auphong2707/dl4se-code-review-dataset huggingface dataset:
Source:
<code>private String getJobCoordinationZkPath(Config config) { JobConfig jobConfig = new JobConfig(config); String appId = new ApplicationConfig(config).getGlobalAppId(); String jobName = jobConfig.getName().isDefined() ? jobConfig.getName().get() : DEFAULT_JOB_NAME; String jobId = jobConfig.getJobId().isDefined() ? jobConfig.getJobId().get() <START> : String.valueOf(System.currentTimeMillis()); END> return String.format(JOB_COORDINATOR_ZK_PATH_FORMAT, appId, jobName, jobId); }</code><technical_language>I jobId defaults 1. is currentTimeMillis here? this path processors? I missing</technical_language>

Target:
private String getJobCoordinationZkPath(Config config) { JobConfig jobConfig = new JobConfig(config); String appId = new ApplicationConfig(config).getGlobalAppId(); String jobName = jobConfig.getName().isDefined() ? jobConfig.getName().get() : DEFAULT_JOB_NAME; String jobId = jobConfig.getJobId().isDefined() ? jobConfig.getJobId().get() : DEFAULT_JOB_ID; return String.format(JOB_COORDINATOR_ZK_PATH_FORMAT, appId, jobName, jobId); }
Source:
<code>public float getFloat() { <START> return delegate.getFloat(); <END> }</code><technical_language>if isNullResult, throw IllegalStateException defensively</technical_language>

Target:
public float getFloat() { if (isNullResult) { throw new IllegalStateException("Cannot return primitive float for Null Value"); } return delegate.getFloat(); }
Source:
<code>private void processMessageBody(final Message message) throws XMLStreamException, IOException { boolean isLarge = false; for (int i = 0; i < reader.getAttributeCount(); i++) { String attributeName = reader.getAttributeLocalName(i); if (XmlDataConstants.MESSAGE_IS_LARGE.equals(attributeName)) { isLarge = Boolean.parseBoolean(reader.getAttributeValue(i)); } } reader.next(); <START> ActiveMQServerLogger.LOGGER.debug("XMLStreamReader impl: " + reader); <END> if (isLarge) { tempFileName = UUID.randomUUID().toString() + ".tmp"; ActiveMQServerLogger.LOGGER.debug("Creating temp file " + tempFileName + " for large message."); try (OutputStream out = new FileOutputStream(tempFileName)) { getMessageBodyBytes(new MessageBodyBytesProcessor() { @Override public void processBodyBytes(byte[] bytes) throws IOException { out.write(bytes); } }); } FileInputStream fileInputStream = new FileInputStream(tempFileName); BufferedInputStream bufferedInput = new BufferedInputStream(fileInputStream); ((ClientMessage) message).setBodyInputStream(bufferedInput); } else { getMessageBodyBytes(new MessageBodyBytesProcessor() { @Override public void processBodyBytes(byte[] bytes) throws IOException { message.getBodyBuffer().writeBytes(bytes); } }); } }</code><technical_language>if (log.isDebug()) log.debug(...) get a logger for this class. This is change I in longer long ago</technical_language>

Target:
private void processMessageBody(final Message message) throws XMLStreamException, IOException { boolean isLarge = false; for (int i = 0; i < reader.getAttributeCount(); i++) { String attributeName = reader.getAttributeLocalName(i); if (XmlDataConstants.MESSAGE_IS_LARGE.equals(attributeName)) { isLarge = Boolean.parseBoolean(reader.getAttributeValue(i)); } } reader.next(); if (logger.isDebugEnabled()) { logger.debug("XMLStreamReader impl: " + reader); } if (isLarge) { tempFileName = UUID.randomUUID().toString() + ".tmp"; if (logger.isDebugEnabled()) { logger.debug("Creating temp file " + tempFileName + " for large message."); } try (OutputStream out = new FileOutputStream(tempFileName)) { getMessageBodyBytes(new MessageBodyBytesProcessor() { @Override public void processBodyBytes(byte[] bytes) throws IOException { out.write(bytes); } }); } FileInputStream fileInputStream = new FileInputStream(tempFileName); BufferedInputStream bufferedInput = new BufferedInputStream(fileInputStream); ((ClientMessage) message).setBodyInputStream(bufferedInput); } else { getMessageBodyBytes(new MessageBodyBytesProcessor() { @Override public void processBodyBytes(byte[] bytes) throws IOException { message.getBodyBuffer().writeBytes(bytes); } }); } }
Source:
<code>public void start(StartContext context) throws StartException { preStart(context); serverService.getValue().registerListener(this); try { final InetSocketAddress socketAddress = binding.getValue().getSocketAddress(); openListener = createOpenListener(); final ChannelListener<AcceptingChannel<StreamConnection>> acceptListener = ChannelListeners.openListenerAdapter(openListener); HttpHandler handler = serverService.getValue().getRoot(); for(HandlerWrapper wrapper : listenerHandlerWrappers) { handler = wrapper.wrap(handler); } openListener.setRootHandler(handler); startListening(worker.getValue(), socketAddress, acceptListener); registerBinding(); } catch (IOException e) { cleanFailedStart(); if (e instanceof BindException) { final StringBuilder sb = new StringBuilder().append(e.getMessage()); final InetSocketAddress socketAddress = binding.getValue().getSocketAddress(); if (socketAddress != null) sb.append(" ").append(socketAddress); throw new StartException(sb.toString()); } else { <START> throw new StartException("Could not start http listener", e); <END> } } }</code><technical_language>This some localization. original code it. it, message is wrong, this code handles listeners http ones. this</technical_language>

Target:
public void start(StartContext context) throws StartException { preStart(context); serverService.getValue().registerListener(this); try { final InetSocketAddress socketAddress = binding.getValue().getSocketAddress(); openListener = createOpenListener(); final ChannelListener<AcceptingChannel<StreamConnection>> acceptListener = ChannelListeners.openListenerAdapter(openListener); HttpHandler handler = serverService.getValue().getRoot(); for(HandlerWrapper wrapper : listenerHandlerWrappers) { handler = wrapper.wrap(handler); } openListener.setRootHandler(handler); startListening(worker.getValue(), socketAddress, acceptListener); registerBinding(); } catch (IOException e) { cleanFailedStart(); if (e instanceof BindException) { final StringBuilder sb = new StringBuilder().append(e.getLocalizedMessage()); final InetSocketAddress socketAddress = binding.getValue().getSocketAddress(); if (socketAddress != null) sb.append(" ").append(socketAddress); throw new StartException(sb.toString()); } else { throw UndertowLogger.ROOT_LOGGER.couldNotStartListener(name, e); } } }
Source:
<code>public Optional<AuthorData> createFrom(DataHolder dataHolder) { if (!(dataHolder instanceof ItemStack)) { return Optional.absent(); } <START> if (!(((ItemStack) dataHolder).getItem() == Items.written_book)) { <END> return Optional.absent(); } if (!((ItemStack) dataHolder).hasTagCompound()) { return Optional.absent(); } final String rawAuthor = ((ItemStack) dataHolder).getTagCompound().getString("author"); final AuthorData data = create(); data.setValue(Texts.of(rawAuthor)); return Optional.of(data); }</code><technical_language>able store information Items.writable_book well</technical_language>

