Examples with FileListParameter com.genericworkflownodes.knime.parameter.FileListParameter used on opensource projects

Example 6 with FileListParameter

use of com.genericworkflownodes.knime.parameter.FileListParameter in project GenericKnimeNodes by genericworkflownodes.

the class DynamicGenericNodeModel method getOutputBaseNames.

/**
 * Tries to guess the optimal output file names given all the input edges.
 * The file names will be extracted from the configuration, hence the file
 * names need to be transferred into config prior to using this method. See
 * {@link GenericKnimeNodeModel#transferIncomingPorts2Config(PortObject[])}.
 *
 * @return A list of base names for the output files.
 * @throws Exception
 */
private List<String> getOutputBaseNames() throws Exception {
    // 1. we select always the list with the highest number of files.
    // 2. we prefer lists over files (independent of the number of
    // elements).
    // 3. we prefer files over prefixes since we assume that prefixes are
    // often indices or reference data
    // 4. ignore optional parameters
    List<String> basenames = new ArrayList<String>();
    // find the port
    int naming_port = 0;
    int max_size = -1;
    boolean seen_prefix = false;
    boolean isFileParameter = false;
    for (int i = 0; i < m_nodeConfig.getInputPorts().size(); ++i) {
        Port port = m_nodeConfig.getInputPorts().get(i);
        String name = port.getName();
        Parameter<?> p = m_nodeConfig.getParameter(name);
        // we don't assume that optional ports are naming relevant
        if (p.isOptional()) {
            continue;
        }
        if (p instanceof FileListParameter) {
            FileListParameter flp = (FileListParameter) p;
            if (max_size == -1 || (isFileParameter && (max_size <= flp.getValue().size()))) {
                max_size = flp.getValue().size();
                naming_port = i;
            } else if (flp.getValue().size() != max_size) {
                throw new Exception("The number of output files cannot be determined since multiple input file lists with disagreeing numbers exist.");
            }
        } else if (max_size == -1 || seen_prefix) {
            // is a regular incoming port but we have no better option
            max_size = 1;
            naming_port = i;
            // indicating that we have (for now) selected a file parameter
            // which will be overruled by any FileListParameter
            isFileParameter = true;
            seen_prefix = port.isPrefix();
        }
    }
    if (m_nodeConfig.getInputPorts().size() > 0) {
        // generate the filenames if there are input ports
        // without ports, the names are set in transferOutgoingPorts2Config
        Port port = m_nodeConfig.getInputPorts().get(naming_port);
        String name = port.getName();
        Parameter<?> p = m_nodeConfig.getParameter(name);
        if (p instanceof FileListParameter) {
            // we have multiple base names
            FileListParameter flp = (FileListParameter) p;
            for (String fName : flp.getValue()) {
                basenames.add(FilenameUtils.getBaseName(fName));
            }
        } else {
            // we only have a single basename
            // FilenameUtils.getBaseName()
            basenames.add(FilenameUtils.getBaseName(((FileParameter) p).getValue()));
        }
    }
    return basenames;
}

Example 7 with FileListParameter

use of com.genericworkflownodes.knime.parameter.FileListParameter in project GenericKnimeNodes by genericworkflownodes.

the class GenericKnimeNodeModel 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);
        // Before we know about its extension, a port is reset to active
        port.setActive(true);
        String name = port.getName();
        String ext = "";
        boolean isPrefix = port.isPrefix();
        if (!isPrefix) {
            ext = getOutputType(i);
        }
        if (ext.toLowerCase().equals("inactive")) {
            port.setActive(false);
            outPorts.add(InactiveBranchPortObject.INSTANCE);
            continue;
        }
        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.");
            }
            PortObject 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());
            }
            // 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()) {
            PortObject po;
            // 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);
            }
            // remember output file
            outPorts.add(po);
        } else {
            throw new Exception("Invalid connection between ports and parameters.");
        }
    }
    return outPorts;
}

Example 8 with FileListParameter

use of com.genericworkflownodes.knime.parameter.FileListParameter in project GenericKnimeNodes by genericworkflownodes.

the class DockerCommandGenerator method extractParamterValues.

private List<List<? extends CommandLineElement>> extractParamterValues(CLIElement cliElement, List<CommandLineElement> dockerCommands, Map<String, String> hostDockerMap) throws IOException {
    List<List<? extends CommandLineElement>> extractedParameterValues = new ArrayList<List<? extends CommandLineElement>>();
    for (CLIMapping cliMapping : cliElement.getMapping()) {
        if (nodeConfig.getParameterKeys().contains(cliMapping.getReferenceName())) {
            Parameter<?> p = nodeConfig.getParameter(cliMapping.getReferenceName());
            if (!p.isNull()) {
                if (p instanceof ListParameter) {
                    ListParameter lp = (ListParameter) p;
                    if (lp.getStrings().size() > 0) {
                        final List<CommandLineElement> tmp = new ArrayList<CommandLineElement>();
                        for (final String s : lp.getStrings()) {
                            tmp.add(new CommandLineFixedString(s));
                        }
                        extractedParameterValues.add(tmp);
                    }
                } else if (p instanceof FileParameter) {
                    extractedParameterValues.add(handleFileParameter(((FileParameter) p).getValue(), dockerCommands, hostDockerMap));
                } else if (p instanceof FileListParameter) {
                    List<String> fl = ((FileListParameter) p).getValue();
                    if (fl.size() > 0) {
                        for (String hostFile : fl) {
                            extractedParameterValues.add(handleFileParameter(hostFile, dockerCommands, hostDockerMap));
                        }
                    }
                } else {
                    List<CommandLineElement> l = new ArrayList<CommandLineElement>();
                    l.add(new CommandLineParameter(p));
                    extractedParameterValues.add(l);
                }
            }
        }
    }
    return extractedParameterValues;
}