List of usage examples for org.apache.commons.io FilenameUtils concat
public static String concat(String basePath, String fullFilenameToAdd)
From source file:edu.cornell.med.icb.goby.modes.TestSplicedSamHelper.java
@Test // Test right soft clip: public void testSamToCompactTrickCase5() throws IOException { SAMToCompactMode importer = new SAMToCompactMode(); importer.setInputFile("test-data/splicedsamhelper/tricky-spliced-5.sam"); final String outputFilename = FilenameUtils.concat(BASE_TEST_DIR, "spliced-output-alignment-5"); importer.setOutputFile(outputFilename); importer.execute();//from ww w. j av a2 s .c om AlignmentReader reader = new AlignmentReaderImpl(outputFilename); assertTrue(reader.hasNext()); Alignments.AlignmentEntry first = reader.next(); assertEquals(0, first.getQueryIndex()); assertEquals(0, first.getFragmentIndex()); assertEquals(71428 - 1, first.getPosition()); }
From source file:com.enioka.jqm.tools.MiscTest.java
@Test public void testMultiLog() throws Exception { PrintStream out_ini = System.out; PrintStream err_ini = System.err; Helpers.setSingleParam("logFilePerLaunch", "true", em); CreationTools.createJobDef(null, true, "App", null, "jqm-tests/jqm-test-datetimemaven/target/test.jar", TestHelpers.qVip, 42, "MarsuApplication", null, "Franquin", "ModuleMachin", "other", "other", true, em);/*w w w. java 2 s. c o m*/ int i = JobRequest.create("MarsuApplication", "TestUser").submit(); addAndStartEngine(); TestHelpers.waitFor(1, 20000, em); String fileName = StringUtils.leftPad("" + i, 10, "0") + ".stdout.log"; File f = new File(FilenameUtils.concat(((MultiplexPrintStream) System.out).rootLogDir, fileName)); Assert.assertEquals(1, TestHelpers.getOkCount(em)); Assert.assertEquals(0, TestHelpers.getNonOkCount(em)); Assert.assertTrue(f.exists()); System.setErr(err_ini); System.setOut(out_ini); }
From source file:edu.cornell.med.icb.goby.readers.sam.TestGobyPaperTop5000s.java
/** * The first 1M alignments of UAN. This large dataset does not exist on the testing server. * * @throws java.io.IOException error//w w w . j av a2 s . com */ // @Test public void testRoundTrip1M() throws IOException { final RoundTripAlignment rtc = new RoundTripAlignment(); rtc.inputGenomeFilename = findThousandGenome(); rtc.sourceBamFilename = "test-data/splicedsamhelper/1M.bam"; rtc.destGobyBasename = FilenameUtils.concat(BASE_TEST_OUTPUT_DIR, "1M"); rtc.destBamFilename = FilenameUtils.concat(BASE_TEST_OUTPUT_DIR, "1M.bam"); rtc.canonicalMdzForComparison = false; final long start = System.currentTimeMillis(); rtc.testRoundTripAny(); System.out.printf("Execution time in ms=%d%n", System.currentTimeMillis() - start); }
From source file:edu.cornell.med.icb.goby.alignments.TestIterateSortedAlignment.java
@Test public void testIterateSortedReferenceInsertions() throws IOException { final String basename = "align-skip-to-1-concat"; final String basenamePath = FilenameUtils.concat(BASE_TEST_DIR, basename); final AlignmentWriterImpl writer = new AlignmentWriterImpl(basenamePath); writer.setNumAlignmentEntriesPerChunk(1); final int numTargets = 3; final int[] targetLengths = new int[numTargets]; for (int referenceIndex = 0; referenceIndex < numTargets; referenceIndex++) { targetLengths[referenceIndex] = 1000; }/*from ww w . j a v a2 s. c o m*/ writer.setTargetLengths(targetLengths); // we write this alignment sorted: writer.setSorted(true); Alignments.AlignmentEntry.Builder newEntry; newEntry = prepareAlignmentEntryWithReferenceInsertion(0, 1, 100, 30, false, new int[] { 4, 3 }); writer.appendEntry(newEntry.build()); writer.close(); writer.printStats(System.out); final Int2IntMap positionMap = new Int2IntOpenHashMap(); final IntSet variantReadIndices = new IntOpenHashSet(); IterateSortedAlignmentsListImpl iterator = new IterateSortedAlignmentsListImpl() { @Override public void observeVariantBase(ConcatSortedAlignmentReader sortedReaders, Alignments.AlignmentEntry alignmentEntry, Int2ObjectMap<DiscoverVariantPositionData> positionToBases, Alignments.SequenceVariation var, char toChar, char fromChar, byte toQual, int currentReferenceIndex, int currentRefPosition, int currentReadIndex) { variantReadIndices.add(currentReadIndex); } @Override public void processPositions(int referenceIndex, int intermediatePosition, DiscoverVariantPositionData positionBaseInfos) { int coverage = 0; for (PositionBaseInfo info : positionBaseInfos) { coverage += info.to != '-' ? 