Target:
public Optional<AuthorData> createFrom(DataHolder dataHolder) { if (!(dataHolder instanceof ItemStack)) { return Optional.absent(); } if (((ItemStack) dataHolder).getItem() != Items.written_book) { return Optional.absent(); } if (!((ItemStack) dataHolder).hasTagCompound()) { return Optional.absent(); } final String rawAuthor = ((ItemStack) dataHolder).getTagCompound().getString("author"); return Optional.of(create().setValue(Texts.of(rawAuthor))); }
Source:
<code>public void test_relativeYearFraction( DayCount dayCount, int y1, int m1, int d1, int y2, int m2, int d2, Double value) { double expected = (value == SIMPLE_30_360 ? calc360(y1, m1, d1, y2, m2, d2) : value); LocalDate date1 = LocalDate.of(y1, m1, d1); LocalDate date2 = LocalDate.of(y2, m2, d2); <START> assertEquals(dayCount.relativeYearFraction(date1, date2), expected, 0d); <END> }</code><technical_language>tolerance of zero? leave call 2-arg assertEquals</technical_language>

Target:
public void test_relativeYearFraction( DayCount dayCount, int y1, int m1, int d1, int y2, int m2, int d2, Double value) { double expected = (value == SIMPLE_30_360 ? calc360(y1, m1, d1, y2, m2, d2) : value); LocalDate date1 = LocalDate.of(y1, m1, d1); LocalDate date2 = LocalDate.of(y2, m2, d2); assertEquals(dayCount.relativeYearFraction(date1, date2), expected, TOLERANCE_ZERO); }
Source:
<code>private RemoteServerDialog(RemoteServerDialogForm form, RemoteServer.Test serverTester) { this.form = form; this.form.onConnect(server -> { form.setTestingConnection(); new SwingWorker<Response<Boolean>, Void>() { @Override protected Response<Boolean> doInBackground() { return serverTester.test(server); } @Override protected void done() { try { Response<Boolean> response = get(); if (response.isSuccess()) { triggerConnect(server); form.hideDialog(); } else showError( response.isRedirection() ? "Redirection detected" : response.isUnauthorized() ? "Wrong credentials" : response.isNotFound() ? "Aggregate not found" : "", response.isRedirection() ? "Unexpected error" : "Configuration error" ); } catch (InterruptedException ignore) { } catch (ExecutionException e) { if (e.getCause() != null) { showError(e.getCause().getMessage(), "Unexpected error"); } } form.unsetTestingConnection(); <START> form.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); <END> } }.execute(); }); }</code><technical_language>a bit confused, is this needed here? I mean, dealing changing wait cursor default cursor in RemoteServerDialogForm.java</technical_language>

Target:
private RemoteServerDialog(RemoteServerDialogForm form, RemoteServer.Test serverTester) { this.form = form; this.form.onConnect(server -> { form.setTestingConnection(); new SwingWorker<Response<Boolean>, Void>() { @Override protected Response<Boolean> doInBackground() { return serverTester.test(server); } @Override protected void done() { try { Response<Boolean> response = get(); if (response.isSuccess()) { triggerConnect(server); form.hideDialog(); } else showError( response.isRedirection() ? "Redirection detected" : response.isUnauthorized() ? "Wrong credentials" : response.isNotFound() ? "Aggregate not found" : "", response.isRedirection() ? "Unexpected error" : "Configuration error" ); } catch (InterruptedException ignore) { } catch (ExecutionException e) { if (e.getCause() != null) { showError(e.getCause().getMessage(), "Unexpected error"); } } form.unsetTestingConnection(); } }.execute(); }); }
Source:
<code>public void computeAABB(AABB aabb, Transform xf, int childIndex) { assert childIndex < m_count; final Vec2 lower = aabb.lowerBound; final Vec2 upper = aabb.upperBound; int i1 = childIndex; int i2 = childIndex + 1; if (i2 == m_count) { i2 = 0; } final Vec2 vi1 = m_vertices[i1]; final Vec2 vi2 = m_vertices[i2]; final Rotation xfq = xf.q; final Vec2 xfp = xf.p; float v1x = (xfq.c * vi1.x - xfq.s * vi1.y) + xfp.x; <START> float v1y = xfq.s * vi1.x + xfq.c * vi1.y + xfp.y; <END> float v2x = (xfq.c * vi2.x - xfq.s * vi2.y) + xfp.x; float v2y = xfq.s * vi2.x + xfq.c * vi2.y + xfp.y; lower.x = v1x < v2x ? v1x : v2x; lower.y = v1y < v2y ? v1y : v2y; upper.x = v1x > v2x ? v1x : v2x; upper.y = v1y > v2y ? v1y : v2y; }</code><technical_language>Please revert equations consistent</technical_language>

Target:
public void computeAABB(AABB aabb, Transform xf, int childIndex) { assert childIndex < m_count; final Vec2 lower = aabb.lowerBound; final Vec2 upper = aabb.upperBound; int i1 = childIndex; int i2 = childIndex + 1; if (i2 == m_count) { i2 = 0; } final Vec2 vi1 = m_vertices[i1]; final Vec2 vi2 = m_vertices[i2]; final Rotation xfq = xf.q; final Vec2 xfp = xf.p; float v1x = (xfq.c * vi1.x - xfq.s * vi1.y) + xfp.x; float v1y = (xfq.s * vi1.x + xfq.c * vi1.y) + xfp.y; float v2x = (xfq.c * vi2.x - xfq.s * vi2.y) + xfp.x; float v2y = xfq.s * vi2.x + xfq.c * vi2.y + xfp.y; lower.x = v1x < v2x ? v1x : v2x; lower.y = v1y < v2y ? v1y : v2y; upper.x = v1x > v2x ? v1x : v2x; upper.y = v1y > v2y ? v1y : v2y; }
Source:
<code>public File persist( final IncrementalIndex index, final Interval dataInterval, File outDir, IndexSpec indexSpec, ProgressIndicator progress, @Nullable SegmentWriteOutMediumFactory segmentWriteOutMediumFactory ) throws IOException { if (index.isEmpty()) { throw new IAE("Trying to persist an empty index!"); } final DateTime firstTimestamp = index.getMinTime(); final DateTime lastTimestamp = index.getMaxTime(); if (!(dataInterval.contains(firstTimestamp) && dataInterval.contains(lastTimestamp))) { throw new IAE( "interval[%s] does not encapsulate the full range of timestamps[%s, %s]", dataInterval, firstTimestamp, lastTimestamp ); } FileUtils.forceMkdir(outDir); log.info("Starting persist for interval[%s], rows[%,d]", dataInterval, index.size()); return merge( <START> Collections.<IndexableAdapter>singletonList( <END> new IncrementalIndexAdapter( dataInterval, index, indexSpec.getBitmapSerdeFactory().getBitmapFactory() ) ), false, index.getMetricAggs(), outDir, indexSpec, progress, segmentWriteOutMediumFactory ); }</code><technical_language>Collections.singletonList</technical_language>

