Examples with ReferencedFile org.knime.core.internal.ReferencedFile used on opensource projects

Example 51 with ReferencedFile

use of org.knime.core.internal.ReferencedFile in project knime-core by knime.

the class FileNodePersistor method loadPorts.

/**
 * @noreference
 * @nooverride
 */
void loadPorts(final Node node, final ExecutionMonitor exec, final NodeSettingsRO settings, final Map<Integer, BufferedDataTable> loadTblRep, final WorkflowDataRepository dataRepository) throws IOException, InvalidSettingsException, CanceledExecutionException {
    final int nrOutPorts = node.getNrOutPorts();
    if (getLoadVersion().isOlderThan(LoadVersion.V200)) {
        // skip flow variables port (introduced in v2.2)
        for (int i = 1; i < nrOutPorts; i++) {
            int oldIndex = getOldPortIndex(i);
            ExecutionMonitor execPort = exec.createSubProgress(1.0 / nrOutPorts);
            exec.setMessage("Port " + oldIndex);
            PortType type = node.getOutputType(i);
            boolean isDataPort = BufferedDataTable.class.isAssignableFrom(type.getPortObjectClass());
            if (m_isConfigured) {
                PortObjectSpec spec = loadPortObjectSpec(node, settings, oldIndex);
                setPortObjectSpec(i, spec);
            }
            if (m_isExecuted) {
                PortObject object;
                if (isDataPort) {
                    object = loadBufferedDataTable(node, settings, execPort, loadTblRep, oldIndex, dataRepository);
                } else {
                    throw new IOException("Can't restore model ports of old 1.x workflows. Execute node again.");
                }
                String summary = object != null ? object.getSummary() : null;
                setPortObject(i, object);
                setPortObjectSummary(i, summary);
            }
            execPort.setProgress(1.0);
        }
    } else {
        if (nrOutPorts == 1) {
            // only the mandatory flow variable port
            return;
        }
        NodeSettingsRO portsSettings = loadPortsSettings(settings);
        exec.setMessage("Reading outport data");
        for (String key : portsSettings.keySet()) {
            NodeSettingsRO singlePortSetting = portsSettings.getNodeSettings(key);
            ExecutionMonitor subProgress = exec.createSubProgress(1 / (double) nrOutPorts);
            int index = loadPortIndex(singlePortSetting);
            if (index < 0 || index >= nrOutPorts) {
                throw new InvalidSettingsException("Invalid outport index in settings: " + index);
            }
            String portDirN = singlePortSetting.getString("port_dir_location");
            if (portDirN != null) {
                ReferencedFile portDir = new ReferencedFile(getNodeDirectory(), portDirN);
                subProgress.setMessage("Port " + index);
                loadPort(node, portDir, singlePortSetting, subProgress, index, loadTblRep, dataRepository);
            }
            subProgress.setProgress(1.0);
        }
    }
}

Example 52 with ReferencedFile

use of org.knime.core.internal.ReferencedFile in project knime-core by knime.

the class BufferedDataTable method loadFromFile.

