List of usage examples for org.apache.commons.io IOUtils closeQuietly
public static void closeQuietly(OutputStream output)
OutputStream. From source file:de.tudarmstadt.ukp.csniper.resbuild.EvaluationItemFixer.java
public static void main(String[] args) { connect(HOST, DATABASE, USER, PASSWORD); Map<Integer, String> items = new HashMap<Integer, String>(); Map<Integer, String> failed = new HashMap<Integer, String>(); // fetch coveredTexts of dubious items and clean it PreparedStatement select = null; try {/*from www . j a v a 2 s . c o m*/ StringBuilder selectQuery = new StringBuilder(); selectQuery.append("SELECT * FROM EvaluationItem "); selectQuery.append("WHERE LOCATE(coveredText, ' ') > 0 "); selectQuery.append("OR LOCATE('" + LRB + "', coveredText) > 0 "); selectQuery.append("OR LOCATE('" + RRB + "', coveredText) > 0 "); selectQuery.append("OR LEFT(coveredText, 1) = ' ' "); selectQuery.append("OR RIGHT(coveredText, 1) = ' ' "); select = connection.prepareStatement(selectQuery.toString()); log.info("Running query [" + selectQuery.toString() + "]."); ResultSet rs = select.executeQuery(); while (rs.next()) { int id = rs.getInt("id"); String coveredText = rs.getString("coveredText"); try { // special handling of double whitespace: in this case, re-fetch the text if (coveredText.contains(" ")) { coveredText = retrieveCoveredText(rs.getString("collectionId"), rs.getString("documentId"), rs.getInt("beginOffset"), rs.getInt("endOffset")); } // replace bracket placeholders and trim the text coveredText = StringUtils.replace(coveredText, LRB, "("); coveredText = StringUtils.replace(coveredText, RRB, ")"); coveredText = coveredText.trim(); items.put(id, coveredText); } catch (IllegalArgumentException e) { failed.put(id, e.getMessage()); } } } catch (SQLException e) { log.error("Exception while selecting: " + e.getMessage()); } finally { closeQuietly(select); } // write logs BufferedWriter bwf = null; BufferedWriter bws = null; try { bwf = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(new File(LOG_FAILED)), "UTF-8")); for (Entry<Integer, String> e : failed.entrySet()) { bwf.write(e.getKey() + " - " + e.getValue() + "\n"); } bws = new BufferedWriter( new OutputStreamWriter(new FileOutputStream(new File(LOG_SUCCESSFUL)), "UTF-8")); for (Entry<Integer, String> e : items.entrySet()) { bws.write(e.getKey() + " - " + e.getValue() + "\n"); } } catch (IOException e) { log.error("Got an IOException while writing the log files."); } finally { IOUtils.closeQuietly(bwf); IOUtils.closeQuietly(bws); } log.info("Texts for [" + items.size() + "] items need to be cleaned up."); // update the dubious items with the cleaned coveredText PreparedStatement update = null; try { String updateQuery = "UPDATE EvaluationItem SET coveredText = ? WHERE id = ?"; update = connection.prepareStatement(updateQuery); int i = 0; for (Entry<Integer, String> e : items.entrySet()) { int id = e.getKey(); String coveredText = e.getValue(); // update item in database update.setString(1, coveredText); update.setInt(2, id); update.executeUpdate(); log.debug("Updating " + id + " with [" + coveredText + "]"); // show percentage of updated items i++; int part = (int) Math.ceil((double) items.size() / 100); if (i % part == 0) { log.info(i / part + "% finished (" + i + "/" + items.size() + ")."); } } } catch (SQLException e) { log.error("Exception while updating: " + e.getMessage()); } finally { closeQuietly(update); } closeQuietly(connection); }
From source file:com.revo.deployr.client.example.data.io.auth.stateful.preload.RepoFileInRepoFileOut.java
public static void main(String args[]) throws Exception { RClient rClient = null;// ww w. jav a2 s . c o m RProject rProject = null; try { /* * Determine DeployR server endpoint. */ String endpoint = System.getProperty("endpoint"); log.info("[ CONFIGURATION ] Using endpoint=" + endpoint); /* * Establish RClient connection to DeployR server. * * An RClient connection is the mandatory starting * point for any application using the client library. */ rClient = RClientFactory.createClient(endpoint); log.info("[ CONNECTION ] Established anonymous " + "connection [ RClient ]."); /* * Build a basic authentication token. */ RAuthentication rAuth = new RBasicAuthentication(System.getProperty("username"), System.getProperty("password")); /* * Establish an authenticated handle with the DeployR * server, rUser. Following this call the rClient * connection is operating as an authenticated connection * and all calls on rClient inherit the access permissions * of the authenticated user, rUser. */ RUser rUser = rClient.login(rAuth); log.info("[ AUTHENTICATION ] Upgraded to authenticated " + "connection [ RUser ]."); /* * Create a ProjectCreationOptions instance * to specify data inputs that "pre-heat" the R session * workspace or working directory for your project. */ ProjectCreationOptions creationOpts = new ProjectCreationOptions(); /* * Preload