Example #1
0
    def addOrganSpecificInformation(self, biomarkers, statements, normalizer, catalog):
        '''Populate biomarkers with body system (aka "organ") details.'''
        for uri, predicates in statements.items():
            try:
                if predicates[_typeURI][0] != _bmOrganDataTypeURI:
                    continue
                biomarker = biomarkers[predicates[_biomarkerPredicateURI][0]]
            except KeyError:
                continue

            organName = unicode(predicates[_organPredicateURI][0])
            results = catalog(Title=organName, object_provides=IBodySystem.__identifier__)
            if len(results) < 1:
                _logger.warn('Unknown organ %s for biomarker %s', organName, biomarker.title)
                continue
            organObjID = normalizer(organName)
            biomarkerBodySystem = biomarker[biomarker.invokeFactory('Biomarker Body System', organObjID)]
            biomarkerBodySystem.setTitle(results[0].Title)
            biomarkerBodySystem.setBodySystem(results[0].UID)
            updateObject(biomarkerBodySystem, uri, predicates, catalog)
            self.addBiomarkerToOrganGroup(biomarker, organName, catalog)
            if _hasBiomarkerOrganStudyDatasPredicateURI in predicates:
                bags = predicates[_hasBiomarkerOrganStudyDatasPredicateURI]
                self.addStudiesToOrgan(biomarkerBodySystem, bags, statements, normalizer, catalog)
            certificationURIs = predicates.get(_certificationPredicateURI, [])
            # TODO: make a separate Certification type so we don't rely on these fixed values.
            # Although we'll likely never have ohter certifications.
            for certificationURI in certificationURIs:
                if certificationURI == _cliaCertificationURI:
                    biomarkerBodySystem.cliaCertification = True
                elif certificationURI == _fdaCeritificationURI:
                    biomarkerBodySystem.fdaCertification = True
            biomarkerBodySystem.reindexObject()
Example #2
0
 def updateBiomarker(self, obj, uri, predicates, context, statements):
     '''Update a biomarker. Sets various attributes and then adjusts workflow & security.'''
     updateObject(obj, uri, predicates, context)
     if _accessPredicateURI in predicates:
         groupIDs = [unicode(i) for i in predicates[_accessPredicateURI]]
         obj.accessGroups = groupIDs
         settings = [
             dict(type='group', roles=[u'Reader'], id=i) for i in groupIDs
         ]
         sharing = getMultiAdapter((obj, TestRequest()), name=u'sharing')
         sharing.update_role_settings(settings)
     if _hasBiomarkerStudyDatasPredicateURI in predicates:
         catalog = getToolByName(context, 'portal_catalog')
         protocolUIDs, piUIDs = [], []
         bag = statements[predicates[_hasBiomarkerStudyDatasPredicateURI]
                          [0]]
         for subjectURI, objects in bag.iteritems():
             if subjectURI == _typeURI: continue
             # Assume anything else is a list item pointing to BiomarkerStudyData objects
             for bmsd in [statements[i] for i in objects]:
                 # Right now, we use just the "referencesStudy" predicate, if it's present
                 if _referencesStudyPredicateURI not in bmsd: continue
                 results = catalog(identifier=unicode(
                     bmsd[_referencesStudyPredicateURI][0]),
                                   object_provides=IProtocol.__identifier__)
                 protocolUIDs.extend([j.UID for j in results])
                 piUIDs.extend([j.piUID for j in results])
                 for k in [j.getObject() for j in results]:
                     self._addBiomarkerToProtocol(obj, k)
         obj.setProtocols(protocolUIDs)
         obj.setPiUIDs(piUIDs)
Example #3
0
 def updateBiomarker(self, obj, uri, predicates, context, statements):
     '''Update a biomarker. Sets various attributes and then adjusts workflow & security.'''
