def handle_edit(self):
policy = ICheckinCheckoutPolicy(self.context)
obj = policy.getWorkingCopy()
#baseline = policy.getBaseline()
if obj is None:
obj = self.context
state = get_state(obj)
if state in ['private', 'sent']:
url = '{0}/edit'.format(obj.absolute_url())
return self.request.response.redirect(url)
elif state == 'published':
# create copy, go to it
wc = self._checkout()
url = '{0}/edit'.format(wc.absolute_url())
return self.request.response.redirect(url)
elif state == 'pending':
# retract object, go to it
transition(obj, to_state='sent')
url = '{0}/edit'.format(obj.absolute_url())
return self.request.response.redirect(url)
raise ValueError ('unknown state')
def handle_edit(self):
obj = get_working_copy(self.context)
# TODO: use the stagingbehavior API to get the best object, in all cases
print "WC: ", obj
print "Baseline: ", get_baseline(self.context)
if obj is None:
obj = self.context
state = get_state(obj)
if state == 'private':
url = '{0}/edit'.format(obj.absolute_url())
return self.request.response.redirect(url)
elif state == 'published':
# create copy, go to it
wc = self._checkout()
url = '{0}/edit'.format(wc.absolute_url())
return self.request.response.redirect(url)
elif state == 'pending':
# create copy, go to it
transition(obj, to_state='private')
url = '{0}/edit'.format(obj.absolute_url())
return self.request.response.redirect(url)
raise ValueError('unknown state')
def publishReport(self, justDoIt=False, duplicate=False):
"""
"""
request = self.REQUEST
alsoProvides(request, IDisableCSRFProtection)
new_version = self
if duplicate:
new_version = content.copy(source=self, id=self.getId(), safe_id=True)
# copy modules into the report?
# We would lose all the reference information, which is important for the situation overview
#mods = self.myModules()
#for mod in mods:
# content.copy(source=mod, target=new_version, safe_id=True)
# create PDF, upload it
data = self.restrictedTraverse("@@pdfprint")._generatePDF(raw=True)
nice_filename = 'report_%s_%s.pdf' % (self.getId(), datetime.now().strftime('%Y%m%d'))
nice_filename = safe_unicode(nice_filename)
field = NamedBlobFile(data=data, filename=nice_filename)
fid = new_version.invokeFactory(id=nice_filename, type_name="File", title=self.Title(), description="")
f = new_version._getOb(fid)
f.file = field
f.reindexObject()
content.transition(new_version, transition="publish")
if not justDoIt:
portalMessage(self, _("The report has been published."), "info")
return self.restrictedTraverse("@@view")()
def handle_edit(self):
obj = get_working_copy(self.context)
# TODO: use the stagingbehavior API to get the best object, in all cases
print "WC: ", obj
print "Baseline: ", get_baseline(self.context)
if obj is None:
obj = self.context
state = get_state(obj)
if state == "private":
url = "{0}/edit".format(obj.absolute_url())
return self.request.response.redirect(url)
elif state == "published":
# create copy, go to it
wc = self._checkout()
url = "{0}/edit".format(wc.absolute_url())
return self.request.response.redirect(url)
elif state == "pending":
# create copy, go to it
transition(obj, to_state="private")
url = "{0}/edit".format(obj.absolute_url())
return self.request.response.redirect(url)
raise ValueError("unknown state")
def _checkout(self):
# NOTE: this code is copied from plone.app.iterate.browser.checkout
context = aq_inner(self.context)
# containers = list(self._containers())
location = self.context.aq_parent #containers[0]['name']
# We want to redirect to a specific template, else we might
# end up downloading a file
control = getMultiAdapter((context, self.request),
name=u"iterate_control")
if not control.checkout_allowed():
raise CheckoutException(u"Not allowed")
policy = ICheckinCheckoutPolicy(context)
wc = policy.checkout(location)
transition(wc, to_state='sent')
# we do this for metadata update side affects which will update lock info
context.reindexObject('review_state')
IStatusMessage(self.request).addStatusMessage(_("Check-out created"),
type='info')
#view_url = wc.restrictedTraverse("@@plone_context_state").view_url()
return wc
def __call__(self):
changed = 0
not_changed = 0
logger.info("Changing workflow states to not_started...")
for nda in self.ndas:
state = get_wf_state_id(nda)
if hasattr(nda, 'saved_assessment_data'):
data = nda.saved_assessment_data.last()
if data:
not_changed += 1
continue
if state == 'in_work':
changed += 1
logger.info("State changing for {}".format(nda.__repr__()))
transition(obj=nda, to_state='not_started')
logger.info("States changed: {}, Not changed: {}".format(
changed, not_changed))
return "Done"
def create_comments_folder(self, content):
for id, title, trans in [
(u'tl', 'Discussion track with Topic Leads', 'open_for_tl'),
(u'ec', 'Discussion track with EC', 'open_for_ec'),
]:
if id not in content.contentIds():
dt = create(content,
'wise.msfd.commentsfolder',
id=id,
title=title)
transition(obj=dt, transition=trans)
def publishModule(self, justDoIt=False):
"""
"""
request = self.REQUEST
alsoProvides(request, IDisableCSRFProtection)
new_version = content.copy(source=self, id=self.getId(), safe_id=True)
content.transition(new_version, transition="publish")
if not justDoIt:
portalMessage(self, _("The module has been published."), "info")
return self.restrictedTraverse("@@view")()
def process_results(self, path):
self.path = path
self.run = self.get_run(path)
if not self.run:
return
# import results and files from path
log = self.process_results_xlsx(path)
log += self.process_out_figures(path)
log += self.process_raw_flipped(path)
# transition run to 'resulted'
self.run.import_log = log
transition(self.run, 'result')
# send result report
self.create_pdf_files()
def handleApply(self, action):
data, errors = self.extractData()
if errors:
self.status = self.formErrorsMessage
return
action = data['workflow_action']
msg = data['message'].strip()
IAnnotations(self.request)[ANNOT_KEY] = msg
notify(WorkflowMessageEvent(self.context))
transition(obj=self.context, transition=action, comment=msg)
self.status = msg = u"Message will be further processed."