from the DeployR repository the following * binary R object input file: * /testuser/example-data-io/hipStar.rData */ ProjectPreloadOptions preloadWorkspace = new ProjectPreloadOptions(); preloadWorkspace.filename = "hipStar.rData"; preloadWorkspace.directory = "example-data-io"; preloadWorkspace.author = "testuser"; creationOpts.preloadWorkspace = preloadWorkspace; log.info("[ PRELOAD INPUT ] Repository binary file input " + "set on project creation, [ ProjectCreationOptions.preloadWorkspace ]."); /* * Create a temporary project (R session) passing a * ProjectCreationOptions to "pre-heat" data into the * workspace and/or working directory. */ rProject = rUser.createProject(creationOpts); log.info("[ GO STATEFUL ] Created stateful temporary " + "R session [ RProject ]."); /* * Create a ProjectExecutionOptions instance * to specify data inputs and output to the * execution of the repository-managed R script. * * This options object can be used to pass standard * execution model parameters on execution calls. All * fields are optional. * * See the Standard Execution Model chapter in the * Client Library Tutorial on the DeployR website for * further details. */ ProjectExecutionOptions execOpts = new ProjectExecutionOptions(); /* * Request storage of entire workspace as a * binary rData file to the DeployR-repository * following the execution. * * Alternatively, you could use storageOptions.objects * to store individual objects from the workspace. */ ProjectStorageOptions storageOptions = new ProjectStorageOptions(); // Use random file name for this example. storageOptions.workspace = Long.toHexString(Double.doubleToLongBits(Math.random())); storageOptions.directory = "example-data-io"; execOpts.storageOptions = storageOptions; log.info("[ EXEC OPTION ] Repository storage request " + "set on execution [ ProjectExecutionOptions.storageOptions ]."); /* * Execute a public analytics Web service as an authenticated * user based on a repository-managed R script: * /testuser/example-data-io/dataIO.R */ RProjectExecution exec = rProject.executeScript("dataIO.R", "example-data-io", "testuser", null, execOpts); log.info("[ EXECUTION ] Stateful R script " + "execution completed [ RProjectExecution ]."); /* * Retrieve repository-managed file(s) that were * generated by the execution per ProjectStorageOptions. * * Outputs generated by an execution can be used in any * number of ways by client applications, including: * * 1. Use output data to perform further calculations. * 2. Display output data to an end-user. * 3. Write output data to a database. * 4. Pass output data along to another Web service. * 5. etc. */ List<RRepositoryFile> repoFiles = exec.about().repositoryFiles; for (RRepositoryFile repoFile : repoFiles) { log.info("[ DATA OUTPUT ] Retrieved repository " + "file output " + repoFile.about().filename + " [ RRepositoryFile ]."); InputStream fis = null; try { fis = repoFile.download(); } catch (Exception ex) { log.warn("Repository-managed file download " + ex); } finally { IOUtils.closeQuietly(fis); try { // Clean-up after example. repoFile.delete(); } catch (Exception dex) { log.warn("Repository-managed file delete " + dex); } } } } catch (Exception ex) { log.warn("Unexpected runtime exception=" + ex); } finally { try { if (rProject != null) { /* * Close rProject before application exits. */ rProject.close(); } } catch (Exception fex) { } try { if (rClient != null) { /* * Release rClient connection before application exits. */ rClient.release(); } } catch (Exception fex) { } } }
From source file:com.l2jfree.loginserver.tools.L2GameServerRegistrar.java
/** * Launches the interactive game server registration. * /*ww w. j a va 2s . c o m*/ * @param args ignored */ public static void main(String[] args) { // LOW rework this crap Util.printSection("Game Server Registration"); _log.info("Please choose:"); _log.info("list - list registered game servers"); _log.info("reg - register a game server"); _log.info("rem - remove a registered game server"); _log.info("hexid - generate a legacy hexid file"); _log.info("quit - exit this application"); BufferedReader br = new BufferedReader(new InputStreamReader(System.in)); L2GameServerRegistrar reg = new L2GameServerRegistrar(); String line; try { RegistrationState next = RegistrationState.INITIAL_CHOICE; while ((line = br.readLine()) != null) { line = line.trim().toLowerCase(); switch (reg.getState()) { case GAMESERVER_ID: try { int id = Integer.parseInt(line); if (id < 1 || id > 127) throw new IllegalArgumentException("ID must be in [1;127]."); reg.setId(id); reg.setState(next); } catch (RuntimeException e) { _log.info("You must input a number between 1 and 127"); } if (reg.getState() == RegistrationState.ALLOW_BANS) { Connection con = null; try { con = L2Database.getConnection(); PreparedStatement ps = con .prepareStatement("SELECT allowBans FROM gameserver WHERE id = ?"); ps.setInt(1, reg.getId()); ResultSet