def get_age(datetime_from, datetime_to=None):
"""Returns the elapsed time in years, months and days between the two
dates passed in."""
if not datetime_to:
datetime_to = DateTime()
if not bapi.is_date(datetime_from) or not bapi.is_date(datetime_to):
bapi.fail("Only DateTime and datetype types are supported")
dfrom = DT2dt(bapi.to_date(datetime_from)).replace(tzinfo=None)
dto = DT2dt(bapi.to_date(datetime_to)).replace(tzinfo=None)
diff = relativedelta(dto, dfrom)
return (diff.years, diff.months, diff.days)
def get_current_age(self, dob):
"""Returns a dict with keys "years", "months", "days"
"""
if not api.is_date(dob):
return {}
delta = patient_api.get_relative_delta(dob)
return {
"years": delta.years,
"months": delta.months,
"days": delta.days,
}
def process_form(self, instance, field, form, empty_marker=None,
emptyReturnsMarker=False, validating=True):
value = form.get(field.getName())
# Not interested in the hidden field, but in the age + dob specific
if isinstance(value, (list, tuple)):
value = value[0] or None
# Allow non-required fields
if not value:
return None, {}
# handle DateTime object when creating partitions
if api.is_date(value):
self.set_age_selected(instance, False)
return value, {}
# Grab the input for DoB first
dob = value.get("dob", "")
dob = patient_api.to_datetime(dob)
age_selected = value.get("selector") == "age"
# remember what was slected
self.set_age_selected(instance, age_selected)
# Maybe user entered age instead of DoB
if age_selected:
# Validate the age entered
ymd = map(lambda p: value.get(p), ["years", "months", "days"])
if not any(ymd):
# No values set
return None
# Age in ymd format
ymd = filter(lambda p: p[0], zip(ymd, 'ymd'))
ymd = "".join(map(lambda p: "".join(p), ymd))
# Calculate the DoB
dob = patient_api.get_birth_date(ymd)
return dob, {}
def addToJSON(self, analysis, service_uid, item):
""" Adds an analysis item to the self.anjson dict that will be used
after the page is rendered to generate a QC Chart
"""
parent = api.get_parent(analysis)
qcid = parent.id
serviceref = "%s (%s)" % (item['Service'], item['Keyword'])
trows = self.anjson.get(serviceref, {})
anrows = trows.get(qcid, [])
rr = parent.getResultsRangeDict()
cap_date = item['obj'].getResultCaptureDate
cap_date = api.is_date(cap_date) and \
cap_date.strftime('%Y-%m-%d %I:%M %p') or ''
if service_uid in rr:
specs = rr.get(service_uid, None)
try:
smin = float(specs.get('min', 0))
smax = float(specs.get('max', 0))
error = float(specs.get('error', 0))
target = float(specs.get('result', 0))
result = float(item['Result'])
error_amount = ((target / 100) * error) if target > 0 else 0
upper = smax + error_amount
lower = smin - error_amount
anrow = {
'date': cap_date,
'min': smin,
'max': smax,
'target': target,
'error': error,
'erroramount': error_amount,
'upper': upper,
'lower': lower,
'result': result,
'unit': item['Unit'],
'id': item['uid']
}
anrows.append(anrow)
trows[qcid] = anrows
self.anjson[serviceref] = trows
except:
pass
def add_analysis(self, analysis):
"""Adds an analysis to be consumed by the Analyses Chart machinery (js)
:param analysis_object: analysis to be rendered in the chart
"""
analysis_object = api.get_object(analysis)
result = analysis_object.getResult()
results_range = analysis_object.getResultsRange()
range_result = results_range.get('result', None)
range_min = results_range.get('min', None)
range_max = results_range.get('max', None)
# All them must be floatable
for value in [result, range_result, range_min, range_max]:
if not api.is_floatable(value):
return
cap_date = analysis_object.getResultCaptureDate()
cap_date = api.is_date(cap_date) and \
cap_date.strftime('%Y-%m-%d %I:%M %p') or ''
if not cap_date:
return
# Create json
ref_sample_id = analysis_object.getSample().getId()
as_keyword = analysis_object.getKeyword()
as_name = analysis_object.Title()
as_ref = '{} ({})'.format(as_name, as_keyword)
as_rows = self.analyses_dict.get(as_ref, {})
an_rows = as_rows.get(ref_sample_id, [])
an_rows.append({
'date': cap_date,
'target': api.to_float(range_result),
'upper': api.to_float(range_max),
'lower': api.to_float(range_min),
'result': api.to_float(result),
'unit': analysis_object.getUnit(),
'id': api.get_uid(analysis_object)
})
as_rows[ref_sample_id] = an_rows
self.analyses_dict[as_ref] = as_rows
def folderitems(self):
items = AnalysesView.folderitems(self)
items.sort(key=itemgetter('CaptureDate'), reverse=True)
for item in items:
obj = item['obj']
