def workflow_script_sample_due(self):
if skip(self, "sample_due"):
return
# All associated AnalysisRequests are also transitioned
for ar in self.getAnalysisRequests():
doActionFor(ar, "sample_due")
ar.reindexObject()
def workflow_script_sample_due(self):
if skip(self, "sample_due"):
return
# All associated AnalysisRequests are also transitioned
for ar in self.getAnalysisRequests():
doActionFor(ar, "sample_due")
ar.reindexObject()
def test_default_stickers(self):
"""https://jira.bikalabs.com/browse/WINE-44: display SampleID or
SamplePartition ID depending on bikasetup.ShowPartitions value
"""
folder = self.portal.bika_setup.bika_analysisservices
services = [_createObjectByType("AnalysisService", folder, tmpID()),
_createObjectByType("AnalysisService", folder, tmpID())]
services[0].processForm()
services[1].processForm()
services[0].edit(title="Detect Dust")
services[1].edit(title="Detect water")
service_uids = [s.UID for s in services]
folder = self.portal.clients
client = _createObjectByType("Client", folder, tmpID())
client.processForm()
folder = self.portal.clients.objectValues("Client")[0]
contact = _createObjectByType("Contact", folder, tmpID())
contact.processForm()
contact.edit(Firstname="Bob", Surname="Dobbs", email="*****@*****.**")
folder = self.portal.bika_setup.bika_sampletypes
sampletype = _createObjectByType("SampleType", folder, tmpID())
sampletype.processForm()
sampletype.edit(title="Air", Prefix="AIR")
values = {'Client': client.UID(),
'Contact': contact.UID(),
'SamplingDate': '2015-01-01',
'SampleType': sampletype.UID()}
for stemp in getStickerTemplates():
# create and receive AR
ar = create_analysisrequest(client, {}, values, service_uids)
ar.bika_setup.setShowPartitions(False)
doActionFor(ar, 'receive')
self.assertEquals(ar.portal_workflow.getInfoFor(ar, 'review_state'), 'sample_received')
# check sticker text
ar.REQUEST['items'] = ar.getId()
ar.REQUEST['template'] = stemp.get('id')
sticker = Sticker(ar, ar.REQUEST)()
pid = ar.getSample().objectValues("SamplePartition")[0].getId()
self.assertNotIn(pid, sticker, "Sticker must not contain partition ID %s"%pid)
# create and receive AR
ar = create_analysisrequest(client, {}, values, service_uids)
ar.bika_setup.setShowPartitions(True)
doActionFor(ar, 'receive')
self.assertEquals(ar.portal_workflow.getInfoFor(ar, 'review_state'), 'sample_received')
# check sticker text
ar.REQUEST['items'] = ar.getId()
ar.REQUEST['template'] = stemp.get('id')
sticker = Sticker(ar, ar.REQUEST)()
pid = ar.getSample().objectValues("SamplePartition")[0].getId()
self.assertIn(pid, sticker, "Sticker must contain partition ID %s"%pid)
def workflow_script_verify(self):
if skip(self, "verify"):
return
workflow = getToolByName(self, 'portal_workflow')
self.reindexObject(idxs=["review_state", ])
if not "verify all analyses" in self.REQUEST['workflow_skiplist']:
# verify all analyses in this self.
analyses = self.getAnalyses()
for analysis in analyses:
state = workflow.getInfoFor(analysis, 'review_state', '')
if state != 'to_be_verified':
continue
doActionFor(analysis, "verify")
def workflow_script_preserve(self):
"""This action can happen in the Sample UI, so we transition all
self partitions that are still 'to_be_preserved'
"""
workflow = getToolByName(self, "portal_workflow")
parts = self.objectValues("SamplePartition")
tbs = [sp for sp in parts if workflow.getInfoFor(sp, "review_state") == "to_be_preserved"]
for sp in tbs:
doActionFor(sp, "preserve")
# All associated AnalysisRequests are also transitioned
for ar in self.getAnalysisRequests():
doActionFor(ar, "preserve")
ar.reindexObject()
def workflow_script_receive(self):
workflow = getToolByName(self, "portal_workflow")
self.setDateReceived(DateTime())
self.reindexObject(idxs=["review_state", "getDateReceived"])
# Receive all self partitions that are still 'sample_due'
parts = self.objectValues("SamplePartition")
sample_due = [sp for sp in parts if workflow.getInfoFor(sp, "review_state") == "sample_due"]
for sp in sample_due:
workflow.doActionFor(sp, "receive")
# when a self is received, all associated
# AnalysisRequests are also transitioned
for ar in self.getAnalysisRequests():
doActionFor(ar, "receive")
def workflow_script_to_be_preserved(self):
if skip(self, "to_be_preserved"):
return
workflow = getToolByName(self, "portal_workflow")
parts = self.objectValues("SamplePartition")
# Transition our children
tbs = [sp for sp in parts if workflow.getInfoFor(sp, "review_state") == "to_be_preserved"]
for sp in tbs:
doActionFor(sp, "to_be_preserved")
# All associated AnalysisRequests are also transitioned
for ar in self.getAnalysisRequests():
doActionFor(ar, "to_be_preserved")
ar.reindexObject()
def workflow_script_retract(self):
if skip(self, "retract"):
return
workflow = getToolByName(self, 'portal_workflow')
self.reindexObject(idxs=["review_state", ])
if not "retract all analyses" in self.REQUEST['workflow_skiplist']:
