def __init__(self, *args, **kwargs):
super(AnalysisSettingsForm, self).__init__(*args, **kwargs)
# initialize choices when form instance created
references = models.ReferenceGenome.objects.filter(
index_version=settings.TMAP_VERSION, enabled=True)
self.fields['reference'].choices = [('', 'none')] + [
(v[0], "%s (%s)" % (v[0], v[1]))
for v in references.values_list('short_name', 'name')
]
bedfiles = dict_bed_hotspot()
self.fields['targetRegionBedFile'].choices = [('', '')] + [
(v.file, v.path.split("/")[-1].replace(".bed", ""))
for v in bedfiles.get('bedFiles', [])
]
self.fields['hotSpotRegionBedFile'].choices = [('', '')] + [
(v.file, v.path.split("/")[-1].replace(".bed", ""))
for v in bedfiles.get('hotspotFiles', [])
]
self.fields['barcodeKitName'].choices = [('', '')] + list(
models.dnaBarcode.objects.order_by('name').distinct(
'name').values_list('name', 'name'))
adapters = models.ThreePrimeadapter.objects.all().order_by(
'-isDefault', 'name')
self.fields['threePrimeAdapter'].choices = [
(v[1], "%s (%s)" % (v[0], v[1]))
for v in adapters.values_list('name', 'sequence')
]
def __init__(self):
super(ReferenceStepData, self).__init__()
self.resourcePath = 'rundb/plan/page_plan/page_plan_reference.html'
self._dependsOn = [StepNames.APPLICATION]
references = list(ReferenceGenome.objects.all().filter(
index_version=settings.TMAP_VERSION))
self.file_dict = dict_bed_hotspot()
self.prepopulatedFields[ReferenceFieldNames.REFERENCES] = references
self.prepopulatedFields[
ReferenceFieldNames.TARGET_BED_FIELS] = self.file_dict[
ReferenceFieldNames.BED_FILES]
self.prepopulatedFields[
ReferenceFieldNames.HOT_SPOT_BED_FILES] = self.file_dict[
ReferenceFieldNames.HOT_SPOT_FILES]
self.prepopulatedFields[ReferenceFieldNames.SHOW_HOT_SPOT_BED] = False
self.prepopulatedFields[ReferenceFieldNames.REFERENCE_MISSING] = False
self.prepopulatedFields[
ReferenceFieldNames.TARGED_BED_FILE_MISSING] = False
self.prepopulatedFields[
ReferenceFieldNames.HOT_SPOT_BED_FILE_MISSING] = False
self.savedFields[ReferenceFieldNames.REFERENCE] = None
self.savedFields[ReferenceFieldNames.TARGET_BED_FILE] = None
self.savedFields[ReferenceFieldNames.HOT_SPOT_BED_FILE] = None
self.prepopulatedFields[ReferenceFieldNames.REFERENCE_SHORT_NAMES] = [
ref.short_name for ref in references
]
def _validate_target_bed(input, selectedTemplate, planObj):
"""
validate target region BED file case-insensitively with leading/trailing blanks in the input ignored
"""
errorMsg = None
if input:
bedFileDict = dict_bed_hotspot()
value = input.strip()
isValidated = False
for bedFile in bedFileDict.get("bedFiles"):
if value == bedFile.file or value == bedFile.path:
isValidated = True
planObj.get_easObj().targetRegionBedFile = bedFile.file
# elif value.lower() == bedFile.file.lower() or value.lower() == bedFile.path.lower():
# isValidated = True
# planObj.get_easObj().targetRegionBedFile = bedFile.file
if not isValidated:
logger.exception(format_exc())
errorMsg = input + " not found."
