def generate_delivery_pdf(context, ars_or_samples):
if not ars_or_samples:
logger.warn("No Analysis Requests or Samples provided")
return
if ISample.providedBy(ars_or_samples) or \
IAnalysisRequest.providedBy(ars_or_samples):
return generate_delivery_pdf(context, [ars_or_samples])
if not isinstance(ars_or_samples, list):
logger.warn("Type not supported: {}".format(repr(ars_or_samples)))
return
html = DeliveryFormPdf(context,
context.REQUEST,
analysis_requests=ars_or_samples).template()
html = safe_unicode(html).encode("utf-8")
filename = "delivery"
pdf_fn = tempfile.mktemp(suffix=".pdf")
pdf = createPdf(htmlreport=html, outfile=pdf_fn)
if not pdf:
ar_ids = map(lambda ar: ar.id, ars_or_samples)
logger.warn(
"Unable to generate the PDF of delivery form for {}".format(
' '.join(ar_ids)))
return None
def _attach_to_ar(pdf, ar_brain_or_obj):
ar = api.get_object(ar_brain_or_obj)
attid = ar.aq_parent.generateUniqueId('Attachment')
att = _createObjectByType("Attachment", ar.aq_parent, attid)
att.setAttachmentFile(open(pdf_fn))
# Awkward workaround to rename the file
attf = att.getAttachmentFile()
attf.filename = '%s.pdf' % filename
att.setAttachmentFile(attf)
att.unmarkCreationFlag()
renameAfterCreation(att)
atts = ar.getAttachment() + [att] if ar.getAttachment() else [att]
atts = [a.UID() for a in atts]
ar.setAttachment(atts)
for ar_or_sample in ars_or_samples:
# Attach the pdf to the Analysis Request
if ISample.providedBy(ar_or_sample):
for ar in ar_or_sample.getAnalysisRequests():
_attach_to_ar(pdf, ar)
elif IAnalysisRequest.providedBy(ar_or_sample):
_attach_to_ar(pdf, ar_or_sample)
return pdf_fn
def __init__(self, context, request):
super(RequisitionFormPdf, self).__init__(context, request)
self.analysis_requests = []
if ISample.providedBy(context):
self.analysis_requests = context.getAnalysisRequests()
elif IAnalysisRequest.providedBy(context):
self.analysis_requests = [context]
def __init__(self, context, request, analysis_requests=None):
super(DeliveryFormPdf, self).__init__(context, request)
self.analysis_requests = analysis_requests
if not self.analysis_requests:
if ISample.providedBy(context):
self.analysis_requests = context.getAnalysisRequests()
elif IAnalysisRequest.providedBy(context):
self.analysis_requests = [context]
def get_sample(instance):
"""Returns the sample associated to this instance, if any. Otherwise,
returns None"""
if ISample.providedBy(instance):
return instance
if IAnalysisRequest.providedBy(instance):
return get_sample(instance.getSample())
if ISamplePartition.providedBy(instance):
return get_sample(instance.aq_parent)
return None
def __init__(self, context, request, analysis_requests=None, lab_department=None):
super(InternalDeliveryFormPdf, self).__init__(context, request)
self.analysis_requests = analysis_requests
self.lab_department = lab_department
if not self.analysis_requests:
if ISample.providedBy(context):
self.analysis_requests = context.getAnalysisRequests()
elif IAnalysisRequest.providedBy(context):
self.analysis_requests = [context]
def folderitems(self, full_objects=False):
items = BikaListingView.folderitems(self)
bsc = getToolByName(self.context, 'bika_setup_catalog')
brains = bsc(portal_type='SampleType', inactive_state='active')
biospecimen_types = [{
'ResultValue': brain.UID,
'ResultText': brain.title
} for brain in brains]
ret = []
for x, item in enumerate(items):