rs = ps.executeQuery(); if (rs.next()) { _log.info("A game server is already registered on ID " + reg.getId()); reg.setState(RegistrationState.INITIAL_CHOICE); } else _log.info("Allow account bans from this game server? [y/n]:"); ps.close(); } catch (SQLException e) { _log.error("Could not remove a game server!", e); } finally { L2Database.close(con); } } else if (reg.getState() == RegistrationState.REMOVE) { Connection con = null; try { con = L2Database.getConnection(); PreparedStatement ps = con.prepareStatement("DELETE FROM gameserver WHERE id = ?"); ps.setInt(1, reg.getId()); int cnt = ps.executeUpdate(); if (cnt == 0) _log.info("No game server registered on ID " + reg.getId()); else _log.info("Game server removed."); ps.close(); } catch (SQLException e) { _log.error("Could not remove a game server!", e); } finally { L2Database.close(con); } reg.setState(RegistrationState.INITIAL_CHOICE); } else if (reg.getState() == RegistrationState.GENERATE) { Connection con = null; try { con = L2Database.getConnection(); PreparedStatement ps = con .prepareStatement("SELECT authData FROM gameserver WHERE id = ?"); ps.setInt(1, reg.getId()); ResultSet rs = ps.executeQuery(); if (rs.next()) { reg.setAuth(rs.getString("authData")); byte[] b = HexUtil.hexStringToBytes(reg.getAuth()); Properties pro = new Properties(); pro.setProperty("ServerID", String.valueOf(reg.getId())); pro.setProperty("HexID", HexUtil.hexToString(b)); BufferedOutputStream os = new BufferedOutputStream( new FileOutputStream("hexid.txt")); pro.store(os, "the hexID to auth into login"); IOUtils.closeQuietly(os); _log.info("hexid.txt has been generated."); } else _log.info("No game server registered on ID " + reg.getId()); rs.close(); ps.close(); } catch (SQLException e) { _log.error("Could not generate hexid.txt!", e); } finally { L2Database.close(con); } reg.setState(RegistrationState.INITIAL_CHOICE); } break; case ALLOW_BANS: try { if (line.length() != 1) throw new IllegalArgumentException("One char required."); else if (line.charAt(0) == 'y') reg.setTrusted(true); else if (line.charAt(0) == 'n') reg.setTrusted(false); else throw new IllegalArgumentException("Invalid choice."); byte[] auth = Rnd.nextBytes(new byte[BYTES]); reg.setAuth(HexUtil.bytesToHexString(auth)); Connection con = null; try { con = L2Database.getConnection(); PreparedStatement ps = con.prepareStatement( "INSERT INTO gameserver (id, authData, allowBans) VALUES (?, ?, ?)"); ps.setInt(1, reg.getId()); ps.setString(2, reg.getAuth()); ps.setBoolean(3, reg.isTrusted()); ps.executeUpdate(); ps.close(); _log.info("Registered game server on ID " + reg.getId()); _log.info("The authorization string is:"); _log.info(reg.getAuth()); _log.info("Use it when registering this login server."); _log.info("If you need a legacy hexid file, use the 'hexid' command."); } catch (SQLException e) { _log.error("Could not register gameserver!", e); } finally { L2Database.close(con); } reg.setState(RegistrationState.INITIAL_CHOICE); } catch (IllegalArgumentException e) { _log.info("[y/n]?"); } break; default: if (line.equals("list")) { Connection con = null; try { con = L2Database.getConnection(); PreparedStatement ps = con.prepareStatement("SELECT id, allowBans FROM gameserver"); ResultSet rs = ps.executeQuery(); while (rs.next()) _log.info("ID: " + rs.getInt("id") + ", trusted: " + rs.getBoolean("allowBans")); rs.close(); ps.close(); } catch (SQLException e) { _log.error("Could not register gameserver!", e); } finally { L2Database.close(con); } reg.setState(RegistrationState.INITIAL_CHOICE); } else if (line.equals("reg")) { _log.info("Enter the desired ID:"); reg.setState(RegistrationState.GAMESERVER_ID); next = RegistrationState.ALLOW_BANS; } else if (line.equals("rem")) { _log.info("Enter game server ID:"); reg.setState(RegistrationState.GAMESERVER_ID); next = RegistrationState.REMOVE; } else if (line.equals("hexid")) { _log.info("Enter game server ID:"); reg.setState(RegistrationState.GAMESERVER_ID); next = RegistrationState.GENERATE; } else if (line.equals("quit")) Shutdown.exit(TerminationStatus.MANUAL_SHUTDOWN); else _log.info("Incorrect command."); break; } } } catch (IOException e) { _log.fatal("Could not process input!", e); } finally { IOUtils.closeQuietly(br); } }
From source file:gov.nih.nci.ncicb.tcga.dcc.dam.util.TempClinicalDataLoader.java
