def __call__(self, result=None, specification=None, **kwargs): translate = self.context.translate path = '++resource++bika.lims.images' alerts = {} # We look for IResultOutOfRange adapters for this object for name, adapter in getAdapters((self.context, ), IResultOutOfRange): ret = adapter(result) if not ret: continue spec = ret["spec_values"] if spec: rngstr = " ({0} {1}, {2}, {3})".format(t(_("min")), str(spec['min']), t(_("max")), str(spec['max'])) else: rngstr = "" if ret["out_of_range"]: if ret["acceptable"]: message = "{0}{1}".format(t(_('Result in shoulder range')), rngstr) icon = path + '/warning.png' else: message = "{0}{1}".format(t(_('Result out of range')), rngstr) icon = path + '/exclamation.png' alerts[self.context.UID()] = [ { 'icon': icon, 'msg': message, 'field': 'Result', }, ] break return alerts
def __call__(self, result=None, **kwargs): translate = self.context.translate path = '++resource++bika.lims.images' alerts = {} # We look for IResultOutOfRange adapters for this object for name, adapter in getAdapters((self.context, ), IResultOutOfRange): ret = adapter(result) if not ret: continue spec = ret["spec_values"] rngstr = "{0} {1}, {2} {3}".format( t(_("min")), str(spec['min']), t(_("max")), str(spec['max'])) if ret["out_of_range"]: if ret["acceptable"]: message = "{0} ({1})".format( t(_('Result in shoulder range')), rngstr ) icon = path + '/warning.png' else: message = "{0} ({1})".format( t(_('Result out of range')), rngstr ) icon = path + '/exclamation.png' alerts[self.context.UID()] = [ { 'icon': icon, 'msg': message, 'field': 'Result', }, ] break return alerts
def __call__(self): self.selection_macros = SelectionMacrosView(self.context, self.request) self.icon = self.portal_url + "/++resource++bika.lims.images/report_big.png" self.additional_reports = [] adapters = getAdapters((self.context, ), IAdministrationReport) for name, adapter in adapters: report_dict = adapter(self.context, self.request) report_dict['id'] = name self.additional_reports.append(report_dict) return self.template()
def ResultOutOfRange(self, analysis): """ Template wants to know, is this analysis out of range? We scan IResultOutOfRange adapters, and return True if any IAnalysis adapters trigger a result. """ adapters = getAdapters((analysis, ), IResultOutOfRange) spec = self.get_analysis_spec(analysis) for name, adapter in adapters: if not spec: return False if adapter(specification=spec): return True
def __call__(self): self.selection_macros = SelectionMacrosView(self.context, self.request) self.icon = self.portal_url + "/++resource++bika.lims.images/report_big.png" self.getAnalysts = getUsers(self.context, ['Manager', 'LabManager', 'Analyst']) self.additional_reports = [] adapters = getAdapters((self.context, ), IProductivityReport) for name, adapter in adapters: report_dict = adapter(self.context, self.request) report_dict['id'] = name self.additional_reports.append(report_dict) return self.template()
def __call__(self, result=None, **kwargs): workflow = getToolByName(self.context, 'portal_workflow') items = self.context.getAnalyses() field_icons = {} for obj in items: obj = obj.getObject() if hasattr(obj, 'getObject') else obj uid = obj.UID() astate = workflow.getInfoFor(obj, 'review_state') if astate == 'retracted': continue adapters = getAdapters((obj, ), IFieldIcons) for name, adapter in adapters: alerts = adapter(obj) if alerts: if uid in field_icons: field_icons[uid].extend(alerts[uid]) else: field_icons[uid] = alerts[uid] return field_icons
def __call__(self, result=None, **kwargs): translate = self.context.translate path = "++resource++bika.lims.images" alerts = {} for name, adapter in getAdapters((self.context,), IResultOutOfRange): ret = adapter(result, **kwargs) if not ret: continue out_of_range = ret["out_of_range"] spec = ret["spec_values"] if out_of_range: message = t( _( "Relative percentage difference, ${variation_here} %, is out of valid range (${variation} %))", mapping={"variation_here": ret["variation_here"], "variation": ret["variation"]}, ) ) alerts[self.context.UID()] = [{"msg": message, "field": "Result", "icon": path + "/exclamation.png"}] break return alerts
def isVisible(self, instance, mode='view', default=None, field=None): """decide if a field is visible in a given mode -> 'state'. see Products.Archetypes.Widget.TypesWidget#isVisible for details about the default behaviour. """ # First get the original value, to use as our default vis_dic = getattr(aq_base(self), 'visible', _marker) state = default if default else 'visible' if vis_dic is _marker: return state if type(vis_dic) is DictType: state = vis_dic.get(mode, state) elif not vis_dic: state = 'invisible' elif vis_dic < 0: state = 'hidden' if not field: return state # call any IATWidgetVisibility adapters adapters = {} for adapter in getAdapters((instance, ), IATWidgetVisibility): sort_val = getattr(adapter[1], 'sort', 1000) if sort_val not in adapters: adapters[sort_val] = [] adapters[sort_val].append(adapter) keys = sorted(adapters.keys()) keys.reverse() for key in keys: for adapter in adapters[key]: oldstate = state state = adapter[1](instance, mode, field, state) # if state != oldstate: # adapter_name = adapter[1].__repr__().split(" ")[0].split(".")[-1] # print "%-25s %-25s adapter:%s"%(field.getName(), "%s->%s"%(oldstate, state), adapter_name) return state
def __call__(self, result=None, **kwargs): translate = self.context.translate path = "++resource++bika.lims.images" alerts = {} for name, adapter in getAdapters((self.context, ), IResultOutOfRange): ret = adapter(result, **kwargs) if not ret: continue out_of_range = ret["out_of_range"] spec = ret["spec_values"] if out_of_range: message = t(_("Relative percentage difference, ${variation_here} %, is out of valid range (${variation} %))", mapping={'variation_here': ret['variation_here'], 'variation': ret['variation'], } )) alerts[self.context.UID()] = [ { 'msg': message, 'field': 'Result', 'icon': path + '/exclamation.png', }, ] break return alerts
