroupName))
errors = []
errors = validate_targetRegionBedFile_for_runType(targetRegionBedFile, runType, reference, "", applicationGroupName, "Target Regions BED File")
if errors:
self.validationErrors[field_name] = ''.join(errors)
else:
self.validationErrors.pop(field_name, None)
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 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)
def validateField_in_section(self, field_name, new_field_value):
"""
field validation for a step that acts as a section to another step
"""
# logger.debug("at validateField_in_section field_name=%s; new_field_value=%s" %(field_name, new_field_value))
if field_name == ReferenceFieldNames.REFERENCE:
if new_field_value and new_field_value not in [
ref.short_name for ref in self.prepopulatedFields[
ReferenceFieldNames.REFERENCES]
]:
self.prepopulatedFields[
ReferenceFieldNames.REFERENCE_MISSING] = True
self.validationErrors[
field_name] = validation.invalid_not_found_error(
_("workflow.step.reference.fields.default_reference.label"
),
new_field_value,
) # Reference Library not found: %s" % new_field_value
else:
self.prepopulatedFields[
ReferenceFieldNames.REFERENCE_MISSING] = False
self.validationErrors.pop(field_name, None)
# if the plan has been sequenced, do not enforce the target bed file to be selected
if self.prepopulatedFields[ReferenceFieldNames.PLAN_STATUS] != "run":
if field_name == ReferenceFieldNames.TARGET_BED_FILE:
reference = self.savedFields[ReferenceFieldNames.REFERENCE]
targetRegionBedFile = new_field_value
runType = (
self.prepopulatedFields[ReferenceFieldNames.RUN_TYPE]
if self.prepopulatedFields[ReferenceFieldNames.RUN_TYPE]
else "")
applicationGroupName = self.prepopulatedFields[
ReferenceFieldNames.APPLICATION_GROUP_NAME]
logger.debug(
" validateField_in_section reference=%s; targetBed=%s; runType=%s; applicationGroupName=%s"
% (reference, new_field_value, runType,
applicationGroupName))
errors = []
isSameRefInfoPerSample = self.savedFields[
ReferenceFieldNames.SAME_REF_INFO_PER_SAMPLE]
if isSameRefInfoPerSample:
errors = validate_targetRegionBedFile_for_runType(
targetRegionBedFile,
field_label=
_("workflow.step.reference.fields.default_targetBedFile.label"
),
runType=runType,
reference=reference,
nucleotideType="",
applicationGroupName=applicationGroupName,
)
if errors:
self.validationErrors[field_name] = "".join(errors)
else:
self.validationErrors.pop(field_name, None)
