List of usage examples for org.apache.commons.io FileUtils writeStringToFile
public static void writeStringToFile(File file, String data) throws IOException
From source file:ch.sbb.releasetrain.git.GITAccessor.java
public void reset() { writeModel();/*from ww w. j a va2s . c om*/ repo = client.gitRepo(model.getConfigUrl(), model.getConfigBranch(), model.getConfigUser(), model.getEncPassword()); err = ""; read = false; write = false; repo.reset(); try { repo.cloneOrPull(); read = true; File dir = repo.directory(); FileUtils.writeStringToFile(new File(dir, "test.txt"), new Date().toString()); repo.addCommitPush(); write = true; FileUtils.forceDelete(new File(dir, "test.txt")); repo.addCommitPush(); } catch (Exception e) { log.error(e.getMessage(), e); err = e.getMessage(); } }
From source file:edu.pitt.dbmi.facebase.hd.domain.InstructionsText.java
/** Makes the actual text file (ie. FBuserAgreement.txt). * Uses apache commons FileUtils.writeStringToFile() to turn the String into a file. * * @throws IOException/*from w w w . j ava 2 s . c o m*/ * @return size of the file. */ public long makeFiles() throws IOException { log.debug("InstructionsText.makeFiles() called, about to write to file:"); log.debug(destinationFile); FileUtils.writeStringToFile(destinationFile, fileContents); return destinationFile.length(); }
From source file:com.mtgi.io.RelocatableFileTest.java
@Test public void testRelocate() throws IOException, ClassNotFoundException { FileUtils.writeStringToFile(source, "here is some data"); output.writeObject(inst);//from w ww. j a v a2s . co m output.close(); assertTrue("original file still here", inst.getLocalFile().isFile()); assertEquals("source file is unchanged", "here is some data", FileUtils.readFileToString(inst.getLocalFile())); RelocatableFile transferred = (RelocatableFile) new ObjectInputStream( new ByteArrayInputStream(buffer.toByteArray())).readObject(); assertNotNull("file loaded", transferred); assertNotNull("local file defined", transferred.getLocalFile()); assertTrue("local file exists", transferred.getLocalFile().isFile()); assertFalse("reloaded file points to a new path", inst.getLocalFile().getCanonicalPath().equals(transferred.getLocalFile().getCanonicalPath())); assertEquals("transferred file contains source data", "here is some data", FileUtils.readFileToString(transferred.getLocalFile())); assertTrue("transferred file is closed", transferred.getLocalFile().delete()); }
From source file:Pathway2RDFv2.java
public static void main(String[] args) throws ParserConfigurationException, SAXException, IOException, ServiceException, ClassNotFoundException, IDMapperException, ParseException { int softwareVersion = 0; int schemaVersion = 0; int latestRevision = 0; BioDataSource.init();//w w w. j a va 2 s . c o m Class.forName("org.bridgedb.rdb.IDMapperRdb"); File dir = new File("/Users/andra/Downloads/bridge"); File[] bridgeDbFiles = dir.listFiles(); IDMapperStack mapper = new IDMapperStack(); for (File bridgeDbFile : bridgeDbFiles) { System.out.println(bridgeDbFile.getAbsolutePath()); mapper.addIDMapper("idmapper-pgdb:" + bridgeDbFile.getAbsolutePath()); } Model bridgeDbmodel = ModelFactory.createDefaultModel(); InputStream in = new FileInputStream("/tmp/BioDataSource.ttl"); bridgeDbmodel.read(in, "", "TURTLE"); WikiPathwaysClient client = new WikiPathwaysClient( new URL("http://www.wikipathways.org/wpi/webservice/webservice.php")); basicCalls.printMemoryStatus(); //Map wikipathway organisms to NCBI organisms HashMap<String, String> organismTaxonomy = wpRelatedCalls.getOrganismsTaxonomyMapping(); //HashMap<String, String> miriamSources = new HashMap<String, String>(); // HashMap<String, Str ing> miriamLinks = basicCalls.getMiriamUriBridgeDb(); //Document wikiPathwaysDom = basicCalls.openXmlFile(args[0]); Document wikiPathwaysDom = basicCalls.openXmlFile("/tmp/WpGPML.xml"); //initiate the Jena model to be populated Model model = ModelFactory.createDefaultModel(); Model voidModel = ModelFactory.createDefaultModel(); voidModel.setNsPrefix("xsd", XSD.getURI()); voidModel.setNsPrefix("void", Void.getURI()); voidModel.setNsPrefix("wprdf", "http://rdf.wikipathways.org/"); voidModel.setNsPrefix("pav", Pav.getURI()); voidModel.setNsPrefix("prov", Prov.getURI()); voidModel.setNsPrefix("dcterms", DCTerms.getURI()); voidModel.setNsPrefix("biopax", Biopax_level3.getURI()); voidModel.setNsPrefix("gpml", Gpml.getURI()); voidModel.setNsPrefix("wp", Wp.getURI()); voidModel.setNsPrefix("foaf", FOAF.getURI()); voidModel.setNsPrefix("hmdb", "http://identifiers.org/hmdb/"); voidModel.setNsPrefix("freq", Freq.getURI()); voidModel.setNsPrefix("dc", DC.getURI()); setModelPrefix(model); //Populate void.ttl Calendar now = Calendar.getInstance(); Literal nowLiteral = voidModel.createTypedLiteral(now); Literal titleLiteral = voidModel.createLiteral("WikiPathways-RDF VoID Description", "en"); Literal descriptionLiteral = voidModel .createLiteral("This is the VoID description for a WikiPathwyas-RDF dataset.", "en"); Resource voidBase = voidModel.createResource("http://rdf.wikipathways.org/"); Resource identifiersOrg = voidModel.createResource("http://identifiers.org"); Resource wpHomeBase = voidModel.createResource("http://www.wikipathways.org/"); Resource authorResource = voidModel .createResource("http://semantics.bigcat.unimaas.nl/figshare/search_author.php?author=waagmeester"); Resource apiResource = voidModel .createResource("http://www.wikipathways.org/wpi/webservice/webservice.php"); Resource mainDatadump = voidModel.createResource("http://rdf.wikipathways.org/wpContent.ttl.gz"); Resource license = voidModel.createResource("http://creativecommons.org/licenses/by/3.0/"); Resource instituteResource = voidModel.createResource("http://dbpedia.org/page/Maastricht_University"); voidBase.addProperty(RDF.type, Void.Dataset); voidBase.addProperty(DCTerms.title, titleLiteral); voidBase.addProperty(DCTerms.description, descriptionLiteral); voidBase.addProperty(FOAF.homepage, wpHomeBase); voidBase.addProperty(DCTerms.license, license); voidBase.addProperty(Void.uriSpace, voidBase); voidBase.addProperty(Void.uriSpace, identifiersOrg); voidBase.addProperty(Pav.importedBy, authorResource); voidBase.addProperty(Pav.importedFrom, apiResource); voidBase.addProperty(Pav.importedOn, nowLiteral); voidBase.addProperty(Void.dataDump, mainDatadump); voidBase.addProperty(Voag.frequencyOfChange, Freq.Irregular); voidBase.addProperty(Pav.createdBy, authorResource); voidBase.addProperty(Pav.createdAt, instituteResource); voidBase.addLiteral(Pav.createdOn, nowLiteral); voidBase.addProperty(DCTerms.subject, Biopax_level3.Pathway); voidBase.addProperty(Void.exampleResource, voidModel.createResource("http://identifiers.org/ncbigene/2678")); voidBase.addProperty(Void.exampleResource, voidModel.createResource("http://identifiers.org/pubmed/15215856")); voidBase.addProperty(Void.exampleResource, voidModel.createResource("http://identifiers.org/hmdb/HMDB02005")); voidBase.addProperty(Void.exampleResource, voidModel.createResource("http://rdf.wikipathways.org/WP15")); voidBase.addProperty(Void.exampleResource, voidModel.createResource("http://identifiers.org/obo.chebi/17242")); for (String organism : organismTaxonomy.values()) { voidBase.addProperty(DCTerms.subject, voidModel.createResource("http://dbpedia.org/page/" + organism.replace(" ", "_"))); } voidBase.addProperty(Void.vocabulary, Biopax_level3.NAMESPACE); voidBase.addProperty(Void.vocabulary, voidModel.createResource(Wp.getURI())); voidBase.addProperty(Void.vocabulary, voidModel.createResource(Gpml.getURI())); voidBase.addProperty(Void.vocabulary, FOAF.NAMESPACE); voidBase.addProperty(Void.vocabulary, Pav.NAMESPACE); //Custom Properties String baseUri = "http://rdf.wikipathways.org/"; NodeList pathwayElements = wikiPathwaysDom.getElementsByTagName("Pathway"); //BioDataSource.init(); for (int i = 0; i < pathwayElements.getLength(); i++) { Model pathwayModel = createPathwayModel(); String wpId = pathwayElements.item(i).getAttributes().getNamedItem("identifier").getTextContent(); String revision = pathwayElements.item(i).getAttributes().getNamedItem("revision").getTextContent(); String pathwayOrganism = ""; if (pathwayElements.item(i).getAttributes().getNamedItem("Organism") != null) pathwayOrganism = pathwayElements.item(i).getAttributes().getNamedItem("Organism").getTextContent() .trim(); if (Integer.valueOf(revision) > latestRevision) { latestRevision = Integer.valueOf(revision); } File f = new File("/tmp/" + args[0] + "/" + wpId + "_r" + revision + ".ttl"); System.out.println(f.getName()); if (!f.exists()) { Resource voidPwResource = wpRelatedCalls.addVoidTriples(voidModel, voidBase, pathwayElements.item(i), client); Resource pwResource = wpRelatedCalls.addPathwayLevelTriple(pathwayModel, pathwayElements.item(i), organismTaxonomy); // Get the comments NodeList commentElements = ((Element) pathwayElements.item(i)).getElementsByTagName("Comment"); wpRelatedCalls.addCommentTriples(pathwayModel, pwResource, commentElements, wpId, revision); // Get the Groups NodeList groupElements = ((Element) pathwayElements.item(i)).getElementsByTagName("Group"); for (int n = 0; n < groupElements.getLength(); n++) { wpRelatedCalls.addGroupTriples(pathwayModel, pwResource, groupElements.item(n), wpId, revision); } // Get all the Datanodes NodeList dataNodesElement = ((Element) pathwayElements.item(i)).getElementsByTagName("DataNode"); for (int j = 0; j < dataNodesElement.getLength(); j++) { wpRelatedCalls.addDataNodeTriples(pathwayModel, pwResource, dataNodesElement.item(j), wpId, revision, bridgeDbmodel, mapper); } // Get all the lines NodeList linesElement = ((Element) pathwayElements.item(i)).getElementsByTagName("Line"); for (int k = 0; k < linesElement.getLength(); k++) { wpRelatedCalls.addLineTriples(pathwayModel, pwResource, linesElement.item(k), wpId, revision); } //Get all the labels NodeList labelsElement = ((Element) pathwayElements.item(i)).getElementsByTagName("Label"); for (int l = 0; l < labelsElement.getLength(); l++) { wpRelatedCalls.addLabelTriples(pathwayModel, pwResource, labelsElement.item(l), wpId, revision); } NodeList referenceElements = ((Element) pathwayElements.item(i)) .getElementsByTagName("bp:PublicationXref"); for (int m = 0; m < referenceElements.getLength(); m++) { wpRelatedCalls.addReferenceTriples(pathwayModel, pwResource, referenceElements.item(m), wpId, revision); } NodeList referenceElements2 = ((Element) pathwayElements.item(i)) .getElementsByTagName("bp:publicationXref"); for (int m = 0; m < referenceElements2.getLength(); m++) { wpRelatedCalls.addReferenceTriples(pathwayModel, pwResource, referenceElements2.item(m), wpId, revision); } NodeList referenceElements3 = ((Element) pathwayElements.item(i)) .getElementsByTagName("bp:PublicationXRef"); for (int m = 0; m < referenceElements3.getLength(); m++) { wpRelatedCalls.addReferenceTriples(pathwayModel, pwResource, referenceElements3.item(m), wpId, revision); } NodeList ontologyElements = ((Element) pathwayElements.item(i)) .getElementsByTagName("bp:openControlledVocabulary"); for (int n = 0; n < ontologyElements.getLength(); n++) { wpRelatedCalls.addPathwayOntologyTriples(pathwayModel, pwResource, ontologyElements.item(n)); } System.out.println(wpId); basicCalls.saveRDF2File(pathwayModel, "/tmp/" + args[0] + "/" + wpId + "_r" + revision + ".ttl", "TURTLE"); model.add(pathwayModel); pathwayModel.removeAll(); } } Date myDate = new Date(); SimpleDateFormat sdf = new SimpleDateFormat("yyyyMMdd"); String myDateString = sdf.format(myDate); FileUtils.writeStringToFile(new File("latestVersion.txt"), "v" + schemaVersion + "." + softwareVersion + "." + latestRevision + "_" + myDateString); basicCalls.saveRDF2File(model, "/tmp/wpContent_v" + schemaVersion + "." + softwareVersion + "." + latestRevision + "_" + myDateString + ".ttl", "TURTLE"); basicCalls.saveRDF2File(voidModel, "/tmp/void.ttl", "TURTLE"); }
From source file:com.splicemachine.test.MiniZooKeeperCluster.java
private void prepareDir(File dir, int i) throws IOException { try {//from www .j a va 2s . com if (!dir.exists()) { dir.mkdirs(); FileUtils.writeStringToFile(new File(dir, "myid"), "" + i); } } catch (SecurityException e) { throw new IOException("creating dir: " + dir, e); } }