1 : 0; } // store with one-based position positionMap.put(intermediatePosition + 1, coverage); System.out.printf("position: %d listSize: %d%n", intermediatePosition, coverage); } }; iterator.iterate(basenamePath); for (int i = 0; i < 100; i++) { assertEquals("[i=" + i + "] position " + i, 0, positionMap.get(i)); } for (int i = 100; i < 103; i++) { assertEquals("[i=" + i + "] position " + i, 1, positionMap.get(i)); } for (int i = 103; i < 106; i++) { assertEquals("[i=" + i + "] position " + i, 0, positionMap.get(i)); } for (int i = 106; i < 137; i++) { assertEquals("[i=" + i + "] position " + i, 1, positionMap.get(i)); } for (int i = 138; i < 150; i++) { assertEquals("[i=" + i + "] position " + i, 0, positionMap.get(i)); } }
From source file:edu.cornell.med.icb.goby.modes.TestSplicedSamHelper.java
@Test // Test deletion in the read: public void testSamToCompactTrickCase6() throws IOException { SAMToCompactMode importer = new SAMToCompactMode(); importer.setInputFile("test-data/splicedsamhelper/tricky-spliced-6.sam"); final String outputFilename = FilenameUtils.concat(BASE_TEST_DIR, "spliced-output-alignment-6"); importer.setOutputFile(outputFilename); String[] refs = { "NNNNNNTTAGAAAAACAGAGAGAGAAGGAGAGTAAAGGGAGGAGGCGGAGGAGGAGAAAAGAAGAAAGCAGAGANNNNNN" }; RandomAccessSequenceTestSupport genomeTestSupport = new RandomAccessSequenceTestSupport(refs); importer.setGenome(genomeTestSupport); importer.execute();/* w w w. ja v a2s .c o m*/ AlignmentReader reader = new AlignmentReaderImpl(outputFilename); assertTrue(reader.hasNext()); Alignments.AlignmentEntry first = reader.next(); assertEquals(0, first.getQueryIndex()); assertEquals(0, first.getFragmentIndex()); assertEquals(7 - 1, first.getPosition()); }
From source file:com.google.jenkins.plugins.storage.AbstractUpload.java
/** * This is the workhorse API for performing the actual uploads. It is * performed at the workspace, so that all of the {@link FilePath}s should * be local.//w ww. j a v a 2 s . c o m */ private void performUploads(Map<String, String> metadata, String bucketName, String objectPrefix, GoogleRobotCredentials credentials, UploadSpec uploads, TaskListener listener) throws UploadException { try { Storage service = module.getStorageService(credentials); Executor executor = module.newExecutor(); // Ensure the bucket exists, fetching it regardless so that we can // attach its default ACLs to the objects we upload. Bucket bucket = getOrCreateBucket(service, credentials, executor, bucketName); for (FilePath include : uploads.inclusions) { String relativePath = getRelative(include, uploads.workspace); String uploadedFileName = getStrippedFilename(relativePath); String finalName = FilenameUtils .separatorsToUnix(FilenameUtils.concat(objectPrefix, uploadedFileName)); StorageObject object = new StorageObject().setName(finalName).setMetadata(metadata) .setContentDisposition(HttpHeaders.getContentDisposition(include.getName())) .setContentType(detectMIMEType(include.getName())) .setSize(BigInteger.valueOf(include.length())); if (isSharedPublicly()) { object.setAcl(addPublicReadAccess(getDefaultObjectAcl(bucket, listener))); } // Give clients an opportunity to decorate the storage // object before we store it. annotateObject(object, listener); // Log that we are uploading the file and begin executing the upload. listener.getLogger().println(module.prefix(Messages.AbstractUpload_Uploading(relativePath))); performUploadWithRetry(executor, service, bucket, object, include); } } catch (ForbiddenException e) { // If the user doesn't own a bucket then they will end up here. throw new UploadException(Messages.AbstractUpload_ForbiddenFileUpload(), e); } catch (ExecutorException e) { throw new UploadException(Messages.AbstractUpload_ExceptionFileUpload(), e); } catch (IOException e) { throw new UploadException(Messages.AbstractUpload_ExceptionFileUpload(), e); } catch (InterruptedException e) { throw new UploadException(Messages.AbstractUpload_ExceptionFileUpload(), e); } }
From source file:edu.cornell.med.icb.goby.alignments.TestMerge.java
