Examples with Auditable ubic.gemma.model.common.Auditable used on opensource projects

Example 1 with Auditable

use of ubic.gemma.model.common.Auditable in project Gemma by PavlidisLab.

the class SearchServiceImpl method searchForNewlyCreatedUserQueryResults.

@Override
public Map<Class<?>, List<SearchResult>> searchForNewlyCreatedUserQueryResults(UserQuery query) {
    Map<Class<?>, List<SearchResult>> searchResults;
    Map<Class<?>, List<SearchResult>> finalResults = new HashMap<>();
    SearchSettings settings = query.getSearchSettings();
    if (StringUtils.isBlank(settings.getTermUri()) && !settings.getQuery().startsWith("http://")) {
        // fill objects=true, speedySearch=false
        searchResults = this.generalSearch(settings, true, false);
    } else {
        // we only attempt an ontology search if the uri looks remotely like a url.
        searchResults = this.ontologyUriSearch(settings);
    }
    if (searchResults == null) {
        return finalResults;
    }
    for (Class<?> clazz : searchResults.keySet()) {
        List<SearchResult> results = searchResults.get(clazz);
        List<SearchResult> updatedResults = new ArrayList<>();
        if (results.size() == 0)
            continue;
        SearchServiceImpl.log.info("Search for newly createdQuery with settings: " + settings + "; result: " + results.size() + " " + clazz.getSimpleName() + "s");
        for (SearchResult sr : results) {
            // Are SearchResults always auditable? maybe put in some error handling in case they are not or
            // enforce searchSettings object to be of a certain form
            Auditable auditableResult = (Auditable) sr.getResultObject();
            // this list is ordered by date (not descending)
            List<AuditEvent> eventList = auditTrailService.getEvents(auditableResult);
            if (eventList == null || eventList.isEmpty())
                continue;
            for (AuditEvent ae : eventList) {
                // assuming there is only one create event
                if (ae.getAction() == AuditAction.CREATE && ae.getDate().after(query.getLastUsed())) {
                    updatedResults.add(sr);
                    break;
                }
            }
        }
        if (!updatedResults.isEmpty()) {
            finalResults.put(clazz, updatedResults);
        }
    }
    return finalResults;
}

Example 2 with Auditable

use of ubic.gemma.model.common.Auditable in project Gemma by PavlidisLab.

the class AuditEventDaoImplTest method testHandleGetUpdatedSinceDate.

@Test
public void testHandleGetUpdatedSinceDate() {
    Calendar c = Calendar.getInstance();
    c.set(2006, Calendar.DECEMBER, 1);
    Date d = c.getTime();
    Collection<Auditable> objs = auditEventService.getUpdatedSinceDate(d);
    assertTrue(objs.size() > 0);
// for ( AbstractAuditable auditable : objs ) {
// if ( objs instanceof ArrayDesign ) {
// }
// }
}

Example 3 with Auditable

use of ubic.gemma.model.common.Auditable in project Gemma by PavlidisLab.

the class ExpressionExperimentReportServiceImpl method populateEventInformation.

