def _analysis_data(self, analysis):
""" Returns a dict that represents the analysis
"""
decimalmark = analysis.aq_parent.aq_parent.getDecimalMark()
keyword = analysis.getKeyword()
andict = {
'obj': analysis,
'id': analysis.id,
'title': analysis.Title(),
'keyword': keyword,
'scientific_name': analysis.getScientificName(),
'accredited': analysis.getAccredited(),
'point_of_capture': to_utf8(POINTS_OF_CAPTURE.getValue(analysis.getPointOfCapture())),
'category': to_utf8(analysis.getCategoryTitle()),
'result': analysis.getResult(),
'unit': to_utf8(analysis.getUnit()),
'formatted_unit': format_supsub(to_utf8(analysis.getUnit())),
'capture_date': analysis.getResultCaptureDate(),
'request_id': analysis.aq_parent.getId(),
'formatted_result': '',
'uncertainty': analysis.getUncertainty(),
'formatted_uncertainty': '',
'retested': analysis.isRetest(),
'remarks': to_utf8(analysis.getRemarks()),
'outofrange': False,
'type': analysis.portal_type,
'reftype': analysis.getReferenceType() if hasattr(
analysis, 'getReferenceType') else None,
'worksheet': None,
'specs': {},
'formatted_specs': '',
'review_state': api.get_workflow_status_of(analysis),
}
andict['refsample'] = analysis.getSample().id \
if IReferenceAnalysis.providedBy(analysis) \
else analysis.getRequestID()
specs = analysis.getResultsRange()
andict['specs'] = specs
scinot = self.context.bika_setup.getScientificNotationReport()
andict['formatted_result'] = analysis.getFormattedResult(specs=specs, sciformat=int(scinot), decimalmark=decimalmark)
fs = ''
if specs.get('min', None) and specs.get('max', None):
fs = '%s - %s' % (specs['min'], specs['max'])
elif specs.get('min', None):
fs = '> %s' % specs['min']
elif specs.get('max', None):
fs = '< %s' % specs['max']
andict['formatted_specs'] = formatDecimalMark(fs, decimalmark)
andict['formatted_uncertainty'] = format_uncertainty(analysis, analysis.getResult(), decimalmark=decimalmark, sciformat=int(scinot))
# Out of range?
andict['outofrange'] = is_out_of_range(analysis)[0]
return andict
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)
member = mtool.getAuthenticatedMember()
# 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
dmk = self.context.bika_setup.getResultsDecimalMark()
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'] = \
formatDecimalMark(interim_fields[x]['value'], dmk)
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()
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'];
items[i]['structure'] = False;
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'];
items[i]['structure'] = True
# 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")))
after_icons = []
# Submitting user may not verify results unless the user is labman
# or manager and the AS has isSelfVerificationEnabled set to True
if items[i]['review_state'] == 'to_be_verified':
# If multi-verification required, place an informative icon
numverifications = obj.getNumberOfRequiredVerifications()
if numverifications > 1:
# More than one verification required, place an icon
# Get the number of verifications already done:
done = obj.getNumberOfVerifications()
pending = numverifications - done
ratio = float(done)/float(numverifications) \
if done > 0 else 0
scale = '' if ratio < 0.25 else '25' \
if ratio < 0.50 else '50' \
if ratio < 0.75 else '75'
anchor = "<a href='#' title='%s %s %s' " \
"class='multi-verification scale-%s'>%s/%s</a>"
anchor = anchor % (t(_("Multi-verification required")),
str(pending),
t(_("verification(s) pending")),
scale, str(done), str(numverifications))
after_icons.append(anchor)
username = member.getUserName()
allowed = api.user.has_permission(VerifyPermission,
username=username)
if allowed and not obj.isUserAllowedToVerify(member):
after_icons.append(
"<img src='++resource++bika.lims.images/submitted-by-current-user.png' title='%s'/>" %
(t(_("Cannot verify, submitted or verified by current user before")))
)
elif allowed:
if obj.getSubmittedBy() == member.getUser().getId():
after_icons.append(
"<img src='++resource++bika.lims.images/warning.png' title='%s'/>" %
(t(_("Can verify, but submitted by current user")))
)
#If analysis Submitted and Verified by the same person, then warning icon will appear.
