def test_import_ppm(self):
ar = self.add_analysisrequest(
self.client,
dict(Client=self.client.UID(),
Contact=self.contact.UID(),
DateSampled=datetime.now().date().isoformat(),
SampleType=self.sampletype.UID()),
[srv.UID() for srv in self.services])
api.do_transition_for(ar, 'receive')
data = open(fn2, 'rb').read()
import_file = FileUpload(TestFile(cStringIO.StringIO(data), fn2))
request = TestRequest(form=dict(
instrument_results_file_format='xlsx',
submitted=True,
artoapply='received_tobeverified',
results_override='override',
instrument_results_file=import_file,
default_unit='ppm',
instrument=''))
results = importer.Import(self.portal, request)
ag = ar.getAnalyses(full_objects=True, getKeyword='ag107')[0]
al = ar.getAnalyses(full_objects=True, getKeyword='al27')[0]
test_results = eval(results) # noqa
self.assertEqual(ag.getResult(), '1118000.0')
self.assertEqual(al.getResult(), '2228000.0')
def workflow_action_retract_ar(self):
# AR should be retracted
# Can't transition inactive ARs
if not api.is_active(self.context):
message = _('Item is inactive.')
self.context.plone_utils.addPortalMessage(message, 'info')
self.request.response.redirect(self.context.absolute_url())
return
# 1. Copies the AR linking the original one and viceversa
ar = self.context
newar = self.cloneAR(ar)
# 2. The old AR gets a status of 'invalid'
api.do_transition_for(ar, 'retract_ar')
# 3. The new AR copy opens in status 'to be verified'
changeWorkflowState(newar, 'bika_ar_workflow', 'to_be_verified')
# 4. The system immediately alerts the client contacts who ordered
# the results, per email and SMS, that a possible mistake has been
# picked up and is under investigation.
# A much possible information is provided in the email, linking
# to the AR online.
bika_setup = api.get_bika_setup()
if bika_setup.getNotifyOnARRetract():
self.notify_ar_retract(ar, newar)
message = _('${items} invalidated.',
mapping={'items': ar.getRequestID()})
self.context.plone_utils.addPortalMessage(message, 'warning')
self.request.response.redirect(newar.absolute_url())
def workflow_action_retract_ar(self):
# AR should be retracted
# Can't transition inactive ARs
if not api.is_active(self.context):
message = _('Item is inactive.')
self.context.plone_utils.addPortalMessage(message, 'info')
self.request.response.redirect(self.context.absolute_url())
return
# 1. Copies the AR linking the original one and viceversa
ar = self.context
newar = self.cloneAR(ar)
# 2. The old AR gets a status of 'invalid'
api.do_transition_for(ar, 'retract_ar')
# 3. The new AR copy opens in status 'to be verified'
changeWorkflowState(newar, 'bika_ar_workflow', 'to_be_verified')
# 4. The system immediately alerts the client contacts who ordered
# the results, per email and SMS, that a possible mistake has been
# picked up and is under investigation.
# A much possible information is provided in the email, linking
# to the AR online.
bika_setup = api.get_bika_setup()
if bika_setup.getNotifyOnARRetract():
self.notify_ar_retract(ar, newar)
message = _('${items} invalidated.', mapping={'items': ar.getId()})
self.context.plone_utils.addPortalMessage(message, 'warning')
self.request.response.redirect(newar.absolute_url())
def workflow_action_invalidate(self):
# AR should be retracted
# Can't transition inactive ARs
if not api.is_active(self.context):
message = _('Item is inactive.')
self.context.plone_utils.addPortalMessage(message, 'info')
self.request.response.redirect(self.context.absolute_url())
return
# Retract the AR and get the retest
api.do_transition_for(self.context, 'invalidate')
retest = self.context.getRetest()