else:
planObj.get_easObj().targetRegionBedFile = ""
return errorMsg
def __init__(self, sh_type):
super(ReferenceStepData, self).__init__(sh_type)
self.resourcePath = 'rundb/plan/page_plan/page_plan_reference.html'
self._dependsOn = [StepNames.APPLICATION]
references = list(ReferenceGenome.objects.all().filter(index_version=settings.TMAP_VERSION))
self.file_dict = dict_bed_hotspot()
self.prepopulatedFields[ReferenceFieldNames.REFERENCES] = references
self.prepopulatedFields[ReferenceFieldNames.TARGET_BED_FILES] = self.file_dict[ReferenceFieldNames.BED_FILES]
self.prepopulatedFields[ReferenceFieldNames.HOT_SPOT_BED_FILES] = self.file_dict[ReferenceFieldNames.HOT_SPOT_FILES]
self.prepopulatedFields[ReferenceFieldNames.SHOW_HOT_SPOT_BED] = False
self.prepopulatedFields[ReferenceFieldNames.REFERENCE_MISSING] = False
self.prepopulatedFields[ReferenceFieldNames.TARGET_BED_FILE_MISSING] = False
self.prepopulatedFields[ReferenceFieldNames.HOT_SPOT_BED_FILE_MISSING] = False
self.savedFields[ReferenceFieldNames.REFERENCE] = ""
self.savedFields[ReferenceFieldNames.TARGET_BED_FILE] = ""
self.savedFields[ReferenceFieldNames.HOT_SPOT_BED_FILE] = ""
self.prepopulatedFields[ReferenceFieldNames.REQUIRE_TARGET_BED_FILE] = False
self.prepopulatedFields[ReferenceFieldNames.REFERENCE_SHORT_NAMES] = [ref.short_name for ref in references]
self.savedFields[ReferenceFieldNames.MIXED_TYPE_RNA_REFERENCE] = ""
self.savedFields[ReferenceFieldNames.MIXED_TYPE_RNA_TARGET_BED_FILE] = ""
self.savedFields[ReferenceFieldNames.MIXED_TYPE_RNA_HOT_SPOT_BED_FILE] = ""
self.savedFields[ReferenceFieldNames.SAME_REF_INFO_PER_SAMPLE] = True
self.prepopulatedFields[ReferenceFieldNames.PLAN_STATUS] = ""
self.prepopulatedFields[ReferenceFieldNames.RUN_TYPE] = ""
self.prepopulatedFields[ReferenceFieldNames.APPLICATION_GROUP_NAME] = ""
self.sh_type = sh_type
def __init__(self, sh_type):
super(ReferenceStepData, self).__init__(sh_type)
self.resourcePath = 'rundb/plan/page_plan/page_plan_reference.html'
self._dependsOn = [StepNames.APPLICATION]
references = list(ReferenceGenome.objects.all().filter(index_version=settings.TMAP_VERSION))
self.file_dict = dict_bed_hotspot()
self.prepopulatedFields[ReferenceFieldNames.REFERENCES] = references
self.prepopulatedFields[ReferenceFieldNames.TARGET_BED_FILES] = self.file_dict[ReferenceFieldNames.BED_FILES]
self.prepopulatedFields[ReferenceFieldNames.HOT_SPOT_BED_FILES] = self.file_dict[ReferenceFieldNames.HOT_SPOT_FILES]
self.prepopulatedFields[ReferenceFieldNames.SHOW_HOT_SPOT_BED] = False
self.prepopulatedFields[ReferenceFieldNames.REFERENCE_MISSING] = False
self.prepopulatedFields[ReferenceFieldNames.TARGET_BED_FILE_MISSING] = False
self.prepopulatedFields[ReferenceFieldNames.HOT_SPOT_BED_FILE_MISSING] = False
self.savedFields[ReferenceFieldNames.REFERENCE] = ""
self.savedFields[ReferenceFieldNames.TARGET_BED_FILE] = ""
self.savedFields[ReferenceFieldNames.HOT_SPOT_BED_FILE] = ""
self.prepopulatedFields[ReferenceFieldNames.REQUIRE_TARGET_BED_FILE] = False
self.prepopulatedFields[ReferenceFieldNames.REFERENCE_SHORT_NAMES] = [ref.short_name for ref in references]
self.savedFields[ReferenceFieldNames.MIXED_TYPE_RNA_REFERENCE] = ""
self.savedFields[ReferenceFieldNames.MIXED_TYPE_RNA_TARGET_BED_FILE] = ""
self.savedFields[ReferenceFieldNames.MIXED_TYPE_RNA_HOT_SPOT_BED_FILE] = ""
self.savedFields[ReferenceFieldNames.SAME_REF_INFO_PER_SAMPLE] = True
