def test_MultiVerificationType(self):
#Testing when the same user can verify multiple times
self.portal.bika_setup.setNumberOfRequiredVerifications(4)
self.portal.bika_setup.setTypeOfmultiVerification('self_multi_enabled')
client = self.portal.clients['client-1']
sampletype = self.portal.bika_setup.bika_sampletypes['sampletype-1']
values = {'Client': client.UID(),
'Contact': client.getContacts()[0].UID(),
'SamplingDate': '2016-12-12',
'SampleType': sampletype.UID()}
ar = _createObjectByType("AnalysisRequest", client, tmpID())
servs = self.portal.bika_setup.bika_analysisservices
service=servs['analysisservice-3']
service.setSelfVerification(True)
an = create_analysis(ar, service)
member = self.portal.portal_membership.getMemberById('admin')
an.setVerificators(member.getUserName())
an.setNumberOfRequiredVerifications(4)
self.assertEquals(an.isUserAllowedToVerify(member), True)
#Testing when the same user can verify multiple times but not consequetively
self.portal.bika_setup.setTypeOfmultiVerification('self_multi_not_cons')
self.assertEquals(an.isUserAllowedToVerify(member), False)
#Testing when the same user can not verify more than once
self.portal.bika_setup.setTypeOfmultiVerification('self_multi_disabled')
self.assertEquals(an.isUserAllowedToVerify(member), False)
an.addVerificator(TEST_USER_NAME)
self.portal.bika_setup.setTypeOfmultiVerification('self_multi_not_cons')
self.assertEquals(an.isUserAllowedToVerify(member), True)
self.portal.bika_setup.setTypeOfmultiVerification('self_multi_disabled')
self.assertEquals(an.isUserAllowedToVerify(member), False)
def test_MultiVerificationType(self):
bika_setup = self.portal.bika_setup
# Testing when the same user can verify multiple times
bika_setup.setNumberOfRequiredVerifications(4)
bika_setup.setTypeOfmultiVerification('self_multi_enabled')
client = self.portal.clients['client-1']
ar = _createObjectByType("AnalysisRequest", client, tmpID())
servs = bika_setup.bika_analysisservices
service = servs['analysisservice-3']
service.setSelfVerification(True)
an = create_analysis(ar, service)
member = self.portal.portal_membership.getMemberById('admin')
an.setVerificators(member.getUserName())
an.setNumberOfRequiredVerifications(4)
self.assertEquals(an.isUserAllowedToVerify(member), True)
# Testing when the same user can verify multiple times but not
# consequetively
bika_setup.setTypeOfmultiVerification('self_multi_not_cons')
self.assertEquals(an.isUserAllowedToVerify(member), False)
# Testing when the same user can not verify more than once
bika_setup.setTypeOfmultiVerification('self_multi_disabled')
self.assertEquals(an.isUserAllowedToVerify(member), False)
an.addVerificator(TEST_USER_NAME)
bika_setup.setTypeOfmultiVerification('self_multi_not_cons')
self.assertEquals(an.isUserAllowedToVerify(member), True)
bika_setup.setTypeOfmultiVerification('self_multi_disabled')
self.assertEquals(an.isUserAllowedToVerify(member), False)
def after_retract(obj):
"""Function triggered after a 'retract' transition for the analysis passed
in is performed. Retracting an analysis cause its transition to 'retracted'
state and the creation of a new copy of the same analysis as a retest.
Note that retraction only affects to single Analysis and has no other
effect in the status of the Worksheet to which the Analysis is assigned or
to the Analysis Request to which belongs (transition is never proomoted)
This function is called automatically by
bika.lims.workflow.AfterTransitionEventHandler
"""
# TODO Workflow Analysis - review this function
# Rename the analysis to make way for it's successor.
# Support multiple retractions by renaming to *-0, *-1, etc
parent = obj.aq_parent
kw = obj.getKeyword()
analyses = [
x for x in parent.objectValues("Analysis")
if x.getId().startswith(obj.getId())
]
# LIMS-1290 - Analyst must be able to retract, which creates a new
# Analysis. So, _verifyObjectPaste permission check must be cancelled:
parent._verifyObjectPaste = str
# This is needed for tests:
# https://docs.plone.org/develop/plone/content/rename.html
# Testing warning: Rename mechanism relies of Persistent attribute
# called _p_jar to be present on the content object. By default, this is
# not the case on unit tests. You need to call transaction.savepoint() to
# make _p_jar appear on persistent objects.
# If you don't do this, you'll receive a "CopyError" when calling
# manage_renameObjects that the operation is not supported.
transaction.savepoint()
parent.manage_renameObject(kw, "{0}-{1}".format(kw, len(analyses)))
delattr(parent, '_verifyObjectPaste')
# Create new analysis from the retracted obj
analysis = create_analysis(parent, obj)
changeWorkflowState(analysis, "bika_analysis_workflow", "sample_received")
# Assign the new analysis to this same worksheet, if any.
ws = obj.getWorksheet()
if ws:
ws.addAnalysis(analysis)
analysis.reindexObject()
# retract our dependencies
dependencies = obj.getDependencies()
for dependency in dependencies:
doActionFor(dependency, 'retract')
# Retract our dependents
dependents = obj.getDependents()
for dependent in dependents:
doActionFor(dependent, 'retract')
_reindex_request(obj)
def after_retract(obj):
"""Function triggered after a 'retract' transition for the analysis passed
in is performed. Retracting an analysis cause its transition to 'retracted'
state and the creation of a new copy of the same analysis as a retest.
