org.apache.commons.compress.utils.Lists Java Examples

private final List<CfBreakendData> loadChainFinderData(final String sampleId, final String chainDataFile)
{
    try
    {
        final List<String> lines = Files.readAllLines(Paths.get(chainDataFile));

        if(lines.size() <= 2)
            return Lists.newArrayList();

        final Map<String,Integer> fielIndexMap = createFieldsIndexMap(lines.get(0), CF_DATA_DELIMITER);
        lines.remove(0); // header
        lines.remove(lines.size() - 1); // summary row

        return lines.stream().map(x -> CfBreakendData.fromData(x, fielIndexMap)).collect(Collectors.toList());
    }
    catch(IOException e)
    {
        LNX_LOGGER.error("failed to load chain data file({}): {}", chainDataFile.toString(), e.toString());
        return null;
    }

}
 

/**
 * 准备(界面字段等)
 */
@Override
public void prepare() {
    templateId = AliYunMsgForm.getInstance().getMsgTemplateIdTextField().getText();

    if (AliYunMsgForm.getInstance().getTemplateMsgDataTable().getModel().getRowCount() == 0) {
        AliYunMsgForm.initTemplateDataTable();
    }

    DefaultTableModel tableModel = (DefaultTableModel) AliYunMsgForm.getInstance().getTemplateMsgDataTable().getModel();
    int rowCount = tableModel.getRowCount();
    TemplateData templateData;
    templateDataList = Lists.newArrayList();
    for (int i = 0; i < rowCount; i++) {
        String name = ((String) tableModel.getValueAt(i, 0)).trim();
        String value = ((String) tableModel.getValueAt(i, 1)).trim();
        templateData = new TemplateData();
        templateData.setName(name);
        templateData.setValue(value);
        templateDataList.add(templateData);
    }

}
 

/**
 * 准备(界面字段等)
 */
@Override
public void prepare() {
    templateId = MaSubscribeMsgForm.getInstance().getMsgTemplateIdTextField().getText().trim();
    templateUrl = MaSubscribeMsgForm.getInstance().getMsgTemplateUrlTextField().getText().trim();

    if (MaSubscribeMsgForm.getInstance().getTemplateMsgDataTable().getModel().getRowCount() == 0) {
        MaSubscribeMsgForm.initTemplateDataTable();
    }

    DefaultTableModel tableModel = (DefaultTableModel) MaSubscribeMsgForm.getInstance().getTemplateMsgDataTable().getModel();
    int rowCount = tableModel.getRowCount();
    TemplateData templateData;
    templateDataList = Lists.newArrayList();
    for (int i = 0; i < rowCount; i++) {
        String name = ((String) tableModel.getValueAt(i, 0)).trim();
        String value = ((String) tableModel.getValueAt(i, 1)).trim();
        String color = ((String) tableModel.getValueAt(i, 2)).trim();
        templateData = new TemplateData();
        templateData.setName(name);
        templateData.setValue(value);
        templateData.setColor(color);
        templateDataList.add(templateData);
    }
}
 

/**
 * 准备(界面字段等)
 */
@Override
public void prepare() {
    templateId = UpYunMsgForm.getInstance().getMsgTemplateIdTextField().getText();

    if (UpYunMsgForm.getInstance().getTemplateMsgDataTable().getModel().getRowCount() == 0) {
        UpYunMsgForm.initTemplateDataTable();
    }

    DefaultTableModel tableModel = (DefaultTableModel) UpYunMsgForm.getInstance().getTemplateMsgDataTable().getModel();
    int rowCount = tableModel.getRowCount();
    paramList = Lists.newArrayList();
    for (int i = 0; i < rowCount; i++) {
        String value = ((String) tableModel.getValueAt(i, 1));
        paramList.add(value);
    }
}
 

/**
 * 准备(界面字段等)
 */
@Override
public void prepare() {
    templateId = Integer.parseInt(TxYunMsgForm.getInstance().getMsgTemplateIdTextField().getText());

    if (TxYunMsgForm.getInstance().getTemplateMsgDataTable().getModel().getRowCount() == 0) {
        TxYunMsgForm.initTemplateDataTable();
    }

