def getFormattedResult(self, specs=None, decimalmark='.', sciformat=1):
"""Formatted result:
1. If the result is not floatable, return it without being formatted
2. If the analysis specs has hidemin or hidemax enabled and the
result is out of range, render result as '<min' or '>max'
3. If the result is floatable, render it to the correct precision
specs param is optional. A dictionary as follows:
{'min': <min_val>,
'max': <max_val>,
'error': <error>,
'hidemin': <hidemin_val>,
'hidemax': <hidemax_val>}
:param sciformat: 1. The sci notation has to be formatted as aE^+b
2. The sci notation has to be formatted as a·10^b
3. As 2, but with super html entity for exp
4. The sci notation has to be formatted as a·10^b
5. As 4, but with super html entity for exp
By default 1
"""
result = self.getResult()
service = self.getService()
# 1. If the result is not floatable, return it without being formatted
try:
result = float(result)
except:
return result
# 2. If the analysis specs has enabled hidemin or hidemax and the
# result is out of range, render result as '<min' or '>max'
belowmin = False
abovemax = False
if not specs:
uid = self.getServiceUID()
specs = self.aq_parent.getResultsRangeDict().get(uid, {})
hidemin = specs.get('hidemin', '')
hidemax = specs.get('hidemax', '')
try:
belowmin = hidemin and result < float(hidemin) or False
except:
belowmin = False
pass
try:
abovemax = hidemax and result > float(hidemax) or False
except:
abovemax = False
pass
# 2.1. If result is below min and hidemin enabled, return '<min'
if belowmin:
return formatDecimalMark('< %s' % hidemin, decimalmark)
# 2.2. If result is above max and hidemax enabled, return '>max'
if abovemax:
return formatDecimalMark('> %s' % hidemax, decimalmark)
# 3. If the result is floatable, render it to the correct precision
return formatDecimalMark(
format_numeric_result(self, result, sciformat), decimalmark)
def getFormattedResult(self, specs=None, decimalmark='.', sciformat=1):
"""Formatted result:
1. If the result is not floatable, return it without being formatted
2. If the analysis specs has hidemin or hidemax enabled and the
result is out of range, render result as '<min' or '>max'
3. If the result is floatable, render it to the correct precision
specs param is optional. A dictionary as follows:
{'min': <min_val>,
'max': <max_val>,
'error': <error>,
'hidemin': <hidemin_val>,
'hidemax': <hidemax_val>}
:param sciformat: 1. The sci notation has to be formatted as aE^+b
2. The sci notation has to be formatted as a·10^b
3. As 2, but with super html entity for exp
4. The sci notation has to be formatted as a·10^b
5. As 4, but with super html entity for exp
By default 1
"""
result = self.getResult()
service = self.getService()
# 1. If the result is not floatable, return it without being formatted
try:
result = float(result)
except:
return result
# 2. If the analysis specs has enabled hidemin or hidemax and the
# result is out of range, render result as '<min' or '>max'
belowmin = False
abovemax = False
if not specs:
uid = self.getServiceUID()
specs = self.aq_parent.getResultsRangeDict().get(uid, {})
hidemin = specs.get('hidemin', '')
hidemax = specs.get('hidemax', '')
try:
belowmin = hidemin and result < float(hidemin) or False
except:
belowmin = False
pass
try:
abovemax = hidemax and result > float(hidemax) or False
except:
abovemax = False
pass
# 2.1. If result is below min and hidemin enabled, return '<min'
if belowmin:
return formatDecimalMark('< %s' % hidemin, decimalmark)
# 2.2. If result is above max and hidemax enabled, return '>max'
if abovemax:
return formatDecimalMark('> %s' % hidemax, decimalmark)
# 3. If the result is floatable, render it to the correct precision
return formatDecimalMark(format_numeric_result(self, result, sciformat), decimalmark)
def getFormattedResult(self):
"""Formatted result:
1. Print ResultText of matching ResultOptions
2. If the result is not floatable, return it without being formatted
3. If the analysis specs has hidemin or hidemax enabled and the
result is out of range, render result as '<min' or '>max'
4. Otherwise, render numerical value
"""
result = self.getResult()
service = self.getService()
choices = service.getResultOptions()
# 1. Print ResultText of matching ResulOptions
match = [x['ResultText'] for x in choices
if str(x['ResultValue']) == str(result)]
if match:
return match[0]
# 2. If the result is not floatable, return it without being formatted
try:
result = float(result)
except:
return result
# 3. If the analysis specs has enabled hidemin or hidemax and the
# result is out of range, render result as '<min' or '>max'
belowmin = False
abovemax = False
specs = self.getAnalysisSpecs()
specs = specs.getResultsRangeDict() if specs is not None else {}
specs = specs.get(self.getKeyword(), {})
hidemin = specs.get('hidemin', '')
hidemax = specs.get('hidemax', '')
try:
belowmin = hidemin and result < float(hidemin) or False
except:
belowmin = False
pass
try:
abovemax = hidemax and result > float(hidemax) or False
except:
abovemax = False
pass
# 3.1. If result is below min and hidemin enabled, return '<min'
if belowmin:
return '< %s' % hidemin
# 3.2. If result is above max and hidemax enabled, return '>max'
if abovemax:
return '> %s' % hidemax
# Render numerical value
return format_numeric_result(self, result)
def calculate(self, uid=None):
analysis = self.analyses[uid]
form_result = self.current_results[uid]
service = analysis.getService()
precision = service.getPrecision()
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:
# add all our dependent analyses results to the mapping.
# Retrieve value from database if it's not in the current_results.
unsatisfied = False
for dependency_uid, dependency in deps.items():
if dependency_uid in self.ignore_uids:
unsatisfied = True
break
if dependency_uid in self.current_results:
result = self.current_results[dependency_uid]
else:
result = dependency.getResult()
if result == '':
unsatisfied = True
break
key = dependency.getService().getKeyword()
# All mappings must be float, or they are ignored.
try:
mapping[key] = float(self.current_results[dependency_uid])
except:
pass
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
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] = '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))
self.uncertainties.append({
'uid':
uid,
'uncertainty':
analysis.getUncertainty(Result['result'])
})
# 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 getFormattedResult(self, specs=None, decimalmark='.', sciformat=1,
html=True):
"""Formatted result:
1. If the result is a detection limit, returns '< LDL' or '> UDL'
2. Print ResultText of matching ResultOptions
3. If the result is not floatable, return it without being formatted
4. If the analysis specs has hidemin or hidemax enabled and the
result is out of range, render result as '<min' or '>max'
5. If the result is below Lower Detection Limit, show '<LDL'
6. If the result is above Upper Detecion Limit, show '>UDL'
7. Otherwise, render numerical value
:param specs: Optional result specifications, a dictionary as follows:
{'min': <min_val>,
'max': <max_val>,
'error': <error>,
'hidemin': <hidemin_val>,
'hidemax': <hidemax_val>}
:param decimalmark: The string to be used as a decimal separator.
default is '.'
:param sciformat: 1. The sci notation has to be formatted as aE^+b
2. The sci notation has to be formatted as a·10^b
3. As 2, but with super html entity for exp
4. The sci notation has to be formatted as a·10^b
5. As 4, but with super html entity for exp
By default 1
:param html: if true, returns an string with the special characters
escaped: e.g: '<' and '>' (LDL and UDL for results like < 23.4).
"""
result = self.getResult()
# 1. The result is a detection limit, return '< LDL' or '> UDL'
dl = self.getDetectionLimitOperand()
if dl:
try:
res = float(result) # required, check if floatable
res = drop_trailing_zeros_decimal(res)
fdm = formatDecimalMark(res, decimalmark)
hdl = cgi.escape(dl) if html else dl
return '%s %s' % (hdl, fdm)
except (TypeError, ValueError):
logger.warn(
"The result for the analysis %s is a detection limit, "
"but not floatable: %s" % (self.id, result))
return formatDecimalMark(result, decimalmark=decimalmark)
choices = self.getResultOptions()
# 2. Print ResultText of matching ResulOptions
match = [x['ResultText'] for x in choices
if str(x['ResultValue']) == str(result)]
if match:
return match[0]
# 3. If the result is not floatable, return it without being formatted
try:
result = float(result)
except (TypeError, ValueError):
return formatDecimalMark(result, decimalmark=decimalmark)
# 4. If the analysis specs has enabled hidemin or hidemax and the
# result is out of range, render result as '<min' or '>max'
specs = specs if specs else self.getResultsRange()
hidemin = specs.get('hidemin', '')
hidemax = specs.get('hidemax', '')
try:
belowmin = hidemin and result < float(hidemin) or False
except (TypeError, ValueError):
belowmin = False
try:
abovemax = hidemax and result > float(hidemax) or False
except (TypeError, ValueError):
abovemax = False
# 4.1. If result is below min and hidemin enabled, return '<min'
if belowmin:
fdm = formatDecimalMark('< %s' % hidemin, decimalmark)
return fdm.replace('< ', '< ', 1) if html else fdm
# 4.2. If result is above max and hidemax enabled, return '>max'
if abovemax:
fdm = formatDecimalMark('> %s' % hidemax, decimalmark)
return fdm.replace('> ', '> ', 1) if html else fdm
# Below Lower Detection Limit (LDL)?
ldl = self.getLowerDetectionLimit()
if result < ldl:
# LDL must not be formatted according to precision, etc.
# Drop trailing zeros from decimal
ldl = drop_trailing_zeros_decimal(ldl)
fdm = formatDecimalMark('< %s' % ldl, decimalmark)
return fdm.replace('< ', '< ', 1) if html else fdm
# Above Upper Detection Limit (UDL)?
udl = self.getUpperDetectionLimit()
if result > udl:
# UDL must not be formatted according to precision, etc.
# Drop trailing zeros from decimal
udl = drop_trailing_zeros_decimal(udl)
fdm = formatDecimalMark('> %s' % udl, decimalmark)
return fdm.replace('> ', '> ', 1) if html else fdm
# Render numerical values
return format_numeric_result(self, self.getResult(),
decimalmark=decimalmark,
sciformat=sciformat)
def calculate(self, uid=None):
# TODO Move this function to api.analysis.calculate
analysis = self.analyses[uid]
form_result = self.current_results[uid]['result']
calculation = analysis.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.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].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 = analysis.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, calculation._getGlobals())
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
try:
Result['formatted_result'] = format_numeric_result(analysis,
Result['result'])
except ValueError:
# non-float
Result['formatted_result'] = Result['result']
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)
# Render out of range / in shoulder alert info
self._render_range_alert(analysis, Result["result"])
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, ]
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, {})
else:
# Get the specs directly from the analysis. The getResultsRange
# function already takes care about which are the specs to be used:
# AR, client or lab.
specs = analysis.getResultsRange()
# format result
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):
pc = self.portal_catalog
self.checkPermission = self.context.portal_membership.checkPermission
self.now = DateTime()
self.SamplingWorkflowEnabled = self.context.bika_setup.getSamplingWorkflowEnabled()
# Client details (if client is associated)
self.client = None
client_uid = hasattr(self.context, 'getClientUID') and self.context.getClientUID()
if client_uid:
proxies = pc(portal_type='Client', UID=client_uid)
if proxies:
self.client = proxies[0].getObject()
client_address = self.client.getPostalAddress()
if self.contact and not client_address:
client_address = self.contact.getBillingAddress()
if not client_address:
client_address = self.contact.getPhysicalAddress()
if client_address:
_keys = ['address', 'city', 'state', 'zip', 'country']
_list = [client_address.get(v) for v in _keys if client_address.get(v)]
self.client_address = "<br/>".join(_list).replace("\n", "<br/>")
if self.client_address.endswith("<br/>"):
self.client_address = self.client_address[:-5]
else:
self.client_address = None
# Reporter
self.member = self.context.portal_membership.getAuthenticatedMember()
self.username = self.member.getUserName()
self.reporter = self.user_fullname(self.username)
self.reporter_email = self.user_email(self.username)
self.reporter_signature = ""
c = [x for x in self.bika_setup_catalog(portal_type='LabContact')
if x.getObject().getUsername() == self.username]
if c:
sf = c[0].getObject().getSignature()
if sf:
self.reporter_signature = sf.absolute_url() + "/Signature"
# laboratory
self.laboratory = self.context.bika_setup.laboratory
self.accredited = self.laboratory.getLaboratoryAccredited()
lab_address = self.laboratory.getPrintAddress()
if lab_address:
_keys = ['address', 'city', 'state', 'zip', 'country']
_list = [lab_address.get(v) for v in _keys if lab_address.get(v)]
self.lab_address = "<br/>".join(_list).replace("\n", "<br/>")
if self.lab_address.endswith("<br/>"):
self.lab_address = self.lab_address[:-5]
else:
self.lab_address = None
# Analysis Request results
self.ars = []
self.ar_headers = [_("Request ID"),
_("Date Requested"),
_("Sample Type"),
_("Sample Point")]
self.analysis_headers = [_("Analysis Service"),
_("Method"),
_("Result"),
_("Analyst")]
for ar in self.context.getAnalysisRequests():
datecreated = ar.created()
# datereceived = ar.getDateReceived()
# datepublished = ar.getDatePublished()
datalines = []
for analysis in ar.getAnalyses(full_objects=True):
service = analysis.getService()
method = service.getMethod()
sample = ar.getSample()
result = analysis.getResult()
formatted_result = format_numeric_result(analysis, result)
datalines.append({_("Analysis Service"): analysis.getService().Title(),
_("Method"): method and method.Title() or "",
_("Result"): formatted_result,
_("Analyst"): self.user_fullname(analysis.getAnalyst()),
_("Remarks"): analysis.getRemarks()})
self.ars.append({
_("Request ID"): ar.getRequestID(),
_("Date Requested"): self.ulocalized_time(datecreated), # requested->created
_("Sample Type"): sample.getSampleType() and sample.getSampleType().Title() or '',
_("Sample Point"): sample.getSamplePoint() and sample.getSamplePoint().Title() or '',
_("datalines"): datalines,
})
# Create Report
fn = self.context.Title() + " " + self.ulocalized_time(self.now)
report_html = self.template()
debug_mode = App.config.getConfiguration().debug_mode
if debug_mode:
tmp_fd, tmp_fn = tempfile.mkstemp(suffix=".html")
logger.debug("Writing HTML for %s to %s" % (self.context, tmp_fn))
tmp_fd.write(report_html)
tmp_fd.close()
pdf_fd, pdf_fn = tempfile.mkstemp(suffix="pdf")
pdf_fd.close()
pdf = createPdf(report_html, outfile=pdf_fn)
if debug_mode:
logger.debug("Wrote PDF for %s to %s" % (self.context, pdf_fn))
else:
os.remove(pdf_fn)
# XXX Email published batches to who?
# Send PDF to browser
if not pdf.err:
setheader = self.request.RESPONSE.setHeader
setheader('Content-Type', 'application/pdf')
setheader("Content-Disposition", "attachment;filename=\"%s\"" % fn)
self.request.RESPONSE.write(pdf)
def folderitems(self):
rc = getToolByName(self.context, REFERENCE_CATALOG)
bsc = getToolByName(self.context, 'bika_setup_catalog')
analysis_categories = bsc(portal_type="AnalysisCategory", sort_on="sortable_title")
analysis_categories_order = dict([(b.Title, "{:04}".format(a)) for a, b in enumerate(analysis_categories)])
workflow = getToolByName(self.context, 'portal_workflow')
mtool = getToolByName(self.context, 'portal_membership')
checkPermission = mtool.checkPermission
if not self.allow_edit:
can_edit_analyses = False
else:
if self.contentFilter.get('getPointOfCapture', '') == 'field':
can_edit_analyses = checkPermission(EditFieldResults, self.context)
else:
can_edit_analyses = checkPermission(EditResults, self.context)
self.allow_edit = can_edit_analyses
self.show_select_column = self.allow_edit
context_active = isActive(self.context)
self.categories = []
items = super(AnalysesView, self).folderitems(full_objects = True)
# manually skim retracted analyses from the list
new_items = []
for i,item in enumerate(items):
# self.contentsMethod may return brains or objects.
if not ('obj' in items[i]):
continue
obj = hasattr(items[i]['obj'], 'getObject') and \
items[i]['obj'].getObject() or \
items[i]['obj']
if workflow.getInfoFor(obj, 'review_state') == 'retracted' \
and not checkPermission(ViewRetractedAnalyses, self.context):
continue
new_items.append(item)
items = new_items
methods = self.get_methods_vocabulary()
self.interim_fields = {}
self.interim_columns = {}
self.specs = {}
show_methodinstr_columns = False
for i, item in enumerate(items):
# self.contentsMethod may return brains or objects.
obj = hasattr(items[i]['obj'], 'getObject') and \
items[i]['obj'].getObject() or \
items[i]['obj']
if workflow.getInfoFor(obj, 'review_state') == 'retracted' \
and not checkPermission(ViewRetractedAnalyses, self.context):
continue
result = obj.getResult()
service = obj.getService()
calculation = service.getCalculation()
unit = service.getUnit()
keyword = service.getKeyword()
if self.show_categories:
cat = obj.getService().getCategoryTitle()
cat_order = analysis_categories_order.get(cat)
items[i]['category'] = cat
if (cat, cat_order) not in self.categories:
self.categories.append((cat, cat_order))
# Check for InterimFields attribute on our object,
interim_fields = hasattr(obj, 'getInterimFields') \
and obj.getInterimFields() or []