# retract all analyses in this self.
# (NB: don't retract if it's verified)
analyses = self.getAnalyses()
for analysis in analyses:
state = workflow.getInfoFor(analysis, 'review_state', '')
if state not in ('attachment_due', 'to_be_verified',):
continue
doActionFor(analysis, 'retract')
def workflow_script_to_be_preserved(self):
if skip(self, "to_be_preserved"):
return
workflow = getToolByName(self, 'portal_workflow')
parts = self.objectValues('SamplePartition')
# Transition our children
tbs = [sp for sp in parts
if workflow.getInfoFor(sp, 'review_state') == 'to_be_preserved']
for sp in tbs:
doActionFor(sp, "to_be_preserved")
# All associated AnalysisRequests are also transitioned
for ar in self.getAnalysisRequests():
doActionFor(ar, "to_be_preserved")
ar.reindexObject()
def workflow_script_receive(self):
workflow = getToolByName(self, 'portal_workflow')
self.setDateReceived(DateTime())
self.reindexObject(idxs=["review_state", "getDateReceived"])
# Receive all self partitions that are still 'sample_due'
parts = self.objectValues('SamplePartition')
sample_due = [sp for sp in parts
if workflow.getInfoFor(sp, 'review_state') == 'sample_due']
for sp in sample_due:
workflow.doActionFor(sp, 'receive')
# when a self is received, all associated
# AnalysisRequests are also transitioned
for ar in self.getAnalysisRequests():
doActionFor(ar, "receive")
def __call__(self):
if 'transition' in self.request.form:
doActionFor(self.context, self.request.form['transition'])
## render header table
self.header_table = HeaderTableView(self.context, self.request)
## Create Sample Partitions table
parts_table = None
if not self.allow_edit:
p = SamplePartitionsView(self.context, self.request)
p.allow_edit = self.allow_edit
p.show_select_column = self.allow_edit
p.show_workflow_action_buttons = self.allow_edit
p.show_column_toggles = False
p.show_select_all_checkbox = False
p.review_states[0]['transitions'] = [
{
'id': 'empty'
},
] # none
parts_table = p.contents_table()
self.parts = parts_table
## Create Field and Lab Analyses tables
self.tables = {}
if not self.allow_edit:
for poc in POINTS_OF_CAPTURE:
if not self.context.getAnalyses({'getPointOfCapture': poc}):
continue
t = SampleAnalysesView(self.context,
self.request,
getPointOfCapture=poc,
sort_on='getServiceTitle')
t.form_id = "sample_%s_analyses" % poc
if poc == 'field':
t.review_states[0]['columns'].remove('DueDate')
t.show_column_toggles = False
t.review_states[0]['transitions'] = [{
'id': 'submit'
}, {
'id': 'retract'
}, {
'id': 'verify'
}]
self.tables[POINTS_OF_CAPTURE.getValue(
poc)] = t.contents_table()
return self.template()
def workflow_script_preserve(self):
"""This action can happen in the Sample UI, so we transition all
self partitions that are still 'to_be_preserved'
"""
workflow = getToolByName(self, 'portal_workflow')
parts = self.objectValues("SamplePartition")
tbs = [sp for sp in parts
if workflow.getInfoFor(sp, 'review_state') == 'to_be_preserved']
for sp in tbs:
doActionFor(sp, "preserve")
# All associated AnalysisRequests are also transitioned
for ar in self.getAnalysisRequests():
doActionFor(ar, "preserve")
ar.reindexObject()
def workflow_script_verify(self):
if skip(self, "verify"):
return
workflow = getToolByName(self, 'portal_workflow')
self.reindexObject(idxs=[
"review_state",
])
if not "verify all analyses" in self.REQUEST['workflow_skiplist']:
# verify all analyses in this self.
analyses = self.getAnalyses()
for analysis in analyses:
state = workflow.getInfoFor(analysis, 'review_state', '')
if state != 'to_be_verified':
continue
doActionFor(analysis, "verify")
def workflow_script_sample(self):
if skip(self, "sample"):
return
workflow = getToolByName(self, 'portal_workflow')
parts = self.objectValues('SamplePartition')
# This action can happen in the Sample UI. So we transition all
# partitions that are still 'to_be_sampled'
tbs = [sp for sp in parts
if workflow.getInfoFor(sp, 'review_state') == 'to_be_sampled']
for sp in tbs:
doActionFor(sp, "sample")
# All associated AnalysisRequests are also transitioned
for ar in self.getAnalysisRequests():
doActionFor(ar, "sample")
ar.reindexObject()
def workflow_script_submit(self):
# Don't cascade. Shouldn't be submitting WSs directly for now,
# except edge cases where all analyses are already submitted,
# but self was held back until an analyst was assigned.
workflow = getToolByName(self, 'portal_workflow')
self.reindexObject(idxs=["review_state", ])
can_attach = True
for a in self.getAnalyses():
if workflow.getInfoFor(a, 'review_state') in \
('to_be_sampled', 'to_be_preserved', 'sample_due',
'sample_received', 'attachment_due', 'assigned',):
# Note: referenceanalyses and duplicateanalyses can still
# have review_state = "assigned".
can_attach = False
break
if can_attach:
doActionFor(self, 'attach')
def workflow_script_receive(self):
if skip(self, "receive"):
return
sample = self.aq_parent
workflow = getToolByName(self, 'portal_workflow')
sample_state = workflow.getInfoFor(sample, 'review_state')
self.setDateReceived(DateTime())
self.reindexObject(idxs=["getDateReceived", ])
# Transition our analyses
analyses = self.getBackReferences('AnalysisSamplePartition')
for analysis in analyses:
doActionFor(analysis, "receive")
# if all sibling partitions are received, promote sample
if not skip(sample, "receive", peek=True):
due = [sp for sp in sample.objectValues("SamplePartition")
if workflow.getInfoFor(sp, 'review_state') == 'sample_due']
if sample_state == 'sample_due' and not due:
doActionFor(sample, 'receive')
def workflow_script_submit(self):
# Don't cascade. Shouldn't be submitting WSs directly for now,
# except edge cases where all analyses are already submitted,
# but self was held back until an analyst was assigned.
workflow = getToolByName(self, 'portal_workflow')
self.reindexObject(idxs=[
"review_state",
])
can_attach = True
for a in self.getAnalyses():
if workflow.getInfoFor(a, 'review_state') in \
('to_be_sampled', 'to_be_preserved', 'sample_due',
'sample_received', 'attachment_due', 'assigned',):
# Note: referenceanalyses and duplicateanalyses can still
# have review_state = "assigned".
can_attach = False
break
if can_attach:
doActionFor(self, 'attach')
def workflow_script_retract(self):
if skip(self, "retract"):
return
workflow = getToolByName(self, 'portal_workflow')
self.reindexObject(idxs=[
"review_state",
])
if not "retract all analyses" in self.REQUEST['workflow_skiplist']:
