Example usage for org.apache.commons.io FilenameUtils getBaseName

List of usage examples for org.apache.commons.io FilenameUtils getBaseName

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Introduction

In this page you can find the example usage for org.apache.commons.io FilenameUtils getBaseName.

Prototype

public static String getBaseName(String filename)

Source Link

Document

Gets the base name, minus the full path and extension, from a full filename.

Usage

From source file:com.consol.citrus.admin.service.TestCaseServiceImpl.java

@Override
public Long getTestCount(Project project) {
    Long testCount = Long.valueOf(FileUtils.getTestFiles(getTestDirectory(project)).size());

    try {//from   w w w.j  ava2  s.co m
        Resource[] javaSources = new PathMatchingResourcePatternResolver().getResources(
                "file:" + FilenameUtils.separatorsToUnix(getJavaDirectory(project)) + "**/*.java");
        for (Resource resource : javaSources) {
            File file = resource.getFile();
            String testName = FilenameUtils.getBaseName(file.getName());
            String testPackage = file.getParentFile().getAbsolutePath()
                    .substring(getJavaDirectory(project).length()).replace(File.separatorChar, '.');

            if (knownToClasspath(testPackage, testName)) {
                testCount += getTestCaseInfoFromClass(testPackage, testName, file).size();
            } else {
                testCount += getTestCaseInfoFromFile(testPackage, testName, file).size();
            }
        }
    } catch (IOException e) {
        log.warn("Failed to read Java source files - list of test cases for this project is incomplete", e);
    }

    return testCount;
}

From source file:edu.cornell.med.icb.goby.modes.SplitFastaMode.java

/**
 * Split a fasta / fastq file by (a) readlength and (b) the maximum number of
 * entries per file. This will output the files that are written to stdout
 * @throws IOException error reading / writing files.
 *//*from  ww  w  .j av  a  2  s . c  o m*/
@Override
public void execute() throws IOException {
    final FastXReader reader = new FastXReader(inputFile);
    final Int2ObjectMap<PrintStream> outputMap = new Int2ObjectOpenHashMap<PrintStream>();
    final Int2IntMap entriesPerReadLen = new Int2IntOpenHashMap();
    final Int2IntMap filesPerReadLen = new Int2IntOpenHashMap();
    final List<String> removeExt = Arrays.asList("gz", "fa", "mpfa", "fna", "fsa", "fas", "fasta", "fq", "mpfq",
            "fnq", "fsq", "fas", "fastq");
    String inputName = FilenameUtils.getName(inputFile);
    while (true) {
        // Remove the unwanted extensions from the file name
        final String ext = FilenameUtils.getExtension(inputName);
        if (!removeExt.contains(ext)) {
            break;
        }
        inputName = FilenameUtils.getBaseName(inputName);
    }
    final String outputFilenameTemplate = FilenameUtils.getFullPath(inputFile) + inputName
            + "._READLENGTH_._PART_." + reader.getFileType();
    final NumberFormat nf3 = NumberFormat.getInstance();
    nf3.setMinimumIntegerDigits(3);
    final NumberFormat nf2 = NumberFormat.getInstance();
    nf2.setMinimumIntegerDigits(2);
    for (final FastXEntry entry : reader) {
        final int readLen = Math.min(fastxSplitMaxLength, roundReadLen(entry.getReadLength(), splitReadsMod));
        PrintStream out = outputMap.get(readLen);
        if (out == null) {
            filesPerReadLen.put(readLen, 1);
            entriesPerReadLen.put(readLen, 0);
            String outputFilename = outputFilenameTemplate.replaceAll("_READLENGTH_", nf3.format(readLen));
            outputFilename = outputFilename.replaceAll("_PART_", nf2.format(1));
            System.out.println(outputFilename);
            out = new PrintStream(new BufferedOutputStream(new FileOutputStream(outputFilename)));
            outputMap.put(readLen, out);
        }
        int numEntries = entriesPerReadLen.get(readLen);
        if (numEntries == maxReadsPerFile) {
            out.close();
            numEntries = 0;
            int numFiles = filesPerReadLen.get(readLen);
            numFiles++;
            filesPerReadLen.put(readLen, numFiles);
            String outputFilename = outputFilenameTemplate.replaceAll("_READLENGTH_", nf3.format(readLen));
            outputFilename = outputFilename.replaceAll("_PART_", nf2.format(numFiles));
            System.out.println(outputFilename);
            out = new PrintStream(new BufferedOutputStream(new FileOutputStream(outputFilename)));
            outputMap.put(readLen, out);
        }
        out.println(entry.getEntry());
        entriesPerReadLen.put(readLen, numEntries + 1);
    }
    for (final PrintStream out : outputMap.values()) {
        out.close();
    }
    outputMap.clear();
    reader.close();
}

