def _to_service(self, thing):
"""Convert to Analysis Service
:param thing: UID/Catalog Brain/Object/Something
:returns: Analysis Service object or None
"""
# Convert UIDs to objects
if api.is_uid(thing):
thing = api.get_object_by_uid(thing, None)
# Bail out if the thing is not a valid object
if not api.is_object(thing):
logger.warn("'{}' is not a valid object!".format(repr(thing)))
return None
# Ensure we have an object here and not a brain
obj = api.get_object(thing)
if IAnalysisService.providedBy(obj):
return obj
if IAnalysis.providedBy(obj):
return obj.getAnalysisService()
# An object, but neither an Analysis nor AnalysisService?
# This should never happen.
portal_type = api.get_portal_type(obj)
logger.error("ARAnalysesField doesn't accept objects from {} type. "
"The object will be dismissed.".format(portal_type))
return None
def _to_service(self, thing):
"""Convert to Analysis Service
:param thing: UID/Catalog Brain/Object/Something
:returns: Analysis Service object or None
"""
# Convert UIDs to objects
if api.is_uid(thing):
thing = api.get_object_by_uid(thing, None)
# Bail out if the thing is not a valid object
if not api.is_object(thing):
logger.warn("'{}' is not a valid object!".format(repr(thing)))
return None
# Ensure we have an object here and not a brain
obj = api.get_object(thing)
if IAnalysisService.providedBy(obj):
return obj
if IAnalysis.providedBy(obj):
return obj.getAnalysisService()
# An object, but neither an Analysis nor AnalysisService?
# This should never happen.
msg = "ARAnalysesField doesn't accept objects from {} type. " \
"The object will be dismissed.".format(api.get_portal_type(obj))
logger.warn(msg)
return None
def after_verify(obj):
"""Event fired after receive (Process) transition is triggered
"""
logger.info("*** Custom after_verify transition ***")
if IAnalysis.providedBy(obj) or IDuplicateAnalysis.providedBy(obj):
analysis_events.after_verify(obj)
if IAnalysisRequest.providedBy(obj):
_promote_transition(obj, "verify")
def after_submit(obj):
"""Event fired after submit transition is triggered
"""
logger.info("*** Custom after_submit transition ***")
if IAnalysis.providedBy(obj) or IDuplicateAnalysis.providedBy(obj):
analysis_events.after_submit(obj)
if IAnalysisRequest.providedBy(obj):
_promote_transition(obj, "submit")
def _resolve_items_to_service_uids(items):
portal = api.portal.get()
# We need to send a list of service UIDS to setAnalyses function.
# But we may have received one, or a list of:
# AnalysisService instances
# Analysis instances
# service titles
# service UIDs
# service Keywords
service_uids = []
# Maybe only a single item was passed
if type(items) not in (list, tuple):
items = [
items,
]
for item in items:
uid = False
# service objects
if IAnalysisService.providedBy(item):
uid = item.UID()
service_uids.append(uid)
# Analysis objects (shortcut for eg copying analyses from other AR)
if IAnalysis.providedBy(item):
uid = item.getService().UID()
service_uids.append(uid)
# Maybe object UID.
bsc = getToolByName(portal, 'bika_setup_catalog')
brains = bsc(UID=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
# Maybe service Title
bsc = getToolByName(portal, 'bika_setup_catalog')
brains = bsc(portal_type='AnalysisService', title=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
# Maybe service Title
bsc = getToolByName(portal, 'bika_setup_catalog')
brains = bsc(portal_type='AnalysisService', getKeyword=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
if not uid:
raise RuntimeError(
str(item) + " should be the UID, title, keyword "
" or title of an AnalysisService.")
