Examples with ContainerTable org.knime.core.data.container.ContainerTable used on opensource projects

Example 1 with ContainerTable

use of org.knime.core.data.container.ContainerTable in project knime-core by knime.

the class HistogramColumn method loadHistograms.

/**
 * Loads the histograms from the saved internal files.
 *
 * @param histogramsGz The file for the histograms.
 * @param dataArrayGz The data array file for the row keys.
 * @param nominalColumns The nominal columns.
 * @param strategy The strategy used to compute the bins.
 * @param means The mean values for the numeric columns.
 * @return A triple (Pair(Pair(,),)) of histograms, numeric and nominal row keys.
 * @throws IOException Failed to read the files.
 * @throws InvalidSettingsException Something went wrong.
 */
public static Pair<Pair<Map<Integer, ? extends HistogramModel<?>>, Map<Integer, Map<Integer, Set<RowKey>>>>, Map<Integer, Map<DataValue, Set<RowKey>>>> loadHistograms(final File histogramsGz, final File dataArrayGz, final Set<String> nominalColumns, final BinNumberSelectionStrategy strategy, final double[] means) throws IOException, InvalidSettingsException {
    Map<Integer, Map<Integer, Set<RowKey>>> numericKeys = new HashMap<Integer, Map<Integer, Set<RowKey>>>();
    Map<Integer, HistogramNumericModel> histograms = loadHistogramsPrivate(histogramsGz, numericKeys, strategy, means);
    Map<Integer, Map<DataValue, Set<RowKey>>> nominalKeys = new HashMap<Integer, Map<DataValue, Set<RowKey>>>();
    ContainerTable table = DataContainer.readFromZip(dataArrayGz);
    Set<Integer> numericColIndices = numericKeys.keySet();
    for (String colName : nominalColumns) {
        int colIndex = table.getDataTableSpec().findColumnIndex(colName);
        if (colIndex < 0) {
            continue;
        }
        nominalKeys.put(Integer.valueOf(colIndex), new HashMap<DataValue, Set<RowKey>>());
    }
    for (DataRow dataRow : table) {
        for (Integer col : numericColIndices) {
            // Integer col = Integer.valueOf(colIdx);
            HistogramNumericModel hd = histograms.get(col);
            Map<Integer, Set<RowKey>> map = numericKeys.get(col);
            DataCell cell = dataRow.getCell(col.intValue());
            if (!cell.isMissing() && cell instanceof DoubleValue) {
                DoubleValue dv = (DoubleValue) cell;
                Integer bin = Integer.valueOf(hd.findBin(dv));
                if (!map.containsKey(bin)) {
                    map.put(bin, new HashSet<RowKey>());
                }
                map.get(bin).add(dataRow.getKey());
            }
        }
        for (Entry<Integer, Map<DataValue, Set<RowKey>>> entry : nominalKeys.entrySet()) {
            DataCell value = dataRow.getCell(entry.getKey().intValue());
            Map<DataValue, Set<RowKey>> map = entry.getValue();
            if (!map.containsKey(value)) {
                map.put(value, new HashSet<RowKey>());
            }
            map.get(value).add(dataRow.getKey());
        }
    }
    return Pair.create(new Pair<Map<Integer, ? extends HistogramModel<?>>, Map<Integer, Map<Integer, Set<RowKey>>>>(histograms, numericKeys), nominalKeys);
}

Example 2 with ContainerTable

use of org.knime.core.data.container.ContainerTable in project knime-core by knime.

the class DataTableSpecView method dispose.

/**
 * {@inheritDoc}
 * @since 3.6
 */
@Override
public void dispose() {
    TableContentModel contentModel = m_specView.getContentModel();
    DataTable dataTable = contentModel.getDataTable();
    contentModel.setDataTable(null);
    if (dataTable instanceof ContainerTable) {
        ((ContainerTable) dataTable).clear();
    }
}

Example 3 with ContainerTable

use of org.knime.core.data.container.ContainerTable in project knime-core by knime.

the class FileNativeNodeContainerPersistor method loadNCAndWashModelSettings.