Note that retraction only affects to single Analysis and has no other
effect in the status of the Worksheet to which the Analysis is assigned or
to the Analysis Request to which belongs (transition is never proomoted)
This function is called automatically by
bika.lims.workflow.AfterTransitionEventHandler
"""
# TODO Workflow Analysis - review this function
# Rename the analysis to make way for it's successor.
# Support multiple retractions by renaming to *-0, *-1, etc
parent = obj.aq_parent
kw = obj.getKeyword()
analyses = [x for x in parent.objectValues("Analysis")
if x.getId().startswith(obj.getId())]
# LIMS-1290 - Analyst must be able to retract, which creates a new
# Analysis. So, _verifyObjectPaste permission check must be cancelled:
parent._verifyObjectPaste = str
# This is needed for tests:
# https://docs.plone.org/develop/plone/content/rename.html
# Testing warning: Rename mechanism relies of Persistent attribute
# called _p_jar to be present on the content object. By default, this is
# not the case on unit tests. You need to call transaction.savepoint() to
# make _p_jar appear on persistent objects.
# If you don't do this, you'll receive a "CopyError" when calling
# manage_renameObjects that the operation is not supported.
transaction.savepoint()
parent.manage_renameObject(kw, "{0}-{1}".format(kw, len(analyses)))
delattr(parent, '_verifyObjectPaste')
# Create new analysis from the retracted obj
analysis = create_analysis(parent, obj)
changeWorkflowState(
analysis, "bika_analysis_workflow", "sample_received")
# Assign the new analysis to this same worksheet, if any.
ws = obj.getWorksheet()
if ws:
ws.addAnalysis(analysis)
analysis.reindexObject()
# retract our dependencies
dependencies = obj.getDependencies()
for dependency in dependencies:
doActionFor(dependency, 'retract')
# Retract our dependents
dependents = obj.getDependents()
for dependent in dependents:
doActionFor(dependent, 'retract')
_reindex_request(obj)
def after_retract(obj):
"""Function triggered after a 'retract' transition for the analysis passed
in is performed. Retracting an analysis cause its transition to 'retracted'
state and the creation of a new copy of the same analysis as a retest.
Note that retraction only affects to single Analysis and has no other
effect in the status of the Worksheet to which the Analysis is assigned or
to the Analysis Request to which belongs (transition is never proomoted)
This function is called automatically by
bika.lims.workflow.AfterTransitionEventHandler
"""
# TODO Workflow Analysis - review this function
# Rename the analysis to make way for it's successor.
# Support multiple retractions by renaming to *-0, *-1, etc
parent = obj.aq_parent
kw = obj.getKeyword()
analyses = [
x for x in parent.objectValues("Analysis")
if x.getId().startswith(obj.getId())
]
# LIMS-1290 - Analyst must be able to retract, which creates a new
# Analysis. So, _verifyObjectPaste permission check must be cancelled:
parent._verifyObjectPaste = str
parent.manage_renameObject(kw, "{0}-{1}".format(kw, len(analyses)))
delattr(parent, '_verifyObjectPaste')
# Create new analysis from the retracted obj
analysis = create_analysis(parent, obj)
changeWorkflowState(analysis, "bika_analysis_workflow", "sample_received")
# Assign the new analysis to this same worksheet, if any.
ws = obj.getWorksheet()
if ws:
ws.addAnalysis(analysis)
analysis.reindexObject()
# retract our dependencies
dependencies = obj.getDependencies()
for dependency in dependencies:
doActionFor(dependency, 'retract')
# Retract our dependents
dependents = obj.getDependents()
for dependent in dependents:
doActionFor(dependent, 'retract')
_reindex_request(obj)
def after_retract(analysis):
"""Function triggered after a 'retract' transition for the analysis passed
in is performed. The analysis transitions to "retracted" state and a new
copy of the analysis is created. The copy initial state is "unassigned",
unless the the retracted analysis was assigned to a worksheet. In such case,
the copy is transitioned to 'assigned' state too
"""
# Retract our dependents (analyses that depend on this analysis)
cascade_to_dependents(analysis, "retract")
# Retract our dependencies (analyses this analysis depends on)
promote_to_dependencies(analysis, "retract")
# Rename the analysis to make way for it's successor.
# Support multiple retractions by renaming to *-0, *-1, etc
parent = analysis.aq_parent
keyword = analysis.getKeyword()
# Get only those that are analyses and with same keyword as the original
analyses = parent.getAnalyses(full_objects=True)
analyses = filter(lambda an: an.getKeyword() == keyword, analyses)
# TODO This needs to get managed by Id server in a nearly future!
new_id = '{}-{}'.format(keyword, len(analyses))
# Create a copy of the retracted analysis
an_uid = api.get_uid(analysis)
new_analysis = create_analysis(parent,
analysis,
id=new_id,
RetestOf=an_uid)
new_analysis.setResult("")
new_analysis.setResultCaptureDate(None)
new_analysis.reindexObject()
logger.info("Retest for {} ({}) created: {}".format(
keyword, api.get_id(analysis), api.get_id(new_analysis)))