return service_uids
def _resolve_items_to_service_uids(items):
portal = api.portal.get()
# We need to send a list of service UIDS to setAnalyses function.
# But we may have received one, or a list of:
# AnalysisService instances
# Analysis instances
# service titles
# service UIDs
# service Keywords
service_uids = []
# Maybe only a single item was passed
if type(items) not in (list, tuple):
items = [items, ]
for item in items:
uid = False
# service objects
if IAnalysisService.providedBy(item):
uid = item.UID()
service_uids.append(uid)
# Analysis objects (shortcut for eg copying analyses from other AR)
if IAnalysis.providedBy(item):
uid = item.getService().UID()
service_uids.append(uid)
# Maybe object UID.
bsc = getToolByName(portal, 'bika_setup_catalog')
brains = bsc(UID=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
# Maybe service Title
bsc = getToolByName(portal, 'bika_setup_catalog')
brains = bsc(portal_type='AnalysisService', title=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
# Maybe service Keyword
bsc = getToolByName(portal, 'bika_setup_catalog')
brains = bsc(portal_type='AnalysisService', getKeyword=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
if not uid:
raise RuntimeError(
str(item) + " should be the UID, title, keyword "
" or title of an AnalysisService.")
return service_uids
def _get_service_uid(self, item):
if api.is_uid(item):
return item
if not api.is_object(item):
logger.warn("Not an UID: {}".format(item))
return None
obj = api.get_object(item)
if IAnalysisService.providedBy(obj):
return api.get_uid(obj)
if IAnalysis.providedBy(obj) and IRequestAnalysis.providedBy(obj):
return obj.getServiceUID()
# An object, but neither an Analysis nor AnalysisService?
# This should never happen.
msg = "ARAnalysesField doesn't accept objects from {} type. " \
"The object will be dismissed."
logger.warn(msg.format(api.get_portal_type(obj)))
return None
def _resolve_items_to_service_uids(items):
""" Returns a list of service uids without duplicates based on the items
:param items:
A list (or one object) of service-related info items. The list can be
heterogeneous and each item can be:
- Analysis Service instance
- Analysis instance
- Analysis Service title
- Analysis Service UID
- Analysis Service Keyword
If an item that doesn't match any of the criterias above is found, the
function will raise a RuntimeError
"""
portal = None
bsc = None
service_uids = []
# Maybe only a single item was passed
if type(items) not in (list, tuple):
items = [items, ]
for item in items:
# service objects
if IAnalysisService.providedBy(item):
uid = item.UID()
service_uids.append(uid)
continue
# Analysis objects (shortcut for eg copying analyses from other AR)
if IAnalysis.providedBy(item):
uid = item.getService().UID()
service_uids.append(uid)
continue
# An object UID already there?
if (item in service_uids):
continue
# Maybe object UID.
portal = portal if portal else api.portal.get()
bsc = bsc if bsc else getToolByName(portal, 'bika_setup_catalog')
brains = bsc(UID=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
continue
# Maybe service Title
brains = bsc(portal_type='AnalysisService', title=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
continue
# Maybe service Keyword
brains = bsc(portal_type='AnalysisService', getKeyword=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
continue
raise RuntimeError(
str(item) + " should be the UID, title, keyword "
" or title of an AnalysisService.")
return list(set(service_uids))
def _resolve_items_to_service_uids(items):
""" Returns a list of service uids without duplicates based on the items
:param items:
A list (or one object) of service-related info items. The list can be
heterogeneous and each item can be:
- Analysis Service instance
- Analysis instance
- Analysis Service title
- Analysis Service UID
- Analysis Service Keyword
If an item that doesn't match any of the criterias above is found, the
function will raise a RuntimeError
"""
portal = None
bsc = None
service_uids = []
# Maybe only a single item was passed
if type(items) not in (list, tuple):
items = [
items,
]
for item in items:
# service objects
if IAnalysisService.providedBy(item):
uid = item.UID()
service_uids.append(uid)
continue
# Analysis objects (shortcut for eg copying analyses from other AR)
if IAnalysis.providedBy(item):
uid = item.getService().UID()
service_uids.append(uid)
continue
# An object UID already there?
if (item in service_uids):
continue
# Maybe object UID.
portal = portal if portal else api.portal.get()
bsc = bsc if bsc else getToolByName(portal, 'bika_setup_catalog')
brains = bsc(UID=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
continue
# Maybe service Title
brains = bsc(portal_type='AnalysisService', title=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
continue
# Maybe service Keyword
brains = bsc(portal_type='AnalysisService', getKeyword=item)
if brains:
uid = brains[0].UID
service_uids.append(uid)
continue
raise RuntimeError(
str(item) + " should be the UID, title, keyword "
" or title of an AnalysisService.")
