def validate_sample_nucleotideType(value, runType, applicationGroupName, displayedName='Sample Nucleotide Type'):
"""
validate nucleotide type case-insensitively with leading/trailing blanks in the input ignored
"""
errors = []
nucleotideType = ""
try:
runTypeObj = RunType.objects.filter(runType=runType)[0]
value_from_runType = runTypeObj.nucleotideType.upper() if runTypeObj.nucleotideType else ""
except:
value_from_runType = ""
if value:
nucleotideType = value.strip().upper()
if nucleotideType == "FUSIONS": nucleotideType = "RNA"
if value_from_runType:
if value_from_runType == "DNA_RNA":
valid_values = ["DNA", "RNA", "Fusions"]
else:
valid_values = [value_from_runType]
else:
valid_values = ["DNA", "RNA"]
if not validation.is_valid_keyword(nucleotideType, valid_values):
errors.append(validation.invalid_keyword_error(displayedName, valid_values))
else:
# fill in nucleotideType from selected runType or applicationGroup
if value_from_runType and value_from_runType != "DNA_RNA":
nucleotideType = value_from_runType
elif applicationGroupName in ["DNA", "RNA"]:
nucleotideType = applicationGroupName
return errors, nucleotideType
def validate_sample_nucleotideType(nucleotideType,
runType,
displayedName='Sample Nucleotide Type'):
"""
validate nucleotide type case-insensitively with leading/trailing blanks in the input ignored
"""
errors = []
input = ""
valid_values = VALID_NUCLEOTIDE_TYPES
if nucleotideType:
input = nucleotideType.strip().upper()
if runType:
runTypeObjs = RunType.objects.filter(runType=runType)
if runTypeObjs:
runTypeObj = runTypeObjs[0]
if (runTypeObj.nucleotideType
and runTypeObj.nucleotideType.upper() != "DNA_RNA"):
valid_values = [str(runTypeObj.nucleotideType.upper())]
if not validation.is_valid_keyword(input, valid_values):
errors.append(
validation.invalid_keyword_error(displayedName, valid_values))
return errors, input
def validate_sample_nucleotideType(nucleotideType, runType, applicationGroupName, displayedName='Sample Nucleotide Type'):
"""
validate nucleotide type case-insensitively with leading/trailing blanks in the input ignored
"""
errors = []
input = ""
valid_values = VALID_NUCLEOTIDE_TYPES
if nucleotideType:
input = nucleotideType.strip().upper()
if runType:
runTypeObjs = RunType.objects.filter(runType = runType)
if runTypeObjs:
runTypeObj = runTypeObjs[0]
if (runTypeObj.nucleotideType and runTypeObj.nucleotideType.upper() != "DNA_RNA"):
valid_values = [str(runTypeObj.nucleotideType.upper())]
if not validation.is_valid_keyword(input, valid_values):
errors.append(validation.invalid_keyword_error(displayedName, valid_values))
else:
if runType:
runTypeObjs = RunType.objects.filter(runType = runType)
if runTypeObjs:
runTypeObj = runTypeObjs[0]
if (runTypeObj.nucleotideType and runTypeObj.nucleotideType.upper() != "DNA_RNA"):
return errors, runTypeObj.nucleotideType.upper()
else:
#some runType can have more than one nucleotideType
if applicationGroupName in ["DNA", "RNA"]:
return errors, applicationGroupName
return errors, input
def validate_sample_nucleotideType(value, runType, applicationGroupName, displayedName='Sample Nucleotide Type'):
"""
validate nucleotide type case-insensitively with leading/trailing blanks in the input ignored
"""
errors = []
nucleotideType = ""
try:
runTypeObj = RunType.objects.filter(runType=runType)[0]
value_from_runType = runTypeObj.nucleotideType.upper() if runTypeObj.nucleotideType else ""
except:
value_from_runType = ""
if value:
nucleotideType = value.strip().upper()
if nucleotideType == "FUSIONS": nucleotideType = "RNA"
if value_from_runType:
if value_from_runType == "DNA_RNA":
valid_values = ["DNA", "RNA", "Fusions"]
else:
valid_values = [value_from_runType]
else:
valid_values = ["DNA", "RNA"]
if not validation.is_valid_keyword(nucleotideType, valid_values):
errors.append(validation.invalid_keyword_error(displayedName, valid_values))
else:
# fill in nucleotideType from selected runType or applicationGroup
if value_from_runType and value_from_runType != "DNA_RNA":
nucleotideType = value_from_runType
elif applicationGroupName in ["DNA", "RNA"]:
nucleotideType = applicationGroupName
return errors, nucleotideType
def validate_templatingSize(value, displayedName='Templating Size'):
"""
validate templating size case-insensitively with leading/trailing blanks in the input ignored
"""
errors = []
input = ""
valid_values = VALID_TEMPLATING_SIZES
if value:
input = value.strip().upper()
if not validation.is_valid_keyword(input, valid_values):
errors.append(validation.invalid_keyword_error(displayedName, valid_values))
return errors
def validate_nucleotideType(nucleotideType, displayedName='Sample Nucleotide Type'):
"""
validate nucleotide type case-insensitively with leading/trailing blanks in the input ignored
"""
isValid = True
errors = []
input = ""
if nucleotideType:
input = nucleotideType.strip().lower()
if not validation.is_valid_keyword(input, VALID_NUCLEOTIDE_TYPES):
errors.append(validation.invalid_keyword_error(displayedName, VALID_NUCLEOTIDE_TYPES))
isValid = False
