def get_analysis_spec(self, analysis):
if hasattr(analysis, 'getResultsRange'):
return analysis.getResultsRange()
if hasattr(analysis.aq_parent, 'getResultsRange'):
rr = dicts_to_dict(analysis.aq_parent.getResultsRange(), 'keyword')
return rr.get(analysis.getKeyword(), None)
if hasattr(analysis.aq_parent, 'getReferenceResults'):
rr = dicts_to_dict(analysis.aq_parent.getReferenceResults(), 'uid')
return rr.get(analysis.UID(), None)
keyword = analysis.getService().getKeyword()
uid = analysis.UID()
return {'keyword':keyword, 'uid':uid, 'min':'', 'max':'', 'error':''}
def __call__(self, result=None, specification=None):
workflow = getToolByName(self.context, 'portal_workflow')
astate = workflow.getInfoFor(self.context, 'review_state')
if astate == 'retracted':
return None
result = result is not None and str(result) or self.context.getResult()
if result == '':
return None
# if analysis result is not a number, then we assume in range:
try:
result = float(str(result))
except ValueError:
return None
# The spec is found in the parent AR's ResultsRange field.
if not specification:
rr = dicts_to_dict(self.context.aq_parent.getResultsRange(), 'keyword')
specification = rr.get(self.context.getKeyword(), None)
# No specs available, assume in range:
if not specification:
return None
outofrange, acceptable = \
self.isOutOfRange(result,
specification.get('min', ''),
specification.get('max', ''),
specification.get('error', ''))
return {
'out_of_range': outofrange,
'acceptable': acceptable,
'spec_values': specification
}
def __call__(self, result=None, specification=None):
workflow = getToolByName(self.context, 'portal_workflow')
astate = workflow.getInfoFor(self.context, 'review_state')
if astate == 'retracted':
return None
result = result is not None and str(result) or self.context.getResult()
if result == '':
return None
# if analysis result is not a number, then we assume in range:
try:
result = float(str(result))
except ValueError:
return None
# The spec is found in the parent AR's ResultsRange field.
if not specification:
rr = dicts_to_dict(self.context.aq_parent.getResultsRange(),
'keyword')
specification = rr.get(self.context.getKeyword(), None)
# No specs available, assume in range:
if not specification:
return None
outofrange, acceptable = \
self.isOutOfRange(result,
specification.get('min', ''),
specification.get('max', ''),
specification.get('error', ''))
return {
'out_of_range': outofrange,
'acceptable': acceptable,
'spec_values': specification
}
def get_specs_from_request(self, dicts_to_dict_rr=None):
"""Specifications for analyses are given on the request in *Spec
>>> portal = layer['portal']
>>> portal_url = portal.absolute_url()
>>> from plone.app.testing import SITE_OWNER_NAME
>>> from plone.app.testing import SITE_OWNER_PASSWORD
>>> browser = layer['getBrowser'](portal, loggedIn=True, username=SITE_OWNER_NAME, password=SITE_OWNER_PASSWORD)
>>> browser.open(portal_url+"/@@API/create", "&".join([
... "obj_type=AnalysisRequest",
... "Client=portal_type:Client|id:client-1",
... "SampleType=portal_type:SampleType|title:Apple Pulp",
... "Contact=portal_type:Contact|getFullname:Rita Mohale",
... "Services:list=portal_type:AnalysisService|title:Calcium",
... "Services:list=portal_type:AnalysisService|title:Copper",
... "Services:list=portal_type:AnalysisService|title:Magnesium",
... "SamplingDate=2013-09-29",
... "Specification=portal_type:AnalysisSpec|title:Apple Pulp",
... 'ResultsRange=[{"keyword":"Cu","min":5,"max":10,"error":10},{"keyword":"Mg","min":6,"max":11,"error":11}]',
... ]))
>>> browser.contents
'{..."success": true...}'
"""