# Assign the new analysis to this same worksheet, if any.
worksheet = analysis.getWorksheet()
if worksheet:
worksheet.addAnalysis(new_analysis)
# Try to rollback the Analysis Request
if IRequestAnalysis.providedBy(analysis):
doActionFor(analysis.getRequest(), "rollback_to_receive")
reindex_request(analysis)
def add_analysis(self, instance, service, **kwargs):
service_uid = api.get_uid(service)
# Ensure we have suitable parameters
specs = kwargs.get("specs") or {}
# Get the hidden status for the service
hidden = kwargs.get("hidden") or []
hidden = filter(lambda d: d.get("uid") == service_uid, hidden)
hidden = hidden and hidden[0].get("hidden") or service.getHidden()
# Get the price for the service
prices = kwargs.get("prices") or {}
price = prices.get(service_uid) or service.getPrice()
# Gets the analysis or creates the analysis for this service
# Note this returns a list, because is possible to have multiple
# partitions with same analysis
analyses = self.resolve_analyses(instance, service)
if not analyses:
# Create the analysis
keyword = service.getKeyword()
logger.info("Creating new analysis '{}'".format(keyword))
analysis = create_analysis(instance, service)
analyses.append(analysis)
skip = ["cancelled", "retracted", "rejected"]
for analysis in analyses:
# Skip analyses to better not modify
if api.get_review_status(analysis) in skip:
continue
# Set the hidden status
analysis.setHidden(hidden)
# Set the price of the Analysis
analysis.setPrice(price)
# Set the internal use status
parent_sample = analysis.getRequest()
analysis.setInternalUse(parent_sample.getInternalUse())
# Set the result range to the analysis
analysis_rr = specs.get(service_uid) or analysis.getResultsRange()
analysis.setResultsRange(analysis_rr)
analysis.reindexObject()
def after_retract(analysis):
"""Function triggered after a 'retract' transition for the analysis passed
in is performed. The analysis transitions to "retracted" state and a new
copy of the analysis is created. The copy initial state is "unassigned",
unless the the retracted analysis was assigned to a worksheet. In such case,
the copy is transitioned to 'assigned' state too
"""
# Rename the analysis to make way for it's successor.
# Support multiple retractions by renaming to *-0, *-1, etc
parent = analysis.aq_parent
keyword = analysis.getKeyword()
analyses = filter(lambda an: an.getKeyword() == keyword,
parent.objectValues("Analysis"))
# Rename the retracted analysis
# https://docs.plone.org/develop/plone/content/rename.html
# _verifyObjectPaste permission check must be cancelled
parent._verifyObjectPaste = str
retracted_id = '{}-{}'.format(keyword, len(analyses))
# Make sure all persistent objects have _p_jar attribute
transaction.savepoint(optimistic=True)
parent.manage_renameObject(analysis.getId(), retracted_id)
delattr(parent, '_verifyObjectPaste')
# Create a copy of the retracted analysis
analysis_uid = api.get_uid(analysis)
new_analysis = create_analysis(parent, analysis, RetestOf=analysis_uid)
# Assign the new analysis to this same worksheet, if any.
worksheet = analysis.getWorksheet()
if worksheet:
worksheet.addAnalysis(new_analysis)
# Retract our dependents (analyses that depend on this analysis)
cascade_to_dependents(analysis, "retract")
# Try to rollback the Analysis Request
if IRequestAnalysis.providedBy(analysis):
doActionFor(analysis.getRequest(), "rollback_to_receive")
reindex_request(analysis)
def create_ast_analysis(sample, keyword, microorganism, antibiotics):
"""Creates a new AST analysis
"""
# Convert antibiotics to interim fields
interim_fields = map(lambda ab: to_interim(keyword, ab), antibiotics)
# Create a new ID to prevent clashes
new_id = new_analysis_id(sample, keyword)
# Create the analysis
service = get_service(keyword)
analysis = create_analysis(sample, service, id=new_id)
# Assign the name of the microorganism as the title
title = get_analysis_title(keyword, microorganism)
short_title = api.get_title(microorganism)
analysis.setTitle(title)
analysis.setShortTitle(short_title)
# Assign the antibiotics as interim fields
analysis.setInterimFields(interim_fields)
# Compute all combinations of interim/antibiotic and possible result and
# and generate the result options for this analysis (the "Result" field is
# never displayed and is only used for reporting)
result_options = get_result_options(analysis)
analysis.setResultOptions(result_options)
# Apply the IASTAnalysis and IInternalUser marker interfaces
alsoProvides(analysis, IASTAnalysis)
alsoProvides(analysis, IInternalUse)
# Initialize the analysis and reindex
doActionFor(analysis, "initialize")
analysis.reindexObject()
return analysis
def set(self, instance, items, prices=None, specs=None, hidden=None, **kw):
"""Set/Assign Analyses to this AR
:param items: List of Analysis objects/brains, AnalysisService
objects/brains and/or Analysis Service uids
:type items: list
:param prices: Mapping of AnalysisService UID -> price
:type prices: dict
:param specs: List of AnalysisService UID -> Result Range mappings
:type specs: list
:param hidden: List of AnalysisService UID -> Hidden mappings
:type hidden: list
:returns: list of new assigned Analyses
"""
# This setter returns a list of new set Analyses
new_analyses = []
# Current assigned analyses
analyses = instance.objectValues("Analysis")
# Analyses which are in a non-open state must be retained, except those
# that are in a registered state (the sample has not been received)
non_open_analyses = filter(lambda an: not an.isOpen(), analyses)
non_open_analyses = filter(
lambda an: api.get_workflow_status_of(an) != "registered",
non_open_analyses)
# Prevent removing all analyses
#
# N.B.: Non-open analyses are rendered disabled in the HTML form.
# Therefore, their UIDs are not included in the submitted UIDs.
if not items and not non_open_analyses:
logger.warn("Not allowed to remove all Analyses from AR.")
return new_analyses
# Bail out if the items is not a list type
if not isinstance(items, (list, tuple)):
raise TypeError(
"Items parameter must be a tuple or list, got '{}'".format(
type(items)))
# Bail out if the AR is inactive
if not api.is_active(instance):
raise Unauthorized(
"Inactive ARs can not be modified".format(AddAnalysis))
# Bail out if the user has not the right permission
if not check_permission(AddAnalysis, instance):
raise Unauthorized(
"You do not have the '{}' permission".format(AddAnalysis))
# Convert the items to a valid list of AnalysisServices
services = filter(None, map(self._to_service, items))
# Calculate dependencies
# FIXME Infinite recursion error possible here, if the formula includes
# the Keyword of the Service that includes the Calculation
dependencies = map(lambda s: s.getServiceDependencies(), services)
dependencies = list(itertools.chain.from_iterable(dependencies))
# Merge dependencies and services
services = set(services + dependencies)
