def validate_planStatus(planStatus, field_label):
"""
validate planStatus is in ALLOWED_PLAN_STATUS
"""
errors = []
if planStatus:
planStatus = planStatus.strip()
isValid = False
defaultPlanStatus = get_default_planStatus()
for status in defaultPlanStatus:
if planStatus.lower() == status:
isValid = True
if not isValid:
errors.append(
validation.invalid_choice(field_label, planStatus,
defaultPlanStatus)
) # "The plan status(%s) is not valid. Default Values are: %s" % (planStatus, defaultPlanStatus_display))
logger.debug("plan_validator.validate_planStatus() value=%s;" %
(planStatus))
return errors
def validate_runType(runType, field_label):
errors = []
if runType:
runTypeObjs = RunType.objects.filter(runType__iexact=runType)
if not runTypeObjs:
validRunTypes = RunType.objects.values_list("runType", flat=True)
errors.append(
validation.invalid_choice(field_label, runType, validRunTypes))
return errors
def validate_plan_samplePrepProtocol(value, templatingKitName, field_label,
templatingKitName_label):
# validate if input matches the common_CV value or uid
errors = []
if value:
value = value.strip()
(isValid, cv, cvLists) = _validate_spp_value_uid(value)
if not isValid:
cvLists = [cvlist.value for cvlist in cvLists]
cvLists.append("undefined")
validation.invalid_choice(field_label, value, cvLists)
errors.append(
validation.invalid_choice(field_label, value, cvLists))
logger.debug(
"plan_validator.validate_plan_samplePrepProtocol() : Error, %s is not valid. Valid sample kit protocols are: %s"
% (value, cvLists))
else:
# valid spp but still validate if it is compatible with the specified templatingKit
isValid, validSPP_tempKit = _validate_ssp_templatingKit(
cv.categories, templatingKitName, cvLists)
if not isValid:
validSPP_tempKit.append("undefined")
errors.append(
validation.invalid_choice_related_choice(
field_label,
value,
validSPP_tempKit,
templatingKitName_label,
templatingKitName,
)
) # '%s not supported for the specified templatingKit %s. Valid sample prep protocols are: %s ' % (value, templatingKitName, ", ".join(validSPP_tempKit))
logger.debug(
"plan_validator.validate_plan_samplePrepProtocol() : Error,%s %s not supported for this templatingKit %s "
% (field_label, value, templatingKitName))
value = cv.value
return errors, value
def validate_16s_markers(value, field_label):
errors = []
if not value or value == "none":
value = ""
else:
value = value.strip().lower() if value else ""
annotations = SampleAnnotation_CV.objects.filter(
annotationType="16s_markers")
annotationObj = annotations.filter(
value__iexact=value) or annotations.filter(iRValue__iexact=value)
if annotationObj:
value = annotationObj[0].value
else:
choices = annotations.order_by("value").values_list("value",
flat=True)
errors.append(
validation.invalid_choice(field_label, value, choices))
return errors, value
def validate_sampleControlType(value, field_label):
errors = []
value = value.strip().lower() if value else ""
if value:
if value == "none":
value = ""
else:
controlTypes = SampleAnnotation_CV.objects.filter(
annotationType="controlType")
controlType = controlTypes.filter(
value__iexact=value) or controlTypes.filter(
iRValue__iexact=value)
if controlType:
value = controlType[0].value
else:
choices = controlTypes.order_by("value").values_list("value",
flat=True)
errors.append(
validation.invalid_choice(field_label, value, choices))
return errors, value