    DefaultTableModel tableModel = (DefaultTableModel) TxYunMsgForm.getInstance().getTemplateMsgDataTable().getModel();
    int rowCount = tableModel.getRowCount();
    paramList = Lists.newArrayList();
    for (int i = 0; i < rowCount; i++) {
        String value = ((String) tableModel.getValueAt(i, 1));
        paramList.add(value);
    }
}
 

/**
 * 准备(界面字段等)
 */
@Override
public void prepare() {
    templateId = HwYunMsgForm.getInstance().getMsgTemplateIdTextField().getText();

    if (HwYunMsgForm.getInstance().getTemplateMsgDataTable().getModel().getRowCount() == 0) {
        HwYunMsgForm.initTemplateDataTable();
    }

    DefaultTableModel tableModel = (DefaultTableModel) HwYunMsgForm.getInstance().getTemplateMsgDataTable().getModel();
    int rowCount = tableModel.getRowCount();
    paramList = Lists.newArrayList();
    for (int i = 0; i < rowCount; i++) {
        String value = ((String) tableModel.getValueAt(i, 1));
        paramList.add(value);
    }
}
 

public FusionCohortData(final String[] chromosomes, final int[] junctionPositions, final byte[] junctionOrientations,
        final FusionJunctionType[] junctionTypes, final String svType, final String[] geneIds, final String[] geneNames)
{
    mSampleIds = Lists.newArrayList();
    Chromosomes = chromosomes;
    JunctionPositions = junctionPositions;
    JunctionOrientations = junctionOrientations;
    JunctionTypes = junctionTypes;
    SvType = svType;
    GeneIds = geneIds;
    GeneNames = geneNames;

    mSampleCount = 0;
    mTotalFragments = 0;
    mMaxFragments = 0;
}
 

/**
 * 准备(界面字段等)
 */
@Override
public void prepare() {
    templateId = MaTemplateMsgForm.getInstance().getMsgTemplateIdTextField().getText().trim();
    templateUrl = MaTemplateMsgForm.getInstance().getMsgTemplateUrlTextField().getText().trim();
    templateKeyWord = MaTemplateMsgForm.getInstance().getMsgTemplateKeyWordTextField().getText().trim() + ".DATA";

    if (MaTemplateMsgForm.getInstance().getTemplateMsgDataTable().getModel().getRowCount() == 0) {
        MaTemplateMsgForm.initTemplateDataTable();
    }

    DefaultTableModel tableModel = (DefaultTableModel) MaTemplateMsgForm.getInstance().getTemplateMsgDataTable().getModel();
    int rowCount = tableModel.getRowCount();
    TemplateData templateData;
    templateDataList = Lists.newArrayList();
    for (int i = 0; i < rowCount; i++) {
        String name = ((String) tableModel.getValueAt(i, 0)).trim();
        String value = ((String) tableModel.getValueAt(i, 1)).trim();
        String color = ((String) tableModel.getValueAt(i, 2)).trim();
        templateData = new TemplateData();
        templateData.setName(name);
        templateData.setValue(value);
        templateData.setColor(color);
        templateDataList.add(templateData);
    }
}
 

public void init() {
    this.setName(UiConsts.APP_NAME);
    this.setTitle(UiConsts.APP_NAME);
    List<Image> images = Lists.newArrayList();
    images.add(UiConsts.IMAGE_LOGO_1024);
    images.add(UiConsts.IMAGE_LOGO_512);
    images.add(UiConsts.IMAGE_LOGO_256);
    images.add(UiConsts.IMAGE_LOGO_128);
    images.add(UiConsts.IMAGE_LOGO_64);
    images.add(UiConsts.IMAGE_LOGO_48);
    images.add(UiConsts.IMAGE_LOGO_32);
    images.add(UiConsts.IMAGE_LOGO_24);
    images.add(UiConsts.IMAGE_LOGO_16);
    this.setIconImages(images);
    // Mac系统Dock图标
    if (SystemUtil.isMacOs()) {
        Application application = Application.getApplication();
        application.setDockIconImage(UiConsts.IMAGE_LOGO_1024);
        application.setEnabledAboutMenu(false);
        application.setEnabledPreferencesMenu(false);
    }

