def __call__(self):
form = self.request.form
plone.protect.CheckAuthenticator(form)
workflow = getToolByName(self.context, 'portal_workflow')
rc = getToolByName(self.context, REFERENCE_CATALOG)
action, came_from = WorkflowAction._get_form_workflow_action(self)
if action == 'reassign':
selected_worksheets = WorkflowAction._get_selected_items(self)
selected_worksheet_uids = selected_worksheets.keys()
if selected_worksheets:
changes = False
for uid in selected_worksheet_uids:
worksheet = selected_worksheets[uid]
# Double-check the state first
if workflow.getInfoFor(worksheet, 'review_state') == 'open':
worksheet.setAnalyst(form['Analyst'][0][uid])
changes = True
if changes:
message = self.context.translate(PMF('Changes saved.'))
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.request.get_header("referer",
self.context.absolute_url())
self.request.response.redirect(self.destination_url)
else:
# default bika_listing.py/WorkflowAction for other transitions
WorkflowAction.__call__(self)
def __call__(self):
form = self.request.form
plone.protect.CheckAuthenticator(form)
action, came_from = WorkflowAction._get_form_workflow_action(self)
if action == 'submit':
objects = WorkflowAction._get_selected_items(self)
if not objects:
message = self.context.translate(
_b("No analyses have been selected"))
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.context.absolute_url() + \
"/batchbook"
self.request.response.redirect(self.destination_url)
return
for ar_uid, ar in objects.items():
for analysis in ar.getAnalyses(full_objects=True):
kw = analysis.getKeyword()
values = form.get(kw)
analysis.setResult(values[0][ar_uid])
if values[0][ar_uid]:
doActionFor(analysis, 'submit')
message = self.context.translate(_p("Changes saved."))
self.context.plone_utils.addPortalMessage(message, 'info')
self.request.response.redirect(self.request.get('URL'))
return
else:
WorkflowAction.__call__(self)
def workflow_action_save_analyses_button(self):
form = self.request.form
workflow = getToolByName(self.context, 'portal_workflow')
action, came_from = WorkflowAction._get_form_workflow_action(self)
# AR Manage Analyses: save Analyses
ar = self.context
sample = ar.getSample()
objects = WorkflowAction._get_selected_items(self)
if not objects:
message = _("No analyses have been selected")
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.context.absolute_url() + "/analyses"
self.request.response.redirect(self.destination_url)
return
Analyses = objects.keys()
prices = form.get("Price", [None])[0]
specs = {}
if form.get("min", None):
for service_uid in Analyses:
specs[service_uid] = {
"min": form["min"][0][service_uid],
"max": form["max"][0][service_uid],
"error": form["error"][0][service_uid]
}
else:
for service_uid in Analyses:
specs[service_uid] = {"min": "", "max": "", "error": ""}
new = ar.setAnalyses(Analyses, prices=prices, specs=specs)
# link analyses and partitions
# If Bika Setup > Analyses > 'Display individual sample
# partitions' is checked, no Partitions available.
# https://github.com/bikalabs/Bika-LIMS/issues/1030
if 'Partition' in form:
for service_uid, service in objects.items():
part_id = form['Partition'][0][service_uid]
part = sample[part_id]
analysis = ar[service.getKeyword()]
analysis.setSamplePartition(part)
analysis.reindexObject()
if new:
for analysis in new:
# if the AR has progressed past sample_received, we need to bring it back.
ar_state = workflow.getInfoFor(ar, 'review_state')
if ar_state in ('attachment_due', 'to_be_verified'):
# Apply to AR only; we don't want this transition to cascade.
ar.REQUEST['workflow_skiplist'].append(
"retract all analyses")
workflow.doActionFor(ar, 'retract')
ar.REQUEST['workflow_skiplist'].remove(
"retract all analyses")
ar_state = workflow.getInfoFor(ar, 'review_state')
# Then we need to forward new analyses state
analysis.updateDueDate()
changeWorkflowState(analysis, 'bika_analysis_workflow',
ar_state)
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
def __call__(self):
form = self.request.form
CheckAuthenticator(form)
analysis_uids = form.get("uids", [])
if not analysis_uids:
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
return
action, came_from = WorkflowAction._get_form_workflow_action(self)
if action == "submit":
# Submit the form. Saves the results, methods, etc.
# Calls to its parent class AnalysesWorkflowAction
self.workflow_action_submit()
elif action == "assign":
# Assign the analyses
self.do_assign(analysis_uids)
elif action == "unassign":
# Unassign analyses
self.do_unassign(analysis_uids)
elif action == "verify":
# default bika_listing.py/WorkflowAction, but then go to view
# screen.
self.destination_url = self.context.absolute_url()
return self.workflow_action_default(
action="verify", came_from=came_from)
else:
# default bika_listing.py/WorkflowAction for other transitions
WorkflowAction.__call__(self)
def __call__(self):
form = self.request.form
plone.protect.CheckAuthenticator(form)
workflow = getToolByName(self.context, 'portal_workflow')
rc = getToolByName(self.context, REFERENCE_CATALOG)
action, came_from = WorkflowAction._get_form_workflow_action(self)
if action == 'reassign':
selected_worksheets = WorkflowAction._get_selected_items(self)
selected_worksheet_uids = selected_worksheets.keys()
if selected_worksheets:
changes = False
for uid in selected_worksheet_uids:
worksheet = selected_worksheets[uid]
# Double-check the state first
if workflow.getInfoFor(worksheet,
'review_state') == 'open':
worksheet.setAnalyst(form['Analyst'][0][uid])
changes = True
if changes:
message = self.context.translation_service.translate(
PMF('Changes saved.'))
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.request.get_header(
"referer", self.context.absolute_url())
self.request.response.redirect(self.destination_url)
else:
# default bika_listing.py/WorkflowAction for other transitions
WorkflowAction.__call__(self)
def workflow_action_preserve(self):
form = self.request.form
workflow = getToolByName(self.context, 'portal_workflow')
action, came_from = WorkflowAction._get_form_workflow_action(self)
checkPermission = self.context.portal_membership.checkPermission
# Partition Preservation
# the partition table shown in AR and Sample views sends it's
# action button submits here.
objects = WorkflowAction._get_selected_items(self)
transitioned = []
incomplete = []
for obj_uid, obj in objects.items():
part = obj
# can't transition inactive items
if workflow.getInfoFor(part, 'inactive_state', '') == 'inactive':
continue
if not checkPermission(PreserveSample, part):
continue
# grab this object's Preserver and DatePreserved from the form
Preserver = form['getPreserver'][0][obj_uid].strip()
Preserver = Preserver and Preserver or ''
DatePreserved = form['getDatePreserved'][0][obj_uid].strip()
DatePreserved = DatePreserved and DateTime(DatePreserved) or ''
# write them to the sample
part.setPreserver(Preserver)
part.setDatePreserved(DatePreserved)
# transition the object if both values are present
if Preserver and DatePreserved:
workflow.doActionFor(part, action)
transitioned.append(part.id)
else:
incomplete.append(part.id)
part.reindexObject()
part.aq_parent.reindexObject()
message = None
if len(transitioned) > 1:
message = _('${items} are waiting to be received.',
mapping={'items': safe_unicode(', '.join(transitioned))})
self.context.plone_utils.addPortalMessage(message, 'info')
elif len(transitioned) == 1:
message = _('${item} is waiting to be received.',
mapping={'item': safe_unicode(', '.join(transitioned))})
self.context.plone_utils.addPortalMessage(message, 'info')
if not message:
message = _('No changes made.')
self.context.plone_utils.addPortalMessage(message, 'info')
if len(incomplete) > 1:
message = _('${items} are missing Preserver or Date Preserved',
mapping={'items': safe_unicode(', '.join(incomplete))})
self.context.plone_utils.addPortalMessage(message, 'error')
elif len(incomplete) == 1:
message = _('${item} is missing Preserver or Preservation Date',
mapping={'item': safe_unicode(', '.join(incomplete))})
self.context.plone_utils.addPortalMessage(message, 'error')
self.destination_url = self.request.get_header("referer",
self.context.absolute_url())
self.request.response.redirect(self.destination_url)
def workflow_action_preserve(self):
form = self.request.form
workflow = getToolByName(self.context, 'portal_workflow')
action, came_from = WorkflowAction._get_form_workflow_action(self)
checkPermission = self.context.portal_membership.checkPermission
# Partition Preservation
# the partition table shown in AR and Sample views sends it's
# action button submits here.
objects = WorkflowAction._get_selected_items(self)
transitioned = []
incomplete = []
for obj_uid, obj in objects.items():
part = obj
# can't transition inactive items
if workflow.getInfoFor(part, 'inactive_state', '') == 'inactive':
continue
if not checkPermission(PreserveSample, part):
continue
# grab this object's Preserver and DatePreserved from the form
Preserver = form['getPreserver'][0][obj_uid].strip()
Preserver = Preserver and Preserver or ''
DatePreserved = form['getDatePreserved'][0][obj_uid].strip()
DatePreserved = DatePreserved and DateTime(DatePreserved) or ''
# write them to the sample
part.setPreserver(Preserver)
part.setDatePreserved(DatePreserved)
# transition the object if both values are present
if Preserver and DatePreserved:
workflow.doActionFor(part, action)
transitioned.append(part.id)
else:
incomplete.append(part.id)
part.reindexObject()
part.aq_parent.reindexObject()
message = None
if len(transitioned) > 1:
message = _('${items} are waiting to be received.',
mapping={'items': safe_unicode(', '.join(transitioned))})
self.context.plone_utils.addPortalMessage(message, 'info')
elif len(transitioned) == 1:
message = _('${item} is waiting to be received.',
mapping={'item': safe_unicode(', '.join(transitioned))})
self.context.plone_utils.addPortalMessage(message, 'info')
if not message:
message = _('No changes made.')