submitter=obj.getSubmittedBy()
if submitter and obj.wasVerifiedByUser(submitter):
after_icons.append(
"<img src='++resource++bika.lims.images/warning.png' title='%s'/>" %
(t(_("Submited and verified by the same user- "+ submitter)))
)
# 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]
after_icons.append("<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)}))))
items[i]['after']['state_title'] = ' '.join(after_icons)
# 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 _analysis_data(self, analysis, decimalmark=None):
keyword = analysis.getKeyword()
service = analysis.getService()
andict = {'obj': analysis,
'id': analysis.id,
'title': analysis.Title(),
'keyword': keyword,
'scientific_name': service.getScientificName(),
'accredited': service.getAccredited(),
'point_of_capture': to_utf8(POINTS_OF_CAPTURE.getValue(service.getPointOfCapture())),
'category': to_utf8(service.getCategoryTitle()),
'result': analysis.getResult(),
'isnumber': isnumber(analysis.getResult()),
'unit': to_utf8(service.getUnit()),
'formatted_unit': format_supsub(to_utf8(service.getUnit())),
'capture_date': analysis.getResultCaptureDate(),
'request_id': analysis.aq_parent.getId(),
'formatted_result': '',
'uncertainty': analysis.getUncertainty(),
'formatted_uncertainty': '',
'retested': analysis.getRetested(),
'remarks': to_utf8(analysis.getRemarks()),
'resultdm': to_utf8(analysis.getResultDM()),
'outofrange': False,
'type': analysis.portal_type,
'reftype': analysis.getReferenceType() \
if hasattr(analysis, 'getReferenceType')
else None,
'worksheet': None,
'specs': {},
'formatted_specs': ''}
if analysis.portal_type == 'DuplicateAnalysis':
andict['reftype'] = 'd'
ws = analysis.getBackReferences('WorksheetAnalysis')
andict['worksheet'] = ws[0].id if ws and len(ws) > 0 else None
andict['worksheet_url'] = ws[0].absolute_url if ws and len(ws) > 0 else None
andict['refsample'] = analysis.getSample().id \
if analysis.portal_type == 'Analysis' \
else '%s - %s' % (analysis.aq_parent.id, analysis.aq_parent.Title())
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()
andict['specs'] = specs
scinot = self.context.bika_setup.getScientificNotationReport()
andict['formatted_result'] = analysis.getFormattedResult(specs=specs, sciformat=int(scinot), decimalmark=decimalmark)
fs = ''
if specs.get('min', None) and specs.get('max', None):
fs = '%s - %s' % (specs['min'], specs['max'])
elif specs.get('min', None):
fs = '> %s' % specs['min']
elif specs.get('max', None):
fs = '< %s' % specs['max']
andict['formatted_specs'] = formatDecimalMark(fs, decimalmark)
andict['formatted_uncertainty'] = format_uncertainty(analysis, analysis.getResult(), decimalmark=decimalmark, sciformat=int(scinot))
# Out of range?
if specs:
adapters = getAdapters((analysis, ), IResultOutOfRange)
bsc = getToolByName(self.context, "bika_setup_catalog")
for name, adapter in adapters:
ret = adapter(specification=specs)
if ret and ret['out_of_range']:
andict['outofrange'] = True
break
return andict
def _analysis_data(self, analysis, decimalmark=None):
if analysis.UID() in self._cache['_analysis_data']:
return self._cache['_analysis_data'][analysis.UID()]
keyword = analysis.getKeyword()
service = analysis.getService()
andict = {'obj': analysis,
'id': analysis.id,
'title': analysis.Title(),
'keyword': keyword,
'scientific_name': service.getScientificName(),
'accredited': service.getAccredited(),
'point_of_capture': to_utf8(POINTS_OF_CAPTURE.getValue(service.getPointOfCapture())),
'category': to_utf8(service.getCategoryTitle()),
'result': analysis.getResult(),
'isnumber': isnumber(analysis.getResult()),
'unit': to_utf8(service.getUnit()),
'formatted_unit': format_supsub(to_utf8(service.getUnit())),
'capture_date': analysis.getResultCaptureDate(),
'request_id': analysis.aq_parent.getId(),
'formatted_result': '',
'uncertainty': analysis.getUncertainty(),
'formatted_uncertainty': '',
'retested': analysis.getRetested(),
'remarks': to_utf8(analysis.getRemarks()),
'resultdm': to_utf8(analysis.getResultDM()),
'outofrange': False,
'type': analysis.portal_type,
'reftype': analysis.getReferenceType() \
if hasattr(analysis, 'getReferenceType')
else None,
'worksheet': None,
'specs': {},
'formatted_specs': ''}
if analysis.portal_type == 'DuplicateAnalysis':
andict['reftype'] = 'd'
ws = analysis.getBackReferences('WorksheetAnalysis')
andict['worksheet'] = ws[0].id if ws and len(ws) > 0 else None
andict['worksheet_url'] = ws[0].absolute_url if ws and len(ws) > 0 else None
andict['refsample'] = analysis.getSample().id \
if analysis.portal_type == 'Analysis' \
else '%s - %s' % (analysis.aq_parent.id, analysis.aq_parent.Title())
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()
andict['specs'] = specs
scinot = self.context.bika_setup.getScientificNotationReport()
fresult = analysis.getFormattedResult(specs=specs, sciformat=int(scinot), decimalmark=decimalmark)