    ComponentUtil.setPreferSizeAndLocateToCenter(this, 0.8, 0.88);
}
 

protected void flush(@NotNull final GenomePosition position) {
    final List<SageVariant> flushed = Lists.newArrayList();
    final Iterator<SageVariant> iterator = buffer.iterator();
    while (iterator.hasNext()) {
        final SageVariant entry = iterator.next();
        long entryEnd = entry.position() + entry.ref().length() - 1;
        if (!entry.chromosome().equals(position.chromosome()) || entryEnd < position.position() - maxDistance) {
            iterator.remove();
            flushed.add(entry);
        } else {
            break;
        }
    }

    if (!flushed.isEmpty()) {
        preFlush(flushed);
    }

    flushed.forEach(consumer);
    flushed.clear();
}
 

public FusionData(int id, final String[] chromosomes, final int[] junctionPositions, final byte[] junctionOrientations,
        final FusionJunctionType[] junctionTypes, final String svType, final String[] geneIds, final String[] geneNames,
        int splitFrags, int realignedFrags, int discordantFrags, final int[] coverage, final int[] anchorDistance, int cohortCount)
{
    Id = id;
    Chromosomes = chromosomes;
    JunctionPositions = junctionPositions;
    JunctionOrientations = junctionOrientations;
    JunctionTypes = junctionTypes;
    SvType = svType;
    GeneIds = geneIds;
    GeneNames = geneNames;
    SplitFrags = splitFrags;
    RealignedFrags = realignedFrags;
    DiscordantFrags = discordantFrags;
    Coverage = coverage;
    AnchorDistance = anchorDistance;
    CohortCount = cohortCount;

    mRawData = null;
    mKnownFusionType = KnownGeneType.OTHER;
    mRelatedFusionIds = Lists.newArrayList();
    mHasRelatedKnownSpliceSites = false;
    mCohortFrequency = 0;
    mFilter = "";
}
 

public static void setupNew3DVisualizer(final RawDataFile dataFile, final Range<Double> mzRange,
    final Range<Double> rtRange, final Feature featureToShow) {

  final ParameterSet myParameters =
      MZmineCore.getConfiguration().getModuleParameters(Fx3DVisualizerModule.class);
  final Fx3DVisualizerModule myInstance =
      MZmineCore.getModuleInstance(Fx3DVisualizerModule.class);
  myParameters.getParameter(Fx3DVisualizerParameters.dataFiles)
      .setValue(RawDataFilesSelectionType.SPECIFIC_FILES, new RawDataFile[] {dataFile});
  myParameters.getParameter(Fx3DVisualizerParameters.scanSelection)
      .setValue(new ScanSelection(rtRange, 1));
  myParameters.getParameter(Fx3DVisualizerParameters.mzRange).setValue(mzRange);
  
  List<FeatureSelection> featuresList = Lists.newArrayList();
  if (featureToShow != null) {
    FeatureSelection selectedFeature = new FeatureSelection(null, featureToShow, null, null);
    featuresList.add(selectedFeature);
  }
  
  myParameters.getParameter(Fx3DVisualizerParameters.features).setValue(featuresList);
  if (myParameters.showSetupDialog(MZmineCore.getDesktop().getMainWindow(),
      true) == ExitCode.OK) {
    myInstance.runModule(MZmineCore.getProjectManager().getCurrentProject(),
        myParameters.cloneParameterSet(), new ArrayList<Task>());
  }
}
 

private List<String> getLogs(JSONObject logInfo) {
    List<String> logs = Lists.newArrayList();
    if (logInfo.has("log")) {
        try {
            JSONArray logArray = logInfo.getJSONArray("log");

            for (int i=0; i<logArray.length(); i++) {
                logs.add(logArray.getString(i));
            }

        } catch (JSONException e) {
            e.printStackTrace();
        }
    }
    return logs;
}
 