# 4. The system immediately alerts the client contacts who ordered
# the results, per email and SMS, that a possible mistake has been
# picked up and is under investigation.
# A much possible information is provided in the email, linking
# to the AR online.
bika_setup = api.get_bika_setup()
if bika_setup.getNotifyOnARRetract():
self.notify_ar_retract(self.context, retest)
message = _('${items} invalidated.',
mapping={'items': self.context.getId()})
self.context.plone_utils.addPortalMessage(message, 'warning')
self.request.response.redirect(retest.absolute_url())
def doActionFor(instance, action_id):
actionperformed = False
message = ''
if not skip(instance, action_id, peek=True):
try:
api.do_transition_for(instance, action_id)
actionperformed = True
except api.BikaLIMSError as e:
message = str(e)
logger.warn(message)
return actionperformed, message
def doActionFor(instance, action_id):
actionperformed = False
message = ''
if not skip(instance, action_id, peek=True):
try:
api.do_transition_for(instance, action_id)
actionperformed = True
except api.BikaLIMSError as e:
message = str(e)
logger.warn(message)
return actionperformed, message
def doActionFor(instance, action_id):
actionperformed = False
message = ''
if not skip(instance, action_id, peek=True):
try:
api.do_transition_for(instance, action_id)
actionperformed = True
except ploneapi.exc.InvalidParameterError as e:
message = str(e)
logger.warn("Failed to perform transition {} on {}: {}".format(
action_id, instance, message))
return actionperformed, message
def test_LIMS_2371_SignificantFigures(self):
RESULT_VALUES = {
'-22770264': {1: '-2e07', 2: '-2.3e07', 3: '-2.28e07', 4: '-2.277e07', 5: '-2.277e07', 6: '-2.27703e07', 7: '-2.277026e07'},
'-2277.3': {1: '-2000', 2: '-2300', 3: '-2280', 4: '-2277', 5: '-2277.3', 6: '-2277.30', 7: '-2277.300'},
'-40277': {1: '-40000', 2: '-40000', 3: '-40300', 4: '-40280', 5: '-40277', 6: '-40277.0', 7: '-40277.00'},
'-40277.036': {1: '-40000', 2: '-40000', 3: '-40300', 4: '-40280', 5: '-40277', 6: '-40277.0', 7: '-40277.04'},
'47000.01': {1: '50000', 2: '47000', 3: '47000', 4: '47000', 5: '47000', 6: '47000.0', 7: '47000.01', 8: '47000.010', 9: '47000.0100'},
'132': {1: '100', 2: '130', 3: '132', 4: '132.0', 5: '132.00', 6: '132.000'},
'14700.04': {1: '10000', 2: '15000', 3: '14700', 4: '14700', 5: '14700', 6: '14700.0', 7: '14700.04', 8: '14700.040', 9: '14700.0400'},
'1407.0': {1: '1000', 2: '1400', 3: '1410', 4: '1407', 5: '1407.0', 6: '1407.00', 7: '1407.000'},
'0.147': {1: '0.1', 2: '0.15', 3: '0.147', 4: '0.1470', 5: '0.14700'},
'4308': {1: '4000', 2: '4300', 3: '4310', 4: '4308', 5: '4308.0', 6: '4308.00', 7: '4308.000'},
'470000': {1: '500000', 2: '470000', 3: '470000', 4: '470000', 5: '470000', 6: '470000', 7: '470000.0', 8: '470000.00', 9: '470000.000'},
'0.154': {1: '0.2', 2: '0.15', 3: '0.154', 4: '0.1540', 5: '0.15400', 6: '0.154000'},
'0.166': {1: '0.2', 2: '0.17', 3: '0.166', 4: '0.1660', 5: '0.16600', 6: '0.166000'},
'0.156': {1: '0.2', 2: '0.16', 3: '0.156', 4: '0.1560', 5: '0.15600', 6: '0.156000'},
'47841242': {1: '5e07', 2: '4.8e07', 3: '4.78e07', 4: '4.784e07', 5: '4.7841e07', 6: '4.78412e07', 7: '4.784124e07', 8: '4.7841242e07', 9: '4.7841242e07', 10: '4.7841242e07'},
'2.2e-06': {1: '0.000002', 2: '0.0000022', 3: '0.00000220', 4: '0.000002200'},
'19019.19019': {1: '20000', 2: '19000', 3: '19000', 4: '19020', 5: '19019', 6: '19019.2', 7: '19019.19', 8: '19019.190', 9: '19019.1902', 10: '19019.19019'}
}
service = self.service
service.setExponentialFormatPrecision(7) # just a high value
service.setDisplayRounding("SIGNIFICANT_FIGURES")
service.setLowerDetectionLimit('-999999999') # Test results below 0 too
for value, tests in RESULT_VALUES.items():
# Create the AR with modified analysis service
for sig_figures, expected in tests.items():
service.setSignificantFigures(sig_figures)
ar = create_analysisrequest(
self.client,
{},