# valid output for ResultsRange goes here.
specs = []
context = self.context
request = self.request
brains = resolve_request_lookup(context, request, "Specification")
spec_rr = brains[0].getObject().getResultsRange() if brains else {}
spec_rr = dicts_to_dict(spec_rr, 'keyword')
#
bsc = getToolByName(context, "bika_setup_catalog")
req_rr = request.get('ResultsRange', "[]")
try:
req_rr = json.loads(req_rr)
except:
raise BadRequest("Invalid value for ResultsRange (%s)"%req_rr)
req_rr = dicts_to_dict(req_rr, 'keyword')
#
spec_rr.update(req_rr)
return spec_rr.values()
def get_analysis_spec(self, analysis):
if hasattr(analysis, 'getResultsRange'):
return analysis.getResultsRange()
if hasattr(analysis.aq_parent, 'getResultsRange'):
rr = dicts_to_dict(analysis.aq_parent.getResultsRange(), 'keyword')
return rr.get(analysis.getKeyword(), None)
if hasattr(analysis.aq_parent, 'getReferenceResults'):
rr = dicts_to_dict(analysis.aq_parent.getReferenceResults(), 'uid')
return rr.get(analysis.UID(), None)
keyword = analysis.getService().getKeyword()
uid = analysis.UID()
return {
'keyword': keyword,
'uid': uid,
'min': '',
'max': '',
'error': ''
}
def __call__(self):
bsc = getToolByName(self.context, 'bika_setup_catalog')
bac = getToolByName(self.context, 'bika_analysis_catalog')
self.report_content = {}
parms = []
headings = {}
headings['header'] = _("Analyses out of range")
headings['subheader'] = _("Analyses results out of specified range")
count_all = 0
query = {"portal_type": "Analysis",
"sort_order": "reverse"}
spec_uid = self.request.form.get("spec", False)
spec_obj = None
spec_title = ""
if spec_uid:
brains = bsc(UID=spec_uid)
if brains:
spec_obj = brains[0].getObject()
spec_title = spec_obj.Title()
parms.append(
{"title": _("Range spec"),
"value": spec_title,
"type": "text"})
date_query = formatDateQuery(self.context, 'Received')
if date_query:
query['getDateReceived'] = date_query
received = formatDateParms(self.context, 'Received')
else:
received = 'Undefined'
parms.append(
{'title': _('Received'),
'value': received,
'type': 'text'})
wf_tool = getToolByName(self.context, 'portal_workflow')
if self.request.form.has_key('bika_analysis_workflow'):
query['review_state'] = self.request.form['bika_analysis_workflow']
review_state = wf_tool.getTitleForStateOnType(
self.request.form['bika_analysis_workflow'], 'Analysis')
else:
review_state = 'Undefined'
parms.append(
{'title': _('Status'),
'value': review_state,
'type': 'text'})
if self.request.form.has_key('bika_cancellation_workflow'):
query['cancellation_state'] = self.request.form[
'bika_cancellation_workflow']
cancellation_state = wf_tool.getTitleForStateOnType(
self.request.form['bika_cancellation_workflow'], 'Analysis')
else:
cancellation_state = 'Undefined'
parms.append(
{'title': _('Active'),
'value': cancellation_state,
'type': 'text'})
if self.request.form.has_key('bika_worksheetanalysis_workflow'):
query['worksheetanalysis_review_state'] = self.request.form[
'bika_worksheetanalysis_workflow']
ws_review_state = wf_tool.getTitleForStateOnType(
self.request.form['bika_worksheetanalysis_workflow'], 'Analysis')
else:
ws_review_state = 'Undefined'
parms.append(
{'title': _('Assigned to worksheet'),
'value': ws_review_state,
'type': 'text'})
# and now lets do the actual report lines
col_heads = [_('Client'),
_('Request'),
_('Sample type'),
_('Sample point'),
_('Category'),
_('Analysis'),
_('Result'),
_('Min'),
_('Max'),
_('Status'),
]
if isAttributeHidden('Sample', 'SamplePoint'):
col_heads.remove(_('Sample point'))
formats = {'columns': 10,
'col_heads': col_heads,
'class': '',
}
datalines = []
for a_proxy in bac(query):
analysis = a_proxy.getObject()
if analysis.getResult():
try:
result = float(analysis.getResult())
except:
continue
else:
continue
keyword = analysis.getKeyword()
