def getChipDisplayedNameSecondaryPrefix(chipDisplayedName):
"""
Returns all the second portion of the chip displayed name for UI to display
e.g., for chip name "318 Select", return "Select"
"""
isVersionInfoFound, prefixes = Chip.getChipDisplayedNameParts(chipDisplayedName)
return prefixes[-1] if len(prefixes) > 1 else ""
def getChipDisplayedNamePrimaryPrefix(chipDisplayedName):
"""
Returns all the primary chip displayed name for UI to display
e.g., for chip name "318 Select", return 318
"""
isVersionInfoFound, prefixes = Chip.getChipDisplayedNameParts(chipDisplayedName)
return prefixes[0]
def getChipDisplayedNameSecondaryPrefix(chipDisplayedName):
"""
Returns all the second portion of the chip displayed name for UI to display
e.g., for chip name "318 Select", return "Select"
"""
isVersionInfoFound, prefixes = Chip.getChipDisplayedNameParts(chipDisplayedName)
return prefixes[-1] if len(prefixes) > 1 else ""
def getChipDisplayedNamePrimaryPrefix(chipDisplayedName):
"""
Returns all the primary chip displayed name for UI to display
e.g., for chip name "318 Select", return 318
"""
isVersionInfoFound, prefixes = Chip.getChipDisplayedNameParts(chipDisplayedName)
return prefixes[0]
def __init__(self, sh_type):
super(KitsStepData, self).__init__(sh_type)
self.resourcePath = "rundb/plan/page_plan/page_plan_kits.html"
self.prev_step_url = reverse("page_plan_application")
self.next_step_url = reverse("page_plan_plugins")
# 20130827-test
# self._dependsOn.append(StepNames.IONREPORTER)
self._dependsOn.append(StepNames.APPLICATION)
self._dependsOn.append(StepNames.BARCODE_BY_SAMPLE)
self.savedFields[KitsFieldNames.SAMPLE_PREPARATION_KIT] = None
self.prepopulatedFields[
KitsFieldNames.SAMPLE_PREP_KITS] = KitInfo.objects.filter(
kitType="SamplePrepKit", isActive=True).order_by("description")
self.savedFields[KitsFieldNames.LIBRARY_KIT_NAME] = None
self.prepopulatedFields[
KitsFieldNames.LIB_KITS] = KitInfo.objects.filter(
kitType__in=["LibraryKit", "LibraryPrepKit"],
isActive=True).order_by("description")
self.savedFields[KitsFieldNames.LIBRARY_KEY] = None
self.prepopulatedFields[
KitsFieldNames.FORWARD_LIB_KEYS] = LibraryKey.objects.filter(
direction="Forward",
runMode="single").order_by("-isDefault", "name")
self.savedFields[KitsFieldNames.LIBRARY_KEY] = self.prepopulatedFields[
KitsFieldNames.FORWARD_LIB_KEYS][0].sequence
self.savedFields[KitsFieldNames.TF_KEY] = GlobalConfig.get(
).default_test_fragment_key
self.savedFields[KitsFieldNames.FORWARD_3_PRIME_ADAPTER] = None
self.prepopulatedFields[
KitsFieldNames.
FORWARD_3_ADAPTERS] = ThreePrimeadapter.objects.filter(
direction="Forward",
runMode="single").order_by("-isDefault", "chemistryType",
"name")
self.savedFields[
KitsFieldNames.FORWARD_3_PRIME_ADAPTER] = self.prepopulatedFields[
KitsFieldNames.FORWARD_3_ADAPTERS][0].sequence
self.savedFields[KitsFieldNames.FLOW_ORDER] = None
self.prepopulatedFields[
KitsFieldNames.FLOW_ORDERS] = FlowOrder.objects.filter(
isActive=True).order_by("-isDefault", "description")
self.savedFields[KitsFieldNames.FLOW_ORDER] = None
self.savedFields[KitsFieldNames.TEMPLATE_KIT_NAME] = None
# no longer default to OneTouch
# self.savedFields[KitsFieldNames.TEMPLATE_KIT_TYPE] = KitsFieldNames.ONE_TOUCH
self.savedFields[KitsFieldNames.TEMPLATE_KIT_TYPE] = None
oneTouchDict = {
KitsFieldNames.KIT_VALUES:
KitInfo.objects.filter(
kitType__in=["TemplatingKit", "AvalancheTemplateKit"],
isActive=True).exclude(
samplePrep_instrumentType="IA").order_by("description"),
KitsFieldNames.APPLICATION_DEFAULT:
None,
}
isoAmpDict = {
KitsFieldNames.KIT_VALUES:
KitInfo.objects.filter(
kitType__in=["TemplatingKit"],
isActive=True,
samplePrep_instrumentType="IA",
).order_by("description"),
KitsFieldNames.APPLICATION_DEFAULT:
None,
}
ionChefDict = {
KitsFieldNames.KIT_VALUES:
KitInfo.objects.filter(kitType="IonChefPrepKit",
isActive=True).order_by("description"),
KitsFieldNames.APPLICATION_DEFAULT:
None,
}
self.prepopulatedFields[
KitsFieldNames.TEMPLATE_KIT_TYPES] = OrderedDict([
(KitsFieldNames.ONE_TOUCH, oneTouchDict),
(KitsFieldNames.ION_CHEF, ionChefDict),
(KitsFieldNames.ISO_AMP, isoAmpDict),
])
self.ModelsSamplePrepInstrumentToLabelsSamplePrepInstrumentAsDict = {
KitsFieldNames.ONE_TOUCH: SamplePrepInstrument.OT,
KitsFieldNames.ION_CHEF: SamplePrepInstrument.IC,
KitsFieldNames.ISO_AMP: SamplePrepInstrument.IA,
}
self.savedFields[KitsFieldNames.SEQUENCE_KIT_NAME] = None
self.prepopulatedFields[
KitsFieldNames.SEQ_KITS] = KitInfo.objects.filter(
kitType="SequencingKit", isActive=True).order_by("description")
self.savedFields[KitsFieldNames.TEMPLATE_KIT_NAME] = None
self.prepopulatedFields[
KitsFieldNames.TEMPLATE_KITS] = KitInfo.objects.filter(
kitType__in=[
"TemplatingKit", "AvalancheTemplateKit", "IonChefPrepKit"
],
isActive=True,
).order_by("description")
self.savedFields[KitsFieldNames.CONTROL_SEQUENCE] = None
self.prepopulatedFields[
KitsFieldNames.CONTROL_SEQ_KITS] = KitInfo.objects.filter(
kitType="ControlSequenceKit",
isActive=True).order_by("description")
self.savedFields[KitsFieldNames.CHIP_TYPE] = None
self.prepopulatedFields[
KitsFieldNames.