self.context.plone_utils.addPortalMessage(message, 'info')
if len(incomplete) > 1:
message = _('${items} are missing Preserver or Date Preserved',
mapping={'items': safe_unicode(', '.join(incomplete))})
self.context.plone_utils.addPortalMessage(message, 'error')
elif len(incomplete) == 1:
message = _('${item} is missing Preserver or Preservation Date',
mapping={'item': safe_unicode(', '.join(incomplete))})
self.context.plone_utils.addPortalMessage(message, 'error')
self.destination_url = self.request.get_header("referer",
self.context.absolute_url())
self.request.response.redirect(self.destination_url)
def workflow_action_receive(self):
# default bika_listing.py/WorkflowAction, but then
# print automatic labels.
if 'receive' in self.context.bika_setup.getAutoPrintLabels():
size = self.context.bika_setup.getAutoLabelSize()
q = "/sticker?size=%s&items=%s" % (size, self.context.getId())
self.destination_url = self.context.absolute_url() + q
WorkflowAction.__call__(self)
def __call__(self):
form = self.request.form
plone.protect.CheckAuthenticator(form)
action, _ = WorkflowAction._get_form_workflow_action(self)
if action == 'receive' and 'Type' in form:
BiospecimenWorkflowAction.__call__(self)
else:
WorkflowAction.__call__(self)
def workflow_action_receive(self):
# default bika_listing.py/WorkflowAction, but then
# print automatic labels.
if 'receive' in self.context.bika_setup.getAutoPrintLabels():
size = self.context.bika_setup.getAutoLabelSize()
q = "/sticker?size=%s&items=%s" % (size, self.context.getId())
self.destination_url = self.context.absolute_url() + q
WorkflowAction.__call__(self)
def __call__(self):
form = self.request.form
plone.protect.CheckAuthenticator(form)
workflow = getToolByName(self.context, 'portal_workflow')
rc = getToolByName(self.context, REFERENCE_CATALOG)
uc = getToolByName(self.context, 'uid_catalog')
action, came_from = WorkflowAction._get_form_workflow_action(self)
if action == 'duplicate':
selected_services = WorkflowAction._get_selected_items(self)
## Create a copy of the selected services
folder = self.context.bika_setup.bika_analysisservices
created = []
for service in selected_services.values():
_id = folder.invokeFactory('AnalysisService', id = 'tmp')
dup = folder[_id]
dup.setTitle('%s (copy)' % service.Title())
_id = renameAfterCreation(dup)
dup.edit(
description = service.Description(),
PointOfCapture = service.getPointOfCapture(),
ReportDryMatter = service.getReportDryMatter(),
Unit = service.getUnit(),
Precision = service.getPrecision(),
Price = service.getPrice(),
CorporatePrice = service.getCorporatePrice(),
VAT = service.getVAT(),
Calculation = service.getCalculation(),
Instrument = service.getInstrument(),
MaxTimeAllowed = service.getMaxTimeAllowed(),
DuplicateVariation = service.getDuplicateVariation(),
Category = service.getCategory(),
Department = service.getDepartment(),
Accredited = service.getAccredited(),
Uncertainties = service.getUncertainties(),
ResultOptions = service.getResultOptions()
)
created.append(_id)
if len(created) > 1:
message = self.context.translation_service.translate(
_('Services ${services} were successfully created.',
mapping = {'services': ', '.join(created)}))
self.destination_url = self.request.get_header("referer",
self.context.absolute_url())
else:
message = self.context.translation_service.translate(
_('Analysis request ${service} was successfully created.',
mapping = {'service': ', '.join(created)}))
self.destination_url = dup.absolute_url() + "/base_edit"
self.context.plone_utils.addPortalMessage(message, 'info')
self.request.response.redirect(self.destination_url)
else:
# default bika_listing.py/WorkflowAction for other transitions
WorkflowAction.__call__(self)
def workflow_action_save_analyses_button(self):
form = self.request.form
workflow = getToolByName(self.context, 'portal_workflow')
action, came_from = WorkflowAction._get_form_workflow_action(self)
# AR Manage Analyses: save Analyses
ar = self.context
sample = ar.getSample()
objects = WorkflowAction._get_selected_items(self)
if not objects:
message = _("No analyses have been selected")
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.context.absolute_url() + "/analyses"
self.request.response.redirect(self.destination_url)
return
Analyses = objects.keys()
prices = form.get("Price", [None])[0]
specs = {}
if form.get("min", None):
for service_uid in Analyses:
specs[service_uid] = {
"min": form["min"][0][service_uid],
"max": form["max"][0][service_uid],
"error": form["error"][0][service_uid]
}
else:
for service_uid in Analyses:
specs[service_uid] = {"min": "", "max": "", "error": ""}
new = ar.setAnalyses(Analyses, prices=prices, specs=specs)
# link analyses and partitions
# If Bika Setup > Analyses > 'Display individual sample
# partitions' is checked, no Partitions available.
# https://github.com/bikalabs/Bika-LIMS/issues/1030
if 'Partition' in form:
for service_uid, service in objects.items():
part_id = form['Partition'][0][service_uid]
part = sample[part_id]
analysis = ar[service.getKeyword()]
analysis.setSamplePartition(part)
analysis.reindexObject()
if new:
for analysis in new:
# if the AR has progressed past sample_received, we need to bring it back.
ar_state = workflow.getInfoFor(ar, 'review_state')
if ar_state in ('attachment_due', 'to_be_verified'):
# Apply to AR only; we don't want this transition to cascade.
ar.REQUEST['workflow_skiplist'].append("retract all analyses")
workflow.doActionFor(ar, 'retract')
ar.REQUEST['workflow_skiplist'].remove("retract all analyses")
ar_state = workflow.getInfoFor(ar, 'review_state')
# Then we need to forward new analyses state
analysis.updateDueDate()
changeWorkflowState(analysis, 'bika_analysis_workflow', ar_state)
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
def __call__(self):
form = self.request.form
plone.protect.CheckAuthenticator(form)
workflow = getToolByName(self.context, 'portal_workflow')
rc = getToolByName(self.context, REFERENCE_CATALOG)
uc = getToolByName(self.context, 'uid_catalog')
action, came_from = WorkflowAction._get_form_workflow_action(self)
if action == 'duplicate':
selected_services = WorkflowAction._get_selected_items(self)
## Create a copy of the selected services
folder = self.context.bika_setup.bika_analysisservices
created = []
for service in selected_services.values():
_id = folder.invokeFactory('AnalysisService', id='tmp')
dup = folder[_id]
dup.setTitle('%s (copy)' % service.Title())
_id = renameAfterCreation(dup)
dup.edit(description=service.Description(),
PointOfCapture=service.getPointOfCapture(),
ReportDryMatter=service.getReportDryMatter(),
Unit=service.getUnit(),
Precision=service.getPrecision(),
Price=service.getPrice(),
CorporatePrice=service.getCorporatePrice(),
VAT=service.getVAT(),
Calculation=service.getCalculation(),
Instrument=service.getInstrument(),
MaxTimeAllowed=service.getMaxTimeAllowed(),
DuplicateVariation=service.getDuplicateVariation(),
Category=service.getCategory(),
Department=service.getDepartment(),
Accredited=service.getAccredited(),
Uncertainties=service.getUncertainties(),
ResultOptions=service.getResultOptions())
created.append(_id)
if len(created) > 1:
message = self.context.translation_service.translate(
_('Services ${services} were successfully created.',
mapping={'services': ', '.join(created)}))
self.destination_url = self.request.get_header(
"referer", self.context.absolute_url())
else:
message = self.context.translation_service.translate(
_('Analysis request ${service} was successfully created.',
mapping={'service': ', '.join(created)}))
self.destination_url = dup.absolute_url() + "/base_edit"
self.context.plone_utils.addPortalMessage(message, 'info')
self.request.response.redirect(self.destination_url)
else:
# default bika_listing.py/WorkflowAction for other transitions
WorkflowAction.__call__(self)
def __call__(self):
form = self.request.form
plone.protect.CheckAuthenticator(form)
action, _ = WorkflowAction._get_form_workflow_action(self)
if action == 'receive' and 'Type' in form:
BiospecimenWorkflowAction.__call__(self)
elif action == 'receive' and 'AliquotType' in form:
AliquotWorkflowAction.__call__(self)
else:
WorkflowAction.__call__(self)
def __call__(self):
form = self.request.form
plone.protect.CheckAuthenticator(form)
action, _ = WorkflowAction._get_form_workflow_action(self)
if type(action) in (list, tuple):
action = action[0]
# Call out to the workflow action method
method_name = 'workflow_action_' + action
method = getattr(self, method_name, False)
if method:
method()
else:
WorkflowAction.__call__(self)
def __call__(self):
form = self.request.form
plone.protect.CheckAuthenticator(form)
action, _ = WorkflowAction._get_form_workflow_action(self)
if type(action) in (list, tuple):
action = action[0]
# Call out to the workflow action method
method_name = 'workflow_action_' + action
method = getattr(self, method_name, False)
if method:
method()
else:
WorkflowAction.__call__(self)
def workflow_action_keep(self):
workflow = getToolByName(self.context, 'portal_workflow')
action, came_from = WorkflowAction._get_form_workflow_action(self)
objects = WorkflowAction._get_selected_items(self)
for obj_uid, obj in objects.items():
pitem = obj
old_d = pitem.Description()
new_message = "\n*** Restored in Inventory at " + time.strftime("%c") + " ***\n"
pitem.setDescription(old_d + new_message)
pitem.reindexObject()
workflow.doActionFor(pitem, action)
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
def __call__(self):
form = self.request.form
plone.protect.CheckAuthenticator(form)
action, came_from = WorkflowAction._get_form_workflow_action(self)
if type(action) in (list, tuple):
action = action[0]
if type(came_from) in (list, tuple):
came_from = came_from[0]
# Call out to the workflow action method
# Use default bika_listing.py/WorkflowAction for other transitions
method_name = 'workflow_action_' + action
method = getattr(self, method_name, False)
if method:
method()
else:
WorkflowAction.__call__(self)
def workflow_action_sample_due(self):
form = self.request.form
selected_biospecimens = WorkflowAction._get_selected_items(self)
biospecimens = []
for uid in selected_biospecimens.keys():
if not form['Barcode'][0][uid] or \
not form['Type'][0][uid]:
continue
try:
obj = selected_biospecimens.get(uid, None)
obj.getField('Barcode').set(obj, form['Barcode'][0][uid])
obj.getField('SampleType').set(obj, form['Type'][0][uid])
obj.setId(form['Barcode'][0][uid])
obj.edit(SampleID=obj.getId())
obj.reindexObject()
biospecimens.append(obj)
except ReferenceException:
continue
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, 'info')
for biospecimen in biospecimens:
doActionFor(biospecimen, 'sample_due')
for partition in biospecimen.objectValues('SamplePartition'):
doActionFor(partition, 'sample_due')
self.destination_url = self.context.absolute_url()
if form['portal_type'] == 'Kit' or \
form['portal_type'] == 'SampleBatch':
self.destination_url = form['view_url']
self.destination_url += '/biospecimens'
self.request.response.redirect(self.destination_url)
def workflow_action_verify(self):