{'Client': self.client.UID(),
'Contact': self.client.getContacts()[0].UID(),
'SamplingDate': '2015-01-01',
'SampleType': self.sampletype.UID()},
[service.UID()])
do_transition_for(ar, 'receive')
an = ar.getAnalyses()[0].getObject()
an.setResult(value)
self.assertEqual(an.getFormattedResult(), expected)
def test_retract_an_analysis_request(self):
ar = self.create_ar()
# Check "receive" transition -> sample_received
api.do_transition_for(ar, "receive")
self.assertEquals(
api.get_workflow_status_of(ar, "review_state"),
"sample_received"
)
for analysis in ar.getAnalyses(full_objects=True):
analysis.setResult("12")
# Check "submit" transition -> to_be_verified
api.do_transition_for(analysis, "submit")
self.assertEquals(
api.get_workflow_status_of(analysis, "review_state"),
"to_be_verified"
)
# Check "retract" transition -> retracted
api.do_transition_for(analysis, "retract")
self.assertEquals(api.get_workflow_status_of(
analysis, "review_state"), "retracted")
for analysis in ar.getAnalyses(full_objects=True):
if api.get_workflow_status_of(
analysis, "review_state") == "retracted":
continue
# Check "submit" transition -> to_be_verified
analysis.setResult(12)
api.do_transition_for(analysis, "submit")
self.assertEquals(
api.get_workflow_status_of(analysis, "review_state"),
"to_be_verified")
# Check "retract" transition -> "sample_received"
api.do_transition_for(ar, "retract")
self.assertEquals(
api.get_workflow_status_of(ar, "review_state"),
"sample_received")
def test_import_csv_without_filename_suffix(self):
ar = self.add_analysisrequest(
self.client,
dict(Client=self.client.UID(),
Contact=self.contact.UID(),
DateSampled=datetime.now().date().isoformat(),
SampleType=self.sampletype.UID()),
[srv.UID() for srv in self.services])
api.do_transition_for(ar, 'receive')
data = open(fn, 'r').read()
import_file = FileUpload(TestFile(cStringIO.StringIO(data), fn))
request = TestRequest(
form=dict(submitted=True,
artoapply='received_tobeverified',
results_override='override',
instrument_results_file=import_file,
instrument=api.get_uid(self.instrument)))
results = importer.Import(self.portal, request)
ag = ar.getAnalyses(full_objects=True, getKeyword='Ag107')[0]
al = ar.getAnalyses(full_objects=True, getKeyword='Al27')[0]
test_results = eval(results) # noqa
self.assertEqual(ag.getResult(), '0.111')
self.assertEqual(al.getResult(), '0.222')
def test_import_xlsx(self):
ar1 = self.add_analysisrequest(
self.client,
dict(Client=self.client.UID(),
Contact=self.contact.UID(),
DateSampled=datetime.now().date().isoformat(),
SampleType=self.sampletype.UID()),
[srv.UID() for srv in self.services])
ar2 = self.add_analysisrequest(
self.client,
dict(Client=self.client.UID(),
Contact=self.contact.UID(),
DateSampled=datetime.now().date().isoformat(),
SampleType=self.sampletype.UID()),
[srv.UID() for srv in self.services])
api.do_transition_for(ar1, 'receive')
api.do_transition_for(ar2, 'receive')
data = open(fn, 'rb').read()
import_file = FileUpload(TestFile(cStringIO.StringIO(data), fn))
request = TestRequest(
form=dict(submitted=True,
artoapply='received_tobeverified',
results_override='override',
instrument_results_file=import_file,
worksheet='Concentrations',
instrument=api.get_uid(self.instrument)))
results = importer.Import(self.portal, request)
test_results = eval(results) # noqa
ag1 = ar1.getAnalyses(full_objects=True, getKeyword='Ag107')[0]
al1 = ar1.getAnalyses(full_objects=True, getKeyword='Al27')[0]
ag2 = ar2.getAnalyses(full_objects=True, getKeyword='Ag107')[0]
al2 = ar2.getAnalyses(full_objects=True, getKeyword='Al27')[0]
self.assertEqual(ag1.getResult(), '0.111')
self.assertEqual(al1.getResult(), '0.555')
self.assertEqual(ag2.getResult(), '0.222')
self.assertEqual(al2.getResult(), '0.666')
def calculateTotalResults(self, objid, analysis):
""" If an AR(objid) has an analysis that has a calculation
then check if param analysis is used on the calculations formula.