     updateObject(obj, uri, predicates, context)
     if _accessPredicateURI in predicates:
         groupIDs = [unicode(i) for i in predicates[_accessPredicateURI]]
         obj.accessGroups = groupIDs
         settings = [dict(type='group', roles=[u'Reader'], id=i) for i in groupIDs]
         sharing = getMultiAdapter((obj, TestRequest()), name=u'sharing')
         sharing.update_role_settings(settings)
     if _hasBiomarkerStudyDatasPredicateURI in predicates:
         catalog = getToolByName(context, 'portal_catalog')
         protocolUIDs, piUIDs = [], []
         bag = statements[predicates[_hasBiomarkerStudyDatasPredicateURI][0]]
         for subjectURI, objects in bag.iteritems():
             if subjectURI == _typeURI: continue
             # Assume anything else is a list item pointing to BiomarkerStudyData objects
             for bmsd in [statements[i] for i in objects]:
                 # Right now, we use just the "referencesStudy" predicate, if it's present
                 if _referencesStudyPredicateURI not in bmsd: continue
                 results = catalog(
                     identifier=unicode(bmsd[_referencesStudyPredicateURI][0]),
                     object_provides=IProtocol.__identifier__
                 )
                 protocolUIDs.extend([j.UID for j in results])
                 piUIDs.extend([j.piUID for j in results])
                 for k in [j.getObject() for j in results]:
                     self._addBiomarkerToProtocol(obj, k)
         obj.setProtocols(protocolUIDs)
         obj.setPiUIDs(piUIDs)
Example #4
0
File: rdf.py Project: EDRN/eke.ecas
    def __call__(self):
        """We have to override this because ECAS datasets come in with unpredictable RDF types.
        """
        context = aq_inner(self.context)
        catalog = getToolByName(context, "portal_catalog")
        wfTool = getToolByName(context, "portal_workflow")
        rdfDataSource, dsSumDataSource = context.rdfDataSource, context.dsSumDataSource
        if dsSumDataSource:
            context.dataSummary = self.getSummaryData(dsSumDataSource)

        if not rdfDataSource:
            raise RDFIngestException(_(u"This folder has no RDF data source URL."))

        normalizerFunction = queryUtility(IIDNormalizer).normalize
        graph = ConjunctiveGraph()
        graph.parse(URLInputSource(rdfDataSource))
        statements = self._parseRDF(graph)
        createdObjects = []
        for uri, predicates in statements.items():
            objectID = self._generateID(uri, predicates, normalizerFunction)
            title = self._generateTitle(uri, predicates)
            if objectID in context.objectIds():
                dataset = context[objectID]
            else:
                dataset = context[context.invokeFactory("Dataset", objectID)]
            dataset.setTitle(title)
            updateObject(dataset, uri, predicates, context)
            createdObjects.append(CreatedObject(dataset))
            if _collaborativeGroupURI in predicates:
                self.updateCollaborativeGroup(dataset, unicode(predicates[_collaborativeGroupURI][0]), catalog)
            if _protocolPredicateURI in predicates:
                for proto in [
                    i.getObject() for i in catalog(identifier=[unicode(i) for i in predicates[_protocolPredicateURI]])
                ]:
                    uid = dataset.UID()
                    current = [i.UID() for i in proto.datasets]
                    if uid not in current:
                        current.append(uid)
                        proto.setDatasets(current)
                        proto.datasetNames = proto._computeDatasetNames()
                        proto.reindexObject()
            if _accessPredicateURI in predicates:
                groupIDs = [unicode(i) for i in predicates[_accessPredicateURI]]
                dataset.accessGroups = groupIDs
                settings = [dict(type="group", roles=[u"Reader"], id=i) for i in groupIDs]
                sharing = getMultiAdapter((dataset, TestRequest()), name=u"sharing")
                sharing.update_role_settings(settings)
            if _organPredicateURI in predicates:
                bodySystemName = predicates[_organPredicateURI][0].rsplit("/", 1)[-1]
                organs = self.getBodySysteObj(catalog, bodySystemName)
                if len(organs) > 0:
                    dataset.setBodySystem(organs[0])
            self.publishDataset(wfTool, dataset, predicates)
            dataset.reindexObject()
        self.objects = createdObjects

        return self.render and self.template() or len(self.objects)
Example #5
0
File: rdf.py Project: EDRN/eke.site
 def _ingestPeople(self):
     context = aq_inner(self.context)
     catalog = getToolByName(context, 'portal_catalog')
     normalizerFunction = queryUtility(IIDNormalizer).normalize
     graph = ConjunctiveGraph()
     graph.parse(URLInputSource(context.peopleDataSource))
     statements = self._parseRDF(graph)
     createdPeople = {}
     for uri, predicates in statements.items():
         persons = catalog(identifier=unicode(uri), object_provides=IPerson.__identifier__)
         person_list = [p.id for p in persons]
         employmentStatus = self._getNameComponent(_employmentActiveURI, predicates)
         if _siteURI not in predicates:
             # Person without a site, ignore him or her.
             continue
         siteURIs = [unicode(i) for i in predicates[_siteURI]]
         results = catalog(object_provides=ISite.__identifier__, identifier=siteURIs)
         if len(results) == 0:
             # Person with a site, but it's unknown, so again, ignore him or her.
             continue
         for site in [i.getObject() for i in results]:
             if employmentStatus == "Former employee":
                 # Person who is not an current employee anymore
                 # make sure to delete them if they exist
                 if len(persons) > 0:
                     for pid in person_list:
                         if pid in site.objectIds():
                             site.manage_delObjects(pid)
                 continue
             objectID = self._generatePersonID(predicates, normalizerFunction)
             if objectID in site.objectIds():
                 site.manage_delObjects(objectID)
             person = site[site.invokeFactory('Person', objectID)]
             updateObject(person, uri, predicates, context)
             person.siteName = site.title
             person.setDescription(u'Staff, %s, %s' % (safe_unicode(person.siteName), safe_unicode(person.phone)))
             person.memberType = site.memberType
             degrees = []
             for degreePredicateURI in [URIRef(_degreePredicateURIPrefix + unicode(i)) for i in range(1, 4)]:
                 if degreePredicateURI in predicates:
                     degree = unicode(predicates[degreePredicateURI][0])
                     degree.strip()
                     if degree:
                         degrees.append(degree)
             person.setDegrees(degrees)
             if _photoPredicateURI in predicates:
                 url = predicates[_photoPredicateURI][0]
                 contentType = mimetypes.guess_type(url)[0] or 'image/gif'
                 try:
                     with contextlib.closing(urllib2.urlopen(url)) as con:
                         field = person.schema['image']
                         field.set(person, con.read(), content_type=contentType, mimetype=contentType)
                 except urllib2.HTTPError:
                     pass
             person.reindexObject()
             createdPeople[(site.identifier, uri)] = person
     return createdPeople
Example #6
0
 def addStudiesToOrgan(self, biomarkerBodySystem, bags, statements,
                       normalizer, catalog):
     '''Add protocol/study-specific information to a biomarker body system.'''
     # Gather all the URIs
     bmStudyDataURIs = []