# Modify existing AR specs with new form values of selected analyses.
self._update_specs(instance, specs)
# Create a mapping of Service UID -> Hidden status
if hidden is None:
hidden = []
hidden = dict(map(lambda d: (d.get("uid"), d.get("hidden")), hidden))
# Ensure we have a prices dictionary
if prices is None:
prices = dict()
# CREATE/MODIFY ANALYSES
for service in services:
service_uid = api.get_uid(service)
keyword = service.getKeyword()
# Create the Analysis if it doesn't exist
if shasattr(instance, keyword):
analysis = instance._getOb(keyword)
else:
analysis = create_analysis(instance, service)
new_analyses.append(analysis)
# set the hidden status
analysis.setHidden(hidden.get(service_uid, False))
# Set the price of the Analysis
analysis.setPrice(prices.get(service_uid, service.getPrice()))
# DELETE ANALYSES
# Service UIDs
service_uids = map(api.get_uid, services)
# Analyses IDs to delete
delete_ids = []
# Assigned Attachments
assigned_attachments = []
for analysis in analyses:
service_uid = analysis.getServiceUID()
# Skip if the Service is selected
if service_uid in service_uids:
continue
# Skip non-open Analyses
if analysis in non_open_analyses:
continue
# Remember assigned attachments
# https://github.com/senaite/senaite.core/issues/1025
assigned_attachments.extend(analysis.getAttachment())
analysis.setAttachment([])
# If it is assigned to a worksheet, unassign it before deletion.
worksheet = analysis.getWorksheet()
if worksheet:
worksheet.removeAnalysis(analysis)
# Unset the partition reference
# TODO Remove in >v1.3.0 - This is kept for backwards-compatibility
part = analysis.getSamplePartition()
if part:
# From this partition, remove the reference to the current
# analysis that is going to be removed to prevent inconsistent
# states (Sample Partitions referencing to Analyses that do not
# exist anymore
an_uid = api.get_uid(analysis)
part_ans = part.getAnalyses() or []
part_ans = filter(lambda an: api.get_uid(an) != an_uid,
part_ans)
part.setAnalyses(part_ans)
# Unset the Analysis-to-Partition reference
analysis.setSamplePartition(None)
delete_ids.append(analysis.getId())
if delete_ids:
# Note: subscriber might promote the AR
instance.manage_delObjects(ids=delete_ids)
# Remove orphaned attachments
for attachment in assigned_attachments:
# only delete attachments which are no further linked
if not attachment.getLinkedAnalyses():
logger.info("Deleting attachment: {}".format(
attachment.getId()))
attachment_id = api.get_id(attachment)
api.get_parent(attachment).manage_delObjects(attachment_id)
return new_analyses
def set(self, instance, items, prices=None, specs=None, **kwargs):
"""Set/Assign Analyses to this AR
:param items: List of Analysis objects/brains, AnalysisService
objects/brains and/or Analysis Service uids
:type items: list
:param prices: Mapping of AnalysisService UID -> price
:type prices: dict
:param specs: List of AnalysisService UID -> Result Range Record mappings
:type specs: list
:returns: list of new assigned Analyses
"""
# This setter returns a list of new set Analyses
new_analyses = []
# Prevent removing all Analyses
if not items:
logger.warn("Not allowed to remove all Analyses from AR.")
return new_analyses
# Bail out if the items is not a list type
if not isinstance(items, (list, tuple)):
raise TypeError(
"Items parameter must be a tuple or list, got '{}'".format(
type(items)))
# Bail out if the AR in frozen state
if self._is_frozen(instance):
raise ValueError(
"Analyses can not be modified for inactive/verified ARs")
# Convert the items to a valid list of AnalysisServices
services = filter(None, map(self._to_service, items))
# Calculate dependencies
# FIXME Infinite recursion error possible here, if the formula includes
# the Keyword of the Service that includes the Calculation
dependencies = map(lambda s: s.getServiceDependencies(), services)
dependencies = list(itertools.chain.from_iterable(dependencies))
# Merge dependencies and services
services = set(services + dependencies)
# Service UIDs
service_uids = map(api.get_uid, services)
# Modify existing AR specs with new form values of selected analyses.
self._update_specs(instance, specs)
for service in services:
keyword = service.getKeyword()
# Create the Analysis if it doesn't exist
if shasattr(instance, keyword):
analysis = instance._getOb(keyword)
else:
# TODO Entry point for interims assignment and Calculation
# decoupling from Analysis. See comments PR#593
analysis = create_analysis(instance, service)
# TODO Remove when the `create_analysis` function supports this
# Set the interim fields only for new created Analysis
self._update_interims(analysis, service)
new_analyses.append(analysis)
# Set the price of the Analysis
self._update_price(analysis, service, prices)
# delete analyses
delete_ids = []
for analysis in instance.objectValues('Analysis'):
service_uid = analysis.getServiceUID()
# Skip assigned Analyses
if service_uid in service_uids:
continue
# Skip Analyses in frozen states
if self._is_frozen(analysis, "retract"):
logger.warn("Inactive/verified/retracted Analyses can not be "
"removed.")
continue
# If it is assigned to a worksheet, unassign it before deletion.
if self._is_assigned_to_worksheet(analysis):
backrefs = self._get_assigned_worksheets(analysis)
ws = backrefs[0]
ws.removeAnalysis(analysis)
# Unset the partition reference
part = analysis.getSamplePartition()
if part:
# From this partition, remove the reference to the current
# analysis that is going to be removed to prevent inconsistent
# states (Sample Partitions referencing to Analyses that do not
# exist anymore
an_uid = api.get_uid(analysis)
part_ans = part.getAnalyses() or []
part_ans = filter(lambda an: api.get_uid(an) != an_uid, part_ans)
part.setAnalyses(part_ans)
# Unset the Analysis-to-Partition reference
analysis.setSamplePartition(None)
delete_ids.append(analysis.getId())
if delete_ids:
# Note: subscriber might promote the AR
instance.manage_delObjects(ids=delete_ids)
return new_analyses
def set(self, instance, service_uids, prices=None, specs={}, **kwargs):
""" service_uids are the services selected on the AR Add/Edit form.
