def getResultsRange(self):
"""Returns the valid result range for this analysis duplicate, based on
both on the result and duplicate variation set in the original analysis
A Duplicate will be out of range if its result does not match with the
result for the parent analysis plus the duplicate variation in % as the
margin error.
:return: A dictionary with the keys min and max
:rtype: dict
"""
specs = ResultsRangeDict()
analysis = self.getAnalysis()
if not analysis:
return specs
result = analysis.getResult()
if not api.is_floatable(result):
return specs
specs.min = specs.max = result
result = api.to_float(result)
dup_variation = analysis.getDuplicateVariation()
dup_variation = api.to_float(dup_variation)
if not dup_variation:
return specs
margin = abs(result) * (dup_variation / 100.0)
specs.min = str(result - margin)
specs.max = str(result + margin)
return specs
def get_specs(self, service):
"""Returns the analysis specs available in the request for the given uid
"""
uid = api.get_uid(service)
keyword = service.getKeyword()
specs = ResultsRangeDict(keyword=keyword, uid=uid).copy()
for key in specs.keys():
specs_value = self.request.form.get(key, [{}])[0].get(uid, None)
specs[key] = specs_value or specs.get(key)
return specs
def getResultsRange(self):
"""Returns the valid result range for this routine analysis based on the
results ranges defined in the Analysis Request this routine analysis is
assigned to.
A routine analysis will be considered out of range if it result falls
out of the range defined in "min" and "max". If there are values set for
"warn_min" and "warn_max", these are used to compute the shoulders in
both ends of the range. Thus, an analysis can be out of range, but be
within shoulders still.
:return: A dictionary with keys "min", "max", "warn_min" and "warn_max"
:rtype: dict
"""
specs = ResultsRangeDict()
analysis_request = self.getRequest()
if not analysis_request:
return specs
keyword = self.getKeyword()
ar_ranges = analysis_request.getResultsRange()
# Get the result range that corresponds to this specific analysis
an_range = [rr for rr in ar_ranges if rr.get('keyword', '') == keyword]
rr = an_range and an_range[0].copy() or specs
# Calculated Specification
calc_uid = rr.get("calculation")
calc = api.get_object_by_uid(calc_uid, None)
if calc:
spec = rr.copy()
spec["analysis_uid"] = self.UID()
calc_spec = calc.calculate_result(mapping={"spec": spec}, default=rr)
if calc_spec:
rr.update(calc_spec)
return rr
def get_results_range(self):
"""Get the results Range from the AR
"""
spec = self.context.getResultsRange()
if spec:
return dicts_to_dict(spec, "keyword")
return ResultsRangeDict()
def get_formatted_interval(results_range, default=_marker):
"""Returns a string representation of the interval defined by the results
range passed in
:param results_range: a dict or a ResultsRangeDict
"""
if not isinstance(results_range, Mapping):
if default is not _marker:
return default
api.fail("Type not supported")
results_range = ResultsRangeDict(results_range)
min_str = results_range.min if api.is_floatable(results_range.min) else None
max_str = results_range.max if api.is_floatable(results_range.max) else None
if min_str is None and max_str is None:
if default is not _marker:
return default
api.fail("Min and max values are not floatable or not defined")
min_operator = results_range.min_operator
max_operator = results_range.max_operator
if max_str is None:
return "{}{}".format(MIN_OPERATORS.getValue(min_operator), min_str)
if min_str is None:
return "{}{}".format(MAX_OPERATORS.getValue(max_operator), max_str)
# Both values set. Return an interval
min_bracket = min_operator == 'geq' and '[' or '('
max_bracket = max_operator == 'leq' and ']' or ')'
return "{}{};{}{}".format(min_bracket, min_str, max_str, max_bracket)
def getResultsRange(self):
"""Returns the valid result range for this analysis duplicate, based on
both on the result and duplicate variation set in the original analysis
A Duplicate will be out of range if its result does not match with the
result for the parent analysis plus the duplicate variation in % as the
margin error.
