def Import(self):
folder = self.context.bika_setup.bika_products
rows = self.get_rows(3)
bsc = getToolByName(self.context, 'bika_setup_catalog')
suppliers = [o.getObject() for o in bsc(portal_type="Supplier")]
for row in rows:
title = row.get('Title')
description = row.get('description', '')
obj = _createObjectByType('Product', folder, tmpID())
obj.edit(
title=title,
description=description,
Hazardous=self.to_bool(row.get('Hazardous', '')),
Quantity=self.to_int(row.get('Quantity', 0)),
Unit=row.get('Unit', ''),
Price=str(row.get('Price', '0.00'))
)
for supplier in suppliers:
if supplier.Title() == row.get('Suppliers', ''):
obj.setSupplier(supplier)
break
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def Import(self):
pc = getToolByName(self.context, 'portal_catalog')
rows = self.get_rows(3)
for row in rows:
# get the client object
client_list = pc(portal_type="Client", Title=row.get('Client'))
folder = client_list and client_list[0].getObject() or None
if not folder: continue
s_types = row.get('SampleTypes')
a_services = row.get('AnalysisServices')
st_objects = get_project_multi_items(self.context, s_types, 'SampleType', 'bika_setup_catalog')
as_objects = get_project_multi_items(self.context, a_services, 'AnalysisService', 'bika_setup_catalog')
obj = _createObjectByType('Project', folder, tmpID())
obj.edit(
title=row.get('title'),
description=row.get('description'),
StudyType=row.get('StudyType', ''),
AgeHigh=self.to_int(row.get('AgeHigh', 0)),
AgeLow=self.to_int(row.get('AgeLow', 0)),
NumParticipants=self.to_int(row.get('NumParticipants', 0)),
SampleType=st_objects,
Service=as_objects,
DateCreated=row.get('DateCreated', ''),
)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def Import(self):
folder = self.context.donors
rows = self.get_rows(3)
pc = getToolByName(self.context, 'portal_catalog')
for row in rows:
sample_donor_id = row.get('SampleDonorID')
selected_project = row.get('SelectedProject', '')
info_link = row.get('InfoLink')
sex = row.get('Sex')
age = row.get('Age')
age_unit = row.get('AgeUnit')
obj = _createObjectByType('SampleDonor', folder, tmpID())
# get the project
project_list = pc(portal_type="Project", Title=selected_project)
project = project_list and project_list[0].getObject() or None
obj.edit(SampleDonorID=sample_donor_id,
SelectedProject=project,
InfoLink=info_link,
Age=age,
AgeUnit=age_unit)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def Import(self):
pc = getToolByName(self.context, 'bika_catalog')
folder = self.context.freezers
rows = self.get_rows(3)
for row in rows:
if not row['CurrentReading']:
continue
deviceTitle = row.get('MonitoringDevice', None)
mon_device = pc(portal_type='MonitoringDevice', title=deviceTitle)
dev_obj = mon_device[0].getObject() if mon_device else None
if not dev_obj: continue
# Device reading
de_reading = _createObjectByType('DeviceReading', dev_obj, tmpID())
de_reading.setCurrentReading(row['CurrentReading'])
de_reading.setLabel(row['Label'])
de_reading.setUnit(row['Unit'])
de_reading.unmarkCreationFlag()
renameAfterCreation(de_reading)
# Freezer reading
freezer = pc(portal_type="Freezer", Title=row.get('Freezer', None))
fr_obj = freezer[0].getObject() if freezer else None
fr_reading = _createObjectByType('DeviceReading', fr_obj, tmpID())
fr_reading.setCurrentReading(row['CurrentReading'])
fr_reading.setDatetimeRecorded(row['DatetimeRecorded'])
fr_reading.setLabel(row['Label'])
fr_reading.setUnit(row['Unit'])
fr_reading.unmarkCreationFlag()
fr_reading.unmarkCreationFlag()
renameAfterCreation(fr_reading)
def create_sample(context, request, values):
obj = _createObjectByType('Sample', context, tmpID())
