Examples with IWriter de.ipbhalle.metfraglib.interfaces.IWriter used on opensource projects

Example 1 with IWriter

use of de.ipbhalle.metfraglib.interfaces.IWriter in project MetFragRelaunched by ipb-halle.

the class UserOutputDataHandler method createResultsToDownload.

/**
 * @param format
 * @param errorMessages
 * @return
 */
public org.primefaces.model.StreamedContent createResultsToDownload(MetFragResultsContainer metfragResults, String format, Messages errorMessages) {
    System.out.println("downloadResults " + format);
    IWriter candidateWriter = null;
    String filePath = "";
    org.primefaces.model.StreamedContent resource = new org.primefaces.model.DefaultStreamedContent(System.in, "text/csv", "MetFragWeb_Candidates." + format);
    try {
        java.io.File folder = new java.io.File(this.beanSettingsContainer.getRootSessionFolder() + Constants.OS_SPECIFIC_FILE_SEPARATOR + "downloads");
        System.out.println("creating folder " + folder.getAbsolutePath());
        boolean folderExists = true;
        if (!folder.exists())
            folderExists = folder.mkdirs();
        if (!folderExists)
            throw new Exception();
        String mimetype = "";
        if (format.equals("csv")) {
            candidateWriter = new CandidateListWriterCSV();
            mimetype = "text/csv";
        } else if (format.equals("xls")) {
            candidateWriter = new CandidateListWriterXLS();
            mimetype = "application/vnd.ms-excel";
        } else if (format.equals("sdf")) {
            candidateWriter = new CandidateListWriterSDF();
            mimetype = "chemical/x-mdl-sdfile";
        } else {
            System.out.println("Error: Unknown format " + format);
        }
        candidateWriter.write(metfragResults.getScoredCandidateList(), "MetFragWeb_Results", folder.getAbsolutePath());
        filePath = folder.getAbsolutePath() + Constants.OS_SPECIFIC_FILE_SEPARATOR + "MetFragWeb_Results." + format;
        resource = new org.primefaces.model.DefaultStreamedContent(new java.io.FileInputStream(new java.io.File(filePath)), mimetype, "MetFragWeb_Candidates." + format);
        errorMessages.removeKey("buttonDownloadResultsError");
    } catch (Exception e) {
        e.printStackTrace();
        errorMessages.setMessage("buttonDownloadResultsError", "Error when downloading candidates.");
        return resource;
    }
    System.out.println("success " + resource.getContentType() + " " + resource.getName());
    return resource;
}

Example 2 with IWriter

use of de.ipbhalle.metfraglib.interfaces.IWriter in project MetFragRelaunched by ipb-halle.

the class AddMissingNonExplainedPeaks method main.

public static void main(String[] args) throws Exception {
    String paramfile = args[0];
    String resultfile = args[1];
    String outputfile = args[2];
    Settings settings = getSettings(paramfile);
    settings.set(VariableNames.LOCAL_DATABASE_PATH_NAME, resultfile);
    IPeakListReader peakListReader = (IPeakListReader) Class.forName((String) settings.get(VariableNames.METFRAG_PEAK_LIST_READER_NAME)).getConstructor(Settings.class).newInstance(settings);
    SettingsChecker settingsChecker = new SettingsChecker();
    if (!settingsChecker.check(settings)) {
        System.err.println("Problems reading settings");
        return;
    }
    settings.set(VariableNames.PEAK_LIST_NAME, peakListReader.read());
    IDatabase db = null;
    String dbFilename = (String) settings.get(VariableNames.LOCAL_DATABASE_PATH_NAME);
    if (dbFilename.endsWith("psv"))
        db = new LocalPSVDatabase(settings);
    else
        db = new LocalCSVDatabase(settings);
    ArrayList<String> ids = null;
    try {
        ids = db.getCandidateIdentifiers();
    } catch (MultipleHeadersFoundInInputDatabaseException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    CandidateList candidates = null;
    try {
        candidates = db.getCandidateByIdentifier(ids);
    } catch (Exception e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
    }
    if (candidates.getNumberElements() == 0) {
        System.out.println("No candidates found in " + (String) settings.get(VariableNames.LOCAL_DATABASE_PATH_NAME));
        return;
    }
    DefaultPeakList peaklist = (DefaultPeakList) settings.get(VariableNames.PEAK_LIST_NAME);
    for (int i = 0; i < candidates.getNumberElements(); i++) {
        String explPeaks = (String) candidates.getElement(i).getProperty("ExplPeaks");
        String[] explPeaksArray = explPeaks.split(";");
        Double[] explPeaksMasses = null;
        if (!explPeaks.equals("NA"))
            explPeaksMasses = getDoubleArrayFromPeakList(explPeaksArray);
        String nonExplPeaksString = "";
        for (int k = 0; k < peaklist.getNumberElements(); k++) {
            if (explPeaks.equals("NA")) {
                nonExplPeaksString += ((IPeak) peaklist.getElement(k)).getMass() + ";";
            } else if (!isContained(((IPeak) peaklist.getElement(k)).getMass(), explPeaksMasses)) {
                nonExplPeaksString += ((IPeak) peaklist.getElement(k)).getMass() + ";";
            }
        }
        if (nonExplPeaksString.length() == 0)
            nonExplPeaksString = "NA";
        if (nonExplPeaksString.endsWith(";"))
            nonExplPeaksString = nonExplPeaksString.substring(0, nonExplPeaksString.length() - 1);
        candidates.getElement(i).setProperty("NonExplainedMasses", nonExplPeaksString);
    }
    IWriter writer = null;
    if (outputfile.endsWith("psv"))
        writer = new CandidateListWriterPSV();
    else
        writer = new CandidateListWriterCSV();
    writer.write(candidates, outputfile);
}