Target:
public File persist( final IncrementalIndex index, final Interval dataInterval, File outDir, IndexSpec indexSpec, ProgressIndicator progress, @Nullable SegmentWriteOutMediumFactory segmentWriteOutMediumFactory ) throws IOException { if (index.isEmpty()) { throw new IAE("Trying to persist an empty index!"); } final DateTime firstTimestamp = index.getMinTime(); final DateTime lastTimestamp = index.getMaxTime(); if (!(dataInterval.contains(firstTimestamp) && dataInterval.contains(lastTimestamp))) { throw new IAE( "interval[%s] does not encapsulate the full range of timestamps[%s, %s]", dataInterval, firstTimestamp, lastTimestamp ); } FileUtils.forceMkdir(outDir); log.info("Starting persist for interval[%s], rows[%,d]", dataInterval, index.size()); return merge( Collections.singletonList( new IncrementalIndexAdapter( dataInterval, index, indexSpec.getBitmapSerdeFactory().getBitmapFactory() ) ), false, index.getMetricAggs(), outDir, indexSpec, progress, segmentWriteOutMediumFactory ); }
Source:
<code>public Response getDatabaseSegmentDataSourceSegments( @PathParam("dataSourceName") String dataSourceName, @QueryParam("full") String full, List<Interval> intervals ) { List<DataSegment> segments = null; try { segments = metadataStorageCoordinator.getUsedSegmentsForIntervals(dataSourceName, intervals); } catch (IOException ex) { return Response.status(Response.Status.INTERNAL_SERVER_ERROR).entity(ex.getMessage()).build(); } Response.ResponseBuilder builder = Response.status(Response.Status.OK); if (full != null) { return builder.entity(segments).build(); } return builder.entity( Iterables.transform( segments, <START> new Function<DataSegment, Object>() <END> { @Override public Object apply(DataSegment segment) { return segment.getIdentifier(); } } ) ).build(); }</code><technical_language>this return a String, code easier read</technical_language>

Target:
public Response getDatabaseSegmentDataSourceSegments( @PathParam("dataSourceName") String dataSourceName, @QueryParam("full") String full, List<Interval> intervals ) { List<DataSegment> segments = null; try { segments = metadataStorageCoordinator.getUsedSegmentsForIntervals(dataSourceName, intervals); } catch (IOException ex) { return Response.status(Response.Status.INTERNAL_SERVER_ERROR).entity(ex.getMessage()).build(); } Response.ResponseBuilder builder = Response.status(Response.Status.OK); if (full != null) { return builder.entity(segments).build(); } return builder.entity( Iterables.transform( segments, new Function<DataSegment, String>() { @Override public String apply(DataSegment segment) { return segment.getIdentifier(); } } ) ).build(); }
Source:
<code>public void onSocialLoginSuccess(String accessToken, String backend, Task task) { <START> environment.getAnalyticsProvider().trackUserLogin(backend); <END> tryToSetUIInteraction(false); task.setProgressDialog(activityLoginBinding.progress.progressIndicator); }</code><technical_language>this called LoginAPI#finishLogin() method</technical_language>

Target:
public void onSocialLoginSuccess(String accessToken, String backend, Task task) { tryToSetUIInteraction(false); task.setProgressDialog(activityLoginBinding.progress.progressIndicator); }
Source:
<code>public Builder retriesForConnectionFailures(Integer retriesConnectionFailures) { <START> checkNotNull(retriesConnectionFailures, "retriesConnectionFailures"); <END> if (retriesConnectionFailures < 1) { throw new IllegalArgumentException("retriesConnectionFailure should be one or more"); } client.retriesForConnectionFailures = retriesConnectionFailures; return this; }</code><technical_language>If nulls accepted parameter int</technical_language>

Target:
public Builder retriesForConnectionFailures(Integer retriesConnectionFailures) { if (retriesConnectionFailures < 1) { throw new IllegalArgumentException("retriesConnectionFailure should be one or more"); } client.retriesForConnectionFailures = retriesConnectionFailures; return this; }
Source:
<code>public StageResult processAckOnMaster(List<DistStageAck> acks) { StageResult result = super.processAckOnMaster(acks); if (result.isError()) return result; Report.Test test = createTest(testName); <START> int testIteration = test.getIterations().size(); <END> for (ListenersAck ack : Projections.castProject(acks, ListenersAck.class)) { if (ack.stats != null) test.addStatistics(testIteration, ack.getSlaveIndex(), Collections.singletonList(ack.stats)); } return StageResult.SUCCESS; }</code><technical_language>get NPE if testName == null</technical_language>

Target:
public StageResult processAckOnMaster(List<DistStageAck> acks) { StageResult result = super.processAckOnMaster(acks); if (result.isError()) return result; Report.Test test = createTest(testName, null); if (test != null) { int testIteration = test.getIterations().size(); for (ListenersAck ack : Projections.castProject(acks, ListenersAck.class)) { if (ack.stats != null) test.addStatistics(testIteration, ack.getSlaveIndex(), Collections.singletonList(ack.stats)); } } return StageResult.SUCCESS; }
Source:
<code>public void setSelectionRange(int beginIndex, int endIndex) { if (fTableItemCount > 0) { <START> int begin = Math.min(beginIndex, fTableItemCount - 1); <END> begin = Math.max(begin, 0); int end = Math.min(endIndex, fTableItemCount - 1); end = Math.max(end, 0); fSelectedBeginRank = begin; fSelectedEventRank = end; if ((begin < fTableTopEventRank + fFrozenRowCount && begin >= fFrozenRowCount) || (begin >= fTableTopEventRank + fFullyVisibleRows)) { int lastPageTopEntryRank = Math.max(0, fTableItemCount - fFullyVisibleRows); fTableTopEventRank = Math.max(0, Math.min(lastPageTopEntryRank, begin - fFrozenRowCount - fFullyVisibleRows / 2)); } if (fFullyVisibleRows < fTableItemCount) { fSlider.setSelection(fTableTopEventRank); } refreshTable(); } }</code><technical_language>combine in line? original code that</technical_language>