# st_loc_list = pc(portal_type='StoragePosition', Title=values.get('StorageLocation'))
# storage_location = st_loc_list and st_loc_list[0].getObject() or None
obj.edit(
title=values['title'],
description=values['description'],
Project=values['Project'],
AllowSharing=values['AllowSharing'],
SampleType=values['SampleType'],
StorageLocation=values['StorageLocation'],
SubjectID=values['SubjectID'],
Barcode=values['Barcode'],
Volume=values['Volume'],
Unit=values['Unit'],
LinkedSample=values['LinkedSample'],
DateCreated=values['DateCreated'],
)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
if values.has_key('APISource'):
obj.api_source = values['APISource']
from baobab.lims.subscribers.sample import ObjectInitializedEventHandler
ObjectInitializedEventHandler(obj, None)
return obj
def Import(self):
folder = self.context.bika_setup.bika_stockitems
rows = self.get_rows(3)
bsc = getToolByName(self.context, 'bika_setup_catalog')
pc = getToolByName(self.context, 'portal_catalog')
for row in rows:
products = bsc(portal_type="Product", title=row.get('Product'))
product = products and products[0].getObject() or None
description = row.get('description', '')
st_loc_list = pc(portal_type='UnmanagedStorage',
Title=row.get('StorageLocation'))
storage_location = st_loc_list and st_loc_list[0].getObject(
) or None
obj = _createObjectByType('StockItem', folder, tmpID())
obj.edit(
Product=product,
StorageLocation=storage_location,
description=description,
Quantity=self.to_int(row.get('Quantity', 0)),
orderId=row.get('InvoiceNzr', ''),
batchId=row.get('BatchNr', ''),
receivedBy=row.get('ReceivedBy'),
dateReceived=row.get('DateReceived', ''),
)
new_quantity = int(product.getQuantity()) + int(
row.get('Quantity'))
product.setQuantity(new_quantity)
product.reindexObject()
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def Import(self):
folder = self.context.bika_setup.bika_storagetypes
rows = self.get_rows(3)
for row in rows:
title = row.get('title')
description = row.get('description', '')
obj = _createObjectByType('StorageType', folder, tmpID())
obj.edit(title=title, description=description)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def Import(self):
folder = self.context.monitoring_devices
rows = self.get_rows(3)
for row in rows:
title = row.get('title', '')
if not title: continue
description = row.get('description', '')
obj = _createObjectByType('MonitoringDevice', folder, tmpID())
obj.edit(title=title,
description=description,
MACAddress=row.get('MACAddress'))
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def Import(self):
folder = self.context.lab_hosts
rows = self.get_rows(3)
for row in rows:
if self.isExistingTitle('LabHost', row.get('title')):
continue
title = row.get('title')
description = row.get('description', '')
obj = _createObjectByType('LabHost', folder, tmpID())
obj.edit(
title=title,
description=description,
)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def Import(self):
folder = self.context.bika_setup.bika_kittemplates
rows = self.get_rows(3)
catalog = getToolByName(self.context, 'bika_setup_catalog')
for row in rows:
template_name = row.get('templateName')
kit_component = Kit_Components(self, self.workbook,
self.dataset_project,
self.dataset_name, template_name,
catalog)
product_list = kit_component.get_product_list()
obj = _createObjectByType('KitTemplate', folder, tmpID())
obj.edit(title=template_name, ProductList=product_list)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def Import(self):
folder = self.context.disease_ontologies
rows = self.get_rows(3)
for row in rows:
title = row.get('title')
