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 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_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, 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_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_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 validate_projects(value, displayedName='Project Name', delim=','):
"""
validate projects case-insensitively with leading/trailing blanks in the input ignored
"""
errors = []
trimmed_projects = ""
if value:
for project in value.split(delim):
trimmed_project = project.strip()
if trimmed_project:
trimmed_projects = trimmed_projects + trimmed_project + delim
if not validation.is_valid_chars(trimmed_project):
errors.append(
validation.invalid_chars_error(displayedName))
if not validation.is_valid_length(trimmed_project,
PROJECT_NAME_LENGTH):
errors.append(
validation.invalid_length_error(
displayedName, PROJECT_NAME_LENGTH))
if errors:
break
return errors, trimmed_projects
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_sampleName(sampleName):
displayedTerm = "Sample name"
isValid, errorMessage = _validate_textValue_mandatory(
sampleName, displayedTerm)
if not isValid:
return isValid, errorMessage
isValid, errorMessage = _validate_textValue(sampleName, displayedTerm)
if not isValid:
return isValid, errorMessage
isValid, errorMessage = _validate_textValue_leadingChars(
sampleName, displayedTerm)
if not isValid:
return isValid, errorMessage
if not validation.is_valid_length(sampleName.strip(),
MAX_LENGTH_SAMPLE_NAME):
errorMessage = validation.invalid_length_error(
"Error, Sample name", MAX_LENGTH_SAMPLE_NAME
) + ". It is currently %s characters long." % str(
len(sampleName.strip()))
return isValid, errorMessage
return True, None
def validate_notes(value, displayedName='Notes'):
errors = []
if not validation.is_valid_chars(value):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_length(value, MAX_LENGTH_NOTES):
errors.append(validation.invalid_length_error(displayedName, MAX_LENGTH_NOTES))
return errors
def validate_sample_id(value, displayedName='Sample Id'):
errors = []
if not validation.is_valid_chars(value):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_length(value, MAX_LENGTH_SAMPLE_ID):
errors.append(validation.invalid_length_error(displayedName, MAX_LENGTH_SAMPLE_ID))
return errors
def validate_sample_id(value, displayedName="Sample Id"):
errors = []
if not validation.is_valid_chars(value):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_length(value, MAX_LENGTH_SAMPLE_ID):
errors.append(validation.invalid_length_error(displayedName, MAX_LENGTH_SAMPLE_ID))
return errors
def validate_notes(value, displayedName="Notes"):
errors = []
if not validation.is_valid_chars(value):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_length(value, MAX_LENGTH_NOTES):
errors.append(validation.invalid_length_error(displayedName, MAX_LENGTH_NOTES))
return errors
def _validate_optional_text(value, maxLength, displayedTerm):
isValid, errorMessage = _validate_textValue(value.strip(), displayedTerm)
if not isValid:
return isValid, errorMessage
if not validation.is_valid_length(value.strip(), maxLength):
errorMessage = validation.invalid_length_error("Error, " + displayedTerm, maxLength) + ". It is currently %s characters long." % str(len(value.strip()))
return isValid, errorMessage
return True, None
def validate_sample_tube_label(value, displayedName='Sample Tube Label'):
errors = []
if value:
if not validation.is_valid_chars(value):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_length(value, MAX_LENGTH_SAMPLE_TUBE_LABEL):
errors.append(validation.invalid_length_error(displayedName, MAX_LENGTH_SAMPLE_TUBE_LABEL))
return errors
def validate_sample_tube_label(value, displayedName="Sample Tube Label"):
errors = []
if value:
if not validation.is_valid_chars(value):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_length(value, MAX_LENGTH_SAMPLE_TUBE_LABEL):
errors.append(validation.invalid_length_error(displayedName, MAX_LENGTH_SAMPLE_TUBE_LABEL))
return errors
def validate_sample_id(value, field_label):
errors = []
if not validation.is_valid_chars(value):
errors.append(validation.invalid_chars_error(field_label))
if not validation.is_valid_length(value, MAX_LENGTH_SAMPLE_ID):
errors.append(
validation.invalid_length_error(field_label, MAX_LENGTH_SAMPLE_ID,
value))
return errors
def _validate_optional_text(value, maxLength, displayedTerm):
isValid, errorMessage = _validate_textValue(value.strip(), displayedTerm)
if not isValid:
return isValid, errorMessage