Target:
public void setSelectionRange(int beginIndex, int endIndex) { if (fTableItemCount > 0) { int begin = Math.max(Math.min(beginIndex, fTableItemCount - 1), 0); int end = Math.max(Math.min(endIndex, fTableItemCount - 1), 0); int selection = fSelectedBeginRank != begin ? begin : end; fSelectedBeginRank = begin; fSelectedEventRank = end; if ((selection < fTableTopEventRank + fFrozenRowCount && selection >= fFrozenRowCount) || (selection >= fTableTopEventRank + fFullyVisibleRows)) { int lastPageTopEntryRank = Math.max(0, fTableItemCount - fFullyVisibleRows); fTableTopEventRank = Math.max(0, Math.min(lastPageTopEntryRank, selection - fFrozenRowCount - fFullyVisibleRows / 2)); } if (fFullyVisibleRows < fTableItemCount) { fSlider.setSelection(fTableTopEventRank); } refreshTable(); } }
Source:
<code>public void retrieveEdit() throws Exception { RestResponse r = adminSession.get(urlEdit()); assertThat(r.getStatusCode()).isEqualTo(SC_NO_CONTENT); assertThat(modifier.createEdit(change, ps)).isEqualTo(RefUpdate.Result.NEW); Optional<ChangeEdit> edit = editUtil.byChange(change); assertThat(modifier.modifyFile(edit.get(), FILE_NAME, CONTENT_NEW)) .isEqualTo(RefUpdate.Result.FORCED); edit = editUtil.byChange(change); EditInfo info = toEditInfo(false); assertThat(info.commit.commit).isEqualTo(edit.get().getRevision().get()); <START> assertThat(info.commit.parents.size()).isEqualTo(1); <END> edit = editUtil.byChange(change); editUtil.delete(edit.get()); r = adminSession.get(urlEdit()); assertThat(r.getStatusCode()).isEqualTo(SC_NO_CONTENT); }</code><technical_language>assertThat(info.commit.parents).hasSize(1)</technical_language>

Target:
public void retrieveEdit() throws Exception { RestResponse r = adminSession.get(urlEdit()); assertThat(r.getStatusCode()).isEqualTo(SC_NO_CONTENT); assertThat(modifier.createEdit(change, ps)).isEqualTo(RefUpdate.Result.NEW); Optional<ChangeEdit> edit = editUtil.byChange(change); assertThat(modifier.modifyFile(edit.get(), FILE_NAME, CONTENT_NEW)) .isEqualTo(RefUpdate.Result.FORCED); edit = editUtil.byChange(change); EditInfo info = toEditInfo(false); assertThat(info.commit.commit).isEqualTo(edit.get().getRevision().get()); assertThat(info.commit.parents).hasSize(1); edit = editUtil.byChange(change); editUtil.delete(edit.get()); r = adminSession.get(urlEdit()); assertThat(r.getStatusCode()).isEqualTo(SC_NO_CONTENT); }
Source:
<code>private JPanel pnlOnVertex(){ CategorizedPoint point = (CategorizedPoint) getLegend(); <START> JRadioButton bVertex = new JRadioButton(ON_VERTEX); <END> bVertex.addActionListener( EventHandler.create(ActionListener.class, point, "setOnVertex")); bVertex.addActionListener( EventHandler.create(ActionListener.class, this, "onClickVertex")); boolean onVertex = ((PointSymbolizer)point.getSymbolizer()).isOnVertex(); bVertex.setSelected(onVertex); JRadioButton bCentroid = new JRadioButton(ON_CENTROID); bCentroid.addActionListener( EventHandler.create(ActionListener.class, point, "setOnCentroid")); bCentroid.addActionListener( EventHandler.create(ActionListener.class, this, "onClickCentroid")); bCentroid.setSelected(!onVertex); ButtonGroup bg = new ButtonGroup(); bg.add(bVertex); bg.add(bCentroid); JPanel jp = new JPanel(); jp.add(bVertex); jp.add(bCentroid); return jp; }</code><technical_language>I18n.marktr ON_VERTEX use: java JRadioButton bVertex = new JRadioButton(I18N.tr(ON_VERTEX));</technical_language>

Target:
private JPanel pnlOnVertex(){ CategorizedPoint point = (CategorizedPoint) getLegend(); JRadioButton bVertex = new JRadioButton(I18N.tr(ON_VERTEX)); bVertex.addActionListener( EventHandler.create(ActionListener.class, point, "setOnVertex")); bVertex.addActionListener( EventHandler.create(ActionListener.class, this, "onClickVertex")); boolean onVertex = ((PointSymbolizer)point.getSymbolizer()).isOnVertex(); bVertex.setSelected(onVertex); JRadioButton bCentroid = new JRadioButton(I18N.tr(ON_CENTROID)); bCentroid.addActionListener( EventHandler.create(ActionListener.class, point, "setOnCentroid")); bCentroid.addActionListener( EventHandler.create(ActionListener.class, this, "onClickCentroid")); bCentroid.setSelected(!onVertex); ButtonGroup bg = new ButtonGroup(); bg.add(bVertex); bg.add(bCentroid); JPanel jp = new JPanel(); jp.add(bVertex); jp.add(bCentroid); return jp; }
Source:
<code><START> public Object getEvidence() { <END> return evidence; }</code><technical_language>return type Evidence</technical_language>

