def addReferenceAnalysis(self, service_uid, reference_type):
""" add an analysis to the sample """
rc = getToolByName(self, REFERENCE_CATALOG)
service = rc.lookupObject(service_uid)
analysis = _createObjectByType("ReferenceAnalysis", self, tmpID())
analysis.unmarkCreationFlag()
calculation = service.getCalculation()
interim_fields = calculation and calculation.getInterimFields() or []
renameAfterCreation(analysis)
# maxtime = service.getMaxTimeAllowed() and service.getMaxTimeAllowed() \
# or {'days':0, 'hours':0, 'minutes':0}
# starttime = DateTime()
# max_days = float(maxtime.get('days', 0)) + \
# (
# (float(maxtime.get('hours', 0)) * 3600 + \
# float(maxtime.get('minutes', 0)) * 60)
# / 86400
# )
# duetime = starttime + max_days
analysis.setReferenceType(reference_type)
analysis.setService(service_uid)
analysis.setInterimFields(interim_fields)
return analysis.UID()
def addReferenceAnalysis(self, service_uid, reference_type):
""" add an analysis to the sample """
rc = getToolByName(self, REFERENCE_CATALOG)
service = rc.lookupObject(service_uid)
analysis = _createObjectByType("ReferenceAnalysis", self, tmpID())
analysis.unmarkCreationFlag()
calculation = service.getCalculation()
interim_fields = calculation and calculation.getInterimFields() or []
renameAfterCreation(analysis)
# maxtime = service.getMaxTimeAllowed() and service.getMaxTimeAllowed() \
# or {'days':0, 'hours':0, 'minutes':0}
# starttime = DateTime()
# max_days = float(maxtime.get('days', 0)) + \
# (
# (float(maxtime.get('hours', 0)) * 3600 + \
# float(maxtime.get('minutes', 0)) * 60)
# / 86400
# )
# duetime = starttime + max_days
analysis.setReferenceType(reference_type)
analysis.setService(service_uid)
analysis.setInterimFields(interim_fields)
return analysis.UID()
def create_service(self, src_uid, dst_title, dst_keyword):
folder = self.context.bika_setup.bika_analysisservices
dst_service = _createObjectByType("AnalysisService", folder, tmpID())
# manually set keyword and title
dst_service.setKeyword(dst_keyword)
dst_service.setTitle(dst_title)
dst_service.unmarkCreationFlag()
_id = renameAfterCreation(dst_service)
dst_service = folder[_id]
return dst_service
def create_service(self, src_uid, dst_title, dst_keyword):
folder = self.context.bika_setup.bika_analysisservices
dst_service = _createObjectByType("AnalysisService", folder, tmpID())
# manually set keyword and title
dst_service.setKeyword(dst_keyword)
dst_service.setTitle(dst_title)
dst_service.unmarkCreationFlag()
_id = renameAfterCreation(dst_service)
dst_service = folder[_id]
return dst_service
def test_instrument_calibration(self):
# Getting all instruments
instrument_names = self.portal.bika_setup.bika_instruments.keys()
# Setting calibration dates
for instrument_name in instrument_names:
# Getting each instrument
instrument = self.portal.bika_setup.bika_instruments[
instrument_name]
today = date.today()
# Getting last valid calibration
lastcal = instrument.getLatestValidCalibration()
if not lastcal:
# Creating a new calibration
cal_obj = _createObjectByType("InstrumentCalibration",
instrument, tmpID())
cal_obj.edit(title='test',
DownFrom=today.strftime("%Y/%m/%d"),
DownTo=today.strftime("%Y/%m/%d"),
Instrument=instrument)
cal_obj.unmarkCreationFlag()
renameAfterCreation(cal_obj)
else:
# Updating last calibration
lastcal.setDownTo(today)
lastcal.setDownFrom(today)
# Testing calibration state
for instrument_name in instrument_names:
instrument = self.portal.bika_setup.bika_instruments[
instrument_name]
self.assertTrue(instrument.isCalibrationInProgress())
for instrument_name in instrument_names:
instrument = self.portal.bika_setup.bika_instruments[
instrument_name]
anotherday = '2014/11/27'
lastcal = instrument.getLatestValidCalibration()
lastcal.setDownTo(anotherday)
lastcal.setDownFrom(anotherday)
for instrument_name in instrument_names:
instrument = self.portal.bika_setup.bika_instruments[
instrument_name]
self.assertFalse(instrument.isCalibrationInProgress())
def test_instrument_calibration(self):
# Getting all instruments
instrument_names = self.portal.bika_setup.bika_instruments.keys()
# Setting calibration dates
for instrument_name in instrument_names:
# Getting each instrument
instrument = self.portal.bika_setup.bika_instruments[instrument_name]
today = date.today()
# Getting last valid calibration
lastcal = instrument.getLatestValidCalibration()
if not lastcal:
# Creating a new calibration
cal_obj = _createObjectByType("InstrumentCalibration", instrument, tmpID())
cal_obj.edit(
title='test',
DownFrom=today.strftime("%Y/%m/%d"),
DownTo=today.strftime("%Y/%m/%d"),
Instrument=instrument
)
cal_obj.unmarkCreationFlag()
renameAfterCreation(cal_obj)
else:
# Updating last calibration
lastcal.setDownTo(today)
lastcal.setDownFrom(today)
# Testing calibration state
for instrument_name in instrument_names:
instrument = self.portal.bika_setup.bika_instruments[instrument_name]
self.assertTrue(instrument.isCalibrationInProgress())
for instrument_name in instrument_names:
instrument = self.portal.bika_setup.bika_instruments[instrument_name]
anotherday = '2014/11/27'
lastcal = instrument.getLatestValidCalibration()
lastcal.setDownTo(anotherday)
lastcal.setDownFrom(anotherday)
for instrument_name in instrument_names:
instrument = self.portal.bika_setup.bika_instruments[instrument_name]
self.assertFalse(instrument.isCalibrationInProgress())
def _renameAfterCreation(self, check_auto_id=False):
from lims.idserver import renameAfterCreation
renameAfterCreation(self)
def workflow_script_reject(self):
"""Copy real analyses to RejectAnalysis, with link to real
create a new worksheet, with the original analyses, and new
duplicates and references to match the rejected
worksheet.