# default bika_listing.py/WorkflowAction, but then go to view screen.
self.destination_url = self.context.absolute_url()
action, came_from = WorkflowAction._get_form_workflow_action(self)
if type(came_from) in (list, tuple):
came_from = came_from[0]
return self.workflow_action_default(action="verify", came_from=came_from)
def workflow_action_deactivate(self):
context = self.context
selected_elements = WorkflowAction._get_selected_items(self)
catalog = getToolByName(self, 'portal_catalog')
# import pdb;pdb.set_trace()
for uid in selected_elements.keys():
try:
obj = selected_elements.get(uid, None)
units = []
if obj.portal_type in ['ManagedStorage', 'UnmanagedStorage']:
units.append(obj)
else:
unit_path = '/'.join(obj.getPhysicalPath())
brains = catalog(portal_type=[
'StorageUnit', 'UnmanagedStorage', 'ManagedStorage'
],
path={
'query': unit_path,
'level': 0
})
units += [brain.getObject() for brain in brains]
for unit in units:
review_state = context.portal_workflow.getInfoFor(
unit, 'inactive_state')
if review_state == 'active':
context.portal_workflow.doActionFor(unit, 'deactivate')
except ReferenceException:
pass
self.request.response.redirect(context.absolute_url())
def workflow_action_verify(self):
# default bika_listing.py/WorkflowAction, but then go to view screen.
self.destination_url = self.context.absolute_url()
action, came_from = WorkflowAction._get_form_workflow_action(self)
if type(came_from) in (list, tuple):
came_from = came_from[0]
return self.workflow_action_default(action='verify', came_from=came_from)
def workflow_action_aliquot_receive(self):
form = self.request.form
selected_aliquots = WorkflowAction._get_selected_items(self)
aliquots = []
for uid in selected_aliquots.keys():
if not form["AliquotType"][0][uid] or not form["Volume"][0][uid] or not form["Unit"][0][uid]:
continue
try:
aliquot = selected_aliquots.get(uid, None)
aliquot.getField("SampleType").set(aliquot, form["AliquotType"][0][uid])
aliquot.getField("Volume").set(aliquot, form["Volume"][0][uid])
unit = "ml"
for u in VOLUME_UNITS:
if u["ResultValue"] == form["Unit"][0][uid]:
unit = u["ResultText"]
aliquot.getField("Unit").set(aliquot, unit)
aliquot.reindexObject()
aliquots.append(aliquot)
except ReferenceException:
continue
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, "info")
for aliquot in aliquots:
doActionFor(aliquot, "receive")
for partition in aliquot.objectValues("SamplePartition"):
doActionFor(partition, "receive")
self.destination_url = self.context.absolute_url()
if self.context.portal_type == "Project":
self.destination_url += "/aliquots"
self.request.response.redirect(self.destination_url)
def __call__(self):
form = self.request.form
plone.protect.CheckAuthenticator(form)
action, came_from = WorkflowAction._get_form_workflow_action(self)
if type(action) in (list, tuple):
action = action[0]
if type(came_from) in (list, tuple):
came_from = came_from[0]
# Call out to the workflow action method
# Use default bika_listing.py/WorkflowAction for other transitions
method_name = 'workflow_action_' + action
method = getattr(self, method_name, False)
if method:
method()
else:
WorkflowAction.__call__(self)
def workflow_action_schedule_sampling(self):
"""
This function prevent the transition if the fields "SamplingDate"
and "ScheduledSamplingSampler" are uncompleted.
:return: bool
"""
from bika.lims.utils.workflow import schedulesampling
message = "Not expected transition."
# In Samples Folder we have to get each selected item
if interfaces.ISamplesFolder.providedBy(self.context):
select_objs = WorkflowAction._get_selected_items(self)
message = _("Transition done.")
for key in select_objs.keys():
sample = select_objs[key]
# Getting the sampler
sch_sampl = (
self.request.form.get("getScheduledSamplingSampler", None)[0].get(key)
if self.request.form.get("getScheduledSamplingSampler", None)
else ""
)
# Getting the date
sampl_date = (
self.request.form.get("getSamplingDate", None)[0].get(key)
if self.request.form.get("getSamplingDate", None)
else ""
)
# Setting both values
sample.setScheduledSamplingSampler(sch_sampl)
sample.setSamplingDate(sampl_date)
# Transitioning the sample
success, errmsg = schedulesampling.doTransition(sample)
if errmsg == "missing":
message = _(
"'Sampling date' and 'Define the Sampler for the"
+ " scheduled sampling' must be completed and saved "
+ "in order to schedule a sampling. Element: %s" % sample.getId()
)
elif errmsg == "cant_trans":
message = _("The item %s can't be transitioned." % sample.getId())
else:
message = _("Transition done.")
self.context.plone_utils.addPortalMessage(message, "info")
else:
success, errmsg = schedulesampling.doTransition(self.context)
if errmsg == "missing":
message = _(
"'Sampling date' and 'Define the Sampler for the"
+ " scheduled sampling' must be completed and saved in "
+ "order to schedule a sampling."
)
elif errmsg == "cant_trans":
message = _("The item can't be transitioned.")
else:
message = _("Transition done.")
self.context.plone_utils.addPortalMessage(message, "info")
# Reload the page in order to show the portal message
self.request.response.redirect(self.context.absolute_url())
return success
def __call__(self):
form = self.request.form
plone.protect.CheckAuthenticator(form)
workflow = getToolByName(self.context, 'portal_workflow')
rc = getToolByName(self.context, REFERENCE_CATALOG)
action, came_from = WorkflowAction._get_form_workflow_action(self)
if action == 'reassign':
mtool = getToolByName(self.context, 'portal_membership')
if not mtool.checkPermission(ManageWorksheets, self.context):
# Redirect to WS list
msg = _('You do not have sufficient privileges to '
'manage worksheets.')
self.context.plone_utils.addPortalMessage(msg, 'warning')
portal = getToolByName(self.context,
'portal_url').getPortalObject()
self.destination_url = portal.absolute_url() + "/worksheets"
self.request.response.redirect(self.destination_url)
return
selected_worksheets = WorkflowAction._get_selected_items(self)
selected_worksheet_uids = selected_worksheets.keys()
if selected_worksheets:
changes = False
for uid in selected_worksheet_uids:
worksheet = selected_worksheets[uid]
# Double-check the state first
if workflow.getInfoFor(worksheet,
'review_state') == 'open':
worksheet.setAnalyst(form['Analyst'][0][uid])
worksheet.reindexObject(idxs=['getAnalyst'])
changes = True
if changes:
message = PMF('Changes saved.')