def __call__(self): CheckAuthenticator(self.request) page = self.request['page'] nr_rows = self.request['rows'] sord = self.request['sord'] sidx = self.request['sidx'] colModel = json.loads(_u(self.request.get('colModel', '[]'))) discard_empty = json.loads(_c(self.request.get('discard_empty', "[]"))) rows = [] brains = [] for name, adapter in getAdapters((self.context, self.request), IReferenceWidgetVocabulary): brains.extend(adapter()) for p in brains: row = {'UID': getattr(p, 'UID'), 'Title': getattr(p, 'Title')} other_fields = [x for x in colModel if x['columnName'] not in row.keys()] instance = schema = None discard = False # This will be faster if the columnNames are catalog indexes for field in other_fields: fieldname = field['columnName'] # Prioritize method retrieval over field retrieval from schema obj = p.getObject() value = getattr(obj, fieldname, None) if not value or hasattr(value, 'im_self'): value = getattr(p, fieldname, None) if not value: if instance is None: instance = p.getObject() schema = instance.Schema() if fieldname in schema: value = schema[fieldname].get(instance) elif hasattr(instance, fieldname): value = getattr(instance, fieldname) if callable(value): value = value() if fieldname in discard_empty and not value: discard = True break # ' ' instead of '' because empty div fields don't render # correctly in combo results table row[fieldname] = value and value or ' ' if discard is False: rows.append(row) rows = sorted(rows, cmp=lambda x, y: cmp( str(x).lower(), str(y).lower()), key=itemgetter(sidx and sidx or 'Title')) if sord == 'desc': rows.reverse() pages = len(rows) / int(nr_rows) pages += divmod(len(rows), int(nr_rows))[1] and 1 or 0 start = (int(page) - 1) * int(nr_rows) end = int(page) * int(nr_rows) ret = {'page': page, 'total': pages, 'records': len(rows), 'rows': rows[start:end]} return json.dumps(ret)
def read(context, request): tag = AuthenticatorView(context, request).authenticator() pattern = '<input .*name="(\w+)".*value="(\w+)"' _authenticator = re.match(pattern, tag).groups()[1] ret = { "url": router.url_for("read", force_external=True), "success": True, "error": False, "objects": [], "_authenticator": _authenticator, } debug_mode = True #App.config.getConfiguration().debug_mode "Commented by Yasir" catalog_name = request.get("catalog_name", "portal_catalog") if not catalog_name: raise ValueError("bad or missing catalog_name: " + catalog_name) catalog = getToolByName(context, catalog_name) indexes = catalog.indexes() contentFilter = {} for index in indexes: if index in request: if index == 'review_state' and "{" in request[index]: continue contentFilter[index] = safe_unicode(request[index]) if "%s[]"%index in request: value = request["%s[]"%index] contentFilter[index] = [safe_unicode(v) for v in value] if 'limit' in request: try: contentFilter['sort_limit'] = int(request["limit"]) except ValueError: pass sort_on = request.get('sort_on', 'id') contentFilter['sort_on'] = sort_on # sort order sort_order = request.get('sort_order', '') if sort_order: contentFilter['sort_order'] = sort_order else: sort_order = 'ascending' contentFilter['sort_order'] = 'ascending' include_fields = get_include_fields(request) if debug_mode: logger.info("contentFilter: " + str(contentFilter)) # Get matching objects from catalog proxies = catalog(**contentFilter) # batching items page_nr = int(request.get("page_nr", 0)) try: page_size = int(request.get("page_size", 10)) except ValueError: page_size = 10 # page_size == 0: show all if page_size == 0: page_size = len(proxies) first_item_nr = page_size * page_nr if first_item_nr > len(proxies): first_item_nr = 0 page_proxies = proxies[first_item_nr:first_item_nr + page_size] for proxy in page_proxies: obj_data = {} # Place all proxy attributes into the result. obj_data.update(load_brain_metadata(proxy, include_fields)) # Place all schema fields ino the result. obj = proxy.getObject() obj_data.update(load_field_values(obj, include_fields)) obj_data['path'] = "/".join(obj.getPhysicalPath()) # call any adapters that care to modify this data. adapters = getAdapters((obj, ), IJSONReadExtender) for name, adapter in adapters: adapter(request, obj_data) ret['objects'].append(obj_data) ret['total_objects'] = len(proxies) ret['first_object_nr'] = first_item_nr last_object_nr = first_item_nr + len(page_proxies) if last_object_nr > ret['total_objects']: last_object_nr = ret['total_objects'] ret['last_object_nr'] = last_object_nr if debug_mode: logger.info("{0} objects returned".format(len(ret['objects']))) return ret
def _analysis_data(self, analysis): """ Returns a dict that represents the analysis """ decimalmark = analysis.aq_parent.aq_parent.getDecimalMark() keyword = analysis.getKeyword() service = analysis.getService() andict = {'obj': analysis, 'id': analysis.id, 'title': analysis.Title(), 'keyword': keyword, 'scientific_name': service.getScientificName(), 'accredited': service.getAccredited(), 'point_of_capture': to_utf8(POINTS_OF_CAPTURE.getValue(service.getPointOfCapture())), 'category': to_utf8(service.getCategoryTitle()), 'result': analysis.getResult(), 'unit': to_utf8(service.getUnit()), 'formatted_unit': format_supsub(to_utf8(service.getUnit())), 'capture_date': analysis.getResultCaptureDate(), 'request_id': analysis.aq_parent.getId(), 'formatted_result': '', 'uncertainty': analysis.getUncertainty(), 'formatted_uncertainty': '', 'retested': analysis.getRetested(), 'remarks': to_utf8(analysis.getRemarks()), 'resultdm': to_utf8(analysis.getResultDM()), 'outofrange': False, 'type': analysis.portal_type, 'reftype': analysis.getReferenceType() \ if hasattr(analysis, 'getReferenceType') else None, 'worksheet': None, 'specs': {}, 'formatted_specs': ''} andict['refsample'] = analysis.getSample().id \ if analysis.portal_type == 'Analysis' \ else '%s - %s' % (analysis.aq_parent.id, analysis.aq_parent.Title()) # Which analysis specs must be used? # Try first with those defined at AR Publish Specs level if analysis.portal_type == 'ReferenceAnalysis': # The analysis is a Control or Blank. We might use the # reference results instead other specs uid = analysis.getServiceUID() specs = analysis.aq_parent.getResultsRangeDict().get(uid, {}) elif analysis.portal_type == 'DuplicateAnalysis': specs = analysis.getAnalysisSpecs() else: ar = analysis.aq_parent specs = ar.getPublicationSpecification() if not specs or keyword not in specs.getResultsRangeDict(): specs = analysis.getAnalysisSpecs() specs = specs.getResultsRangeDict().get(keyword, {}) \ if specs else {} andict['specs'] = specs scinot = self.context.bika_setup.getScientificNotationReport() andict['formatted_result'] = analysis.getFormattedResult( specs=specs, sciformat=int(scinot), decimalmark=decimalmark) fs = '' if specs.get('min', None) and specs.get('max', None): fs = '%s - %s' % (specs['min'], specs['max']) elif specs.get('min', None): fs = '> %s' % specs['min'] elif specs.get('max', None): fs = '< %s' % specs['max'] andict['formatted_specs'] = formatDecimalMark(fs, decimalmark) andict['formatted_uncertainty'] = format_uncertainty( analysis, analysis.getResult(), decimalmark=decimalmark, sciformat=int(scinot)) # Out of range? if specs: adapters = getAdapters((analysis, ), IResultOutOfRange) bsc = getToolByName(self.context, "bika_setup_catalog") for name, adapter in adapters: ret = adapter(specification=specs) if ret and ret['out_of_range']: andict['outofrange'] = True break return andict
