def get_template_data_for_export(templateId):
''' generates data for template export to CSV file
'''
template = PlannedExperiment.objects.get(pk=int(templateId))
name = "exported " + getPlanDisplayedName(template).strip()
runType = RunType.objects.get(runType=template.runType)
data = [
( PlanCSVcolumns.TEMPLATE_NAME, name[:MAX_LENGTH_PLAN_NAME]),
( PlanCSVcolumns.FAVORITE, template.isFavorite ),
( PlanCSVcolumns.APPLICATION, template.applicationGroup.description if template.applicationGroup else '' ),
( PlanCSVcolumns.RUNTYPE, runType.alternate_name ),
( PlanCSVcolumns.SAMPLE_GROUP, template.sampleGrouping.displayedName if template.sampleGrouping else '' ),
( PlanCSVcolumns.BARCODE_SET, template.get_barcodeId() ),
( PlanCSVcolumns.COLUMN_CHIP_TYPE, _get_chip_type_description(template) ),
( PlanCSVcolumns.COLUMN_SAMPLE_PREP_KIT, _get_sample_prep_kit_description(template) ),
( PlanCSVcolumns.COLUMN_LIBRARY_KIT, _get_lib_kit_description(template) ),
( PlanCSVcolumns.LIBRARY_KEY, template.get_libraryKey() ),
( PlanCSVcolumns.TF_KEY, template.get_tfKey() ),
( PlanCSVcolumns.THREEPRIME_ADAPTER, template.get_forward3primeadapter() ),
( PlanCSVcolumns.FLOW_ORDER, template.experiment.flowsInOrder or "default" ),
( PlanCSVcolumns.COLUMN_TEMPLATING_KIT, _get_template_kit_description(template) ),
( PlanCSVcolumns.COLUMN_TEMPLATING_SIZE, _get_templating_size(template) ),
( PlanCSVcolumns.COLUMN_SEQ_KIT, _get_seq_kit_description(template) ),
( PlanCSVcolumns.COLUMN_CONTROL_SEQ_KIT, _get_control_seq_kit_description(template) ),
( PlanCSVcolumns.COLUMN_LIBRARY_READ_LENGTH, _get_library_read_length(template) ),
( PlanCSVcolumns.CALIBRATION_MODE, template.latestEAS.base_recalibration_mode ),
( PlanCSVcolumns.MARK_DUPLICATES, template.latestEAS.isDuplicateReads ),
( PlanCSVcolumns.REALIGN, template.latestEAS.realign ),
( PlanCSVcolumns.COLUMN_FLOW_COUNT, template.get_flows() ),
( PlanCSVcolumns.COLUMN_REF, _get_reference(template) ),
( PlanCSVcolumns.COLUMN_TARGET_BED, _get_target_regions_bed_file(template) ),
( PlanCSVcolumns.COLUMN_HOTSPOT_BED,_get_hotspot_regions_bed_file(template) )
]
# add fusions reference for DNA/Fusions application
if runType.runType == 'AMPS_DNA_RNA':
data.extend([
( PlanCSVcolumns.FUSIONS_REF, template.get_mixedType_rna_library() ),
( PlanCSVcolumns.FUSIONS_TARGET_BED, _get_fusions_target_regions_bed_file(template) )
])
data.extend([
( PlanCSVcolumns.COLUMN_BEAD_LOAD_PCT, _get_bead_loading_qc(template) ),
( PlanCSVcolumns.COLUMN_KEY_SIGNAL_PCT, _get_key_signal_qc(template) ),
( PlanCSVcolumns.COLUMN_USABLE_SEQ_PCT, _get_usable_seq_qc(template) ),
( PlanCSVcolumns.COLUMN_PLUGINS, _get_plugins(template, TOKEN_DELIMITER) ),
( PlanCSVcolumns.COLUMN_PROJECTS, _get_projects(template, TOKEN_DELIMITER) ),
( PlanCSVcolumns.CATEGORIES, template.categories ),
( PlanCSVcolumns.COLUMN_NOTES, _get_notes(template) ),
( PlanCSVcolumns.COLUMN_LIMS_DATA, _get_LIMS_data(template) ),
])
# add custom analysis args
if template.latestEAS.custom_args:
args = template.latestEAS.get_cmdline_args()
data.append((PlanCSVcolumns.CUSTOM_ARGS, True))
data.extend([(key, args[key]) for key in sorted(args)])
return zip(*data)
def get_template_data_for_export(templateId):
''' generates data for template export to CSV file
'''
template = PlannedExperiment.objects.get(pk=int(templateId))
name = "exported " + getPlanDisplayedName(template).strip()
runType = RunType.objects.get(runType=template.runType)
data = [
( PlanCSVcolumns.TEMPLATE_NAME, name[:MAX_LENGTH_PLAN_NAME]),
( PlanCSVcolumns.FAVORITE, template.isFavorite ),
( PlanCSVcolumns.APPLICATION, template.applicationGroup.description if template.applicationGroup else '' ),
( PlanCSVcolumns.RUNTYPE, runType.alternate_name ),
( PlanCSVcolumns.SAMPLE_GROUP, template.sampleGrouping.displayedName if template.sampleGrouping else '' ),
( PlanCSVcolumns.BARCODE_SET, template.get_barcodeId() ),
( PlanCSVcolumns.COLUMN_CHIP_TYPE, _get_chip_type_description(template) ),