     # The RDF may contain an empty <hasBiomarkerStudyDatas/>, which means that
     # there will be just an empty Literal '' in the bags list (which will be a
     # one item list). In that case, don't bother adding studies.
     if len(bags) == 1 and unicode(bags[0]) == u'':
         return
     for bag in bags:
         preds = statements[bag]
         del preds[_typeURI]
         bmStudyDataURIs.extend(flatten(preds.values()))
     for studyURI in bmStudyDataURIs:
         bmStudyDataPredicates = statements[studyURI]
         if _referencesStudyPredicateURI not in bmStudyDataPredicates:
             continue
         studies = self.findObjectsByIdentifiers(catalog, [
             unicode(i)
             for i in bmStudyDataPredicates[_referencesStudyPredicateURI]
         ])
         if len(studies) < 1:
             _logger.warn(
                 'Study "%s" not found for biomarker body system "%r"',
                 bmStudyDataPredicates[_referencesStudyPredicateURI][0],
                 biomarkerBodySystem.identifier)
             continue
         identifier = str(
             studies[0].identifier.split('/')[-1]) + '-' + normalizer(
                 studies[0].title)
         bodySystemStudy = None
         if identifier not in biomarkerBodySystem.keys():
             bodySystemStudy = biomarkerBodySystem[
                 biomarkerBodySystem.invokeFactory('Body System Study',
                                                   identifier)]
         else:
             bodySystemStudy = biomarkerBodySystem[identifier]
         updateObject(bodySystemStudy, studyURI, bmStudyDataPredicates,
                      catalog)
         bodySystemStudy.title = studies[0].title
         bodySystemStudy.description = studies[0].description
         bodySystemStudy.setProtocol(studies[0].UID())
         self._addBiomarkerToProtocol(
             aq_parent(aq_inner(aq_parent(aq_inner(bodySystemStudy)))),
             studies[0])
         if _sensitivityDatasPredicateURI in bmStudyDataPredicates:
             bags = bmStudyDataPredicates[_sensitivityDatasPredicateURI]
             self.addStatistics(bodySystemStudy, bags, statements,
                                normalizer, catalog)
         bodySystemStudy.reindexObject()
Example #7
0
 def addStatistics(self, bodySystemStudy, bags, statements, normalizer, catalog):
     '''Add study statistics to a body system study.  The bags are
     RDF-style collections of URIRefs to statistics found in the
     statements.'''
     # Gather all the URIs
     sensitivityURIs = []
     for bag in bags:
         preds = statements[bag]
         del preds[_typeURI]
         sensitivityURIs.extend(flatten(preds.values()))
     # For each set of statistics...
     for sensitivityURI in sensitivityURIs:
         predicates = statements[sensitivityURI]
         stats = bodySystemStudy[bodySystemStudy.invokeFactory('Study Statistics', uuid.uuid1())]
         updateObject(stats, sensitivityURI, predicates, catalog)
         stats.title = sensitivityURI
         stats.reindexObject()
Example #8
0
 def addStatistics(self, bodySystemStudy, bags, statements, normalizer,
                   catalog):
     '''Add study statistics to a body system study.  The bags are
     RDF-style collections of URIRefs to statistics found in the
     statements.'''
     # Gather all the URIs
     sensitivityURIs = []
     for bag in bags:
         preds = statements[bag]
         del preds[_typeURI]
         sensitivityURIs.extend(flatten(preds.values()))
     # For each set of statistics...
     for sensitivityURI in sensitivityURIs:
         predicates = statements[sensitivityURI]
         stats = bodySystemStudy[bodySystemStudy.invokeFactory(
             'Study Statistics', uuid.uuid1())]
         updateObject(stats, sensitivityURI, predicates, catalog)
         stats.title = sensitivityURI
         stats.reindexObject()
Example #9
0
 def addStudiesToOrgan(self, biomarkerBodySystem, bags, statements, normalizer, catalog):
     '''Add protocol/study-specific information to a biomarker body system.'''
     # Gather all the URIs
     bmStudyDataURIs = []