return isValid, errors, input
def validate_pcrPlateRow(pcrPlateRow, displayedName='PCR Plate Position'):
"""
validate PCR plate row case-insensitively with leading/trailing blanks in the input ignored
"""
isValid = True
errors = []
input = ""
if pcrPlateRow:
input = pcrPlateRow.strip().upper()
validValues = views_helper._get_pcrPlateRow_valid_values(None)
if not validation.is_valid_keyword(input, validValues):
errors.append(validation.invalid_keyword_error(displayedName, validValues))
isValid = False
return isValid, errors, input
def validate_pcrPlateRow(pcrPlateRow, displayedName='PCR Plate Position'):
"""
validate PCR plate row case-insensitively with leading/trailing blanks in the input ignored
"""
isValid = True
errors = []
input = ""
if pcrPlateRow:
input = pcrPlateRow.strip().upper()
validValues = views_helper._get_pcrPlateRow_valid_values(None)
if not validation.is_valid_keyword(input, validValues):
errors.append(
validation.invalid_keyword_error(displayedName, validValues))
isValid = False
return isValid, errors, input
def validate_pcrPlateCol(pcrPlateCol, displayedName='PCR Plate Position'):
"""
validate PCR plate row case-insensitively with leading/trailing blanks in the input ignored
"""
isValid = True
errors = []
input = ""
if pcrPlateCol:
valid_tuples = SampleSetItem.ALLOWED_AMPLISEQ_PCR_PLATE_COLUMNS_V1
input = pcrPlateCol.strip().upper()
validValues = views_helper._get_pcrPlateCol_valid_values(None)
if not validation.is_valid_keyword(input, validValues):
errors.append(validation.invalid_keyword_error(displayedName, validValues))
isValid = False
return isValid, errors, input
def validate_pcrPlateCol(pcrPlateCol, displayedName='PCR Plate Position'):
"""
validate PCR plate row case-insensitively with leading/trailing blanks in the input ignored
"""
isValid = True
errors = []
input = ""
if pcrPlateCol:
valid_tuples = SampleSetItem.ALLOWED_AMPLISEQ_PCR_PLATE_COLUMNS_V1
input = pcrPlateCol.strip().upper()
validValues = views_helper._get_pcrPlateCol_valid_values(None)
if not validation.is_valid_keyword(input, validValues):
errors.append(
validation.invalid_keyword_error(displayedName, validValues))
isValid = False
return isValid, errors, input
def validate_nucleotideType(nucleotideType,
displayedName='Sample Nucleotide Type'):
"""
validate nucleotide type case-insensitively with leading/trailing blanks in the input ignored
"""
isValid = True
errors = []
input = ""
if nucleotideType:
input = nucleotideType.strip().lower()
if not validation.is_valid_keyword(input, VALID_NUCLEOTIDE_TYPES):
errors.append(
validation.invalid_keyword_error(displayedName,
VALID_NUCLEOTIDE_TYPES))
isValid = False
return isValid, errors, input
def validate_libPrepType(libPrepType, displayedTerm="Library Prep Type"):
"""
validate libPrepType with leading/trailing blanks in the input ignored
"""
isValid = True
errors = []
inputData = ""
if libPrepType:
inputData = libPrepType.strip()
validValues = views_helper._get_libraryPrepType_choices(None)
if not validation.is_valid_keyword(inputData, validValues):
errors.append(validation.invalid_keyword_error(displayedTerm, validValues))
errors = ''.join(errors).replace("are ,", ":")
isValid = False
return isValid, errors, libPrepType
isValid = True
return isValid, None, None
def validate_samplesetStatus(samplesetStatus, displayedTerm="Status"):
"""
validate samplesetStatus with leading/trailing blanks in the input ignored
"""
isValid = True
errors = []
inputData = ""
if samplesetStatus:
inputData = samplesetStatus.strip().lower()
validValues = views_helper._get_sampleset_choices(None)
if not validation.is_valid_keyword(inputData, validValues):
errors.append(validation.invalid_keyword_error(displayedTerm, validValues))
errors = ''.join(errors).replace("are ,", ":")
isValid = False
return isValid, errors, samplesetStatus
isValid = True
return isValid, None, None
def validate_libPrepType(libPrepType, displayedTerm="Library Prep Type"):
"""
validate libPrepType with leading/trailing blanks in the input ignored
"""
isValid = True
errors = []
inputData = ""
if libPrepType:
inputData = libPrepType.strip()
validValues = views_helper._get_libraryPrepType_choices(None)
if not validation.is_valid_keyword(inputData, validValues):
errors.append(
validation.invalid_keyword_error(displayedTerm, validValues))
errors = ''.join(errors).replace("are ,", ":")
isValid = False
return isValid, errors, libPrepType
isValid = True
return isValid, None, None
def validate_samplesetStatus(samplesetStatus, displayedTerm="Status"):
"""
validate samplesetStatus with leading/trailing blanks in the input ignored
"""
isValid = True
errors = []
inputData = ""
if samplesetStatus:
inputData = samplesetStatus.strip().lower()
validValues = views_helper._get_sampleset_choices(None)
if not validation.is_valid_keyword(inputData, validValues):
errors.append(
validation.invalid_keyword_error(displayedTerm, validValues))
errors = ''.join(errors).replace("are ,", ":")
isValid = False
return isValid, errors, samplesetStatus
isValid = True
return isValid, None, None