From source file:me.jaimegarza.syntax.test.java.TestJavaPackedParser.java

@Test
public void test03Runtime() throws ParsingException, AnalysisException, OutputException, MalformedURLException,
        ClassNotFoundException, InstantiationException, IllegalAccessException, SecurityException,
        NoSuchMethodException, IllegalArgumentException, InvocationTargetException {
    generateLanguageFile(packedArgs);//from   ww  w. j  av a2  s .  co m

    File source = new File(tmpLanguageFile);
    File sourceDir = source.getParentFile();
    CompilationResult result = compileJavaFile(source, sourceDir);
    Assert.assertEquals(result.getErrors().length, 0, "Syntax errors found trying to execute");

    URL urls[] = new URL[1];
    urls[0] = sourceDir.toURI().toURL();
    URLClassLoader classLoader = URLClassLoader.newInstance(urls, this.getClass().getClassLoader());
    String className = FilenameUtils.getBaseName(tmpLanguageFile);
    Class<?> clazz = classLoader.loadClass(className);
    Object parser = clazz.newInstance();
    Method setVerbose = parser.getClass().getMethod("setVerbose", boolean.class);
    Method parse = parser.getClass().getMethod("parse");
    Method getTotal = parser.getClass().getMethod("getTotal");
    setVerbose.invoke(parser, true);
    parse.invoke(parser);
    Object o = getTotal.invoke(parser);
    Assert.assertTrue(o instanceof Integer);
    Integer i = (Integer) o;
    Assert.assertEquals((int) i, -17, "total does not match");
}

From source file:be.fedict.eid.dss.portal.control.bean.UploadBean.java

@Override
public void listener(UploadEvent event) throws Exception {
    this.log.debug("listener");
    UploadItem item = event.getUploadItem();
    this.log.debug("filename: #0", item.getFileName());
    this.filename = item.getFileName();
    this.log.debug("content type: #0", item.getContentType());
    String extension = FilenameUtils.getExtension(this.filename).toLowerCase();
    this.contentType = supportedFileExtensions.get(extension);
    if (null == this.contentType) {
        /*//w  w  w.j a v  a 2s  .  c o  m
         * Unsupported content-type is converted to a ZIP container.
         */
        ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
        ZipOutputStream zipOutputStream = new ZipOutputStream(outputStream);
        ZipEntry zipEntry = new ZipEntry(this.filename);
        zipOutputStream.putNextEntry(zipEntry);
        IOUtils.write(item.getData(), zipOutputStream);
        zipOutputStream.close();
        this.filename = FilenameUtils.getBaseName(this.filename) + ".zip";
        this.document = outputStream.toByteArray();
        this.contentType = "application/zip";
        return;
    }
    this.log.debug("file size: #0", item.getFileSize());
    this.log.debug("data bytes available: #0", (null != item.getData()));
    if (null != item.getData()) {
        this.document = item.getData();
        return;
    }
    File file = item.getFile();
    if (null != file) {
        this.log.debug("tmp file: #0", file.getAbsolutePath());
        this.document = FileUtils.readFileToByteArray(file);
    }
}

From source file:MSUmpire.LCMSPeakStructure.LCMSPeakMS1.java

public String GetDefaultPepXML() {
    return FilenameUtils.separatorsToUnix(FilenameUtils.getFullPath(ScanCollectionName) + "interact-"
            + FilenameUtils.getBaseName(ScanCollectionName) + ".pep.xml");
}

From source file:com.googlecode.dex2jar.tools.JarAccessCmd.java

@Override
protected void doCommandLine() throws Exception {
    if (remainingArgs.length != 1) {
        usage();//from  w ww  . j  a  va 2 s . co m
        return;
    }

    File jar = new File(remainingArgs[0]);
    if (!jar.exists()) {
        System.err.println(jar + " is not exists");
        usage();
        return;
    }

    if (output == null) {
        if (jar.isDirectory()) {
            output = new File(jar.getName() + "-access.jar");
        } else {
            output = new File(FilenameUtils.getBaseName(jar.getName()) + "-access.jar");
        }
    }

    if (output.exists() && !forceOverwrite) {
        System.err.println(output + " exists, use --force to overwrite");
        usage();
        return;
    }

    final int rf = ~str2acc(removeFieldAccess);
    final int rm = ~str2acc(removeMethodAccess);
    final int rc = ~str2acc(removeClassAccess);

    final int af = str2acc(addFieldAccess);
    final int am = str2acc(addMethodAccess);
    final int ac = str2acc(addClassAccess);

    final int flags = removeDebug ? ClassReader.SKIP_DEBUG : 0;
    final OutHandler fo = FileOut.create(output, true);
    try {
        new FileWalker().withStreamHandler(new StreamHandler() {