     # The RDF may contain an empty <hasBiomarkerStudyDatas/>, which means that
     # there will be just an empty Literal '' in the bags list (which will be a
     # one item list). In that case, don't bother adding studies.
     if len(bags) == 1 and unicode(bags[0]) == u'':
         return
     for bag in bags:
         preds = statements[bag]
         del preds[_typeURI]
         bmStudyDataURIs.extend(flatten(preds.values()))
     for studyURI in bmStudyDataURIs:
         bmStudyDataPredicates = statements[studyURI]
         if _referencesStudyPredicateURI not in bmStudyDataPredicates:
             continue
         studies = self.findObjectsByIdentifiers(catalog,
             [unicode(i) for i in bmStudyDataPredicates[_referencesStudyPredicateURI]])
         if len(studies) < 1:
             _logger.warn('Study "%s" not found for biomarker body system "%r"',
                 bmStudyDataPredicates[_referencesStudyPredicateURI][0],
                 biomarkerBodySystem.identifier
             )
             continue
         identifier = str(studies[0].identifier.split('/')[-1]) + '-' + normalizer(studies[0].title)
         bodySystemStudy = None
         if identifier not in biomarkerBodySystem.keys():
             bodySystemStudy = biomarkerBodySystem[biomarkerBodySystem.invokeFactory('Body System Study', identifier)]
         else:
             bodySystemStudy = biomarkerBodySystem[identifier]
         updateObject(bodySystemStudy, studyURI, bmStudyDataPredicates, catalog)
         bodySystemStudy.title = studies[0].title
         bodySystemStudy.description = studies[0].description
         bodySystemStudy.setProtocol(studies[0].UID())
         self._addBiomarkerToProtocol(aq_parent(aq_inner(aq_parent(aq_inner(bodySystemStudy)))), studies[0])
         if _sensitivityDatasPredicateURI in bmStudyDataPredicates:
             bags = bmStudyDataPredicates[_sensitivityDatasPredicateURI]
             self.addStatistics(bodySystemStudy, bags, statements, normalizer, catalog)
         bodySystemStudy.reindexObject()
Example #10
0
    def addOrganSpecificInformation(self, biomarkers, statements, normalizer,
                                    catalog):
        '''Populate biomarkers with body system (aka "organ") details.'''
        for uri, predicates in statements.items():
            try:
                if predicates[_typeURI][0] != _bmOrganDataTypeURI:
                    continue
                biomarker = biomarkers[predicates[_biomarkerPredicateURI][0]]
            except KeyError:
                continue

            organName = unicode(predicates[_organPredicateURI][0])
            results = catalog(Title=organName,
                              object_provides=IBodySystem.__identifier__)
            if len(results) < 1:
                _logger.warn('Unknown organ %s for biomarker %s', organName,
                             biomarker.title)
                continue
            organObjID = normalizer(organName)
            biomarkerBodySystem = biomarker[biomarker.invokeFactory(
                'Biomarker Body System', organObjID)]
            biomarkerBodySystem.setTitle(results[0].Title)
            biomarkerBodySystem.setBodySystem(results[0].UID)
            updateObject(biomarkerBodySystem, uri, predicates, catalog)
            self.addBiomarkerToOrganGroup(biomarker, organName, catalog)
            if _hasBiomarkerOrganStudyDatasPredicateURI in predicates:
                bags = predicates[_hasBiomarkerOrganStudyDatasPredicateURI]
                self.addStudiesToOrgan(biomarkerBodySystem, bags, statements,
                                       normalizer, catalog)
            certificationURIs = predicates.get(_certificationPredicateURI, [])
            # TODO: make a separate Certification type so we don't rely on these fixed values.
            # Although we'll likely never have ohter certifications.
            for certificationURI in certificationURIs:
                if certificationURI == _cliaCertificationURI:
                    biomarkerBodySystem.cliaCertification = True
                elif certificationURI == _fdaCeritificationURI:
                    biomarkerBodySystem.fdaCertification = True
            biomarkerBodySystem.reindexObject()
Example #11
0
File: rdf.py Project: EDRN/eke.site
 def createObjects(self, objectID, title, uri, predicates, statements, context):
     s = context[context.invokeFactory('Site', objectID)]
     updateObject(s, uri, predicates, context)
     if _memberTypeURI in predicates and len(predicates[_memberTypeURI]) > 0:
         s.memberType = _transformMemberType(unicode(predicates[_memberTypeURI][0]))
     return [CreatedObject(s)]
Example #12
0
 def createObjects(self, objectID, title, uri, predicates, statements, context):
     p = context[context.invokeFactory('Protocol', objectID)]
     updateObject(p, uri, predicates, context)
     return [CreatedObject(p)]
Example #13
0
File: rdf.py Project: EDRN/eke.site
 def __call__(self, rdfDataSource=None):
     '''Ingest and render a results page.'''