public static void main(String[] args) { // first get the db connection properties String url = urlSet.get(args[1]); String user = args[2];// w ww. j a va 2 s.c o m String word = args[3]; // make sure we have the Oracle driver somewhere try { Class.forName("oracle.jdbc.OracleDriver"); Class.forName("org.postgresql.Driver"); } catch (Exception x) { System.out.println("Unable to load the driver class!"); System.exit(0); } // connect to the database try { dbConnection = DriverManager.getConnection(url, user, word); ClinicalBean.setDBConnection(dbConnection); } catch (SQLException x) { x.printStackTrace(); System.exit(1); } final String xmlList = args[0]; BufferedReader br = null; try { final Map<String, String> clinicalFiles = new HashMap<String, String>(); final Map<String, String> biospecimenFiles = new HashMap<String, String>(); final Map<String, String> fullFiles = new HashMap<String, String>(); //noinspection IOResourceOpenedButNotSafelyClosed br = new BufferedReader(new FileReader(xmlList)); // read the file list to get all the files to load while (br.ready()) { final String[] in = br.readLine().split("\\t"); String xmlfile = in[0]; String archive = in[1]; if (xmlfile.contains("_clinical")) { clinicalFiles.put(xmlfile, archive); } else if (xmlfile.contains("_biospecimen")) { biospecimenFiles.put(xmlfile, archive); } else { fullFiles.put(xmlfile, archive); } } Date dateAdded = Calendar.getInstance().getTime(); // NOTE!!! This deletes all data before the load starts, assuming we are re-loading everything. // a better way would be to figure out what has changed and load that, or to be able to load multiple versions of the data in the schema emptyClinicalTables(user); // load any "full" files first -- in case some archives aren't split yet for (final String file : fullFiles.keySet()) { String archive = fullFiles.get(file); System.out.println("Full file " + file + " in " + archive); // need to re-instantiate the disease-specific beans for each file createDiseaseSpecificBeans(xmlList); String disease = getDiseaseName(archive); processFullXmlFile(file, archive, disease, dateAdded); // memory leak or something... have to commit and close all connections and re-get connection // after each file to keep from using too much heap space. this troubles me, but I have never had // the time to figure out why it happens resetConnections(url, user, word); } // now process all clinical files, and insert patients and clinical data for (final String clinicalFile : clinicalFiles.keySet()) { createDiseaseSpecificBeans(xmlList); String archive = clinicalFiles.get(clinicalFile); System.out.println("Clinical file " + clinicalFile + " in " + archive); String disease = getDiseaseName(archive); processClinicalXmlFile(clinicalFile, archive, disease, dateAdded); resetConnections(url, user, word); } // now process biospecimen files for (final String biospecimenFile : biospecimenFiles.keySet()) { createDiseaseSpecificBeans(xmlList); String archive = biospecimenFiles.get(biospecimenFile); String disease = getDiseaseName(archive); System.out.println("Biospecimen file " + biospecimenFile); processBiospecimenXmlFile(biospecimenFile, archive, disease, dateAdded); resetConnections(url, user, word); } // this sets relationships between these clinical tables and data browser tables, since we delete // and reload every time setForeignKeys(); dbConnection.commit(); dbConnection.close(); } catch (Exception e) { e.printStackTrace(); System.exit(-1); } finally { IOUtils.closeQuietly(br); } }
From source file:net.padaf.xmpbox.parser.XMLValueTypeDescriptionManager.java
/** * Sample of using to write/read information * //from w w w . ja va 2s.c o m * @param args * not used * @throws BuildPDFAExtensionSchemaDescriptionException * When errors during building/reading xml file */ public static void main(String[] args) throws BuildPDFAExtensionSchemaDescriptionException { XMLValueTypeDescriptionManager vtMaker = new XMLValueTypeDescriptionManager(); // add Descriptions for (int i = 0; i < 3; i++) { vtMaker.addValueTypeDescription("testType" + i, "nsURI" + i, "prefix" + i, "description" + i); } List<FieldDescription> fieldSample = new ArrayList<FieldDescription>(); for (int i = 0; i < 2; i++) { fieldSample.add(new FieldDescription("fieldName" + i, "valueType" + i, "description" + i)); } vtMaker.addValueTypeDescription("testTypeField", "http://test.withfield.com/vt/", "prefTest", " value type description", fieldSample); // Display XML conversion System.out.println("Display XML Result:"); vtMaker.toXML(System.out); // Sample to show how to build object from XML file ByteArrayOutputStream bos = new ByteArrayOutputStream(); vtMaker.toXML(bos); IOUtils.closeQuietly(bos); // emulate a new reading InputStream is = new ByteArrayInputStream(bos.toByteArray()); vtMaker = new XMLValueTypeDescriptionManager(); vtMaker.loadListFromXML(is); List<ValueTypeDescription> result = vtMaker.getValueTypesDescriptionList(); System.out.println(); System.out.println(); System.out.println("Result of XML Loading :"); for (ValueTypeDescription propertyDescription : result) { System.out.println(propertyDescription.getType() + " :" + propertyDescription.getDescription()); if (propertyDescription.getFields() != null) { Iterator<FieldDescription> fit = propertyDescription.getFields().iterator(); FieldDescription field; while (fit.hasNext()) { field = fit.next(); System.out.println("Field " + field.getName() + " :" + field.getValueType()); } } } }
