Examples with Port com.genericworkflownodes.knime.port.Port used on opensource projects

Example 11 with Port

use of com.genericworkflownodes.knime.port.Port in project GenericKnimeNodes by genericworkflownodes.

the class GalaxyNodeConfigurationReader method readOutPort.

private Port readOutPort(Node portnode) throws Exception {
    Port port = new Port();
    port.setDescription("");
    String extension = DOMHelper.valueOf(portnode, "@format");
    port.addMimeType(extension);
    String portname = DOMHelper.valueOf(portnode, "@name");
    port.setName(portname);
    return port;
}

Example 12 with Port

use of com.genericworkflownodes.knime.port.Port in project GenericKnimeNodes by genericworkflownodes.

the class NodeFactoryXMLTemplate method getInPorts.

/**
 * Returns the xml representation of the input ports.
 *
 * @param nodeConfiguration
 *            The {@link INodeConfiguration} containing the port
 *            information.
 * @return A {@link String} representing the input port part of the xml
 *         config file.
 */
private static String getInPorts(final INodeConfiguration nodeConfiguration) {
    // ports
    String ip = "\t\t<inPort index=\"__IDX__\" name=\"__PORTNAME__ [__MIMETYPE__]\">__PORTDESCR__ [__MIMETYPE____OPT__]</inPort>";
    String inPorts = "";
    int idx = 0;
    for (Port port : nodeConfiguration.getInputPorts()) {
        Parameter<?> parameter = nodeConfiguration.getParameter(port.getName());
        String ipp = ip;
        ipp = ip.replace("__PORTNAME__", parameter.getKey());
        ipp = ipp.replace("__PORTDESCR__", StringEscapeUtils.escapeHtml(port.getDescription()));
        ipp = ipp.replace("__IDX__", String.format("%d", idx++));
        ipp = ipp.replace("__MIMETYPE__", join(port.getMimeTypes(), ","));
        ipp = ipp.replace("__OPT__", (port.isOptional() ? ",opt." : ""));
        inPorts += ipp + "\n";
    }
    return inPorts;
}

Example 13 with Port

use of com.genericworkflownodes.knime.port.Port in project GenericKnimeNodes by genericworkflownodes.

the class DynamicGenericNodeFactory method createNodeModel.

/**
 * {@inheritDoc}
 */
@Override
public DynamicGenericNodeModel createNodeModel() {
    INodeConfiguration tmpConfig;
    try {
        tmpConfig = getNodeConfiguration();
        String[][] inputs = new String[tmpConfig.getInputPorts().size()][];
        String[][] outputs = new String[tmpConfig.getOutputPorts().size()][];
        int i = 0;
        for (Port p : tmpConfig.getInputPorts()) {
            inputs[i++] = p.getMimeTypes().toArray(new String[0]);
        }
        i = 0;
        for (Port p : tmpConfig.getOutputPorts()) {
            outputs[i++] = p.getMimeTypes().toArray(new String[0]);
        }
        return new DynamicGenericNodeModel(tmpConfig, getPluginConfig(), inputs, outputs);
    } catch (Exception e) {
        logger.error("Dynamic node model instantiation failed", e);
    }
    return null;
}

Example 14 with Port

use of com.genericworkflownodes.knime.port.Port in project GenericKnimeNodes by genericworkflownodes.

the class DynamicGenericNodeModel method transferOutgoingPorts2Config.

