def validateStep(self):
self.validationErrors.pop(SavePlanFieldNames.NO_BARCODE, None)
self.validationErrors.pop(SavePlanFieldNames.BAD_BARCODES, None)
samplesTable = json.loads(self.savedFields['samplesTable'])
barcodeSet = self.savedFields[SavePlanFieldNames.BARCODE_SET]
selectedBarcodes = []
for row in samplesTable:
sample_name = row.get(SavePlanFieldNames.SAMPLE_NAME, '').strip()
if sample_name:
if barcodeSet:
selectedBarcodes.append(row.get('barcodeId'))
if barcodeSet:
errors = validate_barcode_sample_association(
selectedBarcodes, barcodeSet)
myErrors = convert(errors)
if myErrors.get("MISSING_BARCODE", ""):
self.validationErrors[
SavePlanFieldNames.NO_BARCODE] = myErrors.get(
"MISSING_BARCODE", "")
if myErrors.get("DUPLICATE_BARCODE", ""):
self.validationErrors[
SavePlanFieldNames.BAD_BARCODES] = myErrors.get(
"DUPLICATE_BARCODE", "")
self.prepopulatedFields['fireValidation'] = "0"
def validateStep(self):
self.validationErrors.pop(SavePlanFieldNames.NO_BARCODE,None)
self.validationErrors.pop(SavePlanFieldNames.BAD_BARCODES,None)
samplesTable = json.loads(self.savedFields['samplesTable'])
barcodeSet = self.savedFields[SavePlanFieldNames.BARCODE_SET]
selectedBarcodes = []
for row in samplesTable:
sample_name = row.get(SavePlanFieldNames.SAMPLE_NAME,'').strip()
if sample_name:
if barcodeSet:
selectedBarcodes.append(row.get('barcodeId'))
if barcodeSet:
errors = validate_barcode_sample_association(selectedBarcodes, barcodeSet)
myErrors = convert(errors)
if myErrors.get("MISSING_BARCODE", ""):
self.validationErrors[SavePlanFieldNames.NO_BARCODE] = myErrors.get("MISSING_BARCODE", "")
if myErrors.get("DUPLICATE_BARCODE", ""):
self.validationErrors[SavePlanFieldNames.BAD_BARCODES] = myErrors.get("DUPLICATE_BARCODE", "")
self.prepopulatedFields['fireValidation'] = "0"
def updateSavedFieldsForSamples(self):
#logger.debug("ENTER barcode_by_sample_step_data.updateSavedFieldsForSamples() self.savedFields[SavePlanFieldNames.BARCODE_SET]=%s" %(self.savedFields[SavePlanFieldNames.BARCODE_SET]))
if self.savedFields[SavePlanFieldNames.BARCODE_SET]:
#convert tuple to string
planReference = str(
self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE])
planHotSptRegionBedFile = str(self.prepopulatedFields[
SavePlanFieldNames.PLAN_HOTSPOT_REGION_BED_FILE])
planTargetRegionBedFile = str(self.prepopulatedFields[
SavePlanFieldNames.PLAN_TARGET_REGION_BED_FILE])
#logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() type(self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE])=%s; self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE]=%s" %(type(self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE]), self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE]))
hasAnyChanges = False
myTable = json.loads(self.savedFields['samplesTable'])
#convert unicode to str
myTable = convert(myTable)
for index, row in enumerate(myTable):
#logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() B4 CHANGES... BARCODE_SET LOOP row=%s" %(row))
sample_name = row.get(SavePlanFieldNames.SAMPLE_NAME,
'').strip()
if sample_name:
sample_nucleotideType = row.get(
SavePlanFieldNames.BARCODE_SAMPLE_NUCLEOTIDE_TYPE, "")
sampleReference = row.get(
SavePlanFieldNames.BARCODE_SAMPLE_REFERENCE, "")
sampleHotSpotRegionBedFile = row.get(
SavePlanFieldNames.
BARCODE_SAMPLE_HOTSPOT_REGION_BED_FILE, "")
sampleTargetRegionBedFile = row.get(
SavePlanFieldNames.
BARCODE_SAMPLE_TARGET_REGION_BED_FILE, "")
runType = self.prepopulatedFields[
SavePlanFieldNames.RUN_TYPE]
if runType == "AMPS_DNA_RNA" and sample_nucleotideType == "RNA":
newSampleReference = sampleReference
newSampleHotspotRegionBedFile = sampleHotSpotRegionBedFile
newSampleTargetRegionBedFile = sampleTargetRegionBedFile
else:
newSampleReference = planReference
newSampleHotspotRegionBedFile = planHotSptRegionBedFile
newSampleTargetRegionBedFile = planTargetRegionBedFile
#logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() BARCODE_SET LOOP planReference=%s; type(newSampleReference)=%s; newSampleReference=%s;" %(planReference, type(newSampleReference), newSampleReference))
#cascade the reference and BED file info to sample if none specified at the sample level
if runType != "AMPS_DNA_RNA":
if not sampleReference:
newSampleReference = planReference
newSampleHotspotRegionBedFile = planHotSptRegionBedFile
newSampleTargetRegionBedFile = planTargetRegionBedFile
hasChanged = False
if newSampleReference != sampleReference:
row[SavePlanFieldNames.