return list(set(service_uids))
def is_out_of_range(brain_or_object, result=_marker):
"""Checks if the result for the analysis passed in is out of range and/or
out of shoulders range.
min max
warn min max warn
·········|---------------|=====================|---------------|·········
----- out-of-range -----><----- in-range ------><----- out-of-range -----
<-- shoulder --><----- in-range ------><-- shoulder -->
:param brain_or_object: A single catalog brain or content object
:param result: Tentative result. If None, use the analysis result
:type brain_or_object: ATContentType/DexterityContentType/CatalogBrain
:returns: Tuple of two elements. The first value is `True` if the result is
out of range and `False` if it is in range. The second value is `True` if
the result is out of shoulder range and `False` if it is in shoulder range
:rtype: (bool, bool)
"""
analysis = api.get_object(brain_or_object)
if not IAnalysis.providedBy(analysis) and \
not IReferenceAnalysis.providedBy(analysis):
api.fail("{} is not supported. Needs to be IAnalysis or "
"IReferenceAnalysis".format(repr(analysis)))
if result is _marker:
result = api.safe_getattr(analysis, "getResult", None)
if result in [None, '']:
# Empty result
return False, False
if IDuplicateAnalysis.providedBy(analysis):
# Result range for duplicate analyses is calculated from the original
# result, applying a variation % in shoulders. If the analysis has
# result options enabled or string results enabled, system returns an
# empty result range for the duplicate: result must match %100 with the
# original result
original = analysis.getAnalysis()
original_result = original.getResult()
# Does original analysis have a valid result?
if original_result in [None, '']:
return False, False
# Does original result type matches with duplicate result type?
if api.is_floatable(result) != api.is_floatable(original_result):
return True, True
# Does analysis has result options enabled or non-floatable?
if analysis.getResultOptions() or not api.is_floatable(original_result):
# Let's always assume the result is 'out from shoulders', cause we
# consider the shoulders are precisely the duplicate variation %
out_of_range = original_result != result
return out_of_range, out_of_range
elif not api.is_floatable(result):
# A non-duplicate with non-floatable result. There is no chance to know
# if the result is out-of-range
return False, False
# Convert result to a float
result = api.to_float(result)
# Note that routine analyses, duplicates and reference analyses all them
# implement the function getResultRange:
# - For routine analyses, the function returns the valid range based on the
# specs assigned during the creation process.
# - For duplicates, the valid range is the result of the analysis the
# the duplicate was generated from +/- the duplicate variation.
# - For reference analyses, getResultRange returns the valid range as
# indicated in the Reference Sample from which the analysis was created.
result_range = api.safe_getattr(analysis, "getResultsRange", None)
if not result_range:
# No result range defined or the passed in object does not suit
return False, False
# Maybe there is a custom adapter
adapters = getAdapters((analysis,), IResultOutOfRange)
for name, adapter in adapters:
ret = adapter(result=result, specification=result_range)
if not ret or not ret.get('out_of_range', False):
continue
if not ret.get('acceptable', True):
# Out of range + out of shoulders
return True, True
# Out of range, but in shoulders
return True, False
result_range = ResultsRangeDict(result_range)
# The assignment of result as default fallback for min and max guarantees
# the result will be in range also if no min/max values are defined
specs_min = api.to_float(result_range.min, result)
specs_max = api.to_float(result_range.max, result)
in_range = False
min_operator = result_range.min_operator
if min_operator == "geq":
in_range = result >= specs_min
else:
in_range = result > specs_min
max_operator = result_range.max_operator
if in_range:
if max_operator == "leq":
in_range = result <= specs_max
else:
in_range = result < specs_max
# If in range, no need to check shoulders
if in_range:
return False, False
# Out of range, check shoulders. If no explicit warn_min or warn_max have
# been defined, no shoulders must be considered for this analysis. Thus, use
# specs' min and max as default fallback values
warn_min = api.to_float(result_range.warn_min, specs_min)
warn_max = api.to_float(result_range.warn_max, specs_max)
in_shoulder = warn_min <= result <= warn_max
return True, not in_shoulder
def is_out_of_range(brain_or_object, result=_marker):
"""Checks if the result for the analysis passed in is out of range and/or
out of shoulders range.
