def validate_sampleSet_values(sampleSetName, sampleSetDesc, isNew = False):
"""
validate the sampleSet input.
returns a boolean isValid and a text string for error message, None if input passes validation
Note: Input length willl not be validated since maxLength has been specified in the form.
"""
isValid = False
if not validation.has_value(sampleSetName):
return isValid, validation.required_error("Error, Sample set name")
else:
if not validation.is_valid_chars(sampleSetName):
return isValid, validation.invalid_chars_error("Error, Sample set name")
if not validation.is_valid_length(sampleSetName, MAX_LENGTH_SAMPLE_SET_DISPLAYED_NAME):
errorMessage = validation.invalid_length_error("Error, Sample set name", MAX_LENGTH_SAMPLE_SET_DISPLAYED_NAME) + ". It is currently %s characters long." % str(len(sampleSetName.strip()))
return isValid, errorMessage
if isNew:
#error if new sample set already exists
existingSampleSets = SampleSet.objects.filter(displayedName = sampleSetName)
if existingSampleSets:
errorMessage = "Error, Sample set %s already exists." % (sampleSetName)
return isValid, errorMessage
if validation.has_value(sampleSetDesc):
if not validation.is_valid_chars(sampleSetDesc):
return isValid, validation.invalid_chars_error("Error, Sample set description")
if not validation.is_valid_length(sampleSetDesc, MAX_LENGTH_SAMPLE_SET_DESCRIPTION):
errorMessage = validation.invalid_length_error("Error, Sample set description", MAX_LENGTH_SAMPLE_SET_DESCRIPTION) + ". It is currently %s characters long." % str(len(sampleSetDesc.strip()))
return isValid, errorMessage
isValid = True
return isValid, None
def validateField(self, field_name, new_field_value):
'''
Flows qc value must be a positive integer
Chip type is required
'''
if field_name == KitsFieldNames.FLOWS:
errors = validate_flows(new_field_value)
if errors:
self.validationErrors[field_name] = ' '.join(errors)
else:
self.validationErrors.pop(field_name, None)
if field_name == KitsFieldNames.CHIP_TYPE and self.prepopulatedFields.get(
'is_chipType_required', True):
if validation.has_value(new_field_value):
self.validationErrors.pop(field_name, None)
else:
self.validationErrors[field_name] = validation.required_error(
"Chip Type")
if field_name == KitsFieldNames.TEMPLATE_KIT_NAME:
if validation.has_value(new_field_value):
self.validationErrors.pop(field_name, None)
else:
self.validationErrors[field_name] = validation.required_error(
"Template Kit")
def validateField(self, field_name, new_field_value):
"""
Flows qc value must be a positive integer
Chip type is required
"""
if field_name == KitsFieldNames.FLOWS:
errors = validate_flows(
new_field_value,
field_label=_("workflow.step.kits.fields.flows.label"))
if errors:
self.validationErrors[field_name] = " ".join(errors)
else:
self.validationErrors.pop(field_name, None)
if field_name == KitsFieldNames.CHIP_TYPE and self.prepopulatedFields.get(
"is_chipType_required", True):
if validation.has_value(new_field_value):
self.validationErrors.pop(field_name, None)
else:
self.validationErrors[field_name] = validation.required_error(
_("workflow.step.kits.fields.chipType.label")
) # "Chip Type"
if field_name == KitsFieldNames.TEMPLATE_KIT_NAME:
if validation.has_value(new_field_value):
self.validationErrors.pop(field_name, None)
else:
self.validationErrors[field_name] = validation.required_error(
_("workflow.step.kits.fields.templatekitname.label")
) # "Template Kit"
if field_name == KitsFieldNames.LIBRARY_READ_LENGTH:
errors = validate_libraryReadLength(
new_field_value,
field_label=_(
"workflow.step.kits.fields.libraryReadLength.label"),
)
if errors:
self.validationErrors[field_name] = " ".join(errors)
else:
self.validationErrors.pop(field_name, None)
if field_name == KitsFieldNames.READ_LENGTH:
if new_field_value:
errors = validate_libraryReadLength(
new_field_value,
field_label=_(
"workflow.step.kits.fields.readLength.label"),
)
if errors:
self.validationErrors[field_name] = " ".join(errors)
else:
self.validationErrors.pop(field_name, None)
self.savedFields[
KitsFieldNames.LIBRARY_READ_LENGTH] = new_field_value
def validate_targetRegionBedFile_for_runType(value, runType, reference, nucleotideType=None, applicationGroupName=None, displayedName="Target Regions BED File", isPrimaryTargetRegion = True):
"""
validate targetRegionBedFile based on the selected reference and the plan's runType
"""
errors = []
value = value.strip() if value else ""
if value:
missing_file = check_uploaded_files(bedfilePaths=[value])
if missing_file:
errors.append("%s : %s not found" % (displayedName, value))
logger.debug("plan_validator.validate_targetRegionBedFile_for_run() SKIPS validation due to no targetRegion file exists in db. value=%s" % (value))
return errors
logger.debug("plan_validator.validate_targetRegionBedFile_for_runType() value=%s; runType=%s; reference=%s; nucleotideType=%s; applicationGroupName=%s" % (value, runType, reference, nucleotideType, applicationGroupName))
if not isPrimaryTargetRegion:
logger.debug("plan_validator.validate_targetRegionBedFile_for_run() SKIPS validation due to no validation rules for non-primary targetRegion. value=%s" %(value))
return errors
if reference:
if runType:
runType = runType.strip()
applProducts = ApplProduct.objects.filter(isActive=True, applType__runType=runType, applicationGroup__name=applicationGroupName) \
or ApplProduct.objects.filter(isActive=True, applType__runType=runType)
if applProducts:
applProduct = applProducts[0]
if applProduct:
if validation.has_value(value) and not applProduct.isTargetRegionBEDFileSupported:
errors.append(displayedName+" selection is not supported for this Application")
else:
isRequired = applProduct.isTargetRegionBEDFileSelectionRequiredForRefSelection
if isRequired and not validation.has_value(value):
# skip for now
if runType in ["AMPS_DNA_RNA","AMPS_HD_DNA_RNA"] and nucleotideType and nucleotideType.upper() == "RNA":
logger.debug("plan_validator.validate_targetRegionBedFile_for_runType() ALLOW MISSING targetRegionBed for runType=%s; nucleotideType=%s" % (runType, nucleotideType))
elif runType in ["AMPS_RNA","AMPS_HD_RNA"]:
logger.debug("plan_validator.validate_targetRegionBedFile_for_runType() ALLOW MISSING targetRegionBed for runType=%s; applicationGroupName=%s" % (runType, applicationGroupName))
else:
errors.append("%s is required for this application" % (displayedName))
elif value:
if not os.path.isfile(value):
errors.append("Missing or Invalid %s - %s" % (displayedName, value))
else:
errors.append("%s Application %s not found" % (displayedName, runType))
else:
errors.append("%s Run type is missing" % (displayedName))
# logger.debug("EXIT plan_validator.validate_targetRegionBedFile_for_runType() errors=%s" %(errors))
return errors
def validateField(self, field_name, new_field_value):
'''
Flows qc value must be a positive integer
Chip type is required
'''
if field_name == KitsFieldNames.FLOWS:
errors = validate_flows(new_field_value)
if errors:
self.validationErrors[field_name] = ' '.join(errors)
else:
self.validationErrors.pop(field_name, None)
if field_name == KitsFieldNames.CHIP_TYPE and self.prepopulatedFields.get(
'is_chipType_required', True):
if validation.has_value(new_field_value):
self.validationErrors.pop(field_name, None)
else:
self.validationErrors[field_name] = validation.required_error(
"Chip Type")
if field_name == KitsFieldNames.TEMPLATE_KIT_NAME:
if validation.has_value(new_field_value):
self.validationErrors.pop(field_name, None)
else:
self.validationErrors[field_name] = validation.required_error(
"Template Kit")
if field_name == KitsFieldNames.LIBRARY_READ_LENGTH:
errors = validate_libraryReadLength(new_field_value)
if errors:
self.validationErrors[field_name] = ' '.join(errors)
else:
self.validationErrors.pop(field_name, None)
if field_name == KitsFieldNames.READ_LENGTH:
if new_field_value:
errors = validate_libraryReadLength(new_field_value)
if errors:
self.validationErrors[field_name] = ' '.join(errors)
else:
self.validationErrors.pop(field_name, None)
self.savedFields[
KitsFieldNames.LIBRARY_READ_LENGTH] = new_field_value
if field_name == KitsFieldNames.TEMPLATING_SIZE:
errors = validate_templatingSize(new_field_value)
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]
#logger.debug("at validateField_in_section reference=%s; REQUIRE_TARGET_BED_FILE=%s; targetBed=%s" %(reference, str(self.prepopulatedFields[ReferenceFieldNames.REQUIRE_TARGET_BED_FILE]), new_field_value))
if self.prepopulatedFields[
ReferenceFieldNames.REQUIRE_TARGET_BED_FILE]:
if reference:
if validation.has_value(new_field_value):
self.validationErrors.pop(field_name, None)
else:
self.validationErrors[
field_name] = validation.required_error(
"Target Regions BED File")
else:
self.validationErrors.pop(field_name, None)
def validate_plan_templating_kit_name(value, field_label, isNewPlan=None):
errors = []
warnings = []
if not validation.has_value(value):
errors.append(validation.required_error(field_label))
else:
value = value.strip()
query_kwargs = {"kitType__in": ["TemplatingKit", "IonChefPrepKit"]}
query_args = (Q(name=value) | Q(description=value), )
kit = KitInfo.objects.filter(*query_args, **query_kwargs)
if not kit:
errors.append(
validation.invalid_not_found_error(field_label, value))
elif kit and not kit[0].isActive:
if isNewPlan:
errors.append(validation.invalid_not_active(
field_label, value))
else:
warnings.append(
validation.invalid_not_active(field_label, value))
return errors, warnings
def validateField_crossField_dependency(self, field_name, new_field_value,
dependent_field_name,
dependent_field_value):
isBarcodeKitRequired = False
if field_name == KitsFieldNames.LIBRARY_KIT_NAME:
if new_field_value:
libKit_objs = KitInfo.objects.filter(
kitType='LibraryKit',
name=new_field_value).order_by("-isActive")
if libKit_objs and len(libKit_objs) > 0:
libKit_obj = libKit_objs[0]
if libKit_obj.categories and (
"bcrequired" in libKit_obj.categories.lower()):
isBarcodeKitRequired = True
if dependent_field_name == KitsFieldNames.BARCODE_KIT_NAME:
if self.prepopulatedFields[
KitsFieldNames.