# determine which specs to use for this particular analysis
# 1) if a spec is given in the query form, use it.
# 2) if a spec is entered directly on the analysis, use it.
# otherwise just continue to the next object.
spec_dict = False
if spec_obj:
rr = spec_obj.getResultsRangeDict()
if keyword in rr:
spec_dict = rr[keyword]
else:
ar = analysis.aq_parent
rr = dicts_to_dict(ar.getResultsRange(), 'keyword')
if keyword in rr:
spec_dict = rr[keyword]
else:
continue
if not spec_dict:
continue
try:
spec_min = float(spec_dict['min'])
spec_max = float(spec_dict['max'])
except ValueError:
continue
if spec_min <= result <= spec_max:
continue
# check if in shoulder: out of range, but in acceptable
# error percentage
shoulder = False
error = 0
try:
error = float(spec_dict.get('error', '0'))
except:
error = 0
pass
error_amount = (result / 100) * error
error_min = result - error_amount
error_max = result + error_amount
if ((result < spec_min) and (error_max >= spec_min)) or \
((result > spec_max) and (error_min <= spec_max)):
shoulder = True
dataline = []
dataitem = {'value': analysis.getClientTitle()}
dataline.append(dataitem)
dataitem = {'value': analysis.getRequestID()}
dataline.append(dataitem)
dataitem = {'value': analysis.aq_parent.getSampleTypeTitle()}
dataline.append(dataitem)
if isAttributeHidden('Sample', 'SamplePoint'):
dataitem = {'value': analysis.aq_parent.getSamplePointTitle()}
dataline.append(dataitem)
dataitem = {'value': analysis.getCategoryTitle()}
dataline.append(dataitem)
dataitem = {'value': analysis.getServiceTitle()}
dataline.append(dataitem)
if shoulder:
dataitem = {'value': analysis.getResult(),
'img_after': '++resource++bika.lims.images/exclamation.png'}
else:
dataitem = {'value': analysis.getResult()}
dataline.append(dataitem)
dataitem = {'value': spec_dict['min']}
dataline.append(dataitem)
dataitem = {'value': spec_dict['max']}
dataline.append(dataitem)
state = wf_tool.getInfoFor(analysis, 'review_state', '')
review_state = wf_tool.getTitleForStateOnType(
state, 'Analysis')
dataitem = {'value': review_state}
dataline.append(dataitem)
datalines.append(dataline)
count_all += 1
# table footer data
footlines = []
footline = []
footitem = {'value': _('Number of analyses out of range for period'),
'colspan': 9,
'class': 'total_label'}
footline.append(footitem)
footitem = {'value': count_all}
footline.append(footitem)
footlines.append(footline)
# report footer data
footnotes = []
footline = []
footitem = {'value': _('Analysis result within error range'),
'img_before': '++resource++bika.lims.images/exclamation.png'
}
footline.append(footitem)
footnotes.append(footline)
self.report_content = {
'headings': headings,
'parms': parms,
'formats': formats,
'datalines': datalines,
'footings': footlines,
'footnotes': footnotes}
title = t(headings['header'])
return {'report_title': title,
'report_data': self.template()}
def get_analysis_spec(self, analysis):
rr = dicts_to_dict(analysis.aq_parent.getResultsRange(), 'keyword')
return rr.get(analysis.getKeyword(), None)
def get_analysis_spec(self, analysis):
rr = dicts_to_dict(analysis.aq_parent.getResultsRange(), 'keyword')
return rr.get(analysis.getKeyword(), None)
def get_spec_from_ar(self, ar, keyword):
empty = {'min': '', 'max': '', 'error': '', 'keyword':keyword}
spec = ar.getResultsRange()
if spec:
return dicts_to_dict(spec, 'keyword').get(keyword, empty)
return empty
def __call__(self):
bsc = getToolByName(self.context, 'bika_setup_catalog')
bac = getToolByName(self.context, 'bika_analysis_catalog')
self.report_content = {}
parms = []
headings = {}
headings['header'] = _("Analyses out of range")
headings['subheader'] = _("Analyses results out of specified range")
count_all = 0
query = {"portal_type": "Analysis", "sort_order": "reverse"}
spec_uid = self.request.form.get("spec", False)
spec_obj = None
spec_title = ""
if spec_uid:
brains = bsc(UID=spec_uid)
if brains:
spec_obj = brains[0].getObject()
spec_title = spec_obj.Title()
parms.append({
"title": _("Range spec"),
"value": spec_title,
"type": "text"
})
date_query = formatDateQuery(self.context, 'Received')
if date_query:
query['getDateReceived'] = date_query
received = formatDateParms(self.context, 'Received')
else:
received = 'Undefined'
parms.append({
'title': _('Received'),
'value': received,
'type': 'text'
})
wf_tool = getToolByName(self.context, 'portal_workflow')
if self.request.form.has_key('bika_analysis_workflow'):
query['review_state'] = self.request.form['bika_analysis_workflow']
review_state = wf_tool.getTitleForStateOnType(
self.request.form['bika_analysis_workflow'], 'Analysis')
else:
review_state = 'Undefined'
parms.append({
'title': _('Status'),
'value': review_state,
'type': 'text'
})
if self.request.form.has_key('bika_cancellation_workflow'):
query['cancellation_state'] = self.request.form[
'bika_cancellation_workflow']
cancellation_state = wf_tool.getTitleForStateOnType(
self.request.form['bika_cancellation_workflow'], 'Analysis')
else:
cancellation_state = 'Undefined'
parms.append({
'title': _('Active'),
'value': cancellation_state,
'type': 'text'
})
if self.request.form.has_key('bika_worksheetanalysis_workflow'):
query['worksheetanalysis_review_state'] = self.request.form[
'bika_worksheetanalysis_workflow']
ws_review_state = wf_tool.getTitleForStateOnType(
self.request.form['bika_worksheetanalysis_workflow'],
'Analysis')
else:
ws_review_state = 'Undefined'
parms.append({
'title': _('Assigned to worksheet'),
'value': ws_review_state,
'type': 'text'
})
# and now lets do the actual report lines
col_heads = [
_('Client'),
_('Request'),
_('Sample type'),
_('Sample point'),
_('Category'),
_('Analysis'),
_('Result'),
_('Min'),
_('Max'),
_('Status'),
]
if isAttributeHidden('Sample', 'SamplePoint'):
col_heads.remove(_('Sample point'))
formats = {
'columns': 10,
'col_heads': col_heads,
'class': '',
}
datalines = []
for a_proxy in bac(query):
analysis = a_proxy.getObject()
if analysis.getResult():
try:
result = float(analysis.getResult())
except:
continue
else:
continue
keyword = analysis.getKeyword()
