def create_test_data(portal):
"""Populates with storage-like test data
"""
if not CREATE_TEST_DATA:
return
logger.info("Creating test data ...")
facilities = portal.senaite_storage
if len(facilities.objectValues()) > 0:
logger.info("There are facilities created already [SKIP]")
return
def get_random(min, max):
if not CREATE_TEST_DATA_RANDOM:
return min
return int(round(random.uniform(min, max)))
# Facilities
for x in range(get_random(3, 8)):
facility = api.create(
facilities,
"StorageFacility",
title="Storage facility {:02d}".format(x + 1),
Phone="123456789",
EmailAddress="storage{:02d}@example.com".format(x + 1),
PhysicalAddress={
"address": "Av. Via Augusta 15 - 25",
"city": "Sant Cugat del Valles",
"zip": "08174",
"state": "",
"country": "Spain",
})
# Fridges
for i in range(get_random(2, 5)):
container = api.create(facility,
"StorageContainer",
title="Fridge {:02d}".format(i + 1),
Rows=get_random(4, 8),
Columns=get_random(4, 6))
# Racks
for j in range(get_random(4, container.get_capacity())):
rack = api.create(container,
"StorageContainer",
title="Rack {:02d}".format(j + 1),
Rows=get_random(3, 4),
Columns=get_random(2, 3))
# Boxes
for k in range(get_random(2, rack.get_capacity())):
box = api.create(rack,
"StorageSamplesContainer",
title="Sample box {:02d}".format(k + 1),
Rows=get_random(5, 10),
Columns=get_random(5, 10))
def create_report(self, parent, pdf, html, uids, metadata):
"""Create a new report object
NOTE: We limit the creation of reports to 1 to avoid conflict errors on
simultaneous publication.
:param parent: parent object where to create the report inside
:returns: ARReport
"""
parent_id = api.get_id(parent)
logger.info("Create Report for {} ...".format(parent_id))
# Manually update the view on the database to avoid conflict errors
parent._p_jar.sync()
# Create the report object
report = api.create(parent,
"ARReport",
AnalysisRequest=api.get_uid(parent),
Pdf=pdf,
Html=html,
ContainedAnalysisRequests=uids,
Metadata=metadata)
# Commit the changes
transaction.commit()
logger.info("Create Report for {} [DONE]".format(parent_id))
return report
def create_attachment(self, container, attachment_file, **kw):
"""Create an Attachment object in the given container
"""
filename = getattr(attachment_file, "filename", "Attachment")
attachment = api.create(container, "Attachment", title=filename)
attachment.edit(AttachmentFile=attachment_file, **kw)
attachment.processForm()
attachment.reindexObject()
logger.info("Created new Attachment {} in {}".format(
repr(attachment), repr(container)))
return attachment
def create_object(container, portal_type, **data):
"""Creates an object slug
:returns: The new created content object
:rtype: object
"""
if "id" in data:
# always omit the id as senaite LIMS generates a proper one
id = data.pop("id")
logger.warn("Passed in ID '{}' omitted! Senaite LIMS "
"generates a proper ID for you".format(id))
try:
# Is there any adapter registered to handle the creation of this type?
adapter = queryAdapter(container, ICreate, name=portal_type)
if adapter and adapter.is_creation_delegated():
logger.info("Delegating 'create' operation of '{}' in '{}'".format(
portal_type, api.get_path(container)))
return adapter.create_object(**data)
# Special case for ARs
# => return immediately w/o update
if portal_type == "AnalysisRequest":
obj = create_analysisrequest(container, **data)
# Omit values which are already set through the helper
data = u.omit(data, "SampleType", "Analyses")
# Set the container as the client, as the AR lives in it
data["Client"] = container
return obj
# Standard content creation
else:
# we want just a minimun viable object and set the data later
obj = api.create(container, portal_type)
# obj = api.create(container, portal_type, **data)
except Unauthorized:
fail(401, "You are not allowed to create this content")
# Update the object with the given data, but omit the id
try:
update_object_with_data(obj, data)
except APIError:
# Failure in creation process, delete the invalid object
# NOTE: We bypass the permission checks
container._delObject(obj.id)
# reraise the error
raise
return obj
def setup_antibiotic_classes(portal):
"""Setup default antibiotic classes if do not exist yet
"""
logger.info("Setup default antibiotic classes ...")