# We don't use here cgi.encode because results fields must be rendered
# using the 'structure' wildcard. The reason is that the result can be
# expressed in sci notation, that may include <sup></sup> html tags.
# Please note the default value for the 'html' parameter from
# getFormattedResult signature is set to True, so the service will
# already take into account LDLs and UDLs symbols '<' and '>' and escape
# them if necessary.
andict['formatted_result'] = fresult;
fs = ''
if specs.get('min', None) and specs.get('max', None):
fs = '%s - %s' % (specs['min'], specs['max'])
elif specs.get('min', None):
fs = '> %s' % specs['min']
elif specs.get('max', None):
fs = '< %s' % specs['max']
andict['formatted_specs'] = formatDecimalMark(fs, decimalmark)
andict['formatted_uncertainty'] = format_uncertainty(analysis, analysis.getResult(), decimalmark=decimalmark, sciformat=int(scinot))
# Out of range?
if specs:
adapters = getAdapters((analysis, ), IResultOutOfRange)
bsc = getToolByName(self.context, "bika_setup_catalog")
for name, adapter in adapters:
ret = adapter(specification=specs)
if ret and ret['out_of_range']:
andict['outofrange'] = True
break
self._cache['_analysis_data'][analysis.UID()] = andict
return andict
def _analysis_data(self, analysis, decimalmark=None):
keyword = analysis.getKeyword()
service = analysis.getService()
andict = {'obj': analysis,
'id': analysis.id,
'title': analysis.Title(),
'keyword': keyword,
'scientific_name': service.getScientificName(),
'accredited': service.getAccredited(),
'point_of_capture': to_utf8(POINTS_OF_CAPTURE.getValue(service.getPointOfCapture())),
'category': to_utf8(service.getCategoryTitle()),
'result': analysis.getResult(),
'isnumber': isnumber(analysis.getResult()),
'unit': to_utf8(service.getUnit()),
'formatted_unit': format_supsub(to_utf8(service.getUnit())),
'capture_date': analysis.getResultCaptureDate(),
'request_id': analysis.aq_parent.getId(),
'formatted_result': '',
'uncertainty': analysis.getUncertainty(),
'formatted_uncertainty': '',
'retested': analysis.getRetested(),
'remarks': to_utf8(analysis.getRemarks()),
'resultdm': to_utf8(analysis.getResultDM()),
'outofrange': False,
'type': analysis.portal_type,
'reftype': analysis.getReferenceType() \
if hasattr(analysis, 'getReferenceType')
else None,
'worksheet': None,
'specs': {},
'formatted_specs': ''}
if analysis.portal_type == 'DuplicateAnalysis':
andict['reftype'] = 'd'
ws = analysis.getBackReferences('WorksheetAnalysis')
andict['worksheet'] = ws[0].id if ws and len(ws) > 0 else None
andict['worksheet_url'] = ws[0].absolute_url if ws and len(
ws) > 0 else None
andict['refsample'] = analysis.getSample().id \
if analysis.portal_type == 'Analysis' \
else '%s - %s' % (analysis.aq_parent.id, analysis.aq_parent.Title())
# Which analysis specs must be used?
# Try first with those defined at AR Publish Specs level
if analysis.portal_type == 'ReferenceAnalysis':
# The analysis is a Control or Blank. We might use the
# reference results instead other specs
uid = analysis.getServiceUID()
specs = analysis.aq_parent.getResultsRangeDict().get(uid, {})
elif analysis.portal_type == 'DuplicateAnalysis':
specs = analysis.getAnalysisSpecs()
else:
ar = analysis.aq_parent
specs = ar.getPublicationSpecification()
if not specs or keyword not in specs.getResultsRangeDict():
specs = analysis.getAnalysisSpecs()
specs = specs.getResultsRangeDict().get(keyword, {}) \
if specs else {}
andict['specs'] = specs
scinot = self.context.bika_setup.getScientificNotationReport()
andict['formatted_result'] = analysis.getFormattedResult(
specs=specs, sciformat=int(scinot), decimalmark=decimalmark)
fs = ''
if specs.get('min', None) and specs.get('max', None):
fs = '%s - %s' % (specs['min'], specs['max'])
elif specs.get('min', None):
fs = '> %s' % specs['min']
elif specs.get('max', None):
fs = '< %s' % specs['max']
andict['formatted_specs'] = formatDecimalMark(fs, decimalmark)
andict['formatted_uncertainty'] = format_uncertainty(
analysis,
analysis.getResult(),
decimalmark=decimalmark,
sciformat=int(scinot))
# Return specs of current analysis
andict['specs_dict'] = analysis.getSpecification().getResultsRangeDict(
).get(analysis.id)
# Out of range?
if specs:
adapters = getAdapters((analysis, ), IResultOutOfRange)
bsc = getToolByName(self.context, "bika_setup_catalog")
for name, adapter in adapters:
ret = adapter(specification=specs)
if ret and ret['out_of_range']:
andict['outofrange'] = True
break
return andict
def folderitems(self):
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)
member = mtool.getAuthenticatedMember()
self.interim_fields = {}
self.interim_columns = {}
self.specs = {}
show_methodinstr_columns = False
dmk = self.context.bika_setup.getResultsDecimalMark()
for item in items:
if 'obj' not in item:
logger.warn(
"Missing 'obj' key in Analysis item '{}'".format(item))