self.prepopulatedFields[ReferenceFieldNames.PLAN_STATUS] = ""
self.prepopulatedFields[ReferenceFieldNames.RUN_TYPE] = ""
self.prepopulatedFields[ReferenceFieldNames.APPLICATION_GROUP_NAME] = ""
self.sh_type = sh_type
def _validate_target_bed(input, selectedTemplate, planObj):
"""
validate target region BED file case-insensitively with leading/trailing blanks in the input ignored
"""
errorMsg = None
if input:
bedFileDict = dict_bed_hotspot()
value = input.strip()
isValidated = False
for bedFile in bedFileDict.get("bedFiles"):
if value == bedFile.file or value == bedFile.path:
isValidated = True
planObj.get_easObj().targetRegionBedFile = bedFile.file
# elif value.lower() == bedFile.file.lower() or value.lower() == bedFile.path.lower():
# isValidated = True
# planObj.get_easObj().targetRegionBedFile = bedFile.file
if not isValidated:
logger.exception(format_exc())
errorMsg = input + " not found."
else:
planObj.get_easObj().targetRegionBedFile = ""
return errorMsg
def __init__(self, *args, **kwargs):
super(AnalysisSettingsForm, self).__init__(*args, **kwargs)
# initialize choices when form instance created
references = models.ReferenceGenome.objects.filter(
index_version=settings.TMAP_VERSION, enabled=True
)
self.fields["reference"].choices = [("", "none")] + [
(v[0], "%s (%s)" % (v[0], v[1]))
for v in references.values_list("short_name", "name")
]
bedfiles = dict_bed_hotspot()
self.fields["targetRegionBedFile"].choices = [("", "")] + [
(v.file, v.path.split("/")[-1].replace(".bed", ""))
for v in bedfiles.get("bedFiles", [])
]
self.fields["hotSpotRegionBedFile"].choices = [("", "")] + [
(v.file, v.path.split("/")[-1].replace(".bed", ""))
for v in bedfiles.get("hotspotFiles", [])
]
self.fields["barcodeKitName"].choices = [("", "")] + list(
models.dnaBarcode.objects.order_by("name")
.distinct("name")
.values_list("name", "name")
)
adapters = models.ThreePrimeadapter.objects.filter(
direction="Forward", runMode="single"
).order_by("-isDefault", "chemistryType", "name")
self.fields["threePrimeAdapter"].choices = [
(v[1], "%s (%s)" % (v[0], v[1]))
for v in adapters.values_list("name", "sequence")
]
def __init__(self, *args, **kwargs):
super(AnalysisSettingsForm, self).__init__(*args, **kwargs)
# initialize choices when form instance created
references = models.ReferenceGenome.objects.filter(index_version=settings.TMAP_VERSION, enabled=True)
self.fields['reference'].choices= [('','none')] + [(v[0],"%s (%s)" % (v[0],v[1])) for v in references.values_list('short_name', 'name')]
bedfiles = dict_bed_hotspot()
self.fields['targetRegionBedFile'].choices= [('','')] + [(v.file, v.path.split("/")[-1].replace(".bed", "")) for v in bedfiles.get('bedFiles',[])]
self.fields['hotSpotRegionBedFile'].choices= [('','')] + [(v.file, v.path.split("/")[-1].replace(".bed", "")) for v in bedfiles.get('hotspotFiles',[])]
self.fields['barcodeKitName'].choices= [('','')]+list(models.dnaBarcode.objects.order_by('name').distinct('name').values_list('name','name'))
adapters = models.ThreePrimeadapter.objects.all().order_by('-isDefault', 'name')
self.fields['threePrimeAdapter'].choices= [(v[1],"%s (%s)" % (v[0],v[1])) for v in adapters.values_list('name', 'sequence')]
def _validate_hotspot_bed(input, selectedTemplate, planObj):
errorMsg = None
if input:
bedFileDict = dict_bed_hotspot()
value = input.strip()
if value in bedFileDict.get("hotspotPaths") or value in bedFileDict.get("hotspotFullPaths"):