     context = aq_inner(self.context)
     catalog = getToolByName(context, 'portal_catalog')
     if rdfDataSource is None:
         rdfDataSource = context.rdfDataSource
     if not rdfDataSource:
         raise RDFIngestException(_(u'This folder has no RDF data source URL.'))
     normalizerFunction = queryUtility(IIDNormalizer).normalize
     graph = ConjunctiveGraph()
     graph.parse(URLInputSource(rdfDataSource))
     statements = self._parseRDF(graph)
     createdObjects = []
     handler = SiteHandler()
     for uri, predicates in statements.items():
         results = catalog(identifier=unicode(uri), object_provides=ISite.__identifier__)
         objectID = handler.generateID(uri, predicates, normalizerFunction)
         #check if homepage URL has rdf datasource in it because of missing http prefix
         if _homePageURI in predicates:
             predicates[_homePageURI][0] = _transformHomePage(predicates[_homePageURI][0], rdfDataSource)
         if len(results) == 1 or objectID in context.keys():
             # Existing site. Update it
             if objectID in context.keys():
                 s = context[objectID]
             else:
                 s = results[0].getObject()
             updateObject(s, uri, predicates, context)
             if _memberTypeURI in predicates and len(predicates[_memberTypeURI]) > 0:
                 s.memberType = _transformMemberType(unicode(predicates[_memberTypeURI][0]))
             # Reset my investigators
             s.setPrincipalInvestigator(None)
             s.setCoPrincipalInvestigators([])
             s.setCoInvestigators([])
             s.setInvestigators([])
             # FIXME:
             # s.manage_delObjects(s.objectIds())
             created = [CreatedObject(s)]
         else:
             if len(results) > 1:
                 # More than one? Nuke 'em all.
                 context.manage_delObjects([s.id for s in results])
             # New site. Create it.
             title = handler.generateTitle(uri, predicates)
             created = handler.createObjects(objectID, title, uri, predicates, statements, context)
         for obj in created:
             obj.reindex()
         createdObjects.extend(created)
     self.objects = createdObjects
     statements, createdSites = self._updateSponsors()
     self._updateSiteIDs(createdSites.values())
     folks = self._ingestPeople()
     warnings = self._updateInvestigators(statements, createdSites, folks)
     for site in createdSites.values():
         site.obj.reindexObject()
     # Set the PI's UID on all members so we can search for everyone who works for his PI'liness
     for createdPerson in folks.itervalues():
         createdPerson.piUID = createdPerson.aq_parent.piUID
     # CA-609: check for sites without any member type
     mailTool = getToolByName(aq_inner(self.context), 'MailHost')
     if mailTool is not None:
         unknowns = ['* %s (%s)' % (i.obj.title, i.obj.siteID) for i in createdSites.values() if not i.obj.memberType]
         if len(unknowns) > 0:
             urlTool = getToolByName(aq_inner(self.context), 'portal_url')
             portal, portalURL = urlTool.getPortalObject(), urlTool()
             src = portal.getProperty('email_from_address', _sa).strip()
             if not src: src = _sa
             charset = portal.getProperty('email_charset', 'utf-8')
             message = _message % {
                 'portalURL':     portalURL,
                 'numberOfSites': len(unknowns),
                 'sitesList':     '\n'.join(unknowns),
             }
             subject = _(u'Notice: the portal ingested some EDRN sites with NO member type')
             try:
                 mailTool.send(message, mto=_na, mfrom=src, subject=subject, charset=charset)
             except (socket.error, smtplib.SMTPException):
                 pass
     self._results = Results(self.objects, warnings)
     return self.renderResults()
Example #14
0
 def __call__(self, rdfDataSource=None):
     '''Ingest and render a results page'''
     context = aq_inner(self.context)
     _logger.info('Study Folder RDF ingest for folder at %s', '/'.join(context.getPhysicalPath()))
     catalog = getToolByName(context, 'portal_catalog')
     if rdfDataSource is None:
         rdfDataSource = context.rdfDataSource
     if not rdfDataSource:
         raise RDFIngestException(_(u'This folder has no RDF data source URL.'))