( PlanCSVcolumns.COLUMN_SAMPLE_PREP_KIT, _get_sample_prep_kit_description(template) ),
( PlanCSVcolumns.COLUMN_LIBRARY_KIT, _get_lib_kit_description(template) ),
( PlanCSVcolumns.LIBRARY_KEY, template.get_libraryKey() ),
( PlanCSVcolumns.TF_KEY, template.get_tfKey() ),
( PlanCSVcolumns.THREEPRIME_ADAPTER, template.get_forward3primeadapter() ),
( PlanCSVcolumns.FLOW_ORDER, template.experiment.flowsInOrder or "default" ),
( PlanCSVcolumns.COLUMN_TEMPLATING_KIT, _get_template_kit_description(template) ),
( PlanCSVcolumns.COLUMN_TEMPLATING_SIZE, _get_templating_size(template) ),
( PlanCSVcolumns.COLUMN_SEQ_KIT, _get_seq_kit_description(template) ),
( PlanCSVcolumns.COLUMN_CONTROL_SEQ_KIT, _get_control_seq_kit_description(template) ),
( PlanCSVcolumns.COLUMN_LIBRARY_READ_LENGTH, _get_library_read_length(template) ),
( PlanCSVcolumns.CALIBRATION_MODE, template.latestEAS.base_recalibration_mode ),
( PlanCSVcolumns.MARK_DUPLICATES, template.latestEAS.isDuplicateReads ),
( PlanCSVcolumns.REALIGN, template.latestEAS.realign ),
( PlanCSVcolumns.COLUMN_FLOW_COUNT, template.get_flows() ),
( PlanCSVcolumns.COLUMN_REF, _get_reference(template) ),
( PlanCSVcolumns.COLUMN_TARGET_BED, _get_target_regions_bed_file(template) ),
( PlanCSVcolumns.COLUMN_HOTSPOT_BED,_get_hotspot_regions_bed_file(template) )
]
# add fusions reference for DNA/Fusions application
if runType.runType == 'AMPS_DNA_RNA':
data.extend([
( PlanCSVcolumns.FUSIONS_REF, template.get_mixedType_rna_library() ),
( PlanCSVcolumns.FUSIONS_TARGET_BED, _get_fusions_target_regions_bed_file(template) )
])
data.extend([
( PlanCSVcolumns.COLUMN_BEAD_LOAD_PCT, _get_bead_loading_qc(template) ),
( PlanCSVcolumns.COLUMN_KEY_SIGNAL_PCT, _get_key_signal_qc(template) ),
( PlanCSVcolumns.COLUMN_USABLE_SEQ_PCT, _get_usable_seq_qc(template) ),
( PlanCSVcolumns.COLUMN_PLUGINS, _get_plugins(template, TOKEN_DELIMITER) ),
( PlanCSVcolumns.COLUMN_PROJECTS, _get_projects(template, TOKEN_DELIMITER) ),
( PlanCSVcolumns.CATEGORIES, template.categories ),
( PlanCSVcolumns.COLUMN_NOTES, _get_notes(template) ),
( PlanCSVcolumns.COLUMN_LIMS_DATA, _get_LIMS_data(template) ),
])
# add custom analysis args
if template.latestEAS.custom_args:
args = template.latestEAS.get_cmdline_args()
data.append((PlanCSVcolumns.CUSTOM_ARGS, True))
data.extend([(key, args[key]) for key in sorted(args)])
return zip(*data)
def get_template_data_for_batch_planning(templateId, single_samples_file):
try:
template = PlannedExperiment.objects.get(pk=int(templateId))
logger.info("plan_csv_writer.get_template_data_for_batch_planning() template retrieved. id=%d;" % (int(templateId)))
hdr = [PlanCSVcolumns.COLUMN_TEMPLATE_NAME, PlanCSVcolumns.COLUMN_PLAN_NAME
]
hdr2 = [PlanCSVcolumns.COLUMN_SAMPLE_PREP_KIT, PlanCSVcolumns.COLUMN_LIBRARY_KIT, PlanCSVcolumns.COLUMN_TEMPLATING_KIT, PlanCSVcolumns.COLUMN_TEMPLATING_SIZE, PlanCSVcolumns.COLUMN_CONTROL_SEQ_KIT, PlanCSVcolumns.COLUMN_SEQ_KIT, PlanCSVcolumns.COLUMN_CHIP_TYPE, PlanCSVcolumns.COLUMN_LIBRARY_READ_LENGTH, PlanCSVcolumns.COLUMN_FLOW_COUNT, PlanCSVcolumns.COLUMN_SAMPLE_TUBE_LABEL, PlanCSVcolumns.COLUMN_BEAD_LOAD_PCT, PlanCSVcolumns.COLUMN_KEY_SIGNAL_PCT, PlanCSVcolumns.COLUMN_USABLE_SEQ_PCT, PlanCSVcolumns.COLUMN_REF, PlanCSVcolumns.COLUMN_TARGET_BED, PlanCSVcolumns.COLUMN_HOTSPOT_BED, PlanCSVcolumns.COLUMN_PLUGINS, PlanCSVcolumns.COLUMN_PROJECTS, PlanCSVcolumns.COLUMN_EXPORT, PlanCSVcolumns.COLUMN_NOTES, PlanCSVcolumns.COLUMN_LIMS_DATA, PlanCSVcolumns.COLUMN_CHIP_BARCODE
]
body = [getPlanDisplayedName(template), ""
]
body2 = [_get_sample_prep_kit_description(template), _get_lib_kit_description(template), _get_template_kit_description(template), _get_templating_size(template), _get_control_seq_kit_description(template), _get_seq_kit_description(template), _get_chip_type_description(template), _get_library_read_length(template), _get_flow_count(template), _get_sample_tube_label(template), _get_bead_loading_qc(template), _get_key_signal_qc(template), _get_usable_seq_qc(template), _get_reference(template), _get_target_regions_bed_file(template), _get_hotspot_regions_bed_file(template), _get_plugins(template, ";"), _get_projects(template, ";"), _get_export(template, ";"), _get_notes(template), _get_LIMS_data(template)