IS_BARCODE_KIT_SELECTION_REQUIRED] or isBarcodeKitRequired:
if validation.has_value(dependent_field_value):
self.validationErrors.pop(dependent_field_name, None)
else:
self.validationErrors[
dependent_field_name] = validation.required_error(
"Barcode Set")
else:
self.validationErrors.pop(dependent_field_name, None)
def validate_plan_templating_kit_name(value,
displayedName="Template Kit",
isNewPlan=None):
errors = []
warnings = []
if not validation.has_value(value):
errors.append(validation.required_error(displayedName))
else:
value = value.strip()
query_kwargs = {"kitType__in": ["TemplatingKit", "IonChefPrepKit"]}
query_args = (Q(name=value) | Q(description=value), )
kit = KitInfo.objects.filter(*query_args, **query_kwargs)
if not kit:
errors.append("%s %s not found" % (displayedName, value))
elif kit and not kit[0].isActive:
if isNewPlan:
errors.append("%s %s not active" % (displayedName, value))
else:
warnings.append("Found inactive %s %s" %
(displayedName, value))
return errors, warnings
def validate_sampleAttribute_definition(attributeName, attributeDescription):
"""
validate the sample attribute definition
return a boolean isValid and a text string for error message, None if input passes validation
Note: Input length will not be validated since maxLength has been specified in the form.
"""
isValid = False
if not validation.has_value(attributeName):
return isValid, validation.required_error("Error, Attribute name")
if not validation.is_valid_chars(attributeName.strip()):
return isValid, validation.invalid_chars_error("Error, Attribute name")
if not validation.is_valid_length(attributeName.strip(), MAX_LENGTH_SAMPLE_ATTRIBUTE_DISPLAYED_NAME):
errorMessage = validation.invalid_length_error("Error, User-defined sample attribute", MAX_LENGTH_SAMPLE_ATTRIBUTE_DISPLAYED_NAME) + ". It is currently %s characters long." % str(len((attributeName.strip())))
return isValid, errorMessage
if not validation.is_valid_chars(attributeDescription):
return isValid, validation.invalid_chars_error("Error, Attribute description")
if not validation.is_valid_length(attributeDescription.strip(), MAX_LENGTH_SAMPLE_ATTRIBUTE_DESCRIPTION):
errorMessage = validation.invalid_length_error("Error, User-defined sample attribute description", MAX_LENGTH_SAMPLE_ATTRIBUTE_DESCRIPTION) + ". It is currently %s characters long." % str(len(attributeDescription.strip()))
return isValid, errorMessage
isValid = True
return isValid, None
def validate_sampleAttribute(attribute, value):
"""
validate the sample attribute value for the attribute of interest
return a boolean isValid and a text string for error message, None if input passes validation
Note: Input length will not be validated since maxLength has been specified in the form.
"""
isValid = False
if not attribute:
return isValid, "Error, No sample attribute to validate."