if not items[x].has_key('obj'):
continue
obj = items[x]['obj']
if not ISample.providedBy(obj):
continue
items[x]['Type'] = obj.getSampleType() and obj.getSampleType(
).Title() or ''
items[x]['Volume'] = obj.getField('Volume').get(obj)
items[x]['Unit'] = VOLUME_UNITS[0]['ResultText']
items[x]['SubjectID'] = obj.getField('SubjectID').get(obj)
kit = obj.getField('Kit').get(obj)
project = obj.getField('Project').get(obj)
items[x]['Kit'] = kit
items[x]['Project'] = project
if project:
items[x]['replace']['Project'] = \
'<a href="%s">%s</a>' % (project.absolute_url(),
project.Title())
if kit:
items[x]['replace']['Kit'] = \
'<a href="%s">%s</a>' % (kit.absolute_url(), kit.Title())
# TODO: IF STATUS IS RECEIVED EXECUTE THIS
# items[x]['replace']['Type'] = \
# '<a href="%s">%s</a>' % (obj.getSampleType().absolute_url(),
# obj.getSampleType().Title())
items[x]['Barcode'] = obj.getField('Barcode').get(obj)
items[x]['replace']['Title'] = "<a href='%s'>%s</a>" % \
(items[x]['url'], items[x]['Title'])
# TODO: SPECIFY OBJ STATES WHERE USER CAN EDIT BARCODE
if self.allow_edit and isActive(self.context) and \
getSecurityManager().checkPermission(ManageProjects, obj):
if items[x]['review_state'] == "sample_registered":
items[x]['allow_edit'] = ['Type', 'Barcode']
items[x]['choices']['Type'] = biospecimen_types
elif items[x]['review_state'] == "sample_due":
items[x]['allow_edit'] = ['SubjectID', 'Volume', 'Unit']
if not items[x]['Unit']:
items[x]['choices']['Unit'] = VOLUME_UNITS
ret.append(item)
return ret
def after_process(obj):
"""Event fired after process (Process) transition is triggered
"""
logger.info("*** Custom after_process transition ***")
if IAnalysisRequest.providedBy(obj):
# Generate a derived AR (and Sample) for every single partition
create_requests_from_partitions(obj)
elif ISample.providedBy(obj):
# We do not permit partitioning directly from Sample!
# sample_events._cascade_transition(obj, 'process')
pass
def after_send_to_lab(obj):
""" Event fired after send_to_lab transition is triggered.
"""
logger.info("*** Custom after_send_to_lab transition ***")
if IAnalysisRequest.providedBy(obj):
# Promote to sample
sample = obj.getSample()
if sample:
doActionFor(sample, 'send_to_lab')
elif ISample.providedBy(obj):
sample_events._cascade_transition(obj, 'send_to_lab')
def workflow_action_download_requisition(self):
if ISample.providedBy(self.context):
# TODO, Concatenate the PDFs of all ocntaine ARs
logger.info("This is a sample!")
elif IAnalysisRequest.providedBy(self.context):
# Redirect to the requisition PDF
req_att = self.get_last_requisition_attachment(self.context)
if not req_att:
return
self.destination_url = '{}/at_download/AttachmentFile'.format(
req_att.absolute_url())
self.request.response.redirect(self.destination_url)
def after_send_to_pot(obj):
"""Event fired after sending to point of testing
"""
logger.info("*** Custom after_send_to_pot transition ***")
if IAnalysisRequest.providedBy(obj):
# Transition Analyses to sample_due
ans = obj.getAnalyses(full_objects=True, cancellation_state='active')
for analysis in ans:
doActionFor(analysis, 'sample_due')
# Promote to parent AR
_promote_cascade(obj, "send_to_pot")
elif ISample.providedBy(obj):
sample_events._cascade_transition(obj, 'send_to_pot')
def get_sample_from_values(context, values):
"""values may contain a UID or a direct Sample object.