     normalizerFunction = queryUtility(IIDNormalizer).normalize
     t0 = time.time()
     graph = ConjunctiveGraph()
     graph.parse(URLInputSource(rdfDataSource))
     statements = self._parseRDF(graph)
     delta = time.time() - t0
     _logger.info('Took %f seconds to read and parse %s', delta, rdfDataSource)
     createdObjects = []
     handler = StudyHandler()
     t0 = time.time()
     # First gather the protocol-to-involved investigator sites
     protocolToInvolvedSites = {}
     for uri, predicates in statements.items():
         typeURI = predicates[_typeURI][0]
         if typeURI == _siteSpecificTypeURI:
             protocolID, siteID = os.path.basename(urlparse.urlparse(unicode(uri)).path).split(u'-')
             siteIDs = protocolToInvolvedSites.get(protocolID, set())
             siteIDs.add(siteID)
             protocolToInvolvedSites[protocolID] = siteIDs
     # Now go through each protocol
     for uri, predicates in statements.items():
         typeURI = predicates[_typeURI][0]
         if typeURI == _siteSpecificTypeURI: continue
         if unicode(uri) == u'http://edrn.nci.nih.gov/data/protocols/0':
             # Bad data from DMCC
             continue
         results = catalog(identifier=unicode(uri), object_provides=IProtocol.__identifier__)
         objectID = handler.generateID(uri, predicates, normalizerFunction)
         isProject = unicode(predicates.get(_projectFlagURI, ['Protocol'])[0]) == u'Project'
         if len(results) == 1 or objectID in context.keys():
             # Existing protocol. Update it.
             if objectID in context.keys():
                 p = context[objectID]
             else:
                 p = results[0].getObject()
             oldID = p.id
             updateObject(p, uri, predicates, context)
             p.project = True if isProject else False
             newID = handler.generateID(uri, predicates, normalizerFunction)
             if oldID != newID:
                 # Need to update the object ID too
                 p.setId(newID)
             # And set the involved investigator sites
             self.setInvolvedInvestigatorSites(catalog, p, protocolToInvolvedSites)
             created = [CreatedObject(p)]
         else:
             if len(results) > 1:
                 # More than one? WTF? Nuke 'em all.
                 context.manage_delObjects([p.id for p in results])
             # New protocol. Create it.
             title = handler.generateTitle(uri, predicates)
             created = handler.createObjects(objectID, title, uri, predicates, statements, context)
             for createdObject in created:
                 createdObject.obj.project = True if isProject else False
                 self.setInvolvedInvestigatorSites(catalog, createdObject.obj, protocolToInvolvedSites)
         for obj in created:
             obj.reindex()
         createdObjects.extend(created)
     _logger.info('Took %f seconds to process %d statements', time.time() - t0, len(statements))
     self.objects = createdObjects
     t0 = time.time()
     self.updateCollaborativeGroups(createdObjects, catalog)
     _logger.info('Took %f seconds to update collaborative groups', time.time() - t0)
     # Now add involved investigator sites to protocols
     self._results = Results(self.objects, warnings=[])
     return self.renderResults()
Example #15
0
 def createObjects(self, objectID, title, uri, predicates, statements, context):
     disease = context[context.invokeFactory('Disease', objectID)]
     updateObject(disease, uri, predicates)
     if _bodySystemsAffectedPredURI in predicates:
         disease.setAffectedOrgans(getUIDsFromURIs(context, predicates[_bodySystemsAffectedPredURI]))
     return [CreatedObject(disease)]
Example #16
0
 def createObjects(self, objectID, title, uri, predicates, statements, context):
     bodySystem = context[context.invokeFactory('Body System', objectID)]
     updateObject(bodySystem, uri, predicates)
     return [CreatedObject(bodySystem)]
Example #17
0
 def createObjects(self, objectID, title, uri, predicates, statements, context):
     resource = context[context.invokeFactory('Knowledge Object', objectID)]
     updateObject(resource, uri, predicates)
     return [CreatedObject(resource)]