if not validation.has_value(value):
if attribute.isMandatory:
return isValid, "Error, "+ validation.required_error(attribute.displayedName)
else:
aValue = value.strip()
if attribute.dataType.dataType == "Text" and not validation.is_valid_chars(aValue):
return isValid, "Error, "+ validation.invalid_chars_error(attribute.displayedName)
if attribute.dataType.dataType == "Integer" and not aValue.isdigit():
return isValid, "Error, "+ attribute.displayedName + ERROR_MSG_INVALID_DATATYPE
if not validation.is_valid_chars(aValue):
return isValid, "Error, "+ validation.invalid_chars_error(attribute.displayedName)
if not validation.is_valid_length(aValue, MAX_LENGTH_SAMPLE_ATTRIBUTE_VALUE):
errorMessage = validation.invalid_length_error("Error, User-defined sample attribute value", MAX_LENGTH_SAMPLE_ATTRIBUTE_VALUE) + ". It is currently %s characters long." % str(len(aValue.strip()))
return isValid, errorMessage
isValid = True
return isValid, 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]
#logger.debug("at validateField_in_section reference=%s; REQUIRE_TARGET_BED_FILE=%s; targetBed=%s" %(reference, str(self.prepopulatedFields[ReferenceFieldNames.REQUIRE_TARGET_BED_FILE]), new_field_value))
if self.prepopulatedFields[ReferenceFieldNames.REQUIRE_TARGET_BED_FILE]:
if reference:
if validation.has_value(new_field_value):
self.validationErrors.pop(field_name, None)
else:
self.validationErrors[field_name] = validation.required_error("Target Regions BED File")
else:
self.validationErrors.pop(field_name, None)
def validate_targetRegionBedFile_for_runType(value, runType, reference, nucleotideType = None, displayedName="Target Regions BED File"):
"""
validate targetRegionBedFile based on the selected reference and the plan's runType
"""
errors = []
logger.debug("plan_validator.validate_targetRegionBedFile_for_runType() value=%s; runType=%s; reference=%s; nucleotideType=%s" %(value, runType, reference, nucleotideType))
if reference:
if runType:
runType = runType.strip()
applProducts = ApplProduct.objects.filter(applType__runType = runType)
if applProducts:
applProduct = applProducts[0]
if applProduct:
isRequired = applProduct.isTargetRegionBEDFileSelectionRequiredForRefSelection
if isRequired and not validation.has_value(value):
#skip for now
if runType == "AMPS_DNA_RNA" and nucleotideType and nucleotideType.upper() == "RNA":
logger.debug("plan_validator.validate_targetRegionBedFile_for_runType() ALLOW MISSING targetRegionBed for runType=%s; nucleotideType=%s" %(runType, nucleotideType))
else:
errors.append("%s is required for this application" %(displayedName))
else:
errors.append("%s Application %s not found" %(displayedName, runType))
else:
errors.append("%s Run type is missing" %(displayedName))
##logger.debug("EXIT plan_validator.validate_targetRegionBedFile_for_runType() errors=%s" %(errors))
return errors
def validateField(self, field_name, new_field_value):
'''
Flows qc value must be a positive integer
Chip type is required
'''
if field_name == KitsFieldNames.FLOWS:
errors = validate_flows(new_field_value)
if errors:
self.validationErrors[field_name] = ' '.join(errors)
else:
self.validationErrors.pop(field_name, None)
if field_name == KitsFieldNames.CHIP_TYPE and self.prepopulatedFields.get('is_chipType_required',True):
if validation.has_value(new_field_value):
self.validationErrors.pop(field_name, None)
else:
self.validationErrors[field_name] = validation.required_error("Chip Type")
if field_name == KitsFieldNames.TEMPLATE_KIT_NAME:
if validation.has_value(new_field_value):
self.validationErrors.pop(field_name, None)
else:
self.validationErrors[field_name] = validation.required_error("Template Kit")
if field_name == KitsFieldNames.LIBRARY_READ_LENGTH:
errors = validate_libraryReadLength(new_field_value)
if errors:
self.validationErrors[field_name] = ' '.join(errors)
else:
self.validationErrors.pop(field_name, None)
if field_name == KitsFieldNames.READ_LENGTH:
if new_field_value:
errors = validate_libraryReadLength(new_field_value)
if errors:
self.validationErrors[field_name] = ' '.join(errors)
else:
self.validationErrors.pop(field_name, None)
self.savedFields[KitsFieldNames.LIBRARY_READ_LENGTH] = new_field_value
if field_name == KitsFieldNames.TEMPLATING_SIZE:
errors = validate_templatingSize(new_field_value)
if errors:
self.validationErrors[field_name] = ' '.join(errors)
else:
self.validationErrors.pop(field_name, None)
def validate_reference_short_name(value, displayedName='Reference'):
errors = []
if validation.has_value(value):
value = value.strip()
reference = ReferenceGenome.objects.filter(short_name=value, enabled=True)
if not reference.exists():
errors.append(validation.invalid_not_found_error(displayedName, value))
return errors
def validate_barcode_kit_name(value, displayedName="Barcode Kit"):
errors = []
if validation.has_value(value):
value = value.strip()
kits = dnaBarcode.objects.filter(name=value)
if not kits:
errors.append("%s %s not found" % (displayedName, value))
return errors
def validate_barcode_kit_name(value, displayedName="Barcode Kit"):
errors = []