Example 3 with IWriter

use of de.ipbhalle.metfraglib.interfaces.IWriter in project MetFragRelaunched by ipb-halle.

the class CommandLineTool method main.

/**
 * @param args
 */
public static void main(String[] args) {
    /*
		 * read in commandline arguments
		 */
    java.util.Hashtable<String, String> commandLineArguments = processCommandLineArguments(args);
    if (commandLineArguments == null) {
        System.exit(1);
    }
    if (printHelp) {
        printHelp();
        System.exit(0);
    }
    File parameterFile = null;
    MetFragGlobalSettings settings = null;
    if (commandLineArguments.containsKey(VariableNames.PARAMETER_FILE_NAME)) {
        parameterFile = new File((String) commandLineArguments.get(VariableNames.PARAMETER_FILE_NAME));
        if (!parameterFile.exists()) {
            logger.error("Parameter file " + parameterFile.getAbsolutePath() + " not found!");
            System.exit(1);
        }
        if (!parameterFile.canRead()) {
            logger.error("Parameter file " + parameterFile.getAbsolutePath() + " has no read permissions!");
            System.exit(1);
        }
        if (!parameterFile.isFile()) {
            logger.error("Parameter file " + parameterFile.getAbsolutePath() + " is no regular file!");
            System.exit(1);
        }
        /*
			 * read settings
			 */
        try {
            settings = MetFragGlobalSettings.readSettings(parameterFile, logger);
        } catch (Exception e) {
            logger.error("Error reading parameter file " + parameterFile);
            System.exit(1);
        }
    }
    /*
		 * read additional parameters
		 */
    try {
        if (settings == null) {
            settings = MetFragGlobalSettings.readSettings(commandLineArguments, logger);
        } else {
            MetFragGlobalSettings.readSettings(commandLineArguments, settings, logger);
        }
    } catch (Exception e2) {
        logger.error(e2.getMessage());
        logger.error("Error reading settings");
        System.exit(1);
    }
    // check settings with SettingsChecker
    SettingsChecker settingsChecker = new SettingsChecker();
    if (!settingsChecker.check(settings)) {
        System.exit(2);
    }
    /*
		 * load hd plugin
		 */
    HydrogenDeuteriumPlugin hdPlugin = new HydrogenDeuteriumPlugin();
    if (!hdPlugin.load(settings))
        System.exit(3);
    // init the MetFrag process
    CombinedMetFragProcess mp = new CombinedMetFragProcess(settings);
    // retrieve candidates from database
    try {
        boolean candidatesRetrieved = mp.retrieveCompounds();
        if (!candidatesRetrieved)
            throw new Exception();
    } catch (Exception e1) {
        e1.printStackTrace();
        logger.error("Error when retrieving compounds.");
        System.exit(4);
    }
    // run the MetFrag process -> in silico fragmentation, fragment-peak-assignment, scoring
    try {
        mp.run();
    } catch (Exception e1) {
        e1.printStackTrace();
        logger.error("Error when processing compounds.");
        System.exit(5);
    }
    // fetch the scored candidate list
    CandidateList scoredCandidateList = mp.getCandidateList();
    /*
		 * store the results
		 */
    try {
        /*
			 * store candidates in your specified format
			 */
        if (settings.get(VariableNames.METFRAG_CANDIDATE_WRITER_NAME) != null) {
            String[] candidateWriterNames = (String[]) settings.get(VariableNames.METFRAG_CANDIDATE_WRITER_NAME);
            for (int k = 0; k < candidateWriterNames.length; k++) {
                IWriter candidateWriter = (IWriter) Class.forName(ClassNames.getClassNameOfCandidateListWriter(candidateWriterNames[k])).getConstructor().newInstance();
                try {
                    Object ResultsFile = settings.get(VariableNames.STORE_RESULTS_FILE_NAME);
                    if (ResultsFile != null)
                        candidateWriter.writeFile(new File((String) ResultsFile), scoredCandidateList, settings);
                    else
                        candidateWriter.write(scoredCandidateList, (String) settings.get(VariableNames.SAMPLE_NAME), (String) settings.get(VariableNames.STORE_RESULTS_PATH_NAME), settings);
                } catch (Exception e) {
                    e.printStackTrace();
                    logger.error("Error: Could not write candidate file.");
                    System.exit(6);
                }
            }
        }
        /*
			 * store candidates fragments in your specified format
			 */