From source file:com.doculibre.constellio.lang.html.HtmlLangDetector.java
public static void main(String[] args) throws Exception { //java.net.URL url = new java.net.URL("http://www.gouv.qc.ca"); java.net.URL url = new java.net.URL("http://andrew.triumf.ca/multilingual/samples/french.meta.html"); java.net.URLConnection connection = url.openConnection(); java.io.InputStream is = null; String content = null;//from ww w .ja v a2s . com try { is = connection.getInputStream(); content = IOUtils.toString(is); } finally { IOUtils.closeQuietly(is); } HtmlLangDetector langDetector = new HtmlLangDetector(); System.out.println(langDetector.getLang(content)); }
From source file:com.revo.deployr.client.example.data.io.anon.discrete.exec.MultipleDataInMultipleDataOut.java
public static void main(String args[]) throws Exception { RClient rClient = null;//from w w w. j a v a 2 s . com try { /* * Determine DeployR server endpoint. */ String endpoint = System.getProperty("endpoint"); log.info("[ CONFIGURATION ] Using endpoint=" + endpoint); /* * Establish RClient connection to DeployR server. * * An RClient connection is the mandatory starting * point for any application using the client library. */ rClient = RClientFactory.createClient(endpoint); log.info("[ CONNECTION ] Established anonymous " + "connection [ RClient ]."); /* * Create the AnonymousProjectExecutionOptions object * to specify data inputs and output to the script. * * This options object can be used to pass standard * execution model parameters on execution calls. All * fields are optional. * * See the Standard Execution Model chapter in the * Client Library Tutorial on the DeployR website for * further details. */ AnonymousProjectExecutionOptions options = new AnonymousProjectExecutionOptions(); /* * MultipleDataInMultipleDataOut Example Note: * * The inputs sent on this example are contrived * and superfluous as the hipStar.rData binary R * object input and the hipStarUrl input perform * the exact same purpose...to load the Hip STAR * dataset into the workspace ahead of execution. * * The example is provided to simply demonstrate * the mechanism of specifying multiple inputs. */ /* * Preload from the DeployR repository the following * binary R object input file: * /testuser/example-data-io/hipStar.rData * * As this is an anonymous operation "hipStar.rData" * must have it's repository-managed access controls * set to "public". */ ProjectPreloadOptions preloadWorkspace = new ProjectPreloadOptions(); preloadWorkspace.filename = "hipStar.rData"; preloadWorkspace.directory = "example-data-io"; preloadWorkspace.author = "testuser"; options.preloadWorkspace = preloadWorkspace; log.info("[ DATA INPUT ] Repository binary file input " + "set on execution, [ ProjectExecutionOptions.preloadWorkspace ]."); /* * Load an R object literal "hipStarUrl" into the * workspace prior to script execution. * * The R script checks for the existence of "hipStarUrl" * in the workspace and if present uses the URL path * to load the Hipparcos star dataset from the DAT file * at that location. */ RData hipStarUrl = RDataFactory.createString("hipStarUrl", HIP_DAT_URL); List<RData> rinputs = Arrays.asList(hipStarUrl); options.rinputs = rinputs; log.info("[ DATA INPUT ] External data source input " + "set on execution, [ ProjectPreloadOptions.rinputs ]."); /* * Request the retrieval of the "hip" data.frame and * two vector objects from the workspace following the * execution. The corresponding R objects are named as * follows: * 'hip', hipDim', 'hipNames'. */ options.routputs = Arrays.asList("hip", "hipDim", "hipNames"); log.info("[ EXEC OPTION ] DeployR-encoded R object request " + "set on execution [ ProjectExecutionOptions.routputs ]."); /* * Execute a public analytics Web service as an anonymous * user based on a repository-managed R script: * /testuser/example-data-io/dataIO.R */ RScriptExecution exec = rClient.executeScript("dataIO.R", "example-data-io", "testuser", null, options); log.info("[ EXECUTION ] Discrete R script " + "execution completed [ RScriptExecution ]."); /* * Retrieve multiple outputs following the execution: * * 1. R console output. * 2. R console output. * 3. R console output. * 4. R console output. * 5. R console output. */ String console = exec.about().console; log.info("[ DATA OUTPUT ] Retrieved R console " + "output [ String ]."); /* * Retrieve the requested R object data encodings from * the workspace follwing the script execution. * * See the R Object Data Decoding chapter in the * Client Library Tutorial on the DeployR website for * further details. */ List<RData> objects = exec.about().workspaceObjects; for (RData rData : objects) { if (rData instanceof RDataFrame) { log.info("[ DATA OUTPUT ] Retrieved DeployR-encoded R " + "object output " + rData.getName() + " [ RDataFrame ]."); List<RData> hipSubsetVal = ((RDataFrame) rData).getValue(); } else if (rData instanceof RNumericVector) { log.info("[ DATA OUTPUT ] Retrieved DeployR-encoded R " + "object output " + rData.getName() + " [ RNumericVector ]."); List<Double> hipDimVal = ((RNumericVector) rData).getValue(); log.info("[ DATA OUTPUT ] Retrieved DeployR-encoded R " + "object " + rData.getName() + " value=" + hipDimVal); } else if (rData instanceof RStringVector) { log.info("[ DATA OUTPUT ] Retrieved DeployR-encoded R " + "object output " + rData.getName() + " [ RStringVector ]."); List<String> hipNamesVal = ((RStringVector) rData).getValue(); log.info("[ DATA OUTPUT ] Retrieved DeployR-encoded R " + "object " + rData.getName() + " value=" + hipNamesVal); } else { log.info("Unexpected DeployR-encoded R object returned, " + "object name=" + rData.getName() + ", encoding=" + rData.getClass()); } } /* * Retrieve the working directory files (artifact) * was generated by the execution. */ List<RProjectFile> wdFiles = exec.about().artifacts; for (RProjectFile wdFile : wdFiles) { log.info("[ DATA OUTPUT ] Retrieved working directory " + "file output " + wdFile.about().filename + " [ RProjectFile ]."); InputStream fis = null; try { fis = wdFile.download(); } catch (Exception ex) { log.warn("Working directory binary file " + ex); } finally { IOUtils.closeQuietly(fis); } } /* * Retrieve R graphics device plots (results) called * unnamedplot*.png that was generated by the execution. */ List<RProjectResult> results = exec.about().results; for (RProjectResult result : results) { log.info("[ DATA OUTPUT ] Retrieved graphics device " + "plot output " + result.about().filename + " [ RProjectResult ]."); InputStream fis = null; try { fis = result.download(); } catch (Exception ex) { log.warn("Graphics device plot " + ex); } finally { IOUtils.closeQuietly(fis); } } } catch (Exception ex) { log.warn("Unexpected runtime exception=" + ex); } finally { try { if (rClient != null) { /* * Release rClient connection before application exits. */ rClient.release(); } } catch (Exception fex) { } } }
From source file:com.revo.deployr.client.example.data.io.auth.discrete.exec.MultipleDataInMultipleDataOut.java
public static void main(String args[]) throws Exception { RClient rClient = null;//w ww.j av a 2s . c o m try { /* * Determine DeployR server endpoint. */ String endpoint = System.getProperty("endpoint"); log.info("[ CONFIGURATION ] Using endpoint=" + endpoint); /* * Establish RClient connection to DeployR server. * * An RClient connection is the mandatory starting * point for any application using the client library. */ rClient = RClientFactory.createClient(endpoint); log.info("[ CONNECTION ] Established anonymous " + "connection [ RClient ]."); /* * Build a basic authentication token. */ RAuthentication rAuth = new RBasicAuthentication(System.getProperty("username"), System.getProperty("password")); /* * Establish an authenticated handle with the DeployR * server, rUser. Following this call the rClient * connection is operating as an authenticated connection * and all calls on rClient inherit the access permissions * of the authenticated user, rUser. */ RUser rUser = rClient.login(rAuth); log.info("[ AUTHENTICATION ] Upgraded to authenticated " + "connection [ RUser ]."); /* * Create the AnonymousProjectExecutionOptions object * to specify data inputs and output to the script. * * This options object can be used to pass standard * execution model parameters on execution calls. All * fields are optional. * * See the Standard Execution Model chapter in the * Client Library Tutorial on the DeployR website for * further details. */ AnonymousProjectExecutionOptions options = new AnonymousProjectExecutionOptions(); /* * MultipleDataInMultipleDataOut Example Note: * * The inputs sent on this example are contrived * and superfluous as the hipStar.rData binary R * object input and the hipStarUrl input perform * the exact same purpose...to load the Hip STAR * dataset into the workspace ahead of execution. * * The example is provided to simply demonstrate * the mechanism of specifying multiple inputs. */ /* * Preload from the DeployR repository the following * binary R object input file: * /testuser/example-data-io/hipStar.rData */ ProjectPreloadOptions preloadWorkspace = new ProjectPreloadOptions(); preloadWorkspace.filename = "hipStar.rData"; preloadWorkspace.directory = "example-data-io"; preloadWorkspace.author = "testuser"; options.preloadWorkspace = preloadWorkspace; log.info("[ DATA INPUT ] Repository binary file input " + "set on execution, [ ProjectExecutionOptions.preloadWorkspace ]."); /* * Load an R object literal "hipStarUrl" into the * workspace prior to script execution. * * The R script checks for the existence of "hipStarUrl" * in the workspace and if present uses the URL path * to load the Hipparcos star dataset from the DAT file * at that location. */ RData hipStarUrl = RDataFactory.createString("hipStarUrl", HIP_DAT_URL); List<RData> rinputs = Arrays.asList(hipStarUrl); options.rinputs = rinputs; log.info("[ DATA INPUT ] External data source input " + "set on execution, [ ProjectPreloadOptions.rinputs ]."); /* * Request the retrieval of the "hip" data.frame and * two vector objects from the workspace following the * execution. The corresponding R objects are named as * follows: * 'hip', hipDim', 'hipNames'. */ options.routputs = Arrays.asList("hip", "hipDim", "hipNames"); log.info("[ EXEC OPTION ] DeployR-encoded R object request " + "set on execution [ ProjectExecutionOptions.routputs ]."); /* * Execute an analytics Web service as an authenticated * user based on a repository-managed R script: * /testuser/example-data-io/dataIO.R */ RScriptExecution exec = rClient.executeScript("dataIO.R", "example-data-io", "testuser", null, options); log.info("[ EXECUTION ] Discrete R script " + "execution completed [ RScriptExecution ]."); /* * Retrieve multiple outputs following the execution: * * 1. R console output. * 2. R console output. * 3. R console output. * 4. R console output. * 5. R console output. */ String console = exec.about().console; log.info("[ DATA OUTPUT ] Retrieved R console " + "output [ String ]."); /* * Retrieve the requested R object data encodings from * the workspace follwing the script execution. * * See the R Object Data Decoding chapter in the * Client Library Tutorial on the DeployR website for * further details. */ List<RData> objects = exec.about().workspaceObjects; for (RData rData : objects) { if (rData instanceof RDataFrame) { log.info("[ DATA OUTPUT ] Retrieved DeployR-encoded R " + "object output " + rData.getName() + " [ RDataFrame ]."); List<RData> hipSubsetVal = ((RDataFrame) rData).getValue(); } else if (rData instanceof RNumericVector) { log.info("[ DATA OUTPUT ] Retrieved DeployR-encoded R " + "object output " + rData.getName() + " [ RNumericVector ]."); List<Double> hipDimVal = ((RNumericVector) rData).getValue(); log.info("[ DATA OUTPUT ] Retrieved DeployR-encoded R " + "object " + rData.getName() + " value=" + hipDimVal); } else if (rData instanceof RStringVector) { log.info("[ DATA OUTPUT ] Retrieved DeployR-encoded R " + "object output " + rData.getName() + " [ RStringVector ]."); List<String> hipNamesVal = ((RStringVector) rData).getValue(); log.info("[ DATA OUTPUT ] Retrieved DeployR-encoded R " + "object " + rData.getName() + " value=" + hipNamesVal); } else { log.info("Unexpected DeployR-encoded R object returned, " + "object name=" + rData.getName() + ", encoding=" + rData.getClass()); } } /* * Retrieve the working directory files (artifact) * was generated by the execution. */ List<RProjectFile> wdFiles = exec.about().artifacts; for (RProjectFile wdFile : wdFiles) { log.info("[ DATA OUTPUT ] Retrieved working directory " + "file output " + wdFile.about().filename + " [ RProjectFile ]."); InputStream fis = null; try { fis = wdFile.download(); } catch (Exception ex) { log.warn("Working directory binary file " + ex); } finally { IOUtils.closeQuietly(fis); } } /* * Retrieve R graphics device plots (results) called * unnamedplot*.png that was generated by the execution. */ List<RProjectResult> results = exec.about().results; for (RProjectResult result : results) { log.info("[ DATA OUTPUT ] Retrieved graphics device " + "plot output " + result.about().filename + " [ RProjectResult ]."); InputStream fis = null; try { fis = result.download(); } catch (Exception ex) { log.warn("Graphics device plot " + ex); } finally { IOUtils.closeQuietly(fis); } } } catch (Exception ex) { log.warn("Unexpected runtime exception=" + ex); } finally { try { if (rClient != null) { /* * Release rClient connection before application exits. */ rClient.release(); } } catch (Exception fex) { } } }
From source file:ezbake.deployer.cli.EzDeployerCli.java
public static void main(String[] args) throws TException, IOException { int returnVal = 43; try {//from w ww.java 2 s .com EzDeployerCli cli = new EzDeployerCli(args); try { returnVal = cli.run(); } finally { IOUtils.closeQuietly(cli); } } catch (DeploymentException e) { // A deployment exception won't be useful to print out the stack trace. System.out.println(Strings.repeat("\n", 3)); System.err.println("Error: " + e.getMessage()); System.out.println(Strings.repeat("\n", 3)); returnVal = 15; } catch (Exception e) { e.printStackTrace(); returnVal = 13; } finally { System.out.println("Finished"); } System.exit(returnVal); }
From source file:com.revo.deployr.client.example.data.io.auth.stateful.exec.MultipleDataInMultipleDataOut.java