if validation.has_value(value):
value = value.strip()
kits = dnaBarcode.objects.filter(name=value)
if not kits:
errors.append("%s %s not found" % (displayedName, value))
return errors
def validate_reference_short_name(value, displayedName='Reference'):
errors = []
if validation.has_value(value):
value = value.strip()
reference = ReferenceGenome.objects.filter(short_name=value, enabled=True)
if not reference.exists():
generic_not_found_error = validation.invalid_not_found_error(displayedName, value)
error_fixing_message = ". To import it, visit Settings > References > Import Preloaded Ion References"
reference_error_message = generic_not_found_error.strip() + error_fixing_message
errors.append(reference_error_message)
return errors
def validate_reference_short_name(value, displayedName='Reference'):
errors = []
if validation.has_value(value):
value = value.strip()
reference = ReferenceGenome.objects.filter(short_name=value, enabled=True)
if not reference.exists():
generic_not_found_error = validation.invalid_not_found_error(displayedName, value)
error_fixing_message = ". To import it, visit Settings > References > Import Preloaded Ion References"
reference_error_message = generic_not_found_error.strip() + error_fixing_message
errors.append(reference_error_message)
return errors
def validate_plan_name(value, displayedName='Plan Name'):
errors = []
if not validation.has_value(value):
errors.append(validation.required_error(displayedName))
if not validation.is_valid_chars(value):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_length(value, MAX_LENGTH_PLAN_NAME):
errors.append(validation.invalid_length_error(displayedName, MAX_LENGTH_PLAN_NAME))
return errors
def validate_plan_name(value, displayedName="Plan Name"):
errors = []
if not validation.has_value(value):
errors.append(validation.required_error(displayedName))
if not validation.is_valid_chars(value):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_length(value, MAX_LENGTH_PLAN_NAME):
errors.append(validation.invalid_length_error(displayedName, MAX_LENGTH_PLAN_NAME))
return errors
def validate_targetRegionBedFile_for_runType(value, runType, reference, nucleotideType=None, applicationGroupName=None, displayedName="Target Regions BED File"):
"""
validate targetRegionBedFile based on the selected reference and the plan's runType
"""
errors = []
value = value.strip() if value else ""
logger.debug("plan_validator.validate_targetRegionBedFile_for_runType() value=%s; runType=%s; reference=%s; nucleotideType=%s; applicationGroupName=%s" % (value, runType, reference, nucleotideType, applicationGroupName))
if reference:
if runType:
runType = runType.strip()
applProducts = ApplProduct.objects.filter(isActive=True, applType__runType=runType, applicationGroup__name=applicationGroupName) \
or ApplProduct.objects.filter(isActive=True, applType__runType=runType)
if applProducts:
applProduct = applProducts[0]
if applProduct:
if validation.has_value(value) and not applProduct.isTargetRegionBEDFileSupported:
errors.append(displayedName+" selection is not supported for this Application")
else:
isRequired = applProduct.isTargetRegionBEDFileSelectionRequiredForRefSelection
if isRequired and not validation.has_value(value):
# skip for now
if runType == "AMPS_DNA_RNA" and nucleotideType and nucleotideType.upper() == "RNA":
logger.debug("plan_validator.validate_targetRegionBedFile_for_runType() ALLOW MISSING targetRegionBed for runType=%s; nucleotideType=%s" % (runType, nucleotideType))
elif runType == "AMPS_RNA" and applicationGroupName and applicationGroupName in ["DNA + RNA", "DNA and Fusions"]:
logger.debug("plan_validator.validate_targetRegionBedFile_for_runType() ALLOW MISSING targetRegionBed for runType=%s; applicationGroupName=%s" % (runType, applicationGroupName))
else:
errors.append("%s is required for this application" % (displayedName))
elif value:
if not os.path.isfile(value):
errors.append("Missing or Invalid %s - %s" % (displayedName, value))
else:
errors.append("%s Application %s not found" % (displayedName, runType))
else:
errors.append("%s Run type is missing" % (displayedName))
# logger.debug("EXIT plan_validator.validate_targetRegionBedFile_for_runType() errors=%s" %(errors))
return errors
def validate_barcode_kit_name(value, field_label):
errors = []
if validation.has_value(value):
value = value.strip()
kits = dnaBarcode.objects.filter(name=value)
if not kits:
errors.append(
validation.invalid_not_found_error(
field_label,
value)) # "%s %s not found" % (displayedName, value)
return errors
def validate_sequencing_kit_name(value, displayedName="Sequencing Kit"):
errors = []
if validation.has_value(value):
value = value.strip()
kit = KitInfo.objects.filter(kitType__in = ["SequencingKit"], name = value)
if not kit:
kit = KitInfo.objects.filter(kitType__in = ["SequencingKit"], description = value)
if not kit:
errors.append("%s %s not found" %(displayedName, value))
return errors
def validate_sampleDescription(sampleDescription):
isValid = False
if validation.has_value(sampleDescription):