        if (settings.get(VariableNames.METFRAG_CANDIDATE_FRAGMENT_WRITER_NAME) != null) {
            IWriter candidateWriter = (IWriter) Class.forName(ClassNames.getClassNameOfFragmentListWriter((String) settings.get(VariableNames.METFRAG_CANDIDATE_FRAGMENT_WRITER_NAME))).getConstructor().newInstance();
            try {
                candidateWriter.write(scoredCandidateList, (String) settings.get(VariableNames.SAMPLE_NAME), (String) settings.get(VariableNames.STORE_RESULTS_PATH_NAME), settings);
            } catch (Exception e) {
                logger.error(e.getMessage());
                logger.error("Error: Could not write fragment files.");
                System.exit(7);
            }
        }
        /*
			 * store candidates in your specified image format
			 */
        if (settings.get(VariableNames.METFRAG_CANDIDATE_IMAGE_GENERATOR_NAME) != null) {
            IWriter imageWriter = (IWriter) Class.forName((String) settings.get(VariableNames.METFRAG_IMAGE_WRITER_NAME)).getConstructor().newInstance();
            IImageGenerator imageGenerator = (IImageGenerator) Class.forName((String) settings.get(VariableNames.METFRAG_CANDIDATE_IMAGE_GENERATOR_NAME)).getConstructor().newInstance();
            for (int i = 0; i < scoredCandidateList.getNumberElements(); i++) {
                try {
                    RenderedImage renderedImage = imageGenerator.generateImage(scoredCandidateList.getElement(i));
                    DefaultList imageList = new DefaultList();
                    imageList.addElement(renderedImage);
                    imageWriter.write(imageList, (String) settings.get(VariableNames.SAMPLE_NAME) + "_" + scoredCandidateList.getElement(i).getIdentifier(), (String) settings.get(VariableNames.STORE_RESULTS_PATH_NAME));
                } catch (Exception e) {
                    logger.error("Error: Could not write candidate image files.");
                    System.exit(8);
                }
            }
        }
        /*
			 * store candidate fragments in your specified image format
			 */
        if (settings.get(VariableNames.METFRAG_FRAGMENT_IMAGE_GENERATOR_NAME) != null) {
            IWriter imageWriter = (IWriter) Class.forName((String) settings.get(VariableNames.METFRAG_IMAGE_WRITER_NAME)).getConstructor().newInstance();
            IImageGenerator imageGenerator = (IImageGenerator) Class.forName((String) settings.get(VariableNames.METFRAG_FRAGMENT_IMAGE_GENERATOR_NAME)).getConstructor().newInstance();
            for (int i = 0; i < scoredCandidateList.getNumberElements(); i++) {
                MatchList matchList = scoredCandidateList.getElement(i).getMatchList();
                for (int j = 0; j < matchList.getNumberElements(); j++) {
                    try {
                        scoredCandidateList.getElement(i).initialisePrecursorCandidate();
                        RenderedImage renderedImage = imageGenerator.generateImage(scoredCandidateList.getElement(i).getPrecursorMolecule(), (DefaultBitArrayFragment) matchList.getElement(j).getBestMatchedFragment());
                        DefaultList imageList = new DefaultList();
                        imageList.addElement(renderedImage);
                        imageWriter.write(imageList, (String) settings.get(VariableNames.SAMPLE_NAME) + "_" + scoredCandidateList.getElement(i).getIdentifier() + "_fragment_id" + (j + 1), (String) settings.get(VariableNames.STORE_RESULTS_PATH_NAME));
                        scoredCandidateList.getElement(i).resetPrecursorMolecule();
                    } catch (Exception e) {
                        logger.error("Error: Could not write fragment image files.");
                        System.exit(9);
                    }
                }
            }
        }
    } catch (InstantiationException e) {
        e.printStackTrace();
        System.exit(10);
    } catch (IllegalAccessException e) {
        e.printStackTrace();
        System.exit(10);
    } catch (IllegalArgumentException e) {
        e.printStackTrace();
        System.exit(10);
    } catch (InvocationTargetException e) {
        e.printStackTrace();
        System.exit(10);
    } catch (NoSuchMethodException e) {
        e.printStackTrace();
        System.exit(10);
    } catch (SecurityException e) {
        e.printStackTrace();
        System.exit(10);
    } catch (ClassNotFoundException e) {
        e.printStackTrace();
        System.exit(10);
    }
}

Example 4 with IWriter

use of de.ipbhalle.metfraglib.interfaces.IWriter in project MetFragRelaunched by ipb-halle.

the class MetFragRestService method startMetFrag.