show_message(message=msg, request=self.request, type='info')
return self.request.response.redirect(self.context.absolute_url())
def handleApply(self, action):
data, errors = self.extractData()
if errors:
self.status = self.formErrorsMessage
return
action = data['workflow_action']
msg = data['message'].strip()
IAnnotations(self.request)[ANNOT_KEY] = msg
notify(WorkflowMessageEvent(self.context))
transition(obj=self.context, transition=action, comment=msg)
self.status = msg = u"Message will be further processed."
show_message(message=msg, request=self.request, type='info')
return self.request.response.redirect(self.context.absolute_url())
def setUp(self):
"""Custom shared utility setup for tests."""
self.portal = self.layer['portal']
self.workflow = api.portal.get_tool('portal_workflow')
# in tests we have to manually map content types to workflows
self.workflow.setChainForPortalTypes(['News Item'],
'simple_publication_workflow')
# add test item
content.create(type='News Item',
title='Tést item',
container=self.portal)
self.newsitem = self.portal['test-item']
# publish the item
content.transition(obj=self.newsitem, transition='publish')
def _attempt_invalid_transition(
self,
obj=None,
transition=None,
end_state=None,
):
self.assertIsNotNone(obj)
self.assertIn(transition, TRANSITIONS)
self.assertIn(end_state, STATES.keys())
error_str = ''
try:
content.transition(obj=obj, transition=transition)
except InvalidParameterError as e:
error_str = e.message
found_expected_error = 'Invalid transition' in error_str
self.assertTrue(found_expected_error)
self.assertEqual(content.get_state(obj=obj), end_state)
def after_queue(instance):
"""
"""
assayrequests, clinicalaliquots, ichips, qcaliquots = run_objects(instance)
for obj in set(qcaliquots):
transition(obj, "queue")
for obj in set(clinicalaliquots):
transition(obj, "queue")
for obj in set(ichips):
transition(obj, "queue")
for obj in set(assayrequests):
transition(obj, "queue")
def send_to_tl(self):
regions = self.get_regions()
for region in regions:
descriptors = self.get_descriptors(region)
for desc in descriptors:
assessments = self.get_articles(desc)
for assessment in assessments:
state_id = self.get_wf_state_id(assessment)
if state_id == 'approved':
transition(obj=assessment, to_state='in_work')
IStatusMessage(self.request).add(u'Sent to TL', type='info')
url = self.context.absolute_url()
return self.request.response.redirect(url)
def setUp(self):
"""Custom shared utility setup for tests."""
self.portal = self.layer['portal']
self.workflow = api.portal.get_tool('portal_workflow')
# in tests we have to manually map content types to workflows
self.workflow.setChainForPortalTypes(
['News Item'],
'simple_publication_workflow'
)
# add test item
content.create(
type='News Item',
title='Tést item',
container=self.portal
)
self.newsitem = self.portal['test-item']
# publish the item
content.transition(obj=self.newsitem, transition='publish')
def _verify_allowed_transition_by_role(
self,
obj=None,
initial_state=None,
role=None,
transition=None,
destination_state=None,
end_state=None,
):
self.assertIsNotNone(obj)
self.assertIn(initial_state, STATES.keys())
self.assertIn(role, ROLES)
self.assertIn(transition, TRANSITIONS)
self.assertIn(destination_state, STATES.keys())
self.assertIn(end_state, STATES.keys())
self.assertEqual(content.get_state(obj=obj), initial_state)
self._switch_role(obj, role)
content.transition(obj=obj, transition=transition)
self.assertEqual(content.get_state(obj=obj), destination_state)
# send it back to the end state
self._transition_to_state(obj, destination_state=end_state)
def add_comment(self):
form = self.request.form
question_id = form.get('q').lower()
thread_id = form.get('thread_id')
transition_id = 'open_for_{}'.format(thread_id)
text = form.get('text')
folder = self.context
if question_id in folder.contentIds():
q_folder = folder[question_id]
# Due to a bug, For 'EC' the wrong state was given (opened_for_tl)
# transition to the correct state if necessary
current_state = get_state(q_folder)
correct_state = 'opened_for_{}'.format(thread_id)
if current_state != 'closed' and current_state != correct_state:
transition(obj=q_folder, transition='close')
transition(obj=q_folder, transition=transition_id)
else: # initially create the question folder for comments
q_folder = create(folder,
'wise.msfd.commentsfolder',
id=question_id,
title='Comments for question ' + question_id)
transition(obj=q_folder, transition=transition_id)
comment = create(q_folder, 'wise.msfd.comment', text=text)
logger.info('Added comment %r in %r:, %r', q_folder, comment, text)
return self.template()
def _transition_and_or_roles_test(
self,
fast,
initial_state,
transition,
end_state,
authorized_roles,
):
if fast:
self.assertEqual(content.get_state(obj=self.test_obj),
initial_state)
content.transition(obj=self.test_obj, transition=transition)
self.assertEqual(content.get_state(obj=self.test_obj), end_state)
else:
self._verify_transition_by_all_roles(
obj=self.test_obj,
initial_state=initial_state,
authorized_roles=authorized_roles,
transition=transition,
destination_state=end_state,
end_state=initial_state,
)
def after_cancel_run(instance):
"""When cancelling a test run, objects that were linked here must
be freed for use in a future test run, or cancelled.