# retract all analyses in this self.
# (NB: don't retract if it's verified)
analyses = self.getAnalyses()
for analysis in analyses:
state = workflow.getInfoFor(analysis, 'review_state', '')
if state not in (
'attachment_due',
'to_be_verified',
):
continue
doActionFor(analysis, 'retract')
def __call__(self):
if 'transition' in self.request.form:
doActionFor(self.context, self.request.form['transition'])
## render header table
self.header_table = HeaderTableView(self.context, self.request)
## Create Sample Partitions table
parts_table = None
if not self.allow_edit:
p = SamplePartitionsView(self.context, self.request)
p.allow_edit = self.allow_edit
p.show_select_column = self.allow_edit
p.show_workflow_action_buttons = self.allow_edit
p.show_column_toggles = False
p.show_select_all_checkbox = False
p.review_states[0]['transitions'] = [{'id': 'empty'},] # none
parts_table = p.contents_table()
self.parts = parts_table
## Create Field and Lab Analyses tables
self.tables = {}
if not self.allow_edit:
for poc in POINTS_OF_CAPTURE:
if not self.context.getAnalyses({'getPointOfCapture': poc}):
continue
t = SampleAnalysesView(self.context,
self.request,
getPointOfCapture = poc,
sort_on = 'getServiceTitle')
t.form_id = "sample_%s_analyses" % poc
if poc == 'field':
t.review_states[0]['columns'].remove('DueDate')
t.show_column_toggles = False
t.review_states[0]['transitions'] = [{'id':'submit'},
{'id':'retract'},
{'id':'verify'}]
self.tables[POINTS_OF_CAPTURE.getValue(poc)] = t.contents_table()
return self.template()
def workflow_script_receive(self):
if skip(self, "receive"):
return
sample = self.aq_parent
workflow = getToolByName(self, 'portal_workflow')
sample_state = workflow.getInfoFor(sample, 'review_state')
self.setDateReceived(DateTime())
self.reindexObject(idxs=[
"getDateReceived",
])
# Transition our analyses
analyses = self.getBackReferences('AnalysisSamplePartition')
for analysis in analyses:
doActionFor(analysis, "receive")
# if all sibling partitions are received, promote sample
if not skip(sample, "receive", peek=True):
due = [
sp for sp in sample.objectValues("SamplePartition")
if workflow.getInfoFor(sp, 'review_state') == 'sample_due'
]
if sample_state == 'sample_due' and not due:
doActionFor(sample, 'receive')
def workflow_script_preserve(self):
workflow = getToolByName(self, 'portal_workflow')
sample = self.aq_parent
# Transition our analyses
analyses = self.getBackReferences('AnalysisSamplePartition')
if analyses:
for analysis in analyses:
doActionFor(analysis, "preserve")
# if all our siblings are now up to date, promote sample and ARs.
parts = sample.objectValues("SamplePartition")
if parts:
lower_states = ['to_be_sampled', 'to_be_preserved', ]
escalate = True
for part in parts:
if workflow.getInfoFor(part, 'review_state') in lower_states:
escalate = False
if escalate:
doActionFor(sample, "preserve")
for ar in sample.getAnalysisRequests():
doActionFor(ar, "preserve")
def workflow_script_preserve(self):
workflow = getToolByName(self, 'portal_workflow')
sample = self.aq_parent
# Transition our analyses
analyses = self.getBackReferences('AnalysisSamplePartition')
if analyses:
for analysis in analyses:
doActionFor(analysis, "preserve")
# if all our siblings are now up to date, promote sample and ARs.
parts = sample.objectValues("SamplePartition")
if parts:
lower_states = [
'to_be_sampled',
'to_be_preserved',
]
escalate = True
for part in parts:
if workflow.getInfoFor(part, 'review_state') in lower_states:
escalate = False
if escalate:
doActionFor(sample, "preserve")
for ar in sample.getAnalysisRequests():
doActionFor(ar, "preserve")
def _add_services_to_ar(self, ar, analyses):
#Add Services
service_uids = [i.split(':')[0] for i in analyses]
new_analyses = ar.setAnalyses(service_uids)
ar.setRequestID(ar.getId())
ar.reindexObject()
event.notify(ObjectInitializedEvent(ar))
ar.at_post_create_script()
SamplingWorkflowEnabled = \
self.bika_setup.getSamplingWorkflowEnabled()
wftool = getToolByName(self, 'portal_workflow')
# Create sample partitions
parts = [{'services': [],
'container':[],
'preservation':'',
'separate':False}]
sample = ar.getSample()
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']
else:
part = _createObjectByType("SamplePartition", sample, tmpID())
parts[_i]['object'] = part
container = None
preservation = p['preservation']
parts[_i]['prepreserved'] = False
part.unmarkCreationFlag()
part.edit(
Container=container,
Preservation=preservation,
)
part._renameAfterCreation()
if SamplingWorkflowEnabled:
wftool.doActionFor(part, 'sampling_workflow')
else:
wftool.doActionFor(part, 'no_sampling_workflow')
parts_and_services[part.id] = p['services']
if SamplingWorkflowEnabled:
wftool.doActionFor(ar, 'sampling_workflow')
else:
wftool.doActionFor(ar, 'no_sampling_workflow')
# 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)
part.edit(
Analyses=analyses,
)
for analysis in new_analyses:
analysis.setSamplePartition(part)
# 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)
for analysis in ar.objectValues('Analysis'):
doActionFor(analysis, lowest_state)
doActionFor(ar, lowest_state)
def create_analysisrequest(context, request, values):
"""Create an AR.
:param context the container in which the AR will be created (Client)
:param request the request object
:param values a dictionary containing fieldname/value pairs, which
will be applied. Some fields will have specific code to handle them,
and others will be directly written to the schema.
:return the new AR instance
Special keys present (or required) in the values dict, which are not present
in the schema:
- Partitions: data about partitions to be created, and the
analyses that are to be assigned to each.
- Prices: custom prices set in the HTML form.