]
# position of the fields below are based on the template selected and whether IR has been installed on the TS
if _has_ir_v1_0(template):
hdr2.append(PlanCSVcolumns.COLUMN_IR_V1_0_WORKFLOW)
body2.append("")
# has_ir_beyond_v1_0 = _has_ir_beyond_v1_0(template)
if _is_barcoded(template):
if single_samples_file:
hdr.extend(_get_barcoded_sample_headers(template, PlanCSVcolumns.COLUMN_BC_SAMPLE_KEY))
body.extend(_get_barcoded_sample_names(template))
# if has_ir_beyond_v1_0:
# hdr.extend(_get_barcoded_sample_IR_beyond_v1_0_headers(template, PlanCSVcolumns.COLUMN_BC_SAMPLE_KEY, ))
# body.extend(_get_barcoded_sample_IR_beyond_v1_0_workflows(template))
else:
hdr.append(PlanCSVcolumns.COLUMN_SAMPLE_FILE_HEADER)
body.append("")
else:
hdr.append(PlanCSVcolumns.COLUMN_SAMPLE)
body.append(_get_sample_name(template))
hdr.append(PlanCSVcolumns.COLUMN_SAMPLE_ID)
body.append(_get_sample_id(template))
# if has_ir_beyond_v1_0:
# hdr.append(PlanCSVcolumns.COLUMN_IR_V1_X_WORKFLOW)
# body.append(_get_sample_IR_beyond_v1_0_workflows(template))
hdr.extend(hdr2)
body.extend(body2)
return hdr, body
except:
logger.exception(format_exc())
return [], [], []
def updateTemplateSpecificStepHelper(self, step_helper, planned_experiment):
'''
Updates the template specific step helper with template specific info from the planned experiment.
'''
save_template_step_data = step_helper.steps[StepNames.SAVE_TEMPLATE]
planDisplayedName = getPlanDisplayedName(planned_experiment)
if step_helper.sh_type == StepHelperType.COPY_TEMPLATE:
save_template_step_data.savedFields['templateName'] = "Copy of " + planDisplayedName
else:
save_template_step_data.savedFields['templateName'] = planDisplayedName
save_template_step_data.savedFields['setAsFavorite'] = planned_experiment.isFavorite
def getStepHelperForTemplatePlannedExperiment(self, pe_id, step_helper_type=StepHelperType.EDIT_TEMPLATE, sampleset_id=None):
'''
Get a step helper from a template planned experiment.
'''
step_helper = StepHelper(sh_type=step_helper_type, previous_template_id=pe_id)
planned_experiment = PlannedExperiment.objects.get(pk=pe_id)
if not planned_experiment.isReusable:
raise ValueError("You must pass in a template id, not a plan id.")
planDisplayedName = getPlanDisplayedName(planned_experiment)
step_helper.parentName = planDisplayedName
self.updateUniversalStepHelper(step_helper, planned_experiment)
if step_helper.isPlan() and step_helper.isPlanBySample():
self.updatePlanBySampleSpecificStepHelper(step_helper, planned_experiment, sampleset_id)
elif step_helper.isPlan():
self.updatePlanSpecificStepHelper(step_helper, planned_experiment, True)
else:
self.updateTemplateSpecificStepHelper(step_helper, planned_experiment)
return step_helper
def getStepHelperForPlanPlannedExperiment(self, pe_id, step_helper_type=StepHelperType.EDIT_PLAN):
'''
Get a plan step helper from a plan planned experiment.
'''
step_helper = StepHelper(sh_type=step_helper_type, previous_plan_id=pe_id)
planned_experiment = PlannedExperiment.objects.get(pk=pe_id)
planDisplayedName = getPlanDisplayedName(planned_experiment)
step_helper.parentName = planDisplayedName
if planned_experiment.isReusable:
raise ValueError("You must pass in a plan id, not a template id.")
self.updateUniversalStepHelper(step_helper, planned_experiment)
if step_helper.isPlan() and step_helper.isPlanBySample():
self.updatePlanBySampleSpecificStepHelper(step_helper, planned_experiment, planned_experiment.sampleSet.pk)
elif step_helper.isPlan():
self.updatePlanSpecificStepHelper(step_helper, planned_experiment)
else:
raise ValueError("Can not create templates from plans.")
