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, action, objects):
# Store invalid instruments-ref.analyses
invalid_instrument_refs = defaultdict(set)
# Get interims data
interims_data = self.get_interims_data()
for analysis in objects:
uid = api.get_uid(analysis)
# Need to save remarks?
remarks = self.get_form_value("Remarks", uid, default="")
analysis.setRemarks(remarks)
# Need to save the instrument?
instrument = self.get_form_value("Instrument", uid, None)
if instrument is not None:
# Could be an empty string
instrument = instrument or None
analysis.setInstrument(instrument)
if instrument and IReferenceAnalysis.providedBy(analysis):
if is_out_of_range(analysis):
# This reference analysis is out of range, so we have
# to retract all analyses assigned to this same
# instrument that are awaiting for verification
invalid_instrument_refs[uid].add(analysis)
else:
# The reference result is valid, so make the instrument
# available again for further analyses
instrument.setDisposeUntilNextCalibrationTest(False)
# Need to save the method?
method = self.get_form_value("Method", uid, default=None)
if method is not None:
method = method or None
analysis.setMethod(method)
# Need to save analyst?
analyst = self.get_form_value("Analyst", uid, default=None)
if analyst is not None:
analysis.setAnalyst(analyst)
# Save uncertainty
uncertainty = self.get_form_value("Uncertainty", uid, "")
analysis.setUncertainty(uncertainty)
# Save detection limit
dlimit = self.get_form_value("DetectionLimit", uid, "")
analysis.setDetectionLimitOperand(dlimit)
# Interim fields
interims = interims_data.get(uid, analysis.getInterimFields())
analysis.setInterimFields(interims)
# Save Hidden
hidden = self.get_form_value("Hidden", uid, "")
analysis.setHidden(hidden == "on")
# Result
result = self.get_form_value("Result",
uid,
default=analysis.getResult())
analysis.setResult(result)
# Submit all analyses
transitioned = self.do_action(action, objects)
if not transitioned:
return self.redirect(message=_("No changes made"), level="warning")
# If a reference analysis with an out-of-range result and instrument
# assigned has been submitted, retract then routine analyses that are
# awaiting for verification and with same instrument associated
retracted = list()
for invalid_instrument_uid in invalid_instrument_refs.keys():
query = dict(
getInstrumentUID=invalid_instrument_uid,
portal_type=['Analysis', 'DuplicateAnalysis'],
review_state='to_be_verified',
cancellation_state='active',
)
brains = api.search(query, CATALOG_ANALYSIS_LISTING)
for brain in brains:
analysis = api.get_object(brain)
failed_msg = '{0}: {1}'.format(
ulocalized_time(DateTime(), long_format=1),
_("Instrument failed reference test"))
an_remarks = analysis.getRemarks()
analysis.setRemarks('. '.join([an_remarks, failed_msg]))
retracted.append(analysis)
# If some analyses have been retracted because instrument failed a
# reference test, then generate a pdf report
if self.do_action("retract", retracted):
# Create the Retracted Analyses List
portal_url = api.get_url(api.get_portal())
report = AnalysesRetractedListReport(self.context, self.request,
portal_url,
'Retracted analyses',
retracted)
# Attach the pdf to all ReferenceAnalysis that failed (accessible
# from Instrument's Internal Calibration Tests list
pdf = report.toPdf()
for ref in invalid_instrument_refs.values():
ref.setRetractedAnalysesPdfReport(pdf)
# Send the email
try:
report.sendEmail()
except Exception as err_msg:
message = "Unable to send email: {}".format(err_msg)
logger.warn(message)
# Redirect to success view
return self.success(transitioned)
def workflow_action_submit(self):
uids = self.get_selected_uids()
if not uids:
message = _('No items selected.')
self.context.plone_utils.addPortalMessage(message, 'info')
self.request.response.redirect(self.context.absolute_url())
return
if not is_active(self.context):
message = _('Item is inactive.')