- ResultsRange: Specification values entered in the HTML form.
"""
# Gather neccesary tools
workflow = getToolByName(context, 'portal_workflow')
bc = getToolByName(context, 'bika_catalog')
# Create new sample or locate the existing for secondary AR
if values['Sample']:
secondary = True
if ISample.providedBy(values['Sample']):
sample = values['Sample']
else:
sample = bc(UID=values['Sample'])[0].getObject()
samplingworkflow_enabled = sample.getSamplingWorkflowEnabled()
else:
secondary = False
samplingworkflow_enabled = context.bika_setup.getSamplingWorkflowEnabled()
sample = create_sample(context, request, values)
# Create the Analysis Request
ar = _createObjectByType('AnalysisRequest', context, tmpID())
ar.setSample(sample)
# processform renames the sample, this requires values to contain the Sample.
values['Sample'] = sample
ar.processForm(REQUEST=request, values=values)
# Object has been renamed
ar.edit(RequestID=ar.getId())
# Set initial AR state
workflow_action = 'sampling_workflow' if samplingworkflow_enabled \
else 'no_sampling_workflow'
workflow.doActionFor(ar, workflow_action)
# Set analysis request analyses
ar.setAnalyses(values['Analyses'],
prices=values.get("Prices", []),
specs=values.get('ResultsRange', []))
analyses = ar.getAnalyses(full_objects=True)
skip_receive = ['to_be_sampled', 'sample_due', 'sampled', 'to_be_preserved']
if secondary:
# Only 'sample_due' and 'sample_recieved' samples can be selected
# for secondary analyses
doActionFor(ar, 'sampled')
doActionFor(ar, 'sample_due')
sample_state = workflow.getInfoFor(sample, 'review_state')
if sample_state not in skip_receive:
doActionFor(ar, 'receive')
for analysis in analyses:
doActionFor(analysis, 'sample_due')
analysis_state = workflow.getInfoFor(analysis, 'review_state')
if analysis_state not in skip_receive:
doActionFor(analysis, 'receive')
if not secondary:
# Create sample partitions
partitions = []
for n, partition in enumerate(values['Partitions']):
# Calculate partition id
partition_prefix = sample.getId() + "-P"
partition_id = '%s%s' % (partition_prefix, n + 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
)
# now assign analyses to this partition.
obj = partition['object']
for analysis in analyses:
if analysis.getService().UID() in partition['services']:
analysis.setSamplePartition(obj)
partitions.append(partition)
# If Preservation is required for some partitions,
# and the SamplingWorkflow is disabled, we need
# to transition to to_be_preserved manually.
if not samplingworkflow_enabled:
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)
doActionFor(ar, lowest_state)
# Transition pre-preserved partitions
for p in partitions:
if 'prepreserved' in p and p['prepreserved']:
part = p['object']
state = workflow.getInfoFor(part, 'review_state')
if state == 'to_be_preserved':
workflow.doActionFor(part, 'preserve')
# Return the newly created Analysis Request
return ar
def create_analysisrequest(context, request, values):
"""Create an AR.
:param context the container in which the AR will be created (Client)
:param request the request object
:param values a dictionary containing fieldname/value pairs, which
will be applied. Some fields will have specific code to handle them,
and others will be directly written to the schema.
:return the new AR instance
Special keys present (or required) in the values dict, which are not present
in the schema:
- Partitions: data about partitions to be created, and the
analyses that are to be assigned to each.
- Prices: custom prices set in the HTML form.
- ResultsRange: Specification values entered in the HTML form.
"""
# Gather neccesary tools
workflow = getToolByName(context, 'portal_workflow')
bc = getToolByName(context, 'bika_catalog')
# Create new sample or locate the existing for secondary AR
if values['Sample']:
secondary = True
if ISample.providedBy(values['Sample']):
sample = values['Sample']
else:
sample = bc(UID=values['Sample'])[0].getObject()
samplingworkflow_enabled = sample.getSamplingWorkflowEnabled()
else:
secondary = False
samplingworkflow_enabled = context.bika_setup.getSamplingWorkflowEnabled(
)
sample = create_sample(context, request, values)
# Create the Analysis Request
ar = _createObjectByType('AnalysisRequest', context, tmpID())
ar.setSample(sample)
# processform renames the sample, this requires values to contain the Sample.
values['Sample'] = sample
ar.processForm(REQUEST=request, values=values)
# Object has been renamed
ar.edit(RequestID=ar.getId())
# Set initial AR state
workflow_action = 'sampling_workflow' if samplingworkflow_enabled \
else 'no_sampling_workflow'
workflow.doActionFor(ar, workflow_action)
# Set analysis request analyses
ar.setAnalyses(values['Analyses'],
prices=values.get("Prices", []),
specs=values.get('ResultsRange', []))
analyses = ar.getAnalyses(full_objects=True)
skip_receive = [
'to_be_sampled', 'sample_due', 'sampled', 'to_be_preserved'
]
if secondary:
# Only 'sample_due' and 'sample_recieved' samples can be selected
# for secondary analyses
doActionFor(ar, 'sampled')
doActionFor(ar, 'sample_due')
sample_state = workflow.getInfoFor(sample, 'review_state')
if sample_state not in skip_receive:
doActionFor(ar, 'receive')
for analysis in analyses:
doActionFor(analysis, 'sample_due')
analysis_state = workflow.getInfoFor(analysis, 'review_state')
if analysis_state not in skip_receive:
doActionFor(analysis, 'receive')
if not secondary:
# Create sample partitions
partitions = []
for n, partition in enumerate(values['Partitions']):
# Calculate partition id
partition_prefix = sample.getId() + "-P"
partition_id = '%s%s' % (partition_prefix, n + 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)
# now assign analyses to this partition.
obj = partition['object']
for analysis in analyses:
if analysis.getService().UID() in partition['services']:
analysis.setSamplePartition(obj)
partitions.append(partition)