isValid, errorMessage = _validate_textValue(sampleDescription, "Sample description ")
if not isValid:
return isValid, errorMessage
if not validation.is_valid_length(sampleDescription.strip(), MAX_LENGTH_SAMPLE_DESCRIPTION):
errorMessage = validation.invalid_length_error("Error, Sample description", MAX_LENGTH_SAMPLE_DESCRIPTION) + ". It is currently %s characters long." % str(len(sampleDescription.strip()))
return isValid, errorMessage
return True, None
def validate_sequencing_kit_name(value, displayedName="Sequencing Kit"):
errors = []
if validation.has_value(value):
value = value.strip()
kit = KitInfo.objects.filter(kitType__in=["SequencingKit"], name=value)
if not kit:
kit = KitInfo.objects.filter(kitType__in=["SequencingKit"], description=value)
if not kit:
errors.append("%s %s not found" % (displayedName, value))
return errors
def validateField(self, field_name, new_field_value):
'''
Flows qc value must be a positive integer
Chip type is required
'''
if field_name == KitsFieldNames.FLOWS:
errors = validate_flows(new_field_value)
if errors:
self.validationErrors[field_name] = ' '.join(errors)
else:
self.validationErrors.pop(field_name, None)
if field_name == KitsFieldNames.CHIP_TYPE and self.prepopulatedFields.get('is_chipType_required',True):
if validation.has_value(new_field_value):
self.validationErrors.pop(field_name, None)
else:
self.validationErrors[field_name] = validation.required_error("Chip Type")
if field_name == KitsFieldNames.TEMPLATE_KIT_NAME:
if validation.has_value(new_field_value):
self.validationErrors.pop(field_name, None)
else:
self.validationErrors[field_name] = validation.required_error("Template Kit")
def validate_plan_name(value, field_label):
errors = []
if not validation.has_value(value):
errors.append(validation.required_error(field_label))
if not validation.is_valid_chars(value):
errors.append(validation.invalid_chars_error(field_label))
if not validation.is_valid_length(value, MAX_LENGTH_PLAN_NAME):
errors.append(
validation.invalid_length_error(field_label, MAX_LENGTH_PLAN_NAME,
value))
return errors
def validate_plan_templating_kit_name(value, displayedName="Template Kit"):
errors = []
if not validation.has_value(value):
errors.append(validation.required_error(displayedName))
else:
value = value.strip()
kit = KitInfo.objects.filter(kitType__in = ["TemplatingKit", "IonChefPrepKit"], name = value)
if not kit:
kit = KitInfo.objects.filter(kitType__in = ["TemplatingKit", "IonChefPrepKit"], description = value)
if not kit:
errors.append("%s %s not found" %(displayedName, value))
return errors
def validate_plan_templating_kit_name(value, displayedName="Template Kit"):
errors = []
if not validation.has_value(value):
errors.append(validation.required_error(displayedName))
else:
value = value.strip()
kit = KitInfo.objects.filter(kitType__in=["TemplatingKit", "IonChefPrepKit"], name=value)
if not kit:
kit = KitInfo.objects.filter(kitType__in=["TemplatingKit", "IonChefPrepKit"], description=value)
if not kit:
errors.append("%s %s not found" % (displayedName, value))
return errors
def check_uploaded_files(referenceNames=[], bedfilePaths=[]):
''' checks if reference or BED files are missing '''
missing_files = {}
for reference in referenceNames:
ref_err = validate_reference_short_name(reference)
if ref_err:
missing_files.setdefault('references',[]).append(reference)
content = Content.objects.filter(publisher__name="BED")
for bedfile in bedfilePaths:
bedfile_err = validation.has_value(bedfile) and (content.filter(path=bedfile).count() == 0
and content.filter(file=bedfile).count() == 0)
if bedfile_err:
missing_files.setdefault('bedfiles',[]).append(bedfile)
return missing_files
def check_uploaded_files(referenceNames=[], bedfilePaths=[]):
''' checks if reference or BED files are missing '''
missing_files = {}
for reference in referenceNames:
ref_err = validate_reference_short_name(reference)
if ref_err:
missing_files.setdefault('references', []).append(reference)
content = Content.objects.filter(publisher__name="BED")
for bedfile in bedfilePaths:
bedfile_err = validation.has_value(bedfile) and content.filter(
path=bedfile).count() == 0
if bedfile_err:
missing_files.setdefault('bedfiles', []).append(bedfile)
return missing_files
def validate_reference_short_name(value, field_label):
errors = []
if validation.has_value(value):
value = value.strip()
reference = ReferenceGenome.objects.filter(short_name=value,
enabled=True)
if not reference.exists():
generic_not_found_error = validation.invalid_not_found_error(
field_label, value)
error_fixing_message = ugettext_lazy(
"references_genome_download.messages.help.import"
) # "To import it, visit Settings > References > Import Preloaded Ion References"
reference_error_message = (generic_not_found_error.strip() +
error_fixing_message.strip()
) # avoid lazy
errors.append(reference_error_message)
return errors
def validate_optional_kit_name(value, kitType, field_label, isNewPlan=None):
errors = []
warnings = []
if validation.has_value(value):
kit = get_kitInfo_by_name_or_description(value, kitType)
if not kit:
errors.append(
