def _validate_textValue_leadingChars(value, displayedTerm):
isValid = False
if value and not validation.is_valid_leading_chars(value):
return isValid, "Error, " + validation.invalid_leading_chars(
displayedTerm)
return True, None
def validate_barcoded_sample_info(
sampleName, sampleId, nucleotideType, runTypeName, sampleReference, displayedName="Barcoded Sample"
):
errors = []
if not validation.is_valid_chars(sampleName):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_leading_chars(sampleName):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_length(sampleName, MAX_LENGTH_SAMPLE_NAME):
errors.append(validation.invalid_length_error(displayedName, MAX_LENGTH_SAMPLE_NAME))
sample_id_errors = validate_sample_id(sampleId)
if sample_id_errors:
errors.extend(sample_id_errors)
sample_nucleotideType = ""
nucleotideType_errors, sample_nucleotideType = validate_sample_nucleotideType(nucleotideType, runTypeName)
if nucleotideType_errors:
errors.extend(nucleotideType_errors)
ref_errors, ref_short_name = validate_reference(sampleReference, displayedName="Sample Reference")
##logger.debug("plan_validator.validate_barcoded_sample_info() sampleReference=%s; ref_short_name=%s" %(sampleReference, ref_short_name))
if ref_errors:
errors.extend(ref_errors)
##logger.debug("plan_validator.validate_barcoded_sample_info() errors=%s" %(errors))
return errors, ref_short_name, sample_nucleotideType
def validate_sample_name(value,
displayedName='Sample Name',
isTemplate=None,
barcodeId=None):
errors = []
if not value:
if not isTemplate:
errors.append(validation.required_error(displayedName))
else:
if isTemplate:
errors.append(
"Invalid input. Sample information cannot be saved in the template"
)
if barcodeId:
errors.append(
"Invalid input. Barcode kit should not be provided (%s) for non barcoded plan"
% barcodeId)
if not validation.is_valid_chars(value):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_leading_chars(value):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_length(value, MAX_LENGTH_SAMPLE_NAME):
errors.append(
validation.invalid_length_error(displayedName,
MAX_LENGTH_SAMPLE_NAME))
return errors
def validate_barcoded_sample_info(sampleName, sampleId, nucleotideType, sampleReference, runType, applicationGroupName, displayedName='Barcoded Sample'):
errors = []
if not validation.is_valid_chars(sampleName):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_leading_chars(sampleName):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_length(sampleName, MAX_LENGTH_SAMPLE_NAME):
errors.append(validation.invalid_length_error(displayedName, MAX_LENGTH_SAMPLE_NAME))
sample_id_errors = validate_sample_id(sampleId)
if sample_id_errors:
errors.extend(sample_id_errors)
nucleotideType_errors, sample_nucleotideType = validate_sample_nucleotideType(nucleotideType, runType, applicationGroupName)
if (nucleotideType_errors):
errors.extend(nucleotideType_errors)
ref_displayedName = "Sample Reference" if nucleotideType != "RNA" else "RNA Sample Reference"
ref_errors, ref_short_name = validate_reference(sampleReference, runType, applicationGroupName, displayedName=ref_displayedName)
if (ref_errors):
errors.extend(ref_errors)
return errors, ref_short_name, sample_nucleotideType
def validate_barcoded_sample_info(sampleName, sampleId, nucleotideType, sampleReference, runType, applicationGroupName, displayedName='Barcoded Sample'):
errors = []
if not validation.is_valid_chars(sampleName):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_leading_chars(sampleName):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_length(sampleName, MAX_LENGTH_SAMPLE_NAME):
errors.append(validation.invalid_length_error(displayedName, MAX_LENGTH_SAMPLE_NAME))
sample_id_errors = validate_sample_id(sampleId)
if sample_id_errors:
errors.extend(sample_id_errors)
nucleotideType_errors, sample_nucleotideType = validate_sample_nucleotideType(nucleotideType, runType, applicationGroupName)
if (nucleotideType_errors):
errors.extend(nucleotideType_errors)
ref_displayedName = "Sample Reference" if nucleotideType != "RNA" else "RNA Sample Reference"
ref_errors, ref_short_name = validate_reference(sampleReference, runType, applicationGroupName, displayedName=ref_displayedName)
if (ref_errors):
errors.extend(ref_errors)
return errors, ref_short_name, sample_nucleotideType
def validate_barcoded_sample_info(sampleName,
sampleId,
nucleotideType,
sampleReference,
sampleRnaReference,
runType,
applicationGroupName,
displayedName='Barcoded Sample'):
errors = []