continue
# self.contentsMethod may return brains or objects.
obj = api.get_object(item["obj"])
if workflow.getInfoFor(obj, 'review_state') == 'retracted' \
and not checkPermission(ViewRetractedAnalyses, self.context):
logger.info("Skipping retracted analysis {}".format(
obj.getId()))
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)
item['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'] = \
formatDecimalMark(interim_fields[x]['value'], dmk)
self.interim_fields[obj.UID()] = interim_fields
item['service_uid'] = service.UID()
item['Service'] = service.Title()
item['Keyword'] = keyword
item['Unit'] = format_supsub(unit) if unit else ''
item['Result'] = ''
item['formatted_result'] = ''
item['interim_fields'] = interim_fields
item['Remarks'] = obj.getRemarks()
item['Uncertainty'] = ''
item['DetectionLimit'] = ''
item['retested'] = obj.getRetested()
item['class']['retested'] = 'center'
item['result_captured'] = self.ulocalized_time(
obj.getResultCaptureDate(), long_format=0)
item['calculation'] = calculation and True or False
try:
item['Partition'] = obj.getSamplePartition().getId()
except AttributeError:
item['Partition'] = ''
if obj.portal_type == "ReferenceAnalysis":
item['DueDate'] = self.ulocalized_time(
obj.aq_parent.getExpiryDate(), long_format=0)
else:
item['DueDate'] = self.ulocalized_time(obj.getDueDate(),
long_format=1)
cd = obj.getResultCaptureDate()
item['CaptureDate'] = cd and self.ulocalized_time(
cd, long_format=1) or ''
item['Attachments'] = ''
item['allow_edit'] = []
tblrowclass = item.get('table_row_class')
if obj.portal_type == 'ReferenceAnalysis':
item['st_uid'] = obj.aq_parent.UID()
item['table_row_class'] = ' '.join(
[tblrowclass, 'qc-analysis'])
elif obj.portal_type == 'DuplicateAnalysis' and \
obj.getAnalysis().portal_type == 'ReferenceAnalysis':
item['st_uid'] = obj.aq_parent.UID()
item['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 ''
item['st_uid'] = st_uid
if checkPermission(ManageBika, self.context):
# service_uid = service.UID()
# latest = rc.lookupObject(service_uid).version_id
item['Service'] = service.Title()
item['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:
item['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()]:
item['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 item['calculation'] or \
(item['calculation'] and self.interim_fields[obj.UID()]):
item['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()
item['Analyst'] = analyst
item['choices']['Analyst'] = self.getAnalysts()
else:
item['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>"
item['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:
item['Result'] = result
scinot = self.context.bika_setup.getScientificNotationResults()
item['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(
) is True:
unc = obj.getUncertainty(result)
item['allow_edit'].append('Uncertainty')
item['Uncertainty'] = unc if unc else ''
item['before']['Uncertainty'] = '± '
item['after'][
'Uncertainty'] = '<em class="discreet" style="white-space:nowrap;"> %s</em>' % item[
'Unit']
item['structure'] = False
elif fu:
item['Uncertainty'] = fu
item['before']['Uncertainty'] = '± '
item['after'][
'Uncertainty'] = '<em class="discreet" style="white-space:nowrap;"> %s</em>' % item[
'Unit']
item['structure'] = True
# 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() is 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:
item['Specification'] = ""
if 'Result' in item['allow_edit']:
item['allow_edit'].remove('Result')
item['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 = ""
item['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
item[f['keyword']] = f
item['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()
item['replace']['DueDate'] = \
self.ulocalized_time(duedate, long_format=1)
if item['review_state'] not in [
'to_be_sampled', 'to_be_preserved', 'sample_due',
'published'
]:
if (resultdate and resultdate > duedate) \
or (not resultdate and DateTime() > duedate):
item['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")))
after_icons = []
# Submitting user may not verify results unless the user is labman
# or manager and the AS has isSelfVerificationEnabled set to True
if item['review_state'] == 'to_be_verified':
# If multi-verification required, place an informative icon
numverifications = obj.getNumberOfRequiredVerifications()
if numverifications > 1:
# More than one verification required, place an icon
# Get the number of verifications already done:
done = obj.getNumberOfVerifications()
pending = numverifications - done
ratio = float(done) / float(numverifications) \
if done > 0 else 0
scale = '' if ratio < 0.25 else '25' \
if ratio < 0.50 else '50' \
if ratio < 0.75 else '75'
anchor = "<a href='#' title='%s %s %s' " \
"class='multi-verification scale-%s'>%s/%s</a>"
anchor = anchor % (t(
_("Multi-verification required")), str(pending),
t(_("verification(s) pending")), scale,
str(done), str(numverifications))
after_icons.append(anchor)
username = member.getUserName()
allowed = ploneapi.user.has_permission(VerifyPermission,
username=username)
if allowed and not obj.isUserAllowedToVerify(member):
after_icons.append(
"<img src='++resource++bika.lims.images/submitted-by-current-user.png' title='%s'/>"
% (t(
_("Cannot verify, submitted or verified by current user before"
))))
elif allowed:
if obj.getSubmittedBy() == member.getUser().getId():
after_icons.append(
"<img src='++resource++bika.lims.images/warning.png' title='%s'/>"
%
(t(_("Can verify, but submitted by current user")))
)
# If analysis Submitted and Verified by the same person, then warning icon will appear.
submitter = obj.getSubmittedBy()
if submitter and obj.wasVerifiedByUser(submitter):
after_icons.append(
"<img src='++resource++bika.lims.images/warning.png' title='%s'/>"
% (t(
_("Submited and verified by the same user- " +
submitter))))
# add icon for assigned analyses in AR views
if self.context.portal_type == 'AnalysisRequest':
obj = item['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]
after_icons.append(
"<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)
}))))
item['after']['state_title'] = ' '.join(after_icons)
# 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 folderitem(self, obj, item, index):
"""Service triggered each time an item is iterated in folderitems.