validation.invalid_not_found_error(field_label, value))
elif kit and not kit.isActive:
if isNewPlan:
errors.append(validation.invalid_not_active(
field_label, value))
else:
warnings.append(
validation.invalid_not_active(field_label, value))
return errors, warnings
def validateField_crossField_dependency(self, field_name, new_field_value, dependent_field_name, dependent_field_value):
isBarcodeKitRequired = False
if field_name == KitsFieldNames.LIBRARY_KIT_NAME:
if new_field_value:
libKit_objs = KitInfo.objects.filter(kitType='LibraryKit', name = new_field_value).order_by("-isActive")
if libKit_objs and len(libKit_objs) > 0:
libKit_obj = libKit_objs[0]
if libKit_obj.categories and ("bcrequired" in libKit_obj.categories.lower()):
isBarcodeKitRequired = True
if dependent_field_name == KitsFieldNames.BARCODE_KIT_NAME:
if self.prepopulatedFields[KitsFieldNames.IS_BARCODE_KIT_SELECTION_REQUIRED] or isBarcodeKitRequired:
if validation.has_value(dependent_field_value):
self.validationErrors.pop(dependent_field_name, None)
else:
self.validationErrors[dependent_field_name] = validation.required_error("Barcode Set")
else:
self.validationErrors.pop(dependent_field_name, None)
def validate_optional_kit_name(value, kitType, displayedName=None, isNewPlan=None):
errors = []
warnings = []
if validation.has_value(value):
value = value.strip()
query_kwargs = {"kitType__in": kitType}
query_args = (Q(name__iexact=value) | Q(description__iexact=value),)
kit = KitInfo.objects.filter(*query_args, **query_kwargs)
if not kit:
errors.append("%s %s not found" % (displayedName, value))
elif kit and not kit[0].isActive:
if isNewPlan:
errors.append("%s %s not active" % (displayedName, value))
else:
warnings.append("Found inactive %s %s" % (displayedName, value))
return errors, warnings
def validate_plan_templating_kit_name(value, displayedName="Template Kit", isNewPlan=None):
errors = []
warnings = []
if not validation.has_value(value):
errors.append(validation.required_error(displayedName))
else:
value = value.strip()
query_kwargs = {"kitType__in": ["TemplatingKit", "IonChefPrepKit"]}
query_args = (Q(name=value) | Q(description=value), )
kit = KitInfo.objects.filter(*query_args, **query_kwargs)
if not kit:
errors.append("%s %s not found" % (displayedName, value))
elif kit and not kit[0].isActive:
if isNewPlan:
errors.append("%s %s not active" % (displayedName, value))
else:
warnings.append("Found inactive %s %s" % (displayedName, value))
return errors, warnings
def check_uploaded_files(referenceNames=[],
bedfilePaths=[],
referenceNames_label="Reference"):
""" checks if reference or BED files are missing
referenceNames_label='Reference'
"""
missing_files = {}
for reference in referenceNames:
ref_err = validate_reference_short_name(
reference, field_label=referenceNames_label)
if ref_err:
missing_files.setdefault("references", []).append(reference)
content = Content.objects.filter(publisher__name="BED")
for bedfile in bedfilePaths:
bedfile_err = validation.has_value(bedfile) and (
content.filter(path=bedfile).count() == 0
and content.filter(file=bedfile).count() == 0)
if bedfile_err:
missing_files.setdefault("bedfiles", []).append(bedfile)
return missing_files
def _validate_textValue_mandatory(value, displayedTerm):
isValid = False
if not validation.has_value(value):
return isValid, "Error, " + validation.required_error(displayedTerm)
return True, None
def validate_targetRegionBedFile_for_runType(
value,
field_label,
runType,
reference,
nucleotideType=None,
applicationGroupName=None,
isPrimaryTargetRegion=True,
barcodeId="",
runType_label=ugettext_lazy(
"workflow.step.application.fields.runType.label"),
):
"""
validate targetRegionBedFile based on the selected reference and the plan's runType
"""
errors = []
value = value.strip() if value else ""
if value:
missing_file = check_uploaded_files(bedfilePaths=[value])
if missing_file:
errors.append("%s : %s not found" % (field_label, value))
logger.debug(
"plan_validator.validate_targetRegionBedFile_for_run() SKIPS validation due to no targetRegion file exists in db. value=%s"
% (value))
return errors
logger.debug(
"plan_validator.validate_targetRegionBedFile_for_runType() value=%s; runType=%s; reference=%s; nucleotideType=%s; applicationGroupName=%s"
% (value, runType, reference, nucleotideType, applicationGroupName))
if not isPrimaryTargetRegion:
logger.debug(
"plan_validator.validate_targetRegionBedFile_for_run() SKIPS validation due to no validation rules for non-primary targetRegion. value=%s"
% (value))
return errors
if reference:
if runType:
runType = runType.strip()
applProducts = ApplProduct.objects.filter(
isActive=True,
applType__runType=runType,
applicationGroup__name=applicationGroupName,
) or ApplProduct.objects.filter(isActive=True,
applType__runType=runType)
if applProducts:
applProduct = applProducts[0]
if applProduct:
if (validation.has_value(value) and
not applProduct.isTargetRegionBEDFileSupported):
errors.append(
validation.invalid_invalid_related(
field_label,
ScientificApplication.verbose_name))
else:
isRequired = (
applProduct.