- cancels iChip and Aliquot objects
- make_available on AssayRequest objects.
"""
assayrequests, clinicalaliquots, ichips, qcaliquots = run_objects(instance)
for obj in set(qcaliquots):
transition(obj, "make_available")
for obj in set(clinicalaliquots):
transition(obj, "make_available")
for obj in set(ichips):
transition(obj, "make_available")
for obj in set(assayrequests):
transition(obj, "make_available")
def store_aliquot(self, uid, usn, aliquot_type, target_box_type):
# get active box from workflow state, if one doesn't exist make it,
# check for aliquot space in box, if none make a new box
aliquot_type = aliquot_type # Bulk or Working
target_box_type = target_box_type # CommercialBox, RandDBox, QCBox
# find the active box of the type we need,
brains = find(portal_type=target_box_type, review_state='active')
if brains is not None:
for brain in brains:
cb = brain.getObject()
if cb.box_type == aliquot_type:
if cb.remaining_volume > 0:
box_to_use = cb.UID
entry_key = str(len(cb.aliquot.keys()) + 1)
entry_value = [usn, uid] # Aliquot ID, UID
# thing to add it to cb.aliquot_dic
else:
# change box workflow to full
try:
transition(cb, "filled")
except:
msg = "Could not transition %s, action='filled'" % \
cb.Title
raise ObjectInInvalidState(msg)
# see if rack has empty space, if not bail, and
# alert user make a new aliquot_type, and return
# this UID
rack = cb.aq_parent
new_box = api.content.create(
container=rack,
type=target_box_type,
title="",
box_type=aliquot_type,
max_samples=81,
remaining_volume=80,
aliquot_dic={u'1', [usn, uid]})
else:
print "No Active Box for Parameters sent"
def store_aliquot(self, uid, usn, aliquot_type, target_box_type):
# get active box from workflow state, if one doesn't exist make it,
# check for aliquot space in box, if none make a new box
aliquot_type = aliquot_type # Bulk or Working
target_box_type = target_box_type # CommercialBox, RandDBox, QCBox
# find the active box of the type we need,
brains = find(portal_type=target_box_type, review_state='active')
if brains is not None:
for brain in brains:
cb = brain.getObject()
if cb.box_type == aliquot_type:
if cb.remaining_volume > 0:
box_to_use = cb.UID
entry_key = str(len(cb.aliquot.keys()) + 1)
entry_value = [usn, uid] # Aliquot ID, UID
# thing to add it to cb.aliquot_dic
else:
# change box workflow to full
try:
transition(cb, "filled")
except:
msg = "Could not transition %s, action='filled'" % \
cb.Title
raise ObjectInInvalidState(msg)
# see if rack has empty space, if not bail, and
# alert user make a new aliquot_type, and return
# this UID
rack = cb.aq_parent
new_box = api.content.create(
container=rack,
type=target_box_type,
title="",
box_type=aliquot_type,
max_samples=81,
remaining_volume=80,
aliquot_dic={u'1', [usn, uid]})
else:
print "No Active Box for Parameters sent"
def after_begin_process(instance):
"""
"""
assayrequests, clinicalaliquots, ichips, qcaliquots = run_objects(instance)
for obj in set(qcaliquots):
transition(obj, "begin_process")
for obj in set(clinicalaliquots):
transition(obj, "begin_process")
for obj in set(assayrequests):
transition(obj, "begin_process")
def transition_plate_contents(self, ichips, aliquots, action_id):
"""Chips, aliquots, and assay requests move together through
identical states during the test run.
"""
transitioned = []
try:
for ichip in ichips:
if ichip not in transitioned:
transition(ichip, action_id)
transitioned.append(ichip)
except InvalidParameterError:
# noinspection PyUnboundLocalVariable
msg = "Can't invoke '%s' transition on %s" % (action_id, ichip)
raise ObjectInInvalidState(msg)
try:
for aliquot in aliquots:
if aliquot not in transitioned:
transition(aliquot, action_id)
transitioned.append(aliquot)
except InvalidParameterError:
# noinspection PyUnboundLocalVariable
msg = "Can't invoke '%s' transition on %s" % (action_id, aliquot)
raise ObjectInInvalidState(msg)
# get AssayRequests associated with all aliquots, and queue them.
for aliquot in aliquots:
sample = self.get_parent_sample_from_aliquot(aliquot)
if IClinicalSample.providedBy(sample):
assayrequest = self.get_assay_request_from_sample(sample)
wf = get_tool('portal_workflow')
t_ids = [t['id'] for t in wf.getTransitionsFor(assayrequest)]
if action_id in t_ids \
and assayrequest not in transitioned:
transition(assayrequest, action_id)
transitioned.append(assayrequest)
def transition_plate_contents(self, ichips, aliquots, action_id):
"""Chips, aliquots, and assay requests move together through
identical states during the test run.