# TODO-performance: getting an object
# Note here the object in items[i]['obj'] is a brain, cause the
# base class (AnalysesView), calls folderitems(.., classic=False).
obj = obj.getObject()
imgtype = ""
if obj.portal_type == 'ReferenceAnalysis':
antype = QCANALYSIS_TYPES.getValue(obj.getReferenceType())
if obj.getReferenceType() == 'c':
imgtype = "<img title='%s' src='%s/++resource++bika.lims.images/control.png'/> " % (
antype, self.context.absolute_url())
if obj.getReferenceType() == 'b':
imgtype = "<img title='%s' src='%s/++resource++bika.lims.images/blank.png'/> " % (
antype, self.context.absolute_url())
item['replace']['Partition'] = "<a href='%s'>%s</a>" % (
obj.aq_parent.absolute_url(), obj.aq_parent.id)
elif obj.portal_type == 'DuplicateAnalysis':
antype = QCANALYSIS_TYPES.getValue('d')
imgtype = "<img title='%s' src='%s/++resource++bika.lims.images/duplicate.png'/> " % (
antype, self.context.absolute_url())
item['sortcode'] = '%s_%s' % (obj.getSample().id,
obj.getKeyword())
else:
item['sortcode'] = '%s_%s' % (obj.getSample().id,
obj.getKeyword())
item['before']['Service'] = imgtype
# Get retractions field
pdf = obj.getRetractedAnalysesPdfReport()
title = ''
anchor = ''
try:
if pdf:
filesize = 0
title = _('Retractions')
anchor = "<a class='pdf' target='_blank' href='%s/at_download/RetractedAnalysesPdfReport'>%s</a>" % \
(obj.absolute_url(), _("Retractions"))
filesize = pdf.get_size()
filesize = filesize / 1024 if filesize > 0 else 0
except:
# POSKeyError: 'No blob file'
# Show the record, but not the link
title = _('Retraction report unavailable')
anchor = title
item['Retractions'] = title
item['replace']['Retractions'] = anchor
# Create json
qcid = obj.aq_parent.getId()
serviceref = "%s (%s)" % (item['Service'], item['Keyword'])
trows = self.anjson.get(serviceref, {})
anrows = trows.get(qcid, [])
# anid = '%s.%s' % (item['getReferenceAnalysesGroupID'],
# item['id'])
rr = obj.aq_parent.getResultsRangeDict()
uid = obj.getServiceUID()
if uid in rr:
specs = rr[uid]
try:
smin = float(specs.get('min', 0))
smax = float(specs.get('max', 0))
error = float(specs.get('error', 0))
target = float(specs.get('result', 0))
result = float(item['Result'])
error_amount = ((target / 100) *
error) if target > 0 else 0
upper = smax + error_amount
lower = smin - error_amount
cap_date = obj.getResultCaptureDate()
cap_date = api.is_date(cap_date) and \
cap_date.strftime('%Y-%m-%d %I:%M %p') or ''
anrow = {
'date': cap_date,
'min': smin,
'max': smax,
'target': target,
'error': error,
'erroramount': error_amount,
'upper': upper,
'lower': lower,
'result': result,
'unit': item['Unit'],
'id': item['uid']
}
anrows.append(anrow)
trows[qcid] = anrows
self.anjson[serviceref] = trows
except:
pass
return items