def calculate(self, uid=None): analysis = self.analyses[uid] form_result = self.current_results[uid]['result'] service = analysis.getService() calculation = service.getCalculation() if analysis.portal_type == 'ReferenceAnalysis': deps = {} else: deps = {} for dep in analysis.getDependencies(): deps[dep.UID()] = dep path = '++resource++bika.lims.images' mapping = {} # values to be returned to form for this UID Result = {'uid': uid, 'result': form_result} try: Result['result'] = float(form_result) except: if form_result == "0/0": Result['result'] = "" if calculation: ''' We need first to create the map of available parameters acording to the interims, analyses and wildcards: params = { <as-1-keyword> : <analysis_result>, <as-1-keyword>.<wildcard-1> : <wildcard_1_value>, <as-1-keyword>.<wildcard-2> : <wildcard_2_value>, <interim-1> : <interim_result>, ... } ''' # Get dependent analyses results and wildcard values to the # mapping. If dependent analysis without result found, # break and abort calculation unsatisfied = False for dependency_uid, dependency in deps.items(): if dependency_uid in self.ignore_uids: unsatisfied = True break # LIMS-1769. Allow to use LDL and UDL in calculations. # https://jira.bikalabs.com/browse/LIMS-1769 analysisvalues = {} if dependency_uid in self.current_results: analysisvalues = self.current_results[dependency_uid] else: # Retrieve the result and DLs from the analysis analysisvalues = { 'keyword': dependency.getKeyword(), 'result': dependency.getResult(), 'ldl': dependency.getLowerDetectionLimit(), 'udl': dependency.getUpperDetectionLimit(), 'belowldl': dependency.isBelowLowerDetectionLimit(), 'aboveudl': dependency.isAboveUpperDetectionLimit(), } if analysisvalues['result'] == '': unsatisfied = True break key = analysisvalues.get('keyword', dependency.getService().getKeyword()) # Analysis result # All result mappings must be float, or they are ignored. try: mapping[key] = float(analysisvalues.get('result')) mapping['%s.%s' % (key, 'RESULT')] = float( analysisvalues.get('result')) mapping['%s.%s' % (key, 'LDL')] = float( analysisvalues.get('ldl')) mapping['%s.%s' % (key, 'UDL')] = float( analysisvalues.get('udl')) mapping['%s.%s' % (key, 'BELOWLDL')] = int( analysisvalues.get('belowldl')) mapping['%s.%s' % (key, 'ABOVEUDL')] = int( analysisvalues.get('aboveudl')) except: # If not floatable, then abort! unsatisfied = True break if unsatisfied: # unsatisfied means that one or more result on which we depend # is blank or unavailable, so we set blank result and abort. self.results.append({ 'uid': uid, 'result': '', 'formatted_result': '' }) return None # Add all interims to mapping for i_uid, i_data in self.item_data.items(): for i in i_data: # if this interim belongs to current analysis and is blank, # return an empty result for this analysis. if i_uid == uid and i['value'] == '': self.results.append({ 'uid': uid, 'result': '', 'formatted_result': '' }) return None # All interims must be float, or they are ignored. try: i['value'] = float(i['value']) except: pass # all interims are ServiceKeyword.InterimKeyword if i_uid in deps: key = "%s.%s" % (deps[i_uid].getService().getKeyword(), i['keyword']) mapping[key] = i['value'] # this analysis' interims get extra reference # without service keyword prefix if uid == i_uid: mapping[i['keyword']] = i['value'] # Grab values for hidden InterimFields for only for current calculation # we can't allow non-floats through here till we change the eval's # interpolation hidden_fields = [] c_fields = calculation.getInterimFields() s_fields = service.getInterimFields() for field in c_fields: if field.get('hidden', False): hidden_fields.append(field['keyword']) try: mapping[field['keyword']] = float(field['value']) except ValueError: pass # also grab stickier defaults from AnalysisService for field in s_fields: if field['keyword'] in hidden_fields: try: mapping[field['keyword']] = float(field['value']) except ValueError: pass # convert formula to a valid python string, ready for interpolation formula = calculation.getMinifiedFormula() formula = formula.replace('[', '%(').replace(']', ')f') try: formula = eval("'%s'%%mapping" % formula, { "__builtins__": None, 'math': math, 'context': self.context }, {'mapping': mapping}) # calculate result = eval(formula) Result['result'] = result self.current_results[uid]['result'] = result except TypeError as e: # non-numeric arguments in interim mapping? alert = { 'field': 'Result', 'icon': path + '/exclamation.png', 'msg': "{0}: {1} ({2}) ".format(t(_("Type Error")), html_quote(str(e.args[0])), formula) } if uid in self.alerts: self.alerts[uid].append(alert) else: self.alerts[uid] = [ alert, ] except ZeroDivisionError as e: Result['result'] = '0/0' Result['formatted_result'] = '0/0' self.current_results[uid]['result'] = '0/0' self.results.append(Result) alert = { 'field': 'Result', 'icon': path + '/exclamation.png', 'msg': "{0}: {1} ({2}) ".format(t(_("Division by zero")), html_quote(str(e.args[0])), formula) } if uid in self.alerts: self.alerts[uid].append(alert) else: self.alerts[uid] = [ alert, ] return None except KeyError as e: alert = { 'field': 'Result', 'icon': path + '/exclamation.png', 'msg': "{0}: {1} ({2}) ".format(t(_("Key Error")), html_quote(str(e.args[0])), formula) } if uid in self.alerts: self.alerts[uid].append(alert) else: self.alerts[uid] = [ alert, ] # format result belowmin = False abovemax = False # Some analyses will not have AnalysisSpecs, eg, ReferenceAnalysis if hasattr(analysis, 'getAnalysisSpecs'): specs = analysis.getAnalysisSpecs() specs = specs.getResultsRangeDict() if specs is not None else {} specs = specs.get(analysis.getKeyword(), {}) hidemin = specs.get('hidemin', '') hidemax = specs.get('hidemax', '') if Result.get('result', ''): fresult = Result['result'] try: belowmin = hidemin and fresult < float(hidemin) or False except ValueError: belowmin = False pass try: abovemax = hidemax and fresult > float(hidemax) or False except ValueError: abovemax = False pass if belowmin is True: Result['formatted_result'] = '< %s' % hidemin elif abovemax is True: Result['formatted_result'] = '> %s' % hidemax else: try: Result['formatted_result'] = format_numeric_result( analysis, Result['result']) except ValueError: # non-float Result['formatted_result'] = Result['result'] # calculate Dry Matter result # if parent is not an AR, it's never going to be calculable dm = hasattr(analysis.aq_parent, 'getReportDryMatter') and \ analysis.aq_parent.getReportDryMatter() and \ analysis.getService().getReportDryMatter() if dm: dry_service = self.context.bika_setup.getDryMatterService() # get the UID of the DryMatter Analysis from our parent AR dry_analysis = [ a for a in analysis.aq_parent.getAnalyses(full_objects=True) if a.getService().UID() == dry_service.UID() ] if dry_analysis: dry_analysis = dry_analysis[0] dry_uid = dry_analysis.UID() # get the current DryMatter analysis result from the form if dry_uid in self.current_results: try: dry_result = float(self.current_results[dry_uid]) except: dm = False else: try: dry_result = float(dry_analysis.getResult()) except: dm = False else: dm = False Result['dry_result'] = dm and dry_result and \ '%.2f' % ((Result['result'] / dry_result) * 100) or '' self.results.append(Result) # if App.config.getConfiguration().debug_mode: # logger.info("calc.py: %s->%s %s" % (analysis.aq_parent.id, # analysis.id, # Result)) # LIMS-1808 Uncertainty calculation on DL # https://jira.bikalabs.com/browse/LIMS-1808 flres = Result.get('result', None) if flres and isnumber(flres): flres = float(flres) anvals = self.current_results[uid] isldl = anvals.get('isldl', False) isudl = anvals.get('isudl', False) ldl = anvals.get('ldl', 0) udl = anvals.get('udl', 0) ldl = float(ldl) if isnumber(ldl) else 0 udl = float(udl) if isnumber(udl) else 10000000 belowldl = (isldl or flres < ldl) aboveudl = (isudl or flres > udl) unc = '' if (belowldl or aboveudl) else analysis.getUncertainty( Result.get('result')) if not (belowldl or aboveudl): self.uncertainties.append({'uid': uid, 'uncertainty': unc}) # maybe a service who depends on us must be recalculated. if analysis.portal_type == 'ReferenceAnalysis': dependents = [] else: dependents = analysis.getDependents() if dependents: for dependent in dependents: dependent_uid = dependent.UID() # ignore analyses that no longer exist. if dependent_uid in self.ignore_uids or \ dependent_uid not in self.analyses: continue self.calculate(dependent_uid) # These self.alerts are just for the json return. # we're placing the entire form's results in kwargs. adapters = getAdapters((analysis, ), IFieldIcons) for name, adapter in adapters: alerts = adapter(result=Result['result'], form_results=self.current_results) if alerts: if analysis.UID() in self.alerts: self.alerts[analysis.UID()].extend(alerts[analysis.UID()]) else: self.alerts[analysis.UID()] = alerts[analysis.UID()]
def __call__(self): CheckAuthenticator(self.request) page = self.request['page'] nr_rows = self.request['rows'] sord = self.request['sord'] sidx = self.request['sidx'] colModel = json.loads(_u(self.request.get('colModel', '[]'))) discard_empty = json.loads(_c(self.request.get('discard_empty', "[]"))) rows = [] brains = [] for name, adapter in getAdapters((self.context, self.request), IReferenceWidgetVocabulary): brains.extend(adapter()) for p in brains: row = {'UID': getattr(p, 'UID'), 'Title': getattr(p, 'Title')} other_fields = [ x for x in colModel if x['columnName'] not in row.keys() ] instance = schema = None discard = False # This will be faster if the columnNames are catalog indexes for field in other_fields: fieldname = field['columnName'] # Prioritize method retrieval over field retrieval from schema obj = p.getObject() value = getattr(obj, fieldname, None) if not value or hasattr(value, 'im_self'): value = getattr(p, fieldname, None) if not value: if instance is None: instance = p.getObject() schema = instance.Schema() if fieldname in schema: value = schema[fieldname].get(instance) elif hasattr(instance, fieldname): value = getattr(instance, fieldname) if callable(value): value = value() if fieldname in discard_empty and not value: discard = True break # ' ' instead of '' because empty div fields don't render # correctly in combo results table row[fieldname] = value and value or ' ' if discard is False: rows.append(row) rows = sorted(rows, cmp=lambda x, y: cmp(str(x).lower(), str(y).lower()), key=itemgetter(sidx and sidx or 'Title')) if sord == 'desc': rows.reverse() pages = len(rows) / int(nr_rows) pages += divmod(len(rows), int(nr_rows))[1] and 1 or 0 start = (int(page) - 1) * int(nr_rows) end = int(page) * int(nr_rows) ret = { 'page': page, 'total': pages, 'records': len(rows), 'rows': rows[start:end] } return json.dumps(ret)
def getSetupDatas(self): datasets = [] adapters = getAdapters((self.context, ), ISetupDataSetList) for name, adapter in adapters: datasets.extend(adapter()) return datasets
def getProjectName(self): adapters = getAdapters((self.context, ), ISetupDataSetList) productnames = [name for name, adapter in adapters] if len(productnames) == 1: productnames[0] = 'bika.lims' return productnames[len(productnames) - 1]
def calculate(self, uid=None): analysis = self.analyses[uid] form_result = self.current_results[uid]['result'] service = analysis.getService() calculation = service.getCalculation() if analysis.portal_type == 'ReferenceAnalysis': deps = {} else: deps = {} for dep in analysis.getDependencies(): deps[dep.UID()] = dep path = '++resource++bika.lims.images' mapping = {} # values to be returned to form for this UID Result = {'uid': uid, 'result': form_result} try: Result['result'] = float(form_result) except: if form_result == "0/0": Result['result'] = "" if calculation: ''' We need first to create the map of available parameters acording to the interims, analyses and wildcards: params = { <as-1-keyword> : <analysis_result>, <as-1-keyword>.<wildcard-1> : <wildcard_1_value>, <as-1-keyword>.<wildcard-2> : <wildcard_2_value>, <interim-1> : <interim_result>, ... } ''' # Get dependent analyses results and wildcard values to the # mapping. If dependent analysis without result found, # break and abort calculation unsatisfied = False for dependency_uid, dependency in deps.items(): if dependency_uid in self.ignore_uids: unsatisfied = True break # LIMS-1769. Allow to use LDL and UDL in calculations. # https://jira.bikalabs.com/browse/LIMS-1769 analysisvalues = {} if dependency_uid in self.current_results: analysisvalues = self.current_results[dependency_uid] else: # Retrieve the result and DLs from the analysis analysisvalues = { 'keyword': dependency.getKeyword(), 'result': dependency.getResult(), 'ldl': dependency.getLowerDetectionLimit(), 'udl': dependency.getUpperDetectionLimit(), 'belowldl': dependency.isBelowLowerDetectionLimit(), 'aboveudl': dependency.isAboveUpperDetectionLimit(), } if analysisvalues['result']=='': unsatisfied = True break; key = analysisvalues.get('keyword',dependency.getService().getKeyword()) # Analysis result # All result mappings must be float, or they are ignored. try: mapping[key] = float(analysisvalues.get('result')) mapping['%s.