# kick some pretty display values in.
for x in range(len(interim_fields)):
interim_fields[x]['formatted_value'] = \
format_numeric_result(obj, interim_fields[x]['value'])
self.interim_fields[obj.UID()] = interim_fields
items[i]['service_uid'] = service.UID()
items[i]['Service'] = service.Title()
items[i]['Keyword'] = keyword
items[i]['Unit'] = format_supsub(unit) if unit else ''
items[i]['Result'] = ''
items[i]['formatted_result'] = ''
items[i]['interim_fields'] = interim_fields
items[i]['Remarks'] = obj.getRemarks()
items[i]['Uncertainty'] = ''
items[i]['DetectionLimit'] = ''
items[i]['retested'] = obj.getRetested()
items[i]['class']['retested'] = 'center'
items[i]['result_captured'] = self.ulocalized_time(
obj.getResultCaptureDate(), long_format=0)
items[i]['calculation'] = calculation and True or False
try:
items[i]['Partition'] = obj.getSamplePartition().getId()
except AttributeError:
items[i]['Partition'] = ''
if obj.portal_type == "ReferenceAnalysis":
items[i]['DueDate'] = self.ulocalized_time(obj.aq_parent.getExpiryDate(), long_format=0)
else:
items[i]['DueDate'] = self.ulocalized_time(obj.getDueDate(), long_format=1)
cd = obj.getResultCaptureDate()
items[i]['CaptureDate'] = cd and self.ulocalized_time(cd, long_format=1) or ''
items[i]['Attachments'] = ''
item['allow_edit'] = []
client_or_lab = ""
tblrowclass = items[i].get('table_row_class');
if obj.portal_type == 'ReferenceAnalysis':
items[i]['st_uid'] = obj.aq_parent.UID()
items[i]['table_row_class'] = ' '.join([tblrowclass, 'qc-analysis']);
elif obj.portal_type == 'DuplicateAnalysis' and \
obj.getAnalysis().portal_type == 'ReferenceAnalysis':
items[i]['st_uid'] = obj.aq_parent.UID()
items[i]['table_row_class'] = ' '.join([tblrowclass, 'qc-analysis']);
else:
sample = None
if self.context.portal_type == 'AnalysisRequest':
sample = self.context.getSample()
elif self.context.portal_type == 'Worksheet':
if obj.portal_type in ('DuplicateAnalysis', 'RejectAnalysis'):
sample = obj.getAnalysis().getSample()
else:
sample = obj.aq_parent.getSample()
elif self.context.portal_type == 'Sample':
sample = self.context
st_uid = sample.getSampleType().UID() if sample else ''
items[i]['st_uid'] = st_uid
if checkPermission(ManageBika, self.context):
service_uid = service.UID()
latest = rc.lookupObject(service_uid).version_id
items[i]['Service'] = service.Title()
items[i]['class']['Service'] = "service_title"
# Show version number of out-of-date objects
# No: This should be done in another column, if at all.
# The (vX) value confuses some more fragile forms.
# if hasattr(obj, 'reference_versions') and \
# service_uid in obj.reference_versions and \
# latest != obj.reference_versions[service_uid]:
# items[i]['after']['Service'] = "(v%s)" % \
# (obj.reference_versions[service_uid])
# choices defined on Service apply to result fields.
choices = service.getResultOptions()
if choices:
item['choices']['Result'] = choices
# permission to view this item's results
can_view_result = \
getSecurityManager().checkPermission(ViewResults, obj)
# permission to edit this item's results
# Editing Field Results is possible while in Sample Due.
poc = self.contentFilter.get("getPointOfCapture", 'lab')
can_edit_analysis = self.allow_edit and context_active and \
( (poc == 'field' and getSecurityManager().checkPermission(EditFieldResults, obj))
or
(poc != 'field' and getSecurityManager().checkPermission(EditResults, obj)) )
allowed_method_states = ['to_be_sampled',
'to_be_preserved',
'sample_received',
'sample_registered',
'sampled',
'assigned']
# Prevent from being edited if the instrument assigned
# is not valid (out-of-date or uncalibrated), except if
# the analysis is a QC with assigned status
can_edit_analysis = can_edit_analysis \
and (obj.isInstrumentValid() \
or (obj.portal_type == 'ReferenceAnalysis' \
and item['review_state'] in allowed_method_states))
if can_edit_analysis:
items[i]['allow_edit'].extend(['Analyst',
'Result',
'Remarks'])
# if the Result field is editable, our interim fields are too
for f in self.interim_fields[obj.UID()]:
items[i]['allow_edit'].append(f['keyword'])
# if there isn't a calculation then result must be re-testable,
# and if there are interim fields, they too must be re-testable.
if not items[i]['calculation'] or \
(items[i]['calculation'] and self.interim_fields[obj.UID()]):
items[i]['allow_edit'].append('retested')
# TODO: Only the labmanager must be able to change the method
# can_set_method = getSecurityManager().checkPermission(SetAnalysisMethod, obj)
can_set_method = can_edit_analysis \
and item['review_state'] in allowed_method_states
method = obj.getMethod() \
if hasattr(obj, 'getMethod') and obj.getMethod() \
else service.getMethod()
# Display the methods selector if the AS has at least one
# method assigned
item['Method'] = ''
item['replace']['Method'] = ''
if can_set_method:
voc = self.get_methods_vocabulary(obj)
if voc:
# The service has at least one method available
item['Method'] = method.UID() if method else ''
item['choices']['Method'] = voc
item['allow_edit'].append('Method')
show_methodinstr_columns = True
elif method:
# This should never happen
# The analysis has set a method, but its parent
# service hasn't any method available O_o
item['Method'] = method.Title()
item['replace']['Method'] = "<a href='%s'>%s</a>" % \
(method.absolute_url(), method.Title())
show_methodinstr_columns = True
elif method:
# Edition not allowed, but method set
item['Method'] = method.Title()
item['replace']['Method'] = "<a href='%s'>%s</a>" % \
(method.absolute_url(), method.Title())
show_methodinstr_columns = True
# TODO: Instrument selector dynamic behavior in worksheet Results
# Only the labmanager must be able to change the instrument to be used. Also,
# the instrument selection should be done in accordance with the method selected
# can_set_instrument = service.getInstrumentEntryOfResults() and getSecurityManager().checkPermission(SetAnalysisInstrument, obj)
can_set_instrument = service.getInstrumentEntryOfResults() \
and can_edit_analysis \
and item['review_state'] in allowed_method_states
item['Instrument'] = ''
item['replace']['Instrument'] = ''
if service.getInstrumentEntryOfResults():
instrument = None
# If the analysis has an instrument already assigned, use it
if service.getInstrumentEntryOfResults() \
and hasattr(obj, 'getInstrument') \
and obj.getInstrument():
instrument = obj.getInstrument()
# Otherwise, use the Service's default instrument
elif service.getInstrumentEntryOfResults():
instrument = service.getInstrument()
if can_set_instrument:
# Edition allowed
voc = self.get_instruments_vocabulary(obj)
if voc:
# The service has at least one instrument available
item['Instrument'] = instrument.UID() if instrument else ''
item['choices']['Instrument'] = voc
item['allow_edit'].append('Instrument')
show_methodinstr_columns = True
elif instrument:
# This should never happen
# The analysis has an instrument set, but the
# service hasn't any available instrument
item['Instrument'] = instrument.Title()
item['replace']['Instrument'] = "<a href='%s'>%s</a>" % \
(instrument.absolute_url(), instrument.Title())
show_methodinstr_columns = True
elif instrument:
# Edition not allowed, but instrument set
item['Instrument'] = instrument.Title()
item['replace']['Instrument'] = "<a href='%s'>%s</a>" % \
(instrument.absolute_url(), instrument.Title())
show_methodinstr_columns = True
else:
# Manual entry of results, instrument not allowed
item['Instrument'] = _('Manual')
msgtitle = t(_(
"Instrument entry of results not allowed for ${service}",
mapping={"service": safe_unicode(service.Title())},
))
item['replace']['Instrument'] = \
'<a href="#" title="%s">%s</a>' % (msgtitle, t(_('Manual')))
# Sets the analyst assigned to this analysis
if can_edit_analysis:
analyst = obj.getAnalyst()
# widget default: current user
if not analyst:
analyst = mtool.getAuthenticatedMember().getUserName()
items[i]['Analyst'] = analyst
item['choices']['Analyst'] = self.getAnalysts()
else:
items[i]['Analyst'] = obj.getAnalystName()
# If the user can attach files to analyses, show the attachment col
can_add_attachment = \
getSecurityManager().checkPermission(AddAttachment, obj)
if can_add_attachment or can_view_result:
attachments = ""
if hasattr(obj, 'getAttachment'):
for attachment in obj.getAttachment():
af = attachment.getAttachmentFile()
icon = af.icon
attachments += "<span class='attachment' attachment_uid='%s'>" % (attachment.UID())
if icon: attachments += "<img src='%s/%s'/>" % (self.portal_url, icon)
attachments += '<a href="%s/at_download/AttachmentFile"/>%s</a>' % (attachment.absolute_url(), af.filename)
if can_edit_analysis:
attachments += "<img class='deleteAttachmentButton' attachment_uid='%s' src='%s'/>" % (attachment.UID(), "++resource++bika.lims.images/delete.png")
attachments += "</br></span>"
items[i]['replace']['Attachments'] = attachments[:-12] + "</span>"
