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

Example 6 with FileParameter

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

the class GenericKnimeNodeModel 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 FileParameter

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

the class CTDConfigurationReaderTest method testSeqAnCTD.

@Test
public void testSeqAnCTD() throws Exception {
    CTDConfigurationReader reader = new CTDConfigurationReader();
    assertNotNull(reader);
    INodeConfiguration config = reader.read(TestDataSource.class.getResourceAsStream("sam2matrix.ctd"));
    assertEquals("Metagenomics", config.getCategory());
    assertEquals("http://www.seqan.de", config.getDocUrl());
    // <ITEM name="out" value="" type="output-file"
    // description="Output file." supported_formats="*.tsv" required="true"
    // advanced="false" />
    FileParameter fp_out = (FileParameter) config.getParameter("sam2matrix.out");
    assertNotNull(fp_out);
    assertEquals("Output file.", fp_out.getDescription());
    assertEquals(1, fp_out.getPort().getMimeTypes().size());
    assertEquals("tsv", fp_out.getPort().getMimeTypes().get(0));
    assertFalse(fp_out.isOptional());
    assertFalse(fp_out.isAdvanced());
    // <ITEMLIST name="mapping" type="input-file"
    // description="File containing the mappings." supported_formats="*.sam"
    // required="true" advanced="false" >
    FileListParameter flp_mapping = (FileListParameter) config.getParameter("sam2matrix.mapping");
    assertNotNull(flp_mapping);
    assertEquals("File containing the mappings.", flp_mapping.getDescription());
    assertEquals(1, flp_mapping.getPort().getMimeTypes().size());
    assertEquals("sam", flp_mapping.getPort().getMimeTypes().get(0));
    assertFalse(flp_mapping.isOptional());
    assertFalse(flp_mapping.isAdvanced());
    // <ITEM name="reads" value="" type="input-file"
    // description="File containing the reads contained in the mapping file(s)."
    // supported_formats="*.fa,*.fasta,*.fq,*.fastq" required="true"
    // advanced="false" />
    FileParameter fp_reads = (FileParameter) config.getParameter("sam2matrix.reads");
    assertNotNull(fp_reads);
    assertEquals("File containing the reads contained in the mapping file(s).", fp_reads.getDescription());
    assertEquals(4, fp_reads.getPort().getMimeTypes().size());
    assertEquals("fa", fp_reads.getPort().getMimeTypes().get(0));
    assertEquals("fasta", fp_reads.getPort().getMimeTypes().get(1));
    assertEquals("fq", fp_reads.getPort().getMimeTypes().get(2));
    assertEquals("fastq", fp_reads.getPort().getMimeTypes().get(3));
    assertFalse(fp_reads.isOptional());
    assertFalse(fp_reads.isAdvanced());
    // <ITEMLIST name="reference" type="string"
    // description="Name of the file used as reference of the corresponding sam file. If not specified the names of the mapping files are taken"
    // required="false" advanced="false" >
    StringListParameter slp_reference = (StringListParameter) config.getParameter("sam2matrix.reference");
    assertNotNull(slp_reference);
    assertEquals("Name of the file used as reference of the corresponding sam file. If not specified the names of the mapping files are taken", slp_reference.getDescription());
    assertTrue(slp_reference.isOptional());
    assertFalse(slp_reference.isAdvanced());
    // the parameter following parameters were tagged with gkn-ignore and
    // hence should not be parsed
    assertNull(config.getParameter("sam2matrix.write-ctd-file-ext"));
    assertNull(config.getParameter("sam2matrix.out-file-ext"));
    assertNull(config.getParameter("sam2matrix.mapping-file-ext"));
    assertNull(config.getParameter("sam2matrix.reads-file-ext"));
}

Example 8 with FileParameter

use of com.genericworkflownodes.knime.parameter.FileParameter 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 9 with FileParameter

use of com.genericworkflownodes.knime.parameter.FileParameter 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);
        }
    }
}

Example 10 with FileParameter

use of com.genericworkflownodes.knime.parameter.FileParameter 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;
}