%s' % (key, 'RESULT')] = float(analysisvalues.get('result')) mapping['%s.%s' % (key, 'LDL')] = float(analysisvalues.get('ldl')) mapping['%s.%s' % (key, 'UDL')] = float(analysisvalues.get('udl')) mapping['%s.%s' % (key, 'BELOWLDL')] = int(analysisvalues.get('belowldl')) mapping['%s.%s' % (key, 'ABOVEUDL')] = int(analysisvalues.get('aboveudl')) except: # If not floatable, then abort! unsatisfied = True break if unsatisfied: # unsatisfied means that one or more result on which we depend # is blank or unavailable, so we set blank result and abort. self.results.append({'uid': uid, 'result': '', 'formatted_result': ''}) return None # Add all interims to mapping for i_uid, i_data in self.item_data.items(): for i in i_data: # if this interim belongs to current analysis and is blank, # return an empty result for this analysis. if i_uid == uid and i['value'] == '': self.results.append({'uid': uid, 'result': '', 'formatted_result': ''}) return None # All interims must be float, or they are ignored. try: i['value'] = float(i['value']) except: pass # all interims are ServiceKeyword.InterimKeyword if i_uid in deps: key = "%s.%s" % (deps[i_uid].getService().getKeyword(), i['keyword']) mapping[key] = i['value'] # this analysis' interims get extra reference # without service keyword prefix if uid == i_uid: mapping[i['keyword']] = i['value'] # Grab values for hidden InterimFields for only for current calculation # we can't allow non-floats through here till we change the eval's # interpolation hidden_fields = [] c_fields = calculation.getInterimFields() s_fields = service.getInterimFields() for field in c_fields: if field.get('hidden', False): hidden_fields.append(field['keyword']) try: mapping[field['keyword']] = float(field['value']) except ValueError: pass # also grab stickier defaults from AnalysisService for field in s_fields: if field['keyword'] in hidden_fields: try: mapping[field['keyword']] = float(field['value']) except ValueError: pass # convert formula to a valid python string, ready for interpolation formula = calculation.getMinifiedFormula() formula = formula.replace('[', '%(').replace(']', ')f') try: formula = eval("'%s'%%mapping" % formula, {"__builtins__": None, 'math': math, 'context': self.context}, {'mapping': mapping}) # calculate result = eval(formula) Result['result'] = result self.current_results[uid]['result'] = result except TypeError as e: # non-numeric arguments in interim mapping? alert = {'field': 'Result', 'icon': path + '/exclamation.png', 'msg': "{0}: {1} ({2}) ".format( t(_("Type Error")), html_quote(str(e.args[0])), formula)} if uid in self.alerts: self.alerts[uid].append(alert) else: self.alerts[uid] = [alert, ] except ZeroDivisionError as e: Result['result'] = '0/0' Result['formatted_result'] = '0/0' self.current_results[uid]['result'] = '0/0' self.results.append(Result) alert = {'field': 'Result', 'icon': path + '/exclamation.png', 'msg': "{0}: {1} ({2}) ".format( t(_("Division by zero")), html_quote(str(e.args[0])), formula)} if uid in self.alerts: self.alerts[uid].append(alert) else: self.alerts[uid] = [alert, ] return None except KeyError as e: alert = {'field': 'Result', 'icon': path + '/exclamation.png', 'msg': "{0}: {1} ({2}) ".format( t(_("Key Error")), html_quote(str(e.args[0])), formula)} if uid in self.alerts: self.alerts[uid].append(alert) else: self.alerts[uid] = [alert, ] # format result belowmin = False abovemax = False # Some analyses will not have AnalysisSpecs, eg, ReferenceAnalysis if hasattr(analysis, 'getAnalysisSpecs'): specs = analysis.getAnalysisSpecs() specs = specs.getResultsRangeDict() if specs is not None else {} specs = specs.get(analysis.getKeyword(), {}) hidemin = specs.get('hidemin', '') hidemax = specs.get('hidemax', '') if Result.get('result', ''): fresult = Result['result'] try: belowmin = hidemin and fresult < float(hidemin) or False except ValueError: belowmin = False pass try: abovemax = hidemax and fresult > float(hidemax) or False except ValueError: abovemax = False pass if belowmin is True: Result['formatted_result'] = '< %s' % hidemin elif abovemax is True: Result['formatted_result'] = '> %s' % hidemax else: try: Result['formatted_result'] = format_numeric_result(analysis, Result['result']) except ValueError: # non-float Result['formatted_result'] = Result['result'] # calculate Dry Matter result # if parent is not an AR, it's never going to be calculable dm = hasattr(analysis.aq_parent, 'getReportDryMatter') and \ analysis.aq_parent.getReportDryMatter() and \ analysis.getService().getReportDryMatter() if dm: dry_service = self.context.bika_setup.getDryMatterService() # get the UID of the DryMatter Analysis from our parent AR dry_analysis = [a for a in analysis.aq_parent.getAnalyses(full_objects=True) if a.getService().UID() == dry_service.UID()] if dry_analysis: dry_analysis = dry_analysis[0] dry_uid = dry_analysis.UID() # get the current DryMatter analysis result from the form if dry_uid in self.current_results: try: dry_result = float(self.current_results[dry_uid]) except: dm = False else: try: dry_result = float(dry_analysis.getResult()) except: dm = False else: dm = False Result['dry_result'] = dm and dry_result and \ '%.2f' % ((Result['result'] / dry_result) * 100) or '' self.results.append(Result) # if App.config.getConfiguration().debug_mode: # logger.info("calc.py: %s->%s %s" % (analysis.aq_parent.id, # analysis.id, # Result)) # LIMS-1808 Uncertainty calculation on DL # https://jira.bikalabs.com/browse/LIMS-1808 flres = Result.get('result', None) if flres and isnumber(flres): flres = float(flres) anvals = self.current_results[uid] isldl = anvals.get('isldl', False) isudl = anvals.get('isudl', False) ldl = anvals.get('ldl',0) udl = anvals.get('udl',0) ldl = float(ldl) if isnumber(ldl) else 0 udl = float(udl) if isnumber(udl) else 10000000 belowldl = (isldl or flres < ldl) aboveudl = (isudl or flres > udl) unc = '' if (belowldl or aboveudl) else analysis.getUncertainty(Result.get('result')) if not (belowldl or aboveudl): self.uncertainties.append({'uid': uid, 'uncertainty': unc}) # maybe a service who depends on us must be recalculated. if analysis.portal_type == 'ReferenceAnalysis': dependents = [] else: dependents = analysis.getDependents() if dependents: for dependent in dependents: dependent_uid = dependent.UID() # ignore analyses that no longer exist. if dependent_uid in self.ignore_uids or \ dependent_uid not in self.analyses: continue self.calculate(dependent_uid) # These self.alerts are just for the json return. # we're placing the entire form's results in kwargs. adapters = getAdapters((analysis, ), IFieldIcons) for name, adapter in adapters: alerts = adapter(result=Result['result'], form_results=self.current_results) if alerts: if analysis.UID() in self.alerts: self.alerts[analysis.UID()].extend(alerts[analysis.UID()]) else: self.alerts[analysis.UID()] = alerts[analysis.UID()]
