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

Example 21 with ContainerTable

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

the class WorkflowLoadHelper method createTemplateLoadPersistor.

/**
 * Create persistor for a workflow or template.
 * @noreference Clients should only be required to load projects using
 * {@link WorkflowManager#loadProject(File, ExecutionMonitor, WorkflowLoadHelper)}
 * @param directory The directory to load from
 * @param templateSourceURI URI of the link to the template (will load a template and when the template is
 * instantiated and put into the workflow a link is created)
 * @return The persistor
 * @throws IOException If an IO error occured
 * @throws UnsupportedWorkflowVersionException If the workflow is of an unsupported version
 */
public final TemplateNodeContainerPersistor createTemplateLoadPersistor(final File directory, final URI templateSourceURI) throws IOException, UnsupportedWorkflowVersionException {
    if (directory == null) {
        throw new NullPointerException("Arguments must not be null.");
    }
    String fileName = getDotKNIMEFileName();
    if (!directory.isDirectory() || !directory.canRead()) {
        throw new IOException("Can't read metanode/template directory " + directory);
    }
    // template.knime or workflow.knime
    ReferencedFile dotKNIMERef = new ReferencedFile(new ReferencedFile(directory), fileName);
    File dotKNIME = dotKNIMERef.getFile();
    if (!dotKNIME.isFile()) {
        throw new IOException("No \"" + fileName + "\" file in directory \"" + directory.getAbsolutePath() + "\"");
    }
    NodeSettingsRO settings = NodeSettings.loadFromXML(new BufferedInputStream(new FileInputStream(dotKNIME)));
    // CeBIT 2006 version did not contain a version string.
    String versionString;
    if (settings.containsKey(WorkflowLoadHelper.CFG_VERSION)) {
        try {
            versionString = settings.getString(WorkflowLoadHelper.CFG_VERSION);
        } catch (InvalidSettingsException e) {
            throw new IOException("Can't read version number from \"" + dotKNIME.getAbsolutePath() + "\"", e);
        }
    } else {
        versionString = "0.9.0";
    }
    // might also be FUTURE
    LoadVersion version = FileWorkflowPersistor.parseVersion(versionString);
    boolean isSetDirtyAfterLoad = false;
    StringBuilder versionDetails = new StringBuilder(versionString);
    String createdBy = settings.getString(WorkflowLoadHelper.CFG_CREATED_BY, null);
    Version createdByVersion = null;
    if (createdBy != null) {
        versionDetails.append(" (created by KNIME ").append(createdBy).append(")");
        try {
            createdByVersion = new Version(createdBy);
        } catch (IllegalArgumentException e) {
            // ideally this goes into the 'LoadResult' but it's not instantiated yet
            LOGGER.warn(String.format("Unable to parse version string \"%s\" (file \"%s\"): %s", createdBy, dotKNIME.getAbsolutePath(), e.getMessage()), e);
        }
    }
    // added 3.5.0
    boolean isNightly = settings.getBoolean(CFG_NIGHTLY, false);
    boolean isRunningNightly = KNIMEConstants.isNightlyBuild();
    boolean isFutureWorkflow = createdByVersion != null && !new Version(KNIMEConstants.VERSION).isSameOrNewer(createdByVersion);
    if (version == LoadVersion.FUTURE || isFutureWorkflow || (!isRunningNightly && isNightly)) {
        switch(getUnknownKNIMEVersionLoadPolicy(version, createdByVersion, isNightly)) {
            case Abort:
                StringBuilder e = new StringBuilder("Unable to load ");
                e.append(isTemplateFlow() ? "template, " : "workflow, ");
                if (version == LoadVersion.FUTURE || isFutureWorkflow) {
                    e.append("it was created with a future version of KNIME (").append(createdBy).append("). ");
                    e.append("You are running ").append(KNIMEConstants.VERSION).append(".");
                } else {
                    e.append("it was created with a nightly build of KNIME (version ").append(createdBy).append("). ");
                    e.append("You are running ").append(KNIMEConstants.VERSION).append(".");
                }
                throw new UnsupportedWorkflowVersionException(e.toString());
            default:
                isSetDirtyAfterLoad = true;
        }
    } else if (version.isOlderThan(LoadVersion.V200)) {
        LOGGER.warn("The current KNIME version (" + KNIMEConstants.VERSION + ") is different from the one that " + "created the workflow (" + version + ") you are trying to load. In some rare cases, it  " + "might not be possible to load all data or some nodes can't be configured. " + "Please re-configure and/or re-execute these nodes.");
    }
    final MetaNodeTemplateInformation templateInfo;
    if (isTemplateFlow() && templateSourceURI != null) {
        try {
            templateInfo = MetaNodeTemplateInformation.load(settings, version);
            CheckUtils.checkSetting(Role.Template.equals(templateInfo.getRole()), "Role is not '%s' but '%s'", Role.Template, templateInfo.getRole());
        } catch (InvalidSettingsException e) {
            throw new IOException(String.format("Attempting to load template from \"%s\" but can't locate template information: %s", dotKNIME.getAbsolutePath(), e.getMessage()), e);
        }
    } else if (isTemplateFlow()) {
        // LOGGER.coding("Supposed to instantiate a template but the link URI is not set");
        // metanode template from node repository
        templateInfo = null;
    } else {
        templateInfo = null;
    }
    final TemplateNodeContainerPersistor persistor;
    // TODO only create new hash map if workflow is a project?
    HashMap<Integer, ContainerTable> tableRep = new GlobalTableRepository();
    WorkflowFileStoreHandlerRepository fileStoreHandlerRepository = new WorkflowFileStoreHandlerRepository();
    // ordinary workflow is loaded
    if (templateInfo == null) {
        persistor = new FileWorkflowPersistor(tableRep, fileStoreHandlerRepository, dotKNIMERef, this, version, !isTemplateFlow());
    } else {
        // some template is loaded
        switch(templateInfo.getNodeContainerTemplateType()) {
            case MetaNode:
                final ReferencedFile workflowDotKNIME;
                if (version.isOlderThan(LoadVersion.V2100)) {
                    // before 2.10 everything was stored in template.knime
                    workflowDotKNIME = dotKNIMERef;
                } else {
                    workflowDotKNIME = new ReferencedFile(dotKNIMERef.getParent(), WorkflowPersistor.WORKFLOW_FILE);
                }
                persistor = new FileWorkflowPersistor(tableRep, fileStoreHandlerRepository, workflowDotKNIME, this, version, !isTemplateFlow());
                break;
            case SubNode:
                final ReferencedFile settingsDotXML = new ReferencedFile(dotKNIMERef.getParent(), SingleNodeContainerPersistor.SETTINGS_FILE_NAME);
                persistor = new FileSubNodeContainerPersistor(settingsDotXML, this, version, tableRep, fileStoreHandlerRepository, true);
                break;
            default:
                throw new IllegalStateException("Unsupported template type");
        }
    }
    if (templateInfo != null) {
        persistor.setOverwriteTemplateInformation(templateInfo.createLink(templateSourceURI));
        persistor.setNameOverwrite(directory.getName());
    }
    if (isSetDirtyAfterLoad) {
        persistor.setDirtyAfterLoad();
    }
    return persistor;
}

