def _is_frozen(self, brain_or_object, *frozen_transitions):
"""Check if the passed in object is frozen: the object is cancelled,
inactive or has been verified at some point
:param brain_or_object: Analysis or AR Brain/Object
:param frozen_transitions: additional transitions that freeze the object
:returns: True if the object is frozen
"""
if not api.is_active(brain_or_object):
return True
object = api.get_object(brain_or_object)
frozen_trans = set(frozen_transitions)
frozen_trans.add('verify')
performed_transitions = set(getReviewHistoryActionsList(object))
if frozen_trans.intersection(performed_transitions):
return True
return False
def _is_frozen(self, brain_or_object):
"""Check if the passed in object is frozen: the object is cancelled,
inactive or has been verified at some point
:param brain_or_object: Analysis or AR Brain/Object
:returns: True if the object is frozen
"""
if not api.is_active(brain_or_object):
return True
if api.get_workflow_status_of(brain_or_object) in FROZEN_STATES:
return True
# Check the review history if one of the frozen transitions was done
object = api.get_object(brain_or_object)
performed_transitions = set(getReviewHistoryActionsList(object))
if set(FROZEN_TRANSITIONS).intersection(performed_transitions):
return True
return False
def _create_ar(self, context, request):
"""Creates AnalysisRequest object, with supporting Sample, Partition
and Analysis objects. The client is retrieved from the obj_path
key in the request.
Required request parameters:
- Contact: One client contact Fullname. The contact must exist
in the specified client. The first Contact with the specified
value in it's Fullname field will be used.
- SampleType_<index> - Must be an existing sample type.
Optional request parameters:
- CCContacts: A list of contact Fullnames, which will be copied on
all messages related to this AR and it's sample or results.
- CCEmails: A list of email addresses to include as above.
- Sample_id: Create a secondary AR with an existing sample. If
unspecified, a new sample is created.
- Specification: a lookup to set Analysis specs default values
for all analyses
- Analysis_Specification: specs (or overrides) per analysis, using
a special lookup format.
&Analysis_Specification:list=<Keyword>:min:max:error&...
"""
wftool = getToolByName(context, 'portal_workflow')
bc = getToolByName(context, 'bika_catalog')
bsc = getToolByName(context, 'bika_setup_catalog')
pc = getToolByName(context, 'portal_catalog')
ret = {
"url": router.url_for("create", force_external=True),
"success": True,
"error": False,
}
SamplingWorkflowEnabled = context.bika_setup.getSamplingWorkflowEnabled()
for field in [
'Client',
'SampleType',
'Contact',
'SamplingDate',
'Services']:
self.require(field)
self.used(field)
try:
client = resolve_request_lookup(context, request, 'Client')[0].getObject()
except IndexError:
raise Exception("Client not found")
secondary = False
sample = None
# Sample_id
if 'Sample' in request:
# Secondary AR
try:
sample = resolve_request_lookup(context, request, 'Sample')[0].getObject()
except IndexError:
raise Exception("Sample not found")
secondary = True
else:
# Primary AR
sample = _createObjectByType("Sample", client, tmpID())
sample.unmarkCreationFlag()
fields = set_fields_from_request(sample, request)
for field in fields:
self.used(field)
sample._renameAfterCreation()
sample.setSampleID(sample.getId())
sample.setSamplingWorkflowEnabled(SamplingWorkflowEnabled)
event.notify(ObjectInitializedEvent(sample))
sample.at_post_create_script()
ret['sample_id'] = sample.getId()
parts = [{'services': [],
'container': [],
'preservation': '',
'separate': False}]
specs = self.get_specs_from_request()
ar = _createObjectByType("AnalysisRequest", client, tmpID())
ar.unmarkCreationFlag()
fields = set_fields_from_request(ar, request)
for field in fields:
self.used(field)
ar.setSample(sample)
ar._renameAfterCreation()
ret['ar_id'] = ar.getId()
brains = resolve_request_lookup(context, request, 'Services')
service_uids = [p.UID for p in brains]
# If there is a profile, add its services' UIDs
brains = resolve_request_lookup(context, request, 'Profiles')
profiles_uids = [p.UID for p in brains]
profiles_uids = ','.join(profiles_uids)
profiles_dict = {'Profiles': profiles_uids}