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.request.get_header(
"referer", self.context.absolute_url())
self.request.response.redirect(self.destination_url)
else:
# default bika_listing.py/WorkflowAction for other transitions
WorkflowAction.__call__(self)
def workflow_action_publish(self):
action, came_from = WorkflowAction._get_form_workflow_action(self)
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
# AR publish preview
self.request.response.redirect(self.context.absolute_url() + "/publish")
def workflow_action_publish(self):
action, came_from = WorkflowAction._get_form_workflow_action(self)
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
# AR publish preview
self.request.response.redirect(self.context.absolute_url() + "/publish")
def workflow_action_save_partitions_button(self):
form = self.request.form
# Sample Partitions or AR Manage Analyses: save Partition Table
sample = self.context.portal_type == 'Sample' and self.context or\
self.context.getSample()
part_prefix = sample.getId() + "-P"
nr_existing = len(sample.objectIds())
nr_parts = len(form['PartTitle'][0])
# add missing parts
if nr_parts > nr_existing:
for i in range(nr_parts - nr_existing):
part = _createObjectByType("SamplePartition", sample, tmpID())
part.setDateReceived = DateTime()
part.processForm()
# remove excess parts
if nr_existing > nr_parts:
for i in range(nr_existing - nr_parts):
part = sample['%s%s' % (part_prefix, nr_existing - i)]
analyses = part.getAnalyses()
for a in analyses:
a.setSamplePartition(None)
sample.manage_delObjects([
'%s%s' % (part_prefix, nr_existing - i),
])
# modify part container/preservation
for part_uid, part_id in form['PartTitle'][0].items():
part = sample["%s%s" %
(part_prefix, part_id.split(part_prefix)[1])]
part.edit(
Container=form['getContainer'][0][part_uid],
Preservation=form['getPreservation'][0][part_uid],
)
part.reindexObject()
# Adding the Security Seal Intact checkbox's value to the container object
container_uid = form['getContainer'][0][part_uid]
uc = getToolByName(self.context, 'uid_catalog')
cbr = uc(UID=container_uid)
if cbr and len(cbr) > 0:
container_obj = cbr[0].getObject()
else:
continue
value = form.get('setSecuritySealIntact', {}).get(part_uid,
'') == 'on'
container_obj.setSecuritySealIntact(value)
objects = WorkflowAction._get_selected_items(self)
if not objects:
message = _("No items have been selected")
self.context.plone_utils.addPortalMessage(message, 'info')
if self.context.portal_type == 'Sample':
# in samples his table is on 'Partitions' tab
self.destination_url = self.context.absolute_url() +\
"/partitions"
else:
# in ar context this table is on 'ManageAnalyses' tab
self.destination_url = self.context.absolute_url() +\
"/analyses"
self.request.response.redirect(self.destination_url)
def workflow_action_schedule_sampling(self):
"""
This function prevent the transition if the fields "SamplingDate"
and "ScheduledSamplingSampler" are uncompleted.
:return: bool
"""
from bika.lims.utils.workflow import schedulesampling
message = 'Not expected transition.'
# In Samples Folder we have to get each selected item
if interfaces.ISamplesFolder.providedBy(self.context):
select_objs = WorkflowAction._get_selected_items(self)
message = _('Transition done.')
for key in select_objs.keys():
sample = select_objs[key]
# Getting the sampler
sch_sampl = self.request.form.get(
'getScheduledSamplingSampler', None)[0].get(key) if\
self.request.form.get(
'getScheduledSamplingSampler', None) else ''
# Getting the date
sampl_date = self.request.form.get(
'getSamplingDate', None)[0].get(key) if\
self.request.form.get(
'getSamplingDate', None) else ''
# Setting both values
sample.setScheduledSamplingSampler(sch_sampl)
sample.setSamplingDate(sampl_date)
# Transitioning the sample
success, errmsg = schedulesampling.doTransition(sample)
if errmsg == 'missing':
message = _(
"'Sampling date' and 'Define the Sampler for the" +
" scheduled sampling' must be completed and saved " +
"in order to schedule a sampling. Element: %s" %
sample.getId())
elif errmsg == 'cant_trans':
message = _(
"The item %s can't be transitioned." % sample.getId())
else:
message = _('Transition done.')
self.context.plone_utils.addPortalMessage(message, 'info')
else:
success, errmsg = schedulesampling.doTransition(self.context)
if errmsg == 'missing':
message = _(
"'Sampling date' and 'Define the Sampler for the" +
" scheduled sampling' must be completed and saved in " +
"order to schedule a sampling.")
elif errmsg == 'cant_trans':
message = _("The item can't be transitioned.")
else:
message = _('Transition done.')
self.context.plone_utils.addPortalMessage(message, 'info')
# Reload the page in order to show the portal message
self.request.response.redirect(self.context.absolute_url())
return success
def __call__(self):
form = self.request.form
CheckAuthenticator(form)
workflow = getToolByName(self.context, 'portal_workflow')
rc = getToolByName(self.context, REFERENCE_CATALOG)
action, came_from = WorkflowAction._get_form_workflow_action(self)
if action == 'reassign':
mtool = getToolByName(self.context, 'portal_membership')
if not mtool.checkPermission(ManageWorksheets, self.context):
# Redirect to WS list
msg = _('You do not have sufficient privileges to '
'manage worksheets.')
self.context.plone_utils.addPortalMessage(msg, 'warning')
portal = getToolByName(self.context, 'portal_url').getPortalObject()
self.destination_url = portal.absolute_url() + "/worksheets"
self.request.response.redirect(self.destination_url)
return
selected_worksheets = WorkflowAction._get_selected_items(self)
selected_worksheet_uids = selected_worksheets.keys()
if selected_worksheets:
changes = False
for uid in selected_worksheet_uids:
worksheet = selected_worksheets[uid]
# Double-check the state first
if workflow.getInfoFor(worksheet, 'review_state') == 'open':
worksheet.setAnalyst(form['Analyst'][0][uid])
worksheet.reindexObject(idxs=['getAnalyst'])
changes = True
if changes:
message = PMF('Changes saved.')
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.request.get_header("referer",
self.context.absolute_url())
self.request.response.redirect(self.destination_url)
else:
# default bika_listing.py/WorkflowAction for other transitions
WorkflowAction.__call__(self)
def __call__(self):
form = self.request.form
CheckAuthenticator(form)
action, came_from = WorkflowAction._get_form_workflow_action(self)
if action == "reassign":
mtool = api.get_tool("portal_membership")
if not mtool.checkPermission(ManageWorksheets, self.context):
# Redirect to WS list
msg = _("You do not have sufficient privileges to "
"manage worksheets.")
self.context.plone_utils.addPortalMessage(msg, "warning")
portal = api.get_portal()
self.destination_url = portal.absolute_url() + "/worksheets"
self.request.response.redirect(self.destination_url)
return
selected_worksheets = WorkflowAction._get_selected_items(self)
selected_worksheet_uids = selected_worksheets.keys()
if selected_worksheets:
changes = False
for uid in selected_worksheet_uids:
worksheet = selected_worksheets[uid]
# Double-check the state first
if api.get_workflow_status_of(worksheet) == "open":
analyst = form["Analyst"][0][uid]
worksheet.setAnalyst(analyst)
worksheet.reindexObject(idxs=["getAnalyst"])
changes = True
if changes:
message = _("Changes saved.")
self.context.plone_utils.addPortalMessage(message, "info")
self.destination_url = self.request.get_header(
"referer", self.context.absolute_url())
self.request.response.redirect(self.destination_url)
else:
# default bika_listing.py/WorkflowAction for other transitions
WorkflowAction.__call__(self)
def workflow_action_save_partitions_button(self):
form = self.request.form
# Sample Partitions or AR Manage Analyses: save Partition Table
sample = self.context.portal_type == 'Sample' and self.context or\
self.context.getSample()
part_prefix = sample.getId() + "-P"
nr_existing = len(sample.objectIds())
nr_parts = len(form['PartTitle'][0])
# add missing parts
if nr_parts > nr_existing:
for i in range(nr_parts - nr_existing):
part = _createObjectByType("SamplePartition", sample, tmpID())
part.setDateReceived = DateTime()
part.processForm()
# remove excess parts
if nr_existing > nr_parts:
for i in range(nr_existing - nr_parts):
part = sample['%s%s' % (part_prefix, nr_existing - i)]
for a in part.getBackReferences("AnalysisSamplePartition"):
a.setSamplePartition(None)
sample.manage_delObjects(['%s%s' % (part_prefix, nr_existing - i), ])
# modify part container/preservation
for part_uid, part_id in form['PartTitle'][0].items():
part = sample["%s%s" % (part_prefix, part_id.split(part_prefix)[1])]
part.edit(
Container=form['getContainer'][0][part_uid],
Preservation=form['getPreservation'][0][part_uid],
)
part.reindexObject()
# Adding the Security Seal Intact checkbox's value to the container object
container_uid = form['getContainer'][0][part_uid]
uc = getToolByName(self.context, 'uid_catalog')
cbr = uc(UID=container_uid)
if cbr and len(cbr) > 0:
container_obj = cbr[0].getObject()
else:
continue
value = form.get('setSecuritySealIntact', {}).get(part_uid, '') == 'on'
container_obj.setSecuritySealIntact(value)
objects = WorkflowAction._get_selected_items(self)
if not objects:
message = _("No items have been selected")
self.context.plone_utils.addPortalMessage(message, 'info')
if self.context.portal_type == 'Sample':
# in samples his table is on 'Partitions' tab
self.destination_url = self.context.absolute_url() +\
"/partitions"
else:
# in ar context this table is on 'ManageAnalyses' tab
self.destination_url = self.context.absolute_url() +\
"/analyses"
self.request.response.redirect(self.destination_url)
def workflow_action_publish(self):
action, came_from = WorkflowAction._get_form_workflow_action(self)
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
# AR publish preview
uids = self.request.form.get('uids', [self.context.UID()])
items = ",".join(uids)
self.request.response.redirect(self.context.portal_url() +
"/analysisrequests/publish?items=" +
items)
def workflow_action_copy_to_new(self):