"""
if ISample.providedBy(values['Sample']):
sample = values['Sample']
else:
bc = getToolByName(context, 'bika_catalog')
brains = bc(UID=values['Sample'])
if brains:
sample = brains[0].getObject()
else:
raise RuntimeError(
"create_analysisrequest: invalid sample value provided. values=%s" % values)
if not sample:
raise RuntimeError(
"create_analysisrequest: invalid sample value provided. values=%s" % values)
def generate_requisition_pdf(ar_or_sample):
if not ar_or_sample:
logger.warn("No Analysis Request or Sample provided")
return
if ISample.providedBy(ar_or_sample):
for ar in ar_or_sample.getAnalysisRequests():
generate_requisition_pdf(ar)
return
elif not IAnalysisRequest.providedBy(ar_or_sample):
logger.warn("Type not supported: {}".format(repr(ar_or_sample)))
return
html = RequisitionFormPdf(ar_or_sample, ar_or_sample.REQUEST).template()
html = safe_unicode(html).encode('utf-8')
filename = '%s-requisition' % ar_or_sample.id
pdf_fn = tempfile.mktemp(suffix=".pdf")
pdf = createPdf(htmlreport=html, outfile=pdf_fn)
if not pdf:
logger.warn(
"Unable to generate the PDF of requisition form for {}".format(
ar_or_sample.id))
return
# Attach the pdf to the Analysis Request
attid = ar_or_sample.aq_parent.generateUniqueId('Attachment')
att = _createObjectByType("Attachment", ar_or_sample.aq_parent, attid)
att.setAttachmentFile(open(pdf_fn))
att.setReportOption('i') # Ignore in report
# Try to assign the Requisition Attachment Type
query = dict(portal_type='AttachmentType', title='Requisition')
brains = api.search(query, 'bika_setup_catalog')
if brains:
att_type = api.get_object(brains[0])
att.setAttachmentType(att_type)
# Awkward workaround to rename the file
attf = att.getAttachmentFile()
attf.filename = '%s.pdf' % filename
att.setAttachmentFile(attf)
att.unmarkCreationFlag()
renameAfterCreation(att)
atts = ar_or_sample.getAttachment() + [att] if \
ar_or_sample.getAttachment() else [att]
atts = [a.UID() for a in atts]
ar_or_sample.setAttachment(atts)
os.remove(pdf_fn)
def get_sample_from_values(context, values):
"""values may contain a UID or a direct Sample object.
"""
if ISample.providedBy(values['Sample']):
sample = values['Sample']
else:
bc = getToolByName(context, 'bika_catalog')
brains = bc(UID=values['Sample'])
if brains:
sample = brains[0].getObject()
else:
raise RuntimeError(
"create_analysisrequest: invalid sample value provided. values=%s" % values)
if not sample:
raise RuntimeError(
"create_analysisrequest: invalid sample value provided. values=%s" % values)
return sample
def after_receive(obj):
"""Event fired after receive (Process) transition is triggered
"""
logger.info("*** Custom after_receive transition ***")
if IAnalysisRequest.providedBy(obj):
# Transition Analyses to sample_due
ans = obj.getAnalyses(full_objects=True, cancellation_state='active')
for analysis in ans:
doActionFor(analysis, 'receive')
# Promote to parent AR
_promote_cascade(obj, "receive")
elif ISample.providedBy(obj):
sample_events._cascade_transition(obj, 'receive')
def after_deliver(obj):
""" Event fired after delivery transition is triggered.
