def validateField(self, field_name, new_field_value):
self.validationErrors.pop(field_name, None)
if field_name == SaveTemplateStepDataFieldNames.TEMPLATE_NAME:
errors = validate_plan_name(
new_field_value,
field_label=_(
"workflow.step.savetemplate.fields.templateName.label"),
) #'Template Name'
if errors:
self.validationErrors[field_name] = "\n".join(errors)
elif field_name == SaveTemplateStepDataFieldNames.NOTE:
errors = validate_notes(
new_field_value,
field_label=_("workflow.step.savetemplate.fields.note.label"),
)
if errors:
self.validationErrors[field_name] = "\n".join(errors)
# validate all qc thresholds must be positive integers
elif field_name in self.qcNames:
errors = validate_QC(new_field_value,
ModelsQcTypeToLabelsQcType(field_name))
if errors:
self.validationErrors[field_name] = errors[0]
else:
for section, sectionObj in list(self.step_sections.items()):
self.validationErrors.pop(field_name, None)
def validateField(self, field_name, new_field_value):
'''
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)
def validateField(self, field_name, new_field_value):
'''
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)
def validateField(self, field_name, new_field_value):
"""
All qc thresholds must be positive integers
"""
errors = validate_QC(new_field_value,
ModelsQcTypeToLabelsQcType(field_name))
if errors:
self.validationErrors[field_name] = errors[0]
else:
self.validationErrors.pop(field_name, None)
def validateField(self, field_name, new_field_value):
self.validationErrors.pop(field_name, None)
if field_name == SavePlanBySampleFieldNames.NOTE:
errors = validate_notes(new_field_value)
if errors:
self.validationErrors[field_name] = '\n'.join(errors)
'''
All qc thresholds must be positive integers
'''
if field_name in self.qcNames:
errors = validate_QC(new_field_value, field_name)
if errors:
self.validationErrors[field_name] = errors[0]
else:
self.validationErrors.pop(field_name, None)
def validateField(self, field_name, new_field_value):
self.validationErrors.pop(field_name, None)
if field_name == SavePlanBySampleFieldNames.NOTE:
errors = validate_notes(new_field_value)
if errors:
self.validationErrors[field_name] = '\n'.join(errors)
'''
All qc thresholds must be positive integers
'''
if field_name in self.qcNames:
errors = validate_QC(new_field_value, field_name)
if errors:
self.validationErrors[field_name] = errors[0]
else:
self.validationErrors.pop(field_name, None)
def _validate_qc_pct(input, selectedTemplate, planObj, displayedName):
"""
validate QC threshold with leading/trailing blanks in the input ignored
"""
errorMsg = None
qcValue = None
if input:
value = input.strip()
errors = validate_QC(value, displayedName)
if errors:
errorMsg = ' '.join(errors)
else:
qcValue = int(value)
else:
qcValue = 1
return errorMsg, qcValue
def _validate_qc_pct(input, selectedTemplate, planObj, displayedName):
"""
validate QC threshold with leading/trailing blanks in the input ignored
"""
errorMsg = None
qcValue = None
if input:
value = input.strip()
errors = validate_QC(value, displayedName)
if errors:
errorMsg = ' '.join(errors)
else:
qcValue = int(value)
else:
qcValue = 1
return errorMsg, qcValue
def validateField(self, field_name, new_field_value):
self.validationErrors.pop(field_name, None)
if field_name == SaveTemplateStepDataFieldNames.TEMPLATE_NAME:
errors = validate_plan_name(new_field_value, 'Template Name')
if errors:
self.validationErrors[field_name] = '\n'.join(errors)
elif field_name == SaveTemplateStepDataFieldNames.NOTE:
errors = validate_notes(new_field_value)
if errors:
self.validationErrors[field_name] = '\n'.join(errors)
# validate all qc thresholds must be positive integers
elif field_name in self.qcNames:
errors = validate_QC(new_field_value, field_name)
if errors:
self.validationErrors[field_name] = errors[0]
def validateField(self, field_name, new_field_value):
self.validationErrors.pop(field_name, None)
if field_name == SaveTemplateStepDataFieldNames.TEMPLATE_NAME:
errors = validate_plan_name(new_field_value, 'Template Name')
if errors:
self.validationErrors[field_name] = '\n'.join(errors)
elif field_name == SaveTemplateStepDataFieldNames.NOTE:
errors = validate_notes(new_field_value)
if errors:
self.validationErrors[field_name] = '\n'.join(errors)
# validate all qc thresholds must be positive integers
elif field_name in self.qcNames:
errors = validate_QC(new_field_value, field_name)
if errors:
self.validationErrors[field_name] = errors[0]
def validateField(self, field_name, new_field_value):
self.validationErrors.pop(field_name, None)
if field_name == SaveTemplateStepDataFieldNames.TEMPLATE_NAME:
errors = validate_plan_name(new_field_value, "Template Name")
if errors:
self.validationErrors[field_name] = "\n".join(errors)
elif field_name == SaveTemplateStepDataFieldNames.NOTE:
errors = validate_notes(new_field_value)
if errors:
self.validationErrors[field_name] = "\n".join(errors)
# validate all qc thresholds must be positive integers
elif field_name in self.qcNames:
errors = validate_QC(new_field_value, field_name)
if errors:
self.validationErrors[field_name] = errors[0]
else:
for section, sectionObj in self.step_sections.items():
self.validationErrors.pop(field_name, None)
def validateField(self, field_name, new_field_value):
self.validationErrors.pop(field_name, None)
if field_name == SavePlanBySampleFieldNames.NOTE:
errors = validate_notes(
new_field_value,
field_label=_(
"workflow.step.saveplan.bysample.fields.note.label"),
)
if errors:
self.validationErrors[field_name] = "\n".join(errors)
"""
All qc thresholds must be positive integers
"""
if field_name in self.qcNames:
errors = validate_QC(new_field_value,
ModelsQcTypeToLabelsQcType(field_name))
if errors:
self.validationErrors[field_name] = errors[0]
else:
self.validationErrors.pop(field_name, None)
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)