# If Preservation is required for some partitions,
# and the SamplingWorkflow is disabled, we need
# to transition to to_be_preserved manually.
if not samplingworkflow_enabled:
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)
doActionFor(ar, lowest_state)
# Transition pre-preserved partitions
for p in partitions:
if 'prepreserved' in p and p['prepreserved']:
part = p['object']
state = workflow.getInfoFor(part, 'review_state')
if state == 'to_be_preserved':
workflow.doActionFor(part, 'preserve')
# Return the newly created Analysis Request
return ar
def __call__(self):
ar = self.context
workflow = getToolByName(self.context, 'portal_workflow')
if 'transition' in self.request.form:
doActionFor(self.context, self.request.form['transition'])
# Contacts get expanded for view
contact = self.context.getContact()
contacts = []
for cc in self.context.getCCContact():
contacts.append(cc)
if contact in contacts:
contacts.remove(contact)
ccemails = []
for cc in contacts:
ccemails.append(
"%s <<a href='mailto:%s'>%s</a>>" %
(cc.Title(), cc.getEmailAddress(), cc.getEmailAddress()))
# CC Emails become mailto links
emails = self.context.getCCEmails()
if isinstance(emails, str):
emails = emails and [
emails,
] or []
cc_emails = []
cc_hrefs = []
for cc in emails:
cc_emails.append(cc)
cc_hrefs.append("<a href='mailto:%s'>%s</a>" % (cc, cc))
# render header table
self.header_table = HeaderTableView(self.context, self.request)()
# Create Partitions View for this ARs sample
p = SamplePartitionsView(self.context.getSample(), self.request)
p.show_column_toggles = False
self.parts = p.contents_table()
# Create Field and Lab Analyses tables
self.tables = {}
for poc in POINTS_OF_CAPTURE:
if self.context.getAnalyses(getPointOfCapture=poc):
t = self.createAnalysesView(
ar,
self.request,
getPointOfCapture=poc,
show_categories=self.context.bika_setup.
getCategoriseAnalysisServices())
t.allow_edit = True
t.form_id = "%s_analyses" % poc
t.review_states[0]['transitions'] = [{
'id': 'submit'
}, {
'id': 'retract'
}, {
'id': 'verify'
}]
t.show_workflow_action_buttons = True
t.show_select_column = True
if getSecurityManager().checkPermission(EditFieldResults, self.context) \
and poc == 'field':
t.review_states[0]['columns'].remove('DueDate')
self.tables[POINTS_OF_CAPTURE.getValue(
poc)] = t.contents_table()
# Un-captured field analyses may cause confusion
if ar.getAnalyses(getPointOfCapture='field',
review_state=['sampled', 'sample_due']):
message = _("There are field analyses without submitted results.")
self.addMessage(message, 'info')
# Create QC Analyses View for this AR
show_cats = self.context.bika_setup.getCategoriseAnalysisServices()
qcview = self.createQCAnalyesView(ar,
self.request,
show_categories=show_cats)
qcview.allow_edit = False
qcview.show_select_column = False
qcview.show_workflow_action_buttons = False
qcview.form_id = "%s_qcanalyses"
qcview.review_states[0]['transitions'] = [{
'id': 'submit'
}, {
'id': 'retract'
}, {
'id': 'verify'
}]
self.qctable = qcview.contents_table()
# Create the ResultsInterpretation by department view
from dependencies.dependency import ARResultsInterpretationView
self.riview = ARResultsInterpretationView(ar, self.request)
# If a general retracted is done, rise a waring
if workflow.getInfoFor(ar, 'review_state') == 'sample_received':
allstatus = list()
for analysis in ar.getAnalyses():
status = workflow.getInfoFor(analysis.getObject(),
'review_state')
if status not in ['retracted', 'to_be_verified', 'verified']:
allstatus = []
break
else:
allstatus.append(status)
if len(allstatus) > 0:
self.addMessage("General Retract Done", 'warning')
# If is a retracted AR, show the link to child AR and show a warn msg
if workflow.getInfoFor(ar, 'review_state') == 'invalid':
childar = hasattr(ar, 'getChildAnalysisRequest') \
and ar.getChildAnalysisRequest() or None
message = _(
'These results have been withdrawn and are '
'listed here for trace-ability purposes. Please follow '
'the link to the retest')
if childar:
message = (message + " %s.") % childar.getRequestID()
else:
message = message + "."
self.addMessage(message, 'warning')
# If is an AR automatically generated due to a Retraction, show it's
# parent AR information
if hasattr(ar, 'getParentAnalysisRequest') \
and ar.getParentAnalysisRequest():
par = ar.getParentAnalysisRequest()
message = _(
'This Analysis Request has been '
'generated automatically due to '
'the retraction of the Analysis '
'Request ${retracted_request_id}.',
mapping={'retracted_request_id': par.getRequestID()})
self.addMessage(message, 'info')
self.renderMessages()
return self.template()
def __call__(self):
ar = self.context
workflow = getToolByName(self.context, 'portal_workflow')
if 'transition' in self.request.form:
doActionFor(self.context, self.request.form['transition'])
# Contacts get expanded for view
contact = self.context.getContact()
contacts = []
for cc in self.context.getCCContact():
contacts.append(cc)
if contact in contacts:
contacts.remove(contact)
ccemails = []
for cc in contacts:
ccemails.append("%s <<a href='mailto:%s'>%s</a>>"
% (cc.Title(), cc.getEmailAddress(), cc.getEmailAddress()))
# CC Emails become mailto links
emails = self.context.getCCEmails()
if isinstance(emails, str):
emails = emails and [emails, ] or []
cc_emails = []
cc_hrefs = []
for cc in emails:
cc_emails.append(cc)
cc_hrefs.append("<a href='mailto:%s'>%s</a>" % (cc, cc))
# render header table
self.header_table = HeaderTableView(self.context, self.request)()
# Create Partitions View for this ARs sample
p = SamplePartitionsView(self.context.getSample(), self.request)
p.show_column_toggles = False
self.parts = p.contents_table()
# Create Field and Lab Analyses tables
self.tables = {}
for poc in POINTS_OF_CAPTURE:
if self.context.getAnalyses(getPointOfCapture=poc):
t = self.createAnalysesView(ar,
self.request,
getPointOfCapture=poc,
show_categories=self.context.bika_setup.getCategoriseAnalysisServices())
t.allow_edit = True
t.form_id = "%s_analyses" % poc
t.review_states[0]['transitions'] = [{'id': 'submit'},
{'id': 'retract'},
{'id': 'verify'}]
t.show_workflow_action_buttons = True
t.show_select_column = True
if getSecurityManager().checkPermission(EditFieldResults, self.context) \
and poc == 'field':
t.review_states[0]['columns'].remove('DueDate')
self.tables[POINTS_OF_CAPTURE.getValue(poc)] = t.contents_table()
# Un-captured field analyses may cause confusion
if ar.getAnalyses(getPointOfCapture='field',
review_state=['sampled', 'sample_due']):
message = _("There are field analyses without submitted results.")