            @Override
            public void handle(boolean isDir, String name, StreamOpener current, Object nameObject)
                    throws IOException {
                if (isDir || !name.endsWith(".class")) {
                    fo.write(isDir, name, current == null ? null : current.get(), nameObject);
                    return;
                }

                OutputStream os = null;
                try {
                    InputStream is = current.get();
                    final ClassReader r = new ClassReader(is);
                    ClassWriter cr = new ClassWriter(0);
                    r.accept(new ClassAdapter(cr) {

                        @Override
                        public void visit(int version, int access, String name, String signature,
                                String superName, String[] interfaces) {
                            int na = (access & rc) | ac;
                            if (access != na) {
                                System.out.println("c " + name);
                            }
                            super.visit(version, na, name, signature, superName, interfaces);
                        }

                        @Override
                        public FieldVisitor visitField(int access, String name, String desc, String signature,
                                Object value) {
                            int na = (access & rf) | af;
                            if (na != access) {
                                System.out.println("f " + r.getClassName() + "." + name);
                            }
                            return super.visitField(na, name, desc, signature, value);
                        }

                        @Override
                        public MethodVisitor visitMethod(int access, String name, String desc, String signature,
                                String[] exceptions) {
                            int na = (access & rm) | am;
                            if (na != access) {
                                System.out.println("m " + r.getClassName() + "." + name + desc);
                            }
                            return super.visitMethod(na, name, desc, signature, exceptions);
                        }

                    }, flags | ClassReader.EXPAND_FRAMES);
                    fo.write(isDir, name, cr.toByteArray(), nameObject);
                } catch (IOException ioe) {
                    System.err.println("error in " + name);
                    ioe.printStackTrace(System.err);
                } finally {
                    IOUtils.closeQuietly(os);
                }
            }
        }).walk(jar);
    } finally {
        IOUtils.closeQuietly(fo);
    }
}

From source file:me.jaimegarza.syntax.test.java.TestJavaExpandedParser.java

@Test
public void test03Runtime() throws ParsingException, AnalysisException, OutputException, MalformedURLException,
        ClassNotFoundException, InstantiationException, IllegalAccessException, SecurityException,
        NoSuchMethodException, IllegalArgumentException, InvocationTargetException {
    generateLanguageFile(expandedArgs);/*from w ww  . java 2 s  .com*/

    File source = new File(tmpLanguageFile);
    File sourceDir = source.getParentFile();
    CompilationResult result = compileJavaFile(source, sourceDir);
    Assert.assertEquals(result.getErrors().length, 0, "Syntax errors found trying to execute");

    URL urls[] = new URL[1];
    urls[0] = sourceDir.toURI().toURL();
    URLClassLoader classLoader = URLClassLoader.newInstance(urls, this.getClass().getClassLoader());
    String className = FilenameUtils.getBaseName(tmpLanguageFile);
    Class<?> clazz = classLoader.loadClass(className);
    Object parser = clazz.newInstance();
    Method setVerbose = parser.getClass().getMethod("setVerbose", boolean.class);
    Method parse = parser.getClass().getMethod("parse");
    Method getTotal = parser.getClass().getMethod("getTotal");
    setVerbose.invoke(parser, true);
    parse.invoke(parser);
    Object o = getTotal.invoke(parser);
    Assert.assertTrue(o instanceof Integer);
    Integer i = (Integer) o;
    Assert.assertEquals((int) i, -17, "total does not match");
}

From source file:me.jaimegarza.syntax.test.java.TestJavaExpandedScanner.java

@Test
public void test03Runtime() throws ParsingException, AnalysisException, OutputException, MalformedURLException,
        ClassNotFoundException, InstantiationException, IllegalAccessException, SecurityException,
        NoSuchMethodException, IllegalArgumentException, InvocationTargetException {
    generateLanguageFile(packedArgs);/*w  ww.  j a  v a 2  s.c  o m*/

    File source = new File(tmpLanguageFile);
    File sourceDir = source.getParentFile();
    CompilationResult result = compileJavaFile(source, sourceDir);
    Assert.assertEquals(result.getErrors().length, 0, "Syntax errors found trying to execute");