Target:
public Evidence getEvidence() { return evidence; }
Source:
<code>public Void execute(Context context) { KieSession ksession = ((RegistryContext) context).lookup( KieSession.class ); ProcessInstance processInstance = ksession.getProcessInstance(processInstanceId); DynamicNodeInstance dynamicContext = (DynamicNodeInstance) ((WorkflowProcessInstanceImpl) processInstance).getNodeInstances(true).stream() <START> .filter(ni -> (ni instanceof DynamicNodeInstance) && stage.equals(ni.getNode().getMetaData().get("UniqueId")) || stage.equals(ni.getNodeName())) <END> .findFirst() .orElseThrow(() -> new StageNotFoundException("No stage found with id " + stage)); CaseStage caseStage = caseDef.getCaseStages() .stream() .filter(stage -> stage.getId().equals(dynamicContext.getNode().getMetaData().get("UniqueId"))) .findFirst() .get(); if (!caseStage.getAdHocFragments().stream().anyMatch(fragment -> fragment.getName().equals(fragmentName))) { throw new AdHocFragmentNotFoundException("AdHoc fragment '" + fragmentName + "' not found in case " + ((WorkflowProcessInstanceImpl)processInstance).getCorrelationKey() + " and stage " + stage); } dynamicContext.signalEvent(fragmentName, data); return null; }</code><technical_language>missing parentheses? if NodeInstance is a dynamic nodeName is I for? I guess a ClassCastException. (ni instanceof DynamicNodeInstance) && (stage.equals(ni.getNode().getMetaData().get("UniqueId")) || stage.equals(ni.getNodeName()))</technical_language>

Target:
public Void execute(Context context) { KieSession ksession = ((RegistryContext) context).lookup( KieSession.class ); ProcessInstance processInstance = ksession.getProcessInstance(processInstanceId); DynamicNodeInstance dynamicContext = (DynamicNodeInstance) ((WorkflowProcessInstanceImpl) processInstance).getNodeInstances(true).stream() .filter(ni -> (ni instanceof DynamicNodeInstance) && (stage.equals(ni.getNode().getMetaData().get("UniqueId")) || stage.equals(ni.getNodeName()))) .findFirst() .orElseThrow(() -> new StageNotFoundException("No stage found with id " + stage)); CaseStage caseStage = caseDef.getCaseStages() .stream() .filter(stage -> stage.getId().equals(dynamicContext.getNode().getMetaData().get("UniqueId"))) .findFirst() .get(); if (!caseStage.getAdHocFragments().stream().anyMatch(fragment -> fragment.getName().equals(fragmentName))) { throw new AdHocFragmentNotFoundException("AdHoc fragment '" + fragmentName + "' not found in case " + ((WorkflowProcessInstanceImpl)processInstance).getCorrelationKey() + " and stage " + stage); } dynamicContext.signalEvent(fragmentName, data); return null; }
Source:
<code>public void setReadScopes(final Set<String> readScopes) { <START> this.readScopes = Objects.isNull(readScopes) ? Collections.emptySet() : readScopes; <END> }</code><technical_language>this isNull method? readScopes == null</technical_language>

Target:
public void setReadScopes(final Set<String> readScopes) { this.readScopes = readScopes == null ? Collections.emptySet() : readScopes; }
Source:
<code>protected void postLoad(DAnalysis dAnalysis, Version loadedVersion) { if (loadedVersion.compareTo(MIGRATION_VERSION) < 0) { for (DView dView : dAnalysis.getOwnedViews()) { for (DDiagram dDiagram : Iterables.filter(new DViewQuery(dView).getLoadedRepresentations(), DDiagram.class)) { if <START> (!"SequenceDDiagramSpec".equals(dDiagram.getClass().getSimpleName())) <END> { List<Edge> edgeList = getEdgeList(dDiagram); for (Edge edge : edgeList) { checkAndRepairBendpointsOfEdge(edge); } } } } } }</code><technical_language>explicitly restrict DSemanticDiagramSpec</technical_language>

Target:
protected void postLoad(DAnalysis dAnalysis, Version loadedVersion) { if (loadedVersion.compareTo(MIGRATION_VERSION) < 0) { for (DView dView : dAnalysis.getOwnedViews()) { for (DDiagram dDiagram : Iterables.filter(new DViewQuery(dView).getLoadedRepresentations(), DDiagram.class)) { if ("DSemanticDiagramSpec".equals(dDiagram.getClass().getSimpleName())) { List<Edge> edgeList = getEdgeList(dDiagram); for (Edge edge : edgeList) { checkAndRepairBendpointsOfEdge(edge); } } } } } }
Source:
<code>private RequestCallback getBucketsRequestCallBack() { return new RequestCallback() { @Override public void onResponseReceived(Request request, Response response) { JSONArray bucketsArray = JSONParser.parseStrict(response.getText()).isArray(); List<String> bucketNames = new LinkedList<>(); for (int i = 0; i < bucketsArray.size(); i++) { JSONObject bucketObject = bucketsArray.get(i).isObject(); String bucketName = bucketObject.get(NAME_KEY).isString().stringValue(); <START> bucketNames.add(bucketName); <END> } for (String bucketName : bucketNames) { requestNodeSourcesForBucket(bucketName); } CatalogRequestBuilder.this.importFromCatalogPanel.enableNodeSourceListBox(); } @Override public void onError(Request request, Throwable t) { GWT.log("List buckets from catalog failed. Request was " + request.toString(), t); } }; }</code><technical_language>remove List<String> bucketNames = new LinkedList<>(); simply call requestNodeSourcesForBucket(bucketName) in this loop</technical_language>

Target:
private RequestCallback getBucketsRequestCallBack() { return new RequestCallback() { @Override public void onResponseReceived(Request request, Response response) { JSONArray bucketsArray = JSONParser.parseStrict(response.getText()).isArray(); for (int i = 0; i < bucketsArray.size(); i++) { JSONObject bucketObject = bucketsArray.get(i).isObject(); String bucketName = bucketObject.get(NAME_KEY).isString().stringValue(); requestNodeSourcesForBucket(bucketName); } CatalogRequestBuilder.this.importFromCatalogPanel.enableNodeSourceListBox(); } @Override public void onError(Request request, Throwable t) { CatalogRequestBuilder.this.importFromCatalogPanel.setNodeSourceWindowLabelWithError("List buckets from catalog failed", t); } }; }
Source:
<code>protected String getFile(String stack, String filename) throws IOException { if(stack != null && stack.equalsIgnoreCase("publicdns")) { String catalogTemplateUrl = String.format(CATALOG_RESOURCE_URL, stack); Request temp = Request.Get(catalogTemplateUrl); Response res = temp.execute(); Template template = jsonMapper.readValue(res.returnContent().asBytes(), Template.class); if (template.getDefaultVersion() != null && template.getVersionLinks() != null) { String versionUrl = template.getVersionLinks().get(template.getDefaultVersion()); log.debug("Catalog system template versionUrl is: [{}]", versionUrl); Request versionReq = Request.Get(versionUrl); Response versionRes = versionReq.execute(); Template templateVersion = jsonMapper.readValue(versionRes.returnContent().asBytes(), Template.class); if(templateVersion != null) { if(filename!= null && filename.startsWith("docker-")){ return templateVersion.getDockerCompose(); }else if(filename!= null && filename.startsWith("rancher-")){ return templateVersion.getRancherCompose(); } } log.error("Failed to load template version"); } else { log.error("Failed to load template details"); } return null; } else { <START> String resource = String.format(STACK_RESOURCE, stack, filename); <END> InputStream is = getClass().getResourceAsStream(resource); if (is == null) { return null; } return IOUtils.toString(is); } }</code><technical_language>need fallback logic. catalog now. existing swarm, k8s functionality is currently enabled need worry breaking things</technical_language>