# Get the titles of the existing classes first
folder = api.get_setup().get("antibiotic_classes")
existing = map(api.get_title, folder.objectValues())
# Create the antibiotic classes
for ac in ANTIBIOTIC_CLASSES:
if ac in existing:
logger.warn("Antibiotic class {} already exists [SKIP]".format(ac))
continue
logger.info("Adding antibiotic class: {}".format(ac))
api.create(folder, "AntibioticClass", title=ac)
# Don't know why yet, but after adding the antibiotic classes, the folder
# looses the title
folder.title = "Antibiotic classes"
folder.reindexObject()
logger.info("Setup default antibiotic classes [DONE]")
def create_report(self, parent, pdf, html, uids, metadata, csv_text=None):
"""Create a new report object
NOTE: We limit the creation of reports to 1 to avoid conflict errors on
simultaneous publication.
:param parent: parent object where to create the report inside
:returns: ARReport
"""
parent_id = api.get_id(parent)
logger.info("Create Report for {} ...".format(parent_id))
# Manually update the view on the database to avoid conflict errors
parent._p_jar.sync()
query = {
'portal_type': 'ARReport',
'path': {
'query': api.get_path(parent),
'depth': 1
}
}
brains = api.search(query, 'portal_catalog')
coa_num = '{}-COA-{}'.format(parent_id, len(brains) + 1)
# Create the report object
report = api.create(parent,
"ARReport",
AnalysisRequest=api.get_uid(parent),
Pdf=pdf,
Html=html,
CSV=csv_text,
ContainedAnalysisRequests=uids,
Metadata=metadata)
fld = report.getField('Pdf')
fld.get(report).setFilename(coa_num + ".pdf")
fld.get(report).setContentType('application/pdf')
fld = report.getField('CSV')
fld.get(report).setFilename(coa_num + ".csv")
fld.get(report).setContentType('text/csv')
# Commit the changes
transaction.commit()
logger.info("Create Report for {} [DONE]".format(parent_id))
return report
def setup_antibiotics(portal):
"""Setup default antibiotics if do not exist yet
"""
logger.info("Setup default antibiotics ...")
# Get the titles of the existing antibiotics first
folder = api.get_setup().get("antibiotics")
existing = map(api.get_title, folder.objectValues())
def get_antibiotic_class(name):
query = {
"portal_type": "AntibioticClass",
"title": name,
}
brains = api.search(query)
if len(brains) == 1:
return api.get_object(brains[0])
return None
# Create the antibiotic classes
for name, props in ANTIBIOTICS:
if name in existing:
logger.warn("Antibiotic {} already exists [SKIP]".format(name))
continue
logger.info("Adding antibiotic: {}".format(name))
# Get the antibiotic class by name
a_class_name = props.get("antibiotic_class")
a_class = get_antibiotic_class(a_class_name)
if not a_class:
logger.error("Antibiotic class missing: '{}' [SKIP]".format(
a_class_name))
continue
obj = api.create(folder, "Antibiotic", title=name)
obj.antibiotic_class = api.get_uid(a_class)
obj.abbreviation = props.get("abbreviation")
obj.reindexObject()
# After adding the antibiotic, the folder looses the title
folder.title = "Antibiotics"
folder.reindexObject()
logger.info("Setup default antibiotics [DONE]")
def create_object(container, portal_type, **data):
"""Creates an object slug
:returns: The new created content object
:rtype: object
"""
if "id" in data:
# always omit the id as Bika LIMS generates a proper one
id = data.pop("id")
logger.warn("Passed in ID '{}' omitted! Bika LIMS "
"generates a proper ID for you".format(id))
try:
# Special case for ARs
# => return immediately w/o update
if portal_type == "AnalysisRequest":
obj = create_analysisrequest(container, **data)
# Omit values which are already set through the helper
data = u.omit(data, "SampleType", "Analyses")
# Set the container as the client, as the AR lives in it
data["Client"] = container
# Standard content creation
else:
# we want just a minimun viable object and set the data later
obj = api.create(container, portal_type)
# obj = api.create(container, portal_type, **data)
except Unauthorized:
fail(401, "You are not allowed to create this content")
# Update the object with the given data, but omit the id
try:
update_object_with_data(obj, data) #start point