# Pass the selected AR UIDs in the request, to ar_add.
objects = WorkflowAction._get_selected_items(self)
if not objects:
message = _("No analyses have been selected")
self.context.plone_utils.addPortalMessage(message, 'info')
referer = self.request.get_header("referer")
self.request.response.redirect(referer)
return
url = self.context.absolute_url() + "/ar_add" + \
"?ar_count={0}".format(len(objects)) + \
"©_from={0}".format(",".join(reversed(objects.keys())))
self.request.response.redirect(url)
return
def workflow_action_copy_to_new(self):
# Pass the selected AR UIDs in the request, to ar_add.
objects = WorkflowAction._get_selected_items(self)
if not objects:
message = _("No analyses have been selected")
self.context.plone_utils.addPortalMessage(message, 'info')
referer = self.request.get_header("referer")
self.request.response.redirect(referer)
return
url = self.context.absolute_url() + "/ar_add" + \
"?ar_count={0}".format(len(objects)) + \
"©_from={0}".format(",".join(objects.keys()))
self.request.response.redirect(url)
return
def workflow_action_receive(self):
action, came_from = WorkflowAction._get_form_workflow_action(self)
items = [self.context] if came_from == "workflow_action" else self._get_selected_items().values()
trans, dest = self.submitTransition(action, came_from, items)
if trans and "receive" in self.context.bika_setup.getAutoPrintStickers():
transitioned = [item.id for item in items]
tmpl = self.context.bika_setup.getAutoStickerTemplate()
q = "/sticker?autoprint=1&template=%s&items=" % tmpl
q += ",".join(transitioned)
self.request.response.redirect(self.context.absolute_url() + q)
elif trans:
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, "info")
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
def workflow_action_receive(self):
action, came_from = WorkflowAction._get_form_workflow_action(self)
items = [self.context,] if came_from == 'workflow_action' \
else self._get_selected_items().values()
trans, dest = self.submitTransition(action, came_from, items)
if trans and 'receive' in self.context.bika_setup.getAutoPrintStickers():
transitioned = [item.id for item in items]
tmpl = self.context.bika_setup.getAutoStickerTemplate()
q = "/sticker?template=%s&items=" % tmpl
q += ",".join(transitioned)
self.request.response.redirect(self.context.absolute_url() + q)
elif trans:
message = PMF('Changes saved.')
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
def workflow_action_receive(self):
action, came_from = WorkflowAction._get_form_workflow_action(self)
items = [self.context,] if came_from == 'workflow_action' \
else self._get_selected_items().values()
trans, dest = self.submitTransition(action, came_from, items)
if trans and 'receive' in self.context.bika_setup.getAutoPrintLabels():
transitioned = [item.id for item in items]
size = self.context.bika_setup.getAutoLabelSize()
q = "/sticker?size=%s&items=" % size
q += ",".join(transitioned)
self.request.response.redirect(self.context.absolute_url() + q)
elif trans:
message = PMF('Changes saved.')
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
def workflow_action_sample_due(self):
form = self.request.form
selected_biospecimens = WorkflowAction._get_selected_items(self)
biospecimens = []
for uid in selected_biospecimens.keys():
if not form['Barcode'][0][uid] or \
not form['Type'][0][uid]:
continue
try:
obj = selected_biospecimens.get(uid, None)
if 'Barcode' in form and form['Barcode'][0][uid]:
obj.getField('Barcode').set(obj, form['Barcode'][0][uid])
obj.setId(form['Barcode'][0][uid])
if 'Type' in form and form['Type'][0][uid]:
obj.getField('SampleType').set(obj, form['Type'][0][uid])
if 'FrozenTime' in form and form['FrozenTime'][0][uid]:
if not self.frozen_time_format_is_valid(form['FrozenTime'][0][uid]):
self.context.plone_utils.addPortalMessage('Invalid frozen datetime for %s has been removed. Please complete this batch first and then edit the aliquot separately to enter the frozen time.' % form['Barcode'][0][uid], 'error')
else:
obj.getField('FrozenTime').set(obj, form['FrozenTime'][0][uid])
min_volume = obj.getSampleType().getMinimumVolume()
volume_unit = min_volume.split(' ')
if min_volume and len(volume_unit) == 2:
obj.getField('Volume').set(obj, volume_unit[0])
obj.getField('Unit').set(obj, volume_unit[1])
obj.edit(SampleID=obj.getId())
obj.reindexObject()
biospecimens.append(obj)
except ReferenceException:
continue
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, 'info')
for biospecimen in biospecimens:
doActionFor(biospecimen, 'sample_due')
for partition in biospecimen.objectValues('SamplePartition'):
doActionFor(partition, 'sample_due')
self.destination_url = self.context.absolute_url()
if form['portal_type'] == 'Kit' or \
form['portal_type'] == 'SampleBatch':
self.destination_url = form['view_url']
self.destination_url += '/biospecimens'
self.request.response.redirect(self.destination_url)
def workflow_action_receive(self):
form = self.request.form
# print form
selected_biospecimens = WorkflowAction._get_selected_items(self)
biospecimens = []
for uid in selected_biospecimens.keys():
if not form['Volume'][0][uid] or \
not form['Unit'][0][uid] or \
not form['SubjectID'][0][uid]:
continue
try:
obj = selected_biospecimens.get(uid, None)
obj.getField('Volume').set(obj, form['Volume'][0][uid])
obj.getField('SubjectID').set(obj, form['SubjectID'][0][uid])
if 'Unit' in form and form['Unit'][0][uid]:
unit = 'ml'
for u in VOLUME_UNITS:
if u['ResultText'] == form['Unit'][0][uid]:
unit = u['ResultText']
obj.getField('Unit').set(obj, unit)
location = obj.getStorageLocation()
if location:
doActionFor(location, 'occupy')
obj.reindexObject()
biospecimens.append(obj)
except ReferenceException:
continue
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, 'info')
for biospecimen in biospecimens:
doActionFor(biospecimen, 'receive')
for partition in biospecimen.objectValues('SamplePartition'):
doActionFor(partition, 'receive')
self.destination_url = self.context.absolute_url()
if form['portal_type'] == 'Kit' or \
form['portal_type'] == 'SampleBatch':
self.destination_url = form['view_url']
self.destination_url += '/biospecimens'
self.request.response.redirect(self.destination_url)
def workflow_action_save_partitions_button(self):
form = self.request.form
# Sample Partitions or AR Manage Analyses: save Partition Table
sample = self.context.portal_type == 'Sample' and self.context or\
self.context.getSample()
part_prefix = sample.getId() + "-P"
nr_existing = len(sample.objectIds())
nr_parts = len(form['PartTitle'][0])
# add missing parts
if nr_parts > nr_existing:
for i in range(nr_parts - nr_existing):
part = _createObjectByType("SamplePartition", sample, tmpID())
part.setDateReceived = DateTime()
part.processForm()
# remove excess parts
if nr_existing > nr_parts:
for i in range(nr_existing - nr_parts):
part = sample['%s%s' % (part_prefix, nr_existing - i)]
for a in part.getBackReferences("AnalysisSamplePartition"):
a.setSamplePartition(None)
sample.manage_delObjects([
'%s%s' % (part_prefix, nr_existing - i),
])
# modify part container/preservation
for part_uid, part_id in form['PartTitle'][0].items():
part = sample["%s%s" %
(part_prefix, part_id.split(part_prefix)[1])]
part.edit(
Container=form['getContainer'][0][part_uid],
Preservation=form['getPreservation'][0][part_uid],
)
part.reindexObject()
objects = WorkflowAction._get_selected_items(self)
if not objects:
message = _("No items have been selected")
self.context.plone_utils.addPortalMessage(message, 'info')
if self.context.portal_type == 'Sample':
# in samples his table is on 'Partitions' tab
self.destination_url = self.context.absolute_url() +\
"/partitions"
else:
# in ar context this table is on 'ManageAnalyses' tab
self.destination_url = self.context.absolute_url() +\
"/analyses"
self.request.response.redirect(self.destination_url)
def workflow_action_receive(self):
form = self.request.form
# print form
selected_biospecimens = WorkflowAction._get_selected_items(self)
biospecimens = []
for uid in selected_biospecimens.keys():
if not form['Barcode'][0][uid] or \
not form['Type'][0][uid] or \
not form['Volume'][0][uid] or \
not form['Unit'][0][uid] or \
not form['SubjectID'][0][uid]:
continue
try:
obj = selected_biospecimens.get(uid, None)
obj.getField('Barcode').set(obj, form['Barcode'][0][uid])
obj.getField('SampleType').set(obj, form['Type'][0][uid])
obj.getField('Volume').set(obj, form['Volume'][0][uid])
obj.getField('SubjectID').set(obj, form['SubjectID'][0][uid])
unit = 'ml'
for u in VOLUME_UNITS:
if u['ResultValue'] == form['Unit'][0][uid]:
unit = u['ResultText']
obj.getField('Unit').set(obj, unit)
obj.reindexObject()
biospecimens.append(obj)
except ReferenceException:
continue
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, 'info')
for biospecimen in biospecimens:
doActionFor(biospecimen, 'receive')
for partition in biospecimen.objectValues('SamplePartition'):
doActionFor(partition, 'receive')
self.destination_url = self.context.absolute_url()
if self.context.portal_type == 'Project':
self.destination_url += '/biospecimens'
self.request.response.redirect(self.destination_url)
def workflow_action_publish(self):
action, came_from = WorkflowAction._get_form_workflow_action(self)