/**
 * {@inheritDoc}
 */
@Override
NodeSettingsRO loadNCAndWashModelSettings(final NodeSettingsRO settingsForNode, final NodeSettingsRO modelSettings, final Map<Integer, BufferedDataTable> tblRep, final ExecutionMonitor exec, final LoadResult result) throws InvalidSettingsException, CanceledExecutionException, IOException {
    final FileNodePersistor nodePersistor = createNodePersistor(settingsForNode);
    nodePersistor.preLoad(m_node, result);
    NodeSettingsRO washedModelSettings = modelSettings;
    try {
        if (modelSettings != null) {
            // null if the node never had settings - no reason to load them
            m_node.validateModelSettings(modelSettings);
            m_node.loadModelSettingsFrom(modelSettings);
            // previous versions of KNIME (2.7 and before) kept the model settings only in the node;
            // NodeModel#saveSettingsTo was always called before the dialog was opened (some dialog implementations
            // rely on the exact structure of the NodeSettings ... which may change between versions).
            // We wash the settings through the node so that the model settings are updated (they possibly
            // no longer map to the variable settings loaded further down below - if so, the inconsistency
            // is warned later during configuration)
            NodeSettings washedSettings = new NodeSettings("model");
            m_node.saveModelSettingsTo(washedSettings);
            washedModelSettings = washedSettings;
        }
    } catch (Exception e) {
        final String error;
        if (e instanceof InvalidSettingsException) {
            error = "Loading model settings failed: " + e.getMessage();
        } else {
            error = "Caught \"" + e.getClass().getSimpleName() + "\", " + "Loading model settings failed: " + e.getMessage();
        }
        final LoadNodeModelSettingsFailPolicy pol = getModelSettingsFailPolicy(getMetaPersistor().getState(), nodePersistor.isInactive());
        switch(pol) {
            case IGNORE:
                if (!(e instanceof InvalidSettingsException)) {
                    getLogger().coding(error, e);
                }
                break;
            case FAIL:
                result.addError(error);
                m_node.createErrorMessageAndNotify(error, e);
                setNeedsResetAfterLoad();
                break;
            case WARN:
                m_node.createWarningMessageAndNotify(error, e);
                result.addWarning(error);
                setDirtyAfterLoad();
                break;
        }
    }
    try {
        HashMap<Integer, ContainerTable> globalTableRepository = getGlobalTableRepository();
        WorkflowFileStoreHandlerRepository fileStoreHandlerRepository = getFileStoreHandlerRepository();
        nodePersistor.load(m_node, getParentPersistor(), exec, tblRep, globalTableRepository, fileStoreHandlerRepository, result);
    } catch (final Exception e) {
        String error = "Error loading node content: " + e.getMessage();
        getLogger().warn(error, e);
        needsResetAfterLoad();
        result.addError(error);
    }
    if (nodePersistor.isDirtyAfterLoad()) {
        setDirtyAfterLoad();
    }
    if (nodePersistor.needsResetAfterLoad()) {
        setNeedsResetAfterLoad();
    }
    return washedModelSettings;
}

Example 4 with ContainerTable

use of org.knime.core.data.container.ContainerTable 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 bufferRep The buffer repository (needed for blobs).
 * @param fileStoreHandlerRepository ...
 * @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 HashMap<Integer, ContainerTable> bufferRep, final FileStoreHandlerRepository fileStoreHandlerRepository) 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
        s = NodeSettings.loadFromXML(new BufferedInputStream(new FileInputStream(dataXML)));
        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);
    LAST_ID.set(Math.max(LAST_ID.get(), id + 1));
    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 = s.getString(CFG_TABLE_TYPE);
    BufferedDataTable t;
    if (tableType.equals(TABLE_TYPE_REFERENCE_IN_SAME_NODE)) {
        t = tblRep.get(id);
        if (t == null) {
            throw new InvalidSettingsException("Table reference with ID " + id + " not found in load map");
        }
        return t;
    } else if (tableType.equals(TABLE_TYPE_CONTAINER)) {
        ContainerTable fromContainer;
        if (isVersion11x) {
            fromContainer = DataContainer.readFromZip(fileRef.getFile());
        } else {
            fromContainer = BufferedDataContainer.readFromZipDelayed(fileRef, spec, id, bufferRep, fileStoreHandlerRepository);
        }
        t = new BufferedDataTable(fromContainer, id);
    } else {
        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) {
            if (reference == null) {
                throw new InvalidSettingsException("Reference dir is \"null\"");
            }
            ReferencedFile referenceDirRef = new ReferencedFile(dirRef, reference);
            loadFromFile(referenceDirRef, s, exec, tblRep, bufferRep, fileStoreHandlerRepository);
        }
        if (tableType.equals(TABLE_TYPE_REARRANGE_COLUMN)) {
            t = new BufferedDataTable(new RearrangeColumnsTable(fileRef, s, tblRep, spec, id, bufferRep, fileStoreHandlerRepository));
        } else if (tableType.equals(TABLE_TYPE_JOINED)) {
            JoinedTable jt = JoinedTable.load(s, spec, tblRep);
            t = new BufferedDataTable(jt);
        } else if (tableType.equals(TABLE_TYPE_VOID)) {
            VoidTable jt = VoidTable.load(spec);
            t = new BufferedDataTable(jt);
        } else if (tableType.equals(TABLE_TYPE_CONCATENATE)) {
            ConcatenateTable ct = ConcatenateTable.load(s, spec, tblRep);
            t = new BufferedDataTable(ct);
        } else if (tableType.equals(TABLE_TYPE_WRAPPED)) {
            WrappedTable wt = WrappedTable.load(s, tblRep);
            t = new BufferedDataTable(wt);
        } else if (tableType.equals(TABLE_TYPE_NEW_SPEC)) {
            TableSpecReplacerTable replTable;
            if (isVersion11x) {
                replTable = TableSpecReplacerTable.load11x(fileRef.getFile(), s, tblRep);
            } else {
                replTable = TableSpecReplacerTable.load(s, spec, tblRep);
            }
            t = new BufferedDataTable(replTable);
        } else if (tableType.equals(TABLE_TYPE_EXTENSION)) {
            ExtensionTable et = ExtensionTable.loadExtensionTable(fileRef, spec, s, tblRep, exec);
            t = new BufferedDataTable(et);
        } else {
            throw new InvalidSettingsException("Unknown table identifier: " + tableType);
        }
    }
    t.m_tableID = id;
    tblRep.put(id, t);
    return t;
}