The use of this service prevents the extra-loops in child objects.
:obj: the instance of the class to be foldered
:item: dict containing the properties of the object to be used by
the template
:index: current index of the item
"""
# ensure we have an object and not a brain
obj = api.get_object(obj)
uid = api.get_uid(obj)
url = api.get_url(obj)
title = api.get_title(obj)
# get the category
if self.show_categories_enabled():
category = obj.getCategoryTitle()
if category not in self.categories:
self.categories.append(category)
item["category"] = category
config = self.configuration.get(uid, {})
hidden = config.get("hidden", False)
item["replace"]["Title"] = get_link(url, value=title)
item["Price"] = self.format_price(obj.Price)
item["allow_edit"] = self.get_editable_columns()
item["selected"] = False
item["Hidden"] = hidden
item["selected"] = uid in self.configuration
# Add methods
methods = obj.getMethods()
if methods:
links = map(
lambda m: get_link(
m.absolute_url(), value=m.Title(), css_class="link"),
methods)
item["replace"]["Methods"] = ", ".join(links)
else:
item["methods"] = ""
# Unit
unit = obj.getUnit()
item["Unit"] = unit and format_supsub(unit) or ""
# Icons
after_icons = ""
if obj.getAccredited():
after_icons += get_image("accredited.png", title=_("Accredited"))
if obj.getAttachmentOption() == "r":
after_icons += get_image("attach_reqd.png",
title=_("Attachment required"))
if obj.getAttachmentOption() == "n":
after_icons += get_image("attach_no.png",
title=_("Attachment not permitted"))
if after_icons:
item["after"]["Title"] = after_icons
return item
def folderitem(self, obj, item, index):
"""Prepare a data item for the listing.
:param obj: The catalog brain or content object
:param item: Listing item (dictionary)
:param index: Index of the listing item
:returns: Augmented listing data item
"""
item['Service'] = obj.Title
item['class']['service'] = 'service_title'
item['service_uid'] = obj.getServiceUID
item['Keyword'] = obj.getKeyword
item['Unit'] = format_supsub(obj.getUnit) if obj.getUnit else ''
item['retested'] = obj.getRetested
item['class']['retested'] = 'center'
# Note that getSampleTypeUID returns the type of the Sample, no matter
# if the sample associated to the analysis is a regular Sample (routine
# analysis) or if is a Reference Sample (Reference Analysis). If the
# analysis is a duplicate, it returns the Sample Type of the sample
# associated to the source analysis.
item['st_uid'] = obj.getSampleTypeUID
# Fill item's category
self._folder_item_category(obj, item)
# Fill item's row class
self._folder_item_css_class(obj, item)
# Fill result and/or result options
self._folder_item_result(obj, item)
# Fill calculation and interim fields
self._folder_item_calculation(obj, item)
# Fill method
self._folder_item_method(obj, item)
# Fill instrument
self._folder_item_instrument(obj, item)
# Fill analyst
self._folder_item_analyst(obj, item)
# Fill attachments
self._folder_item_attachments(obj, item)
# Fill uncertainty
self._folder_item_uncertainty(obj, item)
# Fill Detection Limits
self._folder_item_detection_limits(obj, item)
# Fill Specifications
self._folder_item_specifications(obj, item)
# Fill Due Date and icon if late/overdue
self._folder_item_duedate(obj, item)
# Fill verification criteria
self._folder_item_verify_icons(obj, item)
# Fill worksheet anchor/icon
self._folder_item_assigned_worksheet(obj, item)
# Fill reflex analysis icons
self._folder_item_reflex_icons(obj, item)
# Fill hidden field (report visibility)
self._folder_item_report_visibility(obj, item)
# Renders additional icons to be displayed
self._folder_item_fieldicons(obj)
# Renders remarks toggle button
self._folder_item_remarks(obj, item)
return item
def _analysis_data(self, analysis):
""" Returns a dict that represents the analysis
"""
decimalmark = analysis.aq_parent.aq_parent.getDecimalMark()
keyword = analysis.getKeyword()
service = analysis.getService()
andict = {'obj': analysis,
'id': analysis.id,
'title': analysis.Title(),
'keyword': keyword,
'scientific_name': service.getScientificName(),
'accredited': service.getAccredited(),
'point_of_capture': to_utf8(POINTS_OF_CAPTURE.getValue(service.getPointOfCapture())),
'category': to_utf8(service.getCategoryTitle()),
'result': analysis.getResult(),
'unit': to_utf8(service.getUnit()),
'formatted_unit': format_supsub(to_utf8(service.getUnit())),
'capture_date': analysis.getResultCaptureDate(),
'request_id': analysis.aq_parent.getId(),
'formatted_result': '',
'uncertainty': analysis.getUncertainty(),
'formatted_uncertainty': '',
'retested': analysis.getRetested(),
'remarks': to_utf8(analysis.getRemarks()),
'resultdm': to_utf8(analysis.getResultDM()),
'outofrange': False,
'type': analysis.portal_type,
'reftype': analysis.getReferenceType() \
if hasattr(analysis, 'getReferenceType')
else None,
'worksheet': None,
'specs': {},
'formatted_specs': ''}
andict['refsample'] = analysis.getSample().id \
if analysis.portal_type == 'Analysis' \
else '%s - %s' % (analysis.aq_parent.id, analysis.aq_parent.Title())