/**
 * Creates a list of lists of output files (as {@link URI}s) pointing to the
 * files that will be generated by the executed tool.
 *
 * @param jobdir
 *            The working directory of the executable.
 * @param inData
 *            The input data as {@link PortObject} array
 * @return A list of lists of output files
 * @throws Exception
 *             If the input has an invalid configuration.
 */
private List<PortObject> transferOutgoingPorts2Config(final File jobdir, PortObject[] inData, ExecutionContext exec) throws Exception {
    final int nOut = m_nodeConfig.getOutputPorts().size();
    List<PortObject> outPorts = new ArrayList<PortObject>(nOut);
    for (int i = 0; i < nOut; i++) {
        Port port = m_nodeConfig.getOutputPorts().get(i);
        String name = port.getName();
        String ext = "";
        boolean isPrefix = port.isPrefix();
        if (!isPrefix) {
            ext = getOutputType(i);
        }
        Parameter<?> p = m_nodeConfig.getParameter(name);
        // basenames and number of output files guessed from input
        List<String> basenames = getOutputBaseNames();
        if (p instanceof FileListParameter && port.isMultiFile()) {
            // we currently do not support lists of prefixes
            if (isPrefix) {
                throw new InvalidSettingsException("GKN currently does not support lists of prefixes as output.");
            }
            FileListParameter flp = (FileListParameter) p;
            List<String> fileNames = new ArrayList<String>();
            if (basenames.size() == 0) {
                throw new Exception("Cannot determine number of output files if no input file is given.");
            }
            // if MimeType is "Inactive" just create Empty FileStore(Prefix)URIPortObjects
            PortObject fsupo;
            if (!ext.equals("Inactive")) {
                fsupo = new FileStoreURIPortObject(exec.createFileStore(m_nodeConfig.getName() + "_" + i));
                for (int f = 0; f < basenames.size(); ++f) {
                    // create basename: <base_name>_<port_nr>_<outfile_nr>
                    String file_basename = String.format("%s_%d", basenames.get(f), f);
                    File file = ((FileStoreURIPortObject) fsupo).registerFile(file_basename + "." + ext);
                    fileNames.add(file.getAbsolutePath());
                }
            } else {
                fsupo = InactiveBranchPortObject.INSTANCE;
            }
            // add filled portobject
            outPorts.add(fsupo);
            // overwrite existing settings with new values generated by the
            // stash
            flp.setValue(fileNames);
        } else if (p instanceof FileParameter && !port.isMultiFile()) {
            // if MimeType is "Inactive" just create Empty FileStore(Prefix)URIPortObjects
            PortObject po;
            if (!ext.equals("Inactive")) {
                // if we have no basename to use (e.g., Node without input-file)
                // we use the nodename
                String basename;
                if (basenames.isEmpty()) {
                    basename = m_nodeConfig.getName();
                } else {
                    basename = basenames.get(0);
                }
                // create basename: <base_name>_<outfile_nr>
                String fileName = basename;
                if (!isPrefix) {
                    fileName += '.' + ext;
                }
                if (isPrefix) {
                    po = new FileStorePrefixURIPortObject(exec.createFileStore(m_nodeConfig.getName() + "_" + i), fileName);
                    ((FileParameter) p).setValue(((FileStorePrefixURIPortObject) po).getPrefix());
                    LOGGER.debug("> setting param " + name + "->" + ((FileStorePrefixURIPortObject) po).getPrefix());
                } else {
                    po = new FileStoreURIPortObject(exec.createFileStore(m_nodeConfig.getName() + "_" + i));
                    // we do not append the file extension if we have a prefix
                    File file = ((FileStoreURIPortObject) po).registerFile(fileName);
                    ((FileParameter) p).setValue(file.getAbsolutePath());
                    LOGGER.debug("> setting param " + name + "->" + file);
                }
            } else {
                po = InactiveBranchPortObject.INSTANCE;
            }
            // remember output file
            outPorts.add(po);
        } else {
            throw new Exception("Invalid connection between ports and parameters.");
        }
    }
    return outPorts;
}

Example 15 with Port

use of com.genericworkflownodes.knime.port.Port in project GenericKnimeNodes by genericworkflownodes.

the class DynamicGenericNodeModel method transferIncomingPorts2Config.

/**
 * Transfers the incoming ports into the config, that it can be written out
 * into a config file or can be transferred to the command line.
 *
 * @param inData
 *            The incoming port objects.
 * @throws Exception
 */
private void transferIncomingPorts2Config(PortObject[] inData) throws Exception {
    // Transfer settings from the input ports into the configuration object
    for (int i = 0; i < inData.length; i++) {
        // find the internal port for this PortObject
        Port port = m_nodeConfig.getInputPorts().get(i);
        IURIPortObject po = (IURIPortObject) inData[i];
        String name = port.getName();
        // find the associated parameter in the configuration
        Parameter<?> p = m_nodeConfig.getParameter(name);
        boolean isMultiFile = port.isMultiFile();
        boolean isPrefix = port.isPrefix();
        // skip optional and unconnected inport ports
        if (inData[i] == null) {
            ((FileParameter) p).setValue(null);
            continue;
        }
        // connected: check contents
        List<URIContent> uris = po.getURIContents();
        // check validity of subtypes with actual inputs
        if (uris.size() > 1 && (!isMultiFile && !isPrefix)) {
            throw new Exception("IURIPortObject with multiple URIs supplied at single URI port #" + i);
        }
        // port
        if (!(p instanceof IFileParameter)) {
            throw new Exception("Invalid reference from port to non-file parameter. URI port #" + i);
        }
        if (isPrefix) {
            // we pass only the prefix to the tool
            IPrefixURIPortObject puri = (IPrefixURIPortObject) inData[i];
            ((FileParameter) p).setValue(puri.getPrefix());
        } else if (isMultiFile) {
            // we need to collect all filenames and then set them as a batch
            // in the config
            List<String> filenames = new ArrayList<String>();
            for (URIContent uric : uris) {
                URI uri = uric.getURI();
                filenames.add(new File(uri).getAbsolutePath());
            }
            ((FileListParameter) p).setValue(filenames);
        } else {
            // just one filename
            URI uri = uris.get(0).getURI();
            String filename = new File(uri).getAbsolutePath();
            ((FileParameter) p).setValue(filename);
        }
    }
}