Target:
protected String getFile(String stack, String filename) throws IOException { String resource = String.format(STACK_RESOURCE, stack, filename); InputStream is = getClass().getResourceAsStream(resource); if (is == null) { return null; } return IOUtils.toString(is); }
Source:
<code>public void run(){ log.debug("Listening for client commands: "+clientNumber); String result = socket.readLine(); <START> if(result == null) { <END> log.error("Client disconnect, BAIL OUT"); System.exit(-1); } try { JsonObject commandsJSON = parser.parse(result).getAsJsonObject(); Map<Player, PlayerCommand> commands = jsonToPlayerCommands(commandsJSON); for(Player player: commands.keySet()){ registerMove(player, commands.get(player)); } log.debug("Got client commands: "+clientNumber); } catch (Exception e) { log.error("error waiting for commands from client", e); System.exit(-1); } }</code><technical_language>More null..</technical_language>

Target:
public void run(){ log.debug("Listening for client commands: "+clientNumber); String result = socket.readLine(); if(!socket.isValid()) { log.error("Client disconnect, BAIL OUT"); System.exit(-1); } try { JsonObject commandsJSON = parser.parse(result).getAsJsonObject(); Map<Player, PlayerCommand> commands = jsonToPlayerCommands(commandsJSON); for(Player player: commands.keySet()){ registerMove(player, commands.get(player)); } log.debug("Got client commands: "+clientNumber); } catch (Exception e) { log.error("error waiting for commands from client", e); System.exit(-1); } }
Source:
<code>protected HdfsSinkConnectorConfig(ConfigDef configDef, Map<String, String> props) { super(configDef, props); ConfigDef storageCommonConfigDef = StorageCommonConfig.newConfigDef(STORAGE_CLASS_RECOMMENDER); commonConfig = new StorageCommonConfig(storageCommonConfigDef, originalsStrings()); hiveConfig = new HiveConfig(originalsStrings()); ConfigDef partitionerConfigDef = PartitionerConfig.newConfigDef(PARTITIONER_CLASS_RECOMMENDER); partitionerConfig = new PartitionerConfig(partitionerConfigDef, originalsStrings()); this.name = parseName(originalsStrings()); this.hadoopConfig = new Configuration(); addToGlobal(hiveConfig); addToGlobal(partitionerConfig); addToGlobal(commonConfig); addToGlobal(this); this.url = extractUrl(); try { this.topixRegexCaptureGroup = getString(TOPIC_REGEX_CAPTURE_GROUP_CONFIG) != null ? Pattern.compile(getString(TOPIC_REGEX_CAPTURE_GROUP_CONFIG)) : null; } catch (PatternSyntaxException e) { throw new ConfigException( TOPIC_REGEX_CAPTURE_GROUP_CONFIG + " is an invalid regex pattern: ", e ); } <START> partsToReplace = getPartsToReplace(); <END> }</code><technical_language>partsToReplace need a field</technical_language>

Target:
protected HdfsSinkConnectorConfig(ConfigDef configDef, Map<String, String> props) { super(configDef, props); ConfigDef storageCommonConfigDef = StorageCommonConfig.newConfigDef(STORAGE_CLASS_RECOMMENDER); commonConfig = new StorageCommonConfig(storageCommonConfigDef, originalsStrings()); hiveConfig = new HiveConfig(originalsStrings()); ConfigDef partitionerConfigDef = PartitionerConfig.newConfigDef(PARTITIONER_CLASS_RECOMMENDER); partitionerConfig = new PartitionerConfig(partitionerConfigDef, originalsStrings()); this.name = parseName(originalsStrings()); this.hadoopConfig = new Configuration(); addToGlobal(hiveConfig); addToGlobal(partitionerConfig); addToGlobal(commonConfig); addToGlobal(this); this.url = extractUrl(); try { String topicRegex = getString(TOPIC_CAPTURE_GROUPS_REGEX_CONFIG); this.topicRegexCaptureGroup = topicRegex != null ? Pattern.compile(topicRegex) : null; } catch (PatternSyntaxException e) { throw new ConfigException( TOPIC_CAPTURE_GROUPS_REGEX_CONFIG + " is an invalid regex pattern: ", e ); } topicDirGroupsMaxIndex = getMaxIndexToReplace(getString(TOPICS_DIR_CONFIG)); logDirGroupsMaxIndex = getMaxIndexToReplace(getString(LOGS_DIR_CONFIG)); validateDirsAndRegex(); }
Source:
<code>public SourceOperator createOperator(DriverContext driverContext) { checkState(!closed, "Factory is already closed"); OperatorContext operatorContext = driverContext.addOperatorContext(operatorId, sourceId, MergeOperator.class.getSimpleName()); if (exchangeClientCache == null) { exchangeClientCache = CacheBuilder.<URI, ExchangeClient>newBuilder() .build(CacheLoader.from(location -> { <START> ExchangeClient exchangeClient = exchangeClientSupplier.get(driverContext.getPipelineContext().localSystemMemoryContext()); <END> exchangeClient.addLocation(location); exchangeClient.noMoreLocations(); return exchangeClient; })); } return new MergeOperator( operatorContext, sourceId, exchangeClientCache, serdeFactory.createPagesSerde(), pageWithPositionComparatorFactory.create(types, sortChannels, sortOrder), outputChannels, outputTypes); }</code><technical_language>I missing here, do need cache exchange clients? Is expensive create a new exchange client</technical_language>

Target:
public SourceOperator createOperator(DriverContext driverContext) { checkState(!closed, "Factory is already closed"); OperatorContext operatorContext = driverContext.addOperatorContext(operatorId, sourceId, MergeOperator.class.getSimpleName()); return new MergeOperator( operatorContext, sourceId, exchangeClientSupplier, serdeFactory.createPagesSerde(), orderingCompiler.compilePageWithPositionComparator(types, sortChannels, sortOrder), outputChannels, outputTypes); }
Source:
<code>public ConfirmationPageObject enterActivationLink(String email, String password, String wikiURL) { ConfirmationPageObject confirmPage = enterActivationLink(email, password, wikiURL, "english"); <START> return confirmPage; <END> }</code><technical_language>is need variable here, use: return enterActivationLink(email, password, wikiURL, "english");</technical_language>