/**
 * Factory method to restore a table that has been written using
 * the save method.
 * @param dirRef The directory to load from.
 * @param settings The settings to load from.
 * @param exec The exec mon for progress/cancel
 * @param tblRep The table repository
 * @param dataRepository The data repository (needed for blobs and file stores).
 * @return The table as written by save.
 * @throws IOException If reading fails.
 * @throws CanceledExecutionException If canceled.
 * @throws InvalidSettingsException If settings are invalid.
 */
static BufferedDataTable loadFromFile(final ReferencedFile dirRef, final NodeSettingsRO settings, final ExecutionMonitor exec, final Map<Integer, BufferedDataTable> tblRep, final WorkflowDataRepository dataRepository) throws IOException, CanceledExecutionException, InvalidSettingsException {
    File dir = dirRef.getFile();
    NodeSettingsRO s;
    // in version 1.1.x and before, the information was stored in
    // an external data.xml (directly in the node dir)
    boolean isVersion11x;
    File dataXML = new File(dir, TABLE_DESCRIPTION_FILE);
    // loading an exported workflow without data
    if (!dataXML.exists() && settings == null) {
        throw new IOException("No such data file: " + dataXML.getAbsolutePath());
    }
    DataTableSpec spec;
    if (dataXML.exists()) {
        // version 1.2.0 and later
        try (InputStream input = new BufferedInputStream(new FileInputStream(dataXML))) {
            s = NodeSettings.loadFromXML(input);
        }
        spec = loadSpec(dirRef);
        isVersion11x = false;
    } else {
        // version 1.1.x
        s = settings.getNodeSettings(CFG_TABLE_META);
        // needs to be read from zip file!
        spec = null;
        isVersion11x = true;
    }
    int id = s.getInt(CFG_TABLE_ID);
    dataRepository.updateLastId(id);
    String fileName = s.getString(CFG_TABLE_FILE_NAME);
    ReferencedFile fileRef;
    if (fileName != null) {
        fileRef = new ReferencedFile(dirRef, fileName);
        File file = fileRef.getFile();
        if (!file.exists()) {
            throw new IOException("No such data file: " + fileRef);
        }
        if (!file.isFile() || !file.canRead()) {
            throw new IOException("Cannot read file " + fileRef);
        }
    } else {
        // for instance for a column filter node this is null.
        fileRef = null;
    }
    String tableType = CheckUtils.checkSettingNotNull(s.getString(CFG_TABLE_TYPE), "Table type must not be null");
    BufferedDataTable t;
    if (Arrays.asList(TABLE_TYPE_CONTAINER_CUSTOM, TABLE_TYPE_REARRANGE_COLUMN_CUSTOM).contains(tableType)) {
        checkFormat(s);
    }
    if (Arrays.asList(TABLE_TYPE_CONTAINER_COMPRESS, TABLE_TYPE_REARRANGE_COLUMN_COMPRESS).contains(tableType)) {
        checkCompression(s);
    }
    switch(tableType) {
        case TABLE_TYPE_REFERENCE_IN_SAME_NODE:
            return CheckUtils.checkSettingNotNull(tblRep.get(id), "Table reference with ID %d not found in load map", id);
        case TABLE_TYPE_CONTAINER:
            if (isVersion11x) {
                if (fileRef == null) {
                    throw new NullPointerException("Reference on file to load from has not been set.");
                }
                final ContainerTable cont = DataContainer.readFromZip(fileRef.getFile());
                t = new BufferedDataTable(cont, id);
                break;
            }
        // added in 3.6
        case TABLE_TYPE_CONTAINER_CUSTOM:
        case // added in 4.0
        TABLE_TYPE_CONTAINER_COMPRESS:
            final ContainerTable cont = BufferedDataContainer.readFromZipDelayed(fileRef, spec, id, dataRepository);
            t = new BufferedDataTable(cont, id);
            break;
        case TABLE_TYPE_REARRANGE_COLUMN_CUSTOM:
        case TABLE_TYPE_REARRANGE_COLUMN_COMPRESS:
        case TABLE_TYPE_REARRANGE_COLUMN:
        case TABLE_TYPE_JOINED:
        case TABLE_TYPE_VOID:
        case TABLE_TYPE_CONCATENATE:
        case TABLE_TYPE_WRAPPED:
        case TABLE_TYPE_NEW_SPEC:
        case TABLE_TYPE_EXTENSION:
            String[] referenceDirs;
            // (no concatenate table in those versions)
            if (s.containsKey("table_reference")) {
                String refDir = s.getString("table_reference");
                referenceDirs = refDir == null ? new String[0] : new String[] { refDir };
            } else {
                referenceDirs = s.getStringArray(CFG_TABLE_REFERENCE);
            }
            for (String reference : referenceDirs) {
                CheckUtils.checkSettingNotNull(reference, "Reference dir is \"null\"");
                ReferencedFile referenceDirRef = new ReferencedFile(dirRef, reference);
                loadFromFile(referenceDirRef, s, exec, tblRep, dataRepository);
            }
            if (Arrays.asList(TABLE_TYPE_REARRANGE_COLUMN, TABLE_TYPE_REARRANGE_COLUMN_CUSTOM, TABLE_TYPE_REARRANGE_COLUMN_COMPRESS).contains(tableType)) {
                t = new BufferedDataTable(new RearrangeColumnsTable(fileRef, s, tblRep, spec, id, dataRepository, exec), dataRepository);
            } else if (tableType.equals(TABLE_TYPE_JOINED)) {
                JoinedTable jt = JoinedTable.load(s, spec, tblRep, dataRepository);
                t = new BufferedDataTable(jt, dataRepository);
            } else if (tableType.equals(TABLE_TYPE_VOID)) {
                VoidTable jt = VoidTable.load(spec);
                t = new BufferedDataTable(jt, dataRepository);
            } else if (tableType.equals(TABLE_TYPE_CONCATENATE)) {
                ConcatenateTable ct = ConcatenateTable.load(s, spec, tblRep, dataRepository);
                t = new BufferedDataTable(ct, dataRepository);
            } else if (tableType.equals(TABLE_TYPE_WRAPPED)) {
                WrappedTable wt = WrappedTable.load(s, tblRep, dataRepository);
                t = new BufferedDataTable(wt, dataRepository);
            } else if (tableType.equals(TABLE_TYPE_NEW_SPEC)) {
                TableSpecReplacerTable replTable;
                if (isVersion11x) {
                    if (fileRef == null) {
                        throw new NullPointerException("Reference on file to load from has not been set.");
                    }
                    replTable = TableSpecReplacerTable.load11x(fileRef.getFile(), s, tblRep, dataRepository);
                } else {
                    replTable = TableSpecReplacerTable.load(s, spec, tblRep, dataRepository);
                }
                t = new BufferedDataTable(replTable, dataRepository);
            } else if (tableType.equals(TABLE_TYPE_EXTENSION)) {
                ExtensionTable et = ExtensionTable.loadExtensionTable(fileRef, spec, s, tblRep, exec, dataRepository);
                t = new BufferedDataTable(et, dataRepository);
            } else {
                assert false : "Insufficent case switch: " + tableType;
                throw new InvalidSettingsException("Unknown table identifier: " + tableType);
            }
            break;
        default:
            throw new InvalidSettingsException("Unknown table identifier: " + tableType);
    }
    t.m_tableID = id;
    tblRep.put(id, t);
    return t;
}

