def guard_submit(obj):
"""Returns if 'submit' transition can be applied to the worksheet passed in.
By default, the target state for the 'submit' transition for a worksheet is
'to_be_verified', so this guard returns true if all the analyses assigned
to the worksheet have already been submitted. Those analyses that are in a
non-valid state (cancelled, inactive) are dismissed in the evaluation, but
at least one analysis must be in an active state (and submitted) for this
guard to return True. Otherwise, always returns False.
Note this guard depends entirely on the current status of the children.
"""
analyses = obj.getAnalyses()
if not analyses:
# An empty worksheet cannot be submitted
return False
can_submit = False
for analysis in obj.getAnalyses():
# Dismiss analyses that are not active
if not api.is_active(analysis):
continue
# Dismiss analyses that have been rejected or retracted
if api.get_workflow_status_of(analysis) in ["rejected", "retracted"]:
continue
# Worksheet cannot be submitted if there is one analysis not submitted
can_submit = ISubmitted.providedBy(analysis)
if not can_submit:
# No need to look further
return False
# This prevents the submission of the worksheet if all its analyses are in
# a detached status (rejected, retracted or cancelled)
return can_submit
def render_checkbox(self, item, microorganism, antibiotic):
"""Renders the checkbox properties for the item, microorganism and
antibiotic passed-in
"""
uid = api.get_uid(antibiotic)
# Check whether there are analyses assigned
analyses = self.get_analyses_for(microorganism, antibiotic)
analysis = filter(lambda a: a.getKeyword() == REPORT_KEY, analyses)
analysis = analysis and analysis[-1] or None
# Set whether reporting is enabled/disabled
item[uid] = self.is_reporting_enabled(analysis, antibiotic)
# If sample is not in an editable status, no further actions required
if not self.can_add_analyses():
return
item["allow_edit"].append(uid)
if not analyses:
# No analyses assigned for this microorganism
item.setdefault("disabled", []).append(uid)
elif analysis and ISubmitted.providedBy(analysis):
# Analysis assigned, but report info submitted already
item.setdefault("disable", []).append(uid)
def is_submitted_or_submittable(analysis):
"""Returns whether the analysis is submittable or has already been submitted
"""
if ISubmitted.providedBy(analysis):
return True
if wf.isTransitionAllowed(analysis, "submit"):
return True
return False
def update_ast_analysis(analysis, antibiotics, remove=False):
# There is nothing to do if the analysis has been verified
analysis = api.get_object(analysis)
if IVerified.providedBy(analysis):
return
# Convert antibiotics to interim fields
keyword = analysis.getKeyword()
interim_fields = map(lambda ab: to_interim(keyword, ab), antibiotics)
# Get the analysis interim fields
an_interims = copy.deepcopy(analysis.getInterimFields()) or []
an_keys = sorted(map(lambda i: i.get("keyword"), an_interims))
# Remove non-specified antibiotics
if remove:
in_keys = map(lambda i: i.get("keyword"), interim_fields)
an_interims = filter(lambda a: a["keyword"] in in_keys, an_interims)
# Keep analysis' original antibiotics
abx = filter(lambda a: a["keyword"] not in an_keys, interim_fields)
an_interims.extend(abx)