min max
warn min max warn
·········|---------------|=====================|---------------|·········
----- out-of-range -----><----- in-range ------><----- out-of-range -----
<-- shoulder --><----- in-range ------><-- shoulder -->
:param brain_or_object: A single catalog brain or content object
:param result: Tentative result. If None, use the analysis result
:type brain_or_object: ATContentType/DexterityContentType/CatalogBrain
:returns: Tuple of two elements. The first value is `True` if the result is
out of range and `False` if it is in range. The second value is `True` if
the result is out of shoulder range and `False` if it is in shoulder range
:rtype: (bool, bool)
"""
analysis = api.get_object(brain_or_object)
if not IAnalysis.providedBy(analysis) and \
not IReferenceAnalysis.providedBy(analysis):
api.fail("{} is not supported. Needs to be IAnalysis or "
"IReferenceAnalysis".format(repr(analysis)))
if result is _marker:
result = api.safe_getattr(analysis, "getResult", None)
if not api.is_floatable(result):
# Result is empty/None or not a valid number
return False, False
result = api.to_float(result)
# Note that routine analyses, duplicates and reference analyses all them
# implement the function getResultRange:
# - For routine analyses, the function returns the valid range based on the
# specs assigned during the creation process.
# - For duplicates, the valid range is the result of the analysis the
# the duplicate was generated from +/- the duplicate variation.
# - For reference analyses, getResultRange returns the valid range as
# indicated in the Reference Sample from which the analysis was created.
result_range = api.safe_getattr(analysis, "getResultsRange", None)
if not result_range:
# No result range defined or the passed in object does not suit
return False, False
# Maybe there is a custom adapter
adapters = getAdapters((analysis, ), IResultOutOfRange)
for name, adapter in adapters:
ret = adapter(result=result, specification=result_range)
if not ret or not ret.get('out_of_range', False):
continue
if not ret.get('acceptable', True):
# Out of range + out of shoulders
return True, True
# Out of range, but in shoulders
return True, False
# The assignment of result as default fallback for min and max guarantees
# the result will be in range also if no min/max values are defined
specs_min = api.to_float(result_range.get('min', result), result)
specs_max = api.to_float(result_range.get('max', result), result)
if specs_min <= result <= specs_max:
# In range, no need to check shoulders
return False, False
# Out of range, check shoulders. If no explicit warn_min or warn_max have
# been defined, no shoulders must be considered for this analysis. Thus, use
# specs' min and max as default fallback values
warn_min = api.to_float(result_range.get('warn_min', specs_min), specs_min)
warn_max = api.to_float(result_range.get('warn_max', specs_max), specs_max)
in_shoulder = warn_min <= result <= warn_max
return True, not in_shoulder
def is_analysis(self, obj):
"""Checks if the object is an analysis
"""
return IAnalysis.providedBy(obj)
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:
# Using the global WF menu passes the AR as context
# https://github.com/senaite/senaite.core/issues/1306
if not IAnalysis.providedBy(analysis):
continue
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("DetectionLimitOperand", 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")
# Only set result if it differs from the actual value to preserve
# the result capture date
result = self.get_form_value("Result", uid,
default=analysis.getResult())
if result != 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',)
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)