"""
if skip(self, "reject"):
return
utils = getToolByName(self, 'plone_utils')
workflow = self.portal_workflow
def copy_src_fields_to_dst(src, dst):
# These will be ignored when copying field values between analyses
ignore_fields = ['UID',
'id',
'title',
'allowDiscussion',
'subject',
'description',
'location',
'contributors',
'creators',
'effectiveDate',
'expirationDate',
'language',
'rights',
'creation_date',
'modification_date',
'Layout', # ws
'Analyses', # ws
]
fields = src.Schema().fields()
for field in fields:
fieldname = field.getName()
if fieldname in ignore_fields:
continue
getter = getattr(src, 'get'+fieldname,
src.Schema().getField(fieldname).getAccessor(src))
setter = getattr(dst, 'set'+fieldname,
dst.Schema().getField(fieldname).getMutator(dst))
if getter is None or setter is None:
# ComputedField
continue
setter(getter())
analysis_positions = {}
for item in self.getLayout():
analysis_positions[item['analysis_uid']] = item['position']
old_layout = []
new_layout = []
# New worksheet
worksheets = self.aq_parent
new_ws = _createObjectByType('Worksheet', worksheets, tmpID())
new_ws.unmarkCreationFlag()
new_ws_id = renameAfterCreation(new_ws)
copy_src_fields_to_dst(self, new_ws)
new_ws.edit(
Number = new_ws_id,
Remarks = self.getRemarks()
)
# Objects are being created inside other contexts, but we want their
# workflow handlers to be aware of which worksheet this is occurring in.
# We save the worksheet in request['context_uid'].
# We reset it again below.... be very sure that this is set to the
# UID of the containing worksheet before invoking any transitions on
# analyses.
self.REQUEST['context_uid'] = new_ws.UID()
# loop all analyses
analyses = self.getAnalyses()
new_ws_analyses = []
old_ws_analyses = []
for analysis in analyses:
# Skip published or verified analyses
review_state = workflow.getInfoFor(analysis, 'review_state', '')
if review_state in ['published', 'verified', 'retracted']:
old_ws_analyses.append(analysis.UID())
old_layout.append({'position': position,
'type':'a',
'analysis_uid':analysis.UID(),
'container_uid':analysis.aq_parent.UID()})
continue
# Normal analyses:
# - Create matching RejectAnalysis inside old WS
# - Link analysis to new WS in same position
# - Copy all field values
# - Clear analysis result, and set Retested flag
if analysis.portal_type == 'Analysis':
reject = _createObjectByType('RejectAnalysis', self, tmpID())
reject.unmarkCreationFlag()
reject_id = renameAfterCreation(reject)
copy_src_fields_to_dst(analysis, reject)
reject.setAnalysis(analysis)
reject.reindexObject()
analysis.edit(
Result = None,
Retested = True,
)
analysis.reindexObject()
position = analysis_positions[analysis.UID()]
old_ws_analyses.append(reject.UID())
old_layout.append({'position': position,
'type':'r',
'analysis_uid':reject.UID(),
'container_uid':self.UID()})
new_ws_analyses.append(analysis.UID())
new_layout.append({'position': position,
'type':'a',
'analysis_uid':analysis.UID(),
'container_uid':analysis.aq_parent.UID()})
# Reference analyses
# - Create a new reference analysis in the new worksheet
# - Transition the original analysis to 'rejected' state
if analysis.portal_type == 'ReferenceAnalysis':
service_uid = analysis.getService().UID()
reference = analysis.aq_parent
reference_type = analysis.getReferenceType()
new_analysis_uid = reference.addReferenceAnalysis(service_uid,
reference_type)
position = analysis_positions[analysis.UID()]
old_ws_analyses.append(analysis.UID())
old_layout.append({'position': position,
'type':reference_type,
'analysis_uid':analysis.UID(),
'container_uid':reference.UID()})
new_ws_analyses.append(new_analysis_uid)
new_layout.append({'position': position,
'type':reference_type,
'analysis_uid':new_analysis_uid,
'container_uid':reference.UID()})
workflow.doActionFor(analysis, 'reject')
new_reference = reference.uid_catalog(UID=new_analysis_uid)[0].getObject()
workflow.doActionFor(new_reference, 'assign')
analysis.reindexObject()
# Duplicate analyses
# - Create a new duplicate inside the new worksheet
# - Transition the original analysis to 'rejected' state
if analysis.portal_type == 'DuplicateAnalysis':
src_analysis = analysis.getAnalysis()
ar = src_analysis.aq_parent
service = src_analysis.getService()
duplicate_id = new_ws.generateUniqueId('DuplicateAnalysis')
new_duplicate = _createObjectByType('DuplicateAnalysis',
new_ws, duplicate_id)
new_duplicate.unmarkCreationFlag()
copy_src_fields_to_dst(analysis, new_duplicate)
workflow.doActionFor(new_duplicate, 'assign')
new_duplicate.reindexObject()
position = analysis_positions[analysis.UID()]
old_ws_analyses.append(analysis.UID())
old_layout.append({'position': position,
'type':'d',
'analysis_uid':analysis.UID(),
'container_uid':self.UID()})
new_ws_analyses.append(new_duplicate.UID())
new_layout.append({'position': position,
'type':'d',
'analysis_uid':new_duplicate.UID(),
'container_uid':new_ws.UID()})
workflow.doActionFor(analysis, 'reject')
analysis.reindexObject()
new_ws.setAnalyses(new_ws_analyses)
new_ws.setLayout(new_layout)
new_ws.replaces_rejected_worksheet = self.UID()
for analysis in new_ws.getAnalyses():
review_state = workflow.getInfoFor(analysis, 'review_state', '')
if review_state == 'to_be_verified':
changeWorkflowState(analysis, "bika_analysis_workflow", "sample_received")
self.REQUEST['context_uid'] = self.UID()
self.setLayout(old_layout)
self.setAnalyses(old_ws_analyses)
self.replaced_by = new_ws.UID()
def _renameAfterCreation(self, check_auto_id=False):
renameAfterCreation(self)
def create(self, context, request):
"""/@@API/create: Create new object.
Required parameters:
- obj_type = portal_type of new object.
- obj_path = path of new object, from plone site root. - Not required for
obj_type=AnalysisRequest
Optionally:
- obj_id = ID of new object.
All other parameters in the request are matched against the object's
Schema. If a matching field is found in the schema, then the value is
taken from the request and sent to the field's mutator.
Reference fields may have their target value(s) specified with a
delimited string query syntax, containing the portal_catalog search:
<FieldName>=index1:value1|index2:value2
eg to set the Client of a batch:
...@@API/update?obj_path=<path>...
...&Client=title:<client_title>&...
And, to set a multi-valued reference, these both work:
...@@API/update?obj_path=<path>...
...&InheritedObjects:list=title:AR1...
...&InheritedObjects:list=title:AR2...
...@@API/update?obj_path=<path>...
...&InheritedObjects[]=title:AR1...
...&InheritedObjects[]=title:AR2...