Here we are dealing with two types of analysis.
1. Calculated Analysis - Results are calculated.
2. Analysis - Results are captured and not calculated
:param objid: AR ID or Worksheet's Reference Sample IDs
:param analysis: Analysis Object
"""
analyses = self._getZODBAnalyses(objid)
# Filter Analyses With Calculation
analyses_with_calculation = filter(lambda an: an.getCalculation(),
analyses)
for analysis_with_calc in analyses_with_calculation:
# Get the calculation to get the formula so that we can check
# if param analysis keyword is used on the calculation formula
calcultion = analysis_with_calc.getCalculation()
formula = calcultion.getMinifiedFormula()
# The analysis that we are currenly on
analysis_keyword = analysis.getKeyword()
if analysis_keyword not in formula:
continue
# If the analysis_keyword is in the formula, it means that this
# analysis is a dependent on that calculated analysis
calc_passed = analysis_with_calc.calculateResult(
override=self._override[1])
if calc_passed:
api.do_transition_for(analysis_with_calc, "submit")
self.log(
"${request_id}: calculated result for "
"'${analysis_keyword}': '${analysis_result}'",
mapping={
"request_id": objid,
"analysis_keyword": analysis_with_calc.getKeyword(),
"analysis_result": str(analysis_with_calc.getResult())
})
def calculateTotalResults(self, objid, analysis):
""" If an AR(objid) has an analysis that has a calculation
then check if param analysis is used on the calculations formula.
Here we are dealing with two types of analysis.
1. Calculated Analysis - Results are calculated.
2. Analysis - Results are captured and not calculated
:param objid: AR ID or Worksheet's Reference Sample IDs
:param analysis: Analysis Object
"""
analyses = self._getZODBAnalyses(objid)
# Filter Analyses With Calculation
analyses_with_calculation = filter(
lambda an: an.getCalculation(),
analyses)
for analysis_with_calc in analyses_with_calculation:
# Get the calculation to get the formula so that we can check
# if param analysis keyword is used on the calculation formula
calcultion = analysis_with_calc.getCalculation()
formula = calcultion.getMinifiedFormula()
# The analysis that we are currenly on
analysis_keyword = analysis.getKeyword()
if analysis_keyword not in formula:
continue
# If the analysis_keyword is in the formula, it means that this
# analysis is a dependent on that calculated analysis
calc_passed = analysis_with_calc.calculateResult(override=self._override[1])
if calc_passed:
api.do_transition_for(analysis_with_calc, "submit")
self.log(
"${request_id}: calculated result for "
"'${analysis_keyword}': '${analysis_result}'",
mapping={"request_id": objid,
"analysis_keyword": analysis_with_calc.getKeyword(),
"analysis_result": str(analysis_with_calc.getResult())}
)
def test_LIMS_2221_DecimalMarkWithSciNotation(self):
# Notations
# '1' => aE+b / aE-b
# '2' => ax10^b / ax10^-b
# '3' => ax10^b / ax10^-b (with superscript)
# '4' => a·10^b / a·10^-b
# '5' => a·10^b / a·10^-b (with superscript)
matrix = [
# as_prec as_exp not mark result formatted result
# ------- ------ --- ---- ------ ----------------
[0, 0, 1, ',', '0', '0'],
[0, 0, 2, ',', '0', '0'],
[0, 0, 3, ',', '0', '0'],
[0, 0, 4, ',', '0', '0'],
[0, 0, 5, ',', '0', '0'],
[2, 5, 1, ',', '0.01', '0,01'],
[2, 5, 2, ',', '0.01', '0,01'],
[2, 5, 3, ',', '0.01', '0,01'],
[2, 5, 4, ',', '0.01', '0,01'],
[2, 5, 5, ',', '0.01', '0,01'],