return step_helper
def get_template_data_for_batch_planning(templateId):
try:
template = PlannedExperiment.objects.get(pk = int(templateId))
logger.info("plan_csv_writer.get_template_data_for_batch_planning() template retrieved. id=%d;" %(int(templateId)))
hdr = [ COLUMN_TEMPLATE_NAME
, COLUMN_PLAN_NAME
]
hdr2 = [ COLUMN_SAMPLE_PREP_KIT
, COLUMN_LIBRARY_KIT
, COLUMN_TEMPLATING_KIT
, COLUMN_TEMPLATING_SIZE
, COLUMN_CONTROL_SEQ_KIT
, COLUMN_SEQ_KIT
, COLUMN_CHIP_TYPE
, COLUMN_LIBRARY_READ_LENGTH
, COLUMN_FLOW_COUNT
, COLUMN_SAMPLE_TUBE_LABEL
, COLUMN_BEAD_LOAD_PCT
, COLUMN_KEY_SIGNAL_PCT
, COLUMN_USABLE_SEQ_PCT
, COLUMN_REF
, COLUMN_TARGET_BED
, COLUMN_HOTSPOT_BED
, COLUMN_PLUGINS
, COLUMN_PROJECTS
, COLUMN_EXPORT
, COLUMN_NOTES
, COLUMN_LIMS_DATA
]
body = [ getPlanDisplayedName(template)
, ""
]
body2 = [_get_sample_prep_kit_description(template)
, _get_lib_kit_description(template)
, _get_template_kit_description(template)
, _get_templating_size(template)
, _get_control_seq_kit_description(template)
, _get_seq_kit_description(template)
, _get_chip_type_description(template)
, _get_library_read_length(template)
, _get_flow_count(template)
, _get_sample_tube_label(template)
, _get_bead_loading_qc(template)
, _get_key_signal_qc(template)
, _get_usable_seq_qc(template)
, _get_reference(template)
, _get_target_regions_bed_file(template)
, _get_hotspot_regions_bed_file(template)
, _get_plugins(template, ";")
, _get_projects(template, ";")
, _get_export(template, ";")
, _get_notes(template)
, _get_LIMS_data(template)
]
#position of the fields below are based on the template selected and whether IR has been installed on the TS
if _has_ir_v1_0(template):
hdr2.append(COLUMN_IR_V1_0_WORKFLOW)
body2.append("")
#has_ir_beyond_v1_0 = _has_ir_beyond_v1_0(template)
if _is_barcoded(template):
hdr.extend(_get_barcoded_sample_headers(template, COLUMN_BC_SAMPLE_KEY))
body.extend(_get_barcoded_sample_names(template))
#if has_ir_beyond_v1_0:
# hdr.extend(_get_barcoded_sample_IR_beyond_v1_0_headers(template, COLUMN_BC_SAMPLE_KEY, ))
# body.extend(_get_barcoded_sample_IR_beyond_v1_0_workflows(template))
else:
hdr.append(COLUMN_SAMPLE)
body.append(_get_sample_name(template))
hdr.append(COLUMN_SAMPLE_ID)
body.append(_get_sample_id(template))
#if has_ir_beyond_v1_0:
# hdr.append(COLUMN_IR_V1_X_WORKFLOW)
# body.append(_get_sample_IR_beyond_v1_0_workflows(template))
hdr.extend(hdr2)
body.extend(body2)
return hdr, body
except:
logger.exception(format_exc())
return [], [], []
def updatePlanSpecificStepHelper(self, step_helper, planned_experiment, set_template_name=False):
'''
Updates the plan specific step helper with plan specific info from the planned experiment.
If the planned experiment is a template and you'd like the originating template name to show up
in the save plan page pass in set_template_name=True
'''
planDisplayedName = getPlanDisplayedName(planned_experiment)
if set_template_name:
step_helper.steps[StepNames.SAVE_TEMPLATE].savedFields['templateName'] = planDisplayedName
save_plan_step_data = step_helper.steps[StepNames.SAVE_PLAN]
kits_step_data = step_helper.steps[StepNames.KITS]
#Add a "copy of" if we're copying.