"""
transitioned = []
try:
for ichip in ichips:
if ichip not in transitioned:
transition(ichip, action_id)
transitioned.append(ichip)
except InvalidParameterError:
# noinspection PyUnboundLocalVariable
msg = "Can't invoke '%s' transition on %s" % (action_id, ichip)
raise ObjectInInvalidState(msg)
try:
for aliquot in aliquots:
if aliquot not in transitioned:
transition(aliquot, action_id)
transitioned.append(aliquot)
except InvalidParameterError:
# noinspection PyUnboundLocalVariable
msg = "Can't invoke '%s' transition on %s" % (action_id, aliquot)
raise ObjectInInvalidState(msg)
# get AssayRequests associated with all aliquots, and queue them.
for aliquot in aliquots:
sample = self.get_parent_sample_from_aliquot(aliquot)
if IClinicalSample.providedBy(sample):
assayrequest = self.get_assay_request_from_sample(sample)
wf = get_tool('portal_workflow')
t_ids = [t['id'] for t in wf.getTransitionsFor(assayrequest)]
if action_id in t_ids \
and assayrequest not in transitioned:
transition(assayrequest, action_id)
transitioned.append(assayrequest)
def tweaks(context):
""" Additional soer content tweaks
"""
catalog = getToolByName(context, 'portal_catalog')
soer_2010 = context.restrictedTraverse("/www/SITE/soer/2010")
soer_page_2010 = context.restrictedTraverse("/www/SITE/soer/2010/2010")
page_keys = soer_page_2010.Schema().keys()
folder_keys = soer_2010.Schema().keys()
for key in page_keys:
field = soer_page_2010.getField(key)
if not field:
continue
value = field.getAccessor(soer_page_2010)()
# Fix some metadata
if key in folder_keys:
setattr(soer_2010, key, value)
soer_2010.setTitle(soer_page_2010.Title())
soer_2010.setDescription(soer_page_2010.Description())
soer_2010.setEffectiveDate(soer_page_2010.getEffectiveDate())
soer_2010.setCreationDate(soer_page_2010.creation_date)
soer_2010.setSubject(soer_page_2010.Subject())
soer_2010.setCreators(soer_page_2010.Creators())
soer_2010.changeOwnership(soer_page_2010.getOwner())
soer_2010.temporalCoverage = soer_page_2010.temporalCoverage
# Map relatedItems
forwards = soer_page_2010.getRelatedItems()
backs = soer_page_2010.getBackReferences()
if forwards:
soer_2010.setRelatedItems(forwards)
for ob in backs:
related = ob.getRelatedItems()
related.append(soer_2010)
ob.setRelatedItems(related)
# set geotags
geo_page_2010 = getAdapter(soer_page_2010, IGeoTags)
geo_2010 = getAdapter(soer_2010, IGeoTags)
geo_2010._set_tags(geo_page_2010.tags)
soer_2010._p_changed = True
soer_2010.reindexObject()
catalog.reindexObject(soer_2010, update_metadata=True)
transaction.commit()
soer = context.restrictedTraverse("/www/SITE/soer")
content.transition(obj=soer, transition='publish')
soer_2020 = context.restrictedTraverse("/www/SITE/soer/2020")
soer_2020.setExpirationDate(None)
soer_2020._p_changed = True
soer_2020.reindexObject()
catalog.reindexObject(soer_2020, update_metadata=True)
logger.info('Finished tweaking moved soer content ... DONE')
return 'Done moving'
def handleApply(self, action):
data, errors = self.extractData()
if errors:
self.status = self.formErrorsMessage
return
utils._send_emails = False
try:
en_folder = self.context.restrictedTraverse('en')
if 'organisations' in en_folder:
org_folder = en_folder.restrictedTraverse('organisations')
else:
org_folder = content.create(
en_folder,
type='osha.hwccontent.organisationfolder',
title='Organisations')
if 'focalpoints' in en_folder:
fop_folder = en_folder.restrictedTraverse('focalpoints')
else:
fop_folder = content.create(
en_folder,
type='osha.hwccontent.organisationfolder',
title='Focalpoints')
type_mapping = {
u'Organisation': {
'type': 'osha.hwccontent.organisation',
'schema': dict(getFieldsInOrder(IOrganisation)),
'folder': org_folder,
'wf_actions': ('approve_phase_1', ),
},
u'Focalpoint': {
'type': 'osha.hwccontent.focalpoint',
'schema': dict(getFieldsInOrder(IFocalPoint)),
'folder': fop_folder,
'wf_actions': ('publish', ),
}
}
count = 0
for data in json.loads(data['json']):
# Only keep the data that's in the main schema:
type_info = type_mapping[data['_type']]
schema = type_info['schema']
fields = {}
if data['title'].startswith('MC-'):
continue
for name, field in schema.items():
if name in data:
value = data[name]
if value and INamedImageField.providedBy(field):
content_type = data.get('_%s_content_type' % name,
'')
filename = data.get('_%s_filename' % name, None)
value = NamedBlobImage(base64.b64decode(value),
str(content_type), filename)
elif value and IRichText.providedBy(field):
content_type = data.get('_%s_content_type', None)
value = RichTextValue(value, mimeType=content_type)
elif name.find("email") >= 0:
value = value.strip()
fields[name] = value
new_obj = content.create(container=type_info['folder'],
type=type_info['type'],
id=data['id'],
**fields)
for transition in type_info['wf_actions']:
try:
content.transition(new_obj, transition)
except Exception:
logger.exception(
'Could not execute %s transition for %s' %
(transition, '/'.join(new_obj.getPhysicalPath())))
logger.info('Imported %s' % new_obj.getId())
count += 1
# Set status on this form page
self.status = "%s partners imported" % count
except Exception:
# Enable emails again:
utils._send_emails = True
raise
def handle_submit(self):
transition(self.context, to_state='pending')
url = '{0}/'.format(self.context.absolute_url())
return self.request.response.redirect(url)
def make_clinical_sample(
self, usn_from_form, consent_acquired, ana_testing, clin_rash,
clin_seiz_psych, clin_mouth_sores, clin_hair_loss, clin_joint_pain,
clin_inflam, clin_other, clin_other_specify, diag_D89_89,
diag_M32_10, diag_D89_9, diag_M35_9, diag_L93_2, diag_other,
diag_other_specify, provider_nip_clean, provider_signed,
draw_location, draw_tel, phlebotomist_name, draw_signed,
collection_date, shipment_date, test_other_specify,
clinical_impression, ordering_provider_name, site_id,
assay_selection, other_clinical_symptoms, other_inflam,
other_joint_pain):
"""Make a clinical sample via api, set serial number
Need to add option for assay choice at a later date
"""
# logical test order passed via end user
# assign serial number for sample
sn = api.content.find(context=api.portal.get(),
portal_type='ClinicalSample')
all_sn = []
# list of all serial numbers
sn_uid = [s.UID for s in sn]
for i in sn_uid:
value = api.content.get(UID=i)
all_sn.append(value.sample_serial_number)
if len(all_sn) == 0:
serial_number = 10000
else:
serial_number = max(all_sn) + 1
symptoms_choice = []
if clin_rash is not None:
symptoms_choice.append(unicode(clin_rash, "utf-8"))
if clin_seiz_psych is not None:
symptoms_choice.append(unicode(clin_seiz_psych, "utf-8"))
if clin_mouth_sores is not None:
symptoms_choice.append(unicode(clin_mouth_sores, "utf-8"))
if clin_hair_loss is not None:
symptoms_choice.append(unicode(clin_hair_loss, "utf-8"))
if clin_joint_pain is not None:
symptoms_choice.append(unicode(clin_joint_pain, "utf-8"))
if clin_inflam is not None:
symptoms_choice.append(unicode(clin_inflam, "utf-8"))
if clin_other is not None:
symptoms_choice.append(unicode(clin_other, "utf-8"))
# datetime.datetime.strptime
diagnosis_code = []
if diag_D89_89 is not None:
diagnosis_code.append(unicode(diag_D89_89, "utf-8"))
if diag_M32_10 is not None:
diagnosis_code.append(unicode(diag_M32_10, "utf-8"))
if diag_D89_9 is not None:
diagnosis_code.append(unicode(diag_D89_9, "utf-8"))
if diag_M35_9 is not None:
diagnosis_code.append(unicode(diag_M35_9, "utf-8"))
if diag_L93_2 is not None:
diagnosis_code.append(unicode(diag_L93_2, "utf-8"))
if diag_other is not None:
diagnosis_code.append(unicode(diag_other, "utf-8"))
try:
py_collection_date = \
datetime.datetime.strptime(collection_date, "%Y-%m-%d").date()
except:
py_collection_date = None
try:
py_shipment_date = \
datetime.datetime.strptime(shipment_date, "%Y-%m-%d").date()
except:
py_shipment_date = None
# need to split clin_other_specify on ', '
# if clin_other_specify != "":
# Get primary health care provider from site!
site_objects = api.content.find(context=api.portal.get(),
portal_type='Site')
site_uids = [i.UID for i in site_objects]
primary_provider = "null"
for j in site_uids:
site = api.content.get(UID=j)
if site_id == str(site.title):
primary_provider = site.primary_provider
# set permission for clinical sample
cs = api.portal.get()
sample = cs['lims']['samples']
disallow_default_contenttypes(sample)
clinical_sample = api.content.create(
container=sample,
type='ClinicalSample',
id=usn_from_form,
usn=usn_from_form,
safe_id=True,
sample_serial_number=serial_number,
research_consent=consent_acquired,
sample_ordering_healthcare_provider=ordering_provider_name,
sample_ordering_healthcare_provider_signature=provider_signed,
primary_healthcare_provider=primary_provider,
ana_testing=ana_testing,
clinical_impression=clinical_impression,
other_test_ordered=test_other_specify,
symptoms_choice=symptoms_choice,
symptoms_text=clin_other_specify,
phlebotomist_name=phlebotomist_name,
phlebotomist_signature_provided=draw_signed,
collection_date=py_collection_date,
received_date=py_shipment_date,
joint_pain_text=other_joint_pain,
inflammation_text=other_inflam,
other_symptoms_text=other_clinical_symptoms,
)
clinical_sample_uid = clinical_sample.UID()