prices is a service_uid keyed dictionary containing the prices entered
on the form.
specs is a uid keyed dict with values of
{min:, max:, error:}
"""
if not service_uids:
return
assert type(service_uids) in (list, tuple)
workflow = instance.portal_workflow
# one can only edit Analyses up to a certain state.
ar_state = workflow.getInfoFor(instance, 'review_state', '')
assert ar_state in ('sample_registered', 'sampled',
'to_be_sampled', 'to_be_preserved',
'sample_due', 'sample_received',
'attachment_due', 'to_be_verified')
bsc = getToolByName(instance, 'bika_setup_catalog')
services = bsc(UID=service_uids)
new_analyses = []
for service in services:
service_uid = service.UID
service = service.getObject()
keyword = service.getKeyword()
price = prices[service_uid] if prices and service_uid in prices \
else service.getPrice()
vat = Decimal(service.getVAT())
# analysis->InterimFields
calc = service.getCalculation()
interim_fields = calc and list(calc.getInterimFields()) or []
# override defaults from service->InterimFields
service_interims = service.getInterimFields()
sif = dict([[x['keyword'], x.get('value', '')]
for x in service_interims])
for i, i_f in enumerate(interim_fields):
if i_f['keyword'] in sif:
interim_fields[i]['value'] = sif[i_f['keyword']]
service_interims = [x for x in service_interims
if x['keyword'] != i_f['keyword']]
# Add remaining service interims to the analysis
for v in service_interims:
interim_fields.append(v)
# create the analysis if it doesn't exist
if hasattr(instance, keyword):
analysis = instance._getOb(keyword)
else:
analysis = create_analysis(
instance,
service,
keyword,
interim_fields
)
new_analyses.append(analysis)
# Note: subscriber might retract and/or unassign the AR
spec = specs[service_uid] if specs and service_uid in specs \
else None
# If no specification came to us from the form, then we will
# see if there is a spec for this SampleType & AnalysisService
if not spec:
spec = analysis.get_default_specification()
analysis.specification = spec
# XXX Price?
# analysis.setPrice(price)
# delete analyses
delete_ids = []
for analysis in instance.objectValues('Analysis'):
service_uid = analysis.Schema()['Service'].getRaw(analysis)
if service_uid not in service_uids:
# If it is verified or published, don't delete it.
if workflow.getInfoFor(analysis, 'review_state') in ('verified', 'published'):
continue # log it
# If it is assigned to a worksheet, unassign it before deletion.
elif workflow.getInfoFor(analysis, 'worksheetanalysis_review_state') == 'assigned':
ws = analysis.getBackReferences("WorksheetAnalysis")[0]
ws.removeAnalysis(analysis)
# Unset the partition reference
analysis.edit(SamplePartition=None)
delete_ids.append(analysis.getId())
if delete_ids:
# Note: subscriber might promote the AR
instance.manage_delObjects(ids=delete_ids)
return new_analyses
def set(self, instance, service_uids, prices=None, specs=None, **kwargs):
"""Set the 'Analyses' field value, by creating and removing Analysis
objects from the AR.
service_uids is a list:
The UIDs of all services which should exist in the AR. If a service
is not included here, the corrosponding Analysis will be removed.
prices is a dictionary:
key = AnalysisService UID
value = price
specs is a dictionary:
key = AnalysisService UID
value = dictionary: defined in ResultsRange field definition
"""
if not service_uids:
return
assert type(service_uids) in (list, tuple)
bsc = getToolByName(instance, 'bika_setup_catalog')
workflow = getToolByName(instance, 'portal_workflow')
# one can only edit Analyses up to a certain state.
ar_state = workflow.getInfoFor(instance, 'review_state', '')
assert ar_state in ('sample_registered', 'sampled', 'to_be_sampled',
'to_be_preserved', 'sample_due', 'sample_received',
'attachment_due', 'to_be_verified')
# - Modify existing AR specs with new form values for selected analyses.
# - new analysis requests are also using this function, so ResultsRange
# may be undefined. in this case, specs= will contain the entire
# AR spec.
rr = instance.getResultsRange()
specs = specs if specs else []
for s in specs:
s_in_rr = False
for i, r in enumerate(rr):
if s['keyword'] == r['keyword']:
rr[i].update(s)
s_in_rr = True
if not s_in_rr:
rr.append(s)
instance.setResultsRange(rr)
new_analyses = []
proxies = bsc(UID=service_uids)
for proxy in proxies:
service = proxy.getObject()
service_uid = service.UID()
keyword = service.getKeyword()
price = prices[service_uid] if prices and service_uid in prices \
else service.getPrice()
vat = Decimal(service.getVAT())
# analysis->InterimFields
calc = service.getCalculation()
interim_fields = calc and list(calc.getInterimFields()) or []
# override defaults from service->InterimFields
service_interims = service.getInterimFields()
sif = dict([(x['keyword'], x.get('value', ''))
for x in service_interims])
for i, i_f in enumerate(interim_fields):
if i_f['keyword'] in sif:
interim_fields[i]['value'] = sif[i_f['keyword']]
service_interims = [
x for x in service_interims
if x['keyword'] != i_f['keyword']
]
# Add remaining service interims to the analysis
for v in service_interims:
interim_fields.append(v)
# create the analysis if it doesn't exist
if shasattr(instance, keyword):
analysis = instance._getOb(keyword)
else:
analysis = create_analysis(instance, service, keyword,
interim_fields)
new_analyses.append(analysis)
for i, r in enumerate(rr):
if r['keyword'] == analysis.getService().getKeyword():
r['uid'] = analysis.UID()