Example 53 with ReferencedFile

use of org.knime.core.internal.ReferencedFile in project knime-core by knime.

the class FileNodeContainerMetaPersistor method load.

/**
 * {@inheritDoc}
 */
@Override
public boolean load(final NodeSettingsRO settings, final NodeSettingsRO parentSettings, final LoadResult loadResult) {
    boolean isResetRequired = false;
    try {
        m_nodeAnnotationData = loadNodeAnnotationData(settings, parentSettings);
    } catch (InvalidSettingsException e) {
        String error = "Can't load node annotation: " + e.getMessage();
        loadResult.addError(error);
        getLogger().debug(error, e);
        setDirtyAfterLoad();
        m_nodeAnnotationData = null;
    }
    try {
        m_customDescription = loadCustomDescription(settings, parentSettings);
    } catch (InvalidSettingsException e) {
        String error = "Invalid custom description in settings: " + e.getMessage();
        loadResult.addError(error);
        getLogger().debug(error, e);
        setDirtyAfterLoad();
        m_customDescription = null;
    }
    try {
        m_jobManager = loadNodeExecutionJobManager(settings);
    } catch (InvalidSettingsException e) {
        String error = "Can't restore node execution job manager: " + e.getMessage();
        loadResult.addError(error);
        getLogger().debug(error, e);
        isResetRequired = true;
        setDirtyAfterLoad();
    }
    boolean hasJobManagerLoadFailed = m_jobManager == null;
    try {
        if (!hasJobManagerLoadFailed) {
            m_executionJobSettings = loadNodeExecutionJobSettings(settings);
        }
    } catch (InvalidSettingsException e) {
        String error = "Can't restore node execution job manager: " + e.getMessage();
        loadResult.addError(error);
        getLogger().debug(error, e);
        setDirtyAfterLoad();
        isResetRequired = true;
        hasJobManagerLoadFailed = true;
    }
    try {
        if (!hasJobManagerLoadFailed) {
            ReferencedFile jobManagerInternalsDirectory = loadJobManagerInternalsDirectory(getNodeContainerDirectory(), settings);
            if (jobManagerInternalsDirectory != null) {
                m_jobManager.loadInternals(jobManagerInternalsDirectory);
            }
        }
    } catch (Throwable e) {
        String error = "Can't restore node execution job " + "manager internals directory " + e.getMessage();
        loadResult.addError(error);
        getLogger().debug(error, e);
        setDirtyAfterLoad();
        hasJobManagerLoadFailed = true;
    }
    try {
        m_state = loadState(settings, parentSettings);
        switch(m_state) {
            case EXECUTED:
            case EXECUTINGREMOTELY:
                if (getLoadHelper().isTemplateFlow()) {
                    m_state = InternalNodeContainerState.CONFIGURED;
                }
                break;
            default:
        }
    } catch (InvalidSettingsException e) {
        String error = "Can't restore node's state, fallback to " + InternalNodeContainerState.IDLE + ": " + e.getMessage();
        loadResult.addError(error);
        getLogger().debug(error, e);
        setDirtyAfterLoad();
        isResetRequired = true;
        m_state = InternalNodeContainerState.IDLE;
    }
    try {
        if (!getLoadHelper().isTemplateFlow()) {
            m_nodeMessage = loadNodeMessage(settings);
        }
    } catch (InvalidSettingsException ise) {
        String e = "Unable to load node message: " + ise.getMessage();
        loadResult.addError(e);
        getLogger().warn(e, ise);
    }
    m_nodeLock = loadNodeLocks(settings);
    return isResetRequired;
}

Example 54 with ReferencedFile

use of org.knime.core.internal.ReferencedFile in project knime-core by knime.

the class FileSubNodeContainerPersistor method loadExampleInputSpecs.

/**
 * Helper to load the example data spec stored with a component
 *
 * @param settings settings that contain information required to restore the data, i.e. the location, file names,
 *            port types etc.
 * @param nodeDir the directory of the component to load the data spec from
 * @return the loaded port object specs
 * @throws IOException if the data files couldn't be read
 * @throws InvalidSettingsException if the provided settings are not as expected
 */
static PortObjectSpec[] loadExampleInputSpecs(final NodeSettingsRO settings, final ReferencedFile nodeDir) throws IOException, InvalidSettingsException {
    String subDirName = settings.getString("location");
    ReferencedFile subDirFile = new ReferencedFile(nodeDir, subDirName);
    NodeSettingsRO portSettings = settings.getNodeSettings("content");
    Set<String> keySet = portSettings.keySet();
    PortObjectSpec[] result = new PortObjectSpec[keySet.size()];
    for (String s : keySet) {
        NodeSettingsRO singlePortSetting = portSettings.getNodeSettings(s);
        int index = singlePortSetting.getInt("index");
        if (index < 0 || index >= result.length) {
            throw new InvalidSettingsException("Invalid index: " + index);
        }
        String type = singlePortSetting.getString("type");
        PortObjectSpec spec = null;
        if ("null".equals(type)) {
        // object stays null
        } else if ("table".equals(type)) {
            String fileName = singlePortSetting.getString("table_file");
            if (fileName != null) {
                File portFile = new File(subDirFile.getFile(), fileName);
                InputStream in = FileUtil.openInputStream(portFile.toString());
                // http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5077277
                try (ZipInputStream zipIn = new ZipInputStream(new BufferedInputStream(in))) {
                    ZipEntry entry = zipIn.getNextEntry();
                    // functionality to DataContainer ... at least not yet.
                    if ("spec.xml".equals(entry != null ? entry.getName() : "")) {
                        NodeSettingsRO settingsFile = NodeSettings.loadFromXML(zipIn);
                        try {
                            NodeSettingsRO specSettings = settingsFile.getNodeSettings("table.spec");
                            spec = DataTableSpec.load(specSettings);
                        } catch (InvalidSettingsException ise) {
                            IOException ioe = new IOException("Unable to read spec from file");
                            ioe.initCause(ise);
                            throw ioe;
                        }
                    } else {
                        return null;
                    }
                }
            }
        } else if ("flow-vars".equals(type)) {
            spec = FlowVariablePortObjectSpec.INSTANCE;
        } else if ("non-table".equals(type)) {
            String fileName = singlePortSetting.getString("port_file");
            if (fileName != null) {
                File portFile = new File(subDirFile.getFile(), fileName);
                spec = PortUtil.readObjectSpecFromFile(portFile);
            }
        } else {
            CheckUtils.checkSetting(false, "Unknown object reference %s", type);
        }
        result[index] = spec;
    }
    return result;
}