if step_helper.isCopy():
save_plan_step_data.savedFields['planName'] = "Copy of " + planDisplayedName
else:
save_plan_step_data.savedFields['planName'] = planDisplayedName
save_plan_step_data.savedFields['note'] = planned_experiment.get_notes()
if step_helper.isBarcoded():
save_plan_step_data.prepopulatedFields['prevBarcodeId'] = kits_step_data.savedFields['barcodeId']
save_plan_step_data.prepopulatedFields['barcodes'] = list(dnaBarcode.objects.filter(name=kits_step_data.savedFields['barcodeId']).order_by('name', 'index'))
barcodeToIrValues = None
#build a barcodeid to ir info dict
for plugin_name, plugin_dict in planned_experiment.get_selectedPlugins().items():
if 'IonReporter' in plugin_name:
try:
plugin = Plugin.objects.filter(name=plugin_name, active=True)[0]
except:
continue
barcodeToIrValues = {}
save_plan_step_data.prepopulatedFields['selectedIr'] = plugin
save_plan_step_data.prepopulatedFields['irConfigJson'] = json.dumps(plugin.userinputfields)
if PluginFieldNames.USER_INPUT in plugin_dict:
#Handle the old and the new style userinput in the plugin dictionary
if isinstance(plugin_dict[PluginFieldNames.USER_INPUT], dict)\
and "userInputInfo" in plugin_dict[PluginFieldNames.USER_INPUT]\
and len(plugin_dict[PluginFieldNames.USER_INPUT]["userInputInfo"]) > 0:
for valueDict in plugin_dict[PluginFieldNames.USER_INPUT]["userInputInfo"]:
barcodeToIrValues[valueDict['barcodeId']] = valueDict
save_plan_step_data.prepopulatedFields['setid_suffix'] = valueDict['setid'][valueDict['setid'].find('__'):]
elif isinstance(plugin_dict[PluginFieldNames.USER_INPUT], list):
for valueDict in plugin_dict[PluginFieldNames.USER_INPUT]:
barcodeToIrValues[valueDict['barcodeId']] = valueDict
#build a sample to barcode dict
sample_to_barcode = planned_experiment.get_barcodedSamples()
barcodeIdStrToSample = {}
for sample, value in sample_to_barcode.items():
if 'barcodeSampleInfo' in value:
barcodeSampleInfo = value['barcodeSampleInfo']
for barcode, sampleInfo in barcodeSampleInfo.items():
barcodeIdStrToSample[barcode] = {"sampleName": sample}
barcodeIdStrToSample[barcode].update(sampleInfo)
else:
barcodeIdStrList = value['barcodes']
for barcodeIdStr in barcodeIdStrList:
barcodeIdStrToSample[barcodeIdStr] = {"sampleName": sample, "externalId": None, "description": None}
#for each barcode populate the sample and ir info
for barcode in save_plan_step_data.prepopulatedFields['barcodes']:
if barcode.id_str in barcodeIdStrToSample:
save_plan_step_data.savedFields['barcodeSampleName%s' % str(barcode.pk)] = barcodeIdStrToSample[barcode.id_str]["sampleName"]
save_plan_step_data.savedFields['barcodeSampleExternalId%s' % str(barcode.pk)] = barcodeIdStrToSample[barcode.id_str]["externalId"]
save_plan_step_data.savedFields['barcodeSampleDescription%s' % str(barcode.pk)] = barcodeIdStrToSample[barcode.id_str]["description"]
if barcodeToIrValues:
save_plan_step_data.savedFields['irGender%s' % str(barcode.pk)] = barcodeToIrValues[barcode.id_str]['Gender']
save_plan_step_data.savedFields['irWorkflow%s' % str(barcode.pk)] = barcodeToIrValues[barcode.id_str]['Workflow']
#some older plans do not have "Relation" specified - could be due to work-in-progress development code
save_plan_step_data.savedFields['irRelation%s' % str(barcode.pk)] = barcodeToIrValues[barcode.id_str].get('Relation', "")
save_plan_step_data.savedFields['irRelationRole%s' % str(barcode.pk)] = barcodeToIrValues[barcode.id_str]['RelationRole']
save_plan_step_data.savedFields['irSetID%s' % str(barcode.pk)] = barcodeToIrValues[barcode.id_str]['setid'][0:barcodeToIrValues[barcode.id_str]['setid'].find('__')] if barcodeToIrValues[barcode.id_str]['setid'] else ""
else:
save_plan_step_data.savedFields['irGender%s' % str(barcode.pk)] = None
save_plan_step_data.savedFields['irWorkflow%s' % str(barcode.pk)] = None
save_plan_step_data.savedFields['irRelation%s' % str(barcode.pk)] = None
save_plan_step_data.savedFields['irRelationRole%s' % str(barcode.pk)] = None
save_plan_step_data.savedFields['irSetID%s' % str(barcode.pk)] = None
else:
save_plan_step_data.savedFields['barcodeSampleName%s' % str(barcode.pk)] = None
save_plan_step_data.savedFields['barcodeSampleExternalId%s' % str(barcode.pk)] = None
save_plan_step_data.savedFields['barcodeSampleDescription%s' % str(barcode.pk)] = None
save_plan_step_data.savedFields['irGender%s' % str(barcode.pk)] = None
save_plan_step_data.savedFields['irWorkflow%s' % str(barcode.pk)] = None
save_plan_step_data.savedFields['irRelation%s' % str(barcode.pk)] = None
save_plan_step_data.savedFields['irRelationRole%s' % str(barcode.pk)] = None
save_plan_step_data.savedFields['irSetID%s' % str(barcode.pk)] = None
#do not copy sampleTubeLabel since a sample tube is meant for 1 run only
save_plan_step_data.savedFields['barcodeSampleTubeLabel'] = "" if step_helper.isCopy() else planned_experiment.sampleTubeLabel
else:
#when we load a non-barcoded run for editing/copying we know it will only have a single sample.
