def validate_pcrPlateRow_for_existing_samples(row_list, sampleset_ids):
"""
Validates for uniqueness of PCR plate position and mandatory input for AmpliSeqOnChef sample sets
"""
msgs = dict()
count = 0
for row in row_list:
count += 1
pcrPlateRow = row.get(COLUMN_PCR_PLATE_POSITION, "").strip()
for sampleset_id in sampleset_ids:
sampleset = models.SampleSet.objects.get(pk=sampleset_id)
samplesetitems = sampleset.samples.all()
# validate when adding samples to pre-existing sampleset
if samplesetitems.count():
for item in samplesetitems:
pcrPlateRow1 = item.pcrPlateRow
item_id = item.pk
# ensure only 1 pcr plate position per sample
if (pcrPlateRow and pcrPlateRow1
and pcrPlateRow.upper() == pcrPlateRow1.upper()):
isValid = False
errorMessage = validation.format(
ugettext_lazy(
"samplesets.samplesetitem.messages.validate.pcrPlateRow.unique"
),
message_params={
"pcrPlateRow": pcrPlateRow.upper()
},
include_error_prefix=True,
)
msgs[count] = (COLUMN_PCR_PLATE_POSITION, errorMessage)
if (sampleset and not pcrPlateRow and "amps_on_chef"
in sampleset.libraryPrepType.lower()):
errorMessage = validation.format(
ugettext_lazy(
"samplesets.samplesetitem.messages.validate.pcrPlateRow.required"
),
include_error_prefix=True,
)
msgs[count] = (COLUMN_PCR_PLATE_POSITION, errorMessage)
else:
if (sampleset and not pcrPlateRow and "amps_on_chef"
in sampleset.libraryPrepType.lower()):
errorMessage = validation.format(
ugettext_lazy(
"samplesets.samplesetitem.messages.validate.pcrPlateRow.required"
),
include_error_prefix=True,
)
msgs[count] = (COLUMN_PCR_PLATE_POSITION, errorMessage)
return msgs
def validate_barcodes_are_unique(row_list):
barcodekits = []
dnabarcodes = []
msgs = dict()
count = 0
for row in row_list:
count += 1
barcodeKit = row.get(COLUMN_BARCODE_KIT, "").strip()
barcode = row.get(COLUMN_BARCODE, "").strip()
if barcodeKit and barcode:
barcodekits.append(barcodeKit)
if len(set(barcodekits)) > 1:
msgs[count] = (
COLUMN_BARCODE_KIT,
validation.format(
ugettext_lazy(
"samplesets.samplesetitem.messages.validate.barcodekit.notequal"
),
include_error_prefix=True,
),
)
dnabarcode = models.dnaBarcode.objects.filter(
name__iexact=barcodeKit, id_str__iexact=barcode)
if dnabarcode.count() != 1:
# choices = cvs.order_by('value').values_list('value', flat=True)
# validation.invalid_choice(field_label, cvValue, choices, include_error_prefix=True)
msgs[count] = (
COLUMN_BARCODE_KIT,
validation.format(
ugettext_lazy(
"samplesets.samplesetitem.messages.validate.barcodekit.invalid_choice"
),
{
"barcode": barcode,
"barcodeSet": barcodeKit,
"barcodeSetLabel": COLUMN_BARCODE_KIT,
"barcodeLabel": COLUMN_BARCODE,
},
include_error_prefix=True,
),
) # "Error, %s %s is an invalid barcodeKit and barcode combination" % (barcodeKit, barcode)
if dnabarcode.count() > 0:
if dnabarcode[0] in dnabarcodes:
msgs[count] = (
COLUMN_BARCODE,
validation.format(
ugettext_lazy(
"samplesets.samplesetitem.messages.validate.barcode.unique"
),
{"barcode": barcode},
include_error_prefix=True,
),
) # "Error, A barcode can be assigned to only one sample in the sample set and %s has been assigned to another sample" % (barcode)
else:
dnabarcodes.append(dnabarcode[0])
return msgs
def validate_barcodes_for_existing_samples(row_list, sampleset_ids):
msgs = dict()
count = 0
for row in row_list:
count += 1
barcode = row.get(COLUMN_BARCODE, "").strip()
if barcode:
dnabarcode = models.dnaBarcode.objects.filter(
id_str__iexact=barcode)
barcodeKit = dnabarcode[0].name
row[COLUMN_BARCODE] = dnabarcode[0].id_str
else:
barcode = None
barcodeKit = None
for sampleset_id in sampleset_ids:
sampleset = models.SampleSet.objects.get(pk=sampleset_id)
samplesetitems = sampleset.samples.all()
for item in samplesetitems:
# first validate that all barcode kits are the same for all samples
if item.dnabarcode:
barcodeKit1 = item.dnabarcode.name
barcode1 = item.dnabarcode.id_str
else:
barcodeKit1 = None
barcode1 = None
if barcodeKit and barcodeKit1 and barcodeKit != barcodeKit1:
msgs[count] = (
COLUMN_BARCODE,
validation.format(
ugettext_lazy(
"samplesets.samplesetitem.messages.validate.barcodekit.notequal"
),
include_error_prefix=True,
),
)
# next validate that all barcodes are unique per each sample
if barcode and barcode1 and barcode == barcode1:
msgs[count] = (
COLUMN_BARCODE,
validation.format(
ugettext_lazy(
"samplesets.samplesetitem.messages.validate.barcode.unique"
),
{"barcode": barcode},
include_error_prefix=True,
),
)
return msgs