@Async
public static String startMetFrag(CombinedMetFragProcess mp, MetFragGlobalSettings settings, String resultFolderName) throws IOException {
    // retrieve candidates from database
    boolean candidatesRetrieved = false;
    try {
        candidatesRetrieved = mp.retrieveCompounds();
        mp.run();
        CandidateList scoredCandidateList = mp.getCandidateList();
        if (settings.get(VariableNames.METFRAG_CANDIDATE_WRITER_NAME) != null) {
            String[] candidateWriterNames = (String[]) settings.get(VariableNames.METFRAG_CANDIDATE_WRITER_NAME);
            for (int k = 0; k < candidateWriterNames.length; k++) {
                IWriter candidateWriter = (IWriter) Class.forName(ClassNames.getClassNameOfCandidateListWriter(candidateWriterNames[k])).getConstructor().newInstance();
                try {
                    Object ResultsFile = settings.get(VariableNames.STORE_RESULTS_FILE_NAME);
                    if (ResultsFile != null)
                        candidateWriter.writeFile(new File((String) ResultsFile), scoredCandidateList, settings);
                    else
                        candidateWriter.write(scoredCandidateList, (String) settings.get(VariableNames.SAMPLE_NAME), (String) settings.get(VariableNames.STORE_RESULTS_PATH_NAME), settings);
                } catch (Exception e) {
                    e.printStackTrace();
                }
            }
        }
    } catch (Exception e) {
        e.printStackTrace();
        writeStatus("ERROR", (String) settings.get(VariableNames.SAMPLE_NAME), resultFolderName);
        return "Error when fetching candidates.";
    }
    if (!candidatesRetrieved) {
        writeStatus("ERROR", (String) settings.get(VariableNames.SAMPLE_NAME), resultFolderName);
        return "Error when fetching candidates.";
    } else {
        writeStatus("SUCCESS", (String) settings.get(VariableNames.SAMPLE_NAME), resultFolderName);
        return (String) settings.get(VariableNames.SAMPLE_NAME);
    }
}

Example 5 with IWriter

use of de.ipbhalle.metfraglib.interfaces.IWriter in project MetFragRelaunched by ipb-halle.

the class UserOutputDataHandler method createCandidatesToDownload.

/**
 * @param format
 * @param errorMessages
 * @return
 */
public org.primefaces.model.StreamedContent createCandidatesToDownload(String format, Messages errorMessages) {
    System.out.println("downloadCandidates " + format);
    IWriter candidateWriter = null;
    String filePath = "";
    org.primefaces.model.StreamedContent resource = new org.primefaces.model.DefaultStreamedContent(System.in, "text/csv", "MetFragWeb_Candidates." + format);
    try {
        java.io.File folder = new java.io.File(this.beanSettingsContainer.getRootSessionFolder() + Constants.OS_SPECIFIC_FILE_SEPARATOR + "downloads");
        System.out.println("creating folder " + folder.getAbsolutePath());
        boolean folderExists = true;
        if (!folder.exists())
            folderExists = folder.mkdirs();
        if (!folderExists)
            throw new Exception();
        String mimetype = "";
        if (format.equals("csv")) {
            candidateWriter = new CandidateListWriterCSV();
            mimetype = "text/csv";
        } else if (format.equals("xls")) {
            candidateWriter = new CandidateListWriterXLS();
            mimetype = "application/vnd.ms-excel";
        } else if (format.equals("sdf")) {
            candidateWriter = new CandidateListWriterSDF();
            mimetype = "chemical/x-mdl-sdfile";
        } else {
            System.out.println("Error: Unknown format " + format);
        }
        candidateWriter.write(this.beanSettingsContainer.getRetrievedCandidateList(), "MetFragWeb_Candidates", folder.getAbsolutePath());
        filePath = folder.getAbsolutePath() + Constants.OS_SPECIFIC_FILE_SEPARATOR + "MetFragWeb_Candidates." + format;
        resource = new org.primefaces.model.DefaultStreamedContent(new java.io.FileInputStream(new java.io.File(filePath)), mimetype, "MetFragWeb_Candidates." + format);
        errorMessages.removeKey("buttonDownloadCompoundsError");
    } catch (Exception e) {
        errorMessages.setMessage("buttonDownloadCompoundsError", "Error when downloading candidates.");
        return resource;
    }
    System.out.println("success " + resource.getContentType() + " " + resource.getName());
    return resource;
}