[2, 1, 1, ',', '0.123', '1,2e-01'],
[2, 1, 2, ',', '0.123', '1,2x10^-1'],
[2, 1, 3, ',', '0.123', '1,2x10<sup>-1</sup>'],
[2, 1, 4, ',', '0.123', '1,2·10^-1'],
[2, 1, 5, ',', '0.123', '1,2·10<sup>-1</sup>'],
[2, 1, 1, ',', '1.234', '1,23'],
[2, 1, 2, ',', '1.234', '1,23'],
[2, 1, 3, ',', '1.234', '1,23'],
[2, 1, 4, ',', '1.234', '1,23'],
[2, 1, 5, ',', '1.234', '1,23'],
[2, 1, 1, ',', '12.345', '1,235e01'],
[2, 1, 2, ',', '12.345', '1,235x10^1'],
[2, 1, 3, ',', '12.345', '1,235x10<sup>1</sup>'],
[2, 1, 4, ',', '12.345', '1,235·10^1'],
[2, 1, 5, ',', '12.345', '1,235·10<sup>1</sup>'],
[4, 3, 1, ',', '-123.45678', '-123,4568'],
[4, 3, 2, ',', '-123.45678', '-123,4568'],
[4, 3, 3, ',', '-123.45678', '-123,4568'],
[4, 3, 4, ',', '-123.45678', '-123,4568'],
[4, 3, 5, ',', '-123.45678', '-123,4568'],
[4, 3, 1, ',', '-1234.5678', '-1,2345678e03'],
[4, 3, 2, ',', '-1234.5678', '-1,2345678x10^3'],
[4, 3, 3, ',', '-1234.5678', '-1,2345678x10<sup>3</sup>'],
[4, 3, 4, ',', '-1234.5678', '-1,2345678·10^3'],
[4, 3, 5, ',', '-1234.5678', '-1,2345678·10<sup>3</sup>'],
]
serv = self.service
serv.setLowerDetectionLimit('-99999') # test results below 0 too
prevm = []
an = None
bs = get_bika_setup()
for m in matrix:
as_prec = m[0]
as_exp = m[1]
notation = m[2]
_dm = m[3]
_result = m[4]
_expected = m[5]
bs.setResultsDecimalMark(_dm)
# Create the AR and set the values to the AS, but only if necessary
if not an or prevm[0] != as_prec or prevm[1] != as_exp:
serv.setPrecision(as_prec)
serv.setExponentialFormatPrecision(as_exp)
self.assertEqual(serv.getPrecision(), as_prec)
self.assertEqual(
serv.Schema().getField('Precision').get(serv), as_prec)
self.assertEqual(serv.getExponentialFormatPrecision(), as_exp)
self.assertEqual(
serv.Schema().getField(
'ExponentialFormatPrecision').get(serv), as_exp)
values = {'Client': self.client.UID(),
'Contact': self.client.getContacts()[0].UID(),
'SamplingDate': '2015-01-01',
'SampleType': self.sampletype.UID()}
ar = create_analysisrequest(self.client, {}, values,
[serv.UID()])
do_transition_for(ar, 'receive')
an = ar.getAnalyses()[0].getObject()
prevm = m
an.setResult(_result)
self.assertEqual(an.getResult(), _result)
self.assertEqual(an.Schema().getField('Result').get(an), _result)
decimalmark = bs.getResultsDecimalMark()
fr = an.getFormattedResult(sciformat=notation,
decimalmark=decimalmark)
self.assertEqual(fr, _expected)
def create_analysisrequest(context,
request,
values,
analyses=None,
partitions=None,
specifications=None,
prices=None):
"""This is meant for general use and should do everything necessary to
create and initialise an AR and any other required auxilliary objects
(Sample, SamplePartition, Analysis...)
:param context:
The container in which the ARs will be created.
:param request:
The current Request object.
:param values:
a dict, where keys are AR|Sample schema field names.
:param analyses:
Analysis services list. If specified, augments the values in
values['Analyses']. May consist of service objects, UIDs, or Keywords.
:param partitions:
A list of dictionaries, if specific partitions are required. If not
specified, AR's sample is created with a single partition.
:param specifications:
These values augment those found in values['Specifications']
:param prices:
Allow different prices to be set for analyses. If not set, prices
are read from the associated analysis service.