def __call__(self): form = self.request.form portal = getSite() workbook = None if 'setupexisting' in form and 'existing' in form and form['existing']: fn = form['existing'].split(":") self.dataset_project = fn[0] self.dataset_name = fn[1] path = 'setupdata/%s/%s.xlsx' % \ (self.dataset_name, self.dataset_name) filename = resource_filename(self.dataset_project, path) try: workbook = load_workbook( filename=filename) # , use_iterators=True) except AttributeError: print "" print traceback.format_exc() print "Error while loading ", path elif 'setupfile' in form and 'file' in form and form[ 'file'] and 'projectname' in form and form['projectname']: self.dataset_project = form['projectname'] tmp = tempfile.mktemp() file_content = form['file'].read() open(tmp, 'wb').write(file_content) workbook = load_workbook(filename=tmp) # , use_iterators=True) self.dataset_name = 'uploaded' assert (workbook is not None) adapters = [[name, adapter] for name, adapter in list( getAdapters((self.context, ), ISetupDataImporter))] for sheetname in workbook.get_sheet_names(): transaction.savepoint() ad_name = sheetname.replace(" ", "_") if ad_name in [a[0] for a in adapters]: adapter = [a[1] for a in adapters if a[0] == ad_name][0] adapter(self, workbook, self.dataset_project, self.dataset_name) adapters = [a for a in adapters if a[0] != ad_name] for name, adapter in adapters: transaction.savepoint() adapter(self, workbook, self.dataset_project, self.dataset_name) check = len(self.deferred) while len(self.deferred) > 0: new = self.solve_deferred() logger.info("solved %s of %s deferred references" % (check - new, check)) if new == check: raise Exception("%s unsolved deferred references: %s" % (len(self.deferred), self.deferred)) check = new logger.info("Rebuilding bika_setup_catalog") bsc = getToolByName(self.context, 'bika_setup_catalog') bsc.clearFindAndRebuild() logger.info("Rebuilding bika_catalog") bc = getToolByName(self.context, 'bika_catalog') bc.clearFindAndRebuild() logger.info("Rebuilding bika_analysis_catalog") bac = getToolByName(self.context, 'bika_analysis_catalog') bac.clearFindAndRebuild() message = PMF("Changes saved.") self.context.plone_utils.addPortalMessage(message) self.request.RESPONSE.redirect(portal.absolute_url())
def folderitems(self, full_objects = False): """ >>> portal = layer['portal'] >>> portal_url = portal.absolute_url() >>> from plone.app.testing import SITE_OWNER_NAME >>> from plone.app.testing import SITE_OWNER_PASSWORD Test page batching https://github.com/bikalabs/Bika-LIMS/issues/1276 When visiting the second page, the Water sampletype should be displayed: >>> browser = layer['getBrowser'](portal, loggedIn=True, username=SITE_OWNER_NAME, password=SITE_OWNER_PASSWORD) >>> browser.open(portal_url+"/bika_setup/bika_sampletypes/folder_view?", ... "list_pagesize=10&list_review_state=default&list_pagenumber=2") >>> browser.contents '...Water...' """ #self.contentsMethod = self.context.getFolderContents if not hasattr(self, 'contentsMethod'): self.contentsMethod = getToolByName(self.context, self.catalog) context = aq_inner(self.context) plone_layout = getMultiAdapter((context, self.request), name = u'plone_layout') plone_utils = getToolByName(context, 'plone_utils') plone_view = getMultiAdapter((context, self.request), name = u'plone') portal_properties = getToolByName(context, 'portal_properties') portal_types = getToolByName(context, 'portal_types') workflow = getToolByName(context, 'portal_workflow') site_properties = portal_properties.site_properties norm = getUtility(IIDNormalizer).normalize if self.request.get('show_all', '').lower() == 'true' \ or self.show_all == True \ or self.pagesize == 0: show_all = True else: show_all = False pagenumber = int(self.request.get('pagenumber', 1) or 1) pagesize = self.pagesize start = (pagenumber - 1) * pagesize end = start + pagesize - 1 if (hasattr(self, 'And') and self.And) \ or (hasattr(self, 'Or') and self.Or): # if contentsMethod is capable, we do an AdvancedQuery. if hasattr(self.contentsMethod, 'makeAdvancedQuery'): aq = self.contentsMethod.makeAdvancedQuery(self.contentFilter) if hasattr(self, 'And') and self.And: tmpAnd = And() for q in self.And: tmpAnd.addSubquery(q) aq &= tmpAnd if hasattr(self, 'Or') and self.Or: tmpOr = Or() for q in self.Or: tmpOr.addSubquery(q) aq &= tmpOr brains = self.contentsMethod.evalAdvancedQuery(aq) else: # otherwise, self.contentsMethod must handle contentFilter brains = self.contentsMethod(self.contentFilter) else: brains = self.contentsMethod(self.contentFilter) results = [] self.page_start_index = 0 current_index = -1 for i, obj in enumerate(brains): # we don't know yet if it's a brain or an object path = hasattr(obj, 'getPath') and obj.getPath() or \ "/".join(obj.getPhysicalPath()) if hasattr(obj, 'getObject'): obj = obj.getObject() # check if the item must be rendered or not (prevents from # doing it later in folderitems) and dealing with paging if not self.isItemAllowed(obj): continue # avoid creating unnecessary info for items outside the current # batch; only the path is needed for the "select all" case... # we only take allowed items into account current_index += 1 if not show_all and not (start <= current_index <= end): results.append(dict(path = path, uid = obj.UID())) continue uid = obj.UID() title = obj.Title() description = obj.Description() icon = plone_layout.getIcon(obj) url = obj.absolute_url() relative_url = obj.absolute_url(relative = True) fti = portal_types.get(obj.portal_type) if fti is not None: type_title_msgid = fti.Title() else: type_title_msgid = obj.portal_type url_href_title = '%s at %s: %s' % ( t(type_title_msgid), path, to_utf8(description)) modified = self.ulocalized_time(obj.modified()), # element css classes type_class = 'contenttype-' + \ plone_utils.normalizeString(obj.portal_type) state_class = '' states = {} for w in workflow.getWorkflowsFor(obj): state = w._getWorkflowStateOf(obj).id states[w.state_var] = state state_class += "state-%s " % state results_dict = dict( obj = obj, id = obj.getId(), title = title, uid = uid, path = path, url = url, fti = fti, item_data = json.dumps([]), url_href_title = url_href_title, obj_type = obj.Type, size = obj.getObjSize, modified = modified, icon = icon.html_tag(), type_class = type_class, # a list of lookups for single-value-select fields choices = {}, state_class = state_class, relative_url = relative_url, view_url = url, table_row_class = "", category = 'None', # a list of names of fields that may be edited on this item allow_edit = [], # a list of names of fields that are compulsory (if editable) required = [], # "before", "after" and replace: dictionary (key is column ID) # A snippet of HTML which will be rendered # before/after/instead of the table cell content. before = {}, # { before : "<a href=..