# Only display data bearing fields if we have ViewResults
# permission, otherwise just put an icon in Result column.
if can_view_result:
items[i]['Result'] = result
scinot = self.context.bika_setup.getScientificNotationResults()
dmk = self.context.bika_setup.getResultsDecimalMark()
items[i]['formatted_result'] = obj.getFormattedResult(sciformat=int(scinot),decimalmark=dmk)
# LIMS-1379 Allow manual uncertainty value input
# https://jira.bikalabs.com/browse/LIMS-1379
fu = format_uncertainty(obj, result, decimalmark=dmk, sciformat=int(scinot))
fu = fu if fu else ''
if can_edit_analysis and service.getAllowManualUncertainty() == True:
unc = obj.getUncertainty(result)
item['allow_edit'].append('Uncertainty')
items[i]['Uncertainty'] = unc if unc else ''
items[i]['before']['Uncertainty'] = '± ';
items[i]['after']['Uncertainty'] = '<em class="discreet" style="white-space:nowrap;"> %s</em>' % items[i]['Unit'];
elif fu:
items[i]['Uncertainty'] = fu
items[i]['before']['Uncertainty'] = '± ';
items[i]['after']['Uncertainty'] = '<em class="discreet" style="white-space:nowrap;"> %s</em>' % items[i]['Unit'];
# LIMS-1700. Allow manual input of Detection Limits
# LIMS-1775. Allow to select LDL or UDL defaults in results with readonly mode
# https://jira.bikalabs.com/browse/LIMS-1700
# https://jira.bikalabs.com/browse/LIMS-1775
if can_edit_analysis and \
hasattr(obj, 'getDetectionLimitOperand') and \
hasattr(service, 'getDetectionLimitSelector') and \
service.getDetectionLimitSelector() == True:
isldl = obj.isBelowLowerDetectionLimit()
isudl = obj.isAboveUpperDetectionLimit()
dlval=''
if isldl or isudl:
dlval = '<' if isldl else '>'
item['allow_edit'].append('DetectionLimit')
item['DetectionLimit'] = dlval
choices=[{'ResultValue': '<', 'ResultText': '<'},
{'ResultValue': '>', 'ResultText': '>'}]
item['choices']['DetectionLimit'] = choices
self.columns['DetectionLimit']['toggle'] = True
srv = obj.getService()
defdls = {'min':srv.getLowerDetectionLimit(),
'max':srv.getUpperDetectionLimit(),
'manual':srv.getAllowManualDetectionLimit()}
defin = '<input type="hidden" id="DefaultDLS.%s" value=\'%s\'/>'
defin = defin % (obj.UID(), json.dumps(defdls))
item['after']['DetectionLimit'] = defin
# LIMS-1769. Allow to use LDL and UDL in calculations.
# https://jira.bikalabs.com/browse/LIMS-1769
# Since LDL, UDL, etc. are wildcards that can be used
# in calculations, these fields must be loaded always
# for 'live' calculations.
if can_edit_analysis:
dls = {'default_ldl': 'none',
'default_udl': 'none',
'below_ldl': False,
'above_udl': False,
'is_ldl': False,
'is_udl': False,
'manual_allowed': False,
'dlselect_allowed': False}
if hasattr(obj, 'getDetectionLimits'):
dls['below_ldl'] = obj.isBelowLowerDetectionLimit()
dls['above_udl'] = obj.isBelowLowerDetectionLimit()
dls['is_ldl'] = obj.isLowerDetectionLimit()
dls['is_udl'] = obj.isUpperDetectionLimit()
dls['default_ldl'] = service.getLowerDetectionLimit()
dls['default_udl'] = service.getUpperDetectionLimit()
dls['manual_allowed'] = service.getAllowManualDetectionLimit()
dls['dlselect_allowed'] = service.getDetectionLimitSelector()
dlsin = '<input type="hidden" id="AnalysisDLS.%s" value=\'%s\'/>'
dlsin = dlsin % (obj.UID(), json.dumps(dls))
item['after']['Result'] = dlsin
else:
items[i]['Specification'] = ""
if 'Result' in items[i]['allow_edit']:
items[i]['allow_edit'].remove('Result')
items[i]['before']['Result'] = \
'<img width="16" height="16" ' + \
'src="%s/++resource++bika.lims.images/to_follow.png"/>' % \
(self.portal_url)
# Everyone can see valid-ranges
spec = self.get_analysis_spec(obj)
if spec:
min_val = spec.get('min', '')
min_str = ">{0}".format(min_val) if min_val else ''
max_val = spec.get('max', '')
max_str = "<{0}".format(max_val) if max_val else ''
error_val = spec.get('error', '')
error_str = "{0}%".format(error_val) if error_val else ''
rngstr = ",".join([x for x in [min_str, max_str, error_str] if x])
else:
rngstr = ""
items[i]['Specification'] = rngstr
# Add this analysis' interim fields to the interim_columns list
for f in self.interim_fields[obj.UID()]:
if f['keyword'] not in self.interim_columns and not f.get('hidden', False):
self.interim_columns[f['keyword']] = f['title']
# and to the item itself
items[i][f['keyword']] = f
items[i]['class'][f['keyword']] = 'interim'
# check if this analysis is late/overdue
resultdate = obj.aq_parent.getDateSampled() \
if obj.portal_type == 'ReferenceAnalysis' \
else obj.getResultCaptureDate()
duedate = obj.aq_parent.getExpiryDate() \
if obj.portal_type == 'ReferenceAnalysis' \
else obj.getDueDate()
items[i]['replace']['DueDate'] = \
self.ulocalized_time(duedate, long_format=1)
if items[i]['review_state'] not in ['to_be_sampled',
'to_be_preserved',
'sample_due',
'published']:
if (resultdate and resultdate > duedate) \
or (not resultdate and DateTime() > duedate):
items[i]['replace']['DueDate'] = '%s <img width="16" height="16" src="%s/++resource++bika.lims.images/late.png" title="%s"/>' % \
(self.ulocalized_time(duedate, long_format=1),
self.portal_url,
t(_("Late Analysis")))
# Submitting user may not verify results (admin can though)
if items[i]['review_state'] == 'to_be_verified' and \
not checkPermission(VerifyOwnResults, obj):
user_id = getSecurityManager().getUser().getId()
self_submitted = False
try:
review_history = list(workflow.getInfoFor(obj, 'review_history'))
review_history.reverse()
for event in review_history:
if event.get('action') == 'submit':
if event.get('actor') == user_id:
self_submitted = True
break
if self_submitted:
items[i]['after']['state_title'] = \
"<img src='++resource++bika.lims.images/submitted-by-current-user.png' title='%s'/>" % \
(t(_("Cannot verify: Submitted by current user")))
except WorkflowException:
pass
# add icon for assigned analyses in AR views
if self.context.portal_type == 'AnalysisRequest':
obj = items[i]['obj']
if obj.portal_type in ['ReferenceAnalysis',
'DuplicateAnalysis'] or \
workflow.getInfoFor(obj, 'worksheetanalysis_review_state') == 'assigned':
br = obj.getBackReferences('WorksheetAnalysis')
if len(br) > 0:
ws = br[0]
items[i]['after']['state_title'] = \
"<a href='%s'><img src='++resource++bika.lims.images/worksheet.png' title='%s'/></a>" % \
(ws.absolute_url(),
t(_("Assigned to: ${worksheet_id}",
mapping={'worksheet_id': safe_unicode(ws.id)})))
# the TAL requires values for all interim fields on all
# items, so we set blank values in unused cells
for item in items:
for field in self.interim_columns:
if field not in item:
item[field] = ''
# XXX order the list of interim columns
interim_keys = self.interim_columns.keys()
interim_keys.reverse()
# add InterimFields keys to columns
for col_id in interim_keys:
if col_id not in self.columns:
self.columns[col_id] = {'title': self.interim_columns[col_id],
'input_width': '6',
'input_class': 'ajax_calculate numeric',
'sortable': False}
if can_edit_analyses:
new_states = []
for state in self.review_states:
# InterimFields are displayed in review_state
# They are anyway available through View.columns though.
# In case of hidden fields, the calcs.py should check calcs/services
# for additional InterimFields!!
pos = 'Result' in state['columns'] and \
state['columns'].index('Result') or len(state['columns'])
for col_id in interim_keys:
if col_id not in state['columns']:
state['columns'].insert(pos, col_id)
# retested column is added after Result.
pos = 'Result' in state['columns'] and \
state['columns'].index('Uncertainty') + 1 or len(state['columns'])
state['columns'].insert(pos, 'retested')
new_states.append(state)