From source file:com.cedarsoft.serialization.serializers.jackson.registry.RegistrySerializerDirTest.java
License:asdf
@Before public void setup() { baseDir = TestUtils.createEmptyTmpDir(); access = new DirBasedObjectsAccess(baseDir); serializer = new RegistrySerializer<String, Registry<String>>( new DirBasedRegistrySerializingStrategy<String>(access) { @Nonnull//ww w .j av a 2s. c o m @Override protected String deserialize(@Nonnull String id, @Nonnull File dir) throws IOException { return FileUtils.readFileToString(new File(dir, "data")); } @Override protected void serialize(@Nonnull String object, @Nonnull String id, @Nonnull File dir) throws IOException { File data = new File(dir, "data"); FileUtils.writeStringToFile(data, object); } }, new RegistrySerializer.IdResolver<String>() { @Override @Nonnull public String getId(@Nonnull String object) { return object; } }); }
From source file:com.leclercb.taskunifier.gui.components.license.LicenseUtils.java
public static void saveLicense(String license) throws Exception { try {/* w w w . j av a2 s .c o m*/ CheckUtils.isNotNull(license); license = license.trim(); File file = new File(Main.getLicenseFile()); FileUtils.writeStringToFile(file, license); LICENSE = null; Main.reloadProVersion(); } catch (Exception e) { GuiLogger.getLogger().log(Level.SEVERE, "Cannot save license", e); } }
From source file:net.nicholaswilliams.java.teamcity.plugin.linux.TestAbstractLinuxPropertiesLocator.java
@Test public void testLocateProperties02() throws IOException { File pluginRoot = new File("."); File versionFile = new File(pluginRoot, "version.properties"); FileUtils.writeStringToFile(versionFile, ""); final Capture<Map<String, String>> capture = new Capture<Map<String, String>>(); this.locator.locateLinuxProperties(capture(capture)); expectLastCall().andAnswer(new IAnswer<Void>() { @Override//from w w w. j a v a 2s.com public Void answer() throws Throwable { assertTrue("The properties map should be empty.", capture.getValue().isEmpty()); capture.getValue().put("yourLinuxProperty02", "3.9.1"); return null; } }); replay(this.locator); try { Map<String, String> properties = this.locator.locateProperties(pluginRoot); assertNotNull("The properties should not be null.", properties); assertEquals("The linux property is not correct.", "3.9.1", properties.get("yourLinuxProperty02")); assertFalse("The version property should not be present.", properties.containsKey(LinuxPropertiesLocator.PLUGIN_VERSION_KEY)); } finally { FileUtils.forceDelete(versionFile); } }
From source file:com.seleniumtests.connectors.extools.SoapUi.java
/** * Start SOAP UI with a project file as string. Useful when project file is stored in test resource and we only access the stream * @param projectString project string * @param projectName project name//from www .j a v a 2 s . c o m * @return */ public String executeWithProjectString(String projectString, String projectName) { File tmpFile; try { tmpFile = File.createTempFile("project-" + projectName, ".xml"); FileUtils.writeStringToFile(tmpFile, projectString); } catch (IOException e) { throw new ScenarioException("Cannot write project file", e); } return executeWithProjectFile(tmpFile); }
From source file:net.big_oh.postoffice.PostOfficeIntegrationTest.java
@Before public void setUp() throws Exception { attachment1 = File.createTempFile(this.getClass().getSimpleName(), ".txt"); FileUtils.writeStringToFile(attachment1, "first attachment"); attachment2 = File.createTempFile(this.getClass().getSimpleName(), ".txt"); FileUtils.writeStringToFile(attachment2, "second attachment"); Properties postOfficeProperties = PostOfficeServiceFactory.readDefaultPostOfficeProperties(); String smtpPassword = System.getProperty(PostOfficeServiceFactory.PROPERTY_KEY_SMTP_PASSWORD); assertNotNull("Failed to locate SMTP password in expected system property: " + PostOfficeServiceFactory.PROPERTY_KEY_SMTP_PASSWORD, smtpPassword); postOfficeProperties.setProperty(PostOfficeServiceFactory.PROPERTY_KEY_SMTP_PASSWORD, smtpPassword); postOfficeService = PostOfficeServiceFactory.getInstance(postOfficeProperties); }