The Analysis_Specification parameter is special, it mimics
the format of the python dictionaries, and only service Keyword
can be used to reference services. Even if the keyword is not
actively required, it must be supplied:
<service_keyword>:min:max:error tolerance
The function returns a dictionary as a json string:
{
runtime: Function running time.
error: true or string(message) if error. false if no error.
success: true or string(message) if success. false if no success.
}
>>> portal = layer['portal']
>>> portal_url = portal.absolute_url()
>>> from plone.app.testing import SITE_OWNER_NAME
>>> from plone.app.testing import SITE_OWNER_PASSWORD
Simple AR creation, no obj_path parameter is required:
>>> browser = layer['getBrowser'](portal, loggedIn=True, username=SITE_OWNER_NAME, password=SITE_OWNER_PASSWORD)
>>> browser.open(portal_url+"/@@API/create", "&".join([
... "obj_type=AnalysisRequest",
... "Client=portal_type:Client|id:client-1",
... "SampleType=portal_type:SampleType|title:Apple Pulp",
... "Contact=portal_type:Contact|getFullname:Rita Mohale",
... "Services:list=portal_type:AnalysisService|title:Calcium",
... "Services:list=portal_type:AnalysisService|title:Copper",
... "Services:list=portal_type:AnalysisService|title:Magnesium",
... "SamplingDate=2013-09-29",
... "Specification=portal_type:AnalysisSpec|title:Apple Pulp",
... ]))
>>> browser.contents
'{..."success": true...}'
If some parameters are specified and are not located as existing fields or properties
of the created instance, the create should fail:
>>> browser = layer['getBrowser'](portal, loggedIn=True, username=SITE_OWNER_NAME, password=SITE_OWNER_PASSWORD)
>>> browser.open(portal_url+"/@@API/create?", "&".join([
... "obj_type=Batch",
... "obj_path=/batches",
... "title=Test",
... "Thing=Fish"
... ]))
>>> browser.contents
'{...The following request fields were not used: ...Thing...}'
Now we test that the AR create also fails if some fields are spelled wrong
>>> browser = layer['getBrowser'](portal, loggedIn=True, username=SITE_OWNER_NAME, password=SITE_OWNER_PASSWORD)
>>> browser.open(portal_url+"/@@API/create", "&".join([
... "obj_type=AnalysisRequest",
... "thing=Fish",
... "Client=portal_type:Client|id:client-1",
... "SampleType=portal_type:SampleType|title:Apple Pulp",
... "Contact=portal_type:Contact|getFullname:Rita Mohale",
... "Services:list=portal_type:AnalysisService|title:Calcium",
... "Services:list=portal_type:AnalysisService|title:Copper",
... "Services:list=portal_type:AnalysisService|title:Magnesium",
... "SamplingDate=2013-09-29"
... ]))
>>> browser.contents
'{...The following request fields were not used: ...thing...}'
"""
savepoint = transaction.savepoint()
self.context = context
self.request = request
self.unused = [x for x in self.request.form.keys()]
self.used("form.submitted")
self.used("__ac_name")
self.used("__ac_password")
# always require obj_type
self.require("obj_type")
obj_type = self.request['obj_type']
self.used("obj_type")
# AnalysisRequest shortcut: creates Sample, Partition, AR, Analyses.
if obj_type == "AnalysisRequest":
try:
return self._create_ar(context, request)
except:
savepoint.rollback()
raise
# Other object types require explicit path as their parent
self.require("obj_path")
obj_path = self.request['obj_path']
if not obj_path.startswith("/"):
obj_path = "/" + obj_path
self.used("obj_path")
site_path = request['PATH_INFO'].replace("/@@API/create", "")
parent = context.restrictedTraverse(str(site_path + obj_path))
# normal permissions still apply for this user
if not getSecurityManager().checkPermission(AccessJSONAPI, parent):
msg = "You don't have the '{0}' permission on {1}".format(
AccessJSONAPI, parent.absolute_url())
raise Unauthorized(msg)
obj_id = request.get("obj_id", "")
_renameAfterCreation = False
if not obj_id:
_renameAfterCreation = True
obj_id = tmpID()
self.used(obj_id)
ret = {
"url": router.url_for("create", force_external=True),
"success": True,
"error": False,
}
try:
obj = _createObjectByType(obj_type, parent, obj_id)
obj.unmarkCreationFlag()
if _renameAfterCreation:
renameAfterCreation(obj)
ret['obj_id'] = obj.getId()
used_fields = set_fields_from_request(obj, request)
for field in used_fields:
self.used(field)
obj.reindexObject()
obj.aq_parent.reindexObject()
event.notify(ObjectInitializedEvent(obj))
obj.at_post_create_script()
except:
savepoint.rollback()
raise
if self.unused:
raise BadRequest("The following request fields were not used: %s. Request aborted." % self.unused)
return ret
def cloneAR(self, ar):
newar = _createObjectByType("AnalysisRequest", ar.aq_parent, tmpID())
newar.title = ar.title
newar.description = ar.description
newar.setContact(ar.getContact())
newar.setCCContact(ar.getCCContact())
newar.setCCEmails(ar.getCCEmails())
newar.setBatch(ar.getBatch())
newar.setTemplate(ar.getTemplate())
newar.setProfile(ar.getProfile())
newar.setSamplingDate(ar.getSamplingDate())
newar.setSampleType(ar.getSampleType())
newar.setSamplePoint(ar.getSamplePoint())
newar.setStorageLocation(ar.getStorageLocation())
newar.setSamplingDeviation(ar.getSamplingDeviation())
newar.setPriority(ar.getPriority())
newar.setSampleCondition(ar.getSampleCondition())
newar.setSample(ar.getSample())
newar.setClientOrderNumber(ar.getClientOrderNumber())
newar.setClientReference(ar.getClientReference())
newar.setClientSampleID(ar.getClientSampleID())
newar.setDefaultContainerType(ar.getDefaultContainerType())
newar.setAdHoc(ar.getAdHoc())
newar.setComposite(ar.getComposite())
newar.setReportDryMatter(ar.getReportDryMatter())
newar.setInvoiceExclude(ar.getInvoiceExclude())
newar.setAttachment(ar.getAttachment())
newar.setInvoice(ar.getInvoice())
newar.setDateReceived(ar.getDateReceived())
newar.setMemberDiscount(ar.getMemberDiscount())
# Set the results for each AR analysis
ans = ar.getAnalyses(full_objects=True)
for an in ans:
nan = _createObjectByType("Analysis", newar, an.getKeyword())
nan.setService(an.getService())
nan.setCalculation(an.getCalculation())
nan.setInterimFields(an.getInterimFields())
nan.setResult(an.getResult())
nan.setResultDM(an.getResultDM())
nan.setRetested = False,
nan.setMaxTimeAllowed(an.getMaxTimeAllowed())
nan.setDueDate(an.getDueDate())
nan.setDuration(an.getDuration())
nan.setReportDryMatter(an.getReportDryMatter())
nan.setAnalyst(an.getAnalyst())
nan.setInstrument(an.getInstrument())
nan.setSamplePartition(an.getSamplePartition())
nan.unmarkCreationFlag()
notify(ObjectInitializedEvent(nan))
changeWorkflowState(nan, 'bika_analysis_workflow',
'to_be_verified')
nan.reindexObject()
newar.reindexObject()
newar.aq_parent.reindexObject()
renameAfterCreation(newar)
newar.setRequestID(newar.getId())
if hasattr(ar, 'setChildAnalysisRequest'):
ar.setChildAnalysisRequest(newar)
newar.setParentAnalysisRequest(ar)
return newar
def publishFromHTML(self, aruid, results_html):
# The AR can be published only and only if allowed
uc = getToolByName(self.context, 'uid_catalog')
ars = uc(UID=aruid)
if not ars or len(ars) != 1:
return []
ar = ars[0].getObject();
wf = getToolByName(ar, 'portal_workflow')
allowed_states = ['verified', 'published']
