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 __call__(self):
form = self.request.form
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 __call__(self):
form = self.request.form
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 __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 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 __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 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() + "/portal_factory/" + \
"AnalysisRequest/Request new analyses/ar_add" + \
"?ar_count={0}".format(len(objects)) + \
"©_from={0}".format(",".join(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() + "/portal_factory/" + \
"AnalysisRequest/Request new analyses/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?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_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_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_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 = bsc(UID=service_uid)[0].getObject()
keyword = service.getKeyword()
specs[service_uid] = {
"min": form["min"][0][service_uid],
"max": form["max"][0][service_uid],
"error": form["error"][0][service_uid],
"keyword": keyword,
"uid": service_uid,
}
else:
for service_uid in Analyses:
service = bsc(UID=service_uid)[0].getObject()
keyword = service.getKeyword()
specs[service_uid] = {"min": "", "max": "", "error": "",
"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()
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 workflow_action_submit(self):
form = self.request.form
rc = getToolByName(self.context, REFERENCE_CATALOG)
action, came_from = WorkflowAction._get_form_workflow_action(self)
checkPermission = self.context.portal_membership.checkPermission
if not isActive(self.context):
message = _('Item is inactive.')
self.context.plone_utils.addPortalMessage(message, 'info')
self.request.response.redirect(self.context.absolute_url())
return
# calcs.js has kept item_data and form input interim values synced,
# so the json strings from item_data will be the same as the form values
item_data = {}
if 'item_data' in form:
if isinstance(form['item_data'], list):
for i_d in form['item_data']:
for i, d in json.loads(i_d).items():
item_data[i] = d
else:
item_data = json.loads(form['item_data'])
selected_analyses = WorkflowAction._get_selected_items(self)
results = {}
hasInterims = {}
# check that the form values match the database
# save them if not.
for uid, result in self.request.form.get('Result', [{}])[0].items():
# if the AR has ReportDryMatter set, get dry_result from form.
dry_result = ''
if hasattr(self.context, 'getReportDryMatter') \
and self.context.getReportDryMatter():
for k, v in self.request.form['ResultDM'][0].items():
if uid == k:
dry_result = v
break
if uid in selected_analyses:
analysis = selected_analyses[uid]
else:
analysis = rc.lookupObject(uid)
if not analysis:
# ignore result if analysis object no longer exists
continue
results[uid] = result
interimFields = item_data[uid]
if len(interimFields) > 0:
hasInterims[uid] = True
else:
hasInterims[uid] = False
retested = 'retested' in form and uid in form['retested']
remarks = form.get('Remarks', [
{},
])[0].get(uid, '')
# Don't save uneccessary things
# https://github.com/bikalabs/Bika-LIMS/issues/766:
# Somehow, using analysis.edit() fails silently when
# logged in as Analyst.
if analysis.getInterimFields() != interimFields or \
analysis.getRetested() != retested or \
analysis.getRemarks() != remarks:
analysis.setInterimFields(interimFields)
analysis.setRetested(retested)
analysis.setRemarks(remarks)
# save results separately, otherwise capture date is rewritten
if analysis.getResult() != result or \
analysis.getResultDM() != dry_result:
analysis.setResultDM(dry_result)
analysis.setResult(result)
methods = self.request.form.get('Method', [{}])[0]
instruments = self.request.form.get('Instrument', [{}])[0]
analysts = self.request.form.get('Analyst', [{}])[0]
uncertainties = self.request.form.get('Uncertainty', [{}])[0]
dlimits = self.request.form.get('DetectionLimit', [{}])[0]
# discover which items may be submitted
submissable = []
for uid, analysis in selected_analyses.items():
analysis_active = isActive(analysis)
# Need to save the instrument?
if uid in instruments and analysis_active:
# TODO: Add SetAnalysisInstrument permission
# allow_setinstrument = sm.checkPermission(SetAnalysisInstrument)
allow_setinstrument = True
# ---8<-----
if allow_setinstrument == True:
# The current analysis allows the instrument regards
# to its analysis service and method?
if (instruments[uid] == ''):
previnstr = analysis.getInstrument()
if previnstr:
previnstr.removeAnalysis(analysis)
analysis.setInstrument(None)
elif analysis.isInstrumentAllowed(instruments[uid]):
previnstr = analysis.getInstrument()
if previnstr:
previnstr.removeAnalysis(analysis)
analysis.setInstrument(instruments[uid])
instrument = analysis.getInstrument()
instrument.addAnalysis(analysis)
# Need to save the method?
if uid in methods and analysis_active:
# TODO: Add SetAnalysisMethod permission
# allow_setmethod = sm.checkPermission(SetAnalysisMethod)
allow_setmethod = True
# ---8<-----
if allow_setmethod == True and analysis.isMethodAllowed(
methods[uid]):
analysis.setMethod(methods[uid])
# Need to save the analyst?
if uid in analysts and analysis_active:
analysis.setAnalyst(analysts[uid])
# Need to save the uncertainty?
if uid in uncertainties and analysis_active:
analysis.setUncertainty(uncertainties[uid])
# Need to save the detection limit?
if analysis_active:
analysis.setDetectionLimitOperand(dlimits.get(uid, None))
if uid not in results or not results[uid]:
continue
can_submit = True
# guard_submit does a lot of the same stuff, too.
# the code there has also been commented.
# we must find a better way to allow dependencies to control
# this process.
# for dependency in analysis.getDependencies():
# dep_state = workflow.getInfoFor(dependency, 'review_state')
# if hasInterims[uid]:
# if dep_state in ('to_be_sampled', 'to_be_preserved',
# 'sample_due', 'sample_received',
# 'attachment_due', 'to_be_verified',):
# can_submit = False
# break
# else:
# if dep_state in ('to_be_sampled', 'to_be_preserved',
# 'sample_due', 'sample_received',):
# can_submit = False
# break
if can_submit and analysis not in submissable:
submissable.append(analysis)
# and then submit them.
for analysis in submissable:
doActionFor(analysis, 'submit')
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, 'info')
if checkPermission(EditResults, self.context):
self.destination_url = self.context.absolute_url(
) + "/manage_results"
else:
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
def workflow_action_submit(self):
form = self.request.form
rc = getToolByName(self.context, REFERENCE_CATALOG)
action, came_from = WorkflowAction._get_form_workflow_action(self)
checkPermission = self.context.portal_membership.checkPermission
if not isActive(self.context):
message = _('Item is inactive.')
self.context.plone_utils.addPortalMessage(message, 'info')
self.request.response.redirect(self.context.absolute_url())
return
# calcs.js has kept item_data and form input interim values synced,
# so the json strings from item_data will be the same as the form values
item_data = {}
if 'item_data' in form:
if isinstance(form['item_data'], list):
for i_d in form['item_data']:
for i, d in json.loads(i_d).items():
item_data[i] = d
else:
item_data = json.loads(form['item_data'])
selected_analyses = WorkflowAction._get_selected_items(self)
results = {}
hasInterims = {}
# check that the form values match the database
# save them if not.
for uid, result in self.request.form.get('Result', [{}])[0].items():
# if the AR has ReportDryMatter set, get dry_result from form.
dry_result = ''
if hasattr(self.context, 'getReportDryMatter') \
and self.context.getReportDryMatter():
for k, v in self.request.form['ResultDM'][0].items():
if uid == k:
dry_result = v
break
if uid in selected_analyses:
analysis = selected_analyses[uid]
else:
analysis = rc.lookupObject(uid)
if not analysis:
# ignore result if analysis object no longer exists
continue
results[uid] = result
interimFields = item_data[uid]
if len(interimFields) > 0:
hasInterims[uid] = True
else:
hasInterims[uid] = False
retested = 'retested' in form and uid in form['retested']
remarks = form.get('Remarks', [{}, ])[0].get(uid, '')