# XXX Price?
# analysis.setPrice(price)
# We add rr to the AR after we create all the analyses
instance.setResultsRange(rr)
# delete analyses
delete_ids = []
for analysis in instance.objectValues('Analysis'):
service_uid = analysis.Schema()['Service'].getRaw(analysis)
if service_uid not in service_uids:
# If it is verified or published, don't delete it.
if workflow.getInfoFor(analysis,
'review_state') in ('verified',
'published'):
continue # log it
# If it is assigned to a worksheet, unassign it before deletion.
elif workflow.getInfoFor(
analysis,
'worksheetanalysis_review_state') == 'assigned':
ws = analysis.getBackReferences("WorksheetAnalysis")[0]
ws.removeAnalysis(analysis)
# Unset the partition reference
analysis.edit(SamplePartition=None)
delete_ids.append(analysis.getId())
if delete_ids:
# Note: subscriber might promote the AR
instance.manage_delObjects(ids=delete_ids)
return new_analyses
def set(self, instance, service_uids, prices=None, specs=None, **kwargs):
"""Set the 'Analyses' field value, by creating and removing Analysis
objects from the AR.
service_uids is a list:
The UIDs of all services which should exist in the AR. If a service
is not included here, the corrosponding Analysis will be removed.
prices is a dictionary:
key = AnalysisService UID
value = price
specs is a dictionary:
key = AnalysisService UID
value = dictionary: defined in ResultsRange field definition
"""
if not service_uids:
return
assert type(service_uids) in (list, tuple)
bsc = getToolByName(instance, 'bika_setup_catalog')
workflow = getToolByName(instance, 'portal_workflow')
# one can only edit Analyses up to a certain state.
ar_state = workflow.getInfoFor(instance, 'review_state', '')
assert ar_state in ('sample_registered', 'sampled',
'to_be_sampled', 'to_be_preserved',
'sample_due', 'sample_received',
'attachment_due', 'to_be_verified')
# - Modify existing AR specs with new form values for selected analyses.
# - new analysis requests are also using this function, so ResultsRange
# may be undefined. in this case, specs= will contain the entire
# AR spec.
rr = instance.getResultsRange()
specs = specs if specs else []
for s in specs:
s_in_rr = False
for i, r in enumerate(rr):
if s['keyword'] == r['keyword']:
rr[i].update(s)
s_in_rr = True
if not s_in_rr:
rr.append(s)
instance.setResultsRange(rr)
new_analyses = []
proxies = bsc(UID=service_uids)
for proxy in proxies:
service = proxy.getObject()
service_uid = service.UID()
keyword = service.getKeyword()
price = prices[service_uid] if prices and service_uid in prices \
else service.getPrice()
vat = Decimal(service.getVAT())
# analysis->InterimFields
calc = service.getCalculation()
interim_fields = calc and list(calc.getInterimFields()) or []
# override defaults from service->InterimFields
service_interims = service.getInterimFields()
sif = dict([(x['keyword'], x.get('value', ''))
for x in service_interims])
for i, i_f in enumerate(interim_fields):
if i_f['keyword'] in sif:
interim_fields[i]['value'] = sif[i_f['keyword']]
service_interims = [x for x in service_interims
if x['keyword'] != i_f['keyword']]
# Add remaining service interims to the analysis
for v in service_interims:
interim_fields.append(v)
# create the analysis if it doesn't exist
if shasattr(instance, keyword):
analysis = instance._getOb(keyword)
else:
analysis = create_analysis(
instance,
service,
keyword,
interim_fields
)
new_analyses.append(analysis)
for i, r in enumerate(rr):
if r['keyword'] == analysis.getService().getKeyword():
r['uid'] = analysis.UID()
# XXX Price?
# analysis.setPrice(price)
# We add rr to the AR after we create all the analyses
instance.setResultsRange(rr)
# delete analyses
delete_ids = []
for analysis in instance.objectValues('Analysis'):
service_uid = analysis.Schema()['Service'].getRaw(analysis)
if service_uid not in service_uids:
# If it is verified or published, don't delete it.
if workflow.getInfoFor(analysis, 'review_state') in ('verified', 'published'):
continue # log it
# If it is assigned to a worksheet, unassign it before deletion.
elif workflow.getInfoFor(analysis, 'worksheetanalysis_review_state') == 'assigned':
ws = analysis.getBackReferences("WorksheetAnalysis")[0]
ws.removeAnalysis(analysis)
# Unset the partition reference
analysis.edit(SamplePartition=None)
delete_ids.append(analysis.getId())
if delete_ids:
# Note: subscriber might promote the AR
instance.manage_delObjects(ids=delete_ids)
return new_analyses
def set(self, instance, items, prices=None, specs=None, **kwargs):
"""Set/Assign Analyses to this AR
:param items: List of Analysis objects/brains, AnalysisService
objects/brains and/or Analysis Service uids
:type items: list
:param prices: Mapping of AnalysisService UID -> price
:type prices: dict
:param specs: List of AnalysisService UID -> Result Range Record mappings
:type specs: list
:returns: list of new assigned Analyses
"""
# This setter returns a list of new set Analyses
new_analyses = []
# Prevent removing all Analyses
if not items:
logger.warn("Not allowed to remove all Analyses from AR.")