Example 5 with ContainerTable

use of org.knime.core.data.container.ContainerTable in project knime-core by knime.

the class BufferedDataTable method save.

/**
 * Saves the table to a directory and writes some settings to the argument
 * NodeSettingsWO object. It will also write the reference table in case
 * this node is responsible for it (i.e. this node created the reference
 * table).
 * @param dir The directory to write to.
 * @param savedTableIDs Ids of tables that were previously saved, used to identify
 * tables that are referenced by the same nodes multiple times.
 * @param exec The progress monitor for cancellation.
 * @throws IOException If writing fails.
 * @throws CanceledExecutionException If canceled.
 */
void save(final File dir, final Set<Integer> savedTableIDs, final ExecutionMonitor exec) throws IOException, CanceledExecutionException {
    NodeSettings s = new NodeSettings(CFG_TABLE_META);
    Integer bufferedTableID = getBufferedTableId();
    s.addInt(CFG_TABLE_ID, bufferedTableID);
    File outFile = new File(dir, TABLE_FILE);
    if (!savedTableIDs.add(bufferedTableID)) {
        s.addString(CFG_TABLE_TYPE, TABLE_TYPE_REFERENCE_IN_SAME_NODE);
    } else if (m_delegate instanceof ContainerTable) {
        s.addString(CFG_TABLE_TYPE, TABLE_TYPE_CONTAINER);
        m_delegate.saveToFile(outFile, s, exec);
    } else {
        if (m_delegate instanceof RearrangeColumnsTable) {
            s.addString(CFG_TABLE_TYPE, TABLE_TYPE_REARRANGE_COLUMN);
        } else if (m_delegate instanceof TableSpecReplacerTable) {
            s.addString(CFG_TABLE_TYPE, TABLE_TYPE_NEW_SPEC);
        } else if (m_delegate instanceof WrappedTable) {
            s.addString(CFG_TABLE_TYPE, TABLE_TYPE_WRAPPED);
        } else if (m_delegate instanceof JoinedTable) {
            s.addString(CFG_TABLE_TYPE, TABLE_TYPE_JOINED);
        } else if (m_delegate instanceof VoidTable) {
            s.addString(CFG_TABLE_TYPE, TABLE_TYPE_VOID);
        } else if (m_delegate instanceof ConcatenateTable) {
            s.addString(CFG_TABLE_TYPE, TABLE_TYPE_CONCATENATE);
        } else {
            assert m_delegate instanceof ExtensionTable;
            s.addString(CFG_TABLE_TYPE, TABLE_TYPE_EXTENSION);
        }
        BufferedDataTable[] references = m_delegate.getReferenceTables();
        ArrayList<String> referenceDirs = new ArrayList<String>();
        for (BufferedDataTable reference : references) {
            if (reference.getOwner() == getOwner() && !savedTableIDs.contains(reference.getBufferedTableId())) {
                int index = referenceDirs.size();
                String dirName = "r" + index;
                File subDir = new File(dir, dirName);
                if (!subDir.mkdir() && !subDir.isDirectory()) {
                    throw new IOException("Could not create directory " + subDir.getAbsolutePath());
                }
                if (!subDir.canWrite()) {
                    throw new IOException("Unable to write directory " + subDir.getAbsolutePath());
                }
                referenceDirs.add(dirName);
                reference.save(subDir, savedTableIDs, exec);
            }
        }
        s.addStringArray(CFG_TABLE_REFERENCE, referenceDirs.toArray(new String[referenceDirs.size()]));
        m_delegate.saveToFile(outFile, s, exec);
    }
    // only write the data file to the settings if it has been created
    if (outFile.exists()) {
        s.addString(CFG_TABLE_FILE_NAME, TABLE_FILE);
    } else {
        s.addString(CFG_TABLE_FILE_NAME, null);
    }
    saveSpec(getDataTableSpec(), dir);
    File dataXML = new File(dir, TABLE_DESCRIPTION_FILE);
    s.saveToXML(new BufferedOutputStream(new FileOutputStream(dataXML)));
}