ColumnRowType buildColumnRowType() {
    OLAPRel olapChild = (OLAPRel) getInput(0);
    ColumnRowType inputColumnRowType = olapChild.getColumnRowType();

    List<TblColRef> columns = new ArrayList<>();
    // the input col always be collected by left
    columns.addAll(inputColumnRowType.getAllColumns());

    // add window aggregate calls column
    for (Group group : groups) {
        List<TupleExpression> sourceColOuter = Lists.newArrayList();
        group.keys.asSet().stream().map(inputColumnRowType::getTupleExpressionByIndex).forEach(sourceColOuter::add);
        group.orderKeys.getFieldCollations().stream().map(RelFieldCollation::getFieldIndex)
                .map(inputColumnRowType::getTupleExpressionByIndex).forEach(sourceColOuter::add);
        for (AggregateCall aggrCall : group.getAggregateCalls(this)) {
            TblColRef aggrCallCol = TblColRef.newInnerColumn(aggrCall.getName(),
                    TblColRef.InnerDataTypeEnum.LITERAL);
            List<TupleExpression> sourceColInner = Lists.newArrayList(sourceColOuter.iterator());
            aggrCall.getArgList().stream().filter(i -> i < inputColumnRowType.size())
                    .map(inputColumnRowType::getTupleExpressionByIndex).forEach(sourceColInner::add);
            aggrCallCol.setSubTupleExps(sourceColInner);
            columns.add(aggrCallCol);
        }
    }
    return new ColumnRowType(columns);
}
 

@Test
public void createTemporaryTableTest() throws SQLException {
    String temporaryTableName = null;
    Connection connection = null;
    try {
        List<Long> idList = Lists.newArrayList();
        for (int i = 0; i < 1000000; i++) {
            idList.add(idWorker.nextId());
        }
        connection = this.dataSource.getConnection();
        long startTime = System.currentTimeMillis();
        temporaryTableName = JdbcUtils.createTemporaryTable(connection, idList);
        long endTime = System.currentTimeMillis();
        System.out.println(endTime - startTime);
    } catch (Exception e) {
        e.printStackTrace();
    } finally {
        if (StringUtils.isNotEmpty(temporaryTableName)) {
            JdbcUtils.dropTemporaryTable(connection, temporaryTableName);
        }
        JdbcUtils.close(connection);
    }
}
 

/**
 * 数据字典选择
 *
 * @return
 */
@ApiOperation(value = "数据字典选择", notes = "数据字典选择")
@ApiImplicitParam(paramType = "path", name = "parentId", value = "父ID", required = true, dataType = "Integer")
@GetMapping("/select/{parentId}")
public CommonResult<List<SelectTreeNode>> select(@PathVariable("parentId") Long parentId) {
    Map<String, Object> params = Maps.newHashMap();
    if (parentId != null && 0 != parentId) {
        params.put("parentId", parentId);
    }
    List<SysDic> dicList = sysDicService.selectDicList(params);
    List<SelectTreeNode> treeNodeList = Lists.newArrayList();
    if (!dicList.isEmpty()) {
        dicList.forEach(dic -> {
            SelectTreeNode selectTreeNode = new SelectTreeNode();
            selectTreeNode.setId(dic.getId().toString());
            selectTreeNode.setParentId(dic.getParentId().toString());
            selectTreeNode.setName(dic.getVarName());
            treeNodeList.add(selectTreeNode);
        });
    }
    treeNodeList.add(SelectTreeNode.createParent());
    return CommonResult.success(treeNodeList);
}
 

/**
 * 角色信息
 */
@ApiOperation(value = "角色信息", notes = "角色信息")
@ApiImplicitParam(paramType = "path", name = "roleId", value = "主键ID", dataType = "Integer", required = true)
@GetMapping("/info/{roleId}")
@RequiresPermissions("sys/role/info")
public CommonResult<SysRole> info(@PathVariable("roleId") Long roleId) {
    SysRole role = sysRoleService.getById(roleId);
    //查询角色对应的菜单
    List<Long> resourceIdList = sysRoleResourceService.selectResourceIdListByRoleId(roleId);
    role.setResourceIdList(resourceIdList);
    List<SysRoleResource> roleResourceList = sysRoleResourceService.selectResourceNodeListByRoleId(roleId);
    List<TreeNode> treeNodeList = Lists.newArrayList();
    if (!roleResourceList.isEmpty()) {
        roleResourceList.forEach(roleResource -> {
            TreeNode treeNode = new TreeNode();
            treeNode.setId(roleResource.getResourceId().toString());
            treeNode.setLabel(roleResource.getResource().getName());
            treeNodeList.add(treeNode);
        });
    }
    role.setResourceNodeList(treeNodeList);
    return CommonResult.success(role);
}
 