description = row.get('description', '')
version = row.get('Version')
code = row.get('Code')
free_text = row.get('FreeText')
obj = _createObjectByType('DiseaseOntology', folder, tmpID())
obj.edit(title=title,
description=description,
Version=version,
Code=code,
FreeText=free_text)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def create_biospecimen(self, row):
barcode = str(row.get('Barcode'))
project = self.get_project(row.get('Project', ''))
sample_type = self.get_sample_type(row.get('SampleType', ''))
volume = self.get_volume(row.get('Volume', ''))
title = row.get('title', barcode)
self.confirm_unique_title(barcode)
storage_location = self.get_storage_location(row.get('StorageLocation', ''))
sampling_date = row.get('SamplingDate', '')
if storage_location:
storage_wf_state = self._wf.getInfoFor(storage_location, 'review_state')
if storage_wf_state == 'occupied':
raise ExcelSheetError('Import Error Sample %s: Storage %s already occupied.' % (title, storage_location.Title()))
date_created = row.get('DateCreated', datetime.strftime(datetime.now(), '%Y-%m-%d %H:%M'))
if not date_created:
date_created = datetime.strftime(datetime.now(), '%Y-%m-%d %H:%M')
member = self.get_member()
obj = _createObjectByType('Sample', project, tmpID())
obj.edit(
title=title,
description=row.get('description'),
Project=project,
SampleType=sample_type,
StorageLocation=storage_location,
SubjectID=row.get('SubjectID'),
Barcode=barcode,
Volume=volume,
Unit=row.get('Unit'),
BabyNumber=row.get('BabyNo', ''),
DateCreated=date_created,
SamplingDate=sampling_date,
# FrozenTime=row.get('FrozenTime'),
ChangeUserName=member,
ChangeDateTime=date_created,
)
obj.reindexObject()
obj.unmarkCreationFlag()
renameAfterCreation(obj)
from baobab.lims.subscribers.sample import ObjectInitializedEventHandler
ObjectInitializedEventHandler(obj, None)
def Import(self):
folder = self.context.organisms
rows = self.get_rows(3)
for row in rows:
if self.isExistingTitle('Organism', row.get('title')):
continue
title = row.get('title')
genus = row.get('genus', '')
species = row.get('species', '')
obj = _createObjectByType('Organism', folder, tmpID())
obj.edit(
title=title,
Genus=genus,
Species=species,
)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def Import(self):
pc = getToolByName(self.context, 'portal_catalog')
rows = self.get_rows(3)
for row in rows:
# get the project
project_list = pc(portal_type="Project", Title=row.get('Project'))
if project_list:
project = project_list[0].getObject()
else:
continue
# get the kit template if it exists
bsc = getToolByName(self.context, 'bika_setup_catalog')
kit_template_list = bsc(portal_type="KitTemplate",
title=row.get('KitTemplate'))
kit_template = kit_template_list and kit_template_list[
0].getObject() or None
stock_items = []
try:
if kit_template:
stock_items = self.assign_stock_items(
kit_template, row, bsc, pc)
except ValueError as e:
continue
obj = _createObjectByType('Kit', project, tmpID())
obj.edit(
title=row.get('title'),
description=row.get('description'),
Project=project,
KitTemplate=kit_template,
FormsThere=row.get('FormsThere'),
DateCreated=row.get('DateCreated', ''),
)
if kit_template:
obj.setStockItems(stock_items)
update_quantity_products(obj, bsc)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def Import(self):
folder = self.context.freezers
rows = self.get_rows(3)
pc = getToolByName(self.context, 'bika_catalog')
for row in rows:
title = row.get('title', '')
if not title: continue
description = row.get('description', '')
deviceTitle = row.get('MonitoringDevice', '')
device = pc(portal_type='MonitoringDevice', title=deviceTitle)