/**
 * Fills in event and security information from the database. This will only retrieve the latest event (if any).
 * This is rather slow so should be avoided if the information isn't needed.
 */
@Override
public void populateEventInformation(Collection<ExpressionExperimentDetailsValueObject> vos) {
    StopWatch timer = new StopWatch();
    timer.start();
    Collection<Long> ids = EntityUtils.getIds(vos);
    // do this ahead to avoid round trips - this also filters...
    Collection<ExpressionExperiment> ees = expressionExperimentService.load(ids);
    if (ees.size() == 0) {
        return;
    }
    Map<Long, ExpressionExperiment> eeMap = EntityUtils.getIdMap(ees);
    Map<Long, Date> lastArrayDesignUpdates = expressionExperimentService.getLastArrayDesignUpdate(ees);
    Collection<Class<? extends AuditEventType>> typesToGet = Arrays.asList(eventTypes);
    Map<Class<? extends AuditEventType>, Map<Auditable, AuditEvent>> events = this.getEvents(ees, typesToGet);
    Map<Auditable, AuditEvent> linkAnalysisEvents = events.get(LinkAnalysisEvent.class);
    Map<Auditable, AuditEvent> missingValueAnalysisEvents = events.get(MissingValueAnalysisEvent.class);
    Map<Auditable, AuditEvent> rankComputationEvents = events.get(ProcessedVectorComputationEvent.class);
    Map<Auditable, AuditEvent> differentialAnalysisEvents = events.get(DifferentialExpressionAnalysisEvent.class);
    Map<Auditable, AuditEvent> batchFetchEvents = events.get(BatchInformationFetchingEvent.class);
    Map<Auditable, AuditEvent> pcaAnalysisEvents = events.get(PCAAnalysisEvent.class);
    Map<Long, Collection<AuditEvent>> sampleRemovalEvents = this.getSampleRemovalEvents(ees);
    /*
         * add in the last events of interest for all eeVos This step is remarkably slow.
         */
    for (ExpressionExperimentDetailsValueObject eeVo : vos) {
        Long id = eeVo.getId();
        ExpressionExperiment ee = eeMap.get(id);
        if (linkAnalysisEvents.containsKey(ee)) {
            AuditEvent event = linkAnalysisEvents.get(ee);
            if (event != null) {
                Date date = event.getDate();
                eeVo.setDateLinkAnalysis(date);
                eeVo.setLinkAnalysisEventType(event.getEventType().getClass().getSimpleName());
            }
        }
        if (missingValueAnalysisEvents.containsKey(ee)) {
            AuditEvent event = missingValueAnalysisEvents.get(ee);
            if (event != null) {
                Date date = event.getDate();
                eeVo.setDateMissingValueAnalysis(date);
                eeVo.setMissingValueAnalysisEventType(event.getEventType().getClass().getSimpleName());
            }
        }
        if (rankComputationEvents.containsKey(ee)) {
            AuditEvent event = rankComputationEvents.get(ee);
            if (event != null) {
                Date date = event.getDate();
                eeVo.setDateProcessedDataVectorComputation(date);
                eeVo.setProcessedDataVectorComputationEventType(event.getEventType().getClass().getSimpleName());
            }
        }
        if (differentialAnalysisEvents.containsKey(ee)) {
            AuditEvent event = differentialAnalysisEvents.get(ee);
            if (event != null) {
                Date date = event.getDate();
                eeVo.setDateDifferentialAnalysis(date);
            }
        }
        if (pcaAnalysisEvents.containsKey(ee)) {
            AuditEvent event = pcaAnalysisEvents.get(ee);
            if (event != null) {
                Date date = event.getDate();
                eeVo.setDatePcaAnalysis(date);
                eeVo.setPcaAnalysisEventType(event.getEventType().getClass().getSimpleName());
            }
        }
        if (batchFetchEvents.containsKey(ee)) {
            AuditEvent event = batchFetchEvents.get(ee);
            if (event != null) {
                Date date = event.getDate();
                eeVo.setDateBatchFetch(date);
                eeVo.setBatchFetchEventType(event.getEventType().getClass().getSimpleName());
            }
        }
        if (lastArrayDesignUpdates.containsKey(id)) {
            Date date = lastArrayDesignUpdates.get(id);
            eeVo.setDateArrayDesignLastUpdated(date);
        }
        if (sampleRemovalEvents.containsKey(id)) {
            Collection<AuditEvent> removalEvents = sampleRemovalEvents.get(id);
            // we find we are getting lazy-load exceptions from this guy.
            eeVo.auditEvents2SampleRemovedFlags(removalEvents);
        }
    }
    if (timer.getTime() > 1000)
        log.info("Retrieving audit events took " + timer.getTime() + "ms");
}

Example 4 with Auditable

use of ubic.gemma.model.common.Auditable in project Gemma by PavlidisLab.

the class TableMaintenanceUtilImpl method updateGene2CsEntries.