@Test
public void testDoubleLists() {
    final long LIST_SIZE = 6;

    List<Double> data = Lists.newArrayList();
    for (int i = 0; i < LIST_SIZE; ++i) {
        data.add(Double.valueOf(i));
    }

    Data listOfDouble = new JData.DataBuilder().addListDouble(KEY, data).build();
    assertEquals(ValueType.DOUBLE, listOfDouble.listType(KEY));

    List<?> actual = listOfDouble.getList(KEY, ValueType.DOUBLE);
    for (int i = 0 ; i < LIST_SIZE; ++i) {
        assertEquals(data.get(i), actual.get(i));
    }
}
 

@Test
public void testBooleanList() {
    final long LIST_SIZE = 6;

    List<Boolean> data = Lists.newArrayList();
    for (int i = 0; i < LIST_SIZE; ++i) {
        data.add(i % 2 == 0);
    }
    Data listOfBoolean = Data.singletonList(KEY, data, ValueType.BOOLEAN);
    assertEquals(ValueType.BOOLEAN, listOfBoolean.listType(KEY));

    List<?> actual = listOfBoolean.getList(KEY, ValueType.BOOLEAN);
    for (int i = 0 ; i < LIST_SIZE; ++i) {
        assertEquals(data.get(i), actual.get(i));
    }
}
 

@Test
public void testsNumericLists() {
    final long LIST_SIZE = 6;

    List<Long> numbers = Lists.newArrayList();
    for (long i = 0; i < LIST_SIZE; ++i) {
        numbers.add(i);
    }
    Data listOfNumbers = new JData.DataBuilder().
            addListInt64(KEY, numbers).
            build();
    assertEquals(ValueType.INT64, listOfNumbers.listType(KEY));

    List<?> actual = listOfNumbers.getList(KEY, ValueType.INT64);
    assertEquals(numbers, actual);
    for (int i = 0 ; i < LIST_SIZE; ++i) {
        assertEquals(numbers.get(i), actual.get(i));
    }
}
 

ColumnRowType buildColumnRowType() {
    OLAPRel olapChild = (OLAPRel) getInput(0);
    ColumnRowType inputColumnRowType = olapChild.getColumnRowType();

    List<TblColRef> columns = new ArrayList<>();
    // the input col always be collected by left
    columns.addAll(inputColumnRowType.getAllColumns());

    // add window aggregate calls column
    for (Group group : groups) {
        List<TupleExpression> sourceColOuter = Lists.newArrayList();
        group.keys.asSet().stream().map(inputColumnRowType::getTupleExpressionByIndex).forEach(sourceColOuter::add);
        group.orderKeys.getFieldCollations().stream().map(RelFieldCollation::getFieldIndex)
                .map(inputColumnRowType::getTupleExpressionByIndex).forEach(sourceColOuter::add);
        for (AggregateCall aggrCall : group.getAggregateCalls(this)) {
            TblColRef aggrCallCol = TblColRef.newInnerColumn(aggrCall.getName(),
                    TblColRef.InnerDataTypeEnum.LITERAL);
            List<TupleExpression> sourceColInner = Lists.newArrayList(sourceColOuter.iterator());
            aggrCall.getArgList().stream().filter(i -> i < inputColumnRowType.size())
                    .map(inputColumnRowType::getTupleExpressionByIndex).forEach(sourceColInner::add);
            aggrCallCol.setSubTupleExps(sourceColInner);
            columns.add(aggrCallCol);
        }
    }
    return new ColumnRowType(columns);
}
 

private List<String> getLogs(JSONObject logInfo) {
    List<String> logs = Lists.newArrayList();
    if (logInfo.has("log")) {
        try {
            JSONArray logArray = logInfo.getJSONArray("log");

            for (int i=0; i<logArray.length(); i++) {
                logs.add(logArray.getString(i));
            }