>" } after = {}, replace = {}, ) try: rs = workflow.getInfoFor(obj, 'review_state') st_title = workflow.getTitleForStateOnType(rs, obj.portal_type) st_title = t(PMF(st_title)) except: rs = 'active' st_title = None if rs: results_dict['review_state'] = rs for state_var, state in states.items(): if not st_title: st_title = workflow.getTitleForStateOnType( state, obj.portal_type) results_dict[state_var] = state results_dict['state_title'] = st_title # extra classes for individual fields on this item { field_id : "css classes" } results_dict['class'] = {} for name, adapter in getAdapters((obj, ), IFieldIcons): auid = obj.UID() if hasattr(obj, 'UID') and callable(obj.UID) else None if not auid: continue alerts = adapter() # logger.info(str(alerts)) if alerts and auid in alerts: if auid in self.field_icons: self.field_icons[auid].extend(alerts[auid]) else: self.field_icons[auid] = alerts[auid] # Search for values for all columns in obj for key in self.columns.keys(): if hasattr(obj, key): # if the key is already in the results dict # then we don't replace it's value if results_dict.has_key(key): continue value = getattr(obj, key) if callable(value): value = value() results_dict[key] = value results.append(results_dict) return results
def read(context, request): tag = AuthenticatorView(context, request).authenticator() pattern = '<input .*name="(\w+)".*value="(\w+)"' _authenticator = re.match(pattern, tag).groups()[1] ret = { "url": router.url_for("read", force_external=True), "success": True, "error": False, "objects": [], "_authenticator": _authenticator, } debug_mode = True #App.config.getConfiguration().debug_mode "Commented by Yasir" catalog_name = request.get("catalog_name", "portal_catalog") if not catalog_name: raise ValueError("bad or missing catalog_name: " + catalog_name) catalog = getToolByName(context, catalog_name) indexes = catalog.indexes() contentFilter = {} for index in indexes: if index in request: if index == 'review_state' and "{" in request[index]: continue contentFilter[index] = safe_unicode(request[index]) if "%s[]" % index in request: value = request["%s[]" % index] contentFilter[index] = [safe_unicode(v) for v in value] if 'limit' in request: try: contentFilter['sort_limit'] = int(request["limit"]) except ValueError: pass sort_on = request.get('sort_on', 'id') contentFilter['sort_on'] = sort_on # sort order sort_order = request.get('sort_order', '') if sort_order: contentFilter['sort_order'] = sort_order else: sort_order = 'ascending' contentFilter['sort_order'] = 'ascending' include_fields = get_include_fields(request) if debug_mode: logger.info("contentFilter: " + str(contentFilter)) # Get matching objects from catalog proxies = catalog(**contentFilter) # batching items page_nr = int(request.get("page_nr", 0)) try: page_size = int(request.get("page_size", 10)) except ValueError: page_size = 10 # page_size == 0: show all if page_size == 0: page_size = len(proxies) first_item_nr = page_size * page_nr if first_item_nr > len(proxies): first_item_nr = 0 page_proxies = proxies[first_item_nr:first_item_nr + page_size] for proxy in page_proxies: obj_data = {} # Place all proxy attributes into the result. obj_data.update(load_brain_metadata(proxy, include_fields)) # Place all schema fields ino the result. obj = proxy.getObject() obj_data.update(load_field_values(obj, include_fields)) obj_data['path'] = "/".join(obj.getPhysicalPath()) # call any adapters that care to modify this data. adapters = getAdapters((obj, ), IJSONReadExtender) for name, adapter in adapters: adapter(request, obj_data) ret['objects'].append(obj_data) ret['total_objects'] = len(proxies) ret['first_object_nr'] = first_item_nr last_object_nr = first_item_nr + len(page_proxies) if last_object_nr > ret['total_objects']: last_object_nr = ret['total_objects'] ret['last_object_nr'] = last_object_nr if debug_mode: logger.info("{0} objects returned".format(len(ret['objects']))) return ret
def __call__(self): """Create and render selected report """ # if there's an error, we return productivity.pt which requires these. self.selection_macros = SelectionMacrosView(self.context, self.request) self.additional_reports = [] adapters = getAdapters((self.context, ), IProductivityReport) for name, adapter in adapters: report_dict = adapter(self.context, self.request) report_dict['id'] = name self.additional_reports.append(report_dict) report_id = self.request.get('report_id', '') if not report_id: message = _("No report specified in request") self.logger.error(message) self.context.plone_utils.addPortalMessage(message, 'error') return self.template() self.date = DateTime() username = self.context.portal_membership.getAuthenticatedMember().getUserName() self.reporter = self.user_fullname(username) self.reporter_email = self.user_email(username) # signature image self.reporter_signature = "" c = [x for x in self.bika_setup_catalog(portal_type='LabContact') if x.getObject().getUsername() == username] if c: sf = c[0].getObject().getSignature() if sf: self.reporter_signature = sf.absolute_url() + "/Signature" lab = self.context.bika_setup.laboratory self.laboratory = lab self.lab_title = lab.getName() self.lab_address = lab.getPrintAddress() self.lab_email = lab.getEmailAddress() self.lab_url = lab.getLabURL() client = logged_in_client(self.context) if client: clientuid = client.UID() self.client_title = client.Title() self.client_address = client.getPrintAddress() else: clientuid = None self.client_title = None self.client_address = None # Render form output # the report can add file names to this list; they will be deleted # once the PDF has been generated. temporary plot image files, etc. self.request['to_remove'] = [] if "report_module" in self.request: module = self.request["report_module"] else: module = "bika.lims.browser.reports.