Target:
public ConfirmationPageObject enterActivationLink(String email, String password, String wikiURL) { return enterActivationLink(email, password, wikiURL, default_lang); }
Source:
<code>public Object postProcessAfterInitialization(Object bean, String beanName) throws BeansException { if (bean instanceof Executor && !(bean instanceof ThreadPoolTaskExecutor)) { Method execute = ReflectionUtils.findMethod(bean.getClass(), "execute", Runnable.class); boolean methodFinal = Modifier.isFinal(execute.getModifiers()); boolean classFinal = Modifier.isFinal(bean.getClass().getModifiers()); boolean cglibProxy = !methodFinal && !classFinal; Executor executor = (Executor) bean; try { return createProxy(bean, cglibProxy, executor); } catch (AopConfigException e) { if (cglibProxy) { if (log.isDebugEnabled()) { log.debug("Exception occurred while trying to create a proxy, falling back to JDK proxy", e); } return createProxy(bean, false, executor); } throw e; } } else if (bean instanceof ThreadPoolTaskExecutor) { boolean classFinal = Modifier.isFinal(bean.getClass().getModifiers()); boolean cglibProxy = !classFinal; ThreadPoolTaskExecutor executor = (ThreadPoolTaskExecutor) bean; <START> AsyncProperties asyncProperties = asyncConfigurationProperties(); <END> if (!asyncProperties.getIgnoredBeans().contains(beanName)) { return createThreadPoolTaskExecutorProxy(bean, cglibProxy, executor); } else { log.info("Not instrumenting bean " + beanName); } } return bean; }</code><technical_language>need a test for</technical_language>

Target:
public Object postProcessAfterInitialization(Object bean, String beanName) throws BeansException { if (bean instanceof Executor && !(bean instanceof ThreadPoolTaskExecutor)) { Method execute = ReflectionUtils.findMethod(bean.getClass(), "execute", Runnable.class); boolean methodFinal = Modifier.isFinal(execute.getModifiers()); boolean classFinal = Modifier.isFinal(bean.getClass().getModifiers()); boolean cglibProxy = !methodFinal && !classFinal; Executor executor = (Executor) bean; try { return createProxy(bean, cglibProxy, executor); } catch (AopConfigException e) { if (cglibProxy) { if (log.isDebugEnabled()) { log.debug("Exception occurred while trying to create a proxy, falling back to JDK proxy", e); } return createProxy(bean, false, executor); } throw e; } } else if (bean instanceof ThreadPoolTaskExecutor) { if (isProxyNeeded(beanName)) { boolean classFinal = Modifier.isFinal(bean.getClass().getModifiers()); boolean cglibProxy = !classFinal; ThreadPoolTaskExecutor executor = (ThreadPoolTaskExecutor) bean; return createThreadPoolTaskExecutorProxy(bean, cglibProxy, executor); } else { log.info("Not instrumenting bean " + beanName); } } return bean; }
Source:
<code>public void shouldUnsetOtherPreferredIdentifiers() throws Exception { PatientIdentifier nonPreferred = service.getPatientIdentifierByUuid(getUuid()); long originalCount = getAllCount(); SimpleObject patientIdentifier = new SimpleObject(); patientIdentifier.add("identifier", "abc123ez"); patientIdentifier.add("identifierType", "2f470aa8-1d73-43b7-81b5-01f0c0dfa53c"); patientIdentifier.add("location", RestTestConstants1_8.LOCATION_UUID); patientIdentifier.add("preferred", true); String json = new ObjectMapper().writeValueAsString(patientIdentifier); MockHttpServletRequest req = request(RequestMethod.POST, getURI()); req.setContent(json.getBytes()); SimpleObject newPatientIdentifier = deserialize(handle(req)); assertNotNull(PropertyUtils.getProperty(newPatientIdentifier, "uuid")); assertEquals(originalCount + 1, getAllCount()); String preferredUuid = (String) PropertyUtils.getProperty(newPatientIdentifier, "uuid"); PatientIdentifier preferredIdentifer = service.getPatientIdentifierByUuid(preferredUuid); <START> System.out.print("none prefered is " + nonPreferred.isPreferred()); <END> System.out.print("prefered is " + preferredIdentifer.isPreferred()); assertEquals(nonPreferred.isPreferred(), false); assertEquals(preferredIdentifer.isPreferred(), true); }</code><technical_language>looked this? <LINK_0></technical_language>

Target:
public void shouldUnsetOtherPreferredIdentifiers() throws Exception { PatientIdentifier exisitingIdentifier = service.getPatientIdentifierByUuid(getUuid()); long originalCount = getAllCount(); assertTrue(exisitingIdentifier.isPreferred()); SimpleObject patientIdentifier = new SimpleObject(); patientIdentifier.add("identifier", "abc123ez"); patientIdentifier.add("identifierType", "2f470aa8-1d73-43b7-81b5-01f0c0dfa53c"); patientIdentifier.add("location", RestTestConstants1_8.LOCATION_UUID); patientIdentifier.add("preferred", true); String json = new ObjectMapper().writeValueAsString(patientIdentifier); MockHttpServletRequest req = request(RequestMethod.POST, getURI()); req.setContent(json.getBytes()); SimpleObject newPatientIdentifier = deserialize(handle(req)); Object uuid = PropertyUtils.getProperty(newPatientIdentifier, "uuid"); assertNotNull(uuid); assertEquals(originalCount + 1, getAllCount()); PatientIdentifier newIdentifer = service.getPatientIdentifierByUuid(uuid.toString()); assertFalse(exisitingIdentifier.isPreferred()); assertTrue(newIdentifer.isPreferred()); assertEquals(newIdentifer.getIdentifier(), "abc123ez"); }
Source:
<code><START> protected static boolean hasPlaceholder(@NotNull String formatString) { <END> return StringUtil.contains(formatString, "%"); }</code><technical_language>inspection is client of this method, move method inspection</technical_language>