# Which analysis specs must be used?
# Try first with those defined at AR Publish Specs level
if analysis.portal_type == 'ReferenceAnalysis':
# The analysis is a Control or Blank. We might use the
# reference results instead other specs
uid = analysis.getServiceUID()
specs = analysis.aq_parent.getResultsRangeDict().get(uid, {})
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()
andict['specs'] = specs
scinot = self.context.bika_setup.getScientificNotationReport()
andict['formatted_result'] = analysis.getFormattedResult(
specs=specs, sciformat=int(scinot), decimalmark=decimalmark)
fs = ''
if specs.get('min', None) and specs.get('max', None):
fs = '%s - %s' % (specs['min'], specs['max'])
elif specs.get('min', None):
fs = '> %s' % specs['min']
elif specs.get('max', None):
fs = '< %s' % specs['max']
andict['formatted_specs'] = formatDecimalMark(fs, decimalmark)
andict['formatted_uncertainty'] = format_uncertainty(
analysis,
analysis.getResult(),
decimalmark=decimalmark,
sciformat=int(scinot))
# Out of range?
if specs:
adapters = getAdapters((analysis, ), IResultOutOfRange)
bsc = getToolByName(self.context, "bika_setup_catalog")
for name, adapter in adapters:
ret = adapter(specification=specs)
if ret and ret['out_of_range']:
andict['outofrange'] = True
break
return andict
def get_formatted_unit(self, analysis):
"""Return formatted Unit
"""
return format_supsub(to_utf8(analysis.Unit))
def _analysis_data(self, analysis):
""" Returns a dict that represents the analysis
"""
decimalmark = analysis.aq_parent.aq_parent.getDecimalMark()
keyword = analysis.getKeyword()
andict = {
'obj': analysis,
'id': analysis.id,
'title': analysis.Title(),
'keyword': keyword,
'scientific_name': analysis.getScientificName(),
'accredited': analysis.getAccredited(),
'point_of_capture': to_utf8(POINTS_OF_CAPTURE.getValue(analysis.getPointOfCapture())),
'category': to_utf8(analysis.getCategoryTitle()),
'result': analysis.getResult(),
'unit': to_utf8(analysis.getUnit()),
'formatted_unit': format_supsub(to_utf8(analysis.getUnit())),
'capture_date': analysis.getResultCaptureDate(),
'request_id': analysis.aq_parent.getId(),
'formatted_result': '',
'uncertainty': analysis.getUncertainty(),
'formatted_uncertainty': '',
'retested': analysis.getRetested(),
'remarks': to_utf8(analysis.getRemarks()),
'resultdm': to_utf8(analysis.getResultDM()),
'outofrange': False,
'type': analysis.portal_type,
'reftype': analysis.getReferenceType() if hasattr(
analysis, 'getReferenceType') else None,
'worksheet': None,
'specs': {},
'formatted_specs': '',
'review_state': api.get_workflow_status_of(analysis),
}
andict['refsample'] = analysis.getSample().id \
if analysis.portal_type == 'Analysis' \
else '%s - %s' % (analysis.aq_parent.id, analysis.aq_parent.Title())
# Which analysis specs must be used?
# Try first with those defined at AR Publish Specs level
if analysis.portal_type == 'ReferenceAnalysis':
# The analysis is a Control or Blank. We might use the
# reference results instead other specs
uid = analysis.getServiceUID()
specs = analysis.aq_parent.getResultsRangeDict().get(uid, {})
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()
andict['specs'] = specs
scinot = self.context.bika_setup.getScientificNotationReport()
andict['formatted_result'] = analysis.getFormattedResult(specs=specs, sciformat=int(scinot), decimalmark=decimalmark)
fs = ''
if specs.get('min', None) and specs.get('max', None):
fs = '%s - %s' % (specs['min'], specs['max'])
elif specs.get('min', None):
fs = '> %s' % specs['min']
elif specs.get('max', None):
fs = '< %s' % specs['max']
andict['formatted_specs'] = formatDecimalMark(fs, decimalmark)
andict['formatted_uncertainty'] = format_uncertainty(analysis, analysis.getResult(), decimalmark=decimalmark, sciformat=int(scinot))