save_plan_step_data.prepopulatedFields['prevBarcodeId'] = None
save_plan_step_data.savedFields['sampleName1'] = planned_experiment.get_sampleDisplayedName()
#do not copy sampleTubeLabel since a sample tube is meant for 1 run only
save_plan_step_data.savedFields['tubeLabel1'] = "" if step_helper.isCopy() else planned_experiment.sampleTubeLabel
save_plan_step_data.savedFields['sampleExternalId1'] = planned_experiment.get_sample_external_id()
save_plan_step_data.savedFields['sampleDescription1'] = planned_experiment.get_sample_description()
#if there was ir info we grab it
for plugin_name, plugin_dict in planned_experiment.get_selectedPlugins().items():
if 'IonReporter' in plugin_name:
try:
plugin = Plugin.objects.filter(name=plugin_name, active=True)[0]
except:
continue
save_plan_step_data.prepopulatedFields['selectedIr'] = plugin
save_plan_step_data.prepopulatedFields['irConfigJson'] = json.dumps(plugin.userinputfields)
sample_ir_values = None
if PluginFieldNames.USER_INPUT in plugin_dict:
#Handle the old and the new style userinput in the plugin dictionary
if isinstance(plugin_dict[PluginFieldNames.USER_INPUT], dict)\
and "userInputInfo" in plugin_dict[PluginFieldNames.USER_INPUT]\
and len(plugin_dict[PluginFieldNames.USER_INPUT]["userInputInfo"])>0:
sample_ir_values = plugin_dict[PluginFieldNames.USER_INPUT]["userInputInfo"][0]
save_plan_step_data.prepopulatedFields['setid_suffix'] = plugin_dict[PluginFieldNames.USER_INPUT]["userInputInfo"][0]['setid'][plugin_dict[PluginFieldNames.USER_INPUT]["userInputInfo"][0]['setid'].find('__'):]
elif isinstance(plugin_dict[PluginFieldNames.USER_INPUT], list)\
and len(plugin_dict[PluginFieldNames.USER_INPUT])>0:
sample_ir_values = plugin_dict[PluginFieldNames.USER_INPUT][0]
if sample_ir_values:
save_plan_step_data.savedFields['irWorkflow1'] = sample_ir_values['Workflow']
save_plan_step_data.savedFields['irGender1'] = sample_ir_values['Gender']
save_plan_step_data.savedFields['irRelation1'] = sample_ir_values['Relation']
save_plan_step_data.savedFields['irRelationRole1'] = sample_ir_values['RelationRole']
save_plan_step_data.savedFields['irSetID1'] = str(sample_ir_values['setid'])[0:str(sample_ir_values['setid']).find('__')]
save_plan_step_data.updateSavedObjectsFromSavedFields()
def updatePlanBySampleSpecificStepHelper(self, step_helper, planned_experiment, sampleset_id):
"""
"""
barcoding_step = step_helper.steps[StepNames.BARCODE_BY_SAMPLE]
save_plan_step = step_helper.steps[StepNames.SAVE_PLAN_BY_SAMPLE]
planDisplayedName = getPlanDisplayedName(planned_experiment)
step_helper.steps[StepNames.IONREPORTER].savedFields['irworkflow'] = planned_experiment.irworkflow
if step_helper.isCopy():
save_plan_step.savedFields[SavePlanBySampleFieldNames.TEMPLATE_NAME] = "Copy of " + planDisplayedName
else:
save_plan_step.savedFields[SavePlanBySampleFieldNames.TEMPLATE_NAME] = planDisplayedName
if sampleset_id:
sampleset = SampleSet.objects.get(pk=sampleset_id)
if sampleset.SampleGroupType_CV:
step_helper.steps[StepNames.APPLICATION].savedFields['sampleGrouping'] = sampleset.SampleGroupType_CV.pk
else:
sampleset = planned_experiment.sampleSet
save_plan_step.savedObjects[SavePlanBySampleFieldNames.SAMPLESET] = sampleset
samplesetitems = list(sampleset.samples.all())
all_barcodes = dnaBarcode.objects.values('name', 'id_str', 'sequence')
barcodekits = set(map(lambda x : x['name'], all_barcodes))
barcoding_step.prepopulatedFields['accountId'] = step_helper.steps[StepNames.IONREPORTER].savedFields['irAccountId']
barcoding_step.prepopulatedFields['all_barcodes'] = sorted(all_barcodes, key=lambda x : x['id_str'])
barcoding_step.prepopulatedFields['irworkflow'] = planned_experiment.irworkflow
barcoding_step.prepopulatedFields['pe_irworkflow'] = planned_experiment.irworkflow
dnabarcodes_grouped = [
dict(
name = barcodekit,
barcodes = sorted([
dict( id_str = str(dnabarcode['id_str']),
sequence = str(dnabarcode['sequence'])) \
for dnabarcode in all_barcodes if dnabarcode['name'] == barcodekit], key=lambda z: z['id_str'])) \
for barcodekit in barcodekits]
if step_helper.isBarcoded():
# planned_dnabarcodes = dnaBarcode.objects.filter(name=planned_experiment.get_barcodeId()).values('id_str', 'sequence').order_by('id_str')
planned_dnabarcodes = list(dnaBarcode.objects.filter(name=planned_experiment.get_barcodeId()).order_by('id_str'))