if not validation.is_valid_chars(sampleName):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_leading_chars(sampleName):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_length(sampleName, MAX_LENGTH_SAMPLE_NAME):
errors.append(
validation.invalid_length_error(displayedName,
MAX_LENGTH_SAMPLE_NAME))
sample_id_errors = validate_sample_id(sampleId)
if sample_id_errors:
errors.extend(sample_id_errors)
sample_nucleotideType = ""
nucleotideType_errors, sample_nucleotideType = validate_sample_nucleotideType(
nucleotideType, runType, applicationGroupName)
if (nucleotideType_errors):
errors.extend(nucleotideType_errors)
if runType == "AMPS_DNA_RNA" and sample_nucleotideType.upper() == "RNA":
rna_ref_errors, rna_ref_short_name = validate_reference(
sampleRnaReference,
runType,
applicationGroupName,
displayedName="RNA Sample Reference")
logger.debug(
"plan_validator.validate_barcoded_sample_info() sampleRnaReference=%s; rna_ref_short_name=%s"
% (sampleRnaReference, rna_ref_short_name))
if (rna_ref_errors):
errors.extend(rna_ref_errors)
else:
rna_ref_errors = []
rna_ref_short_name = ""
ref_errors, ref_short_name = validate_reference(
sampleReference,
runType,
applicationGroupName,
displayedName="Sample Reference")
##logger.debug("plan_validator.validate_barcoded_sample_info() sampleReference=%s; ref_short_name=%s" %(sampleReference, ref_short_name))
if (ref_errors):
errors.extend(ref_errors)
return errors, ref_short_name, rna_ref_short_name, sample_nucleotideType
def validate_sample_name(value, displayedName="Sample Name"):
errors = []
if not validation.is_valid_chars(value):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_leading_chars(value):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_length(value, MAX_LENGTH_SAMPLE_NAME):
errors.append(validation.invalid_length_error(displayedName, MAX_LENGTH_SAMPLE_NAME))
return errors
def validate_sample_name(value, displayedName='Sample Name'):
errors = []
if not validation.is_valid_chars(value):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_leading_chars(value):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_length(value, MAX_LENGTH_SAMPLE_NAME):
errors.append(validation.invalid_length_error(displayedName, MAX_LENGTH_SAMPLE_NAME))
return errors
def validate_field(self, value, bad_samples, validate_leading_chars=True, max_length=MAX_LENGTH_SAMPLE_NAME):
exists = False
if value:
exists = True
if not validation.is_valid_chars(value):
bad_samples.append(value)
if validate_leading_chars and value not in bad_samples and not validation.is_valid_leading_chars(value):
bad_samples.append(value)
if value not in bad_samples and not validation.is_valid_length(value, max_length):
bad_samples.append(value)
return exists
def validate_barcoded_sample_info(
sampleName,
sampleName_label,
sampleExternalId,
sampleExternalId_label,
nucleotideType,
nucleotideType_label,
sampleReference,
sampleReference_label,
runType,
applicationGroupName,
):
errors = []
if not validation.is_valid_chars(sampleName):
errors.append(validation.invalid_chars_error(sampleName_label))
if not validation.is_valid_leading_chars(sampleName):
errors.append(validation.invalid_leading_chars(sampleName_label))
if not validation.is_valid_length(sampleName, MAX_LENGTH_SAMPLE_NAME):
errors.append(
validation.invalid_length_error(sampleName_label,
MAX_LENGTH_SAMPLE_NAME,
sampleName))
sample_id_errors = validate_sample_id(sampleExternalId,
field_label=sampleExternalId_label)
if sample_id_errors:
errors.extend(sample_id_errors)
nucleotideType_errors, sample_nucleotideType = validate_sample_nucleotideType(
nucleotideType,
runType,
applicationGroupName,
field_label=nucleotideType_label)
if nucleotideType_errors:
errors.extend(nucleotideType_errors)
ref_errors, ref_short_name = validate_reference(
sampleReference,
field_label=sampleReference_label,
runType=runType,
applicationGroupName=applicationGroupName,
application_label=ScientificApplication.verbose_name,
)
if ref_errors:
errors.extend(ref_errors)
return errors, ref_short_name, sample_nucleotideType
def validate_sample_name(value, displayedName='Sample Name', isTemplate=None, barcodeId=None):
errors = []
if not value:
if not isTemplate:
errors.append(validation.required_error(displayedName))
else:
if isTemplate:
errors.append("Invalid input. Sample information cannot be saved in the template")
if barcodeId:
errors.append("Invalid input. Barcode kit should not be provided (%s) for non barcoded plan" % barcodeId)
if not validation.is_valid_chars(value):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_leading_chars(value):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_length(value, MAX_LENGTH_SAMPLE_NAME):