return new_analyses
# Bail out if the items is not a list type
if not isinstance(items, (list, tuple)):
raise TypeError(
"Items parameter must be a tuple or list, got '{}'".format(
type(items)))
# Bail out if the AR in frozen state
if self._is_frozen(instance):
raise ValueError(
"Analyses can not be modified for inactive/verified ARs")
# Convert the items to a valid list of AnalysisServices
services = filter(None, map(self._to_service, items))
# Calculate dependencies
# FIXME Infinite recursion error possible here, if the formula includes
# the Keyword of the Service that includes the Calculation
dependencies = map(lambda s: s.getServiceDependencies(), services)
dependencies = list(itertools.chain.from_iterable(dependencies))
# Merge dependencies and services
services = set(services + dependencies)
# Service UIDs
service_uids = map(api.get_uid, services)
# Modify existing AR specs with new form values of selected analyses.
self._update_specs(instance, specs)
for service in services:
keyword = service.getKeyword()
# Create the Analysis if it doesn't exist
if shasattr(instance, keyword):
analysis = instance._getOb(keyword)
else:
# TODO Entry point for interims assignment and Calculation
# decoupling from Analysis. See comments PR#593
analysis = create_analysis(instance, service)
# TODO Remove when the `create_analysis` function supports this
# Set the interim fields only for new created Analysis
self._update_interims(analysis, service)
new_analyses.append(analysis)
# Set the price of the Analysis
self._update_price(analysis, service, prices)
# delete analyses
delete_ids = []
for analysis in instance.objectValues('Analysis'):
service_uid = analysis.getServiceUID()
# Skip assigned Analyses
if service_uid in service_uids:
continue
# Skip Analyses in frozen states
if self._is_frozen(analysis):
logger.warn("Inactive/verified Analyses can not be removed.")
continue
# If it is assigned to a worksheet, unassign it before deletion.
if self._is_assigned_to_worksheet(analysis):
backrefs = self._get_assigned_worksheets(analysis)
ws = backrefs[0]
ws.removeAnalysis(analysis)
# Unset the partition reference
analysis.edit(SamplePartition=None)
delete_ids.append(analysis.getId())
if delete_ids:
# Note: subscriber might promote the AR
instance.manage_delObjects(ids=delete_ids)
return new_analyses
def set(self, instance, items, prices=None, specs=None, **kwargs):
"""Set the 'Analyses' field value, by creating and removing Analysis
objects from the AR.
items is a list that contains the items to be set:
The list can contain Analysis objects/brains, AnalysisService
objects/brains and/or Analysis Service uids.
prices is a dictionary:
key = AnalysisService UID
value = price
specs is a dictionary:
key = AnalysisService UID
value = dictionary: defined in ResultsRange field definition
"""
if not items:
return
assert isinstance(items,
(list, tuple)), "items must be a list or a tuple"
# Convert the items list to a list of service uids and remove empties
service_uids = map(self._get_service_uid, items)
service_uids = filter(None, service_uids)
bsc = getToolByName(instance, 'bika_setup_catalog')
workflow = getToolByName(instance, 'portal_workflow')
# one can only edit Analyses up to a certain state.
ar_state = workflow.getInfoFor(instance, 'review_state', '')
assert ar_state in ('sample_registered', 'sampled', 'to_be_sampled',
'to_be_preserved', 'sample_due', 'sample_received',
'attachment_due', 'to_be_verified')
# - Modify existing AR specs with new form values for selected analyses.
# - new analysis requests are also using this function, so ResultsRange
# may be undefined. in this case, specs= will contain the entire
# AR spec.
rr = instance.getResultsRange()
specs = specs if specs else []
for s in specs:
s_in_rr = False
for i, r in enumerate(rr):
if s['keyword'] == r['keyword']:
rr[i].update(s)
s_in_rr = True
if not s_in_rr:
rr.append(s)
instance.setResultsRange(rr)
new_analyses = []
proxies = bsc(UID=service_uids)
for proxy in proxies:
service = proxy.getObject()
keyword = service.getKeyword()
# analysis->InterimFields
calc = service.getCalculation()
interim_fields = calc and list(calc.getInterimFields()) or []
# override defaults from service->InterimFields
service_interims = service.getInterimFields()
sif = dict([(x['keyword'], x.get('value', ''))
for x in service_interims])
for i, i_f in enumerate(interim_fields):
if i_f['keyword'] in sif:
interim_fields[i]['value'] = sif[i_f['keyword']]
service_interims = [
x for x in service_interims
if x['keyword'] != i_f['keyword']
]
# Add remaining service interims to the analysis
for v in service_interims:
interim_fields.append(v)
# create the analysis if it doesn't exist
if shasattr(instance, keyword):
analysis = instance._getOb(keyword)
else:
analysis = create_analysis(instance, service)
new_analyses.append(analysis)
for i, r in enumerate(rr):
if r['keyword'] == analysis.getKeyword():
r['uid'] = analysis.UID()
# delete analyses
delete_ids = []
for analysis in instance.objectValues('Analysis'):
service_uid = analysis.getServiceUID()
if service_uid not in service_uids:
# If it is verified or published, don't delete it.
state = workflow.getInfoFor(analysis, 'review_state')
if state in ('verified', 'published'):
continue
# If it is assigned to a worksheet, unassign it before deletion.
state = workflow.getInfoFor(analysis,
'worksheetanalysis_review_state')
if state == 'assigned':
ws = analysis.getBackReferences("WorksheetAnalysis")[0]
ws.removeAnalysis(analysis)
# Unset the partition reference
analysis.edit(SamplePartition=None)
delete_ids.append(analysis.getId())
if delete_ids:
# Note: subscriber might promote the AR
instance.manage_delObjects(ids=delete_ids)
return new_analyses
def set(self, instance, service_uids, prices=None, specs={}, **kwargs):
""" service_uids are the services selected on the AR Add/Edit form.
prices is a service_uid keyed dictionary containing the prices entered
on the form.