device_obj = device[0].getObject() if device else None
obj = _createObjectByType('Freezer', folder, tmpID())
obj.edit(
title=title,
description=description,
MonitoringDevice=device_obj,
)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
notify(ObjectInitializedEvent(obj))
def create_freezer_readings(self, readings, freezer):
# Device Reading
# slice out \xb0C on the result because it throws an ascii error
# unit defaults to °C so we can avoid the ascii error
current_reading = readings['channels'][0]
# Date comes back as u'/Date(1619779624000+0000)/'
record_date = readings['datetime']
record_date = dt.fromtimestamp(
int(re.findall(r"\d+", record_date)[0]) / 1000)
freezer_reading = _createObjectByType('DeviceReading', freezer,
tmpID())
freezer_reading.setCurrentReading(float(current_reading[0:-2]))
freezer_reading.setDatetimeRecorded(DT(record_date))
unit = freezer_reading.getUnit() + str(current_reading[-1])
freezer_reading.setUnit(unit)
freezer_reading.unmarkCreationFlag()
renameAfterCreation(freezer_reading)
return 'Done'
def create_sample_type(context, request, values):
obj = _createObjectByType('SampleType', context, tmpID())
# st_loc_list = pc(portal_type='StoragePosition', Title=values.get('StorageLocation'))
# storage_location = st_loc_list and st_loc_list[0].getObject() or None
obj.edit(
title=values['title'],
description=values['description'],
RetentionPeriod=values['RetentionPeriod'],
Hazardous=to_bool(values['Hazardous']),
#SampleMatrix=samplematrix,
Prefix=values['Prefix'],
MinimumVolume=values['MinimumVolume'],
#ContainerType=containertype
)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
return obj
def create_biospecimen(self, row):
barcode = str(row.get('Barcode'))
batch_id = str(row.get('BatchID', ''))
brains = self._bc(portal_type='SampleBatch', title=batch_id)
if brains:
batch = brains[0].getObject()
else:
raise ExcelSheetError('Import Error Sample %s: Batch %s not found.' % (barcode, batch_id))
parent = self.get_linked_sample(str(row.get('Parent', '')))
if not parent:
raise ExcelSheetError('Import Error Sample %s: Parent %s not found.' % (barcode, row.get('Parent', '')))
project_obj = batch.getProject()
sample_type = self.get_sample_type(row.get('SampleType', ''))
volume = self.get_volume(row.get('Volume', ''))
sampling_date = row.get('SamplingTime', '')
title = row.get('Title', barcode)
self.confirm_unique_title(barcode)
storage_location = self.get_storage_location(row.get('StorageLocation', ''))
if storage_location:
storage_wf_state = analysis_state = self._wf.getInfoFor(storage_location, 'review_state')
if storage_wf_state == 'occupied':
raise ExcelSheetError('Import Error Sample %s: Storage %s already occupied.' % (barcode, storage_location.Title()))
obj = _createObjectByType('Sample', project_obj, tmpID())
field_b = obj.getField('Batch')
field_b.set(obj, batch)
date_created = row.get('DateCreated', datetime.strftime(datetime.now(), '%Y-%m-%d %H:%M'))
if not date_created:
date_created = datetime.strftime(datetime.now(), '%Y-%m-%d %H:%M')
unit = row.get('Unit', '')
if not unit:
raise ExcelSheetError(
'Import Error Sample %s: Unit is a compulsory field.' % barcode)
member = self.get_member()
obj.edit(
title=title,
description=row.get('description'),
Project=project_obj,
SampleType=sample_type,
StorageLocation=storage_location,
SubjectID=row.get('SubjectID'),
Barcode=barcode,
Volume=volume,
Unit=row.get('Unit'),
# BabyNumber=row.get('BabyNo', ''),
DateCreated=date_created,
LinkedSample=parent,
SamplingDate=sampling_date,
FrozenTime=row.get('FrozenTime'),
ChangeUserName=member,
ChangeDateTime=date_created,
)
obj.reindexObject()