errors.append(validation.invalid_length_error(displayedName, MAX_LENGTH_SAMPLE_NAME))
return errors
def validate_sample_name(
value,
field_label,
isTemplate=None,
isTemplate_label=PlanTemplate.verbose_name,
barcodeId=None,
barcodeId_label=ugettext_lazy("workflow.step.kits.fields.barcodeId.label"),
): # TODO: i18n
errors = []
if not value:
if not isTemplate:
errors.append(validation.required_error(field_label))
else:
if isTemplate:
errors.append(
validation.format(
ugettext_lazy(
"template.messages.validation.invalidsamples"),
{"name": isTemplate_label},
)
) # "Invalid input. Sample information cannot be saved in the %(name)s"
if barcodeId:
errors.append(
validation.format(
ugettext_lazy(
"plannedexperiment.messages.validation.nonbarcoded.barcodesetnotrequired"
),
{
"barcodeSetName": barcodeId_label,
"barcodeSetValue": barcodeId
},
)
) # "Invalid input. %(barcodeSetName)s (%(barcodeSetValue)s) should not be provided for non barcoded plan"
if not validation.is_valid_chars(value):
errors.append(validation.invalid_chars_error(field_label))
if not validation.is_valid_leading_chars(value):
errors.append(validation.invalid_leading_chars(field_label))
if not validation.is_valid_length(value, MAX_LENGTH_SAMPLE_NAME):
errors.append(
validation.invalid_length_error(field_label,
MAX_LENGTH_SAMPLE_NAME, value))
return errors
def validate_barcoded_sample_info(applicationGroupName, runType, sampleName, sampleId, nucleotideType, runTypeName, sampleReference, sampleRnaReference, displayedName='Barcoded Sample'):
errors = []
if not validation.is_valid_chars(sampleName):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_leading_chars(sampleName):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_length(sampleName, MAX_LENGTH_SAMPLE_NAME):
errors.append(validation.invalid_length_error(displayedName, MAX_LENGTH_SAMPLE_NAME))
sample_id_errors = validate_sample_id(sampleId)
if sample_id_errors:
errors.extend(sample_id_errors)
sample_nucleotideType = ""
nucleotideType_errors, sample_nucleotideType = validate_sample_nucleotideType(nucleotideType, runTypeName, applicationGroupName)
if (nucleotideType_errors):
errors.extend(nucleotideType_errors)
if runType == "AMPS_DNA_RNA" and sample_nucleotideType.upper() == "RNA":
rna_ref_errors, rna_ref_short_name = validate_reference(sampleRnaReference, displayedName = "RNA Sample Reference")
logger.debug("plan_validator.validate_barcoded_sample_info() sampleRnaReference=%s; rna_ref_short_name=%s" %(sampleRnaReference, rna_ref_short_name))
if (rna_ref_errors):
errors.extend(rna_ref_errors)
else:
rna_ref_errors = []
rna_ref_short_name = ""
ref_errors, ref_short_name = validate_reference(sampleReference, displayedName = "Sample Reference")
##logger.debug("plan_validator.validate_barcoded_sample_info() sampleReference=%s; ref_short_name=%s" %(sampleReference, ref_short_name))
if (ref_errors):
errors.extend(ref_errors)
##logger.debug("plan_validator.validate_barcoded_sample_info() errors=%s" %(errors))
return errors, ref_short_name, rna_ref_short_name, sample_nucleotideType
def validate_barcoded_sample_info(sampleName,
sampleId,
nucleotideType,
runTypeName,
sampleReference,
displayedName='Barcoded Sample'):
errors = []
if not validation.is_valid_chars(sampleName):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_leading_chars(sampleName):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_length(sampleName, MAX_LENGTH_SAMPLE_NAME):
errors.append(
validation.invalid_length_error(displayedName,
MAX_LENGTH_SAMPLE_NAME))
sample_id_errors = validate_sample_id(sampleId)
if sample_id_errors:
errors.extend(sample_id_errors)
sample_nucleotideType = ""
nucleotideType_errors, sample_nucleotideType = validate_sample_nucleotideType(
nucleotideType, runTypeName)
if (nucleotideType_errors):
errors.extend(nucleotideType_errors)
ref_errors, ref_short_name = validate_reference(
sampleReference, displayedName="Sample Reference")
##logger.debug("plan_validator.validate_barcoded_sample_info() sampleReference=%s; ref_short_name=%s" %(sampleReference, ref_short_name))
if (ref_errors):
errors.extend(ref_errors)
##logger.debug("plan_validator.validate_barcoded_sample_info() errors=%s" %(errors))
return errors, ref_short_name, sample_nucleotideType
def _validate_textValue_leadingChars(value, displayedTerm):
isValid = False
if value and not validation.is_valid_leading_chars(value):
return isValid, "Error, " + validation.invalid_leading_chars(displayedTerm)
return True, None