# Out of range?
if specs:
adapters = getAdapters((analysis, ), IResultOutOfRange)
for name, adapter in adapters:
ret = adapter(specification=specs)
if ret and ret['out_of_range']:
andict['outofrange'] = True
break
return andict
def _analysis_data(self, analysis, decimalmark=None):
if analysis.UID() in self._cache['_analysis_data']:
return self._cache['_analysis_data'][analysis.UID()]
keyword = analysis.getKeyword()
service = analysis.getService()
andict = {'obj': analysis,
'id': analysis.id,
'title': analysis.Title(),
'keyword': keyword,
'scientific_name': service.getScientificName(),
'accredited': service.getAccredited(),
'point_of_capture': to_utf8(POINTS_OF_CAPTURE.getValue(service.getPointOfCapture())),
'category': to_utf8(service.getCategoryTitle()),
'result': analysis.getResult(),
'isnumber': isnumber(analysis.getResult()),
'unit': to_utf8(service.getUnit()),
'formatted_unit': format_supsub(to_utf8(service.getUnit())),
'capture_date': analysis.getResultCaptureDate(),
'request_id': analysis.aq_parent.getId(),
'formatted_result': '',
'uncertainty': analysis.getUncertainty(),
'formatted_uncertainty': '',
'retested': analysis.getRetested(),
'remarks': to_utf8(analysis.getRemarks()),
'resultdm': to_utf8(analysis.getResultDM()),
'outofrange': False,
'type': analysis.portal_type,
'reftype': analysis.getReferenceType() \
if hasattr(analysis, 'getReferenceType')
else None,
'worksheet': None,
'specs': {},
'formatted_specs': ''}
if analysis.portal_type == 'DuplicateAnalysis':
andict['reftype'] = 'd'
ws = analysis.getBackReferences('WorksheetAnalysis')
andict['worksheet'] = ws[0].id if ws and len(ws) > 0 else None
andict['worksheet_url'] = ws[0].absolute_url if ws and len(ws) > 0 else None
andict['refsample'] = analysis.getSample().id \
if analysis.portal_type == 'Analysis' \
else '%s - %s' % (analysis.aq_parent.id, analysis.aq_parent.Title())
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()
andict['specs'] = specs
scinot = self.context.bika_setup.getScientificNotationReport()
fresult = analysis.getFormattedResult(specs=specs, sciformat=int(scinot), decimalmark=decimalmark)
# We don't use here cgi.encode because results fields must be rendered
# using the 'structure' wildcard. The reason is that the result can be
# expressed in sci notation, that may include <sup></sup> html tags.
# Please note the default value for the 'html' parameter from
# getFormattedResult signature is set to True, so the service will
# already take into account LDLs and UDLs symbols '<' and '>' and escape
# them if necessary.
andict['formatted_result'] = fresult;
fs = ''
if specs.get('min', None) and specs.get('max', None):
fs = '%s - %s' % (specs['min'], specs['max'])
elif specs.get('min', None):
fs = '> %s' % specs['min']
elif specs.get('max', None):
fs = '< %s' % specs['max']
andict['formatted_specs'] = formatDecimalMark(fs, decimalmark)
andict['formatted_uncertainty'] = format_uncertainty(analysis, analysis.getResult(), decimalmark=decimalmark, sciformat=int(scinot))
# Out of range?
if specs:
adapters = getAdapters((analysis, ), IResultOutOfRange)
bsc = getToolByName(self.context, "bika_setup_catalog")
for name, adapter in adapters:
ret = adapter(specification=specs)
if ret and ret['out_of_range']:
andict['outofrange'] = True
break
self._cache['_analysis_data'][analysis.UID()] = andict
return andict
def folderitem(self, obj, item, index):
"""Service triggered each time an item is iterated in folderitems.
The use of this service prevents the extra-loops in child objects.