"""
# Gather neccesary tools
workflow = getToolByName(context, 'portal_workflow')
bc = getToolByName(context, 'bika_catalog')
# Analyses are analyses services
analyses_services = analyses
analyses = []
# It's necessary to modify these and we don't want to pollute the
# parent's data
values = values.copy()
analyses_services = analyses_services if analyses_services else []
anv = values['Analyses'] if values.get('Analyses', None) else []
analyses_services = anv + analyses_services
if not analyses_services:
raise RuntimeError(
"create_analysisrequest: no analyses services provided")
# Create new sample or locate the existing for secondary AR
if not values.get('Sample', False):
secondary = False
workflow_enabled = context.bika_setup.getSamplingWorkflowEnabled()
sample = create_sample(context, request, values)
else:
secondary = True
sample = get_sample_from_values(context, values)
workflow_enabled = sample.getSamplingWorkflowEnabled()
# Create the Analysis Request
ar = _createObjectByType('AnalysisRequest', context, tmpID())
# Set some required fields manually before processForm is called
ar.setSample(sample)
values['Sample'] = sample
if values.get('DateSampled', False):
#Inject the timezone into a selection by
#datewidget which is timezone naive
#ie. DateSampled is '2017-05-15 01:05'
#but should be '2017/05/15 01:05:00 GMT+2'
#else processForm => reindexObject() sets it to GMT+0 which results in
#an incorrect date record.
tz = DateTime().timezone()
datesampled = DateTime(values['DateSampled'] + ' ' + tz)
values['DateSampled'] = datesampled
ar.processForm(REQUEST=request, values=values)
# Object has been renamed
ar.edit(RequestID=ar.getId())
# Set initial AR state
action = '{0}sampling_workflow'.format('' if workflow_enabled else 'no_')
workflow.doActionFor(ar, action)
# Set analysis request analyses
service_uids = _resolve_items_to_service_uids(analyses_services)
# processForm already has created the analyses, but here we create the
# analyses with specs and prices. This function, even it is called 'set',
# deletes the old analyses, so eventually we obtain the desired analyses.
ar.setAnalyses(service_uids, prices=prices, specs=specifications)
# Gettin the ar objects
analyses = ar.getAnalyses(full_objects=True)
# Continue to set the state of the AR
skip_receive = [
'to_be_sampled', 'sample_due', 'sampled', 'to_be_preserved'
]
if secondary:
# Only 'sample_due' and 'sample_recieved' samples can be selected
# for secondary analyses
doActionFor(ar, 'sampled')
doActionFor(ar, 'sample_due')
sample_state = workflow.getInfoFor(sample, 'review_state')
if sample_state not in skip_receive:
doActionFor(ar, 'receive')
# Set the state of analyses we created.
for analysis in analyses:
revers = analysis.getService().getNumberOfRequiredVerifications()
analysis.setNumberOfRequiredVerifications(revers)
doActionFor(analysis, 'sample_due')
analysis_state = workflow.getInfoFor(analysis, 'review_state')
if analysis_state not in skip_receive:
doActionFor(analysis, 'receive')
if not secondary:
# Create sample partitions
if not partitions:
partitions = values.get('Partitions', [{'services': service_uids}])
for n, partition in enumerate(partitions):
# Calculate partition id
partition['object'] = create_samplepartition(
sample, partition, analyses)
# If Preservation is required for some partitions,
# and the SamplingWorkflow is disabled, we need
# to transition to to_be_preserved manually.
if not workflow_enabled:
to_be_preserved = []
sample_due = []
lowest_state = 'sample_due'
for p in sample.objectValues('SamplePartition'):
if p.getPreservation():
lowest_state = 'to_be_preserved'
to_be_preserved.append(p)
else:
sample_due.append(p)
for p in to_be_preserved:
doActionFor(p, 'to_be_preserved')
for p in sample_due:
doActionFor(p, 'sample_due')
doActionFor(sample, lowest_state)
doActionFor(ar, lowest_state)
# Transition pre-preserved partitions
for p in partitions:
if 'prepreserved' in p and p['prepreserved']:
part = p['object']
state = workflow.getInfoFor(part, 'review_state')
if state == 'to_be_preserved':
workflow.doActionFor(part, 'preserve')
# Once the ar is fully created, check if there are rejection reasons
reject_field = values.get('RejectionReasons', '')
if reject_field and reject_field.get('checkbox', False):
doActionFor(ar, 'reject')
# If the Sampling Workflow field values are valid,
# and the SamplingWorkflow is enabled, we will
# automatically kick off the "sample" transition now
tids = [t['id'] for t in get_transitions_for(ar)]
if 'sample' in tids and ar.getSampler() and ar.getDateSampled():
do_transition_for(ar, 'sample')
# Return the newly created Analysis Request
return ar
def action_add(self):
"""Form action to add a new attachment
Code taken from bika.lims.content.addARAttachment.