BARCODE_SAMPLE_REFERENCE] = newSampleReference
hasChanged = True
if newSampleHotspotRegionBedFile != sampleHotSpotRegionBedFile:
row[SavePlanFieldNames.
BARCODE_SAMPLE_HOTSPOT_REGION_BED_FILE] = newSampleHotspotRegionBedFile
hasChanged = True
if newSampleTargetRegionBedFile != sampleTargetRegionBedFile:
row[SavePlanFieldNames.
BARCODE_SAMPLE_TARGET_REGION_BED_FILE] = newSampleTargetRegionBedFile
hasChanged = True
#logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() hasChanged=%s; row=%s" %(hasChanged, row))
if hasChanged:
myTable[index] = row
#logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() AFTER CHANGES BARCODE_SET LOOP myTable[index]=%s" %(myTable[index]))
hasAnyChanges = True
if hasAnyChanges:
#logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() hasAnyChanges AFTER CHANGES... type=%s; myTable=%s" %(type(myTable), myTable))
#convert list with single quotes to str with double quotes. Then convert it to be unicode
self.savedFields['samplesTable'] = unicode(json.dumps(myTable))
#logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() hasAnyChanges AFTER unicode(json.dumps)... type=%s; self.savedFields[samplesTable]=%s" %(type(self.savedFields['samplesTable']), self.savedFields['samplesTable']))
self.savedObjects['samplesTableList'] = json.loads(
self.savedFields['samplesTable'])
self.updateSavedObjectsFromSavedFields()
def updateSavedFieldsForSamples(self):
#logger.debug("ENTER barcode_by_sample_step_data.updateSavedFieldsForSamples() self.savedFields[SavePlanFieldNames.BARCODE_SET]=%s" %(self.savedFields[SavePlanFieldNames.BARCODE_SET]))
if self.savedFields[SavePlanFieldNames.BARCODE_SET]:
#convert tuple to string
planReference = str(self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE])
planHotSptRegionBedFile = str(self.prepopulatedFields[SavePlanFieldNames.PLAN_HOTSPOT_REGION_BED_FILE])
planTargetRegionBedFile = str(self.prepopulatedFields[SavePlanFieldNames.PLAN_TARGET_REGION_BED_FILE])
#logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() type(self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE])=%s; self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE]=%s" %(type(self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE]), self.prepopulatedFields[SavePlanFieldNames.PLAN_REFERENCE]))
hasAnyChanges = False
myTable = json.loads(self.savedFields['samplesTable'])
#convert unicode to str
myTable = convert(myTable)
for index, row in enumerate(myTable):
#logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() B4 CHANGES... BARCODE_SET LOOP row=%s" %(row))
sample_name = row.get(SavePlanFieldNames.SAMPLE_NAME,'').strip()
if sample_name:
sample_nucleotideType = row.get(SavePlanFieldNames.BARCODE_SAMPLE_NUCLEOTIDE_TYPE, "")
sampleReference = row.get(SavePlanFieldNames.BARCODE_SAMPLE_REFERENCE, "")
sampleHotSpotRegionBedFile = row.get(SavePlanFieldNames.BARCODE_SAMPLE_HOTSPOT_REGION_BED_FILE, "")
sampleTargetRegionBedFile = row.get(SavePlanFieldNames.BARCODE_SAMPLE_TARGET_REGION_BED_FILE, "")
runType = self.prepopulatedFields[SavePlanFieldNames.RUN_TYPE]
if runType == "AMPS_DNA_RNA" and sample_nucleotideType == "RNA":
newSampleReference = sampleReference
newSampleHotspotRegionBedFile = sampleHotSpotRegionBedFile
newSampleTargetRegionBedFile = sampleTargetRegionBedFile
else:
newSampleReference = planReference
newSampleHotspotRegionBedFile = planHotSptRegionBedFile
newSampleTargetRegionBedFile = planTargetRegionBedFile
#logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() BARCODE_SET LOOP planReference=%s; type(newSampleReference)=%s; newSampleReference=%s;" %(planReference, type(newSampleReference), newSampleReference))
#cascade the reference and BED file info to sample if none specified at the sample level
if runType != "AMPS_DNA_RNA":
if not sampleReference:
newSampleReference = planReference
newSampleHotspotRegionBedFile = planHotSptRegionBedFile
newSampleTargetRegionBedFile = planTargetRegionBedFile
hasChanged = False
if newSampleReference != sampleReference:
row[SavePlanFieldNames.BARCODE_SAMPLE_REFERENCE] = newSampleReference
hasChanged = True
if newSampleHotspotRegionBedFile != sampleHotSpotRegionBedFile:
row[SavePlanFieldNames.BARCODE_SAMPLE_HOTSPOT_REGION_BED_FILE] = newSampleHotspotRegionBedFile
hasChanged = True