specs is a uid keyed dict with values of
{min:, max:, error:}
"""
if not service_uids:
return
assert type(service_uids) in (list, tuple)
workflow = instance.portal_workflow
# one can only edit Analyses up to a certain state.
ar_state = workflow.getInfoFor(instance, 'review_state', '')
assert ar_state in ('sample_registered', 'sampled', 'to_be_sampled',
'to_be_preserved', 'sample_due', 'sample_received',
'attachment_due', 'to_be_verified')
bsc = getToolByName(instance, 'bika_setup_catalog')
services = bsc(UID=service_uids)
new_analyses = []
for service in services:
service_uid = service.UID
service = service.getObject()
keyword = service.getKeyword()
price = prices[service_uid] if prices and service_uid in prices \
else service.getPrice()
vat = Decimal(service.getVAT())
# analysis->InterimFields
calc = service.getCalculation()
interim_fields = calc and list(calc.getInterimFields()) or []
# override defaults from service->InterimFields
service_interims = service.getInterimFields()
sif = dict([[x['keyword'], x.get('value', '')]
for x in service_interims])
for i, i_f in enumerate(interim_fields):
if i_f['keyword'] in sif:
interim_fields[i]['value'] = sif[i_f['keyword']]
service_interims = [
x for x in service_interims
if x['keyword'] != i_f['keyword']
]
# Add remaining service interims to the analysis
for v in service_interims:
interim_fields.append(v)
# create the analysis if it doesn't exist
if hasattr(instance, keyword):
analysis = instance._getOb(keyword)
else:
analysis = create_analysis(instance, service, keyword,
interim_fields)
new_analyses.append(analysis)
# Note: subscriber might retract and/or unassign the AR
spec = specs[service_uid] if specs and service_uid in specs \
else None
# If no specification came to us from the form, then we will
# see if there is a spec for this SampleType & AnalysisService
if not spec:
spec = analysis.get_default_specification()
analysis.specification = spec
# XXX Price?
# analysis.setPrice(price)
# delete analyses
delete_ids = []
for analysis in instance.objectValues('Analysis'):
service_uid = analysis.Schema()['Service'].getRaw(analysis)
if service_uid not in service_uids:
# If it is verified or published, don't delete it.
if workflow.getInfoFor(analysis,
'review_state') in ('verified',
'published'):
continue # log it
# If it is assigned to a worksheet, unassign it before deletion.
elif workflow.getInfoFor(
analysis,
'worksheetanalysis_review_state') == 'assigned':
ws = analysis.getBackReferences("WorksheetAnalysis")[0]
ws.removeAnalysis(analysis)
# Unset the partition reference
analysis.edit(SamplePartition=None)
delete_ids.append(analysis.getId())
if delete_ids:
# Note: subscriber might promote the AR
instance.manage_delObjects(ids=delete_ids)
return new_analyses
def doActionToAnalysis(source_analysis, action):
"""
This functions executes the action against the analysis.
:base: a full analysis object. The new analyses will be cloned from it.
:action: a dictionary representing an action row.
[{'action': 'duplicate', ...}, {,}, ...]
:returns: the new analysis
"""
if not IRequestAnalysis.providedBy(source_analysis):
# Only routine analyses (assigned to a Request) are supported
logger.warn("Only IRequestAnalysis are supported in reflex testing")
return None
state = api.get_review_status(source_analysis)
action_id = action.get('action', '')
if action_id == "new_analysis":
# Create a new analysis (different from the original)
service_uid = action.get("new_analysis", "")
if not api.is_uid(service_uid):
logger.error("Not a valid UID: {}".format(service_uid))
return None
service = api.get_object_by_uid(service_uid, None)
if not service or not IAnalysisService.providedBy(service):
logger.error("No valid service for UID {}".format(service_uid))
return None
analysis = create_analysis(source_analysis.aq_parent, service)
analysis.setSamplePartition(source_analysis.getSamplePartition())
changeWorkflowState(analysis, "bika_analysis_workflow",
"sample_received")
elif action_id == 'setvisibility':
target_id = action.get('setvisibilityof', '')
if target_id == "original":
analysis = source_analysis
else:
analysis = _fetch_analysis_for_local_id(source_analysis, target_id)
elif action_id == 'repeat' and state != 'retracted':
# Repeat an analysis consist on cancel it and then create a new
# analysis with the same analysis service used for the canceled
# one (always working with the same sample). It'll do a retract
# action
doActionFor(source_analysis, 'retract')
analysis_request = source_analysis.getRequest()
analysis = analysis_request.getAnalyses(sort_on="created")[-1]
analysis = api.get_object(analysis)
analysis.setResult('')
elif action_id == 'duplicate' or state == 'retracted':
analysis = duplicateAnalysis(source_analysis)
analysis.setResult('')
elif action_id == 'setresult':
target = action.get('setresulton', '')
result_value = action.get('setresultdiscrete', '') or \
action['setresultvalue']
if target == 'original':
analysis = source_analysis.getOriginalReflexedAnalysis()
analysis.setResult(result_value)
elif target == 'new':
# Create a new analysis
analysis = duplicateAnalysis(source_analysis)
analysis.setResult(result_value)
doActionFor(analysis, 'submit')
else:
logger.error("Unknown 'setresulton' directive: {}".format(target))
return None
else:
logger.error("Unknown Reflex Rule action: {}".format(action_id))
return None
analysis.setReflexRuleAction(action_id)
analysis.setIsReflexAnalysis(True)
analysis.setReflexAnalysisOf(source_analysis)
analysis.setReflexRuleActionsTriggered(
source_analysis.getReflexRuleActionsTriggered())
if action.get('showinreport', '') == "invisible":
analysis.setHidden(True)
elif action.get('showinreport', '') == "visible":
analysis.setHidden(False)
# Setting the original reflected analysis
if source_analysis.getOriginalReflexedAnalysis():
analysis.setOriginalReflexedAnalysis(
source_analysis.getOriginalReflexedAnalysis())
else:
analysis.setOriginalReflexedAnalysis(source_analysis)
analysis.setReflexRuleLocalID(action.get('an_result_id', ''))
# Setting the remarks to base analysis
#remarks = get_remarks(action, analysis)
#analysis.setRemarks(remarks)
return analysis