service_uids = get_services_uids(
context=context, analyses_serv=service_uids, values=profiles_dict)
ar.setAnalyses(service_uids, specs=specs)
new_analyses = ar.getAnalyses(full_objects=True)
ar.reindexObject()
event.notify(ObjectInitializedEvent(ar))
ar.at_post_create_script()
# Create sample partitions
parts_and_services = {}
for _i in range(len(parts)):
p = parts[_i]
part_prefix = sample.getId() + "-P"
if '%s%s' % (part_prefix, _i + 1) in sample.objectIds():
parts[_i]['object'] = sample['%s%s' % (part_prefix, _i + 1)]
parts_and_services['%s%s' % (part_prefix, _i + 1)] = p['services']
part = parts[_i]['object']
else:
part = _createObjectByType("SamplePartition", sample, tmpID())
parts[_i]['object'] = part
container = None
preservation = p['preservation']
parts[_i]['prepreserved'] = False
part.edit(
Container=container,
Preservation=preservation,
)
part.processForm()
parts_and_services[part.id] = p['services']
# Add analyses to sample partitions
# XXX jsonapi create AR: right now, all new analyses are linked to the first samplepartition
if new_analyses:
analyses = list(part.getAnalyses())
analyses.extend(new_analyses)
for analysis in new_analyses:
analysis.setSamplePartition(part)
part.setAnalyses(analyses)
action = 'no_sampling_workflow'
if SamplingWorkflowEnabled:
action = 'sampling_workflow'
wftool.doActionFor(ar, action)
if secondary:
# If secondary AR, then we need to manually transition the AR (and its
# children) to fit with the Sample Partition's current state
sampleactions = getReviewHistoryActionsList(sample)
doActionsFor(ar, sampleactions)
else:
# If Preservation is required for some partitions,
# and the SamplingWorkflow is disabled, we need
# to transition to to_be_preserved manually.
if not SamplingWorkflowEnabled:
to_be_preserved = []
sample_due = []
lowest_state = 'sample_due'
for p in sample.objectValues('SamplePartition'):
if p.getPreservation():
lowest_state = 'to_be_preserved'
to_be_preserved.append(p)
else:
sample_due.append(p)
for p in to_be_preserved:
doActionFor(p, 'to_be_preserved')
for p in sample_due:
doActionFor(p, 'sample_due')
doActionFor(sample, lowest_state)
# Transition pre-preserved partitions
for p in parts:
if 'prepreserved' in p and p['prepreserved']:
part = p['object']
state = workflow.getInfoFor(part, 'review_state')
if state == 'to_be_preserved':
doActionFor(part, 'preserve')
if self.unused:
raise BadRequest("The following request fields were not used: %s. Request aborted." % self.unused)
return ret
def create_analysisrequest(client, request, values, analyses=None,
partitions=None, specifications=None, prices=None):
"""This is meant for general use and should do everything necessary to
create and initialise an AR and any other required auxilliary objects
(Sample, SamplePartition, Analysis...)
:param client:
The container (Client) in which the ARs will be created.
:param request:
The current Request object.
:param values:
a dict, where keys are AR|Sample schema field names.
:param analyses:
Analysis services list. If specified, augments the values in
values['Analyses']. May consist of service objects, UIDs, or Keywords.
:param partitions:
A list of dictionaries, if specific partitions are required. If not
specified, AR's sample is created with a single partition.
:param specifications:
These values augment those found in values['Specifications']
:param prices:
Allow different prices to be set for analyses. If not set, prices
are read from the associated analysis service.
"""
# Don't pollute the dict param passed in
values = deepcopy(values)
# Create new sample or locate the existing for secondary AR
secondary = False
sample = None
if not values.get('Sample', False):
sample = create_sample(client, request, values)
else:
sample = get_sample_from_values(client, values)
secondary = True
# Create the Analysis Request
ar = _createObjectByType('AnalysisRequest', client, tmpID())
# Set some required fields manually before processForm is called
ar.setSample(sample)
values['Sample'] = sample
ar.processForm(REQUEST=request, values=values)
ar.edit(RequestID=ar.getId())
# Set analysis request analyses. 'Analyses' param are analyses services
analyses = analyses if analyses else []
service_uids = get_services_uids(
context=client, analyses_serv=analyses, values=values)