self.review_states = new_states
# Allow selecting individual analyses
self.show_select_column = True
# Dry Matter.
# The Dry Matter column is never enabled for reference sample contexts
# and refers to getReportDryMatter in ARs.
if items and \
(hasattr(self.context, 'getReportDryMatter') and \
self.context.getReportDryMatter()):
# look through all items
# if the item's Service supports ReportDryMatter, add getResultDM().
for item in items:
if item['obj'].getService().getReportDryMatter():
item['ResultDM'] = item['obj'].getResultDM()
else:
item['ResultDM'] = ''
if item['ResultDM']:
item['after']['ResultDM'] = "<em class='discreet'>%</em>"
# modify the review_states list to include the ResultDM column
new_states = []
for state in self.review_states:
pos = 'Result' in state['columns'] and \
state['columns'].index('Uncertainty') + 1 or len(state['columns'])
state['columns'].insert(pos, 'ResultDM')
new_states.append(state)
self.review_states = new_states
if self.show_categories:
self.categories = map(lambda x: x[0], sorted(self.categories, key=lambda x: x[1]))
else:
self.categories.sort()
# self.json_specs = json.dumps(self.specs)
self.json_interim_fields = json.dumps(self.interim_fields)
self.items = items
# Method and Instrument columns must be shown or hidden at the
# same time, because the value assigned to one causes
# a value reassignment to the other (one method can be performed
# by different instruments)
self.columns['Method']['toggle'] = show_methodinstr_columns
self.columns['Instrument']['toggle'] = show_methodinstr_columns
return items
def getFormattedResult(self, specs=None):
"""Formatted result:
1. Print ResultText of matching ResultOptions
2. If the result is not floatable, return it without being formatted
3. If the analysis specs has hidemin or hidemax enabled and the
result is out of range, render result as '<min' or '>max'
4. Otherwise, render numerical value
specs param is optional. A dictionary as follows:
{'min': <min_val>,
'max': <max_val>,
'error': <error>,
'hidemin': <hidemin_val>,
'hidemax': <hidemax_val>}
"""
result = self.getResult()
service = self.getService()
choices = service.getResultOptions()
# 1. Print ResultText of matching ResulOptions
match = [
x['ResultText'] for x in choices
if str(x['ResultValue']) == str(result)
]
if match:
return match[0]
# 2. If the result is not floatable, return it without being formatted
try:
result = float(result)
except:
return result
# 3. If the analysis specs has enabled hidemin or hidemax and the
# result is out of range, render result as '<min' or '>max'
belowmin = False
abovemax = False
if not specs:
specs = self.getAnalysisSpecs()
specs = specs.getResultsRangeDict() if specs is not None else {}
specs = specs.get(self.getKeyword(), {})
hidemin = specs.get('hidemin', '')
hidemax = specs.get('hidemax', '')
try:
belowmin = hidemin and result < float(hidemin) or False
except:
belowmin = False
pass
try:
abovemax = hidemax and result > float(hidemax) or False
except:
abovemax = False
pass
# 3.1. If result is below min and hidemin enabled, return '<min'
if belowmin:
return '< %s' % hidemin
# 3.2. If result is above max and hidemax enabled, return '>max'
if abovemax:
return '> %s' % hidemax
# Render numerical value
return format_numeric_result(self, result)
def __call__(self):
pc = self.portal_catalog
self.checkPermission = self.context.portal_membership.checkPermission
self.now = DateTime()
self.SamplingWorkflowEnabled = self.context.bika_setup.getSamplingWorkflowEnabled(
)
# Client details (if client is associated)
self.client = None
client_uid = hasattr(self.context,
'getClientUID') and self.context.getClientUID()
if client_uid:
proxies = pc(portal_type='Client', UID=client_uid)
if proxies:
self.client = proxies[0].getObject()
client_address = self.client.getPostalAddress()
if self.contact and not client_address:
client_address = self.contact.getBillingAddress()
if not client_address:
client_address = self.contact.getPhysicalAddress()
if client_address:
_keys = ['address', 'city', 'state', 'zip', 'country']
_list = [
client_address.get(v) for v in _keys
if client_address.get(v)
]
self.client_address = "<br/>".join(_list).replace(
"\n", "<br/>")
if self.client_address.endswith("<br/>"):
self.client_address = self.client_address[:-5]
else:
self.client_address = None
# Reporter
self.member = self.context.portal_membership.getAuthenticatedMember()
self.username = self.member.getUserName()
self.reporter = self.user_fullname(self.username)
self.reporter_email = self.user_email(self.username)
self.reporter_signature = ""
c = [
x for x in self.bika_setup_catalog(portal_type='LabContact')
if x.getObject().getUsername() == self.username
]
if c:
sf = c[0].getObject().getSignature()
if sf:
self.reporter_signature = sf.absolute_url() + "/Signature"
# laboratory
self.laboratory = self.context.bika_setup.laboratory
self.accredited = self.laboratory.getLaboratoryAccredited()
lab_address = self.laboratory.getPrintAddress()
if lab_address:
_keys = ['address', 'city', 'state', 'zip', 'country']
_list = [lab_address.get(v) for v in _keys if lab_address.get(v)]
self.lab_address = "<br/>".join(_list).replace("\n", "<br/>")
if self.lab_address.endswith("<br/>"):
self.lab_address = self.lab_address[:-5]
else:
self.lab_address = None
# Analysis Request results
self.ars = []
self.ar_headers = [
_("Request ID"),
_("Date Requested"),
_("Sample Type"),
_("Sample Point")
]
self.analysis_headers = [
_("Analysis Service"),
_("Method"),
_("Result"),
_("Analyst")
]
for ar in self.context.getAnalysisRequests():
datecreated = ar.created()
# datereceived = ar.getDateReceived()
# datepublished = ar.getDatePublished()
datalines = []
for analysis in ar.getAnalyses(full_objects=True):
service = analysis.getService()
method = service.getMethod()
sample = ar.getSample()
result = analysis.getResult()
formatted_result = format_numeric_result(analysis, result)
datalines.append({
_("Analysis Service"):
analysis.getService().Title(),
_("Method"):
method and method.Title() or "",
_("Result"):
formatted_result,
_("Analyst"):
self.user_fullname(analysis.getAnalyst()),
_("Remarks"):
analysis.getRemarks()
})
self.ars.append({
_("Request ID"):
ar.getRequestID(),
_("Date Requested"):
self.ulocalized_time(datecreated), # requested->created
_("Sample Type"):
sample.getSampleType() and sample.getSampleType().Title()
or '',
_("Sample Point"):
sample.getSamplePoint() and sample.getSamplePoint().Title()
or '',
_("datalines"):
datalines,
})
# Create Report
fn = self.context.Title() + " " + self.ulocalized_time(self.now)
report_html = self.template()
debug_mode = App.config.getConfiguration().debug_mode
if debug_mode:
tmp_fd, tmp_fn = tempfile.mkstemp(suffix=".html")
logger.debug("Writing HTML for %s to %s" % (self.context, tmp_fn))
tmp_fd.write(report_html)
tmp_fd.close()
pdf_fd, pdf_fn = tempfile.mkstemp(suffix="pdf")
pdf_fd.close()
pdf = createPdf(report_html, outfile=pdf_fn)
if debug_mode:
logger.debug("Wrote PDF for %s to %s" % (self.context, pdf_fn))
else:
os.remove(pdf_fn)
# XXX Email published batches to who?
# Send PDF to browser
if not pdf.err:
setheader = self.request.RESPONSE.setHeader
setheader('Content-Type', 'application/pdf')
setheader("Content-Disposition", "attachment;filename=\"%s\"" % fn)
self.request.RESPONSE.write(pdf)
def folderitems(self):
rc = getToolByName(self.context, REFERENCE_CATALOG)
bsc = getToolByName(self.context, 'bika_setup_catalog')
workflow = getToolByName(self.context, 'portal_workflow')
mtool = getToolByName(self.context, 'portal_membership')
checkPermission = mtool.checkPermission
if not self.allow_edit:
can_edit_analyses = False
else:
if self.contentFilter.get('getPointOfCapture', '') == 'field':
can_edit_analyses = checkPermission(EditFieldResults,
self.context)
else:
can_edit_analyses = checkPermission(EditResults, self.context)
self.allow_edit = can_edit_analyses
self.show_select_column = self.allow_edit
context_active = isActive(self.context)
self.categories = []
items = super(AnalysesView, self).folderitems(full_objects=True)
# manually skim retracted analyses from the list
new_items = []
for i, item in enumerate(items):
# self.contentsMethod may return brains or objects.
if not ('obj' in items[i]):
continue
obj = hasattr(items[i]['obj'], 'getObject') and \
items[i]['obj'].getObject() or \
items[i]['obj']
if workflow.getInfoFor(obj, 'review_state') == 'retracted' \
and not checkPermission(ViewRetractedAnalyses, self.context):
continue
new_items.append(item)
items = new_items
methods = self.get_methods_vocabulary()
self.interim_fields = {}
self.interim_columns = {}
self.specs = {}
show_methodinstr_columns = False
for i, item in enumerate(items):