else:
planned_dnabarcodes = [None]
barcoding_step.prepopulatedFields['samplesetitems'] = samplesetitems
barcoding_step.prepopulatedFields[BarcodeBySampleFieldNames.PLANNED_DNABARCODES] = planned_dnabarcodes
barcoding_step.prepopulatedFields['barcodekits'] = dnabarcodes_grouped
barcoding_step.savedFields[BarcodeBySampleFieldNames.NUMBER_OF_CHIPS] = len(samplesetitems)
barcoding_step.savedFields[BarcodeBySampleFieldNames.BARCODE_ID] = planned_experiment.get_barcodeId()
selected_plugins = planned_experiment.get_selectedPlugins()
if 'IonReporterUploader' in selected_plugins:
try:
user_input_info = selected_plugins['IonReporterUploader']['userInput']['userInputInfo']
except:
user_input_info = selected_plugins['IonReporterUploader']['userInput']
else:
user_input_info = [planned_experiment.get_barcodedSamples()]
result = []
if len(user_input_info) > 0 and len(user_input_info[0].keys()) > 0:
for i in range(len(samplesetitems)):
result.append(self.get_ir_fields_dict_from_user_input_info(user_input_info, user_input_info[i].get('sample', "barcoded--Sample") if i < len(user_input_info) else user_input_info[0].get('sampleName', "barcoded--Sample"), i))
user_input_info = sorted(result, key=lambda d: d.get('barcodeId'))
existing_plan = not planned_experiment.isReusable
if (step_helper.isEdit() or step_helper.isCopy()) and len(user_input_info[0]) > 0:
if user_input_info[0].get('setid'):
barcoding_step.prepopulatedFields['setid_suffix'] = user_input_info[0].get('setid')[user_input_info[0].get('setid').find('__'):]
for i in range(100):
barcoding_step.savedFields['%s%d' % (BarcodeBySampleFieldNames.NUMBER_OF_CHIPS, i)] = i + 1
barcoding_step.savedFields['%s%d' % (BarcodeBySampleFieldNames.SAMPLE_NAME, i)] = None
barcoding_step.savedFields['%s%d' % (BarcodeBySampleFieldNames.SAMPLE_EXTERNAL_ID, i)] = None
barcoding_step.savedFields['%s%d' % (BarcodeBySampleFieldNames.SAMPLE_BARCODE, i)] = None
barcoding_step.savedFields['%s%d' % (BarcodeBySampleFieldNames.WORKFLOW, i)] = None
barcoding_step.savedFields['%s%d' % (BarcodeBySampleFieldNames.GENDER, i)] = None
barcoding_step.savedFields['%s%d' % (BarcodeBySampleFieldNames.SAMPLE_DESCRIPTION, i)] = None
barcoding_step.savedFields['%s%d' % (BarcodeBySampleFieldNames.RELATION_ROLE, i)] = None
barcoding_step.savedFields['%s%d' % ('relation', i)] = None
barcoding_step.savedFields['%s%d' % (BarcodeBySampleFieldNames.SET_ID, i)] = None
if step_helper.isBarcoded():
for i in range(len(planned_dnabarcodes)):
samplesetitem = samplesetitems[i] if i < len(samplesetitems) else None
dnabarcode = planned_dnabarcodes[i] if i < len(planned_dnabarcodes) else None
if existing_plan:
if i < len(user_input_info):
user_input_dict = self.get_ir_fields_dict_from_user_input_info(user_input_info, user_input_info[i].get('sample', "barcoded--Sample"), i)
barcoding_step.savedObjects[BarcodeBySampleFieldNames.BARCODE_TO_SAMPLE]['%s%d' % (user_input_dict.get('barcodeId'), i)] = {
BarcodeBySampleFieldNames.NUMBER_OF_CHIPS : i + 1,
BarcodeBySampleFieldNames.SAMPLE_NAME : user_input_dict.get('sample'),
BarcodeBySampleFieldNames.SAMPLE_DESCRIPTION : user_input_dict.get('sampleDescription'),
BarcodeBySampleFieldNames.SAMPLE_EXTERNAL_ID : user_input_dict.get('sampleExternalId'),
BarcodeBySampleFieldNames.GENDER : user_input_dict.get('Gender'),
BarcodeBySampleFieldNames.RELATION_ROLE : user_input_dict.get('RelationRole'),
BarcodeBySampleFieldNames.WORKFLOW : user_input_dict.get('Workflow'),
BarcodeBySampleFieldNames.BARCODE_ID : user_input_dict.get('barcodeId'),
BarcodeBySampleFieldNames.SET_ID : user_input_dict.get('setid')[0:user_input_dict['setid'].find('__')] if user_input_dict.get('setid') else "",
'relation' : '',
}
else:
barcoding_step.savedObjects[BarcodeBySampleFieldNames.BARCODE_TO_SAMPLE]['%s%d' % (dnabarcode.id_str, i)] = {
BarcodeBySampleFieldNames.NUMBER_OF_CHIPS : i + 1,
BarcodeBySampleFieldNames.SAMPLE_NAME : '',
BarcodeBySampleFieldNames.SAMPLE_DESCRIPTION : '',
BarcodeBySampleFieldNames.SAMPLE_EXTERNAL_ID : '',
BarcodeBySampleFieldNames.GENDER : '',
BarcodeBySampleFieldNames.RELATION_ROLE : '',
BarcodeBySampleFieldNames.WORKFLOW : '',
BarcodeBySampleFieldNames.BARCODE_ID : dnabarcode.id_str,
BarcodeBySampleFieldNames.SET_ID : 0,
'relation' : '',
}