for bedFile in bedFileDict.get("hotspotFiles"):
if value == bedFile.file or value == bedFile.path:
planObj.regionfile = bedFile.file
else:
logger.exception(format_exc())
errorMsg = input + " not found. "
else:
planObj.regionfile = ""
return errorMsg
def _validate_hotspot_bed(input, selectedTemplate, planObj):
errorMsg = None
if input:
bedFileDict = dict_bed_hotspot()
value = input.strip()
if value in bedFileDict.get(
"hotspotPaths") or value in bedFileDict.get(
"hotspotFullPaths"):
for bedFile in bedFileDict.get("hotspotFiles"):
if value == bedFile.file or value == bedFile.path:
planObj.regionfile = bedFile.file
else:
logger.exception(format_exc())
errorMsg = input + " not found. "
else:
planObj.regionfile = ""
return errorMsg
def __init__(self):
super(ReferenceStepData, self).__init__()
self.resourcePath = 'rundb/plan/page_plan/page_plan_reference.html'
self._dependsOn = [StepNames.APPLICATION]
references = list(ReferenceGenome.objects.all().filter(index_version=settings.TMAP_VERSION))
self.file_dict = dict_bed_hotspot()
self.prepopulatedFields[ReferenceFieldNames.REFERENCES] = references
self.prepopulatedFields[ReferenceFieldNames.TARGET_BED_FILES] = self.file_dict[ReferenceFieldNames.BED_FILES]
self.prepopulatedFields[ReferenceFieldNames.HOT_SPOT_BED_FILES] = self.file_dict[ReferenceFieldNames.HOT_SPOT_FILES]
self.prepopulatedFields[ReferenceFieldNames.SHOW_HOT_SPOT_BED] = False
self.prepopulatedFields[ReferenceFieldNames.REFERENCE_MISSING] = False
self.prepopulatedFields[ReferenceFieldNames.TARGED_BED_FILE_MISSING] = False
self.prepopulatedFields[ReferenceFieldNames.HOT_SPOT_BED_FILE_MISSING] = False
self.savedFields[ReferenceFieldNames.REFERENCE] = ""
self.savedFields[ReferenceFieldNames.TARGET_BED_FILE] = ""
self.savedFields[ReferenceFieldNames.HOT_SPOT_BED_FILE] = ""
self.prepopulatedFields[ReferenceFieldNames.REFERENCE_SHORT_NAMES] = [ref.short_name for ref in references]
def validate_hotspot_bed(hotSpotRegionBedFile):
"""
validate hotSpot BED file case-insensitively with leading/trailing blanks in the input ignored
"""
errors = []
if hotSpotRegionBedFile:
bedFileDict = dict_bed_hotspot()
value = hotSpotRegionBedFile.strip()
isValidated = False
for bedFile in bedFileDict.get("hotspotFiles"):
if value == bedFile.file or value == bedFile.path:
isValidated = True
if not isValidated:
errors.append("%s hotSpotRegionBedFile is missing" % (hotSpotRegionBedFile))
logger.debug("plan_validator.validate_hotspot_bed() value=%s;" % (value))
return errors
def validate_hotspot_bed(hotSpotRegionBedFile):
"""
validate hotSpot BED file case-insensitively with leading/trailing blanks in the input ignored
"""
errors = []
if hotSpotRegionBedFile:
bedFileDict = dict_bed_hotspot()
value = hotSpotRegionBedFile.strip()
isValidated = False
for bedFile in bedFileDict.get("hotspotFiles"):
if value == bedFile.file or value == bedFile.path:
isValidated = True
if not isValidated:
errors.append("%s hotSpotRegionBedFile is missing" % (hotSpotRegionBedFile))
logger.debug("plan_validator.validate_hotspot_bed() value=%s;" % (value))
return errors
def get_columns(selection, isBarcoded=True):
columns = []
bedfiles = dict_bed_hotspot()
for field_options in selection:
column = get_column(field_options)
field = column['field']
if not isBarcoded and field == 'barcode_name':
continue
if field == 'reference':
for reference in ReferenceGenome.objects.filter(enabled=True):