Example 55 with ReferencedFile

use of org.knime.core.internal.ReferencedFile in project knime-core by knime.

the class FileSubNodeContainerPersistor method loadExampleInputData.

/**
 * Helper to load example data stored with a component.
 *
 * @param settings settings that contain information required to restore the data, i.e. the location, file names,
 *            port types etc.
 * @param nodeDir the component directory to load the data from
 * @param exec to report progress, listen to cancel events, and, most important, to create the new buffered data
 *            tables
 * @return the loaded port objects
 * @throws IOException if the data files couldn't be read
 * @throws InvalidSettingsException if the provided settings are not as expected
 */
static PortObject[] loadExampleInputData(final NodeSettingsRO settings, final ReferencedFile nodeDir, final ExecutionContext exec) throws IOException, InvalidSettingsException, CanceledExecutionException {
    String subDirName = settings.getString("location");
    ReferencedFile subDirFile = new ReferencedFile(nodeDir, subDirName);
    NodeSettingsRO portSettings = settings.getNodeSettings("content");
    Set<String> keySet = portSettings.keySet();
    PortObject[] result = new PortObject[keySet.size()];
    for (String s : keySet) {
        ExecutionMonitor subProgress = exec.createSubProgress(1.0 / result.length);
        NodeSettingsRO singlePortSetting = portSettings.getNodeSettings(s);
        int index = singlePortSetting.getInt("index");
        if (index < 0 || index >= result.length) {
            throw new InvalidSettingsException("Invalid index: " + index);
        }
        String type = singlePortSetting.getString("type");
        PortObject object = null;
        if ("null".equals(type)) {
        // object stays null
        } else if ("table".equals(type)) {
            String dataFileName = singlePortSetting.getString("table_file");
            if (dataFileName != null) {
                File portFile = new File(subDirFile.getFile(), dataFileName);
                ContainerTable t = DataContainer.readFromZip(portFile);
                object = exec.createBufferedDataTable(t, subProgress);
                t.clear();
            }
        } else if ("flow-vars".equals(type)) {
            object = FlowVariablePortObject.INSTANCE;
        } else if ("non-table".equals(type)) {
            String dataFileName = singlePortSetting.getString("port_file");
            if (dataFileName != null) {
                File portFile = new File(subDirFile.getFile(), dataFileName);
                object = PortUtil.readObjectFromFile(portFile, exec);
            }
        } else {
            CheckUtils.checkSetting(false, "Unknown object reference %s", type);
        }
        result[index] = object;
        subProgress.setProgress(1.0);
    }
    return result;
}