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 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):
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 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 getSetupDatas(self):
datasets = []
adapters = getAdapters((self.context, ), ISetupDataSetList)
for name, adapter in adapters:
datasets.extend(adapter())
return datasets
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
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]