INSTRUMENT_TYPES] = Chip.getInstrumentTypesForActiveChips(
include_undefined=False)
self.prepopulatedFields[KitsFieldNames.CHIP_TYPES] = list(
Chip.objects.filter(isActive=True).order_by(
"description", "name").distinct("description"))
self.savedFields[KitsFieldNames.BARCODE_ID] = None
self.prepopulatedFields[KitsFieldNames.BARCODES] = list(
dnaBarcode.objects.filter(
active=True).values("name").distinct().order_by("name"))
gc = GlobalConfig.get()
self.savedFields[
KitsFieldNames.IS_DUPLICATED_READS] = gc.mark_duplicates
self.savedFields[
KitsFieldNames.BASE_RECALIBRATE] = gc.base_recalibration_mode
self.prepopulatedFields[
KitsFieldNames.BASE_RECALIBRATION_MODES] = OrderedDict()
self.prepopulatedFields[
KitsFieldNames.BASE_RECALIBRATION_MODES]["standard_recal"] = {
"text":
_("workflow.step.kits.base_recalibration_modes.standard_recal"
),
"title":
_("workflow.step.kits.base_recalibration_modes.standard_recal.title"
),
} # "Default Calibration"
self.prepopulatedFields[
KitsFieldNames.BASE_RECALIBRATION_MODES]["panel_recal"] = {
"text":
_("workflow.step.kits.base_recalibration_modes.panel_recal"),
"title":
_("workflow.step.kits.base_recalibration_modes.panel_recal.title"
),
} # "Enable Calibration Standard"
self.prepopulatedFields[
KitsFieldNames.BASE_RECALIBRATION_MODES]["blind_recal"] = {
"text":
_("workflow.step.kits.base_recalibration_modes.blind_recal"),
"title":
_("workflow.step.kits.base_recalibration_modes.blind_recal.title"
),
} # "Blind Calibration"
self.prepopulatedFields[
KitsFieldNames.BASE_RECALIBRATION_MODES]["no_recal"] = {
"text":
_("workflow.step.kits.base_recalibration_modes.no_recal"),
"title":
_("workflow.step.kits.base_recalibration_modes.no_recal.title"
),
} # "No Calibration"
self.savedFields[KitsFieldNames.REALIGN] = gc.realign
self.savedFields[KitsFieldNames.FLOWS] = 0
self.savedFields[KitsFieldNames.LIBRARY_READ_LENGTH] = 0
self.savedFields[KitsFieldNames.READ_LENGTH] = 0
self.prepopulatedFields[
KitsFieldNames.IS_BARCODE_KIT_SELECTION_REQUIRED] = False
self.prepopulatedFields[KitsFieldNames.TEMPLATING_SIZE_CHOICES] = [
"200", "400"
]
self.savedFields[KitsFieldNames.TEMPLATING_SIZE] = ""
# For raptor templating kits, templating size cannot be used to drive UI behavior or db persistence. Use read length instead.
self.prepopulatedFields[KitsFieldNames.READ_LENGTH_CHOICES] = [
"200", "400"
]
self.prepopulatedFields[
KitsFieldNames.FLOWS_FROM_CATEGORY_RULES] = json.dumps(
KitInfo._category_flowCount_rules)
self.savedFields[KitsFieldNames.SAMPLE_PREP_PROTOCOL] = None
self.prepopulatedFields[
KitsFieldNames.SAMPLE_PREP_PROTOCOLS] = common_CV.objects.filter(
isActive=True, cv_type="samplePrepProtocol").order_by("uid")
self.prepopulatedFields[KitsFieldNames.PLAN_CATEGORIES] = ""
self.savedFields[KitsFieldNames.ADVANCED_SETTINGS_CHOICE] = "default"
self.prepopulatedFields[KitsFieldNames.ADVANCED_SETTINGS] = "{}"
self.sh_type = sh_type