@Override
@Transactional
public synchronized void updateGene2CsEntries() {
    if (TableMaintenanceUtilImpl.running.get())
        return;
    TableMaintenanceUtilImpl.log.debug("Running Gene2CS status check");
    String annotation = "";
    try {
        TableMaintenanceUtilImpl.running.set(true);
        Gene2CsStatus status = this.getLastGene2CsUpdateStatus();
        boolean needToRefresh = false;
        if (status == null) {
            needToRefresh = true;
        }
        if (!needToRefresh) {
            Collection<Auditable> newObj = auditEventService.getNewSinceDate(status.getLastUpdate());
            for (Auditable a : newObj) {
                if (a instanceof ArrayDesign) {
                    needToRefresh = true;
                    annotation = a + " is new since " + status.getLastUpdate();
                    TableMaintenanceUtilImpl.log.debug(annotation);
                    break;
                }
            }
        }
        if (!needToRefresh) {
            Collection<Auditable> updatedObj = auditEventService.getUpdatedSinceDate(status.getLastUpdate());
            for (Auditable a : updatedObj) {
                if (a instanceof ArrayDesign) {
                    for (AuditEvent ae : auditEventService.getEvents(a)) {
                        if (ae == null)
                            // legacy of ordered-list which could end up with gaps; should
                            continue;
                        // not be needed any more
                        if (ae.getEventType() != null && ae.getEventType() instanceof ArrayDesignGeneMappingEvent && ae.getDate().after(status.getLastUpdate())) {
                            needToRefresh = true;
                            annotation = a + " had probe mapping done since: " + status.getLastUpdate();
                            TableMaintenanceUtilImpl.log.debug(annotation);
                            break;
                        }
                    }
                }
                if (needToRefresh)
                    break;
            }
        }
        if (needToRefresh) {
            TableMaintenanceUtilImpl.log.debug("Update of GENE2CS initiated");
            this.generateGene2CsEntries();
            Gene2CsStatus updatedStatus = this.writeUpdateStatus(annotation, null);
            this.sendEmail(updatedStatus);
        } else {
            TableMaintenanceUtilImpl.log.debug("No update of GENE2CS needed");
        }
    } catch (Exception e) {
        try {
            TableMaintenanceUtilImpl.log.info("Error during attempt to check status or update GENE2CS", e);
            Gene2CsStatus updatedStatus = this.writeUpdateStatus(annotation, e);
            this.sendEmail(updatedStatus);
        } catch (IOException e1) {
            throw new RuntimeException(e1);
        }
    } finally {
        TableMaintenanceUtilImpl.running.set(false);
    }
}

Example 5 with Auditable

use of ubic.gemma.model.common.Auditable in project Gemma by PavlidisLab.

the class ArrayDesignReportServiceImpl method fillEventInformation.

/**
 * Fill in event information
 */
@Override
public void fillEventInformation(Collection<ArrayDesignValueObject> adVos) {
    if (adVos == null || adVos.size() == 0)
        return;
    StopWatch watch = new StopWatch();
    watch.start();
    Collection<Long> ids = new ArrayList<>();
    for (Object object : adVos) {
        ArrayDesignValueObject adVo = (ArrayDesignValueObject) object;
        Long id = adVo.getId();
        if (id == null)
            continue;
        ids.add(id);
    }
    if (ids.size() == 0)
        return;
    Collection<Class<? extends AuditEventType>> typesToGet = Arrays.asList(eventTypes);
    Collection<ArrayDesign> arrayDesigns = arrayDesignService.load(ids);
    Map<Long, ArrayDesign> idMap = EntityUtils.getIdMap(arrayDesigns);
    Map<Class<? extends AuditEventType>, Map<Auditable, AuditEvent>> events = auditEventService.getLastEvents(arrayDesigns, typesToGet);
    Map<Auditable, AuditEvent> geneMappingEvents = events.get(ArrayDesignGeneMappingEvent.class);
    Map<Auditable, AuditEvent> sequenceUpdateEvents = events.get(ArrayDesignSequenceUpdateEvent.class);
    Map<Auditable, AuditEvent> sequenceAnalysisEvents = events.get(ArrayDesignSequenceAnalysisEvent.class);
    Map<Auditable, AuditEvent> repeatAnalysisEvents = events.get(ArrayDesignRepeatAnalysisEvent.class);
    for (ArrayDesignValueObject adVo : adVos) {
        Long id = adVo.getId();
        ArrayDesign ad = idMap.get(id);
        if (geneMappingEvents.containsKey(ad)) {
            AuditEvent event = geneMappingEvents.get(ad);
            if (event != null) {
                adVo.setLastGeneMapping(event.getDate());
            }
        }
        if (sequenceUpdateEvents.containsKey(ad)) {
            AuditEvent event = sequenceUpdateEvents.get(ad);
            if (event != null) {
                adVo.setLastSequenceUpdate(event.getDate());
            }
        }
        if (sequenceAnalysisEvents.containsKey(ad)) {
            AuditEvent event = sequenceAnalysisEvents.get(ad);
            if (event != null) {
                adVo.setLastSequenceAnalysis(event.getDate());
            }
        }
        if (repeatAnalysisEvents.containsKey(ad)) {
            AuditEvent event = repeatAnalysisEvents.get(ad);
            if (event != null) {
                adVo.setLastRepeatMask(event.getDate());
            }
        }
    }
    watch.stop();
    if (watch.getTime() > 1000)
        ArrayDesignReportServiceImpl.log.info("Added event information in " + watch.getTime() + "ms");
}