# Is there any difference?
new_keys = sorted(map(lambda i: i.get("keyword"), an_interims))
if new_keys == an_keys:
# No changes
return
# If no antibiotics, remove the analysis
if remove and not an_interims:
sample = analysis.getRequest()
sample._delObject(api.get_id(analysis))
return
if ISubmitted.providedBy(analysis):
# Analysis has been submitted already, retract
succeed, message = wf.doActionFor(analysis, "retract")
if not succeed:
path = api.get_path(analysis)
logger.error("Cannot retract analysis '{}'".format(path))
return
# Assign the antibiotics
analysis.setInterimFields(an_interims)
# Compute all combinations of interim/antibiotic and possible result and
# and generate the result options for this analysis (the "Result" field is
# never displayed and is only used for reporting)
result_options = get_result_options(analysis)
analysis.setResultOptions(result_options)
# Apply the IASTAnalysis marker interface (just in case)
alsoProvides(analysis, IASTAnalysis)
analysis.reindexObject()
def has_analyses_in_panic(sample):
"""Returns whether the sample passed in have at least one analysis for which
the result is in panic in accordance with the specifications. Only analyses
in "to_be_verified" status and beyond are considered
"""
analyses = sample.getAnalyses(full_objects=True)
for analysis in analyses:
if ISubmitted.providedBy(analysis) and is_in_panic(analysis):
return True
return False
def verify_and_retest(relative):
if not ISubmitted.providedBy(relative):
# Result not yet submitted, no need to create a retest
return
# Apply the transition manually, but only if analysis can be verified
doActionFor(relative, "verify")
# Create the retest
create_retest(relative)
def update_analyses(self, microorganism, antibiotics):
analyses = self.get_analyses_for(microorganism)
# Filter those that are not yet submitted
analyses = filter(lambda a: not ISubmitted.providedBy(a), analyses)
if not analyses:
if antibiotics:
# Create new analyses
keywords = [ZONE_SIZE_KEY, RESISTANCE_KEY, REPORT_KEY]
utils.create_ast_analyses(self.context, keywords,
microorganism, antibiotics)
elif not antibiotics:
# Remove analyses
analyses_ids = map(api.get_id, analyses)
map(self.context._delObject, analyses_ids) # noqa
else:
# Update analyses
map(
lambda a: utils.update_ast_analysis(
a, antibiotics, remove=True), analyses)
def set(self, instance, items, prices=None, specs=None, hidden=None, **kw):
"""Set/Assign Analyses to this AR
:param items: List of Analysis objects/brains, AnalysisService
objects/brains and/or Analysis Service uids
:type items: list
:param prices: Mapping of AnalysisService UID -> price
:type prices: dict
:param specs: List of AnalysisService UID -> Result Range mappings
:type specs: list
:param hidden: List of AnalysisService UID -> Hidden mappings
:type hidden: list
:returns: list of new assigned Analyses
"""
if items is None:
items = []
# Bail out if the items is not a list type
if not isinstance(items, (list, tuple)):
raise TypeError(
"Items parameter must be a tuple or list, got '{}'".format(
type(items)))
# Bail out if the AR is inactive
if not api.is_active(instance):
raise Unauthorized(
"Inactive ARs can not be modified".format(AddAnalysis))
# Bail out if the user has not the right permission
if not check_permission(AddAnalysis, instance):
raise Unauthorized(
"You do not have the '{}' permission".format(AddAnalysis))
# Convert the items to a valid list of AnalysisServices
services = filter(None, map(self._to_service, items))
# Calculate dependencies
dependencies = map(lambda s: s.getServiceDependencies(), services)
dependencies = list(itertools.chain.from_iterable(dependencies))
# Merge dependencies and services
services = set(services + dependencies)
# Modify existing AR specs with new form values of selected analyses
specs = self.resolve_specs(instance, specs)
# Add analyses
params = dict(prices=prices, hidden=hidden, specs=specs)
map(lambda serv: self.add_analysis(instance, serv, **params), services)
# Get all analyses (those from descendants included)
analyses = instance.objectValues("Analysis")
analyses.extend(self.get_analyses_from_descendants(instance))
# Bail out those not in services list or submitted
uids = map(api.get_uid, services)
to_remove = filter(lambda an: an.getServiceUID() not in uids, analyses)
to_remove = filter(lambda an: not ISubmitted.providedBy(an), to_remove)
# Remove analyses
map(self.remove_analysis, to_remove)
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 remove_cascaded_analyses_of_root_samples(portal):
"""Removes Analyses from Root Samples that belong to Partitions
https://github.com/senaite/senaite.core/issues/1504
"""
logger.info("Removing cascaded analyses from Root Samples...")