self.context.plone_utils.addPortalMessage(message, 'info')
self.request.response.redirect(self.context.absolute_url())
return
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]
# XXX combine data from multiple bika listing tables.
# TODO: Is this necessary?
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'])
# Store affected Analysis Requests
affected_ars = set()
# Store affected Worksheets
affected_ws = set()
# Store invalid instruments-ref.analyses
invalid_instrument_refs = dict()
# We manually query by all analyses uids at once here instead of using
# _get_selected_items from the base class, cause that function fetches
# the objects by uid, but sequentially one by one
query = dict(UID=uids)
for brain in api.search(query, CATALOG_ANALYSIS_LISTING):
uid = api.get_uid(brain)
analysis = api.get_object(brain)
# If not active, do nothing
if not is_active(brain):
continue
# Need to save remarks?
if uid in remarks:
analysis.setRemarks(remarks[uid])
# Retested?
if uid in retested:
analysis.setRetested(retested[uid])
# Need to save the instrument?
if uid in instruments:
instrument = instruments[uid] or None
analysis.setInstrument(instrument)
if instrument and IReferenceAnalysis.providedBy(analysis):
if is_out_of_range(analysis):
# This reference analysis is out of range, so we have
# to retract all analyses assigned to this same
# instrument that are awaiting for verification
if uid not in invalid_instrument_refs:
invalid_instrument_refs[uid] = set()
invalid_instrument_refs[uid].add(analysis)
else:
# The reference result is valid, so make the instrument
# available again for further analyses
instrument.setDisposeUntilNextCalibrationTest(False)
# Need to save the method?
if uid in methods:
method = methods[uid] or None
analysis.setMethod(method)
# Need to save the analyst?
if uid in analysts:
analysis.setAnalyst(analysts[uid])
# Need to save the uncertainty?
if uid in uncertainties:
analysis.setUncertainty(uncertainties[uid])
# Need to save the detection limit?
if uid in dlimits and dlimits[uid]:
analysis.setDetectionLimitOperand(dlimits[uid])
# Need to save results?
submitted = False
if uid in results and results[uid]:
interims = item_data.get(uid, [])
analysis.setInterimFields(interims)
analysis.setResult(results[uid])
# Can the analysis be submitted?
# An analysis can only be submitted if all its dependencies
# are valid and have been submitted already
can_submit = True
invalid_states = [
'to_be_sampled', 'to_be_preserved', 'sample_due',
'sample_received'
]
for dependency in analysis.getDependencies():
if in_state(dependency, invalid_states):
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')
submitted = True
if IRequestAnalysis.providedBy(analysis):
# Store the AR uids to be reindexed later.
affected_ars.add(brain.getParentUID)
if brain.worksheetanalysis_review_state == 'assigned':
worksheet_uid = analysis.getWorksheetUID()
if worksheet_uid:
affected_ws.add(worksheet_uid)
if not submitted:
# Analysis has not been submitted, so we need to reindex the
# object manually, to update catalog's metadata.
analysis.reindexObject()
# If a reference analysis with an out-of-range result and instrument
# assigned has been submitted, retract then routine analyses that are
# awaiting for verification and with same instrument associated
retracted = list()
for invalid_instrument_uid in invalid_instrument_refs.keys():
query = dict(
getInstrumentUID=invalid_instrument_uid,
portal_type=['Analysis', 'DuplicateAnalysis'],
review_state='to_be_verified',
cancellation_state='active',
)
brains = api.search(query, CATALOG_ANALYSIS_LISTING)
for brain in brains:
analysis = api.get_object(brain)
failed_msg = '{0}: {1}'.format(
ulocalized_time(DateTime(), long_format=1),
_("Instrument failed reference test"))
an_remarks = analysis.getRemarks()
analysis.setRemarks('. '.join([an_remarks, failed_msg]))
doActionFor(analysis, 'retract')
retracted.append(analysis)
# If some analyses have been retracted because instrument failed a
# reference test, then generate a pdf report
if retracted:
# Create the Retracted Analyses List
report = AnalysesRetractedListReport(self.context, self.request,
self.portal_url,
'Retracted analyses',
retracted)
# Attach the pdf to all ReferenceAnalysis that failed (accessible
# from Instrument's Internal Calibration Tests list
pdf = report.toPdf()
for ref in invalid_instrument_refs.values():
ref.setRetractedAnalysesPdfReport(pdf)
# Send the email
try:
report.sendEmail()
except:
pass
# Finally, when we are done processing all applicable analyses, we must
# attempt to initiate the submit transition on the ARs and Worksheets
# the processed analyses belong to.
# We stick only to affected_ars, and affected_ws
# Reindex the Analysis Requests for which at least one Analysis has
# been submitted. We do this here because one AR can contain multiple
# Analyses, so better to just reindex the AR once instead of each time.
# AR Catalog contains some metadata that that rely on the Analyses an
# Analysis Request contains.
if affected_ars:
query = dict(UID=list(affected_ars), portal_type="AnalysisRequest")
for ar_brain in api.search(query,
CATALOG_ANALYSIS_REQUEST_LISTING):
if ar_brain.review_state == 'to_be_verified':
continue
ar = api.get_object(ar_brain)
if isTransitionAllowed(ar, "submit"):
doActionFor(ar, "submit")
else:
ar.reindexObject()
if affected_ws:
query = dict(UID=list(affected_ws), portal_type="Worksheet")
for ws_brain in api.search(query, CATALOG_WORKSHEET_LISTING):
if ws_brain.review_state == 'to_be_verified':
continue
ws = api.get_object(ws_brain)
if isTransitionAllowed(ws, "submit"):
doActionFor(ws, "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)
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):
uids = self.get_selected_uids()
if not uids:
message = _('No items selected.')