if not validation.is_valid_length(value.strip(), maxLength):
errorMessage = validation.invalid_length_error(
"Error, " + displayedTerm, maxLength
) + ". It is currently %s characters long." % str(len(value.strip()))
return isValid, errorMessage
return True, None
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_notes(value, field_label=_Experiment.notes.verbose_name):
errors = []
if value:
if not validation.is_valid_chars(value):
errors.append(validation.invalid_chars_error(field_label))
if not validation.is_valid_length(value, MAX_LENGTH_NOTES):
errors.append(
validation.invalid_length_error(field_label, MAX_LENGTH_NOTES,
value))
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_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_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_sampleExternalId(sampleExternalId):
isValid = False
isValid, errorMessage = _validate_textValue(sampleExternalId, "Sample ID ")
if not isValid:
return isValid, errorMessage
if not validation.is_valid_length(sampleExternalId.strip(), MAX_LENGTH_SAMPLE_EXTERNAL_ID):
errorMessage = validation.invalid_length_error("Error, Sample id", MAX_LENGTH_SAMPLE_EXTERNAL_ID) + ". It is currently %s characters long." % str(len(sampleExternalId.strip()))
return isValid, errorMessage
return True, None
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_sample_tube_label(value, field_label):
errors = []
if value:
if not validation.is_valid_chars(value):
errors.append(validation.invalid_chars_error(field_label))
if not validation.is_valid_length(value, MAX_LENGTH_SAMPLE_TUBE_LABEL):
errors.append(
validation.invalid_length_error(field_label,
MAX_LENGTH_SAMPLE_TUBE_LABEL,
value))
return errors
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_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_csv_user_defined_attributes(csvSampleDict, request):
failed = []
customAttributes = SampleAttribute.objects.filter(isActive=True)
for attribute in customAttributes:
newValue = None
if attribute.displayedName not in list(csvSampleDict.keys()):
# add mandatory custom attributes for an imported sample if user has not added it
if attribute.isMandatory:
failed.append((
attribute.displayedName,
validation.required_error(attribute.displayedName,
include_error_prefix=True),
))
else:
newValue = csvSampleDict.get(attribute.displayedName, "").strip()
if not newValue:
continue
if attribute.dataType and attribute.dataType.dataType == "Integer":
isValid, errorMessage = sample_validator._validate_intValue(
newValue, attribute.displayedName)
if not isValid:
failed.append((attribute.displayedName, errorMessage))
if attribute.dataType and attribute.dataType.dataType == "Text":
if not validation.is_valid_length(
newValue,
sample_validator.MAX_LENGTH_SAMPLE_ATTRIBUTE_VALUE):
errorMessage = validation.invalid_length_error(
attribute.displayedName,
sample_validator.MAX_LENGTH_SAMPLE_ATTRIBUTE_VALUE,
newValue,
include_error_prefix=True,
)
failed.append((attribute.displayedName, errorMessage))
logger.debug(
"import_sample_processor._validate_csv_user_defined_attributes() failed=%s"
% (failed))
return failed
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_projects(value, displayedName="Project Name", delim=","):
"""
validate projects case-insensitively with leading/trailing blanks in the input ignored
"""
errors = []
trimmed_projects = ""
if value:
for project in value.split(delim):
trimmed_project = project.strip()
if trimmed_project:
trimmed_projects = trimmed_projects + trimmed_project + delim
if not validation.is_valid_chars(trimmed_project):
errors.append(validation.invalid_chars_error(displayedName))
if not validation.is_valid_length(trimmed_project, PROJECT_NAME_LENGTH):
errors.append(validation.invalid_length_error(displayedName, PROJECT_NAME_LENGTH))
if errors:
break
return errors, trimmed_projects
def validate_sampleName(sampleName):
displayedTerm = "Sample name"
isValid, errorMessage = _validate_textValue_mandatory(sampleName, displayedTerm)
if not isValid:
return isValid, errorMessage
isValid, errorMessage = _validate_textValue(sampleName, displayedTerm)
if not isValid:
return isValid, errorMessage
isValid, errorMessage = _validate_textValue_leadingChars(sampleName, displayedTerm)
if not isValid:
return isValid, errorMessage
if not validation.is_valid_length(sampleName.strip(), MAX_LENGTH_SAMPLE_NAME):
errorMessage = validation.invalid_length_error("Error, Sample name", MAX_LENGTH_SAMPLE_NAME) + ". It is currently %s characters long." % str(len(sampleName.strip()))
return isValid, errorMessage
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