@Before public void setUp() throws IOException { {//from w w w . ja v a2 s. c o m final AlignmentWriterImpl writer = new AlignmentWriterImpl( FilenameUtils.concat(BASE_TEST_DIR, "align-101")); writer.setNumAlignmentEntriesPerChunk(1000); final int numTargets = 2000; final int numQuery = 10; int position = 1; int score = 30; for (int targetIndex = 0; targetIndex < numTargets; targetIndex++) { for (int queryIndex = 0; queryIndex < numQuery; queryIndex++) { writer.setAlignmentEntry(queryIndex, targetIndex, position++, score++, false, constantQueryLength); writer.appendEntry(); numEntriesIn101++; } } numQueries101 = numQuery; writer.close(); } { final AlignmentWriterImpl writer = new AlignmentWriterImpl( FilenameUtils.concat(BASE_TEST_DIR, "transcript-101")); writer.setNumAlignmentEntriesPerChunk(1000); final int numTargets = 5; int position = 1; final int score = 30; final String[] transcriptIds = { "transcriptId1", "transcriptId2", "transcriptId3", "transcriptId4", "transcriptId5", }; final int[] transcriptIndex = { 0, 1, 2, 3, 4 }; final int[] targetLengths = { 1024, 5678, 1237, 9, 143 }; writer.setTargetLengths(targetLengths); final IndexedIdentifier targetIds = new IndexedIdentifier(); for (int i = 0; i < numTargets; i++) { if (transcriptIndex[i] != targetIds.registerIdentifier(new MutableString(transcriptIds[i]))) { assert false : "transcript Index must match"; } } writer.setTargetIdentifiers(targetIds); // make query 0 OK, matches 3 transcripts that belong to the same gene // query 1 matches two transcripts, but 2 genes, not OK. // query 2 OK: 1 transcript 1 gene. writer.setAlignmentEntry(0, transcriptIndex[0], position++, score, false, constantQueryLength); writer.appendEntry(); writer.setAlignmentEntry(0, transcriptIndex[1], position++, score + 1, false, constantQueryLength); writer.appendEntry(); writer.setAlignmentEntry(0, transcriptIndex[2], position++, score + 1, false, constantQueryLength); writer.appendEntry(); writer.setAlignmentEntry(1, transcriptIndex[2], position++, score, false, constantQueryLength); writer.appendEntry(); writer.setAlignmentEntry(1, transcriptIndex[3], position++, score, false, constantQueryLength); writer.appendEntry(); writer.setAlignmentEntry(2, transcriptIndex[4], position++, score, false, constantQueryLength); writer.appendEntry(); writer.close(); } { // Will have too many hits info created for it: final AlignmentWriterImpl writer = new AlignmentWriterImpl( FilenameUtils.concat(BASE_TEST_DIR, "align-102")); writer.setNumAlignmentEntriesPerChunk(1000); final int numTargets = 2000; final int numQuery = 10; int position = 1; int score = 30; for (int targetIndex = 0; targetIndex < numTargets; targetIndex++) { for (int queryIndex = 0; queryIndex < numQuery; queryIndex++) { writer.setAlignmentEntry(queryIndex, targetIndex, position++, score++, false, constantQueryLength); writer.appendEntry(); numEntriesIn102++; } } numQueries102 = numQuery; writer.close(); } { // Will have too many hits info created for it: final AlignmentWriterImpl writer = new AlignmentWriterImpl( FilenameUtils.concat(BASE_TEST_DIR, "align-103")); writer.setNumAlignmentEntriesPerChunk(1000); final int numTargets = 2000; final int numQuery = 10; int position = 1; int score = 30; for (int targetIndex = 0; targetIndex < numTargets; targetIndex++) { for (int queryIndex = 0; queryIndex < numQuery; queryIndex++) { writer.setAlignmentEntry(queryIndex, targetIndex, position++, score++, false, constantQueryLength); writer.appendEntry(); numEntriesIn103++; } } numQueries103 = numQuery; writer.close(); } { // Will have too many hits info created for it: final AlignmentWriterImpl writer = new AlignmentWriterImpl( FilenameUtils.concat(BASE_TEST_DIR, "align-105")); System.out.println("preparing 105"); writer.setNumAlignmentEntriesPerChunk(1000); final int numTargets = 2; final int numQuery = 10; int position = 1; int score = 30; final IndexedIdentifier targetIds = new IndexedIdentifier(); for (int i = 0; i < numTargets; i++) { targetIds.registerIdentifier(new MutableString("target-" + i)); } writer.setTargetIdentifiers(targetIds); for (int targetIndex = 0; targetIndex < numTargets; targetIndex++) { for (int queryIndex = 0; queryIndex < numQuery; queryIndex++) { writer.setAlignmentEntry(queryIndex, targetIndex, position++, score++, false, constantQueryLength); // System.out.println(String.format("Preparing entry: queryIndex: %d targetIndex: %d position: %d score: %d strand: %b", queryIndex, targetIndex, position++, score++, false)); writer.appendEntry(); numEntriesIn105++; } } numQueries105 = numQuery; writer.close(); } { // Will have too many hits info created for it: final AlignmentWriterImpl writer = new AlignmentWriterImpl( FilenameUtils.concat(BASE_TEST_DIR, "align-106")); writer.setNumAlignmentEntriesPerChunk(1000); final int numTargets = 2; final int numQuery = 10; int position = 1; int score = 30; final IndexedIdentifier targetIds = new IndexedIdentifier(); for (int i = 0; i < numTargets; i++) { targetIds.registerIdentifier(new MutableString("target-b-" + i)); } writer.setTargetIdentifiers(targetIds); for (int targetIndex = 0; targetIndex < numTargets; targetIndex++) { for (int queryIndex = 0; queryIndex < numQuery; queryIndex++) { writer.setAlignmentEntry(queryIndex, targetIndex, position++, score++, false, constantQueryLength); writer.appendEntry(); numEntriesIn106++; } } numQueries106 = numQuery; writer.close(); } }
From source file:com.enderville.enderinstaller.ui.Installer.java
private void loadModDescription(String modName) { JPanel p = getModDescriptionPane(); p.removeAll();/*from ww w. ja v a2 s . c o m*/ p.setLayout(new BoxLayout(p, BoxLayout.Y_AXIS)); final String extras = InstallerConfig.getExtraModsFolder(); final String modFolderName = FilenameUtils.concat(extras, modName); File modFolder = new File(modFolderName); if (!modFolder.exists()) { LOGGER.error("Mod folder for " + modName + " does not exist."); } File descrFile = new File(FilenameUtils.concat(modFolderName, "description.txt")); File imgFile = new File(FilenameUtils.concat(modFolderName, "image.png")); if (!descrFile.exists() && !imgFile.exists()) { p.add(new JLabel("<html>No description for:<br>" + modName + "</html>")); } else { if (imgFile.exists()) { try { JLabel label = new JLabel(); BufferedImage img = ImageIO.read(imgFile); label.setIcon(new ImageIcon(img)); p.add(label); } catch (IOException e) { LOGGER.error("Error reading image file: " + imgFile.getPath(), e); } } if (descrFile.exists()) { StringBuilder buffer = new StringBuilder(); try { BufferedReader r = new BufferedReader(new FileReader(descrFile)); String l = null; while ((l = r.readLine()) != null) { buffer.append(l + "\n"); } r.close(); JEditorPane area = new JEditorPane(); area.setContentType("text/html"); area.setText(buffer.toString()); area.setEditable(false); area.addHyperlinkListener(this); area.setCaretPosition(0); p.add(new JScrollPane(area)); } catch (IOException e) { LOGGER.error("Error reading description file: " + descrFile.getPath(), e); } } } p.validate(); p.repaint(); }
From source file:es.urjc.mctwp.image.impl.dicom.DicomImagePlugin.java
/** * Obtains a DICOM representation for single image * // w ww. jav a 2 s . c om * @param single * @return * @throws ImageException */ private List<File> toDicom(SingleImage single, File outputDir) throws ImageException { List<File> result = new ArrayList<File>(); File content = single.getContent(); try { String ext = StringUtils.substringAfterLast(content.getName(), FilenameUtils.EXTENSION_SEPARATOR_STR); if (ext == null) ext = SingleImageDicomImpl.DCM_EXT; File dest = new File(FilenameUtils.concat(outputDir.getAbsolutePath(), single.getId() + FilenameUtils.EXTENSION_SEPARATOR_STR + ext)); FileUtils.copyFile(content, dest); result.add(dest); } catch (Exception e) { logger.error(e.getMessage()); throw new ImageException(e); } return result; }
From source file:edu.cornell.med.icb.goby.modes.TestSplicedSamHelper.java
@Test public void testSamToCompactTrickCase7() throws IOException { SAMToCompactMode importer = new SAMToCompactMode(); importer.setInputFile("test-data/splicedsamhelper/tricky-spliced-7.sam"); final String outputFilename = FilenameUtils.concat(BASE_TEST_DIR, "spliced-output-alignment-7"); importer.setOutputFile(outputFilename); String[] refs = { "NNNNNNTTAGAAAAACAGAGAGAGAAGGAGAGTAAAGGGAGGAGGCGGAGGAGGAGAAAAGAAGAAAGCAGAGANNNNNN" }; RandomAccessSequenceTestSupport genomeTestSupport = new RandomAccessSequenceTestSupport(refs); importer.setGenome(genomeTestSupport); importer.execute();//from w w w .j a v a 2 s .co m AlignmentReader reader = new AlignmentReaderImpl(outputFilename); assertTrue(reader.hasNext()); Alignments.AlignmentEntry first = reader.next(); assertEquals(0, first.getQueryIndex()); assertEquals(0, first.getFragmentIndex()); assertEquals(8 - 1, first.getPosition()); }