"""
logger.info("*** Custom after_deliver transition ***")
if IAnalysisRequest.providedBy(obj):
# Promote to sample
sample = obj.getSample()
if sample:
doActionFor(sample, 'deliver')
obj.reindexObject(idxs=[
"getDateReceived",
])
elif ISample.providedBy(obj):
obj.setDateReceived(DateTime())
obj.reindexObject(idxs=[
"getDateReceived",
])
sample_events._cascade_transition(obj, 'deliver')
def after_no_sampling_workflow(obj):
""" Event fired for no_sampling_workflow that makes the status of the
Analysis request or Sample to become sample_ordered
"""
logger.info("*** Custom after_no_sampling_workflow (order) transition ***")
# Generate the requisition report
if IAnalysisRequest.providedBy(obj):
# Transition Analyses to sample_due
ans = obj.getAnalyses(full_objects=True, cancellation_state='active')
for analysis in ans:
doActionFor(analysis, 'no_sampling_workflow')
# Promote to sample
sample = obj.getSample()
if sample:
doActionFor(sample, 'no_sampling_workflow')
# Generate the delivery pdf
generate_requisition_pdf(obj)
# Set specifications by default
sample_type = obj.getSampleType()
specs = _api.get_field_value(sample_type,
"DefaultAnalysisSpecifications", None)
if specs:
obj.setSpecification(api.get_object(specs))
else:
# Find out suitable specs by Sample Type name
sample_type = obj.getSampleType().Title()
specs_title = "{} - calculated".format(sample_type)
query = dict(portal_type="AnalysisSpec", title=specs_title)
specs = api.search(query, 'bika_setup_catalog')
if specs:
obj.setSpecification(api.get_object(specs[0]))
elif ISample.providedBy(obj):
sample_events._cascade_transition(obj, 'no_sampling_workflow')
def folderitems(self, full_objects=False):
items = super(AliquotsView, self).folderitems(self)
linked_samples = self.context.getBackReferences("SampleSample")
new_items = []
for x, item in enumerate(items):
if not items[x].has_key('obj'):
continue
obj = items[x]['obj']
if not ISample.providedBy(obj) or obj not in linked_samples:
continue
items[x]['Type'] = obj.getSampleType() and obj.getSampleType(
).Title() or ''
items[x]['Volume'] = obj.getField('Volume').get(obj)
items[x]['Unit'] = VOLUME_UNITS[0]['ResultText']
items[x]['SubjectID'] = obj.getField('SubjectID').get(obj)
kit = obj.getField('Kit').get(obj)
project = obj.getField('Project').get(obj)
items[x]['Kit'] = kit
items[x]['Project'] = project
if project:
items[x]['replace']['Project'] = \
'<a href="%s">%s</a>' % (project.absolute_url(),
project.Title())
if kit:
items[x]['replace']['Kit'] = \
'<a href="%s">%s</a>' % (kit.absolute_url(), kit.Title())
items[x]['replace']['Type'] = \
'<a href="%s">%s</a>' % (obj.getSampleType().absolute_url(),
obj.getSampleType().Title())
items[x]['Barcode'] = obj.getField('Barcode').get(obj)
items[x]['replace']['Title'] = "<a href='%s'>%s</a>" % \
(items[x]['url'], items[x]['Title'])
new_items.append(item)
return new_items
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)
# We need to send a list of service UIDS to setAnalyses function.
# But we may have received a list of titles, list of UIDS,
# list of keywords or list of service objects!
service_uids = []
for obj in values['Analyses']:
uid = False
# service objects
if hasattr(obj, 'portal_type') and obj.portal_type == 'AnalysisService':
uid = obj.UID()
# Analysis objects (shortcut for eg copying analyses from other AR)
elif hasattr(obj, 'portal_type') and obj.portal_type == 'Analysis':
uid = obj.getService()
# Maybe already UIDs.
if not uid:
bsc = getToolByName(context, 'bika_setup_catalog')
brains = bsc(portal_type='AnalysisService', UID=obj)
if brains:
uid = brains[0].UID
# Maybe already UIDs.
if not uid:
bsc = getToolByName(context, 'bika_setup_catalog')
brains = bsc(portal_type='AnalysisService', title=obj)
if brains:
uid = brains[0].UID
if uid:
service_uids.append(uid)
else:
logger.info("In analysisrequest.add.create_analysisrequest: cannot "
"find uid of this service: %s" % obj)
# Set analysis request analyses
ar.setAnalyses(service_uids,
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,
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 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['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
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 create_analysisrequest(
context,
request,
values, # {field: value, ...}
analyses=[],
# uid, service or analysis; list of uids, services or analyses
partitions=None,
# list of dictionaries with container, preservation etc)
specifications=None,
prices=None):
"""This is meant for general use and should do everything necessary to
create and initialise the AR and it's requirements.