# Query all root Samples
query = {
"isRootAncestor": True,
"sort_on": "created",
"sort_order": "ascending",
}
root_samples = api.search(query, "bika_catalog_analysisrequest_listing")
total = len(root_samples)
logger.info("{} Samples to check... ".format(total))
to_clean = []
for num, brain in enumerate(root_samples):
logger.debug("Checking Root Sample {}/{}".format(num + 1, total))
# No Partitions, continue...
if not brain.getDescendantsUIDs:
continue
# get the root sample
root_sample = api.get_object(brain)
# get the contained analyses of the root sample
root_analyses = root_sample.objectIds(spec=["Analysis"])
# Mapping of cascaded Analysis -> Partition
analysis_mapping = {}
# check if a root analysis is located as well in one of the partitions
for partition in root_sample.getDescendants():
# get the contained analyses of the partition
part_analyses = partition.objectIds(spec=["Analysis"])
# filter analyses that cascade root analyses
cascaded = filter(lambda an: an in root_analyses, part_analyses)
# keep a mapping of analysis -> partition
for analysis in cascaded:
analysis_mapping[analysis] = partition
if analysis_mapping:
to_clean.append((root_sample, analysis_mapping))
# count the cases for each condition
case_counter = defaultdict(int)
# cleanup cascaded analyses
# mapping maps the analysis id -> partition
for sample, mapping in to_clean:
# go through the cascaded analyses and decide if the cascaded analysis
# should be removed from (a) the root sample or (b) the partition.
for analysis_id, partition in mapping.items():
# analysis from the root sample
root_an = sample[analysis_id]
# WF state from the root sample analysis
root_an_state = api.get_workflow_status_of(root_an)
# analysis from the partition sample
part_an = partition[analysis_id]
# WF state from the partition sample analysis
part_an_state = api.get_workflow_status_of(part_an)
case_counter["{}_{}".format(root_an_state, part_an_state)] += 1
# both analyses have the same WF state
if root_an_state == part_an_state:
# -> remove the analysis from the root sample
sample._delObject(analysis_id)
logger.info(
"Remove analysis '{}' in state '{}' from sample {}: {}".
format(analysis_id, root_an_state, api.get_id(sample),
api.get_url(sample)))
# both are in verified/published state
elif IVerified.providedBy(root_an) and IVerified.providedBy(
part_an):
root_an_result = root_an.getResult()
part_an_result = root_an.getResult()
if root_an_result == part_an_result:
# remove the root analysis
sample._delObject(analysis_id)
logger.info(
"Remove analysis '{}' in state '{}' from sample {}: {}"
.format(analysis_id, root_an_state, api.get_id(sample),
api.get_url(sample)))
else:
# -> unsolvable edge case
# display an error message
logger.error("Analysis '{}' of root sample in state '{}' "
"and Analysis of partition in state {}. "
"Please fix manually: {}".format(
analysis_id, root_an_state, part_an_state,
api.get_url(sample)))
# root analysis is in invalid state
elif root_an_state in ["rejected", "retracted"]:
# -> probably the retest was automatically created in the
# parent instead of the partition
pass
# partition analysis is in invalid state
elif part_an_state in ["rejected", "retracted"]:
# -> probably the retest was automatically created in the
# parent instead of the partition
pass
# root analysis was submitted, but not the partition analysis
elif ISubmitted.providedBy(
root_an) and not ISubmitted.providedBy(part_an):
# -> remove the analysis from the partition
partition._delObject(analysis_id)
logger.info(
"Remove analysis '{}' in state '{}' from partition {}: {}".
format(analysis_id, part_an_state, api.get_id(partition),
api.get_url(partition)))
# partition analysis was submitted, but not the root analysis
elif ISubmitted.providedBy(
part_an) and not ISubmitted.providedBy(root_an):
# -> remove the analysis from the root sample
sample._delObject(analysis_id)
logger.info(
"Remove analysis '{}' in state '{}' from sample {}: {}".