"""
form = self.request.form
parent = api.get_parent(self.context)
attachment_file = form.get('AttachmentFile_file', None)
AttachmentType = form.get('AttachmentType', '')
AttachmentKeys = form.get('AttachmentKeys', '')
ReportOption = form.get('ReportOption', 'a')
# nothing to do if the attachment file is missing
if attachment_file is None:
logger.warn("AttachmentView.action_add_attachment: Attachment file is missing")
return
# create attachment
attachment = self.create_attachment(
parent,
attachment_file,
AttachmentType=AttachmentType,
AttachmentKeys=AttachmentKeys,
ReportOption=ReportOption)
# append the new UID to the end of the current order
self.set_attachments_order(api.get_uid(attachment))
# handle analysis attachment
analysis_uid = form.get("Analysis", None)
if analysis_uid:
rc = api.get_tool("reference_catalog")
analysis = rc.lookupObject(analysis_uid)
others = analysis.getAttachment()
attachments = []
for other in others:
attachments.append(other.UID())
attachments.append(attachment.UID())
analysis.setAttachment(attachments)
# The metadata for getAttachmentUIDs need to get updated,
# otherwise the attachments are not displayed
# https://github.com/senaite/bika.lims/issues/521
analysis.reindexObject()
if api.get_workflow_status_of(analysis) == 'attachment_due':
api.do_transition_for(analysis, 'attach')
else:
others = self.context.getAttachment()
attachments = []
for other in others:
attachments.append(other.UID())
attachments.append(attachment.UID())
self.context.setAttachment(attachments)
if self.request['HTTP_REFERER'].endswith('manage_results'):
self.request.response.redirect('{}/manage_results'.format(
self.context.absolute_url()))
else:
self.request.response.redirect(self.context.absolute_url())
def do_transition_for(brain_or_object, transition):
"""Proxy to bika.lims.api.do_transition_for
"""
return api.do_transition_for(brain_or_object, transition)
def do_transition_for(brain_or_object, transition):
"""Proxy to senaite.api.do_transition_for
"""
return api.do_transition_for(brain_or_object, transition)
def do_transition_for(brain_or_object, transition):
"""Proxy to bika.lims.api.do_transition_for
"""
return api.do_transition_for(brain_or_object, transition)
def action_add(self):
"""Form action to add a new attachment
Code taken from bika.lims.content.addARAttachment.
"""
form = self.request.form
parent = api.get_parent(self.context)
this_file = form.get('AttachmentFile_file', None)
# nothing to do if the attachment file is missing
if this_file is None:
logger.warn(
"AttachmentView.action_add_attachment: Attachment file is missing"
)
return
# create attachment
attachmentid = self.context.generateUniqueId('Attachment')
attachment = api.create(parent, "Attachment", id=attachmentid)
# update the attachment with the values from the form
attachment.edit(
AttachmentFile=this_file,
AttachmentType=form.get('AttachmentType', ''),
AttachmentKeys=form.get('AttachmentKeys', ''),
ReportOption=form.get('ReportOption', 'a'),
)
# process and reindex
attachment.processForm()
attachment.reindexObject()
# append the new UID to the end of the current order
self.set_attachments_order(api.get_uid(attachment))
# handle analysis attachment
analysis_uid = form.get("Analysis", None)
if analysis_uid:
rc = api.get_tool("reference_catalog")
analysis = rc.lookupObject(analysis_uid)
others = analysis.getAttachment()
attachments = []
for other in others:
attachments.append(other.UID())
attachments.append(attachment.UID())
analysis.setAttachment(attachments)
if api.get_workflow_status_of(analysis) == 'attachment_due':
api.do_transition_for(analysis, 'attach')
else:
others = self.context.getAttachment()
attachments = []
for other in others:
attachments.append(other.UID())
attachments.append(attachment.UID())
self.context.setAttachment(attachments)
if self.request['HTTP_REFERER'].endswith('manage_results'):
self.request.response.redirect('{}/manage_results'.format(
self.context.absolute_url()))
else:
self.request.response.redirect(self.context.absolute_url())