obj.unmarkCreationFlag()
renameAfterCreation(obj)
from baobab.lims.subscribers.sample import ObjectInitializedEventHandler
ObjectInitializedEventHandler(obj, None)
def create_biospecimen(self, row):
pc = getToolByName(self.context, 'portal_catalog')
bc = getToolByName(self.context, 'bika_catalog')
# get the project
project_list = pc(portal_type="Project", Title=row.get('Project'))
project = project_list and project_list[0].getObject() or None
if not project: raise
sampletype_list = pc(portal_type="SampleType",
Title=row.get('SampleType'))
sample_type = sampletype_list and sampletype_list[0].getObject(
) or None
if not sample_type: raise
linked_sample_list = pc(portal_type="Sample",
Title=row.get('LinkedSample', ''))
linked_sample = linked_sample_list and linked_sample_list[0].getObject(
) or None
sample_donor_list = bc(portal_type="SampleDonor",
SampleDonorID=row.get('SampleDonor', ''))
sample_donor = sample_donor_list and sample_donor_list[0].getObject(
) or None
disease_ontology_list = bc(portal_type="DiseaseOntology",
Title=row.get('DiseaseOntology', ''))
disease_ontology = disease_ontology_list and disease_ontology_list[
0].getObject() or None
barcode = row.get('Barcode')
if not barcode:
raise
try:
volume = str(row.get('Volume'))
float_volume = float(volume)
if not float_volume:
raise
except:
raise
obj = _createObjectByType('Sample', project, tmpID())
st_loc_list = pc(portal_type='StoragePosition',
Title=row.get('StorageLocation'))
storage_location = st_loc_list and st_loc_list[0].getObject() or None
obj.edit(
title=row.get('title'),
description=row.get('description'),
Project=project,
DiseaseOntology=disease_ontology,
AllowSharing=row.get('AllowSharing'),
Donor=sample_donor,
SampleType=sample_type,
StorageLocation=storage_location,
SubjectID=row.get('SubjectID'),
Barcode=barcode,
Volume=volume,
Unit=row.get('Unit'),
LinkedSample=linked_sample,
DateCreated=row.get('DateCreated'),
AnatomicalSiteTerm=row.get('AnatomicalSiteTerm'),
AnatomicalSiteDescription=row.get('AnatomicalSiteDescription'),
)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
from baobab.lims.subscribers.sample import ObjectInitializedEventHandler
ObjectInitializedEventHandler(obj, None)
def create_virus_sample(self, row):
folder = self.context.virus_samples
project = self.getObject('Project', row.get('Project'))
sample_type = self.getObject('SampleType', row.get('SampleType'))
storage_location = self.getObject('StoragePosition',
row.get('StorageLocation'))
anatomical_material = self.getObject('AnatomicalMaterial',
row.get('AnatomicalMaterial'))
organism = self.getObject('Organism', row.get('Organism'))
collection_device = self.getObject('CollectionDevice',
row.get('CollectionDevice'))
host = self.getObject('Host', row.get('Host'))
host_disease = self.getObject('HostDisease', row.get('HostDisease'))
lab_host = self.getObject('LabHost', row.get('LabHost'))
instrument_type = self.getObject('InstrumentType',
row.get('InstrumentType'))
instrument = self.getObject('Instrument', row.get('Instrument'))
host_age = row.get('HostAge', '')
try:
volume = str(row.get('Volume'))
float_volume = str(float(volume))
if not float_volume:
raise Exception('Volume %s not found' % row.get('Volume'))
except Exception as e:
print('-----Exception in %s' % str(e))
obj = _createObjectByType('VirusSample', folder, tmpID())
# st_loc_list = pc(portal_type='StoragePosition', Title=row.get('StorageLocation'))
# storage_location = st_loc_list and st_loc_list[0].getObject() or None
obj.edit(
title=row.get('title'),
Barcode=row.get('barcode'),
Project=project,
SampleType=sample_type,
StorageLocation=storage_location,