Example 22 with ContainerTable

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

the class TableSorterWorker method doInBackground.

/**
 * {@inheritDoc}
 */
@Override
protected DataTable doInBackground() throws Exception {
    // passed to table sorter for progress
    long rowCount;
    if (m_inputTable instanceof BufferedDataTable) {
        rowCount = ((BufferedDataTable) m_inputTable).size();
    } else if (m_inputTable instanceof ContainerTable) {
        rowCount = ((ContainerTable) m_inputTable).size();
    } else {
        // unknown, no progress
        rowCount = -1;
    }
    publish(new NodeProgress(0.0, "Starting table sort..."));
    Collection<String> sortColNames = new ArrayList<String>(2);
    DataTableSpec spec = m_inputTable.getDataTableSpec();
    for (int i : m_sortOrder.getSortColumnIndices()) {
        String name;
        if (i < 0) {
            // row id
            name = DataTableSorter.ROWKEY_SORT_SPEC.getName();
        } else {
            name = spec.getColumnSpec(i).getName();
        }
        sortColNames.add(name);
    }
    long start = System.currentTimeMillis();
    LOGGER.debug("Starting interactive table sorting on column(s) " + sortColNames);
    boolean[] sortOrders = m_sortOrder.getSortColumnOrder();
    // it DOES NOT respect blobs -- they will be copied (expensive)
    DataTableSorter sorter = new DataTableSorter(m_inputTable, rowCount, sortColNames, sortOrders, false);
    NodeProgressListener progLis = new NodeProgressListener() {