# self.contentsMethod may return brains or objects.
obj = hasattr(items[i]['obj'], 'getObject') and \
items[i]['obj'].getObject() or \
items[i]['obj']
if workflow.getInfoFor(obj, 'review_state') == 'retracted' \
and not checkPermission(ViewRetractedAnalyses, self.context):
continue
result = obj.getResult()
service = obj.getService()
calculation = service.getCalculation()
unit = service.getUnit()
keyword = service.getKeyword()
if self.show_categories:
cat = obj.getService().getCategoryTitle()
items[i]['category'] = cat
if cat not in self.categories:
self.categories.append(cat)
# Check for InterimFields attribute on our object,
interim_fields = hasattr(obj, 'getInterimFields') \
and obj.getInterimFields() or []
# kick some pretty display values in.
for x in range(len(interim_fields)):
interim_fields[x]['formatted_value'] = \
format_numeric_result(obj, interim_fields[x]['value'])
self.interim_fields[obj.UID()] = interim_fields
items[i]['service_uid'] = service.UID()
items[i]['Service'] = service.Title()
items[i]['Keyword'] = keyword
items[i]['Unit'] = format_supsub(unit) if unit else ''
items[i]['Result'] = ''
items[i]['formatted_result'] = ''
items[i]['interim_fields'] = interim_fields
items[i]['Remarks'] = obj.getRemarks()
items[i]['Uncertainty'] = ''
items[i]['DetectionLimit'] = ''
items[i]['retested'] = obj.getRetested()
items[i]['class']['retested'] = 'center'
items[i]['result_captured'] = self.ulocalized_time(
obj.getResultCaptureDate(), long_format=0)
items[i]['calculation'] = calculation and True or False
try:
items[i]['Partition'] = obj.getSamplePartition().getId()
except AttributeError:
items[i]['Partition'] = ''
if obj.portal_type == "ReferenceAnalysis":
items[i]['DueDate'] = self.ulocalized_time(
obj.aq_parent.getExpiryDate(), long_format=0)
else:
items[i]['DueDate'] = self.ulocalized_time(obj.getDueDate(),
long_format=1)
cd = obj.getResultCaptureDate()
items[i]['CaptureDate'] = cd and self.ulocalized_time(
cd, long_format=1) or ''
items[i]['Attachments'] = ''
item['allow_edit'] = []
client_or_lab = ""
tblrowclass = items[i].get('table_row_class')
if obj.portal_type == 'ReferenceAnalysis':
items[i]['st_uid'] = obj.aq_parent.UID()
items[i]['table_row_class'] = ' '.join(
[tblrowclass, 'qc-analysis'])
elif obj.portal_type == 'DuplicateAnalysis' and \
obj.getAnalysis().portal_type == 'ReferenceAnalysis':
items[i]['st_uid'] = obj.aq_parent.UID()
items[i]['table_row_class'] = ' '.join(
[tblrowclass, 'qc-analysis'])
else:
sample = None
if self.context.portal_type == 'AnalysisRequest':
sample = self.context.getSample()
elif self.context.portal_type == 'Worksheet':
if obj.portal_type in ('DuplicateAnalysis',
'RejectAnalysis'):
sample = obj.getAnalysis().getSample()
else:
sample = obj.aq_parent.getSample()
elif self.context.portal_type == 'Sample':
sample = self.context
st_uid = sample.getSampleType().UID() if sample else ''
items[i]['st_uid'] = st_uid
if checkPermission(ManageBika, self.context):
service_uid = service.UID()
latest = rc.lookupObject(service_uid).version_id
items[i]['Service'] = service.Title()
items[i]['class']['Service'] = "service_title"
# Show version number of out-of-date objects
# No: This should be done in another column, if at all.
# The (vX) value confuses some more fragile forms.
# if hasattr(obj, 'reference_versions') and \
# service_uid in obj.reference_versions and \
# latest != obj.reference_versions[service_uid]:
# items[i]['after']['Service'] = "(v%s)" % \
# (obj.reference_versions[service_uid])
# choices defined on Service apply to result fields.
choices = service.getResultOptions()
if choices:
item['choices']['Result'] = choices
# permission to view this item's results
can_view_result = \
getSecurityManager().checkPermission(ViewResults, obj)
# permission to edit this item's results
# Editing Field Results is possible while in Sample Due.
poc = self.contentFilter.get("getPointOfCapture", 'lab')
can_edit_analysis = self.allow_edit and context_active and \
( (poc == 'field' and getSecurityManager().checkPermission(EditFieldResults, obj))
or
(poc != 'field' and getSecurityManager().checkPermission(EditResults, obj)) )
allowed_method_states = [
'to_be_sampled', 'to_be_preserved', 'sample_received',
'sample_registered', 'sampled', 'assigned'
]
# Prevent from being edited if the instrument assigned
# is not valid (out-of-date or uncalibrated), except if
# the analysis is a QC with assigned status
can_edit_analysis = can_edit_analysis \
and (obj.isInstrumentValid() \
or (obj.portal_type == 'ReferenceAnalysis' \
and item['review_state'] in allowed_method_states))
if can_edit_analysis:
items[i]['allow_edit'].extend(['Analyst', 'Result', 'Remarks'])
# if the Result field is editable, our interim fields are too
for f in self.interim_fields[obj.UID()]:
items[i]['allow_edit'].append(f['keyword'])
# if there isn't a calculation then result must be re-testable,
# and if there are interim fields, they too must be re-testable.
if not items[i]['calculation'] or \
(items[i]['calculation'] and self.interim_fields[obj.UID()]):
items[i]['allow_edit'].append('retested')
# TODO: Only the labmanager must be able to change the method
# can_set_method = getSecurityManager().checkPermission(SetAnalysisMethod, obj)
can_set_method = can_edit_analysis \
and item['review_state'] in allowed_method_states
method = obj.getMethod() \
if hasattr(obj, 'getMethod') and obj.getMethod() \
else service.getMethod()
# Display the methods selector if the AS has at least one
# method assigned
item['Method'] = ''
item['replace']['Method'] = ''
if can_set_method:
voc = self.get_methods_vocabulary(obj)
if voc:
# The service has at least one method available
item['Method'] = method.UID() if method else ''
item['choices']['Method'] = voc
item['allow_edit'].append('Method')
show_methodinstr_columns = True
elif method:
# This should never happen
# The analysis has set a method, but its parent
# service hasn't any method available O_o
item['Method'] = method.Title()
item['replace']['Method'] = "<a href='%s'>%s</a>" % \
(method.absolute_url(), method.Title())
show_methodinstr_columns = True
elif method:
# Edition not allowed, but method set
item['Method'] = method.Title()
item['replace']['Method'] = "<a href='%s'>%s</a>" % \
(method.absolute_url(), method.Title())
show_methodinstr_columns = True
# TODO: Instrument selector dynamic behavior in worksheet Results
# Only the labmanager must be able to change the instrument to be used. Also,
# the instrument selection should be done in accordance with the method selected
# can_set_instrument = service.getInstrumentEntryOfResults() and getSecurityManager().checkPermission(SetAnalysisInstrument, obj)
can_set_instrument = service.getInstrumentEntryOfResults() \
and can_edit_analysis \
and item['review_state'] in allowed_method_states
item['Instrument'] = ''
item['replace']['Instrument'] = ''
if service.getInstrumentEntryOfResults():
instrument = None
# If the analysis has an instrument already assigned, use it
if service.getInstrumentEntryOfResults() \
and hasattr(obj, 'getInstrument') \
and obj.getInstrument():
instrument = obj.getInstrument()
# Otherwise, use the Service's default instrument
elif service.getInstrumentEntryOfResults():
instrument = service.getInstrument()
if can_set_instrument:
# Edition allowed
voc = self.get_instruments_vocabulary(obj)
if voc:
# The service has at least one instrument available
item['Instrument'] = instrument.UID(
) if instrument else ''
item['choices']['Instrument'] = voc
item['allow_edit'].append('Instrument')
show_methodinstr_columns = True
elif instrument:
# This should never happen
# The analysis has an instrument set, but the
# service hasn't any available instrument
item['Instrument'] = instrument.Title()
item['replace']['Instrument'] = "<a href='%s'>%s</a>" % \
(instrument.absolute_url(), instrument.Title())
show_methodinstr_columns = True
elif instrument:
# Edition not allowed, but instrument set
item['Instrument'] = instrument.Title()
item['replace']['Instrument'] = "<a href='%s'>%s</a>" % \
(instrument.absolute_url(), instrument.Title())
show_methodinstr_columns = True
else:
# Manual entry of results, instrument not allowed
item['Instrument'] = _('Manual')
msgtitle = t(
_(
"Instrument entry of results not allowed for ${service}",
mapping={"service": safe_unicode(service.Title())},
))
item['replace']['Instrument'] = \
'<a href="#" title="%s">%s</a>' % (msgtitle, t(_('Manual')))
# Sets the analyst assigned to this analysis
if can_edit_analysis:
analyst = obj.getAnalyst()
# widget default: current user
if not analyst:
analyst = mtool.getAuthenticatedMember().getUserName()
items[i]['Analyst'] = analyst
item['choices']['Analyst'] = self.getAnalysts()
else:
items[i]['Analyst'] = obj.getAnalystName()
# If the user can attach files to analyses, show the attachment col
can_add_attachment = \
getSecurityManager().checkPermission(AddAttachment, obj)
if can_add_attachment or can_view_result:
attachments = ""
if hasattr(obj, 'getAttachment'):
for attachment in obj.getAttachment():
af = attachment.getAttachmentFile()
icon = af.getBestIcon()
attachments += "<span class='attachment' attachment_uid='%s'>" % (
attachment.UID())
if icon:
attachments += "<img src='%s/%s'/>" % (
self.portal_url, icon)
attachments += '<a href="%s/at_download/AttachmentFile"/>%s</a>' % (
attachment.absolute_url(), af.filename)
if can_edit_analysis:
attachments += "<img class='deleteAttachmentButton' attachment_uid='%s' src='%s'/>" % (
attachment.UID(),
"++resource++bika.lims.images/delete.png")
attachments += "</br></span>"
items[i]['replace'][
'Attachments'] = attachments[:-12] + "</span>"