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
# publish entire AR.
self.context.setDatePublished(DateTime())
transitioned = self.doPublish(self.context,
self.request,
action,
[self.context, ])()
if len(transitioned) == 1:
message = _(
'${items} published.',
mapping={'items': safe_unicode(', '.join(transitioned))})
else:
message = _("No items were published")
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.request.get_header("referer",
self.context.absolute_url())
self.request.response.redirect(self.destination_url)
def workflow_action_aliquot_receive(self):
form = self.request.form
selected_aliquots = WorkflowAction._get_selected_items(self)
aliquots = []
for uid in selected_aliquots.keys():
if not form['AliquotType'][0][uid] or \
not form['Volume'][0][uid] or \
not form['Unit'][0][uid]:
continue
try:
aliquot = selected_aliquots.get(uid, None)
aliquot.getField('SampleType').set(aliquot,
form['AliquotType'][0][uid])
aliquot.getField('Volume').set(aliquot, form['Volume'][0][uid])
unit = 'ml'
for u in VOLUME_UNITS:
if u['ResultValue'] == form['Unit'][0][uid]:
unit = u['ResultText']
aliquot.getField('Unit').set(aliquot, unit)
aliquot.reindexObject()
aliquots.append(aliquot)
except ReferenceException:
continue
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, 'info')
for aliquot in aliquots:
doActionFor(aliquot, 'receive')
for partition in aliquot.objectValues('SamplePartition'):
doActionFor(partition, 'receive')
self.destination_url = self.context.absolute_url()
if self.context.portal_type == 'Project':
self.destination_url += '/aliquots'
self.request.response.redirect(self.destination_url)
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]
# 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]);
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 submit(self):
""" Saves the form
"""
form = self.request.form
remarks = form.get('Remarks', [{}])[0]
results = form.get('Result', [{}])[0]
retested = form.get('retested', {})
methods = form.get('Method', [{}])[0]
instruments = 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]
selected = WorkflowAction._get_selected_items(self)
workflow = getToolByName(self.context, 'portal_workflow')
rc = getToolByName(self.context, REFERENCE_CATALOG)
sm = getSecurityManager()
hasInterims = {}
# XXX combine data from multiple bika listing tables.
item_data = {}
if 'item_data' in form:
if type(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'])
# Iterate for each selected analysis and save its data as needed
for uid, analysis in selected.items():
allow_edit = sm.checkPermission(EditResults, analysis)
analysis_active = isActive(analysis)
# Need to save remarks?
if uid in remarks and allow_edit and analysis_active:
analysis.setRemarks(remarks[uid])
# Retested?
if uid in retested and allow_edit and analysis_active:
analysis.setRetested(retested[uid])
# 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)
if analysis.meta_type == 'ReferenceAnalysis':
instrument.setDisposeUntilNextCalibrationTest(
False)
# 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 and uid in dlimits and dlimits[uid]:
analysis.setDetectionLimitOperand(dlimits[uid])
# Need to save results?
if uid in results and results[uid] and allow_edit \
and analysis_active:
interims = item_data.get(uid, [])
analysis.setInterimFields(interims)
analysis.setResult(results[uid])
analysis.reindexObject()
can_submit = True
deps = analysis.getDependencies() \
if hasattr(analysis, 'getDependencies') else []
for dependency in deps:
if workflow.getInfoFor(dependency, 'review_state') in \
('to_be_sampled', 'to_be_preserved',
'sample_due', 'sample_received'):
can_submit = False
break
if can_submit:
# doActionFor transitions the analysis to verif pending,
# so must only be done when results are submitted.
doActionFor(analysis, 'submit')
# Maybe some analyses need to be retracted due to a QC failure
# Done here because don't know if the last selected analysis is
# a valid QC for the instrument used in previous analyses.
# If we add this logic in subscribers.analyses, there's the
# possibility to retract analyses before the QC being reached.
self.retractInvalidAnalyses()
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.request.get_header(
"referer", self.context.absolute_url())
self.request.response.redirect(self.destination_url)
def __call__(self):
form = self.request.form
plone.protect.CheckAuthenticator(form)
workflow = getToolByName(self.context, 'portal_workflow')
rc = getToolByName(self.context, REFERENCE_CATALOG)
bsc = getToolByName(self.context, 'bika_setup_catalog')
bac = getToolByName(self.context, 'bika_analysis_catalog')
action, came_from = WorkflowAction._get_form_workflow_action(self)
if action == 'submit':
# Submit the form. Saves the results, methods, etc.
self.submit()
## assign
elif action == 'assign':
if not self.context.checkUserManage():
self.request.response.redirect(self.context.absolute_url())
return
selected_analyses = WorkflowAction._get_selected_items(self)
selected_analysis_uids = selected_analyses.keys()
if selected_analyses:
for uid in selected_analysis_uids:
analysis = rc.lookupObject(uid)
# Double-check the state first
if (workflow.getInfoFor(analysis, 'worksheetanalysis_review_state') == 'unassigned'
and workflow.getInfoFor(analysis, 'review_state') == 'sample_received'
and workflow.getInfoFor(analysis, 'cancellation_state') == 'active'):
self.context.addAnalysis(analysis)
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
## unassign
elif action == 'unassign':
if not self.context.checkUserManage():
self.request.response.redirect(self.context.absolute_url())
return
selected_analyses = WorkflowAction._get_selected_items(self)
selected_analysis_uids = selected_analyses.keys()
for analysis_uid in selected_analysis_uids:
try:
analysis = bac(UID=analysis_uid)[0].getObject()
except IndexError:
# Duplicate analyses are removed when their analyses
# get removed, so indexerror is expected.
continue
if skip(analysis, action, peek=True):
continue
self.context.removeAnalysis(analysis)
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
## verify
elif action == 'verify':
# default bika_listing.py/WorkflowAction, but then go to view screen.
self.destination_url = self.context.absolute_url()
return self.workflow_action_default(action='verify',
came_from='edit')
else:
# default bika_listing.py/WorkflowAction for other transitions
WorkflowAction.__call__(self)
def __call__(self):
form = self.request.form
CheckAuthenticator(form)
workflow = getToolByName(self.context, 'portal_workflow')
rc = getToolByName(self.context, REFERENCE_CATALOG)
bsc = getToolByName(self.context, 'bika_setup_catalog')
bac = getToolByName(self.context, 'bika_analysis_catalog')
action, came_from = WorkflowAction._get_form_workflow_action(self)
if action == 'submit':
# Submit the form. Saves the results, methods, etc.
self.submit()
## assign
elif action == 'assign':
if not self.context.checkUserManage():
self.request.response.redirect(self.context.absolute_url())
return
analysis_uids = form.get("uids", [])
if analysis_uids:
# We retrieve the analyses from the database sorted by AR ID
# ascending, so the positions of the ARs inside the WS are
# consistent with the order of the ARs
catalog = get_tool(CATALOG_ANALYSIS_LISTING)
brains = catalog({'UID': analysis_uids,
'sort_on': 'getRequestID'})
# Now, we need the analyses within a request ID to be sorted by
# sortkey (sortable_title index), so it will appear in the same
# order as they appear in Analyses list from AR view
curr_arid = None
curr_brains = []
sorted_brains = []
for brain in brains:
arid = brain.getRequestID
if curr_arid != arid:
# Sort the brains we've collected until now, that belong to
# the same Analysis Request
curr_brains.sort(key=attrgetter('getPrioritySortkey'))
sorted_brains.extend(curr_brains)
curr_arid = arid
curr_brains = []
# Now we are inside the same AR
curr_brains.append(brain)
continue
# Sort the last set of brains we've collected
curr_brains.sort(key=attrgetter('getPrioritySortkey'))
sorted_brains.extend(curr_brains)
# Add analyses in the worksheet
for brain in sorted_brains:
analysis = brain.getObject()
self.context.addAnalysis(analysis)
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
## unassign
elif action == 'unassign':
if not self.context.checkUserManage():
self.request.response.redirect(self.context.absolute_url())
return
selected_analyses = WorkflowAction._get_selected_items(self)
selected_analysis_uids = selected_analyses.keys()
for analysis_uid in selected_analysis_uids:
try:
analysis = bac(UID=analysis_uid)[0].getObject()
except IndexError:
# Duplicate analyses are removed when their analyses
# get removed, so indexerror is expected.
continue
if skip(analysis, action, peek=True):
continue
self.context.removeAnalysis(analysis)
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
## verify
elif action == 'verify':
# default bika_listing.py/WorkflowAction, but then go to view screen.
self.destination_url = self.context.absolute_url()
return self.workflow_action_default(action='verify',
came_from=came_from)
else:
# default bika_listing.py/WorkflowAction for other transitions
WorkflowAction.__call__(self)
def __call__(self):
form = self.request.form
plone.protect.CheckAuthenticator(form)
workflow = getToolByName(self.context, 'portal_workflow')
pc = getToolByName(self.context, 'portal_catalog')
rc = getToolByName(self.context, REFERENCE_CATALOG)