If the duplicate is from an analysis with result options and/or string
results enabled (with non-numeric value), returns an empty result range
:return: A dictionary with the keys min and max
:rtype: dict
"""
# Get the original analysis
original_analysis = self.getAnalysis()
if not original_analysis:
logger.warn("Orphan duplicate: {}".format(repr(self)))
return {}
# Return empty if results option enabled (exact match expected)
if original_analysis.getResultOptions():
return {}
# Return empty if non-floatable (exact match expected)
original_result = original_analysis.getResult()
if not api.is_floatable(original_result):
return {}
# Calculate the min/max based on duplicate variation %
specs = ResultsRangeDict(uid=self.getServiceUID())
dup_variation = original_analysis.getDuplicateVariation()
dup_variation = api.to_float(dup_variation, default=0)
if not dup_variation:
# We expect an exact match
specs.min = specs.max = original_result
return specs
original_result = api.to_float(original_result)
margin = abs(original_result) * (dup_variation / 100.0)
specs.min = str(original_result - margin)
specs.max = str(original_result + margin)
return specs
def get_panic_tuple(analysis, panic_range=None):
"""Returns a tuple of min_panic and max_panic for the given analysis.
Resolves each item to None if not found or not valid for the analysis.
"""
if panic_range is None:
# Get the panic range directly from the analysis
panic_range = analysis.getResultsRange() or ResultsRangeDict()
panic_min = panic_range.get("min_panic", None)
panic_max = panic_range.get("max_panic", None)
return tuple(map(to_float_or_none, [panic_min, panic_max]))
def get(self, instance, **kwargs):
values = super(ResultsRangesField, self).get(instance, **kwargs)
# If a keyword or an uid has been specified, return the result range
# for that uid or keyword only
if "search_by" in kwargs:
uid_or_keyword = kwargs.get("search_by")
if uid_or_keyword:
return self.getResultRange(values, uid_or_keyword) or {}
return {}
# Convert the dict items to ResultRangeDict for easy handling
from bika.lims.content.analysisspec import ResultsRangeDict
return map(lambda val: ResultsRangeDict(dict(val.items())), values)
def getResultRange(self, values, uid_keyword_service):
if not uid_keyword_service:
return None
if api.is_object(uid_keyword_service):
uid_keyword_service = api.get_uid(uid_keyword_service)
key = "keyword"
if api.is_uid(uid_keyword_service) and uid_keyword_service != "0":
# We always assume a uid of "0" refers to portal
key = "uid"
# Find out the item for the given uid/keyword
from bika.lims.content.analysisspec import ResultsRangeDict
value = filter(lambda v: v.get(key) == uid_keyword_service, values)
return value and ResultsRangeDict(dict(value[0].items())) or None
def getResultsRange(self):
"""Returns the valid result range for this reference analysis based on
the results ranges defined in the Reference Sample from which this
analysis has been created.
A Reference Analysis (control or blank) will be considered out of range
if its results does not match with the result defined on its parent
Reference Sample, with the % error as the margin of error, that will be
used to set the range's min and max values
:return: A dictionary with the keys min and max
:rtype: dict
"""
specs = ResultsRangeDict(result="")
sample = self.getSample()
if not sample:
return specs
service_uid = self.getServiceUID()
sample_range = sample.getResultsRangeDict()
return sample_range.get(service_uid, specs)
def getResultsRange(self):
"""Returns the valid result range for this routine analysis based on the
results ranges defined in the Analysis Request this routine analysis is
assigned to.
A routine analysis will be considered out of range if it result falls
out of the range defined in "min" and "max". If there are values set for
"warn_min" and "warn_max", these are used to compute the shoulders in
both ends of the range. Thus, an analysis can be out of range, but be
within shoulders still.
:return: A dictionary with keys "min", "max", "warn_min" and "warn_max"
:rtype: dict
"""
specs = ResultsRangeDict()
analysis_request = self.getRequest()
if not analysis_request:
return specs
keyword = self.getKeyword()
ar_ranges = analysis_request.getResultsRange()
# Get the result range that corresponds to this specific analysis
an_range = [rr for rr in ar_ranges if rr.get('keyword', '') == keyword]
return an_range and an_range[0] or specs
def folderitem(self, obj, item, index):
"""Service triggered each time an item is iterated in folderitems.
The use of this service prevents the extra-loops in child objects.