Target:
public static boolean hasPlaceholder(@NotNull String formatString) { return StringUtil.containsChar(formatString, '%'); }
Source:
<code>GenericIndexed( ByteBuffer buffer, ObjectStrategy<T> strategy, boolean allowReverseLookup ) { this.theBuffer = buffer; this.strategy = strategy; this.allowReverseLookup = allowReverseLookup; <START> size = theBuffer.getInt(); <END> numElementsPerValueFile = size; int indexOffset = theBuffer.position(); int valuesOffset = theBuffer.position() + (size << 2); buffer.position(valuesOffset); valueBuffers = Lists.newArrayList(buffer.slice()); buffer.position(indexOffset); headerBuffer = buffer.slice(); final ByteBuffer valueBuffer = valueBuffers.get(0); bufferIndexed = new BufferIndexed() { @Override public T get(int index) { if (index < 0) { throw new IAE("Index[%s] < 0", index); } if (index >= size) { throw new IAE(String.format("Index[%s] >= size[%s]", index, size)); } ByteBuffer copyHeaderBuffer = headerBuffer.asReadOnlyBuffer(); final int startOffset; final int endOffset; if (index == 0) { copyHeaderBuffer.position(0); startOffset = 4; endOffset = copyHeaderBuffer.getInt(); } else { copyHeaderBuffer.position((index - 1) * Ints.BYTES); startOffset = copyHeaderBuffer.getInt() + 4; endOffset = copyHeaderBuffer.getInt(); } return _get(valueBuffer.asReadOnlyBuffer(), startOffset, endOffset); } }; }</code><technical_language>Suggested numElements, match format description in header. is for other fields</technical_language>

Target:
GenericIndexed( ByteBuffer buffer, ObjectStrategy<T> strategy, boolean allowReverseLookup ) { this.theBuffer = buffer; this.strategy = strategy; this.allowReverseLookup = allowReverseLookup; size = theBuffer.getInt(); int indexOffset = theBuffer.position(); int valuesOffset = theBuffer.position() + size * Ints.BYTES; buffer.position(valuesOffset); valueBuffers = Lists.newArrayList(buffer.slice()); buffer.position(indexOffset); headerBuffer = buffer.slice(); final ByteBuffer valueBuffer = valueBuffers.get(0); bufferIndexed = new BufferIndexed() { @Override public T get(int index) { checkIndex(index, size); final int startOffset; final int endOffset; if (index == 0) { startOffset = 4; endOffset = headerBuffer.getInt(0); } else { int headerPosition = (index - 1) * Ints.BYTES; startOffset = headerBuffer.getInt(headerPosition) + Ints.BYTES; endOffset = headerBuffer.getInt(headerPosition + Ints.BYTES); } return _get(valueBuffer.asReadOnlyBuffer(), startOffset, endOffset); } }; }
Source:
<code>public void loginAsync_throwExceptionInErrorHandler() throws InterruptedException { final CountDownLatch latch = new CountDownLatch(1); try { SyncCredentials credentials = SyncCredentials.usernamePassword("IWantToHackYou", "GeneralPassword", false); SyncUser.loginAsync(credentials, Constants.AUTH_URL, new SyncUser.Callback() { @Override public void onSuccess(SyncUser user) { fail(); } @Override public void onError(ObjectServerError error) { latch.countDown(); throw new IllegalArgumentException("Boom"); } }); <START> Thread.sleep(1000); END> TestHelper.awaitOrFail(latch); fail(); } catch (IllegalArgumentException e) { assertEquals("Boom", e.getMessage()); } catch (Exception ignored) { fail(); } finally { looperThread.testComplete(); } }</code><technical_language>Is this required</technical_language>

Target:
public void loginAsync_throwExceptionInErrorHandler() throws InterruptedException { final CountDownLatch latch = new CountDownLatch(1); SyncCredentials credentials = SyncCredentials.usernamePassword("IWantToHackYou", "GeneralPassword", false); SyncUser.loginAsync(credentials, Constants.AUTH_URL, new SyncUser.Callback() { @Override public void onSuccess(SyncUser user) { Log.d("REALM", "onSuccess"); fail(); } @Override public void onError(ObjectServerError error) { Log.d("REALM", "onError 1"); latch.countDown(); Log.d("REALM", "onError 2"); throw new IllegalArgumentException("Boom"); } }); Log.d("REALM", "main 1"); TestHelper.awaitOrFail(latch); Log.d("REALM", "main 2"); looperThread.testComplete(); Log.d("REALM", "main 3"); }
Source:
<code>private ReadCountCollection processReadCounts(@Nonnull final ReadCountCollection rawReadCounts) { if (rawReadCounts.columnNames().size() > 1) { return ReadCountCollectionUtils.removeTotallyUncoveredTargets(rawReadCounts, logger); } else { final long numUncoveredTargets = rawReadCounts.records().stream() .filter(rec -> (int)rec.getDouble(0) == 0).count(); final long numAllTargets = rawReadCounts.targets().size(); logger.info("Since only one sample is given for genotyping, the user is responsible for asserting" + <START> " the aptitute of targets. Fully uncovered (irrelevant) targets can not be automatically" + <END> " identified (total targets: " + numAllTargets + ", uncovered targets: " + numUncoveredTargets + ")"); return rawReadCounts; } }</code><technical_language>>aptitude</technical_language>

Target:
private ReadCountCollection processReadCounts(@Nonnull final ReadCountCollection rawReadCounts) { if (rawReadCounts.columnNames().size() > 1) { return ReadCountCollectionUtils.removeTotallyUncoveredTargets(rawReadCounts, logger); } else { final long numUncoveredTargets = rawReadCounts.records().stream() .filter(rec -> (int)rec.getDouble(0) == 0).count(); final long numAllTargets = rawReadCounts.targets().size(); logger.info("Since only one sample is given for genotyping, the user is responsible for asserting" + " the aptitude of targets. Fully uncovered (irrelevant) targets can not be automatically" + " identified (total targets: " + numAllTargets + ", uncovered targets: " + numUncoveredTargets + ")"); return rawReadCounts; } }
Source:
<code>private static String getFieldAlertProperty( int pluginId, String key, String contentDefault, ExtensionExportReport extensionExport) { if (key.contains("risk") || key.contains("reliability")) { return getMessage( <START> extensionExport, "alertreport.export.pluginid." + key, contentDefault); <END> } StringBuilder sbKey = new StringBuilder(50); sbKey.append("alertreport.export.pluginid."); sbKey.append(pluginId); sbKey.append('.'); sbKey.append(key); return getMessage(extensionExport, sbKey.toString(), contentDefault); }</code><technical_language>changed exportreport, worth adding a task tag for review/changes</technical_language>

Target:
private static String getFieldAlertProperty( int pluginId, String key, String contentDefault, ExtensionExportReport extensionExport) { if (key.contains("risk") || key.contains("reliability")) { return getMessage( extensionExport, "exportreport.export.pluginid." + key, contentDefault); } StringBuilder sbKey = new StringBuilder(50); sbKey.append("exportreport.export.pluginid."); sbKey.append(pluginId); sbKey.append('.'); sbKey.append(key); return getMessage(extensionExport, sbKey.toString(), contentDefault); }