self.addMessage(message, 'info')
# Create QC Analyses View for this AR
show_cats = self.context.bika_setup.getCategoriseAnalysisServices()
qcview = self.createQCAnalyesView(ar,
self.request,
show_categories=show_cats)
qcview.allow_edit = False
qcview.show_select_column = False
qcview.show_workflow_action_buttons = False
qcview.form_id = "%s_qcanalyses"
qcview.review_states[0]['transitions'] = [{'id': 'submit'},
{'id': 'retract'},
{'id': 'verify'}]
self.qctable = qcview.contents_table()
# Create the ResultsInterpretation by department view
from dependencies.dependency import ARResultsInterpretationView
self.riview = ARResultsInterpretationView(ar, self.request)
# If a general retracted is done, rise a waring
if workflow.getInfoFor(ar, 'review_state') == 'sample_received':
allstatus = list()
for analysis in ar.getAnalyses():
status = workflow.getInfoFor(analysis.getObject(), 'review_state')
if status not in ['retracted','to_be_verified','verified']:
allstatus = []
break
else:
allstatus.append(status)
if len(allstatus) > 0:
self.addMessage("General Retract Done", 'warning')
# If is a retracted AR, show the link to child AR and show a warn msg
if workflow.getInfoFor(ar, 'review_state') == 'invalid':
childar = hasattr(ar, 'getChildAnalysisRequest') \
and ar.getChildAnalysisRequest() or None
message = _('These results have been withdrawn and are '
'listed here for trace-ability purposes. Please follow '
'the link to the retest')
if childar:
message = (message + " %s.") % childar.getRequestID()
else:
message = message + "."
self.addMessage(message, 'warning')
# If is an AR automatically generated due to a Retraction, show it's
# parent AR information
if hasattr(ar, 'getParentAnalysisRequest') \
and ar.getParentAnalysisRequest():
par = ar.getParentAnalysisRequest()
message = _('This Analysis Request has been '
'generated automatically due to '
'the retraction of the Analysis '
'Request ${retracted_request_id}.',
mapping={'retracted_request_id': par.getRequestID()})
self.addMessage(message, 'info')
self.renderMessages()
return self.template()
def workflow_action_submit(self):
form = self.request.form
rc = getToolByName(self.context, REFERENCE_CATALOG)
action, came_from = WorkflowAction._get_form_workflow_action(self)
checkPermission = self.context.portal_membership.checkPermission
if not isActive(self.context):
message = _('Item is inactive.')
self.context.plone_utils.addPortalMessage(message, 'info')
self.request.response.redirect(self.context.absolute_url())
return
# calcs.js has kept item_data and form input interim values synced,
# so the json strings from item_data will be the same as the form values
item_data = {}
if 'item_data' in form:
if isinstance(form['item_data'], list):
for i_d in form['item_data']:
for i, d in json.loads(i_d).items():
item_data[i] = d
else:
item_data = json.loads(form['item_data'])
selected_analyses = WorkflowAction._get_selected_items(self)
results = {}
hasInterims = {}
# check that the form values match the database
# save them if not.
for uid, result in self.request.form.get('Result', [{}])[0].items():
# if the AR has ReportDryMatter set, get dry_result from form.
dry_result = ''
if hasattr(self.context, 'getReportDryMatter') \
and self.context.getReportDryMatter():
for k, v in self.request.form['ResultDM'][0].items():
if uid == k:
dry_result = v
break
if uid in selected_analyses:
analysis = selected_analyses[uid]
else:
analysis = rc.lookupObject(uid)
if not analysis:
# ignore result if analysis object no longer exists
continue
results[uid] = result
interimFields = item_data[uid]
if len(interimFields) > 0:
hasInterims[uid] = True
else:
hasInterims[uid] = False
retested = 'retested' in form and uid in form['retested']
remarks = form.get('Remarks', [{}, ])[0].get(uid, '')
# Don't save uneccessary things
# https://github.com/bikalabs/Bika-LIMS/issues/766:
# Somehow, using analysis.edit() fails silently when
# logged in as Analyst.
if analysis.getInterimFields() != interimFields or \
analysis.getRetested() != retested or \
analysis.getRemarks() != remarks:
analysis.setInterimFields(interimFields)
analysis.setRetested(retested)
analysis.setRemarks(remarks)
# save results separately, otherwise capture date is rewritten
if analysis.getResult() != result or \
analysis.getResultDM() != dry_result:
analysis.setResultDM(dry_result)
analysis.setResult(result)
methods = self.request.form.get('Method', [{}])[0]
instruments = self.request.form.get('Instrument', [{}])[0]
analysts = self.request.form.get('Analyst', [{}])[0]
uncertainties = self.request.form.get('Uncertainty', [{}])[0]
dlimits = self.request.form.get('DetectionLimit', [{}])[0]
# discover which items may be submitted
submissable = []
for uid, analysis in selected_analyses.items():
analysis_active = isActive(analysis)
# Need to save the instrument?
if uid in instruments and analysis_active:
# TODO: Add SetAnalysisInstrument permission
# allow_setinstrument = sm.checkPermission(SetAnalysisInstrument)
allow_setinstrument = True
# ---8<-----
if allow_setinstrument == True:
# The current analysis allows the instrument regards
# to its analysis service and method?
if (instruments[uid]==''):
previnstr = analysis.getInstrument()
if previnstr:
previnstr.removeAnalysis(analysis)
analysis.setInstrument(None);
elif analysis.isInstrumentAllowed(instruments[uid]):
previnstr = analysis.getInstrument()
if previnstr:
previnstr.removeAnalysis(analysis)
analysis.setInstrument(instruments[uid])
instrument = analysis.getInstrument()
instrument.addAnalysis(analysis)
# Need to save the method?
if uid in methods and analysis_active:
# TODO: Add SetAnalysisMethod permission
# allow_setmethod = sm.checkPermission(SetAnalysisMethod)
allow_setmethod = True
# ---8<-----
if allow_setmethod == True and analysis.isMethodAllowed(methods[uid]):
analysis.setMethod(methods[uid])
# Need to save the analyst?
if uid in analysts and analysis_active:
analysis.setAnalyst(analysts[uid])
# Need to save the uncertainty?
if uid in uncertainties and analysis_active:
analysis.setUncertainty(uncertainties[uid])
# Need to save the detection limit?
if analysis_active:
analysis.setDetectionLimitOperand(dlimits.get(uid, None))
if uid not in results or not results[uid]:
continue
can_submit = True
# guard_submit does a lot of the same stuff, too.
# the code there has also been commented.
# we must find a better way to allow dependencies to control
# this process.
# for dependency in analysis.getDependencies():
# dep_state = workflow.getInfoFor(dependency, 'review_state')
# if hasInterims[uid]:
# if dep_state in ('to_be_sampled', 'to_be_preserved',
# 'sample_due', 'sample_received',
# 'attachment_due', 'to_be_verified',):
# can_submit = False
# break
# else:
# if dep_state in ('to_be_sampled', 'to_be_preserved',
# 'sample_due', 'sample_received',):
# can_submit = False
# break
if can_submit and analysis not in submissable:
submissable.append(analysis)
# and then submit them.
for analysis in submissable:
doActionFor(analysis, 'submit')
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, 'info')
if checkPermission(EditResults, self.context):
self.destination_url = self.context.absolute_url() + "/manage_results"
else:
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
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")
# Sample_id
if 'Sample' in request:
try:
sample = resolve_request_lookup(context, request, 'Sample')[0].getObject()
except IndexError:
raise Exception("Sample not found")
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())
event.notify(ObjectInitializedEvent(sample))
sample.at_post_create_script()
if SamplingWorkflowEnabled:
wftool.doActionFor(sample, 'sampling_workflow')
else:
wftool.doActionFor(sample, 'no_sampling_workflow')
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.UID())
ar._renameAfterCreation()
ret['ar_id'] = ar.getId()
brains = resolve_request_lookup(context, request, 'Services')
service_uids = [p.UID for p in brains]
new_analyses = ar.setAnalyses(service_uids, specs=specs)
ar.setRequestID(ar.getId())
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()
if SamplingWorkflowEnabled:
wftool.doActionFor(part, 'sampling_workflow')
else:
wftool.doActionFor(part, 'no_sampling_workflow')
parts_and_services[part.id] = p['services']
if SamplingWorkflowEnabled:
wftool.doActionFor(ar, 'sampling_workflow')
else:
wftool.doActionFor(ar, 'no_sampling_workflow')
# 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)
part.edit(
Analyses=analyses,
)
for analysis in new_analyses:
analysis.setSamplePartition(part)
# 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)
for analysis in ar.objectValues('Analysis'):
doActionFor(analysis, lowest_state)
doActionFor(ar, lowest_state)
# receive secondary AR
if request.get('Sample_id', ''):
doActionFor(ar, 'sampled')
doActionFor(ar, 'sample_due')
not_receive = ['to_be_sampled', 'sample_due', 'sampled',
'to_be_preserved']
sample_state = wftool.getInfoFor(sample, 'review_state')
if sample_state not in not_receive:
doActionFor(ar, 'receive')
for analysis in ar.getAnalyses(full_objects=1):
doActionFor(analysis, 'sampled')
doActionFor(analysis, 'sample_due')
if sample_state not in not_receive:
doActionFor(analysis, 'receive')
if self.unused:
raise BadRequest("The following request fields were not used: %s. Request aborted." % self.unused)
return ret
def create_analysisrequest(
context,
request,
values,
analyses=[],
partitions=None,
specifications=None,
prices=None
):
# Gather neccesary tools
workflow = getToolByName(context, 'portal_workflow')
bc = getToolByName(context, 'bika_catalog')
# Create new sample or locate the existing for secondary AR
if values.get('Sample'):
secondary = True
if ISample.providedBy(values['Sample']):
sample = values['Sample']
else:
sample = bc(UID=values['Sample'])[0].getObject()
workflow_enabled = sample.getSamplingWorkflowEnabled()
else:
secondary = False
workflow_enabled = context.bika_setup.getSamplingWorkflowEnabled()
sample = create_sample(context, request, values)
# Create the Analysis Request
ar = _createObjectByType('AnalysisRequest', context, tmpID())
ar.setSample(sample)
# processform renames the sample, this requires values to contain the Sample.
values['Sample'] = sample
ar.processForm(REQUEST=request, values=values)
# Object has been renamed
ar.edit(RequestID=ar.getId())
# Set initial AR state
workflow_action = 'sampling_workflow' if workflow_enabled \
else 'no_sampling_workflow'
workflow.doActionFor(ar, workflow_action)
# Set analysis request analyses
analyses = ar.setAnalyses(analyses, prices=prices, specs=specifications)
if secondary:
# Only 'sample_due' and 'sample_recieved' samples can be selected
# for secondary analyses
doActionFor(ar, 'sample')
doActionFor(ar, 'sample_due')
sample_state = workflow.getInfoFor(sample, 'review_state')
if sample_state == 'sample_received':
doActionFor(ar, 'receive')
for analysis in ar.getAnalyses(full_objects=1):
doActionFor(analysis, 'sample')
doActionFor(analysis, 'sample_due')
analysis_transition_ids = [t['id'] for t in workflow.getTransitionsFor(analysis)]
if 'receive' in analysis_transition_ids and sample_state == 'sample_received':
doActionFor(analysis, 'receive')
if not secondary:
# Create sample partitions
if not partitions:
partitions = [{'services':analyses}]
for n, partition in enumerate(partitions):
# Calculate partition id
partition_prefix = sample.getId() + "-P"
partition_id = '%s%s' % (partition_prefix, n + 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
)