XXX The ar-add form's ajaxAnalysisRequestSubmit should be calling this.
"""
# Gather neccesary tools
workflow = getToolByName(context, 'portal_workflow')
bc = getToolByName(context, 'bika_catalog')
# It's necessary to modify these and we don't want to pollute the
# parent's data
values = values.copy()
# Create new sample or locate the existing for secondary AR
if not values.get('Sample', False):
secondary = False
workflow_enabled = context.bika_setup.getSamplingWorkflowEnabled()
sample = create_sample(context, request, values)
else:
secondary = True
if ISample.providedBy(values['Sample']):
sample = values['Sample']
else:
brains = bc(UID=values['Sample'])
if brains:
sample = brains[0].getObject()
if not sample:
raise RuntimeError(
"create_analysisrequest No sample. values=%s" % values)
workflow_enabled = sample.getSamplingWorkflowEnabled()
# Create the Analysis Request
ar = _createObjectByType('AnalysisRequest', context, tmpID())
# Set some required fields manually before processForm is called
ar.setSample(sample)
values['Sample'] = sample
ar.processForm(REQUEST=request, values=values)
# Object has been renamed
ar.edit(RequestID=ar.getId())
# Set initial AR state
action = '{0}sampling_workflow'.format('' if workflow_enabled else 'no_')
workflow.doActionFor(ar, action)
# Set analysis request analyses
service_uids = _resolve_items_to_service_uids(analyses)
analyses = ar.setAnalyses(service_uids, prices=prices, specs=specifications)
if secondary:
# Only 'sample_due' and 'sample_recieved' samples can be selected
# for secondary analyses
api.content.transition(obj=ar, to_state='sampled')
api.content.transition(obj=ar, to_state='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 folderitems(self, full_objects=False):
# Show only ISharable samples for EMS. Skip others.
pm = getToolByName(self.context, 'portal_membership')
roles = pm.getAuthenticatedMember().getRoles()
#print roles
if 'EMS' in roles:
self.contentFilter['object_provides'] = ISharableSample.__identifier__
items = BikaListingView.folderitems(self)
bsc = getToolByName(self.context, 'bika_setup_catalog')
brains = bsc(portal_type='SampleType', inactive_state='active')
biospecimen_types = [
{
'ResultValue': brain.UID,
'ResultText': brain.title
}
for brain in brains
]
ret = []
for x, item in enumerate(items):
if not items[x].has_key('obj'):
continue
obj = items[x]['obj']
if not ISample.providedBy(obj):
continue
items[x]['Type'] = obj.getSampleType() and obj.getSampleType().Title() or ''
items[x]['Volume'] = obj.getField('Volume').get(obj)
items[x]['Unit'] = obj.getField('Unit').get(obj)
items[x]['SubjectID'] = obj.getField('SubjectID').get(obj)
project = obj.getField('Project').get(obj)
if not project:
project = obj.aq_parent
items[x]['Project'] = project
storage_location = obj.getField('StorageLocation').get(obj)
if storage_location:
items[x]['StorageLocation'] = storage_location.Title()
if project:
items[x]['replace']['Project'] = \
'<a href="%s">%s</a>' % (project.absolute_url(),
project.Title())
items[x]['Barcode'] = obj.getField('Barcode').get(obj)
items[x]['replace']['Title'] = "<a href='%s'>%s</a>" % \
(items[x]['url'], items[x]['Title'])
frozen_time = obj.getField('FrozenTime').get(obj)
if frozen_time:
try:
items[x]['FrozenTime'] = frozen_time.strftime("%Y-%m-%d %H:%M")
except:
items[x]['FrozenTime'] = str(frozen_time)
batch = obj.getField('Batch').get(obj)
try:
items[x]['CFGTime'] = batch.getField('CfgDateTime').get(batch).strftime("%Y/%m/%d %H:%M")
except:
items[x]['CFGTime'] = ''
try:
items[x]['SamplingTime'] = obj.getField('SamplingDate').get(obj).strftime("%Y/%m/%d %H:%M")
except:
items[x]['SamplingTime'] = ''
if self.allow_edit and isActive(self.context) and \
getSecurityManager().checkPermission(ModifyPortalContent, obj):
if items[x]['review_state'] == "sample_registered":
items[x]['allow_edit'] = ['Type', 'Barcode', 'FrozenTime']
items[x]['choices']['Type'] = biospecimen_types
elif items[x]['review_state'] == "sample_due":
# items[x]['allow_edit'] = ['SubjectID', 'Volume', 'Unit']
items[x]['allow_edit'] = ['Volume', 'Unit']
if not items[x]['Unit']:
items[x]['choices']['Unit'] = VOLUME_UNITS
elif items[x]['review_state'] == "sample_shipped":
# items[x]['allow_edit'] = ['SubjectID', 'Volume']
items[x]['allow_edit'] = ['Volume']
ret.append(item)
return ret
def generate_delivery_pdf(context, ars_or_samples):
if not ars_or_samples:
logger.warn("No Analysis Requests or Samples provided")
return
if ISample.providedBy(ars_or_samples) or \
IAnalysisRequest.providedBy(ars_or_samples):
return generate_delivery_pdf(context, [ars_or_samples])
if not isinstance(ars_or_samples, list):
logger.warn("Type not supported: {}".format(repr(ars_or_samples)))
return
html = DeliveryFormPdf(context, context.REQUEST,
analysis_requests=ars_or_samples).template()
html = safe_unicode(html).encode("utf-8")
filename = "delivery"
pdf_fn = tempfile.mktemp(suffix=".pdf")
pdf = createPdf(htmlreport=html, outfile=pdf_fn)
if not pdf:
ar_ids = map(lambda ar: ar.id, ars_or_samples)
logger.warn("Unable to generate the PDF of delivery form for {}".
format(' '.join(ar_ids)))
return None
def _attach_to_ar(pdf, ar_brain_or_obj):
ar = api.get_object(ar_brain_or_obj)
# Attach the pdf to the Analysis Request
attid = ar.aq_parent.generateUniqueId('Attachment')
att = _createObjectByType(
"Attachment", ar.aq_parent, attid)
att.setAttachmentFile(open(pdf_fn))
att.setReportOption('i') # Ignore in report
# Try to assign the Requisition Attachment Type
query = dict(portal_type='AttachmentType', title='Delivery')
brains = api.search(query, 'bika_setup_catalog')
if brains:
att_type = api.get_object(brains[0])
att.setAttachmentType(att_type)
# Awkward workaround to rename the file
attf = att.getAttachmentFile()
attf.filename = '%s.pdf' % filename
att.setAttachmentFile(attf)
att.unmarkCreationFlag()
renameAfterCreation(att)
atts = ar.getAttachment() + [att] if ar.getAttachment() else [att]
atts = [a.UID() for a in atts]
ar.setAttachment(atts)
# TODO Create only one Attachment per Client and assign it to all ARs
# There is no need to creat a single Attachment object for each AR. Same
# attachment can be assigned to different ARs and they will resolve the
# attachment correctly later. This will be useful for:
# a) Reduce the database size (less pdfs to store)
# b) workflow_download_delivery can easily return the attachments that are
# different when multiple ARs are selected.
for ar_or_sample in ars_or_samples:
# Attach the pdf to the Analysis Request
if ISample.providedBy(ar_or_sample):
for ar in ar_or_sample.getAnalysisRequests():
_attach_to_ar(pdf, ar)
elif IAnalysisRequest.providedBy(ar_or_sample):
_attach_to_ar(pdf, ar_or_sample)
return pdf_fn
def create_analysisrequest(
context,
request,
values, # {field: value, ...}
analyses=[],
# uid, service or analysis; list of uids, services or analyses
partitions=None,
# list of dictionaries with container, preservation etc)
specifications=None,
prices=None):
"""This is meant for general use and should do everything necessary to
create and initialise the AR and it's requirements.