# Don't save uneccessary things
# https://github.com/bikalabs/Bika-LIMS/issues/766:
# Somehow, using analysis.edit() fails silently when
# logged in as Analyst.
if analysis.getInterimFields() != interimFields or \
analysis.getRetested() != retested or \
analysis.getRemarks() != remarks:
analysis.setInterimFields(interimFields)
analysis.setRetested(retested)
analysis.setRemarks(remarks)
# save results separately, otherwise capture date is rewritten
if analysis.getResult() != result or \
analysis.getResultDM() != dry_result:
analysis.setResultDM(dry_result)
analysis.setResult(result)
methods = self.request.form.get('Method', [{}])[0]
instruments = self.request.form.get('Instrument', [{}])[0]
analysts = self.request.form.get('Analyst', [{}])[0]
uncertainties = self.request.form.get('Uncertainty', [{}])[0]
dlimits = self.request.form.get('DetectionLimit', [{}])[0]
# discover which items may be submitted
submissable = []
for uid, analysis in selected_analyses.items():
analysis_active = isActive(analysis)
# Need to save the instrument?
if uid in instruments and analysis_active:
# TODO: Add SetAnalysisInstrument permission
# allow_setinstrument = sm.checkPermission(SetAnalysisInstrument)
allow_setinstrument = True
# ---8<-----
if allow_setinstrument == True:
# The current analysis allows the instrument regards
# to its analysis service and method?
if (instruments[uid]==''):
previnstr = analysis.getInstrument()
if previnstr:
previnstr.removeAnalysis(analysis)
analysis.setInstrument(None);
elif analysis.isInstrumentAllowed(instruments[uid]):
previnstr = analysis.getInstrument()
if previnstr:
previnstr.removeAnalysis(analysis)
analysis.setInstrument(instruments[uid])
instrument = analysis.getInstrument()
instrument.addAnalysis(analysis)
# Need to save the method?
if uid in methods and analysis_active:
# TODO: Add SetAnalysisMethod permission
# allow_setmethod = sm.checkPermission(SetAnalysisMethod)
allow_setmethod = True
# ---8<-----
if allow_setmethod == True and analysis.isMethodAllowed(methods[uid]):
analysis.setMethod(methods[uid])
# Need to save the analyst?
if uid in analysts and analysis_active:
analysis.setAnalyst(analysts[uid])
# Need to save the uncertainty?
if uid in uncertainties and analysis_active:
analysis.setUncertainty(uncertainties[uid])
# Need to save the detection limit?
if analysis_active:
analysis.setDetectionLimitOperand(dlimits.get(uid, None))
if uid not in results or not results[uid]:
continue
can_submit = True
# guard_submit does a lot of the same stuff, too.
# the code there has also been commented.
# we must find a better way to allow dependencies to control
# this process.
# for dependency in analysis.getDependencies():
# dep_state = workflow.getInfoFor(dependency, 'review_state')
# if hasInterims[uid]:
# if dep_state in ('to_be_sampled', 'to_be_preserved',
# 'sample_due', 'sample_received',
# 'attachment_due', 'to_be_verified',):
# can_submit = False
# break
# else:
# if dep_state in ('to_be_sampled', 'to_be_preserved',
# 'sample_due', 'sample_received',):
# can_submit = False
# break
if can_submit and analysis not in submissable:
submissable.append(analysis)
# and then submit them.
for analysis in submissable:
doActionFor(analysis, 'submit')
message = PMF("Changes saved.")
self.context.plone_utils.addPortalMessage(message, 'info')
if checkPermission(EditResults, self.context):
self.destination_url = self.context.absolute_url() + "/manage_results"
else:
self.destination_url = self.context.absolute_url()
self.request.response.redirect(self.destination_url)
def 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_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 = bsc(UID=service_uid)[0].getObject()
keyword = service.getKeyword()
specs[service_uid] = {
"min": form["min"][0][service_uid],
"max": form["max"][0][service_uid],
"error": form["error"][0][service_uid],
"keyword": keyword,
"uid": service_uid,
}
else:
for service_uid in Analyses:
service = bsc(UID=service_uid)[0].getObject()
keyword = service.getKeyword()
specs[service_uid] = {
"min": "",
"max": "",
"error": "",
"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()
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)