# Publish/Republish allowed?
if wf.getInfoFor(ar, 'review_state') not in allowed_states:
# Pre-publish allowed?
if not ar.getAnalyses(review_state=allowed_states):
return []
# HTML written to debug file
# debug_mode = App.config.getConfiguration().debug_mode "Commented by Yasir"
debug_mode = True #" Added by Yasir"
if debug_mode:
tmp_fn = tempfile.mktemp(suffix=".html")
logger.debug("Writing HTML for %s to %s" % (ar.Title(), tmp_fn))
open(tmp_fn, "wb").write(results_html)
# Create the pdf report (will always be attached to the AR)
# we must supply the file ourself so that createPdf leaves it alone.
# This version replaces 'attachment' links; probably not required,
# so it's repeated below, without these localise_images.
# cleanup, results_html_for_pdf = self.localise_images(results_html)
# pdf_fn = tempfile.mktemp(suffix=".pdf")
# pdf_report = createPdf(htmlreport=results_html_for_pdf, outfile=pdf_fn)
# for fn in cleanup:
# os.remove(fn)
# Create the pdf report (will always be attached to the AR)
# we must supply the file ourself so that createPdf leaves it alone.
pdf_fn = tempfile.mktemp(suffix=".pdf")
pdf_report = createPdf(htmlreport=results_html, outfile=pdf_fn)
# PDF written to debug file
if debug_mode:
logger.debug("Writing PDF for %s to %s" % (ar.Title(), pdf_fn))
else:
os.remove(pdf_fn)
recipients = []
contact = ar.getContact()
lab = ar.bika_setup.laboratory
if pdf_report:
if contact:
recipients = [{
'UID': contact.UID(),
'Username': to_utf8(contact.getUsername()),
'Fullname': to_utf8(contact.getFullname()),
'EmailAddress': to_utf8(contact.getEmailAddress()),
'PublicationModes': contact.getPublicationPreference()
}]
reportid = ar.generateUniqueId('ARReport')
report = _createObjectByType("ARReport", ar, reportid)
report.edit(
AnalysisRequest=ar.UID(),
Pdf=pdf_report,
Html=results_html,
Recipients=recipients
)
report.unmarkCreationFlag()
renameAfterCreation(report)
# Set status to prepublished/published/republished
status = wf.getInfoFor(ar, 'review_state')
transitions = {'verified': 'publish',
'published' : 'republish'}
transition = transitions.get(status, 'prepublish')
try:
wf.doActionFor(ar, transition)
except WorkflowException:
pass
# compose and send email.
# The managers of the departments for which the current AR has
# at least one AS must receive always the pdf report by email.
# https://github.com/bikalabs/Bika-LIMS/issues/1028
mime_msg = MIMEMultipart('related')
mime_msg['Subject'] = self.get_mail_subject(ar)[0]
mime_msg['From'] = formataddr(
(encode_header(lab.getName()), lab.getEmailAddress()))
mime_msg.preamble = 'This is a multi-part MIME message.'
msg_txt = MIMEText(results_html, _subtype='html')
mime_msg.attach(msg_txt)
to = []
mngrs = ar.getResponsible()
for mngrid in mngrs['ids']:
name = mngrs['dict'][mngrid].get('name', '')
email = mngrs['dict'][mngrid].get('email', '')
if (email != ''):
to.append(formataddr((encode_header(name), email)))
if len(to) > 0:
# Send the email to the managers
mime_msg['To'] = ','.join(to)
attachPdf(mime_msg, pdf_report, pdf_fn)
try:
host = getToolByName(ar, 'MailHost')
host.send(mime_msg.as_string(), immediate=True)
except SMTPServerDisconnected as msg:
logger.warn("SMTPServerDisconnected: %s." % msg)
except SMTPRecipientsRefused as msg:
raise WorkflowException(str(msg))
# Send report to recipients
recips = self.get_recipients(ar)
for recip in recips:
if 'email' not in recip.get('pubpref', []) \
or not recip.get('email', ''):
continue
title = encode_header(recip.get('title', ''))
email = recip.get('email')
formatted = formataddr((title, email))
# Create the new mime_msg object, cause the previous one
# has the pdf already attached
mime_msg = MIMEMultipart('related')
mime_msg['Subject'] = self.get_mail_subject(ar)[0]
mime_msg['From'] = formataddr(
(encode_header(lab.getName()), lab.getEmailAddress()))
mime_msg.preamble = 'This is a multi-part MIME message.'
msg_txt = MIMEText(results_html, _subtype='html')
mime_msg.attach(msg_txt)
mime_msg['To'] = formatted
# Attach the pdf to the email if requested
if pdf_report and 'pdf' in recip.get('pubpref'):
attachPdf(mime_msg, pdf_report, pdf_fn)