# processForm already has created the analyses, but here we create the
# analyses with specs and prices. This function, even it is called 'set',
# deletes the old analyses, so eventually we obtain the desired analyses.
ar.setAnalyses(service_uids, prices=prices, specs=specifications)
analyses = ar.getAnalyses(full_objects=True)
# Create sample partitions
if not partitions:
partitions = values.get('Partitions',
[{'services': service_uids}])
part_num = 0
prefix = sample.getId() + "-P"
if secondary:
# Always create new partitions if is a Secondary AR, cause it does
# not make sense to reuse the partitions used in a previous AR!
sparts = sample.getSamplePartitions()
for spart in sparts:
spartnum = int(spart.getId().split(prefix)[1])
if spartnum > part_num:
part_num = spartnum
for n, partition in enumerate(partitions):
# Calculate partition id
partition_id = '%s%s' % (prefix, part_num + 1)
partition['part_id'] = partition_id
# Point to or create sample partition
if partition_id in sample.objectIds():
partition['object'] = sample[partition_id]
else:
partition['object'] = create_samplepartition(
sample,
partition,
analyses
)
part_num += 1
# At this point, we have a fully created AR, with a Sample, Partitions and
# Analyses, but the state of all them is the initial ("sample_registered").
# We can now transition the whole thing (instead of doing it manually for
# each object we created). After and Before transitions will take care of
# cascading and promoting the transitions in all the objects "associated"
# to this Analysis Request.
sampling_workflow_enabled = sample.getSamplingWorkflowEnabled()
action = 'no_sampling_workflow'
if sampling_workflow_enabled:
action = 'sampling_workflow'
# Transition the Analysis Request and related objects to "sampled" (if
# sampling workflow not enabled) or to "to_be_sampled" statuses.
doActionFor(ar, action)
if secondary:
# If secondary AR, then we need to manually transition the AR (and its
# children) to fit with the Sample Partition's current state
sampleactions = getReviewHistoryActionsList(sample)
doActionsFor(ar, sampleactions)
# We need a workaround here in order to transition partitions.
# auto_no_preservation_required and auto_preservation_required are
# auto transitions applied to analysis requests, but partitions don't
# have them, so we need to replace them by the sample_workflow
# equivalent.
if 'auto_no_preservation_required' in sampleactions:
index = sampleactions.index('auto_no_preservation_required')
sampleactions[index] = 'sample_due'
elif 'auto_preservation_required' in sampleactions:
index = sampleactions.index('auto_preservation_required')
sampleactions[index] = 'to_be_preserved'
# We need to transition the partition manually
# Transition pre-preserved partitions
for partition in partitions:
part = partition['object']
doActionsFor(part, sampleactions)
# Transition pre-preserved partitions
for p in partitions:
if 'prepreserved' in p and p['prepreserved']:
part = p['object']
doActionFor(part, 'preserve')
# Once the ar is fully created, check if there are rejection reasons
reject_field = values.get('RejectionReasons', '')
if reject_field and reject_field.get('checkbox', False):
doActionFor(ar, 'reject')
return ar
def _create_ar(self, context, request):
"""Creates AnalysisRequest object, with supporting Sample, Partition
and Analysis objects. The client is retrieved from the obj_path
key in the request.
Required request parameters:
- Contact: One client contact Fullname. The contact must exist
in the specified client. The first Contact with the specified
value in it's Fullname field will be used.
- SampleType_<index> - Must be an existing sample type.
Optional request parameters:
- CCContacts: A list of contact Fullnames, which will be copied on
all messages related to this AR and it's sample or results.
- CCEmails: A list of email addresses to include as above.
- Sample_id: Create a secondary AR with an existing sample. If
unspecified, a new sample is created.
- Specification: a lookup to set Analysis specs default values
for all analyses
- Analysis_Specification: specs (or overrides) per analysis, using
a special lookup format.
&Analysis_Specification:list=<Keyword>:min:max:error&...
