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, 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