except APIError:
# Failure in creation process, delete the invalid object
container.manage_delObjects(obj.id)
# reraise the error
raise
return obj
def create_object(container, portal_type, **data):
"""Creates an object slug
:returns: The new created content object
:rtype: object
"""
if "id" in data:
# always omit the id as Bika LIMS generates a proper one
id = data.pop("id")
logger.warn("Passed in ID '{}' omitted! Bika LIMS "
"generates a proper ID for you" .format(id))
try:
# Special case for ARs
# => return immediately w/o update
if portal_type == "AnalysisRequest":
obj = create_analysisrequest(container, **data)
# Omit values which are already set through the helper
data = u.omit(data, "SampleType", "Analyses")
# Set the container as the client, as the AR lives in it
data["Client"] = container
# Standard content creation
else:
# we want just a minimun viable object and set the data later
obj = api.create(container, portal_type)
# obj = api.create(container, portal_type, **data)
except Unauthorized:
fail(401, "You are not allowed to create this content")
# Update the object with the given data, but omit the id
try:
update_object_with_data(obj, data) #start point
except APIError:
# Failure in creation process, delete the invalid object
container.manage_delObjects(obj.id)
# reraise the error
raise
return obj
def setup_baseline_data(portal):
"""Setups baseline data for testing purposes
"""
setup = portal.bika_setup
client = _api.create(portal.clients,
"Client",
Name="Happy Hills",
ClientID="HH")
contact = _api.create(client,
"Contact",
Firstname="Rita",
Lastname="Mohale")
sample_type = _api.create(setup.bika_sampletypes,
"SampleType",
title="Water",
Prefix="W")
lab_contact = _api.create(setup.bika_labcontacts,
"LabContact",
Firstname="Lab",
Lastname="Manager")
department = _api.create(setup.bika_departments,
"Department",
title="Chemistry",
Manager=lab_contact)
category = _api.create(setup.bika_analysiscategories,
"AnalysisCategory",
title="Metals",
Department=department)
Cu = _api.create(setup.bika_analysisservices,
"AnalysisService",
title="Copper",
Keyword="Cu",
Category=category.UID())
Fe = _api.create(setup.bika_analysisservices,
"AnalysisService",
title="Iron",
Keyword="Fe",
Category=category.UID())
def action_add(self):
"""Form action to add a new attachment
Code taken from bika.lims.content.addARAttachment.
"""
form = self.request.form
parent = api.get_parent(self.context)
this_file = form.get('AttachmentFile_file', None)
# nothing to do if the attachment file is missing
if this_file is None:
logger.warn(
"AttachmentView.action_add_attachment: Attachment file is missing"
)
return
# create attachment
attachmentid = self.context.generateUniqueId('Attachment')
attachment = api.create(parent, "Attachment", id=attachmentid)
# update the attachment with the values from the form
attachment.edit(
AttachmentFile=this_file,
AttachmentType=form.get('AttachmentType', ''),
AttachmentKeys=form.get('AttachmentKeys', ''),
ReportOption=form.get('ReportOption', 'a'),
)
# process and reindex
attachment.processForm()
attachment.reindexObject()
# append the new UID to the end of the current order
self.set_attachments_order(api.get_uid(attachment))
# handle analysis attachment
analysis_uid = form.get("Analysis", None)
if analysis_uid:
rc = api.get_tool("reference_catalog")
analysis = rc.lookupObject(analysis_uid)
others = analysis.getAttachment()
attachments = []
for other in others:
attachments.append(other.UID())
attachments.append(attachment.UID())
analysis.setAttachment(attachments)
if api.get_workflow_status_of(analysis) == 'attachment_due':
api.do_transition_for(analysis, 'attach')
else:
others = self.context.getAttachment()
attachments = []
for other in others:
attachments.append(other.UID())
attachments.append(attachment.UID())
self.context.setAttachment(attachments)
if self.request['HTTP_REFERER'].endswith('manage_results'):
self.request.response.redirect('{}/manage_results'.format(
self.context.absolute_url()))
else:
self.request.response.redirect(self.context.absolute_url())