        } catch (JSONException e) {
            e.printStackTrace();
        }
    }
    return logs;
}
 

public CfSampleData(final String sampleId)
{
    SampleId = sampleId;
    Chains = Maps.newHashMap();
    CfSvList = Lists.newArrayList();
    UnchainedSvList = Lists.newArrayList();
    ClusterChainOverlaps = Lists.newArrayList();
    SvProximityDistance = Maps.newHashMap();
}
 

private static List<TransExonRef> parseTransExonRefs(final String data)
{
    List<TransExonRef> transExonRefs = Lists.newArrayList();

    for(String ref : data.split(ITEM_DELIM, -1))
    {
        String[] items = ref.split(":");
        if(items.length != 4)
            continue;

        transExonRefs.add(new TransExonRef(items[0], Integer.parseInt(items[1]), items[2], Integer.parseInt(items[3])));
    }

    return transExonRefs;
}
 

public static CfBreakendData fromData(final String data, final Map<String,Integer> fieldIndexMap)
{
    // Sample	 Chain	 Breakpoint	 Rearrangement	 Chromosome:position	 Strand
    // Potential chromosomal end loss (left)	 Potential chromosomal end loss (right)	 Deletion bridge partner breakpoint
    // Adjacent breakpoint(s)	 Site annotation
    //CPCT02010452T	 3	 196	 360203	 14:49979403	 1	 0	 0	 195	 |195|197|	 na
    //CPCT02010452T	 3	 197	 360204	 14:49983004	 0	 0	 0	 198	 |196|198|	 na

    String[] items = data.split(CF_DATA_DELIMITER);

    final int chainId = Integer.parseInt(items[fieldIndexMap.get("Chain")]);
    final int breakpointId = Integer.parseInt(items[fieldIndexMap.get("Breakpoint")]);
    final int rearrangeId = Integer.parseInt(items[fieldIndexMap.get("Rearrangement")]);

    final String breakendData = items[fieldIndexMap.get("Chromosome:position")];
    final String chromosome = breakendData.split(":")[0];
    final int position = Integer.parseInt(breakendData.split(":")[1]);

    final byte orientation = items[fieldIndexMap.get("Strand")].equals("0") ? POS_STRAND : NEG_STRAND;

    final boolean[] chromosomeEndLoss = new boolean[] {
            items[fieldIndexMap.get("Potential chromosomal end loss (left)")].equals("1"),
            items[fieldIndexMap.get("Potential chromosomal end loss (right)")].equals("1") };

    final int dbBreakendId = items.length == fieldIndexMap.size() ?
            Integer.parseInt(items[fieldIndexMap.get("Deletion bridge partner breakpoint")]) : NO_ID;

    int adjBndIndex = fieldIndexMap.get("Adjacent breakpoint(s)");
    final String adjacentBreakendData = items.length == fieldIndexMap.size() ? items[adjBndIndex] : items[adjBndIndex - 1];
    int abLength = adjacentBreakendData.length();

    final List<Integer> adjacentBreakendIds = abLength > 2 ?
            Arrays.stream(adjacentBreakendData.substring(0, abLength - 1).substring(1).split("\\|"))
                    .map(x -> Integer.parseInt(x)).collect(Collectors.toList()) : Lists.newArrayList();

    return new CfBreakendData(chainId, breakpointId, rearrangeId, chromosome, position, orientation, chromosomeEndLoss, dbBreakendId, adjacentBreakendIds);
}
 