# determine which specs to use for this particular analysis
# 1) if a spec is given in the query form, use it.
# 2) if a spec is entered directly on the analysis, use it.
# otherwise just continue to the next object.
spec_dict = False
if spec_obj:
rr = spec_obj.getResultsRangeDict()
if keyword in rr:
spec_dict = rr[keyword]
else:
ar = analysis.aq_parent
rr = dicts_to_dict(ar.getResultsRange(), 'keyword')
if keyword in rr:
spec_dict = rr[keyword]
else:
continue
if not spec_dict:
continue
try:
spec_min = float(spec_dict['min'])
spec_max = float(spec_dict['max'])
except ValueError:
continue
if spec_min <= result <= spec_max:
continue
# check if in shoulder: out of range, but in acceptable
# error percentage
shoulder = False
error = 0
try:
error = float(spec_dict.get('error', '0'))
except:
error = 0
pass
error_amount = (result / 100) * error
error_min = result - error_amount
error_max = result + error_amount
if ((result < spec_min) and (error_max >= spec_min)) or \
((result > spec_max) and (error_min <= spec_max)):
shoulder = True
dataline = []
dataitem = {'value': analysis.getClientTitle()}
dataline.append(dataitem)
dataitem = {'value': analysis.getRequestID()}
dataline.append(dataitem)
dataitem = {'value': analysis.aq_parent.getSampleTypeTitle()}
dataline.append(dataitem)
if isAttributeHidden('Sample', 'SamplePoint'):
dataitem = {'value': analysis.aq_parent.getSamplePointTitle()}
dataline.append(dataitem)
dataitem = {'value': analysis.getCategoryTitle()}
dataline.append(dataitem)
dataitem = {'value': analysis.getServiceTitle()}
dataline.append(dataitem)
if shoulder:
dataitem = {
'value': analysis.getResult(),
'img_after': '++resource++bika.lims.images/exclamation.png'
}
else:
dataitem = {'value': analysis.getResult()}
dataline.append(dataitem)
dataitem = {'value': spec_dict['min']}
dataline.append(dataitem)
dataitem = {'value': spec_dict['max']}
dataline.append(dataitem)
state = wf_tool.getInfoFor(analysis, 'review_state', '')
review_state = wf_tool.getTitleForStateOnType(state, 'Analysis')
dataitem = {'value': review_state}
dataline.append(dataitem)
datalines.append(dataline)
count_all += 1
# table footer data
footlines = []
footline = []
footitem = {
'value': _('Number of analyses out of range for period'),
'colspan': 9,
'class': 'total_label'
}
footline.append(footitem)
footitem = {'value': count_all}
footline.append(footitem)
footlines.append(footline)
# report footer data
footnotes = []
footline = []
footitem = {
'value': _('Analysis result within error range'),
'img_before': '++resource++bika.lims.images/exclamation.png'
}
footline.append(footitem)
footnotes.append(footline)
self.report_content = {
'headings': headings,
'parms': parms,
'formats': formats,
'datalines': datalines,
'footings': footlines,
'footnotes': footnotes
}
title = t(headings['header'])
return {'report_title': title, 'report_data': self.template()}
def analysis_specification(self):
ar = self.context.aq_parent
rr = dicts_to_dict(ar.getResultsRange(),'keyword')
return rr[self.context.getService().getKeyword()]
def analysis_specification(self):
ar = self.context.aq_parent
rr = dicts_to_dict(ar.getResultsRange(), 'keyword')
return rr[self.context.getService().getKeyword()]