column["options"].append({
'value':
reference.short_name,
'display':
'%s (%s)' % (reference.short_name, reference.name),
})
if field == 'target_region_filepath':
for bed in bedfiles.get('bedFiles', []):
column["options"].append({
'value': bed.file,
'display': os.path.basename(bed.file),
'reference': bed.meta['reference']
})
if field == 'hotspot_filepath':
for bed in bedfiles.get('hotspotFiles', []):
column["options"].append({
'value': bed.file,
'display': os.path.basename(bed.file),
'reference': bed.meta['reference']
})
columns.append(column)
return columns
def get_columns(selection, isBarcoded=True):
columns = []
bedfiles = dict_bed_hotspot()
for field_options in selection:
column = get_column(field_options)
field = column["field"]
if not isBarcoded and field == "barcode_name":
continue
if field == "reference":
for reference in ReferenceGenome.objects.filter(enabled=True):
column["options"].append({
"value":
reference.short_name,
"display":
"%s (%s)" % (reference.short_name, reference.name),
})
if field == "target_region_filepath":
for bed in bedfiles.get("bedFiles", []):
column["options"].append({
"value": bed.file,
"display": os.path.basename(bed.file),
"reference": bed.meta["reference"],
})
if field == "hotspot_filepath":
for bed in bedfiles.get("hotspotFiles", []):
column["options"].append({
"value": bed.file,
"display": os.path.basename(bed.file),
"reference": bed.meta["reference"],
})
columns.append(column)
return columns
def get_columns(selection, isBarcoded=True):
columns = []
bedfiles = dict_bed_hotspot()
for field_options in selection:
column = get_column(field_options)
field = column['field']
if not isBarcoded and field =='barcode_name':
continue
if field == 'reference':
for reference in ReferenceGenome.objects.filter(enabled=True):
column["options"].append({
'value': reference.short_name,
'display':'%s (%s)' % (reference.short_name, reference.name),
})
if field == 'target_region_filepath':
for bed in bedfiles.get('bedFiles', []):
column["options"].append({
'value': bed.file,
'display': os.path.basename(bed.file),
'reference': bed.meta['reference']
})
if field == 'hotspot_filepath':
for bed in bedfiles.get('hotspotFiles', []):
column["options"].append({
'value': bed.file,
'display': os.path.basename(bed.file),
'reference': bed.meta['reference']
})
columns.append(column)
return columns
def _get_base_planTemplate_data(isForTemplate):
data = {}
#per requirement, we want to display Generic Sequencing as the last entry in the selection list
data["runTypes"] = list(RunType.objects.all().exclude(runType = "GENS").order_by('nucleotideType', 'runType'))
data["secondaryRunTypes"] = list(RunType.objects.filter(runType = "GENS"))
data["barcodes"] = list(dnaBarcode.objects.values('name').distinct().order_by('name'))
##barcodeKitNames = dnaBarcode.objects.values_list('name', flat=True).distinct().order_by('name')
##for barcodeKitName in barcodeKitNames:
## data[barcodeKitName] = dnaBarcode.objects.filter(name=barcodeKitName).order_by('index')
data["barcodeKitInfo"] = list(dnaBarcode.objects.all().order_by('name', 'index'))
references = list(ReferenceGenome.objects.all().filter(index_version=settings.TMAP_VERSION))
data["references"] = references
data["referenceShortNames"] = [ref.short_name for ref in references]
data.update(dict_bed_hotspot())
data["seqKits"] = KitInfo.objects.filter(kitType='SequencingKit', isActive=True).order_by("name")