def workflow_script_import(self):
"""Create objects from valid ARImport
"""
def convert_date_string(datestr):
return datestr.replace('-', '/')
def lookup_sampler_uid(import_user):
#Lookup sampler's uid
found = False
userid = None
user_ids = []
users = getUsers(self, ['LabManager', 'Sampler']).items()
for (samplerid, samplername) in users:
if import_user == samplerid:
found = True
userid = samplerid
break
if import_user == samplername:
user_ids.append(samplerid)
if found:
return userid
if len(user_ids) == 1:
return user_ids[0]
if len(user_ids) > 1:
#raise ValueError('Sampler %s is ambiguous' % import_user)
return ''
#Otherwise
#raise ValueError('Sampler %s not found' % import_user)
return ''
bsc = getToolByName(self, 'bika_setup_catalog')
workflow = getToolByName(self, 'portal_workflow')
client = self.aq_parent
title = _('Submitting AR Import')
description = _('Creating and initialising objects')
bar = ProgressBar(self, self.REQUEST, title, description)
notify(InitialiseProgressBar(bar))
profiles = [x.getObject() for x in bsc(portal_type='AnalysisProfile')]
gridrows = self.schema['SampleData'].get(self)
row_cnt = 0
for therow in gridrows:
row = therow.copy()
row_cnt += 1
# Create Sample
sample = _createObjectByType('Sample', client, tmpID())
sample.unmarkCreationFlag()
# First convert all row values into something the field can take
sample.edit(**row)
sample._renameAfterCreation()
event.notify(ObjectInitializedEvent(sample))
sample.at_post_create_script()
swe = self.bika_setup.getSamplingWorkflowEnabled()
if swe:
workflow.doActionFor(sample, 'sampling_workflow')
else:
workflow.doActionFor(sample, 'no_sampling_workflow')
part = _createObjectByType('SamplePartition', sample, 'part-1')
part.unmarkCreationFlag()
renameAfterCreation(part)
if swe:
workflow.doActionFor(part, 'sampling_workflow')
else:
workflow.doActionFor(part, 'no_sampling_workflow')
container = self.get_row_container(row)
if container:
part.edit(Container=container)
# Profiles are titles, profile keys, or UIDS: convert them to UIDs.
newprofiles = []
for title in row['Profiles']:
objects = [
x for x in profiles
if title in (x.getProfileKey(), x.UID(), x.Title())
]
for obj in objects:
newprofiles.append(obj.UID())
row['Profiles'] = newprofiles
# BBB in bika.lims < 3.1.9, only one profile is permitted
# on an AR. The services are all added, but only first selected
# profile name is stored.
row['Profile'] = newprofiles[0] if newprofiles else None
# Same for analyses
newanalyses = set(
self.get_row_services(row) +
self.get_row_profile_services(row))
row['Analyses'] = []
# get batch
batch = self.schema['Batch'].get(self)
if batch:
row['Batch'] = batch
# Add AR fields from schema into this row's data
row['ClientReference'] = self.getClientReference()
row['ClientOrderNumber'] = self.getClientOrderNumber()
row['Contact'] = self.getContact()
row['DateSampled'] = convert_date_string(row['DateSampled'])
if row['Sampler']:
row['Sampler'] = lookup_sampler_uid(row['Sampler'])
# Create AR
ar = _createObjectByType("AnalysisRequest", client, tmpID())
ar.setSample(sample)
ar.unmarkCreationFlag()
ar.edit(**row)
ar._renameAfterCreation()
ar.setAnalyses(list(newanalyses))
for analysis in ar.getAnalyses(full_objects=True):
analysis.setSamplePartition(part)
ar.at_post_create_script()
if swe:
workflow.doActionFor(ar, 'sampling_workflow')
else:
workflow.doActionFor(ar, 'no_sampling_workflow')
# If the Sampling Workflow field values are valid,
# and the SamplingWorkflow is enabled, we will
# automatically kick off the "sample" transition now
tids = [t['id'] for t in get_transitions_for(ar)]
if 'sample' in tids and ar.getSampler() and ar.getDateSampled():
do_transition_for(ar, 'sample')
progress_index = float(row_cnt) / len(gridrows) * 100
progress = ProgressState(self.REQUEST, progress_index)
notify(UpdateProgressEvent(progress))
# document has been written to, and redirect() fails here
self.REQUEST.response.write(
'<script>document.location.href="%s"</script>' %
(self.aq_parent.absolute_url()))