if newSampleTargetRegionBedFile != sampleTargetRegionBedFile:
row[SavePlanFieldNames.BARCODE_SAMPLE_TARGET_REGION_BED_FILE] = newSampleTargetRegionBedFile
hasChanged = True
#logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() hasChanged=%s; row=%s" %(hasChanged, row))
if hasChanged:
myTable[index] = row
#logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() AFTER CHANGES BARCODE_SET LOOP myTable[index]=%s" %(myTable[index]))
hasAnyChanges = True
if hasAnyChanges:
#logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() hasAnyChanges AFTER CHANGES... type=%s; myTable=%s" %(type(myTable), myTable))
#convert list with single quotes to str with double quotes. Then convert it to be unicode
self.savedFields['samplesTable'] = unicode(json.dumps(myTable))
#logger.debug("barcode_by_sample_step_data.updateSavedFieldsForSamples() hasAnyChanges AFTER unicode(json.dumps)... type=%s; self.savedFields[samplesTable]=%s" %(type(self.savedFields['samplesTable']), self.savedFields['samplesTable']))
self.savedObjects['samplesTableList'] = json.loads(self.savedFields['samplesTable'])
self.updateSavedObjectsFromSavedFields()
def validateStep(self):
any_samples = False
self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_NAME] = []
self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_EXTERNAL_ID] = []
self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_DESCRIPTION] = []
self.validationErrors[SavePlanFieldNames.BAD_TUBE_LABEL] = []
self.validationErrors[SavePlanFieldNames.BAD_IR_SET_ID] = []
self.validationErrors.pop(SavePlanFieldNames.NO_BARCODE,None)
self.validationErrors.pop(SavePlanFieldNames.BAD_BARCODES,None)
barcodeSet = self.savedFields[SavePlanFieldNames.BARCODE_SET]
selectedBarcodes = []
samplesTable = json.loads(self.savedFields['samplesTable'])
#logger.debug("save_plan_step_data - anySamples? samplesTable=%s" %(samplesTable))
for row in samplesTable:
sample_name = row.get(SavePlanFieldNames.SAMPLE_NAME,'').strip()
#logger.debug("save_plan_step_data - anySamples? sampleName=%s" %(sample_name))
if sample_name:
any_samples = True
if validate_sample_name(sample_name):
self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_NAME].append(sample_name)
external_id = row.get(SavePlanFieldNames.SAMPLE_EXTERNAL_ID,'')
if external_id:
self.validate_field(external_id, self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_EXTERNAL_ID])
description = row.get(SavePlanFieldNames.SAMPLE_DESCRIPTION,'')
if description:
self.validate_field(description, self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_DESCRIPTION], False,
MAX_LENGTH_SAMPLE_DESCRIPTION)
ir_set_id = row.get('irSetId','')
if ir_set_id and not (str(ir_set_id).isdigit()):
self.validationErrors[SavePlanFieldNames.BAD_IR_SET_ID].append(ir_set_id)
tube_label = row.get('tubeLabel','')
if validate_sample_tube_label(tube_label):
self.validationErrors[SavePlanFieldNames.BAD_TUBE_LABEL].append(tube_label)
if barcodeSet:
selectedBarcodes.append(row.get('barcodeId'))
if any_samples:
self.validationErrors.pop(SavePlanFieldNames.NO_SAMPLES, None)
else:
self.validationErrors[SavePlanFieldNames.NO_SAMPLES] = "You must enter at least one sample"
if not self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_NAME]:
self.validationErrors.pop(SavePlanFieldNames.BAD_SAMPLE_NAME, None)
if not self.validationErrors[SavePlanFieldNames.BAD_TUBE_LABEL]:
self.validationErrors.pop(SavePlanFieldNames.BAD_TUBE_LABEL, None)
if not self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_EXTERNAL_ID]:
self.validationErrors.pop(SavePlanFieldNames.BAD_SAMPLE_EXTERNAL_ID, None)
if not self.validationErrors[SavePlanFieldNames.BAD_SAMPLE_DESCRIPTION]:
self.validationErrors.pop(SavePlanFieldNames.BAD_SAMPLE_DESCRIPTION, None)
if not self.validationErrors[SavePlanFieldNames.BAD_IR_SET_ID]:
self.validationErrors.pop(SavePlanFieldNames.BAD_IR_SET_ID, None)
if barcodeSet:
errors = validate_barcode_sample_association(selectedBarcodes, barcodeSet)
myErrors = convert(errors)
if myErrors.get("MISSING_BARCODE", ""):
self.validationErrors[SavePlanFieldNames.NO_BARCODE] = myErrors.get("MISSING_BARCODE", "")
if myErrors.get("DUPLICATE_BARCODE", ""):
self.validationErrors[SavePlanFieldNames.BAD_BARCODES] = myErrors.get("DUPLICATE_BARCODE", "")