format(analysis_id, root_an_state, api.get_id(sample),
api.get_url(sample)))
# inconsistent state
else:
logger.warning(
"Can not handle analysis '{}' located in '{}' (state {}) and '{}' (state {})"
.format(analysis_id, repr(sample), root_an_state,
repr(partition), part_an_state))
logger.info("Removing cascaded analyses from Root Samples... [DONE]")
logger.info("State Combinations (root_an_state, part_an_state): {}".format(
sorted(case_counter.items(), key=itemgetter(1), reverse=True)))
def set(self, instance, items, prices=None, specs=None, hidden=None, **kw):
"""Set/Assign Analyses to this AR
:param items: List of Analysis objects/brains, AnalysisService
objects/brains and/or Analysis Service uids
:type items: list
:param prices: Mapping of AnalysisService UID -> price
:type prices: dict
:param specs: List of AnalysisService UID -> Result Range mappings
:type specs: list
:param hidden: List of AnalysisService UID -> Hidden mappings
:type hidden: list
:returns: list of new assigned Analyses
"""
# This setter returns a list of new set Analyses
new_analyses = []
# Current assigned analyses
analyses = instance.objectValues("Analysis")
# Submitted analyses must be retained
submitted = filter(lambda an: ISubmitted.providedBy(an), analyses)
# Prevent removing all analyses
#
# N.B.: Submitted analyses are rendered disabled in the HTML form.
# Therefore, their UIDs are not included in the submitted UIDs.
if not items and not submitted:
logger.warn("Not allowed to remove all Analyses from AR.")
return new_analyses
# Bail out if the items is not a list type
if not isinstance(items, (list, tuple)):
raise TypeError(
"Items parameter must be a tuple or list, got '{}'".format(
type(items)))
# Bail out if the AR is inactive
if not api.is_active(instance):
raise Unauthorized(
"Inactive ARs can not be modified".format(AddAnalysis))
# Bail out if the user has not the right permission
if not check_permission(AddAnalysis, instance):
raise Unauthorized(
"You do not have the '{}' permission".format(AddAnalysis))
# Convert the items to a valid list of AnalysisServices
services = filter(None, map(self._to_service, items))
# Calculate dependencies
# FIXME Infinite recursion error possible here, if the formula includes
# the Keyword of the Service that includes the Calculation
dependencies = map(lambda s: s.getServiceDependencies(), services)
dependencies = list(itertools.chain.from_iterable(dependencies))
# Merge dependencies and services
services = set(services + dependencies)
# Modify existing AR specs with new form values of selected analyses.
self._update_specs(instance, specs)
# Create a mapping of Service UID -> Hidden status
if hidden is None:
hidden = []
hidden = dict(map(lambda d: (d.get("uid"), d.get("hidden")), hidden))
# Ensure we have a prices dictionary
if prices is None:
prices = dict()
# CREATE/MODIFY ANALYSES
for service in services:
service_uid = api.get_uid(service)
keyword = service.getKeyword()
# Create the Analysis if it doesn't exist
if shasattr(instance, keyword):
analysis = instance._getOb(keyword)
else:
analysis = create_analysis(instance, service)
new_analyses.append(analysis)
# set the hidden status
analysis.setHidden(hidden.get(service_uid, False))
# Set the price of the Analysis
analysis.setPrice(prices.get(service_uid, service.getPrice()))
# DELETE ANALYSES
# Service UIDs
service_uids = map(api.get_uid, services)
# Analyses IDs to delete
delete_ids = []
# Assigned Attachments
assigned_attachments = []
for analysis in analyses:
service_uid = analysis.getServiceUID()
# Skip if the Service is selected
if service_uid in service_uids:
continue
# Skip non-open Analyses
if analysis in submitted:
continue
# Remember assigned attachments
# https://github.com/senaite/senaite.core/issues/1025
assigned_attachments.extend(analysis.getAttachment())
analysis.setAttachment([])
# If it is assigned to a worksheet, unassign it before deletion.
worksheet = analysis.getWorksheet()
if worksheet:
worksheet.removeAnalysis(analysis)
delete_ids.append(analysis.getId())
if delete_ids:
# Note: subscriber might promote the AR
instance.manage_delObjects(ids=delete_ids)
# Remove orphaned attachments
for attachment in assigned_attachments:
# only delete attachments which are no further linked
if not attachment.getLinkedAnalyses():
logger.info("Deleting attachment: {}".format(
attachment.getId()))
attachment_id = api.get_id(attachment)
api.get_parent(attachment).manage_delObjects(attachment_id)
return new_analyses