    URL urls[] = new URL[1];
    urls[0] = sourceDir.toURI().toURL();
    URLClassLoader classLoader = URLClassLoader.newInstance(urls, this.getClass().getClassLoader());
    String className = FilenameUtils.getBaseName(tmpLanguageFile);
    Class<?> clazz = classLoader.loadClass(className);
    String lexicalClassName = className + "$StackElement";
    Class<?> lexicalClazz = classLoader.loadClass(lexicalClassName);
    Object parser = clazz.newInstance();
    Method setVerbose = parser.getClass().getMethod("setVerbose", boolean.class);
    Method init = parser.getClass().getMethod("init");
    Method parse = parser.getClass().getMethod("parse", Integer.TYPE, lexicalClazz);
    Method getValidTokens = parser.getClass().getMethod("getValidTokens");
    Method getTotal = parser.getClass().getMethod("getTotal");
    setVerbose.invoke(parser, true);
    init.invoke(parser);
    for (Parameter p : parameters) {
        int[] tokens = (int[]) getValidTokens.invoke(parser);
        Assert.assertTrue(arrayContains(tokens, p.token), "Token " + p.token + " ain't there");
        Object lexicalValue = lexicalClazz.newInstance();
        Method setNumber = lexicalClazz.getMethod("setNumber", Integer.TYPE);
        setNumber.invoke(lexicalValue, p.value);
        parse.invoke(parser, p.token, lexicalValue);
        Object t = getTotal.invoke(parser);
        Assert.assertEquals(((Integer) t).intValue(), p.result, "Result is not " + p.result);
    }
    Object o = getTotal.invoke(parser);
    Assert.assertTrue(o instanceof Integer);
    Integer i = (Integer) o;
    Assert.assertEquals((int) i, -17, "total does not match");
}

From source file:com.haulmont.cuba.desktop.gui.components.DesktopExportDisplay.java

private void openFileAction(String finalFileName, ExportDataProvider dataProvider) {
    File destFile = null;//from w  w w. j a v  a 2s .  co m
    try {
        destFile = File.createTempFile("get_" + FilenameUtils.getBaseName(finalFileName),
                "." + getFileExt(finalFileName));
    } catch (IOException e) {
        String message = messages.getMessage(DesktopExportDisplay.class, "export.tempFileError");
        getFrame().getWindowManager().showNotification(message, Frame.NotificationType.WARNING);
    }

    if (destFile != null) {
        if (Desktop.isDesktopSupported() && saveFile(dataProvider, destFile)) {
            try {
                Desktop.getDesktop().open(destFile);
            } catch (IOException ex) {
                String message = messages.getMessage(DesktopExportDisplay.class, "export.openError");
                getFrame().getWindowManager().showNotification(message, Frame.NotificationType.WARNING);
            }
        }
    }
}

From source file:edu.cornell.med.icb.goby.modes.SequenceVariationStatsMode.java

/**
 * Display sequence variations.//from   w ww  . j a  v  a2s .c  o  m
 *
 * @throws java.io.IOException error reading / writing
 */
@Override
public void execute() throws IOException {
    PrintStream stream = null;
    try {
        stream = outputFilename == null ? System.out : new PrintStream(new FileOutputStream(outputFilename));
        switch (outputFormat) {
        case TAB_DELIMITED:
        case TSV:
            stream.println(
                    "basename\tread-index\tcount-variation-bases\tbases-at-index/all-variations-bases\tbases-at-index/all-reference-bases\tcount-reference-bases");
            break;
        }

        for (final String basename : basenames) {
            alignmentIterator.resetTallies();
            final String[] singleBasename = { basename };
            // Iterate through each alignment and write sequence variations to output file:
            alignmentIterator.iterate(singleBasename);

            final Long2LongMap readIndexTallies = alignmentIterator.getReadIndexVariationTally();
            final double totalNumberOfVariationBases = sum(readIndexTallies.values());
            final double numberOfAlignmentEntries = alignmentIterator.getNumAlignmentEntries();

            final long countReferenceBases = alignmentIterator.getReferenceBaseCount();
            for (final long readIndex : readIndexTallies.keySet()) {
                final long countVariationBasesAtReadIndex = readIndexTallies.get(readIndex);
                final double frequency = ((double) countVariationBasesAtReadIndex)
                        / totalNumberOfVariationBases;
                final double alignFrequency = ((double) countVariationBasesAtReadIndex) / countReferenceBases;

                stream.printf("%s\t%d\t%d\t%s\t%f\t%d%n", FilenameUtils.getBaseName(basename), readIndex,
                        countVariationBasesAtReadIndex, frequency, alignFrequency, countReferenceBases);
            }
            stream.flush();
        }
    } finally {
        if (stream != System.out) {
            IOUtils.closeQuietly(stream);
        }
    }
}