# For now, I will simply ignore mail send under test.
if hasattr(self.portal, 'robotframework'):
continue
msg_string = mime_msg.as_string()
# content of outgoing email written to debug file
if debug_mode:
tmp_fn = tempfile.mktemp(suffix=".email")
logger.debug("Writing MIME message for %s to %s" % (ar.Title(), tmp_fn))
open(tmp_fn, "wb").write(msg_string)
try:
host = getToolByName(ar, 'MailHost')
host.send(msg_string, immediate=True)
except SMTPServerDisconnected as msg:
logger.warn("SMTPServerDisconnected: %s." % msg)
except SMTPRecipientsRefused as msg:
raise WorkflowException(str(msg))
ar.setDatePublished(DateTime())
return [ar]
def cloneAR(self, ar):
newar = _createObjectByType("AnalysisRequest", ar.aq_parent, tmpID())
newar.title = ar.title
newar.description = ar.description
newar.setContact(ar.getContact())
newar.setCCContact(ar.getCCContact())
newar.setCCEmails(ar.getCCEmails())
newar.setBatch(ar.getBatch())
newar.setTemplate(ar.getTemplate())
newar.setProfile(ar.getProfile())
newar.setSamplingDate(ar.getSamplingDate())
newar.setSampleType(ar.getSampleType())
newar.setSamplePoint(ar.getSamplePoint())
newar.setStorageLocation(ar.getStorageLocation())
newar.setSamplingDeviation(ar.getSamplingDeviation())
newar.setPriority(ar.getPriority())
newar.setSampleCondition(ar.getSampleCondition())
newar.setSample(ar.getSample())
newar.setClientOrderNumber(ar.getClientOrderNumber())
newar.setClientReference(ar.getClientReference())
newar.setClientSampleID(ar.getClientSampleID())
newar.setDefaultContainerType(ar.getDefaultContainerType())
newar.setAdHoc(ar.getAdHoc())
newar.setComposite(ar.getComposite())
newar.setReportDryMatter(ar.getReportDryMatter())
newar.setInvoiceExclude(ar.getInvoiceExclude())
newar.setAttachment(ar.getAttachment())
newar.setInvoice(ar.getInvoice())
newar.setDateReceived(ar.getDateReceived())
newar.setMemberDiscount(ar.getMemberDiscount())
# Set the results for each AR analysis
ans = ar.getAnalyses(full_objects=True)
for an in ans:
nan = _createObjectByType("Analysis", newar, an.getKeyword())
nan.setService(an.getService())
nan.setCalculation(an.getCalculation())
nan.setInterimFields(an.getInterimFields())
nan.setResult(an.getResult())
nan.setResultDM(an.getResultDM())
nan.setRetested = False,
nan.setMaxTimeAllowed(an.getMaxTimeAllowed())
nan.setDueDate(an.getDueDate())
nan.setDuration(an.getDuration())
nan.setReportDryMatter(an.getReportDryMatter())
nan.setAnalyst(an.getAnalyst())
nan.setInstrument(an.getInstrument())
nan.setSamplePartition(an.getSamplePartition())
nan.unmarkCreationFlag()
notify(ObjectInitializedEvent(nan))
changeWorkflowState(nan, 'bika_analysis_workflow',
'to_be_verified')
nan.reindexObject()
newar.reindexObject()
newar.aq_parent.reindexObject()
renameAfterCreation(newar)
newar.setRequestID(newar.getId())
if hasattr(ar, 'setChildAnalysisRequest'):
ar.setChildAnalysisRequest(newar)
newar.setParentAnalysisRequest(ar)
return newar
def process(self):
self._parser.parse()
parsed = self._parser.resume()
self._errors = self._parser.errors
self._warns = self._parser.warns
self._logs = self._parser.logs
self._priorizedsearchcriteria = ''
if parsed == False:
return False
# Allowed analysis states
allowed_ar_states_msg = [t(_(s)) for s in self.getAllowedARStates()]
allowed_an_states_msg = [t(_(s)) for s in self.getAllowedAnalysisStates()]
self.log("Allowed Analysis Request states: ${allowed_states}",
mapping={'allowed_states': ', '.join(allowed_ar_states_msg)})
self.log("Allowed analysis states: ${allowed_states}",
mapping={'allowed_states': ', '.join(allowed_an_states_msg)})
# Exclude non existing ACODEs
acodes = []
ancount = 0
arprocessed = []
instprocessed = []
importedars = {}
importedinsts = {}
rawacodes = self._parser.getAnalysisKeywords()
exclude = self.getKeywordsToBeExcluded()
for acode in rawacodes:
if acode in exclude:
continue
service = self.bsc(getKeyword=acode)
if not service:
self.warn('Service keyword ${analysis_keyword} not found',
mapping={"analysis_keyword": acode})
else:
acodes.append(acode)
if len(acodes) == 0:
self.err("Service keywords: no matches found")
searchcriteria = self.getIdSearchCriteria();
#self.log(_("Search criterias: %s") % (', '.join(searchcriteria)))
for objid, results in self._parser.getRawResults().iteritems():
# Allowed more than one result for the same sample and analysis.
# Needed for calibration tests
for result in results:
analyses = self._getZODBAnalyses(objid)
inst = None
if len(analyses) == 0 and self.instrument_uid:
# No registered analyses found, but maybe we need to
# create them first if an instruemnt id has been set in
insts = self.bsc(portal_type='Instrument', UID=self.instrument_uid)
if len(insts) == 0:
# No instrument found
self.err("No Analysis Request with '${allowed_ar_states}' "
"states found, And no QC analyses found for ${object_id}",
mapping={"allowed_ar_states": ', '.join(allowed_ar_states_msg),
"object_id": objid})
self.err("Instrument not found")
continue
inst = insts[0].getObject()
# Create a new ReferenceAnalysis and link it to the Instrument
# Here we have an objid (i.e. R01200012) and
# a dict with results (the key is the AS keyword).
# How can we create a ReferenceAnalysis if we don't know
# which ReferenceSample we might use?
# Ok. The objid HAS to be the ReferenceSample code.
refsample = self.bc(portal_type='ReferenceSample', id=objid)
if refsample and len(refsample) == 1:
refsample = refsample[0].getObject()
elif refsample and len(refsample) > 1:
# More than one reference sample found!
self.err(
"More than one reference sample found for '${object_id}'",
mapping={"object_id": objid})
continue
else:
# No reference sample found!
self.err("No Reference Sample found for ${object_id}",
mapping={"object_id": objid})
continue
# For each acode, create a ReferenceAnalysis and attach it
# to the Reference Sample
service_uids = []
reference_type = 'b' if refsample.getBlank() == True else 'c'
services = self.bsc(portal_type='AnalysisService')
service_uids = [service.UID for service in services \
if service.getObject().getKeyword() in result.keys()]
analyses = inst.addReferences(refsample, service_uids)
elif len(analyses) == 0:
# No analyses found
self.err("No Analysis Request with '${allowed_ar_states}' "
"states neither QC analyses found for ${object_id}",
mapping={
"allowed_ar_states":', '.join(allowed_ar_states_msg),
"object_id": objid})
continue
# Look for timestamp
capturedate = result.get('DateTime',{}).get('DateTime',None)
if capturedate:
del result['DateTime']
for acode, values in result.iteritems():
if acode not in acodes:
# Analysis keyword doesn't exist
continue
ans = [analysis for analysis in analyses \
if analysis.getKeyword() == acode]
if len(ans) > 1:
self.err("More than one analyses found for ${object_id} and ${analysis_keyword)",
mapping={"object_id": objid,
"analysis_keyword": acode})
continue
elif len(ans) == 0:
self.err("No analyses found for ${object_id} and ${analysis_keyword)",
mapping={"object_id": objid,
"analysis_keyword": acode})
continue
analysis = ans[0]
if capturedate:
values['DateTime'] = capturedate
processed = self._process_analysis(objid, analysis, values)
if processed:
ancount += 1
if inst:
# Calibration Test (import to Instrument)
instprocessed.append(inst.UID())
importedinst = inst.title in importedinsts.keys() \
and importedinsts[inst.title] or []
if acode not in importedinst:
importedinst.append(acode)
importedinsts[inst.title] = importedinst
else:
ar = analysis.portal_type == 'Analysis' and analysis.aq_parent or None
if ar and ar.UID:
# Set AR imported info
arprocessed.append(ar.UID())
importedar = ar.getRequestID() in importedars.keys() \
and importedars[ar.getRequestID()] or []
if acode not in importedar:
importedar.append(acode)
importedars[ar.getRequestID()] = importedar
# Create the AttachmentType for mime type if not exists
attuid = None
attachmentType = self.bsc(portal_type="AttachmentType",
title=self._parser.getAttachmentFileType())
if len(attachmentType) == 0:
try:
folder = self.context.bika_setup.bika_attachmenttypes
obj = _createObjectByType("AttachmentType", folder, tmpID())
obj.edit(title=self._parser.getAttachmentFileType(),
description="Autogenerated file type")
obj.unmarkCreationFlag()
renameAfterCreation(obj)
attuid = obj.UID()
except:
attuid = None
self.err(
"Unable to create the Attachment Type ${mime_type}",
mapping={
"mime_type": self._parser.getFileMimeType()})
else:
attuid = attachmentType[0].UID
if attuid is not None:
try:
# Attach the file to the Analysis
wss = analysis.getBackReferences('WorksheetAnalysis')
if wss and len(wss) > 0:
#TODO: Mirar si es pot evitar utilitzar el WS i utilitzar directament l'Anàlisi (útil en cas de CalibrationTest)
ws = wss[0]
attachment = _createObjectByType("Attachment", ws, tmpID())
attachment.edit(
AttachmentFile=self._parser.getInputFile(),
AttachmentType=attuid,
AttachmentKeys='Results, Automatic import')
attachment.reindexObject()
others = analysis.getAttachment()
attachments = []
for other in others:
if other.getAttachmentFile().filename != attachment.getAttachmentFile().filename:
attachments.append(other.UID())
attachments.append(attachment.UID())
analysis.setAttachment(attachments)
except:
# self.err(_("Unable to attach results file '${file_name}' to AR ${request_id}",
# mapping={"file_name": self._parser.getInputFile().filename,
# "request_id": ar.getRequestID()}))
pass
# Calculate analysis dependencies
for aruid in arprocessed:
ar = self.bc(portal_type='AnalysisRequest',
UID=aruid)
ar = ar[0].getObject()
analyses = ar.getAnalyses()
for analysis in analyses:
analysis = analysis.getObject()
if analysis.calculateResult(True, True):
self.log(
"${request_id} calculated result for '${analysis_keyword}': '${analysis_result}'",
mapping={"request_id": ar.getRequestID(),
"analysis_keyword": analysis.getKeyword(),
"analysis_result": str(analysis.getResult())}
)
# Not sure if there's any reason why ReferenceAnalyses have not
# defined the method calculateResult...
# Needs investigation.
#for instuid in instprocessed:
# inst = self.bsc(portal_type='Instrument',UID=instuid)[0].getObject()
# analyses = inst.getAnalyses()
# for analysis in analyses:
# if (analysis.calculateResult(True, True)):
# self.log(_("%s calculated result for '%s': '%s'") %
# (inst.title, analysis.getKeyword(), str(analysis.getResult())))
for arid, acodes in importedars.iteritems():
acodesmsg = ["Analysis %s" % acod for acod in acodes]
self.log("${request_id}: ${analysis_keywords} imported sucessfully",
mapping={"request_id": arid,
"analysis_keywords": acodesmsg})
for instid, acodes in importedinsts.iteritems():
acodesmsg = ["Analysis %s" % acod for acod in acodes]
msg = "%s: %s %s" % (instid, ", ".join(acodesmsg), "imported sucessfully")
self.log(msg)
if self.instrument_uid:
self.log(
"Import finished successfully: ${nr_updated_ars} ARs, "
"${nr_updated_instruments} Instruments and ${nr_updated_results} "
"results updated",
mapping={"nr_updated_ars": str(len(importedars)),
"nr_updated_instruments": str(len(importedinsts)),
"nr_updated_results": str(ancount)})
else:
self.log(
"Import finished successfully: ${nr_updated_ars} ARs and "
"${nr_updated_results} results updated",
mapping={"nr_updated_ars": str(len(importedars)),
"nr_updated_results": str(ancount)})
def _renameAfterCreation(self, check_auto_id=False):
from lims.idserver import renameAfterCreation
renameAfterCreation(self)
def publishFromHTML(self, aruid, results_html):
# The AR can be published only and only if allowed
uc = getToolByName(self.context, 'uid_catalog')
ars = uc(UID=aruid)
if not ars or len(ars) != 1:
return []
ar = ars[0].getObject()
wf = getToolByName(ar, 'portal_workflow')
allowed_states = ['verified', 'published']
# Publish/Republish allowed?
if wf.getInfoFor(ar, 'review_state') not in allowed_states:
# Pre-publish allowed?
if not ar.getAnalyses(review_state=allowed_states):
return []
# HTML written to debug file
# debug_mode = App.config.getConfiguration().debug_mode "Commented by Yasir"
debug_mode = True #" Added by Yasir"
if debug_mode:
tmp_fn = tempfile.mktemp(suffix=".html")
logger.debug("Writing HTML for %s to %s" % (ar.Title(), tmp_fn))
open(tmp_fn, "wb").write(results_html)