"""
wftool = getToolByName(context, 'portal_workflow')
bc = getToolByName(context, 'bika_catalog')
bsc = getToolByName(context, 'bika_setup_catalog')
pc = getToolByName(context, 'portal_catalog')
ret = {
"url": router.url_for("create", force_external=True),
"success": True,
"error": False,
}
SamplingWorkflowEnabled = context.bika_setup.getSamplingWorkflowEnabled(
)
for field in [
'Client', 'SampleType', 'Contact', 'SamplingDate', 'Services'
]:
self.require(field)
self.used(field)
try:
client = resolve_request_lookup(context, request,
'Client')[0].getObject()
except IndexError:
raise Exception("Client not found")
secondary = False
sample = None
# Sample_id
if 'Sample' in request:
# Secondary AR
try:
sample = resolve_request_lookup(context, request,
'Sample')[0].getObject()
except IndexError:
raise Exception("Sample not found")
secondary = True
else:
# Primary AR
sample = _createObjectByType("Sample", client, tmpID())
sample.unmarkCreationFlag()
fields = set_fields_from_request(sample, request)
for field in fields:
self.used(field)
sample._renameAfterCreation()
sample.setSampleID(sample.getId())
sample.setSamplingWorkflowEnabled(SamplingWorkflowEnabled)
event.notify(ObjectInitializedEvent(sample))
sample.at_post_create_script()
ret['sample_id'] = sample.getId()
parts = [{
'services': [],
'container': [],
'preservation': '',
'separate': False
}]
specs = self.get_specs_from_request()
ar = _createObjectByType("AnalysisRequest", client, tmpID())
ar.unmarkCreationFlag()
fields = set_fields_from_request(ar, request)
for field in fields:
self.used(field)
ar.setSample(sample)
ar._renameAfterCreation()
ret['ar_id'] = ar.getId()
brains = resolve_request_lookup(context, request, 'Services')
service_uids = [p.UID for p in brains]
# If there is a profile, add its services' UIDs
brains = resolve_request_lookup(context, request, 'Profiles')
profiles_uids = [p.UID for p in brains]
profiles_uids = ','.join(profiles_uids)
profiles_dict = {'Profiles': profiles_uids}
service_uids = get_services_uids(context=context,
analyses_serv=service_uids,
values=profiles_dict)
ar.setAnalyses(service_uids, specs=specs)
new_analyses = ar.getAnalyses(full_objects=True)
ar.reindexObject()
event.notify(ObjectInitializedEvent(ar))
ar.at_post_create_script()
# Create sample partitions
parts_and_services = {}
for _i in range(len(parts)):
p = parts[_i]
part_prefix = sample.getId() + "-P"
if '%s%s' % (part_prefix, _i + 1) in sample.objectIds():
parts[_i]['object'] = sample['%s%s' % (part_prefix, _i + 1)]
parts_and_services['%s%s' %
(part_prefix, _i + 1)] = p['services']
part = parts[_i]['object']
else:
part = _createObjectByType("SamplePartition", sample, tmpID())
parts[_i]['object'] = part
container = None
preservation = p['preservation']
parts[_i]['prepreserved'] = False
part.edit(
Container=container,
Preservation=preservation,
)
part.processForm()
parts_and_services[part.id] = p['services']
# Add analyses to sample partitions
# XXX jsonapi create AR: right now, all new analyses are linked to the first samplepartition
if new_analyses:
analyses = list(part.getAnalyses())
analyses.extend(new_analyses)
for analysis in new_analyses:
analysis.setSamplePartition(part)
part.setAnalyses(analyses)
action = 'no_sampling_workflow'
if SamplingWorkflowEnabled:
action = 'sampling_workflow'
wftool.doActionFor(ar, action)
if secondary:
# If secondary AR, then we need to manually transition the AR (and its
# children) to fit with the Sample Partition's current state
sampleactions = getReviewHistoryActionsList(sample)
doActionsFor(ar, sampleactions)
else:
# If Preservation is required for some partitions,
# and the SamplingWorkflow is disabled, we need
# to transition to to_be_preserved manually.
if not SamplingWorkflowEnabled:
to_be_preserved = []
sample_due = []
lowest_state = 'sample_due'
for p in sample.objectValues('SamplePartition'):
if p.getPreservation():
lowest_state = 'to_be_preserved'
to_be_preserved.append(p)
else:
sample_due.append(p)
for p in to_be_preserved:
doActionFor(p, 'to_be_preserved')
for p in sample_due:
doActionFor(p, 'sample_due')
doActionFor(sample, lowest_state)
# Transition pre-preserved partitions
for p in parts:
if 'prepreserved' in p and p['prepreserved']:
part = p['object']
state = workflow.getInfoFor(part, 'review_state')
if state == 'to_be_preserved':
doActionFor(part, 'preserve')
if self.unused:
raise BadRequest(
"The following request fields were not used: %s. Request aborted."
% self.unused)
return ret