# Only display data bearing fields if we have ViewResults
# permission, otherwise just put an icon in Result column.
if can_view_result:
items[i]['Result'] = result
scinot = self.context.bika_setup.getScientificNotationResults()
dmk = self.context.bika_setup.getResultsDecimalMark()
items[i]['formatted_result'] = obj.getFormattedResult(
sciformat=int(scinot), decimalmark=dmk)
# LIMS-1379 Allow manual uncertainty value input
# https://jira.bikalabs.com/browse/LIMS-1379
fu = format_uncertainty(obj,
result,
decimalmark=dmk,
sciformat=int(scinot))
fu = fu if fu else ''
if can_edit_analysis and service.getAllowManualUncertainty(
) == True:
unc = obj.getUncertainty(result)
item['allow_edit'].append('Uncertainty')
items[i]['Uncertainty'] = unc if unc else ''
items[i]['before']['Uncertainty'] = '± '
items[i]['after'][
'Uncertainty'] = '<em class="discreet" style="white-space:nowrap;"> %s</em>' % items[
i]['Unit']
elif fu:
items[i]['Uncertainty'] = fu
items[i]['before']['Uncertainty'] = '± '
items[i]['after'][
'Uncertainty'] = '<em class="discreet" style="white-space:nowrap;"> %s</em>' % items[
i]['Unit']
# LIMS-1700. Allow manual input of Detection Limits
# LIMS-1775. Allow to select LDL or UDL defaults in results with readonly mode
# https://jira.bikalabs.com/browse/LIMS-1700
# https://jira.bikalabs.com/browse/LIMS-1775
if can_edit_analysis and \
hasattr(obj, 'getDetectionLimitOperand') and \
hasattr(service, 'getDetectionLimitSelector') and \
service.getDetectionLimitSelector() == True:
isldl = obj.isBelowLowerDetectionLimit()
isudl = obj.isAboveUpperDetectionLimit()
dlval = ''
if isldl or isudl:
dlval = '<' if isldl else '>'
item['allow_edit'].append('DetectionLimit')
item['DetectionLimit'] = dlval
choices = [{
'ResultValue': '<',
'ResultText': '<'
}, {
'ResultValue': '>',
'ResultText': '>'
}]
item['choices']['DetectionLimit'] = choices
self.columns['DetectionLimit']['toggle'] = True
srv = obj.getService()
defdls = {
'min': srv.getLowerDetectionLimit(),
'max': srv.getUpperDetectionLimit(),
'manual': srv.getAllowManualDetectionLimit()
}
defin = '<input type="hidden" id="DefaultDLS.%s" value=\'%s\'/>'
defin = defin % (obj.UID(), json.dumps(defdls))
item['after']['DetectionLimit'] = defin
# LIMS-1769. Allow to use LDL and UDL in calculations.
# https://jira.bikalabs.com/browse/LIMS-1769
# Since LDL, UDL, etc. are wildcards that can be used
# in calculations, these fields must be loaded always
# for 'live' calculations.
if can_edit_analysis:
dls = {
'default_ldl': 'none',
'default_udl': 'none',
'below_ldl': False,
'above_udl': False,
'is_ldl': False,
'is_udl': False,
'manual_allowed': False,
'dlselect_allowed': False
}
if hasattr(obj, 'getDetectionLimits'):
dls['below_ldl'] = obj.isBelowLowerDetectionLimit()
dls['above_udl'] = obj.isBelowLowerDetectionLimit()
dls['is_ldl'] = obj.isLowerDetectionLimit()
dls['is_udl'] = obj.isUpperDetectionLimit()
dls['default_ldl'] = service.getLowerDetectionLimit()
dls['default_udl'] = service.getUpperDetectionLimit()
dls['manual_allowed'] = service.getAllowManualDetectionLimit(
)
dls['dlselect_allowed'] = service.getDetectionLimitSelector(
)
dlsin = '<input type="hidden" id="AnalysisDLS.%s" value=\'%s\'/>'
dlsin = dlsin % (obj.UID(), json.dumps(dls))
item['after']['Result'] = dlsin
else:
items[i]['Specification'] = ""
if 'Result' in items[i]['allow_edit']:
items[i]['allow_edit'].remove('Result')
items[i]['before']['Result'] = \
'<img width="16" height="16" ' + \
'src="%s/++resource++bika.lims.images/to_follow.png"/>' % \
(self.portal_url)
# Everyone can see valid-ranges
spec = self.get_analysis_spec(obj)
if spec:
min_val = spec.get('min', '')
min_str = ">{0}".format(min_val) if min_val else ''
max_val = spec.get('max', '')
max_str = "<{0}".format(max_val) if max_val else ''
error_val = spec.get('error', '')
error_str = "{0}%".format(error_val) if error_val else ''
rngstr = ",".join(
[x for x in [min_str, max_str, error_str] if x])
else:
rngstr = ""
items[i]['Specification'] = rngstr
# Add this analysis' interim fields to the interim_columns list
for f in self.interim_fields[obj.UID()]:
if f['keyword'] not in self.interim_columns and not f.get(
'hidden', False):
self.interim_columns[f['keyword']] = f['title']
# and to the item itself
items[i][f['keyword']] = f
items[i]['class'][f['keyword']] = 'interim'
# check if this analysis is late/overdue
resultdate = obj.aq_parent.getDateSampled() \
if obj.portal_type == 'ReferenceAnalysis' \
else obj.getResultCaptureDate()
duedate = obj.aq_parent.getExpiryDate() \
if obj.portal_type == 'ReferenceAnalysis' \
else obj.getDueDate()
items[i]['replace']['DueDate'] = \
self.ulocalized_time(duedate, long_format=1)
if items[i]['review_state'] not in [
'to_be_sampled', 'to_be_preserved', 'sample_due',
'published'
]:
if (resultdate and resultdate > duedate) \
or (not resultdate and DateTime() > duedate):
items[i]['replace']['DueDate'] = '%s <img width="16" height="16" src="%s/++resource++bika.lims.images/late.png" title="%s"/>' % \
(self.ulocalized_time(duedate, long_format=1),
self.portal_url,
t(_("Late Analysis")))
# Submitting user may not verify results (admin can though)
if items[i]['review_state'] == 'to_be_verified' and \
not checkPermission(VerifyOwnResults, obj):
user_id = getSecurityManager().getUser().getId()
self_submitted = False
try:
review_history = list(
workflow.getInfoFor(obj, 'review_history'))
review_history.reverse()
for event in review_history:
if event.get('action') == 'submit':
if event.get('actor') == user_id:
self_submitted = True
break
if self_submitted:
items[i]['after']['state_title'] = \
"<img src='++resource++bika.lims.images/submitted-by-current-user.png' title='%s'/>" % \
(t(_("Cannot verify: Submitted by current user")))
except WorkflowException:
pass
# add icon for assigned analyses in AR views
if self.context.portal_type == 'AnalysisRequest':
obj = items[i]['obj']
if obj.portal_type in ['ReferenceAnalysis',
'DuplicateAnalysis'] or \
workflow.getInfoFor(obj, 'worksheetanalysis_review_state') == 'assigned':
br = obj.getBackReferences('WorksheetAnalysis')
if len(br) > 0:
ws = br[0]
items[i]['after']['state_title'] = \
"<a href='%s'><img src='++resource++bika.lims.images/worksheet.png' title='%s'/></a>" % \
(ws.absolute_url(),
t(_("Assigned to: ${worksheet_id}",
mapping={'worksheet_id': safe_unicode(ws.id)})))
# the TAL requires values for all interim fields on all
# items, so we set blank values in unused cells
for item in items:
for field in self.interim_columns:
if field not in item:
item[field] = ''
# XXX order the list of interim columns
interim_keys = self.interim_columns.keys()
interim_keys.reverse()
# add InterimFields keys to columns
for col_id in interim_keys:
if col_id not in self.columns:
self.columns[col_id] = {
'title': self.interim_columns[col_id],
'input_width': '6',
'input_class': 'ajax_calculate numeric',
'sortable': False
}
if can_edit_analyses:
new_states = []
for state in self.review_states:
# InterimFields are displayed in review_state
# They are anyway available through View.columns though.
# In case of hidden fields, the calcs.py should check calcs/services
# for additional InterimFields!!
pos = 'Result' in state['columns'] and \
state['columns'].index('Result') or len(state['columns'])
for col_id in interim_keys:
if col_id not in state['columns']:
state['columns'].insert(pos, col_id)
# retested column is added after Result.
pos = 'Result' in state['columns'] and \
state['columns'].index('Uncertainty') + 1 or len(state['columns'])
state['columns'].insert(pos, 'retested')
new_states.append(state)
self.review_states = new_states
# Allow selecting individual analyses
self.show_select_column = True
# Dry Matter.
# The Dry Matter column is never enabled for reference sample contexts
# and refers to getReportDryMatter in ARs.
if items and \
(hasattr(self.context, 'getReportDryMatter') and \
self.context.getReportDryMatter()):
# look through all items
# if the item's Service supports ReportDryMatter, add getResultDM().
for item in items:
if item['obj'].getService().getReportDryMatter():
item['ResultDM'] = item['obj'].getResultDM()
else:
item['ResultDM'] = ''
if item['ResultDM']:
item['after']['ResultDM'] = "<em class='discreet'>%</em>"
# modify the review_states list to include the ResultDM column
new_states = []
for state in self.review_states:
pos = 'Result' in state['columns'] and \
state['columns'].index('Uncertainty') + 1 or len(state['columns'])
state['columns'].insert(pos, 'ResultDM')
new_states.append(state)
self.review_states = new_states
self.categories.sort()
# self.json_specs = json.dumps(self.specs)
self.json_interim_fields = json.dumps(self.interim_fields)
self.items = items
# Method and Instrument columns must be shown or hidden at the
# same time, because the value assigned to one causes
# a value reassignment to the other (one method can be performed
# by different instruments)
self.columns['Method']['toggle'] = show_methodinstr_columns
self.columns['Instrument']['toggle'] = show_methodinstr_columns
return items
def calculate(self, uid=None):
analysis = self.analyses[uid]
form_result = self.current_results[uid]
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:
# add all our dependent analyses results to the mapping.
# Retrieve value from database if it's not in the current_results.
unsatisfied = False
for dependency_uid, dependency in deps.items():
if dependency_uid in self.ignore_uids:
unsatisfied = True
break
if dependency_uid in self.current_results:
result = self.current_results[dependency_uid]
else:
result = dependency.getResult()
if result == '':
unsatisfied = True
break
key = dependency.getService().getKeyword()
# All mappings must be float, or they are ignored.
try:
mapping[key] = float(self.current_results[dependency_uid])
except:
pass
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
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] = '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))
self.uncertainties.append({'uid': uid,
'uncertainty': analysis.getUncertainty(
Result['result'])})
# 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 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 getFormattedResult(self, specs=None, decimalmark='.', sciformat=1,
html=True):
"""Formatted result:
1. If the result is a detection limit, returns '< LDL' or '> UDL'
2. Print ResultText of matching ResultOptions
3. If the result is not floatable, return it without being formatted
4. If the analysis specs has hidemin or hidemax enabled and the
result is out of range, render result as '<min' or '>max'
5. If the result is below Lower Detection Limit, show '<LDL'
6. If the result is above Upper Detecion Limit, show '>UDL'
7. Otherwise, render numerical value
:param specs: Optional result specifications, a dictionary as follows:
{'min': <min_val>,
'max': <max_val>,
'error': <error>,
'hidemin': <hidemin_val>,
'hidemax': <hidemax_val>}
:param decimalmark: The string to be used as a decimal separator.
default is '.'
:param sciformat: 1. The sci notation has to be formatted as aE^+b
2. The sci notation has to be formatted as a·10^b
3. As 2, but with super html entity for exp
4. The sci notation has to be formatted as a·10^b
5. As 4, but with super html entity for exp
By default 1
:param html: if true, returns an string with the special characters
escaped: e.g: '<' and '>' (LDL and UDL for results like < 23.4).
"""
result = self.getResult()
# 1. The result is a detection limit, return '< LDL' or '> UDL'
dl = self.getDetectionLimitOperand()
if dl:
try:
res = float(result) # required, check if floatable
res = drop_trailing_zeros_decimal(res)
fdm = formatDecimalMark(res, decimalmark)
hdl = cgi.escape(dl) if html else dl
return '%s %s' % (hdl, fdm)
except (TypeError, ValueError):
logger.warn(
"The result for the analysis %s is a detection limit, "
"but not floatable: %s" % (self.id, result))
return formatDecimalMark(result, decimalmark=decimalmark)
choices = self.getResultOptions()
# 2. Print ResultText of matching ResulOptions
match = [x['ResultText'] for x in choices
if str(x['ResultValue']) == str(result)]
if match:
return match[0]
# 3. If the result is not floatable, return it without being formatted
try:
result = float(result)
except (TypeError, ValueError):
return formatDecimalMark(result, decimalmark=decimalmark)
# 4. If the analysis specs has enabled hidemin or hidemax and the
# result is out of range, render result as '<min' or '>max'
specs = specs if specs else self.getResultsRange()
hidemin = specs.get('hidemin', '')
hidemax = specs.get('hidemax', '')
try:
belowmin = hidemin and result < float(hidemin) or False
except (TypeError, ValueError):
belowmin = False
try:
abovemax = hidemax and result > float(hidemax) or False
except (TypeError, ValueError):
abovemax = False
# 4.1. If result is below min and hidemin enabled, return '<min'
if belowmin:
fdm = formatDecimalMark('< %s' % hidemin, decimalmark)
return fdm.replace('< ', '< ', 1) if html else fdm
# 4.2. If result is above max and hidemax enabled, return '>max'
if abovemax:
fdm = formatDecimalMark('> %s' % hidemax, decimalmark)
return fdm.replace('> ', '> ', 1) if html else fdm
# Below Lower Detection Limit (LDL)?
ldl = self.getLowerDetectionLimit()
if result < ldl:
# LDL must not be formatted according to precision, etc.
# Drop trailing zeros from decimal
ldl = drop_trailing_zeros_decimal(ldl)
fdm = formatDecimalMark('< %s' % ldl, decimalmark)
return fdm.replace('< ', '< ', 1) if html else fdm
# Above Upper Detection Limit (UDL)?
udl = self.getUpperDetectionLimit()
if result > udl:
# UDL must not be formatted according to precision, etc.
# Drop trailing zeros from decimal
udl = drop_trailing_zeros_decimal(udl)
fdm = formatDecimalMark('> %s' % udl, decimalmark)
return fdm.replace('> ', '> ', 1) if html else fdm
# Render numerical values
return format_numeric_result(self, self.getResult(),
decimalmark=decimalmark,
sciformat=sciformat)
def getFormattedResult(self, specs=None, decimalmark='.', sciformat=1):
"""Formatted result:
1. Print ResultText of matching ResultOptions
2. If the result is not floatable, return it without being formatted
3. If the analysis specs has hidemin or hidemax enabled and the
result is out of range, render result as '<min' or '>max'
4. Otherwise, render numerical value
specs param is optional. A dictionary as follows:
{'min': <min_val>,
'max': <max_val>,
'error': <error>,
'hidemin': <hidemin_val>,
'hidemax': <hidemax_val>}
:param sciformat: 1. The sci notation has to be formatted as aE^+b
2. The sci notation has to be formatted as a·10^b
3. As 2, but with super html entity for exp
4. The sci notation has to be formatted as a·10^b
5. As 4, but with super html entity for exp
By default 1
"""
result = self.getResult()
service = self.getService()
choices = service.getResultOptions()
# 1. Print ResultText of matching ResulOptions
match = [x['ResultText'] for x in choices
if str(x['ResultValue']) == str(result)]
if match:
return match[0]
# 2. If the result is not floatable, return it without being formatted
try:
result = float(result)
except:
return result
# 3. If the analysis specs has enabled hidemin or hidemax and the
# result is out of range, render result as '<min' or '>max'
belowmin = False
abovemax = False
if not specs:
specs = self.getAnalysisSpecs()
specs = specs.getResultsRangeDict() if specs is not None else {}
specs = specs.get(self.getKeyword(), {})
hidemin = specs.get('hidemin', '')
hidemax = specs.get('hidemax', '')
try:
belowmin = hidemin and result < float(hidemin) or False
except:
belowmin = False
pass
try:
abovemax = hidemax and result > float(hidemax) or False
except:
abovemax = False
pass
# 3.1. If result is below min and hidemin enabled, return '<min'
if belowmin:
return formatDecimalMark('< %s' % hidemin, decimalmark)
# 3.2. If result is above max and hidemax enabled, return '>max'
if abovemax:
return formatDecimalMark('> %s' % hidemax, decimalmark)
# Render numerical values
return formatDecimalMark(format_numeric_result(self, result, sciformat=sciformat), decimalmark=decimalmark)