# use came_from to decide which UI action was clicked.
# "workflow_action" is the action name specified in the
# portal_workflow transition url.
came_from = "workflow_action"
action = form.get(came_from, '')
if not action:
# workflow_action_button is the action name specified in
# the bika_listing_view table buttons.
came_from = "workflow_action_button"
action = form.get(came_from, '')
# XXX some browsers agree better than others about our JS ideas.
if type(action) == type([]): action = action[0]
if not action:
if self.destination_url == "":
self.destination_url = self.request.get_header("referer",
self.context.absolute_url())
self.request.response.redirect(self.destination_url)
return
if action in ('prepublish', 'publish', 'prepublish'):
# We pass a list of AR objects to Publish.
# it returns a list of AR IDs which were actually published.
ARs_to_publish = []
transitioned = []
if 'paths' in form:
for path in form['paths']:
item_id = path.split("/")[-1]
item_path = path.replace("/" + item_id, '')
ar = pc(id = item_id,
path = {'query':item_path,
'depth':1})[0].getObject()
# can't publish inactive items
if not(
'bika_inactive_workflow' in workflow.getChainFor(ar) and \
workflow.getInfoFor(ar, 'inactive_state', '') == 'inactive'):
ar.setDatePublished(DateTime())
ARs_to_publish.append(ar)
transitioned = Publish(self.context,
self.request,
action,
ARs_to_publish)()
if len(transitioned) > 1:
message = _('message_items_published',
default = '${items} were published.',
mapping = {'items': ', '.join(transitioned)})
elif len(transitioned) == 1:
message = _('message_item_published',
default = '${items} published.',
mapping = {'items': ', '.join(transitioned)})
else:
message = _('No items were published')
message = self.context.translate(message)
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.request.get_header("referer",
self.context.absolute_url())
self.request.response.redirect(self.destination_url)
else:
# default bika_listing.py/WorkflowAction for other transitions
WorkflowAction.__call__(self)
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():
# Do not save data for analyses that are not selected.
if uid not in selected_analyses:
continue
analysis = selected_analyses[uid]
# never save any part of rows with empty result values.
# https://jira.bikalabs.com/browse/LIMS-1944:
if not result:
continue
# ignore result if analysis object no longer exists
if not analysis:
continue
# Prevent saving data if the analysis is already transitioned
if not (checkPermission(EditResults, analysis)
or checkPermission(EditFieldResults, analysis)):
title = safe_unicode(analysis.getService().Title())
msgid = _('Result for ${analysis} could not be saved because '
'it was already submitted by another user.',
mapping={'analysis': title})
message = safe_unicode(t(msgid))
self.context.plone_utils.addPortalMessage(message)
continue
# 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
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')
# LIMS-2366: Finally, when we are done processing all applicable
# analyses, we must attempt to initiate the submit transition on the
# AR itself. This is for the case where "general retraction" has been
# done, or where the last "received" analysis has been removed, and
# the AR is in state "received" while there are no "received" analyses
# left to trigger the parent transition.
if self.context.portal_type == 'Sample':
ar = self.context.getAnalysisRequests()[0]
elif self.context.portal_type == 'Analysis':
ar = self.context.aq_parent
else:
ar = self.context
doActionFor(ar, '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 retractInvalidAnalyses(self):
""" Retract the analyses with validation pending status for which
the instrument used failed a QC Test.
"""
toretract = {}
instruments = {}
refs = []
rc = getToolByName(self.context, REFERENCE_CATALOG)
selected = WorkflowAction._get_selected_items(self)
for uid in selected.iterkeys():
# We need to do this instead of using the dict values
# directly because all these analyses have been saved before
# and don't know if they already had an instrument assigned
an = rc.lookupObject(uid)
if an.portal_type == 'ReferenceAnalysis':
refs.append(an)
instrument = an.getInstrument()
if instrument and instrument.UID() not in instruments:
instruments[instrument.UID()] = instrument
for instr in instruments.itervalues():
analyses = instr.getAnalysesToRetract()
for a in analyses:
if a.UID() not in toretract:
toretract[a.UID] = a
retracted = []
for analysis in toretract.itervalues():
try:
# add a remark to this analysis
failedtxt = ulocalized_time(DateTime(), long_format=0)
failedtxt = '%s: %s' % (failedtxt,
_("Instrument failed reference test"))
analysis.setRemarks(failedtxt)
# retract the analysis
doActionFor(analysis, 'retract')
retracted.append(analysis)
except:
# Already retracted as a dependant from a previous one?
pass
if len(retracted) > 0:
# Create the Retracted Analyses List
rep = AnalysesRetractedListReport(self.context, self.request,
self.portal_url,
'Retracted analyses', retracted)
# Attach the pdf to the ReferenceAnalysis (accessible
# from Instrument's Internal Calibration Tests list
pdf = rep.toPdf()
for ref in refs:
ref.setRetractedAnalysesPdfReport(pdf)
# Send the email
try:
rep.sendEmail()
except:
pass
# TODO: mostra una finestra amb els resultats publicats d'AS
# que han utilitzat l'instrument des de la seva última
# calibració vàlida, amb els emails, telèfons dels
# contactes associats per a una intervenció manual
pass
def __call__(self):
form = self.request.form
plone.protect.CheckAuthenticator(form)
workflow = getToolByName(self.context, 'portal_workflow')
rc = getToolByName(self.context, REFERENCE_CATALOG)
bsc = getToolByName(self.context, 'bika_setup_catalog')
bac = getToolByName(self.context, 'bika_analysis_catalog')
action, came_from = WorkflowAction._get_form_workflow_action(self)
# XXX combine data from multiple bika listing tables.
item_data = {}
if 'item_data' in form:
if type(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'])
if action == 'submit' and self.request.form.has_key("Result"):
selected_analyses = WorkflowAction._get_selected_items(self)
results = {}
hasInterims = {}
# first save results for entire form
for uid, result in self.request.form['Result'][0].items():
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
if not(getSecurityManager().checkPermission(EditResults, analysis)):
# or changes no longer allowed
continue
if not isActive(analysis):
# or it's cancelled
continue
results[uid] = result
service = analysis.getService()
interimFields = item_data[uid]
if len(interimFields) > 0:
hasInterims[uid] = True
else:
hasInterims[uid] = False
unit = service.getUnit()
analysis.edit(
Result = result,
InterimFields = interimFields,
Retested = form.has_key('retested') and \
form['retested'].has_key(uid),
Unit = unit and unit or '')
# discover which items may be submitted
submissable = []
for uid, analysis in selected_analyses.items():
if uid not in results:
continue
can_submit = True
if hasattr(analysis, 'getDependencies'):
dependencies = analysis.getDependencies()
for dependency in dependencies:
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
for dependency in dependencies:
if workflow.getInfoFor(dependency, 'review_state') in \
('to_be_sampled', 'to_be_preserved',
'sample_due', 'sample_received'):
can_submit = False
if can_submit:
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')
self.destination_url = self.request.get_header("referer",
self.context.absolute_url())
self.request.response.redirect(self.destination_url)
## assign
elif action == 'assign':
if not(getSecurityManager().checkPermission(EditWorksheet, self.context)):
self.request.response.redirect(self.context.absolute_url())
return
selected_analyses = WorkflowAction._get_selected_items(self)
selected_analysis_uids = selected_analyses.keys()
if selected_analyses:
for uid in selected_analysis_uids:
analysis = rc.lookupObject(uid)
# Double-check the state first
if (workflow.getInfoFor(analysis, 'worksheetanalysis_review_state') == 'unassigned'
and workflow.getInfoFor(analysis, 'review_state') == 'sample_received'
and workflow.getInfoFor(analysis, 'cancellation_state') == 'active'):
self.context.addAnalysis(analysis)
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
## unassign
elif action == 'unassign':
if not(getSecurityManager().checkPermission(EditWorksheet, self.context)):
self.request.response.redirect(self.context.absolute_url())
return
selected_analyses = WorkflowAction._get_selected_items(self)
selected_analysis_uids = selected_analyses.keys()
for analysis_uid in selected_analysis_uids:
try:
analysis = bac(UID=analysis_uid)[0].getObject()
except IndexError:
# Duplicate analyses are removed when their analyses
# get removed, so indexerror is expected.
continue
if skip(analysis, action, peek=True):
continue
self.context.removeAnalysis(analysis)
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
## verify
elif action == 'verify':
# default bika_listing.py/WorkflowAction, but then go to view screen.
self.destination_url = self.context.absolute_url()
WorkflowAction.__call__(self)
else:
# default bika_listing.py/WorkflowAction for other transitions
WorkflowAction.__call__(self)
def __call__(self):
form = self.request.form
plone.protect.CheckAuthenticator(form)
workflow = getToolByName(self.context, 'portal_workflow')
rc = getToolByName(self.context, REFERENCE_CATALOG)
bsc = getToolByName(self.context, 'bika_setup_catalog')
bac = getToolByName(self.context, 'bika_analysis_catalog')
action, came_from = WorkflowAction._get_form_workflow_action(self)
if action == 'submit':
# Submit the form. Saves the results, methods, etc.
self.submit()
## assign
elif action == 'assign':
if not self.context.checkUserManage():
self.request.response.redirect(self.context.absolute_url())
return
selected_analyses = WorkflowAction._get_selected_items(self)
selected_analysis_uids = selected_analyses.keys()
if selected_analyses:
for uid in selected_analysis_uids:
analysis = rc.lookupObject(uid)
# Double-check the state first
if (workflow.getInfoFor(analysis,
'worksheetanalysis_review_state')
== 'unassigned' and workflow.getInfoFor(
analysis, 'review_state') == 'sample_received'
and workflow.getInfoFor(
analysis, 'cancellation_state') == 'active'):
self.context.addAnalysis(analysis)
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
## unassign
elif action == 'unassign':
if not self.context.checkUserManage():
self.request.response.redirect(self.context.absolute_url())
return
selected_analyses = WorkflowAction._get_selected_items(self)
selected_analysis_uids = selected_analyses.keys()
for analysis_uid in selected_analysis_uids:
try:
analysis = bac(UID=analysis_uid)[0].getObject()
except IndexError:
# Duplicate analyses are removed when their analyses
# get removed, so indexerror is expected.
continue
if skip(analysis, action, peek=True):
continue
self.context.removeAnalysis(analysis)
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
## verify
elif action == 'verify':
# default bika_listing.py/WorkflowAction, but then go to view screen.
self.destination_url = self.context.absolute_url()
return self.workflow_action_default(action='verify',
came_from=came_from)
else:
# default bika_listing.py/WorkflowAction for other transitions
WorkflowAction.__call__(self)
def retractInvalidAnalyses(self):
""" Retract the analyses with validation pending status for which
the instrument used failed a QC Test.