XXX The ar-add form's ajaxAnalysisRequestSubmit should be calling this.
"""
# Gather neccesary tools
workflow = getToolByName(context, 'portal_workflow')
bc = getToolByName(context, 'bika_catalog')
# It's necessary to modify these and we don't want to pollute the
# parent's data
values = values.copy()
# Create new sample or locate the existing for secondary AR
if not values.get('Sample', False):
secondary = False
workflow_enabled = context.bika_setup.getSamplingWorkflowEnabled()
sample = create_sample(context, request, values)
else:
secondary = True
if ISample.providedBy(values['Sample']):
sample = values['Sample']
else:
brains = bc(UID=values['Sample'])
if brains:
sample = brains[0].getObject()
if not sample:
raise RuntimeError("create_analysisrequest No sample. values=%s" %
values)
workflow_enabled = sample.getSamplingWorkflowEnabled()
# Create the Analysis Request
ar = _createObjectByType('AnalysisRequest', context, tmpID())
# Set some required fields manually before processForm is called
ar.setSample(sample)
values['Sample'] = sample
ar.processForm(REQUEST=request, values=values)
# Object has been renamed
ar.edit(RequestID=ar.getId())
# Set initial AR state
action = '{0}sampling_workflow'.format('' if workflow_enabled else 'no_')
workflow.doActionFor(ar, action)
# Set analysis request analyses
service_uids = _resolve_items_to_service_uids(analyses)
analyses = ar.setAnalyses(service_uids,
prices=prices,
specs=specifications)
if secondary:
# Only 'sample_due' and 'sample_recieved' samples can be selected
# for secondary analyses
api.content.transition(obj=ar, to_state='sampled')
api.content.transition(obj=ar, to_state='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 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
sample = False
if values['Sample']:
if ISample.providedBy(values['Sample']):
secondary = True
sample = values['Sample']
samplingworkflow_enabled = sample.getSamplingWorkflowEnabled()
else:
brains = bc(UID=values['Sample'])
if brains:
secondary = True
sample = brains[0].getObject()
samplingworkflow_enabled = sample.getSamplingWorkflowEnabled()
if not sample:
secondary = False
sample = create_sample(context, request, values)
samplingworkflow_enabled = context.bika_setup.getSamplingWorkflowEnabled()
# 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)
# We need to send a list of service UIDS to setAnalyses function.
# But we may have received a list of titles, list of UIDS,
# list of keywords or list of service objects!
service_uids = []
for obj in values['Analyses']:
uid = False
# service objects
if hasattr(obj, 'portal_type') and obj.portal_type == 'AnalysisService':
uid = obj.UID()
# Analysis objects (shortcut for eg copying analyses from other AR)
elif hasattr(obj, 'portal_type') and obj.portal_type == 'Analysis':
uid = obj.getService()
# Maybe already UIDs.
if not uid:
bsc = getToolByName(context, 'bika_setup_catalog')
brains = bsc(portal_type='AnalysisService', UID=obj)
if brains:
uid = brains[0].UID
# Maybe already UIDs.
if not uid:
bsc = getToolByName(context, 'bika_setup_catalog')
brains = bsc(portal_type='AnalysisService', title=obj)
if brains:
uid = brains[0].UID
if uid:
service_uids.append(uid)
else:
logger.info("In analysisrequest.add.create_analysisrequest: cannot "
"find uid of this service: %s" % obj)
# Set analysis request analyses
ar.setAnalyses(service_uids,
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
