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 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 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 __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 "Commented by Yasir"
debug_mode = True #"Added by Yasir"
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 __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 "Commented by Yasir"
debug_mode = True #"Added by Yasir"
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 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 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()]