:obj: the instance of the class to be foldered
:item: dict containing the properties of the object to be used by
the template
:index: current index of the item
"""
# ensure we have an object and not a brain
obj = api.get_object(obj)
uid = api.get_uid(obj)
# settings for this analysis
service_settings = self.context.getAnalysisServiceSettings(uid)
hidden = service_settings.get("hidden", obj.getHidden())
# get the category
category = obj.getCategoryTitle()
item["category"] = category
if category not in self.categories:
self.categories.append(category)
price = obj.getPrice()
keyword = obj.getKeyword()
if uid in self.analyses:
analysis = self.analyses[uid]
# Might differ from the service keyword
keyword = analysis.getKeyword()
# Mark the row as disabled if the analysis has been submitted
item["disabled"] = ISubmitted.providedBy(analysis)
# get the hidden status of the analysis
hidden = analysis.getHidden()
# get the price of the analysis
price = analysis.getPrice()
# get the specification of this object
rr = self.get_results_range()
spec = rr.get(keyword, ResultsRangeDict())
item["Title"] = obj.Title()
item["Unit"] = obj.getUnit()
item["Price"] = price
item["before"]["Price"] = self.get_currency_symbol()
item["allow_edit"] = self.get_editable_columns(obj)
item["selected"] = uid in self.selected
item["min"] = str(spec.get("min", ""))
item["max"] = str(spec.get("max", ""))
item["warn_min"] = str(spec.get("warn_min", ""))
item["warn_max"] = str(spec.get("warn_max", ""))
item["Hidden"] = hidden
# Append info link before the service
# see: bika.lims.site.coffee for the attached event handler
item["before"]["Title"] = get_link(
"analysisservice_info?service_uid={}".format(uid),
value="<span class='glyphicon glyphicon-info-sign'></span>",
css_class="service_info")
# Icons
after_icons = ""
if obj.getAccredited():
after_icons += get_image("accredited.png",
title=t(_("Accredited")))
if obj.getAttachmentOption() == "r":
after_icons += get_image("attach_reqd.png",
title=t(_("Attachment required")))
if obj.getAttachmentOption() == "n":
after_icons += get_image("attach_no.png",
title=t(_('Attachment not permitted')))
if after_icons:
item["after"]["Title"] = after_icons
return item
def folderitem(self, obj, item, index):
"""Service triggered each time an item is iterated in folderitems.
The use of this service prevents the extra-loops in child objects.
:obj: the instance of the class to be foldered
:item: dict containing the properties of the object to be used by
the template
:index: current index of the item
"""
# ensure we have an object and not a brain
obj = api.get_object(obj)
uid = api.get_uid(obj)
# settings for this analysis
service_settings = self.context.getAnalysisServiceSettings(uid)
hidden = service_settings.get("hidden", obj.getHidden())
# get the category
category = obj.getCategoryTitle()
item["category"] = category
if category not in self.categories:
self.categories.append(category)
parts = filter(api.is_active, self.get_partitions())
partitions = map(
lambda part: {
"ResultValue": part.Title(),
"ResultText": part.getId()
}, parts)
keyword = obj.getKeyword()
partition = None
if uid in self.analyses:
analysis = self.analyses[uid]
# Might differ from the service keyword
keyword = analysis.getKeyword()
# Mark the row as disabled if the analysis is not in an open state
item["disabled"] = not analysis.isOpen()
# get the hidden status of the analysis
hidden = analysis.getHidden()
# get the partition of the analysis
partition = self.get_partition(analysis)
else:
partition = self.get_partitions()[0]
# get the specification of this object
rr = self.get_results_range()
spec = rr.get(keyword, ResultsRangeDict())
item["Title"] = obj.Title()
item["Unit"] = obj.getUnit()
item["Price"] = obj.getPrice()
item["before"]["Price"] = self.get_currency_symbol()
item["allow_edit"] = self.get_editable_columns(obj)
item["selected"] = uid in self.selected
item["min"] = str(spec.get("min", ""))
item["max"] = str(spec.get("max", ""))
item["warn_min"] = str(spec.get("warn_min", ""))
item["warn_max"] = str(spec.get("warn_max", ""))
item["Hidden"] = hidden
item["Partition"] = partition.getId()
item["choices"]["Partition"] = partitions
# Icons
after_icons = ""
if obj.getAccredited():
after_icons += get_image("accredited.png",
title=t(_("Accredited")))
if obj.getAttachmentOption() == "r":
after_icons += get_image("attach_reqd.png",
title=t(_("Attachment required")))
if obj.getAttachmentOption() == "n":
after_icons += get_image("attach_no.png",
title=t(_('Attachment not permitted')))
if after_icons:
item["after"]["Title"] = after_icons
return item
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)
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 get(self, instance, **kwargs):
from bika.lims.content.analysisspec import ResultsRangeDict
value = super(ResultRangeField, self).get(instance, **kwargs)
if value:
return ResultsRangeDict(dict(value.items()))
return {}
def get_spec_from_ar(self, ar, keyword):
empty = ResultsRangeDict(keyword=keyword)
spec = ar.getResultsRange()
if spec:
return dicts_to_dict(spec, 'keyword').get(keyword, empty)
return empty