# Creates Assay Request Object on Sample Creation, on for each assay
# selected!
for a in assay_selection:
assay_request = api.content.create(container=clinical_sample,
type='AssayRequest',
title=a,
assay_name=a)
transition(assay_request, to_state='to_be_tested')
# add billing program from rec to object
billing_request = api.content.create(
container=assay_request,
type='AssayBillingRequest',
title=usn_from_form,
safe_id=True,
assay_name=a,
sample_id=usn_from_form,
diagnosis_code=diagnosis_code,
diagnosis_code_other=diag_other_specify)
return clinical_sample_uid
def handleApply(self, action):
data, errors = self.extractData()
if errors:
self.status = self.formErrorsMessage
return
utils._send_emails = False
try:
en_folder = self.context.restrictedTraverse('en')
if 'organisations' in en_folder:
org_folder = en_folder.restrictedTraverse('organisations')
else:
org_folder = content.create(en_folder,
type='osha.hwccontent.organisationfolder',
title='Organisations')
if 'focalpoints' in en_folder:
fop_folder = en_folder.restrictedTraverse('focalpoints')
else:
fop_folder = content.create(en_folder,
type='osha.hwccontent.organisationfolder',
title='Focalpoints')
type_mapping = {
u'Organisation': {
'type': 'osha.hwccontent.organisation',
'schema': dict(getFieldsInOrder(IOrganisation)),
'folder': org_folder,
'wf_actions': ('approve_phase_1',),
},
u'Focalpoint': {
'type': 'osha.hwccontent.focalpoint',
'schema': dict(getFieldsInOrder(IFocalPoint)),
'folder': fop_folder,
'wf_actions': ('publish',),
}
}
count = 0
for data in json.loads(data['json']):
# Only keep the data that's in the main schema:
type_info = type_mapping[data['_type']]
schema = type_info['schema']
fields = {}
if data['title'].startswith('MC-'):
continue
for name, field in schema.items():
if name in data:
value = data[name]
if value and INamedImageField.providedBy(field):
content_type = data.get('_%s_content_type' % name, '')
filename = data.get('_%s_filename' % name , None)
value = NamedBlobImage(base64.b64decode(value), str(content_type), filename)
elif value and IRichText.providedBy(field):
content_type = data.get('_%s_content_type', None)
value = RichTextValue(value, mimeType=content_type)
elif name.find("email") >= 0:
value = value.strip()
fields[name] = value
new_obj = content.create(container=type_info['folder'],
type= type_info['type'],
id=data['id'],
**fields)
for transition in type_info['wf_actions']:
try:
content.transition(new_obj, transition)
except Exception:
logger.exception('Could not execute %s transition for %s' % (transition, '/'.join(new_obj.getPhysicalPath())))
logger.info('Imported %s' % new_obj.getId())
count += 1
# Set status on this form page
self.status = "%s partners imported" % count
except Exception:
# Enable emails again:
utils._send_emails = True
raise
def handle_submit(self):
transition(self.context, to_state="pending")
url = "{0}/".format(self.context.absolute_url())
return self.request.response.redirect(url)
def process_results_xlsx(self, path):
"""Take values from path/Out/Results/SLEkey_Results.xlsx, and write
them to the database
"""
run = self.get_run(path)
# Get the first sheet
filename = join(path, 'Out', 'Results', 'SLEkey_Results.xlsx')
wb = openpyxl.load_workbook(filename)
ws = wb.get_sheet_by_name('Sheet1')
# header rows for blocks containg QC and Clinical aliquot/sample info
qc_head_row = self.findnextSerial_Numberrow(ws, 1)
clin_head_row = self.findnextSerial_Numberrow(ws, qc_head_row + 1)
# get column letters of all qc headers that start with "ichip*"
qc_ichip_cols = []
passfail_col = None
for col in all_cols:
coord = "%s%s" % (col, qc_head_row)
val = "%s" % ws[coord].value
if val:
if val.lower().startswith("fina"):
passfail_col = coord
if val.lower().startswith("ichip"):
qc_ichip_cols.append(col)
ichip_passfail_combos = []
if passfail_col:
for row in range(qc_head_row + 1, clin_head_row):
passfail = "%s" % ws["%s%s" % (passfail_col, row)].value
ichip_titles = []
for col in qc_ichip_cols:
ichip_titles.append(ws["%s%s" % (col, row)].value)
ichip_passfail_combos.append([ichip_titles, passfail])
# for each plate
for plate in run.plates:
plate_ichips = []
plate_ichiplot_titles = []
# get all unique ichip lot numbers in a list
for key, uid in plate.items():
if key.startswith('ichip-id'):
ichip = find(UID=uid)[0].getObject()
plate_ichips.append(ichip)
ichiplot_title = ichip.title.upper().split('-')[0]
if ichiplot_title not in plate_ichiplot_titles:
plate_ichiplot_titles.append(ichiplot_title)
for combo in ichip_passfail_combos:
if sorted(plate_ichiplot_titles) == sorted(combo[0]):
for ichip in plate_ichips:
transition(ichip, 'qc_' + combo[1].lower())
