def validate_application_group_for_runType(value, field_label, runType,
runType_label):
errors = []
if value:
value = value.strip()
applicationGroups = ApplicationGroup.objects.filter(
name__iexact=value) | ApplicationGroup.objects.filter(
description__iexact=value)
if applicationGroups:
applicationGroup = applicationGroups[0]
if runType:
runTypeObjs = RunType.objects.filter(runType__iexact=runType)
if runTypeObjs:
associations = runTypeObjs[0].applicationGroups
if not associations.filter(name=applicationGroup.name):
errors.append(
validation.invalid_choice_related_choice(
field_label,
value,
associations.values_list("name", flat=True),
runType_label,
runType,
))
if not runType:
errors.append(validation.missing_error(runType_label))
if not runTypeObjs:
errors.append(
validation.invalid_not_found_error(runType_label, runType))
else:
errors.append(
validation.invalid_not_found_error(field_label, value))
return errors
def validate_reference(referenceName, displayedName="Reference"):
errors = []
ref_short_name = ""
if referenceName:
input = referenceName.strip()
selectedRefs = ReferenceGenome.objects.filter(name=input)
if selectedRefs:
ref_short_name = selectedRefs[0].short_name
else:
selectedRefs = ReferenceGenome.objects.filter(name__iexact=input)
if selectedRefs:
ref_short_name = selectedRefs[0].short_name
else:
selectedRefs = ReferenceGenome.objects.filter(short_name=input)
if selectedRefs:
ref_short_name = selectedRefs[0].short_name
else:
selectedRefs = ReferenceGenome.objects.filter(short_name__iexact=input)
if selectedRefs:
ref_short_name = selectedRefs[0].short_name
else:
errors.append(validation.invalid_not_found_error(displayedName, referenceName))
return errors, ref_short_name
def validate_reference(referenceName, displayedName='Reference'):
errors = []
ref_short_name = ""
if referenceName:
input = referenceName.strip()
selectedRefs = ReferenceGenome.objects.filter(name=input)
if selectedRefs:
ref_short_name = selectedRefs[0].short_name
else:
selectedRefs = ReferenceGenome.objects.filter(name__iexact=input)
if selectedRefs:
ref_short_name = selectedRefs[0].short_name
else:
selectedRefs = ReferenceGenome.objects.filter(short_name=input)
if selectedRefs:
ref_short_name = selectedRefs[0].short_name
else:
selectedRefs = ReferenceGenome.objects.filter(
short_name__iexact=input)
if selectedRefs:
ref_short_name = selectedRefs[0].short_name
else:
errors.append(
validation.invalid_not_found_error(
displayedName, referenceName))
return errors, ref_short_name
def validate_reference(value, field_label, runType, applicationGroupName,
application_label):
errors = []
ref_short_name = ""
value = value.strip() if value else ""
if value:
applProduct = ApplProduct.objects.filter(
isActive=True,
applType__runType=runType,
applicationGroup__name=applicationGroupName,
) or ApplProduct.objects.filter(isActive=True,
applType__runType=runType)
if applProduct and not applProduct[0].isReferenceSelectionSupported:
errors.append(
validation.invalid_invalid_value_related(
field_label, value, application_label))
else:
selectedRefs = (
ReferenceGenome.objects.filter(name=value)
or ReferenceGenome.objects.filter(name__iexact=value)
or ReferenceGenome.objects.filter(short_name=value)
or ReferenceGenome.objects.filter(short_name__iexact=value))
if selectedRefs:
ref_short_name = selectedRefs[0].short_name
else:
errors.append(
validation.invalid_not_found_error(field_label, value))
return errors, ref_short_name
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 validate_reference(value,
runType,
applicationGroupName,
displayedName='Reference'):
errors = []
ref_short_name = ""
value = value.strip() if value else ""
if value:
applProduct = ApplProduct.objects.filter(isActive=True, applType__runType=runType, applicationGroup__name=applicationGroupName) \
or ApplProduct.objects.filter(isActive=True, applType__runType=runType)
if applProduct and not applProduct[0].isReferenceSelectionSupported:
errors.append(displayedName +
" selection is not supported for this Application")
else:
selectedRefs = ReferenceGenome.objects.filter(name=value) or \
ReferenceGenome.objects.filter(name__iexact=value) or \
ReferenceGenome.objects.filter(short_name=value) or \
ReferenceGenome.objects.filter(short_name__iexact=value)
if selectedRefs:
ref_short_name = selectedRefs[0].short_name
else:
errors.append(
validation.invalid_not_found_error(displayedName, value))
return errors, ref_short_name
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_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_sample_grouping(value, field_label):
errors = []
if value:
value = value.strip()
groupings = SampleGroupType_CV.objects.filter(
displayedName__iexact=value)
if not groupings:
errors.append(
validation.invalid_not_found_error(field_label, value))
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_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 validate_library_key(value, field_label):
errors = []
selectedLibKey = None
if not value:
errors.append(validation.required_error(field_label))
else:
try:
selectedLibKey = LibraryKey.objects.get(name__iexact=value.strip())
except LibraryKey.DoesNotExist:
try:
selectedLibKey = LibraryKey.objects.get(
sequence__iexact=value.strip())
except LibraryKey.DoesNotExist:
logger.debug(
"plan_validator.validate_lib_key ...%s not found" % input)
selectedLibKey = None
if not selectedLibKey:
errors.append(
validation.invalid_not_found_error(
field_label, value)) # 'Library key %s not found' % value
return errors, selectedLibKey
def validate_reference(value, runType, applicationGroupName, displayedName='Reference'):
errors = []
ref_short_name = ""
value = value.strip() if value else ""
if value:
applProduct = ApplProduct.objects.filter(isActive=True, applType__runType=runType, applicationGroup__name=applicationGroupName) \
or ApplProduct.objects.filter(isActive=True, applType__runType=runType)
if applProduct and not applProduct[0].isReferenceSelectionSupported:
errors.append(displayedName+" selection is not supported for this Application")
else:
selectedRefs = ReferenceGenome.objects.filter(name=value) or \
ReferenceGenome.objects.filter(name__iexact=value) or \
ReferenceGenome.objects.filter(short_name=value) or \
ReferenceGenome.objects.filter(short_name__iexact=value)
if selectedRefs:
ref_short_name = selectedRefs[0].short_name
else:
errors.append(validation.invalid_not_found_error(displayedName, value))
return errors, ref_short_name
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)