data["libKits"] = KitInfo.objects.filter(kitType='LibraryKit', isActive=True).order_by("name")
data["variantfrequencies"] = VariantFrequencies.objects.all().order_by("name")
#the entry marked as the default will be on top of the list
data["forwardLibKeys"] = LibraryKey.objects.filter(direction='Forward', runMode='single').order_by('-isDefault', 'name')
data["forward3Adapters"] = ThreePrimeadapter.objects.filter(direction='Forward', runMode='single').order_by('-isDefault', 'name')
#pairedEnd does not have special forward library keys
#for TS-4669: remove paired-end from wizard, if there are no active PE lib kits, do not prepare pe keys or adapters
peLibKits = KitInfo.objects.filter(kitType='LibraryKit', runMode='pe', isActive=True)
if (peLibKits.count() > 0):
data["peForwardLibKeys"] = LibraryKey.objects.filter(direction='Forward').order_by('-isDefault', 'name')
data["peForward3Adapters"] = ThreePrimeadapter.objects.filter(direction='Forward', runMode='pe').order_by('-isDefault', 'name')
data["reverseLibKeys"] = LibraryKey.objects.filter(direction='Reverse').order_by('-isDefault', 'name')
data["reverse3Adapters"] = ThreePrimeadapter.objects.filter(direction='Reverse').order_by('-isDefault', 'name')
else:
data["peForwardLibKeys"] = None
data["peForward3Adapters"] = None
data["reverseLibKeys"] = None
data["reverse3Adapters"] = None
#chip types
#note: customer-facing chip names are no longer unique
data['chipTypes'] = list(Chip.objects.filter(isActive=True).order_by('description', 'name').distinct('description'))
#QC
data['qcTypes'] = list(QCType.objects.all().order_by('qcName'))
#project
data['projects'] = list(Project.objects.filter(public=True).order_by('name'))
#templating kit selection
data["templateKits"] = KitInfo.objects.filter(kitType='TemplatingKit', isActive=True).order_by("name")
#control sequence kit selection
data["controlSeqKits"] = KitInfo.objects.filter(kitType='ControlSequenceKit', isActive=True).order_by("name")
#ionChef kit selection
data["ionChefKits"] = KitInfo.objects.filter(kitType='IonChefPrepKit', isActive=True).order_by("name")
#pairedEnd library adapter selection
#for TS-4669: remove paired-end from wizard, if there are no active PE seq kits, do not prepare pe keys or adapters
if (peLibKits.count() > 0):
data["pairedEndLibAdapters"] = KitInfo.objects.filter(kitType='AdapterKit', runMode="pe", isActive=True).order_by('name')
else:
data["pairedEndLibAdapters"] = None
#samplePrep kits
data["samplePrepKits"] = KitInfo.objects.filter(kitType='SamplePrepKit', isActive=True).order_by('name')
data.update(_dict_IR_plugins_uploaders(isForTemplate))
#to allow data entry for multiple non-barcoded samples at the plan wizard
data['nonBarcodedSamples_irConfig_loopCounter'] = [i + 1 for i in range(20)]
return data
def __init__(self, attrs=None, choices=()):
super(bedfiles_Select, self).__init__(attrs=attrs, choices=choices)
bedfiles = dict_bed_hotspot()
self.bedfiles = bedfiles.get(attrs['name'],[])
def _get_base_planTemplate_data(isForTemplate):
data = {}
#per requirement, we want to display Generic Sequencing as the last entry in the selection list
data["runTypes"] = list(RunType.objects.all().exclude(
runType="GENS").order_by('nucleotideType', 'runType'))
data["secondaryRunTypes"] = list(RunType.objects.filter(runType="GENS"))
data["barcodes"] = list(
dnaBarcode.objects.values('name').distinct().order_by('name'))