# 'consume' qc aliquots.
for uid in plate.values():
brains = find(object_provides=IQCAliquot.__identifier__,
UID=uid, review_state='in_process')
if brains:
transition(brains[0].getObject(), 'done')
# find the column at which the following headers are located:
cols = {'Sample_ID': '',
'SLE_key_Score': '',
'SLE_key_Classification': '',
'Assay_QC_Status': ''}
if not all(cols):
msg = "One of the column headers can't be located:" % pformat(cols)
raise SpreadsheetParseError(msg)
for col in all_cols:
coord = "%s%s" % (col, clin_head_row)
value = ws[coord].value
if value in cols:
cols[value] = col
# get values from each row and colum into aliquot_results. results is:
# {sample_id: [SLE_key_Score,
# SLE_key_Classification,
# Assay_QC_Status],}
aliquot_results = {}
first_empty = self.get_first_empty_row(ws, clin_head_row)
for row in range(clin_head_row + 1, first_empty):
sample_id = ws["%s%s" % (cols['Sample_ID'], row)].value
score = ws["%s%s" % (cols['SLE_key_Score'], row)].value
classif = ws["%s%s" % (cols['SLE_key_Classification'], row)].value
status = ws["%s%s" % (cols['Assay_QC_Status'], row)].value
aliquot_results[sample_id] = {
'SLE_key_Score': score,
'SLE_key_Classification': "%s" % classif,
'Assay_QC_Status': "%s" % status
}
log = []
_used_uids = []
for plate in run.plates:
for uid in plate.values():
if uid in _used_uids:
continue
_used_uids.append(uid)
brains = find(UID=uid)
if not brains:
continue
aliquot = brains[0].getObject()
if not IAliquot.providedBy(aliquot):
continue
sample = self.get_sample_from_aliquot(aliquot)
if IClinicalSample.providedBy(sample):
if sample.title not in aliquot_results:
msg = "Sample '%s' not in spreadsheet results: %s" % \
(sample.title, pformat(aliquot_results))
raise RuntimeError(msg)
result = aliquot_results[sample.title]
ar = self.get_ar_from_sample(sample, run.assay_name)
state = result['Assay_QC_Status'].lower()
ar.aliquot_evaluated = aliquot.title
ar.date_resulted = self.get_date(ws)
# assayrequest is associated with multiple aliquots,
# so we only transition if the AR's state is expected.
if get_state(ar) == 'in_process':
transition(ar, 'qc_' + state)
aliquot.numeric_result = result['SLE_key_Score']
aliquot.text_result = result['SLE_key_Classification']
ts = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M")
log.append("%s: Sample: %s, Aliquot: %s, Results: %s, %s" % (
ts,
sample.title,
aliquot.title,
result['SLE_key_Score'],
result['SLE_key_Classification'],
))
return log
def after_release(instance):
"""
"""
for ichip in instance.objectValues():
if get_state(ichip) == "quarantined":
transition(ichip, "release")
def make_clinical_sample(
self, usn_from_form, consent_acquired, ana_testing, clin_rash,
clin_seiz_psych, clin_mouth_sores, clin_hair_loss, clin_joint_pain,
clin_inflam, clin_other, clin_other_specify, diag_D89_89,
diag_M32_10, diag_D89_9, diag_M35_9, diag_L93_2, diag_other,
diag_other_specify, provider_nip_clean, provider_signed,
draw_location, draw_tel, phlebotomist_name, draw_signed,
collection_date, shipment_date, test_other_specify,
clinical_impression, ordering_provider_name, site_id,
assay_selection, other_clinical_symptoms, other_inflam,
other_joint_pain):
"""Make a clinical sample via api, set serial number
Need to add option for assay choice at a later date
"""
# logical test order passed via end user
# assign serial number for sample
sn = api.content.find(context=api.portal.get(),
portal_type='ClinicalSample')
all_sn = []
# list of all serial numbers
sn_uid = [s.UID for s in sn]
for i in sn_uid:
value = api.content.get(UID=i)
all_sn.append(value.sample_serial_number)
if len(all_sn) == 0:
serial_number = 10000
else:
serial_number = max(all_sn) + 1
symptoms_choice = []
if clin_rash is not None:
symptoms_choice.append(unicode(clin_rash, "utf-8"))
if clin_seiz_psych is not None:
symptoms_choice.append(unicode(clin_seiz_psych, "utf-8"))
if clin_mouth_sores is not None:
symptoms_choice.append(unicode(clin_mouth_sores, "utf-8"))
if clin_hair_loss is not None:
symptoms_choice.append(unicode(clin_hair_loss, "utf-8"))
if clin_joint_pain is not None:
symptoms_choice.append(unicode(clin_joint_pain, "utf-8"))
if clin_inflam is not None:
symptoms_choice.append(unicode(clin_inflam, "utf-8"))
if clin_other is not None:
symptoms_choice.append(unicode(clin_other, "utf-8"))
# datetime.datetime.strptime
diagnosis_code = []
if diag_D89_89 is not None:
diagnosis_code.append(unicode(diag_D89_89, "utf-8"))
if diag_M32_10 is not None:
diagnosis_code.append(unicode(diag_M32_10, "utf-8"))
if diag_D89_9 is not None:
diagnosis_code.append(unicode(diag_D89_9, "utf-8"))
if diag_M35_9 is not None:
diagnosis_code.append(unicode(diag_M35_9, "utf-8"))
if diag_L93_2 is not None:
diagnosis_code.append(unicode(diag_L93_2, "utf-8"))
if diag_other is not None:
diagnosis_code.append(unicode(diag_other, "utf-8"))
try:
py_collection_date = \
datetime.datetime.strptime(collection_date, "%Y-%m-%d").date()
except:
py_collection_date = None
try:
py_shipment_date = \
datetime.datetime.strptime(shipment_date, "%Y-%m-%d").date()
except:
py_shipment_date = None
# need to split clin_other_specify on ', '
# if clin_other_specify != "":
# Get primary health care provider from site!
site_objects = api.content.find(context=api.portal.get(),
portal_type='Site')
site_uids = [i.UID for i in site_objects]
primary_provider = "null"
for j in site_uids:
site = api.content.get(UID=j)
if site_id == str(site.title):
primary_provider = site.primary_provider
# set permission for clinical sample
cs = api.portal.get()
sample = cs['lims']['samples']
disallow_default_contenttypes(sample)
clinical_sample = api.content.create(
container=sample,
type='ClinicalSample',
id=usn_from_form,
usn=usn_from_form,
safe_id=True,
sample_serial_number=serial_number,
research_consent=consent_acquired,
sample_ordering_healthcare_provider=ordering_provider_name,
sample_ordering_healthcare_provider_signature=provider_signed,
primary_healthcare_provider=primary_provider,
ana_testing=ana_testing,
clinical_impression=clinical_impression,
other_test_ordered=test_other_specify,
symptoms_choice=symptoms_choice,
symptoms_text=clin_other_specify,
phlebotomist_name=phlebotomist_name,
phlebotomist_signature_provided=draw_signed,
collection_date=py_collection_date,
received_date=py_shipment_date,
joint_pain_text=other_joint_pain,
inflammation_text=other_inflam,
other_symptoms_text=other_clinical_symptoms,
)
clinical_sample_uid = clinical_sample.UID()
# Creates Assay Request Object on Sample Creation, on for each assay
# selected!
for a in assay_selection:
assay_request = api.content.create(
container=clinical_sample,
type='AssayRequest',
title=a,
assay_name=a)
transition(assay_request, to_state='to_be_tested')
# add billing program from rec to object
billing_request = api.content.create(
container=assay_request,
type='AssayBillingRequest',
title=usn_from_form,
safe_id=True,
assay_name=a,
sample_id=usn_from_form,
diagnosis_code=diagnosis_code,
diagnosis_code_other=diag_other_specify)
return clinical_sample_uid
def _recursive_transition_to_state(self, obj, transition_steps):
for transition in transition_steps:
content.transition(obj=obj, transition=transition)
def _publish(obj):
"""Publish the object if it hasn't been published."""
if content.get_state(obj=obj) != 'published':
content.transition(obj=obj, transition='publish')
return True
return False
def votable_update(votable_object, event):
votable = IVoting(votable_object)
if get_state(votable_object) == 'pending':
if votable.average_vote() > 0.5:
transition(votable_object, transition='publish')
def create_demo_content(context):
"""
Initializes demo profile with demo content
:param context:
"""
portal = api.portal.get()
current_dir = os.path.abspath(os.path.dirname(__file__))
json_path = os.path.join(current_dir, "profiles/demo/data/data.json")
with open(json_path) as json_str:
data = json.load(json_str)
api.portal.set_registry_record(
"plonemeeting.portal.core.global_categories", data["categories"])
normalizer = getUtility(IIDNormalizer)
for institution in data["institutions"]:
institution_id = normalizer.normalize(institution["title"])
institution_obj = content.create(
container=portal,
type="Institution",
id=institution_id,
title=institution["title"],
representatives_mappings=institution[
"representatives_mappings"],
plonemeeting_url=institution["plonemeeting_url"],
username=institution["username"],
password=institution["password"],
meeting_config_id=institution["meeting_config_id"],
additional_meeting_query_string_for_list=institution[
"additional_meeting_query_string_for_list"],
additional_published_items_query_string=institution[
"additional_published_items_query_string"],
item_decision_formatting_tal=institution[
"item_decision_formatting_tal"],
info_annex_formatting_tal=institution[
"info_annex_formatting_tal"],
)
content.transition(obj=institution_obj, transition="publish")
user = api.user.create(
username="******".format(institution_obj.id),
email="*****@*****.**",
password="******",
)
group = api.group.get(
format_institution_managers_group_id(institution_obj))
group.addMember(user.id)
for meeting in institution["meetings"]:
date_time = dateutil.parser.parse(meeting["datetime"])
meeting_obj = content.create(
container=institution_obj,
type="Meeting",
title=meeting["title"],
date_time=date_time,
plonemeeting_last_modified=dateutil.parser.parse(
meeting["plonemeeting_last_modified"]),
)
content.transition(obj=meeting_obj,
transition="send_to_project")
content.transition(obj=meeting_obj, transition="publish")
for item in meeting["items"]:
decision = RichTextValue(item["decision"], "text/html",
"text/html")
item_obj = content.create(
container=meeting_obj,
type="Item",
title=item["title"],
sortable_number=item["sortable_number"],
number=item["number"],
representatives_in_charge=item[
"representatives_in_charge"],
decision=decision,
category=item["category"],
plonemeeting_last_modified=dateutil.parser.parse(
meeting["plonemeeting_last_modified"]),
)
if "files" in item:
for file in item["files"]:
create_file(item_obj, file)