self.context.plone_utils.addPortalMessage(message, 'info')
self.request.response.redirect(self.context.absolute_url())
return
if not is_active(self.context):
message = _('Item is inactive.')
self.context.plone_utils.addPortalMessage(message, 'info')
self.request.response.redirect(self.context.absolute_url())
return
form = self.request.form
remarks = form.get('Remarks', [{}])[0]
results = form.get('Result', [{}])[0]
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]
# XXX combine data from multiple bika listing tables.
# TODO: Is this necessary?
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'])
# Store invalid instruments-ref.analyses
invalid_instrument_refs = dict()
# We manually query by all analyses uids at once here instead of using
# _get_selected_items from the base class, cause that function fetches
# the objects by uid, but sequentially one by one
actions_pool = ActionsPool()
query = dict(UID=uids, cancellation_state="active")
for brain in api.search(query, CATALOG_ANALYSIS_LISTING):
uid = api.get_uid(brain)
analysis = api.get_object(brain)
# Need to save remarks?
if uid in remarks:
analysis.setRemarks(remarks[uid])
# Need to save the instrument?
if uid in instruments:
instrument = instruments[uid] or None
analysis.setInstrument(instrument)
if instrument and IReferenceAnalysis.providedBy(analysis):
if is_out_of_range(analysis):
# This reference analysis is out of range, so we have
# to retract all analyses assigned to this same
# instrument that are awaiting for verification
if uid not in invalid_instrument_refs:
invalid_instrument_refs[uid] = set()
invalid_instrument_refs[uid].add(analysis)
else:
# The reference result is valid, so make the instrument
# available again for further analyses
instrument.setDisposeUntilNextCalibrationTest(False)
# Need to save the method?
if uid in methods:
method = methods[uid] or None
analysis.setMethod(method)
# Need to save the analyst?
if uid in analysts:
analysis.setAnalyst(analysts[uid])
# Need to save the uncertainty?
if uid in uncertainties:
analysis.setUncertainty(uncertainties[uid])
# Need to save the detection limit?
analysis.setDetectionLimitOperand(dlimits.get(uid, ""))
interims = item_data.get(uid, analysis.getInterimFields())
analysis.setInterimFields(interims)
analysis.setResult(results.get('uid', analysis.getResult()))
# Add this analysis to the actions pool. We want to submit all them
# together, when all have values set for results, interims, etc.
actions_pool.add(analysis, "submit")
# Submit all analyses
actions_pool.resume()
# If a reference analysis with an out-of-range result and instrument
# assigned has been submitted, retract then routine analyses that are
# awaiting for verification and with same instrument associated
retracted = list()
for invalid_instrument_uid in invalid_instrument_refs.keys():
query = dict(
getInstrumentUID=invalid_instrument_uid,
portal_type=['Analysis', 'DuplicateAnalysis'],
review_state='to_be_verified',
cancellation_state='active',
)
brains = api.search(query, CATALOG_ANALYSIS_LISTING)
for brain in brains:
analysis = api.get_object(brain)
failed_msg = '{0}: {1}'.format(
ulocalized_time(DateTime(), long_format=1),
_("Instrument failed reference test"))
an_remarks = analysis.getRemarks()
analysis.setRemarks('. '.join([an_remarks, failed_msg]))
doActionFor(analysis, 'retract')
retracted.append(analysis)
# If some analyses have been retracted because instrument failed a
# reference test, then generate a pdf report
if retracted:
# Create the Retracted Analyses List
report = AnalysesRetractedListReport(self.context, self.request,
self.portal_url,
'Retracted analyses',
retracted)
# Attach the pdf to all ReferenceAnalysis that failed (accessible
# from Instrument's Internal Calibration Tests list
pdf = report.toPdf()
for ref in invalid_instrument_refs.values():
ref.setRetractedAnalysesPdfReport(pdf)
# Send the email
try:
report.sendEmail()
except:
pass
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)