:obj: the instance of the class to be foldered
:item: dict containing the properties of the object to be used by
the template
:index: current index of the item
"""
cat = obj.getCategoryTitle()
cat_order = self.an_cats_order.get(cat)
if self.do_cats:
# category groups entries
item["category"] = cat
if (cat, cat_order) not in self.categories:
self.categories.append((cat, cat_order))
# Category
category = obj.getCategory()
if category:
title = category.Title()
url = category.absolute_url()
item["Category"] = title
item["replace"]["Category"] = get_link(url, value=title)
# Calculation
calculation = obj.getCalculation()
if calculation:
title = calculation.Title()
url = calculation.absolute_url()
item["Calculation"] = title
item["replace"]["Calculation"] = get_link(url, value=title)
# Methods
methods = obj.getMethods()
if methods:
links = map(
lambda m: get_link(
m.absolute_url(), value=m.Title(), css_class="link"),
methods)
item["replace"]["Methods"] = ", ".join(links)
# Max time allowed
maxtime = obj.MaxTimeAllowed
if maxtime:
item["MaxTimeAllowed"] = self.format_maxtime(maxtime)
# Price
item["Price"] = self.format_price(obj.Price)
# Duplicate Variation
dup_variation = obj.DuplicateVariation
if dup_variation:
item["DuplicateVariation"] = self.format_duplication_variation(
dup_variation)
# Unit
unit = obj.getUnit()
item["Unit"] = unit and format_supsub(unit) or ""
# Icons
after_icons = ""
if obj.getAccredited():
after_icons += get_image("accredited.png", title=_("Accredited"))
if obj.getAttachmentOption() == "r":
after_icons += get_image("attach_reqd.png",
title=_("Attachment required"))
if obj.getAttachmentOption() == "n":
after_icons += get_image("attach_no.png",
title=_("Attachment not permitted"))
if after_icons:
item["after"]["Title"] = after_icons
return item
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]['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:
if self.context.portal_type == 'AnalysisRequest':
sample = self.context.getSample()
st_uid = sample.getSampleType().UID()
items[i]['st_uid'] = st_uid
if st_uid not in self.specs:
proxies = bsc(portal_type = 'AnalysisSpec',
getSampleTypeUID = st_uid)
elif self.context.portal_type == "Worksheet":
if obj.portal_type == "DuplicateAnalysis":
sample = obj.getAnalysis().getSample()
elif obj.portal_type == "RejectAnalysis":
sample = obj.getAnalysis().getSample()
else:
sample = obj.aq_parent.getSample()
st_uid = sample.getSampleType().UID()
items[i]['st_uid'] = st_uid
if st_uid not in self.specs:
proxies = bsc(portal_type = 'AnalysisSpec',
getSampleTypeUID = st_uid)
elif self.context.portal_type == 'Sample':
st_uid = self.context.getSampleType().UID()
items[i]['st_uid'] = st_uid
if st_uid not in self.specs:
proxies = bsc(portal_type = 'AnalysisSpec',
getSampleTypeUID = st_uid)
else:
proxies = []
if st_uid not in self.specs:
for spec in (p.getObject() for p in proxies):
if spec.getClientUID() == obj.getClientUID():
client_or_lab = 'client'
elif spec.getClientUID() == self.context.bika_setup.bika_analysisspecs.UID():
client_or_lab = 'lab'
else:
continue
for keyword, results_range in \
spec.getResultsRangeDict().items():
# hidden form field 'specs' keyed by sampletype uid:
# {st_uid: {'lab/client':{keyword:{min,max,error}}}}
if st_uid in self.specs:
if client_or_lab in self.specs[st_uid]:
self.specs[st_uid][client_or_lab][keyword] = results_range
else:
self.specs[st_uid][client_or_lab] = {keyword: results_range}
else:
self.specs[st_uid] = {client_or_lab: {keyword: results_range}}
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)
items[i]['Uncertainty'] = format_uncertainty(obj, result, decimalmark=dmk, sciformat=int(scinot))
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 get_historicresults(patient):
if not patient:
return [], {}
rows = {}
dates = []
# Retrieve the AR IDs for the current patient
query = {
"portal_type": "AnalysisRequest",
"getPatientUID": api.get_uid(patient),
"review_state": ["verified", "published"],
"sort_on": "getDateSampled",
"sort_order": "descending"
}
brains = api.search(query, CATALOG_ANALYSIS_REQUEST_LISTING)
samples = map(api.get_object, brains)
# Retrieve all analyses
analyses = map(lambda samp: samp.objectValues("Analysis"), samples)
analyses = list(itertools.chain.from_iterable(analyses))
# Build the dictionary of rows
for analysis in analyses:
sample = analysis.aq_parent
sample_type = sample.getSampleType()
row = {
"object": sample_type,
"analyses": {},
}
sample_type_uid = api.get_uid(sample_type)
if sample_type_uid in rows:
row = rows.get(sample_type_uid)
anrow = row.get("analyses")
service_uid = analysis.getServiceUID()
asdict = {
"object": analysis,
"title": api.get_title(analysis),
"keyword": to_utf8(analysis.getKeyword()),
}
if service_uid in anrow:
asdict = anrow.get(service_uid)
if not anrow.get("units", None):
asdict.update(
{"units": format_supsub(to_utf8(analysis.getUnit()))})
date = analysis.getResultCaptureDate() or analysis.created()
date_time = DT2dt(to_date(date)).replace(tzinfo=None)
date_time = datetime.strftime(date_time, "%Y-%m-%d %H:%M")
# If more than one analysis of the same type has been
# performed in the same datetime, get only the last one
if date_time not in asdict.keys():
asdict[date_time] = {
"object": analysis,
"result": analysis.getResult(),
"formattedresult": analysis.getFormattedResult()
}
# Get the specs
# Only the specs applied to the last analysis for that
# sample type will be taken into consideration.
# We assume specs from previous analyses are obsolete.
if "specs" not in asdict.keys():
specs = analysis.getResultsRange()
asdict["specs"] = get_formatted_interval(specs, "")
if date_time not in dates:
dates.append(date_time)
anrow[service_uid] = asdict
row['analyses'] = anrow
rows[sample_type_uid] = row
dates.sort(reverse=False)
return dates, rows