# Create the pdf report (will always be attached to the AR)
# we must supply the file ourself so that createPdf leaves it alone.
# This version replaces 'attachment' links; probably not required,
# so it's repeated below, without these localise_images.
# cleanup, results_html_for_pdf = self.localise_images(results_html)
# pdf_fn = tempfile.mktemp(suffix=".pdf")
# pdf_report = createPdf(htmlreport=results_html_for_pdf, outfile=pdf_fn)
# for fn in cleanup:
# os.remove(fn)
# Create the pdf report (will always be attached to the AR)
# we must supply the file ourself so that createPdf leaves it alone.
pdf_fn = tempfile.mktemp(suffix=".pdf")
pdf_report = createPdf(htmlreport=results_html, outfile=pdf_fn)
# PDF written to debug file
if debug_mode:
logger.debug("Writing PDF for %s to %s" % (ar.Title(), pdf_fn))
else:
os.remove(pdf_fn)
recipients = []
contact = ar.getContact()
lab = ar.bika_setup.laboratory
if pdf_report:
if contact:
recipients = [{
'UID':
contact.UID(),
'Username':
to_utf8(contact.getUsername()),
'Fullname':
to_utf8(contact.getFullname()),
'EmailAddress':
to_utf8(contact.getEmailAddress()),
'PublicationModes':
contact.getPublicationPreference()
}]
reportid = ar.generateUniqueId('ARReport')
report = _createObjectByType("ARReport", ar, reportid)
report.edit(AnalysisRequest=ar.UID(),
Pdf=pdf_report,
Html=results_html,
Recipients=recipients)
report.unmarkCreationFlag()
renameAfterCreation(report)
# Set status to prepublished/published/republished
status = wf.getInfoFor(ar, 'review_state')
transitions = {'verified': 'publish', 'published': 'republish'}
transition = transitions.get(status, 'prepublish')
try:
wf.doActionFor(ar, transition)
except WorkflowException:
pass
# compose and send email.
# The managers of the departments for which the current AR has
# at least one AS must receive always the pdf report by email.
# https://github.com/bikalabs/Bika-LIMS/issues/1028
mime_msg = MIMEMultipart('related')
mime_msg['Subject'] = self.get_mail_subject(ar)[0]
mime_msg['From'] = formataddr(
(encode_header(lab.getName()), lab.getEmailAddress()))
mime_msg.preamble = 'This is a multi-part MIME message.'
msg_txt = MIMEText(results_html, _subtype='html')
mime_msg.attach(msg_txt)
to = []
mngrs = ar.getResponsible()
for mngrid in mngrs['ids']:
name = mngrs['dict'][mngrid].get('name', '')
email = mngrs['dict'][mngrid].get('email', '')
if (email != ''):
to.append(formataddr((encode_header(name), email)))
if len(to) > 0:
# Send the email to the managers
mime_msg['To'] = ','.join(to)
attachPdf(mime_msg, pdf_report, pdf_fn)
try:
host = getToolByName(ar, 'MailHost')
host.send(mime_msg.as_string(), immediate=True)
except SMTPServerDisconnected as msg:
logger.warn("SMTPServerDisconnected: %s." % msg)
except SMTPRecipientsRefused as msg:
raise WorkflowException(str(msg))
# Send report to recipients
recips = self.get_recipients(ar)
for recip in recips:
if 'email' not in recip.get('pubpref', []) \
or not recip.get('email', ''):
continue
title = encode_header(recip.get('title', ''))
email = recip.get('email')
formatted = formataddr((title, email))
# Create the new mime_msg object, cause the previous one
# has the pdf already attached
mime_msg = MIMEMultipart('related')
mime_msg['Subject'] = self.get_mail_subject(ar)[0]
mime_msg['From'] = formataddr(
(encode_header(lab.getName()), lab.getEmailAddress()))
mime_msg.preamble = 'This is a multi-part MIME message.'
msg_txt = MIMEText(results_html, _subtype='html')
mime_msg.attach(msg_txt)
mime_msg['To'] = formatted
# Attach the pdf to the email if requested
if pdf_report and 'pdf' in recip.get('pubpref'):
attachPdf(mime_msg, pdf_report, pdf_fn)
# For now, I will simply ignore mail send under test.
if hasattr(self.portal, 'robotframework'):
continue
msg_string = mime_msg.as_string()
# content of outgoing email written to debug file
if debug_mode:
tmp_fn = tempfile.mktemp(suffix=".email")
logger.debug("Writing MIME message for %s to %s" %
(ar.Title(), tmp_fn))
open(tmp_fn, "wb").write(msg_string)
try:
host = getToolByName(ar, 'MailHost')
host.send(msg_string, immediate=True)
except SMTPServerDisconnected as msg:
logger.warn("SMTPServerDisconnected: %s." % msg)
except SMTPRecipientsRefused as msg:
raise WorkflowException(str(msg))
ar.setDatePublished(DateTime())
return [ar]
def process(self):
self._parser.parse()
parsed = self._parser.resume()
self._errors = self._parser.errors
self._warns = self._parser.warns
self._logs = self._parser.logs
self._priorizedsearchcriteria = ''
if parsed == False:
return False
# Allowed analysis states
allowed_ar_states_msg = [t(_(s)) for s in self.getAllowedARStates()]
allowed_an_states_msg = [
t(_(s)) for s in self.getAllowedAnalysisStates()
]
self.log("Allowed Analysis Request states: ${allowed_states}",
mapping={'allowed_states': ', '.join(allowed_ar_states_msg)})
self.log("Allowed analysis states: ${allowed_states}",
mapping={'allowed_states': ', '.join(allowed_an_states_msg)})
# Exclude non existing ACODEs
acodes = []
ancount = 0
arprocessed = []
instprocessed = []
importedars = {}
importedinsts = {}
rawacodes = self._parser.getAnalysisKeywords()
exclude = self.getKeywordsToBeExcluded()
for acode in rawacodes:
if acode in exclude:
continue
service = self.bsc(getKeyword=acode)
if not service:
self.warn('Service keyword ${analysis_keyword} not found',
mapping={"analysis_keyword": acode})
else:
acodes.append(acode)
if len(acodes) == 0:
self.err("Service keywords: no matches found")
searchcriteria = self.getIdSearchCriteria()
#self.log(_("Search criterias: %s") % (', '.join(searchcriteria)))
for objid, results in self._parser.getRawResults().iteritems():
# Allowed more than one result for the same sample and analysis.
# Needed for calibration tests
for result in results:
analyses = self._getZODBAnalyses(objid)
inst = None
if len(analyses) == 0 and self.instrument_uid:
# No registered analyses found, but maybe we need to
# create them first if an instruemnt id has been set in
insts = self.bsc(portal_type='Instrument',
UID=self.instrument_uid)
if len(insts) == 0:
# No instrument found
self.err(
"No Analysis Request with '${allowed_ar_states}' "
"states found, And no QC analyses found for ${object_id}",
mapping={
"allowed_ar_states":
', '.join(allowed_ar_states_msg),
"object_id":
objid
})
self.err("Instrument not found")
continue
inst = insts[0].getObject()