%s" % report_id try: exec ("from %s import Report" % module) # required during error redirect: the report must have a copy of # additional_reports, because it is used as a surrogate view. Report.additional_reports = self.additional_reports except ImportError: message = "Report %s.Report not found (shouldn't happen)" % module self.logger.error(message) self.context.plone_utils.addPortalMessage(message, 'error') return self.template() # Report must return dict with: # - report_title - title string for pdf/history listing # - report_data - rendered report output = Report(self.context, self.request)() # if CSV output is chosen, report returns None if not output: return if type(output) in (str, unicode, bytes): # remove temporary files for f in self.request['to_remove']: os.remove(f) return output # The report output gets pulled through report_frame.pt self.reportout = output['report_data'] framed_output = self.frame_template() # this is the good part result = createPdf(framed_output) # remove temporary files for f in self.request['to_remove']: os.remove(f) if result: # Create new report object reportid = self.aq_parent.generateUniqueId('Report') report = _createObjectByType("Report", self.aq_parent, reportid) report.edit(Client=clientuid) report.processForm() # write pdf to report object report.edit(title=output['report_title'], ReportFile=result) report.reindexObject() fn = "%s - %s" % (self.date.strftime(self.date_format_short), _u(output['report_title'])) setheader = self.request.RESPONSE.setHeader setheader('Content-Type', 'application/pdf') setheader("Content-Disposition", "attachment;filename=\"%s\"" % _c(fn)) self.request.RESPONSE.write(result) return
def __call__(self): form = self.request.form portal = getSite() workbook = None if 'setupexisting' in form and 'existing' in form and form['existing']: fn = form['existing'].split(":") self.dataset_project = fn[0] self.dataset_name = fn[1] path = 'setupdata/%s/%s.xlsx' % \ (self.dataset_name, self.dataset_name) filename = resource_filename(self.dataset_project, path) try: workbook = load_workbook(filename=filename) # , use_iterators=True) except AttributeError: print "" print traceback.format_exc() print "Error while loading ", path elif 'setupfile' in form and 'file' in form and form['file'] and 'projectname' in form and form['projectname']: self.dataset_project = form['projectname'] tmp = tempfile.mktemp() file_content = form['file'].read() open(tmp, 'wb').write(file_content) workbook = load_workbook(filename=tmp) # , use_iterators=True) self.dataset_name = 'uploaded' assert(workbook is not None) adapters = [[name, adapter] for name, adapter in list(getAdapters((self.context, ), ISetupDataImporter))] for sheetname in workbook.get_sheet_names(): transaction.savepoint() ad_name = sheetname.replace(" ", "_") if ad_name in [a[0] for a in adapters]: adapter = [a[1] for a in adapters if a[0] == ad_name][0] adapter(self, workbook, self.dataset_project, self.dataset_name) adapters = [a for a in adapters if a[0] != ad_name] for name, adapter in adapters: transaction.savepoint() adapter(self, workbook, self.dataset_project, self.dataset_name) check = len(self.deferred) while len(self.deferred) > 0: new = self.solve_deferred() logger.info("solved %s of %s deferred references" % ( check - new, check)) if new == check: raise Exception("%s unsolved deferred references: %s" % ( len(self.deferred), self.deferred)) check = new logger.info("Rebuilding bika_setup_catalog") bsc = getToolByName(self.context, 'bika_setup_catalog') bsc.clearFindAndRebuild() logger.info("Rebuilding bika_catalog") bc = getToolByName(self.context, 'bika_catalog') bc.clearFindAndRebuild() logger.info("Rebuilding bika_analysis_catalog") bac = getToolByName(self.context, 'bika_analysis_catalog') bac.clearFindAndRebuild() message = PMF("Changes saved.") self.context.plone_utils.addPortalMessage(message) self.request.RESPONSE.redirect(portal.absolute_url())
def _analysis_data(self, analysis, decimalmark=None): keyword = analysis.getKeyword() service = analysis.getService() andict = {'obj': analysis, 'id': analysis.id, 'title': analysis.Title(), 'keyword': keyword, 'scientific_name': service.getScientificName(), 'accredited': service.getAccredited(), 'point_of_capture': to_utf8(POINTS_OF_CAPTURE.getValue(service.getPointOfCapture())), 'category': to_utf8(service.getCategoryTitle()), 'result': analysis.getResult(), 'isnumber': isnumber(analysis.getResult()), 'unit': to_utf8(service.getUnit()), 'formatted_unit': format_supsub(to_utf8(service.getUnit())), 'capture_date': analysis.getResultCaptureDate(), 'request_id': analysis.aq_parent.getId(), 'formatted_result': '', 'uncertainty': analysis.getUncertainty(), 'formatted_uncertainty': '', 'retested': analysis.getRetested(), 'remarks': to_utf8(analysis.getRemarks()), 'resultdm': to_utf8(analysis.getResultDM()), 'outofrange': False, 'type': analysis.portal_type, 'reftype': analysis.getReferenceType() \ if hasattr(analysis, 'getReferenceType') else None, 'worksheet': None, 'specs': {}, 'formatted_specs': ''} if analysis.portal_type == 'DuplicateAnalysis': andict['reftype'] = 'd' ws = analysis.getBackReferences('WorksheetAnalysis') andict['worksheet'] = ws[0].id if ws and len(ws) > 0 else None andict['worksheet_url'] = ws[0].absolute_url if ws and len(ws) > 0 else None andict['refsample'] = analysis.getSample().id \ if analysis.portal_type == 'Analysis' \ else '%s - %s' % (analysis.aq_parent.id, analysis.aq_parent.Title()) # Which analysis specs must be used? # Try first with those defined at AR Publish Specs level if analysis.portal_type == 'ReferenceAnalysis': # The analysis is a Control or Blank. We might use the # reference results instead other specs uid = analysis.getServiceUID() specs = analysis.aq_parent.getResultsRangeDict().get(uid, {}) elif analysis.portal_type == 'DuplicateAnalysis': specs = analysis.getAnalysisSpecs(); else: ar = analysis.aq_parent specs = ar.getPublicationSpecification() if not specs or keyword not in specs.getResultsRangeDict(): specs = analysis.getAnalysisSpecs() specs = specs.getResultsRangeDict().get(keyword, {}) \ if specs else {} andict['specs'] = specs scinot = self.context.bika_setup.getScientificNotationReport() andict['formatted_result'] = analysis.getFormattedResult(specs=specs, sciformat=int(scinot), decimalmark=decimalmark) fs = '' if specs.get('min', None) and specs.get('max', None): fs = '%s - %s' % (specs['min'], specs['max']) elif specs.get('min', None): fs = '> %s' % specs['min'] elif specs.get('max', None): fs = '< %s' % specs['max'] andict['formatted_specs'] = formatDecimalMark(fs, decimalmark) andict['formatted_uncertainty'] = format_uncertainty(analysis, analysis.getResult(), decimalmark=decimalmark, sciformat=int(scinot)) # Out of range? if specs: adapters = getAdapters((analysis, ), IResultOutOfRange) bsc = getToolByName(self.context, "bika_setup_catalog") for name, adapter in adapters: ret = adapter(specification=specs) if ret and ret['out_of_range']: andict['outofrange'] = True break return andict