isTargetRegionBEDFileSelectionRequiredForRefSelection
)
if (isRequired and not validation.has_value(value)
and not barcodeId):
# skip for now
if (runType in ["AMPS_DNA_RNA", "AMPS_HD_DNA_RNA"]
and nucleotideType
and nucleotideType.upper() == "RNA"):
logger.debug(
"plan_validator.validate_targetRegionBedFile_for_runType() ALLOW MISSING targetRegionBed for runType=%s; nucleotideType=%s"
% (runType, nucleotideType))
elif runType in ["AMPS_RNA", "AMPS_HD_RNA"]:
logger.debug(
"plan_validator.validate_targetRegionBedFile_for_runType() ALLOW MISSING targetRegionBed for runType=%s; applicationGroupName=%s"
% (runType, applicationGroupName))
else:
errors.append(
validation.invalid_required_related(
field_label,
ScientificApplication.verbose_name))
elif value:
if not os.path.isfile(value):
errors.append(
validation.invalid_invalid_value(
field_label, value))
else:
errors.append(
validation.invalid_invalid_value_related(
runType_label, runType,
ScientificApplication.verbose_name))
else:
errors.append(
validation.invalid_required_related(
runType_label, ScientificApplication.verbose_name))
return errors
def validate_targetRegionBedFile_for_runType(
value,
runType,
reference,
nucleotideType=None,
applicationGroupName=None,
displayedName="Target Regions BED File"):
"""
validate targetRegionBedFile based on the selected reference and the plan's runType
"""
errors = []
value = value.strip() if value else ""
logger.debug(
"plan_validator.validate_targetRegionBedFile_for_runType() value=%s; runType=%s; reference=%s; nucleotideType=%s; applicationGroupName=%s"
% (value, runType, reference, nucleotideType, applicationGroupName))
if reference:
if runType:
runType = runType.strip()
applProducts = ApplProduct.objects.filter(isActive=True, applType__runType=runType, applicationGroup__name=applicationGroupName) \
or ApplProduct.objects.filter(isActive=True, applType__runType=runType)
if applProducts:
applProduct = applProducts[0]
if applProduct:
if validation.has_value(
value
) and not applProduct.isTargetRegionBEDFileSupported:
errors.append(
displayedName +
" selection is not supported for this Application")
else:
isRequired = applProduct.isTargetRegionBEDFileSelectionRequiredForRefSelection
if isRequired and not validation.has_value(value):
# skip for now
if runType == "AMPS_DNA_RNA" and nucleotideType and nucleotideType.upper(
) == "RNA":
logger.debug(
"plan_validator.validate_targetRegionBedFile_for_runType() ALLOW MISSING targetRegionBed for runType=%s; nucleotideType=%s"
% (runType, nucleotideType))
elif runType == "AMPS_RNA" and applicationGroupName and applicationGroupName in [
"DNA + RNA", "DNA and Fusions"
]:
logger.debug(
"plan_validator.validate_targetRegionBedFile_for_runType() ALLOW MISSING targetRegionBed for runType=%s; applicationGroupName=%s"
% (runType, applicationGroupName))
else:
errors.append(
"%s is required for this application" %
(displayedName))
elif value:
if not os.path.isfile(value):
errors.append("Missing or Invalid %s - %s" %
(displayedName, value))
else:
errors.append("%s Application %s not found" %
(displayedName, runType))
else:
errors.append("%s Run type is missing" % (displayedName))
# logger.debug("EXIT plan_validator.validate_targetRegionBedFile_for_runType() errors=%s" %(errors))
return errors