# Create a new ReferenceAnalysis and link it to the Instrument
# Here we have an objid (i.e. R01200012) and
# a dict with results (the key is the AS keyword).
# How can we create a ReferenceAnalysis if we don't know
# which ReferenceSample we might use?
# Ok. The objid HAS to be the ReferenceSample code.
refsample = self.bc(portal_type='ReferenceSample',
id=objid)
if refsample and len(refsample) == 1:
refsample = refsample[0].getObject()
elif refsample and len(refsample) > 1:
# More than one reference sample found!
self.err(
"More than one reference sample found for '${object_id}'",
mapping={"object_id": objid})
continue
else:
# No reference sample found!
self.err("No Reference Sample found for ${object_id}",
mapping={"object_id": objid})
continue
# For each acode, create a ReferenceAnalysis and attach it
# to the Reference Sample
service_uids = []
reference_type = 'b' if refsample.getBlank(
) == True else 'c'
services = self.bsc(portal_type='AnalysisService')
service_uids = [service.UID for service in services \
if service.getObject().getKeyword() in result.keys()]
analyses = inst.addReferences(refsample, service_uids)
elif len(analyses) == 0:
# No analyses found
self.err(
"No Analysis Request with '${allowed_ar_states}' "
"states neither QC analyses found for ${object_id}",
mapping={
"allowed_ar_states":
', '.join(allowed_ar_states_msg),
"object_id": objid
})
continue
# Look for timestamp
capturedate = result.get('DateTime', {}).get('DateTime', None)
if capturedate:
del result['DateTime']
for acode, values in result.iteritems():
if acode not in acodes:
# Analysis keyword doesn't exist
continue
ans = [analysis for analysis in analyses \
if analysis.getKeyword() == acode]
if len(ans) > 1:
self.err(
"More than one analyses found for ${object_id} and ${analysis_keyword)",
mapping={
"object_id": objid,
"analysis_keyword": acode
})
continue
elif len(ans) == 0:
self.err(
"No analyses found for ${object_id} and ${analysis_keyword)",
mapping={
"object_id": objid,
"analysis_keyword": acode
})
continue
analysis = ans[0]
if capturedate:
values['DateTime'] = capturedate
processed = self._process_analysis(objid, analysis, values)
if processed:
ancount += 1
if inst:
# Calibration Test (import to Instrument)
instprocessed.append(inst.UID())
importedinst = inst.title in importedinsts.keys() \
and importedinsts[inst.title] or []
if acode not in importedinst:
importedinst.append(acode)
importedinsts[inst.title] = importedinst
else:
ar = analysis.portal_type == 'Analysis' and analysis.aq_parent or None
if ar and ar.UID:
# Set AR imported info
arprocessed.append(ar.UID())
importedar = ar.getRequestID() in importedars.keys() \
and importedars[ar.getRequestID()] or []
if acode not in importedar:
importedar.append(acode)
importedars[ar.getRequestID()] = importedar
# Create the AttachmentType for mime type if not exists
attuid = None
attachmentType = self.bsc(
portal_type="AttachmentType",
title=self._parser.getAttachmentFileType())
if len(attachmentType) == 0:
try:
folder = self.context.bika_setup.bika_attachmenttypes
obj = _createObjectByType(
"AttachmentType", folder, tmpID())
obj.edit(
title=self._parser.getAttachmentFileType(),
description="Autogenerated file type")
obj.unmarkCreationFlag()
renameAfterCreation(obj)
attuid = obj.UID()
except:
attuid = None
self.err(
"Unable to create the Attachment Type ${mime_type}",
mapping={
"mime_type":
self._parser.getFileMimeType()
})
else:
attuid = attachmentType[0].UID
if attuid is not None:
try:
# Attach the file to the Analysis
wss = analysis.getBackReferences(
'WorksheetAnalysis')
if wss and len(wss) > 0:
#TODO: Mirar si es pot evitar utilitzar el WS i utilitzar directament l'Anàlisi (útil en cas de CalibrationTest)
ws = wss[0]
attachment = _createObjectByType(
"Attachment", ws, tmpID())
attachment.edit(
AttachmentFile=self._parser.
getInputFile(),
AttachmentType=attuid,
AttachmentKeys=
'Results, Automatic import')
attachment.reindexObject()
others = analysis.getAttachment()
attachments = []
for other in others:
if other.getAttachmentFile(
).filename != attachment.getAttachmentFile(
).filename:
attachments.append(other.UID())
attachments.append(attachment.UID())
analysis.setAttachment(attachments)
except:
# self.err(_("Unable to attach results file '${file_name}' to AR ${request_id}",
# mapping={"file_name": self._parser.getInputFile().filename,
# "request_id": ar.getRequestID()}))
pass
# Calculate analysis dependencies
for aruid in arprocessed:
ar = self.bc(portal_type='AnalysisRequest', UID=aruid)
ar = ar[0].getObject()
analyses = ar.getAnalyses()
for analysis in analyses:
analysis = analysis.getObject()
if analysis.calculateResult(True, True):
self.log(
"${request_id} calculated result for '${analysis_keyword}': '${analysis_result}'",
mapping={
"request_id": ar.getRequestID(),
"analysis_keyword": analysis.getKeyword(),
"analysis_result": str(analysis.getResult())
})
# Not sure if there's any reason why ReferenceAnalyses have not
# defined the method calculateResult...
# Needs investigation.
#for instuid in instprocessed:
# inst = self.bsc(portal_type='Instrument',UID=instuid)[0].getObject()
# analyses = inst.getAnalyses()
# for analysis in analyses:
# if (analysis.calculateResult(True, True)):
# self.log(_("%s calculated result for '%s': '%s'") %
# (inst.title, analysis.getKeyword(), str(analysis.getResult())))
for arid, acodes in importedars.iteritems():
acodesmsg = ["Analysis %s" % acod for acod in acodes]
self.log(
"${request_id}: ${analysis_keywords} imported sucessfully",
mapping={
"request_id": arid,
"analysis_keywords": acodesmsg
})
for instid, acodes in importedinsts.iteritems():
acodesmsg = ["Analysis %s" % acod for acod in acodes]
msg = "%s: %s %s" % (instid, ", ".join(acodesmsg),
"imported sucessfully")
self.log(msg)
if self.instrument_uid:
self.log(
"Import finished successfully: ${nr_updated_ars} ARs, "
"${nr_updated_instruments} Instruments and ${nr_updated_results} "
"results updated",
mapping={
"nr_updated_ars": str(len(importedars)),
"nr_updated_instruments": str(len(importedinsts)),
"nr_updated_results": str(ancount)
})
else:
self.log(
"Import finished successfully: ${nr_updated_ars} ARs and "
"${nr_updated_results} results updated",
mapping={
"nr_updated_ars": str(len(importedars)),
"nr_updated_results": str(ancount)
})