"""
toretract = {}
instruments = {}
refs = []
rc = getToolByName(self.context, REFERENCE_CATALOG)
selected = WorkflowAction._get_selected_items(self)
for uid in selected.iterkeys():
# We need to do this instead of using the dict values
# directly because all these analyses have been saved before
# and don't know if they already had an instrument assigned
an = rc.lookupObject(uid)
if an.portal_type == 'ReferenceAnalysis':
refs.append(an)
instrument = an.getInstrument()
if instrument and instrument.UID() not in instruments:
instruments[instrument.UID()] = instrument
for instr in instruments.itervalues():
analyses = instr.getAnalysesToRetract()
for a in analyses:
if a.UID() not in toretract:
toretract[a.UID] = a
retracted = []
for analysis in toretract.itervalues():
try:
# add a remark to this analysis
failedtxt = ulocalized_time(DateTime(), long_format=0)
failedtxt = '%s: %s' % (failedtxt, _("Instrument failed reference test"))
analysis.setRemarks(failedtxt)
# retract the analysis
doActionFor(analysis, 'retract')
retracted.append(analysis)
except:
# Already retracted as a dependant from a previous one?
pass
if len(retracted) > 0:
# Create the Retracted Analyses List
rep = AnalysesRetractedListReport(self.context,
self.request,
self.portal_url,
'Retracted analyses',
retracted)
# Attach the pdf to the ReferenceAnalysis (accessible
# from Instrument's Internal Calibration Tests list
pdf = rep.toPdf()
for ref in refs:
ref.setRetractedAnalysesPdfReport(pdf)
# Send the email
try:
rep.sendEmail()
except:
pass
# TODO: mostra una finestra amb els resultats publicats d'AS
# que han utilitzat l'instrument des de la seva última
# calibració vàlida, amb els emails, telèfons dels
# contactes associats per a una intervenció manual
pass
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():
# Do not save data for analyses that are not selected.
if uid not in selected_analyses:
continue
analysis = selected_analyses[uid]
# never save any part of rows with empty result values.
# https://jira.bikalabs.com/browse/LIMS-1944:
if not result:
continue
# ignore result if analysis object no longer exists
if not analysis:
continue
# Prevent saving data if the analysis is already transitioned
if not (checkPermission(EditResults, analysis) or checkPermission(EditFieldResults, analysis)):
title = safe_unicode(analysis.getService().Title())
msgid = _(
"Result for ${analysis} could not be saved because " "it was already submitted by another user.",
mapping={"analysis": title},
)
message = safe_unicode(t(msgid))
self.context.plone_utils.addPortalMessage(message)
continue
# 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
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")
# LIMS-2366: Finally, when we are done processing all applicable
# analyses, we must attempt to initiate the submit transition on the
# AR itself. This is for the case where "general retraction" has been
# done, or where the last "received" analysis has been removed, and
# the AR is in state "received" while there are no "received" analyses
# left to trigger the parent transition.
if self.context.portal_type == "Sample":
ar = self.context.getAnalysisRequests()[0]
elif self.context.portal_type == "Analysis":
ar = self.context.aq_parent
else:
ar = self.context
doActionFor(ar, "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 workflow_action_verify(self):
# default bika_listing.py/WorkflowAction, but then go to view screen.
self.destination_url = self.context.absolute_url()
WorkflowAction.__call__(self)
def submit(self):
""" Saves the form
"""
form = self.request.form
remarks = form.get('Remarks', [{}])[0]
results = form.get('Result',[{}])[0]
retested = form.get('retested', {})
methods = form.get('Method', [{}])[0]
instruments = 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]
selected = WorkflowAction._get_selected_items(self)
workflow = getToolByName(self.context, 'portal_workflow')
rc = getToolByName(self.context, REFERENCE_CATALOG)
sm = getSecurityManager()
hasInterims = {}
# XXX combine data from multiple bika listing tables.
item_data = {}
if 'item_data' in form:
if type(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'])
# Iterate for each selected analysis and save its data as needed
for uid, analysis in selected.items():
allow_edit = sm.checkPermission(EditResults, analysis)
analysis_active = isActive(analysis)
# Need to save remarks?
if uid in remarks and allow_edit and analysis_active:
analysis.setRemarks(remarks[uid])
# Retested?
if uid in retested and allow_edit and analysis_active:
analysis.setRetested(retested[uid])
# 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)
if analysis.meta_type == 'ReferenceAnalysis':
instrument.setDisposeUntilNextCalibrationTest(False)
# 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 and uid in dlimits and dlimits[uid]:
analysis.setDetectionLimitOperand(dlimits[uid])
# Need to save results?
if uid in results and results[uid] and allow_edit \
and analysis_active:
interims = item_data.get(uid, [])
analysis.setInterimFields(interims)
analysis.setResult(results[uid])
analysis.reindexObject()
can_submit = True
deps = analysis.getDependencies() \
if hasattr(analysis, 'getDependencies') else []
for dependency in deps:
if workflow.getInfoFor(dependency, 'review_state') in \
('to_be_sampled', 'to_be_preserved',
'sample_due', 'sample_received'):
can_submit = False
break
if can_submit:
# doActionFor transitions the analysis to verif pending,
# so must only be done when results are submitted.
doActionFor(analysis, 'submit')
# Maybe some analyses need to be retracted due to a QC failure
# Done here because don't know if the last selected analysis is
# a valid QC for the instrument used in previous analyses.
# If we add this logic in subscribers.analyses, there's the
# possibility to retract analyses before the QC being reached.
self.retractInvalidAnalyses()
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.request.get_header("referer",
self.context.absolute_url())
self.request.response.redirect(self.destination_url)
def workflow_action_save_analyses_button(self):
form = self.request.form
workflow = getToolByName(self.context, 'portal_workflow')
bsc = self.context.bika_setup_catalog
action, came_from = WorkflowAction._get_form_workflow_action(self)
# AR Manage Analyses: save Analyses
ar = self.context
sample = ar.getSample()
objects = WorkflowAction._get_selected_items(self)
if not objects:
message = _("No analyses have been selected")
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.context.absolute_url() + "/analyses"
self.request.response.redirect(self.destination_url)
return
Analyses = objects.keys()
prices = form.get("Price", [None])[0]
# Hidden analyses?
# https://jira.bikalabs.com/browse/LIMS-1324
outs = []
hiddenans = form.get('Hidden', {})
for uid in Analyses:
hidden = hiddenans.get(uid, '')
hidden = True if hidden == 'on' else False
outs.append({'uid': uid, 'hidden': hidden})
ar.setAnalysisServicesSettings(outs)
specs = {}
if form.get("min", None):
for service_uid in Analyses:
service = objects[service_uid]
keyword = service.getKeyword()
specs[service_uid] = {
"min": form["min"][0][service_uid],
"max": form["max"][0][service_uid],
"warn_min": form["warn_min"][0][service_uid],
"warn_max": form["warn_max"][0][service_uid],
"keyword": keyword,
"uid": service_uid,
}
else:
for service_uid in Analyses:
service = objects[service_uid]
keyword = service.getKeyword()
specs[service_uid] = ResultsRangeDict(keyword=keyword,
uid=service_uid)
new = ar.setAnalyses(Analyses, prices=prices, specs=specs.values())
# link analyses and partitions
# If Bika Setup > Analyses > 'Display individual sample
# partitions' is checked, no Partitions available.
# https://github.com/bikalabs/Bika-LIMS/issues/1030
if 'Partition' in form:
for service_uid, service in objects.items():
part_id = form['Partition'][0][service_uid]
part = sample[part_id]
analysis = ar[service.getKeyword()]
analysis.setSamplePartition(part)
analysis.reindexObject()
partans = part.getAnalyses()
partans.append(analysis)
part.setAnalyses(partans)
part.reindexObject()
if new:
ar_state = getCurrentState(ar)
if wasTransitionPerformed(ar, 'to_be_verified'):
# Apply to AR only; we don't want this transition to cascade.
ar.REQUEST['workflow_skiplist'].append("retract all analyses")
workflow.doActionFor(ar, 'retract')
ar.REQUEST['workflow_skiplist'].remove("retract all analyses")
ar_state = getCurrentState(ar)
for analysis in new:
changeWorkflowState(analysis, 'bika_analysis_workflow',
ar_state)
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, 'info')
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