        @Override
        public void progressChanged(final NodeProgressEvent pe) {
            publish(pe.getNodeProgress());
        }
    };
    m_nodeProgressMonitor = new DefaultNodeProgressMonitor();
    ExecutionMonitor exec = new ExecutionMonitor(m_nodeProgressMonitor);
    m_nodeProgressMonitor.addProgressListener(progLis);
    try {
        DataTable result = sorter.sort(exec);
        long elapsedMS = System.currentTimeMillis() - start;
        String time = StringFormat.formatElapsedTime(elapsedMS);
        LOGGER.debug("Interactive table sorting finished (" + time + ")");
        return result;
    } finally {
        m_nodeProgressMonitor.removeProgressListener(progLis);
    }
}

Example 23 with ContainerTable

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

the class DataColumnPropertiesView method dispose.

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

Example 24 with ContainerTable

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

the class LinRegLearnerNodeModel method loadInternals.

/**
 * {@inheritDoc}
 */
@Override
protected void loadInternals(final File internDir, final ExecutionMonitor exec) throws IOException, CanceledExecutionException {
    File inFile = new File(internDir, FILE_SAVE);
    ModelContentRO c = ModelContent.loadFromXML(new BufferedInputStream(new GZIPInputStream(new FileInputStream(inFile))));
    try {
        m_nrRows = c.getInt(CFG_NR_ROWS);
        m_nrRowsSkipped = c.getInt(CFG_NR_ROWS_SKIPPED);
        m_error = c.getDouble(CFG_ERROR);
        ModelContentRO specContent = c.getModelContent(CFG_SPEC);
        DataTableSpec outSpec = DataTableSpec.load(specContent);
        m_actualUsedColumns = specContent.getStringArray(CFG_USED_COLUMNS, (String[]) null);
        ModelContentRO parContent = c.getModelContent(CFG_PARAMS);
        m_params = LinearRegressionContent.instantiateAndLoad(parContent, outSpec);
    } catch (InvalidSettingsException ise) {
        IOException ioe = new IOException("Unable to restore state: " + ise.getMessage());
        ioe.initCause(ise);
        throw ioe;
    }
    File dataFile = new File(internDir, FILE_DATA);
    ContainerTable t = DataContainer.readFromZip(dataFile);
    int rowCount = t.getRowCount();
    m_rowContainer = new DefaultDataArray(t, 1, rowCount, exec);
}

Example 25 with ContainerTable

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

the class PolyRegLearnerNodeModel method loadInternals.

/**
 * {@inheritDoc}
 */
@Override
protected void loadInternals(final File nodeInternDir, final ExecutionMonitor exec) throws IOException, CanceledExecutionException {
    File f = new File(nodeInternDir, "internals.xml");
    if (f.exists()) {
        NodeSettingsRO internals = NodeSettings.loadFromXML(new BufferedInputStream(new FileInputStream(f)));
        try {
            double[] betas = internals.getDoubleArray("betas");
            String[] columnNames = internals.getStringArray("columnNames");
            double squaredError = internals.getDouble("squaredError");
            double[] meanValues = internals.getDoubleArray("meanValues");
            m_viewData = new PolyRegViewData(meanValues, betas, squaredError, columnNames, m_settings.getDegree(), m_settings.getTargetColumn());
        } catch (InvalidSettingsException ex) {
            throw new IOException("Old or corrupt internals", ex);
        }
    } else {
        throw new FileNotFoundException("Internals do not exist");
    }
    f = new File(nodeInternDir, "data.zip");
    if (f.exists()) {
        ContainerTable t = DataContainer.readFromZip(f);
        int rowCount = t.getRowCount();
        m_rowContainer = new DefaultDataArray(t, 1, rowCount, exec);
    } else {
        throw new FileNotFoundException("Internals do not exist");
    }
}