# If Preservation is required for some partitions,
# and the SamplingWorkflow is disabled, we need
# to transition to to_be_preserved manually.
if not workflow_enabled:
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)
doActionFor(ar, lowest_state)
# Transition pre-preserved partitions
for p in partitions:
if 'prepreserved' in p and p['prepreserved']:
part = p['object']
state = workflow.getInfoFor(part, 'review_state')
if state == 'to_be_preserved':
workflow.doActionFor(part, 'preserve')
# Return the newly created Analysis Request
return ar
def workflow_action_submit(self):
form = self.request.form
rc = getToolByName(self.context, REFERENCE_CATALOG)
action, came_from = WorkflowAction._get_form_workflow_action(self)
checkPermission = self.context.portal_membership.checkPermission
if not isActive(self.context):
message = _('Item is inactive.')
self.context.plone_utils.addPortalMessage(message, 'info')
self.request.response.redirect(self.context.absolute_url())
return
# calcs.js has kept item_data and form input interim values synced,
# so the json strings from item_data will be the same as the form values
item_data = {}
if 'item_data' in form:
if isinstance(form['item_data'], list):
for i_d in form['item_data']:
for i, d in json.loads(i_d).items():
item_data[i] = d
else:
item_data = json.loads(form['item_data'])
selected_analyses = WorkflowAction._get_selected_items(self)
results = {}
hasInterims = {}
# check that the form values match the database
# save them if not.
for uid, result in self.request.form.get('Result', [{}])[0].items():
# if the AR has ReportDryMatter set, get dry_result from form.
dry_result = ''
if hasattr(self.context, 'getReportDryMatter') \
and self.context.getReportDryMatter():
for k, v in self.request.form['ResultDM'][0].items():
if uid == k:
dry_result = v
break
if uid in selected_analyses:
analysis = selected_analyses[uid]
else:
analysis = rc.lookupObject(uid)
if not analysis:
# ignore result if analysis object no longer exists
continue
results[uid] = result
interimFields = item_data[uid]
if len(interimFields) > 0:
hasInterims[uid] = True
else:
hasInterims[uid] = False
retested = 'retested' in form and uid in form['retested']
remarks = form.get('Remarks', [
{},
])[0].get(uid, '')
# Don't save uneccessary things
# https://github.com/bikalabs/Bika-LIMS/issues/766:
# Somehow, using analysis.edit() fails silently when
# logged in as Analyst.
if analysis.getInterimFields() != interimFields or \
analysis.getRetested() != retested or \
analysis.getRemarks() != remarks:
analysis.setInterimFields(interimFields)
analysis.setRetested(retested)
analysis.setRemarks(remarks)
# save results separately, otherwise capture date is rewritten
if analysis.getResult() != result or \
analysis.getResultDM() != dry_result:
analysis.setResultDM(dry_result)
analysis.setResult(result)
methods = self.request.form.get('Method', [{}])[0]
instruments = self.request.form.get('Instrument', [{}])[0]
analysts = self.request.form.get('Analyst', [{}])[0]
uncertainties = self.request.form.get('Uncertainty', [{}])[0]
dlimits = self.request.form.get('DetectionLimit', [{}])[0]
# discover which items may be submitted
submissable = []
for uid, analysis in selected_analyses.items():
analysis_active = isActive(analysis)
# Need to save the instrument?
if uid in instruments and analysis_active:
# TODO: Add SetAnalysisInstrument permission
# allow_setinstrument = sm.checkPermission(SetAnalysisInstrument)
allow_setinstrument = True
# ---8<-----
if allow_setinstrument == True:
# The current analysis allows the instrument regards
# to its analysis service and method?
if (instruments[uid] == ''):
previnstr = analysis.getInstrument()
if previnstr:
previnstr.removeAnalysis(analysis)
analysis.setInstrument(None)
elif analysis.isInstrumentAllowed(instruments[uid]):
previnstr = analysis.getInstrument()
if previnstr:
previnstr.removeAnalysis(analysis)
analysis.setInstrument(instruments[uid])
instrument = analysis.getInstrument()
instrument.addAnalysis(analysis)
# Need to save the method?
if uid in methods and analysis_active:
# TODO: Add SetAnalysisMethod permission
# allow_setmethod = sm.checkPermission(SetAnalysisMethod)
allow_setmethod = True
# ---8<-----
if allow_setmethod == True and analysis.isMethodAllowed(
methods[uid]):
analysis.setMethod(methods[uid])
# Need to save the analyst?
if uid in analysts and analysis_active:
analysis.setAnalyst(analysts[uid])
# Need to save the uncertainty?
if uid in uncertainties and analysis_active:
analysis.setUncertainty(uncertainties[uid])
# Need to save the detection limit?
if analysis_active:
analysis.setDetectionLimitOperand(dlimits.get(uid, None))
if uid not in results or not results[uid]:
continue
can_submit = True
# guard_submit does a lot of the same stuff, too.
# the code there has also been commented.
# we must find a better way to allow dependencies to control
# this process.
# for dependency in analysis.getDependencies():
# dep_state = workflow.getInfoFor(dependency, 'review_state')
# if hasInterims[uid]:
# if dep_state in ('to_be_sampled', 'to_be_preserved',
# 'sample_due', 'sample_received',
# 'attachment_due', 'to_be_verified',):
# can_submit = False
# break
# else:
# if dep_state in ('to_be_sampled', 'to_be_preserved',
# 'sample_due', 'sample_received',):
# can_submit = False
# break
if can_submit and analysis not in submissable:
submissable.append(analysis)
# and then submit them.
for analysis in submissable:
doActionFor(analysis, 'submit')
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, 'info')
if checkPermission(EditResults, self.context):
self.destination_url = self.context.absolute_url(
) + "/manage_results"
else:
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)