##barcodeKitNames = dnaBarcode.objects.values_list('name', flat=True).distinct().order_by('name')
##for barcodeKitName in barcodeKitNames:
## data[barcodeKitName] = dnaBarcode.objects.filter(name=barcodeKitName).order_by('index')
data["barcodeKitInfo"] = list(dnaBarcode.objects.all().order_by(
'name', 'index'))
references = list(ReferenceGenome.objects.all().filter(
index_version=settings.TMAP_VERSION))
data["references"] = references
data["referenceShortNames"] = [ref.short_name for ref in references]
data.update(dict_bed_hotspot())
data["seqKits"] = KitInfo.objects.filter(kitType='SequencingKit',
isActive=True).order_by("name")
data["libKits"] = KitInfo.objects.filter(kitType='LibraryKit',
isActive=True).order_by("name")
data["variantfrequencies"] = VariantFrequencies.objects.all().order_by(
"name")
#the entry marked as the default will be on top of the list
data["forwardLibKeys"] = LibraryKey.objects.filter(
direction='Forward', runMode='single').order_by('-isDefault', 'name')
data["forward3Adapters"] = ThreePrimeadapter.objects.filter(
direction='Forward', runMode='single').order_by('-isDefault', 'name')
#pairedEnd does not have special forward library keys
#for TS-4669: remove paired-end from wizard, if there are no active PE lib kits, do not prepare pe keys or adapters
peLibKits = KitInfo.objects.filter(kitType='LibraryKit',
runMode='pe',
isActive=True)
if (peLibKits.count() > 0):
data["peForwardLibKeys"] = LibraryKey.objects.filter(
direction='Forward').order_by('-isDefault', 'name')
data["peForward3Adapters"] = ThreePrimeadapter.objects.filter(
direction='Forward', runMode='pe').order_by('-isDefault', 'name')
data["reverseLibKeys"] = LibraryKey.objects.filter(
direction='Reverse').order_by('-isDefault', 'name')
data["reverse3Adapters"] = ThreePrimeadapter.objects.filter(
direction='Reverse').order_by('-isDefault', 'name')
else:
data["peForwardLibKeys"] = None
data["peForward3Adapters"] = None
data["reverseLibKeys"] = None
data["reverse3Adapters"] = None
#chip types
#note: customer-facing chip names are no longer unique
data['chipTypes'] = list(
Chip.objects.filter(isActive=True).order_by(
'description', 'name').distinct('description'))
#QC
data['qcTypes'] = list(QCType.objects.all().order_by('qcName'))
#project
data['projects'] = list(
Project.objects.filter(public=True).order_by('name'))
#templating kit selection
data["templateKits"] = KitInfo.objects.filter(
kitType='TemplatingKit', isActive=True).order_by("name")
#control sequence kit selection
data["controlSeqKits"] = KitInfo.objects.filter(
kitType='ControlSequenceKit', isActive=True).order_by("name")
#ionChef kit selection
data["ionChefKits"] = KitInfo.objects.filter(
kitType='IonChefPrepKit', isActive=True).order_by("name")
#pairedEnd library adapter selection
#for TS-4669: remove paired-end from wizard, if there are no active PE seq kits, do not prepare pe keys or adapters
if (peLibKits.count() > 0):
data["pairedEndLibAdapters"] = KitInfo.objects.filter(
kitType='AdapterKit', runMode="pe", isActive=True).order_by('name')
else:
data["pairedEndLibAdapters"] = None
#samplePrep kits
data["samplePrepKits"] = KitInfo.objects.filter(
kitType='SamplePrepKit', isActive=True).order_by('name')
data.update(_dict_IR_plugins_uploaders(isForTemplate))
#to allow data entry for multiple non-barcoded samples at the plan wizard
data['nonBarcodedSamples_irConfig_loopCounter'] = [
i + 1 for i in range(20)
]
return data