else:
if i < len(samplesetitems):
#create the saved objects dictionary for the dnabarcode to control
#the order of display of dnabarcode id_str's and sample item names and descriptions
barcoding_step.savedObjects[BarcodeBySampleFieldNames.BARCODE_TO_SAMPLE]['%s%d' % (dnabarcode.id_str, i)] = {
BarcodeBySampleFieldNames.NUMBER_OF_CHIPS : i + 1,
BarcodeBySampleFieldNames.SAMPLE_NAME : samplesetitem.sample.displayedName,
BarcodeBySampleFieldNames.SAMPLE_DESCRIPTION : samplesetitem.sample.description,
BarcodeBySampleFieldNames.SAMPLE_EXTERNAL_ID : samplesetitem.sample.externalId,
BarcodeBySampleFieldNames.GENDER : samplesetitem.gender,
BarcodeBySampleFieldNames.RELATION_ROLE : samplesetitem.relationshipRole,
BarcodeBySampleFieldNames.WORKFLOW : planned_experiment.irworkflow,
BarcodeBySampleFieldNames.BARCODE_ID : dnabarcode.id_str,
BarcodeBySampleFieldNames.SET_ID : samplesetitem.relationshipGroup,
'relation' : '',
}
else:
barcoding_step.savedObjects[BarcodeBySampleFieldNames.BARCODE_TO_SAMPLE]['%s%d' % (dnabarcode.id_str, i)] = {
BarcodeBySampleFieldNames.NUMBER_OF_CHIPS : i + 1,
BarcodeBySampleFieldNames.SAMPLE_NAME : '',
BarcodeBySampleFieldNames.SAMPLE_DESCRIPTION : '',
BarcodeBySampleFieldNames.SAMPLE_EXTERNAL_ID : '',
BarcodeBySampleFieldNames.GENDER : '',
BarcodeBySampleFieldNames.RELATION_ROLE : '',
BarcodeBySampleFieldNames.WORKFLOW : '',
BarcodeBySampleFieldNames.BARCODE_ID : dnabarcode.id_str,
BarcodeBySampleFieldNames.SET_ID : 0,
'relation' : '',
}
#create the saved objects dictionary for each sample set item which holds the dnabarcoding information
#and will be used in the final save process
if i < len(samplesetitems):
barcoding_step.savedObjects[BarcodeBySampleFieldNames.SAMPLE_TO_BARCODE][samplesetitem.sample.displayedName] = {
'barcodeSampleInfo' : {
dnabarcode.id_str : {
'externalId' : samplesetitem.sample.externalId,
'description' : samplesetitem.sample.description,
}
},
'barcodes' : [dnabarcode.id_str]
}
else:
for i in range(20):
samplesetitem = samplesetitems[i] if i < len(samplesetitems) else None
dnabarcode = planned_dnabarcodes[i] if i < len(planned_dnabarcodes) else None
if existing_plan:
if i == planned_experiment.sampleSet_planIndex:
if step_helper.steps[StepNames.IONREPORTER].savedFields['irAccountId'] == '0':
user_input_info = [dict()]
barcoding_step.savedObjects[BarcodeBySampleFieldNames.CHIP_TO_SAMPLE][i] = {
BarcodeBySampleFieldNames.NUMBER_OF_CHIPS : i + 1,
BarcodeBySampleFieldNames.SAMPLE_NAME : planned_experiment.get_sampleDisplayedName(),
BarcodeBySampleFieldNames.SAMPLE_DESCRIPTION : planned_experiment.get_sample_description(),
BarcodeBySampleFieldNames.SAMPLE_EXTERNAL_ID : planned_experiment.get_sample_external_id(),
BarcodeBySampleFieldNames.GENDER : user_input_info[0].get('Gender'),
BarcodeBySampleFieldNames.RELATION_ROLE : user_input_info[0].get('RelationRole'),
BarcodeBySampleFieldNames.WORKFLOW : user_input_info[0].get('Workflow'),
BarcodeBySampleFieldNames.SET_ID : user_input_info[0].get('setid')[0:user_input_info[0]['setid'].find('__')] if user_input_info[0].get('setid') else "",
'relation' : '',
}
else:
if i < len(samplesetitems):
barcoding_step.savedObjects[BarcodeBySampleFieldNames.CHIP_TO_SAMPLE][i] = {
BarcodeBySampleFieldNames.NUMBER_OF_CHIPS : i + 1,
BarcodeBySampleFieldNames.SAMPLE_NAME : samplesetitem.sample.displayedName,
BarcodeBySampleFieldNames.SAMPLE_DESCRIPTION : samplesetitem.sample.description,
BarcodeBySampleFieldNames.SAMPLE_EXTERNAL_ID : samplesetitem.sample.externalId,
BarcodeBySampleFieldNames.GENDER : samplesetitem.gender,
BarcodeBySampleFieldNames.RELATION_ROLE : samplesetitem.relationshipRole,
BarcodeBySampleFieldNames.WORKFLOW : planned_experiment.irworkflow,
BarcodeBySampleFieldNames.SET_ID : samplesetitem.relationshipGroup,
'relation' : '',
}
elif step_helper.steps[StepNames.IONREPORTER].savedFields['irAccountId'] == '0':
barcoding_step.savedObjects[BarcodeBySampleFieldNames.CHIP_TO_SAMPLE][i] = {
BarcodeBySampleFieldNames.NUMBER_OF_CHIPS : i + 1,
BarcodeBySampleFieldNames.SAMPLE_NAME : '',
BarcodeBySampleFieldNames.SAMPLE_DESCRIPTION : '',
BarcodeBySampleFieldNames.SAMPLE_EXTERNAL_ID : '',
BarcodeBySampleFieldNames.GENDER : '',
BarcodeBySampleFieldNames.RELATION_ROLE : '',
BarcodeBySampleFieldNames.WORKFLOW : '',
'relation' : '',
}