/**
 * Example command line: {@code tf delete dir/file.txt}
 * <p>
 * Example stdout:<br>
 * <pre>{@code dir:
 * file.txt}</pre>
 * <p>
 * Example stderr:<br>
 * <pre>{@code The item C:\FullPath\dir\file.txt could not be found in your workspace, or you do not have permission to access it.}</pre>
 */
public TfvcDeleteResult parseOutput(String stdout, String stderr) {
    List<java.nio.file.Path> deletedPaths = Lists.newArrayList();
    List<TfsPath> notFoundFiles = Lists.newArrayList();
    List<String> errorMessages = Lists.newArrayList();

    parseStdErr(stderr, notFoundFiles, errorMessages);
    parseStdOut(stdout, deletedPaths);

    return new TfvcDeleteResult(deletedPaths, notFoundFiles, errorMessages);
}
 

/**
 * Example command line: {@code tf delete dir/file.txt}
 * <p>
 * Example stdout:<br>
 * <pre>{@code dir:
 * file.txt}</pre>
 * <p>
 * Example stderr:<br>
 * <pre>{@code The item C:\FullPath\dir\file.txt could not be found in your workspace, or you do not have permission to access it.}</pre>
 */
@Override
public TfvcCheckoutResult parseOutput(String stdout, String stderr) {
    List<TfsLocalPath> checkedOutFiles = Lists.newArrayList();
    List<TfsLocalPath> notFoundFiles = Lists.newArrayList();
    List<String> errorMessages = Lists.newArrayList();

    parseStdErr(stderr, notFoundFiles, errorMessages);
    parseStdOut(stdout, checkedOutFiles);

    return new TfvcCheckoutResult(checkedOutFiles, notFoundFiles, errorMessages);
}
 

public Collection<String> getOrderedAttributeNames(final Set<String> facetsToConsider) {
	// AD Revised in Aug 2019 for Issue #2869: keep constraints between superspecies and subspecies
	final DirectedGraph<String, Object> dependencies = new DefaultDirectedGraph<>(Object.class);
	final Map<String, VariableDescription> all = new HashMap<>();
	this.visitAllAttributes((d) -> {
		all.put(d.getName(), (VariableDescription) d);
		return true;
	});
	Graphs.addAllVertices(dependencies, all.keySet());
	final VariableDescription shape = getAttribute(SHAPE);
	final Collection<VariableDescription> shapeDependencies =
			shape == null ? Collections.EMPTY_LIST : shape.getDependencies(facetsToConsider, false, true);
	all.forEach((an, var) -> {
		for (final VariableDescription newVar : var.getDependencies(facetsToConsider, false, true)) {
			final String other = newVar.getName();
			// AD Revision in April 2019 for Issue #2624: prevent cycles when building the graph
			if (!dependencies.containsEdge(an, other)) {
				dependencies.addEdge(other, an);
			}
		}
		// Adding a constraint between the shape of the macrospecies and the populations of microspecies
		if (var.isSyntheticSpeciesContainer() && !shapeDependencies.contains(var)) {
			dependencies.addEdge(SHAPE, an);
		}
	});
	// June 2020: moving (back) to Iterables instead of Streams.
	return Lists.newArrayList(new TopologicalOrderIterator<>(dependencies));
	// return StreamEx.of(new TopologicalOrderIterator<>(dependencies)).toList();
}
 

@Override
public UserDetails loadUserByUsername(String username) throws UsernameNotFoundException {
    UserDto user = userService.findByUsername(username);
    if (null == user) {
        throw new UsernameNotFoundException(username);
    }

    List<SimpleGrantedAuthority> authorities = Lists.newArrayList();
    authorities.add(new SimpleGrantedAuthority("USER"));

    return new SecurityUser(user.getUsername(), user.getPassword(), authorities);
}
 

@Override
public List<BrowsePaths> computeAssetPaths(final Asset asset, @Nullable final Component component) {
  String remote = component == null ? getRemoteForMetadataAsset(asset.name()) : getRemoteForPackage(asset.name());
  List<BrowsePaths> paths = Lists.newArrayList(computeComponentPaths(asset, component).iterator());
  paths.addAll(BrowsePaths
      .fromPaths(Lists.newArrayList(
          Splitter.on(DIVIDER).omitEmptyStrings().split(getRelativePath(asset.name(), remote)).iterator()),
          true));
  return paths;
}