def validate_barcode_sample_association(selectedBarcodes, selectedBarcodeKit):
errors = {"MISSING_BARCODE": "", "DUPLICATE_BARCODE": ""}
if not selectedBarcodeKit:
return errors
prior_barcodes = []
if not selectedBarcodes:
errors["MISSING_BARCODE"] = _(
"workflow.step.sample.messages.validate.barcodepersample"
) # "Please select a barcode for each sample"
else:
dupBarcodes = validation.list_duplicates(selectedBarcodes)
for selectedBarcode in dupBarcodes:
# only include unique barcode selection error messages
message = validation.format(
_("workflow.step.sample.messages.validate.barcode.unique"),
{"barcode": selectedBarcode},
) # "Barcode %s selections have to be unique\n" % selectedBarcode
errors["DUPLICATE_BARCODE"] = errors[
"DUPLICATE_BARCODE"] + message + "\n"
# logger.debug("errors=%s" %(errors))
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_pcrPlateRow_are_unique(row_list):
positions = []
msgs = dict()
count = 0
for row in row_list:
count += 1
pcrPlateRow = row.get(COLUMN_PCR_PLATE_POSITION, "").strip().upper()
if pcrPlateRow:
if pcrPlateRow in positions:
msgs[count] = (
COLUMN_PCR_PLATE_POSITION,
validation.format(
ugettext_lazy(
"samplesets.samplesetitem.messages.validate.pcrPlateRow.unique"
),
{"pcrPlateRow": pcrPlateRow},
include_error_prefix=True,
),
)
else:
positions.append(pcrPlateRow)
return msgs
def validate_kit_chip_combination(
bundle,
chipType_label="chipType",
templatingKitName_label="templatingKitName",
sequencekitname_label="sequencekitname",
librarykitname_label="librarykitname",
runType_label="runType",
):
errorMsg = None
chipType = bundle.data.get("chipType", None)
runType = bundle.data.get("runType", None)
templatingKitName = bundle.data.get("templatingKitName", None)
sequencekitname = bundle.data.get("sequencekitname", None)
librarykitname = bundle.data.get("librarykitname", None)
planExp_Kits = [
(templatingKitName, templatingKitName_label),
(sequencekitname, sequencekitname_label),
(librarykitname, librarykitname_label),
]
# since these kits are already been validated, just concentrate on validating the chip/instrument/kits combination
try:
if chipType:
query_args = (Q(name__iexact=chipType)
| Q(description__iexact=chipType), )
selectedChips = Chip.objects.filter(*query_args)
if selectedChips:
selectedChip = selectedChips[0]
for kit_name, kit_label in planExp_Kits:
if not kit_name:
continue
selectedKitInfos = KitInfo.objects.filter(
kitType__in=[
"TemplatingKit",
"IonChefPrepKit",
"SequencingKit",
"LibraryKit",
"LibraryPrepKit",
],
name__iexact=kit_name,
)
if not selectedKitInfos.count():
continue
selectedKitInfo = selectedKitInfos[0]
#
# validate selected chip and kit instrument type combination is supported
#
selectedChip_instType = selectedChip.instrumentType
selectedKit_instType = selectedKitInfo.instrumentType
if (
selectedKit_instType and selectedKit_instType
not in selectedChip_instType
): # BUG: 'proton;S5' not in 'S5' reports True... find alternate way to validate...
# The %(kitLabel)s (%(kitName)s) instrument type of %(kitInstrumentType)s is
# incompatible with the %(chipLabel)s (%(chipName)s) instrument type of
# %(chipInstrumentType)s. Specify a different %(kitLabel)s or %(chipLabel)s.
errorMsg = validation.format(
ugettext_lazy(
"plannedexperiment.messages.validate.invalid.kitandchip.instrumenttype"
),
{
"kitLabel":
kit_label,
"kitName":
selectedKitInfo.name,
"kitInstrumentType":
selectedKitInfo.get_instrument_types_list(),
"chipLabel":
chipType_label,
"chipName":
chipType,
"chipInstrumentType":
selectedChip_instType,
},
)
return errorMsg
#
# if instrument type is valid: validate if chip type of selected kit is in the supported list
#
if selectedKitInfo.chipTypes:
selectedKit_chipTypes = selectedKitInfo.get_chip_types_list(
)
if (selectedKit_chipTypes
and chipType not in selectedKit_chipTypes):
errorMsg = validation.invalid_choice_related_choice(
chipType_label,
chipType,
selectedKit_chipTypes,
kit_label,
selectedKitInfo.name,
)
return errorMsg
#
# if instrument type and chip type are valid: validate if application type of selected kit is in the supported list
#
if (runType and selectedKitInfo.applicationType and runType
not in selectedKitInfo.get_kit_application_list()):
errorMsg = validation.invalid_invalid_value_related_value(
kit_label,
selectedKitInfo.name + "[%s]" %
selectedKitInfo.get_applicationType_display(),
runType_label,
runType,
)
return errorMsg
except Exception as Err:
logger.debug("Error during plan creation %s" % str(Err))
errorMsg = str(Err)
return errorMsg