Volume=float_volume,
Unit=row.get('Unit'),
AnatomicalMaterial=anatomical_material,
AllowSharing=row.get('AllowSharing'),
WillReturnFromShipment=row.get('WillReturnFromShipment'),
# Repository Accession Numbers
BioSampleAccession=row.get('BioSampleAccession'),
# Sample Collector and Processing
SampleCollectedBy=row.get('SampleCollectedBy'),
SampleCollectionDate=row.get('SampleCollectionDate'),
SampleReceivedDate=row.get('SampleReceivedDate'),
GeoLocDate=row.get('GeoLocDate'),
GeoLocState=row.get('GeoLocState'),
Organism=organism,
Isolate=row.get('Isolate'),
PurposeOfSampling=row.get('PurposeOfSampling'),
CollectionDevice=collection_device,
# hhh
CollectionProtocol=row.get('CollectionProtocol'),
SpecimenProcessing=row.get('SpecimenProcessing'),
LabHost=lab_host,
PassageNumber=row.get('PassageNumber'),
PassageMethod=row.get('PassageMethod'),
# Host Information
HostSubjectID=row.get('HostSubjectID'),
Host=host,
HostDisease=host_disease,
HostGender=row.get('HostGender'),
HostAge=str(host_age),
HostAgeUnit=row.get('HostAgeUnit'),
# Host Exposure Information
ExposureCountry=row.get('ExposureCountry'),
ExposureEvent=row.get('ExposureEvent'),
# Sequencing Information
LibraryID=row.get('LibraryID'),
InstrumentType=instrument_type,
Instrument=instrument,
SequencingProtocolName=row.get('SequencingProtocolName'),
)
obj.unmarkCreationFlag()
renameAfterCreation(obj)
from baobab.lims.subscribers.sample import ObjectInitializedEventHandler
ObjectInitializedEventHandler(obj, None)
def Import(self):
folder = self.context.samplebatches
rows = self.get_rows(3)
self._errors = []
self._pc = getToolByName(self.context, 'portal_catalog')
for row in rows:
selected_project = row.get('Project', '')
#import pdb;pdb.set_trace()
if selected_project:
project_list = self._pc(portal_type="Project", Title=selected_project)
project = project_list and project_list[0].getObject() or None
else:
continue
subject_id = row.get('SubjectID')
# sheet_parent_biospecimen = row.get('ParentBiospecimen', '')
# parent_biospecimen = None
# if sheet_parent_biospecimen:
parent_biospecimen_text = str(row.get('ParentBiospecimen', ''))
if parent_biospecimen_text:
parent_biospecimen_list = self._pc(portal_type="Sample", Title=parent_biospecimen_text)
parent_biospecimen = parent_biospecimen_list and parent_biospecimen_list[0].getObject() or None
if not parent_biospecimen:
self._errors.append('Import batch error: Parent %s was not found' % parent_biospecimen_text)
continue
else:
self._errors.append('Import batch error: Parent sample cannot be blank.')
# TODO: VERIFY IT LATER
storage_locations = row.get('StorageLocations', '')
boxes = self.getStorageLocations(storage_locations)
batch_id = str(row.get('BatchID', ''))
obj = _createObjectByType('SampleBatch', folder, tmpID())
date_created = row.get('DateCreated', datetime.strftime(datetime.now(), '%Y-%m-%d %H:%M'))
if not date_created:
date_created = datetime.strftime(datetime.now(), '%Y-%m-%d %H:%M')
member = self.get_member()
obj.edit(
title=batch_id,
Description=row.get('Description', ''),
BatchId=batch_id,
BatchType=row.get('BatchType', ''),
Project=project,
SubjectID=subject_id,
StorageLocation=boxes,
Quantity=row.get('Quantity', 0),
ParentBiospecimen=parent_biospecimen,
DateCreated=date_created,
SerumColour=row.get('SerumColour', ''),
CfgDateTime=row.get('CfgDateTime', ''),
ChangeUserName=member,
ChangeDateTime=date_created,
)
# import pdb;pdb.set_trace()
obj.reindexObject()
obj.unmarkCreationFlag()
renameAfterCreation(obj)
def _renameAfterCreation(self, check_auto_id=False):
from baobab.lims.idserver import renameAfterCreation
renameAfterCreation(self)