public static void main(String args[]) throws Exception { RClient rClient = null;/*from w w w. j a v a 2 s.c o m*/ RProject rProject = null; try { /* * Determine DeployR server endpoint. */ String endpoint = System.getProperty("endpoint"); log.info("[ CONFIGURATION ] Using endpoint=" + endpoint); /* * Establish RClient connection to DeployR server. * * An RClient connection is the mandatory starting * point for any application using the client library. */ rClient = RClientFactory.createClient(endpoint); log.info("[ CONNECTION ] Established anonymous " + "connection [ RClient ]."); /* * Build a basic authentication token. */ RAuthentication rAuth = new RBasicAuthentication(System.getProperty("username"), System.getProperty("password")); /* * Establish an authenticated handle with the DeployR * server, rUser. Following this call the rClient * connection is operating as an authenticated connection * and all calls on rClient inherit the access permissions * of the authenticated user, rUser. */ RUser rUser = rClient.login(rAuth); log.info("[ AUTHENTICATION ] Upgraded to authenticated " + "connection [ RUser ]."); /* * Create a temporary project (R session). * * Optionally: * ProjectCreationOptions options = * new ProjectCreationOptions(); * * Populate options as needed, then: * * rProject = rUser.createProject(options); */ rProject = rUser.createProject(); log.info("[ GO STATEFUL ] Created stateful temporary " + "R session [ RProject ]."); /* * Create a ProjectExecutionOptions instance * to specify data inputs and output to the * execution of the repository-managed R script. * * This options object can be used to pass standard * execution model parameters on execution calls. All * fields are optional. * * See the Standard Execution Model chapter in the * Client Library Tutorial on the DeployR website for * further details. */ ProjectExecutionOptions options = new ProjectExecutionOptions(); /* * MultipleDataInMultipleDataOut Example Note: * * The inputs sent on this example are contrived * and superfluous as the hipStar.rData binary R * object input and the hipStarUrl input perform * the exact same purpose...to load the Hip STAR * dataset into the workspace ahead of execution. * * The example is provided to simply demonstrate * the mechanism of specifying multiple inputs. */ /* * Preload from the DeployR repository the following * binary R object input file: * /testuser/example-data-io/hipStar.rData */ ProjectPreloadOptions preloadWorkspace = new ProjectPreloadOptions(); preloadWorkspace.filename = "hipStar.rData"; preloadWorkspace.directory = "example-data-io"; preloadWorkspace.author = "testuser"; options.preloadWorkspace = preloadWorkspace; log.info("[ DATA INPUT ] Repository binary file input " + "set on execution, [ ProjectExecutionOptions.preloadWorkspace ]."); /* * Load an R object literal "hipStarUrl" into the * workspace prior to script execution. * * The R script checks for the existence of "hipStarUrl" * in the workspace and if present uses the URL path * to load the Hipparcos star dataset from the DAT file * at that location. */ RData hipStarUrl = RDataFactory.createString("hipStarUrl", HIP_DAT_URL); List<RData> rinputs = Arrays.asList(hipStarUrl); options.rinputs = rinputs; log.info("[ DATA INPUT ] External data source input " + "set on execution, [ ProjectExecutionOptions.rinputs ]."); /* * Request the retrieval of the "hip" data.frame and * two vector objects from the workspace following the * execution. The corresponding R objects are named as * follows: * 'hip', hipDim', 'hipNames'. */ options.routputs = Arrays.asList("hip", "hipDim", "hipNames"); log.info("[ EXEC OPTION ] DeployR-encoded R object request " + "set on execution [ ProjectExecutionOptions.routputs ]."); /* * Execute a public analytics Web service as an authenticated * user based on a repository-managed R script: * /testuser/example-data-io/dataIO.R */ RProjectExecution exec = rProject.executeScript("dataIO.R", "example-data-io", "testuser", null, options); log.info("[ EXECUTION ] Stateful R script " + "execution completed [ RProjectExecution ]."); /* * Retrieve multiple outputs following the execution: * * 1. R console output. * 2. R console output. * 3. R console output. * 4. R console output. * 5. R console output. */ String console = exec.about().console; log.info("[ DATA OUTPUT ] Retrieved R console " + "output [ String ]."); /* * Retrieve the requested R object data encodings from * the workspace follwing the script execution. * * See the R Object Data Decoding chapter in the * Client Library Tutorial on the DeployR website for * further details. */ List<RData> objects = exec.about().workspaceObjects; for (RData rData : objects) { if (rData instanceof RDataFrame) { log.info("[ DATA OUTPUT ] Retrieved DeployR-encoded R " + "object output " + rData.getName() + " [ RDataFrame ]."); List<RData> hipSubsetVal = ((RDataFrame) rData).getValue(); } else if (rData instanceof RNumericVector) { log.info("[ DATA OUTPUT ] Retrieved DeployR-encoded R " + "object output " + rData.getName() + " [ RNumericVector ]."); List<Double> hipDimVal = ((RNumericVector) rData).getValue(); log.info("[ DATA OUTPUT ] Retrieved DeployR-encoded R " + "object " + rData.getName() + " value=" + hipDimVal); } else if (rData instanceof RStringVector) { log.info("[ DATA OUTPUT ] Retrieved DeployR-encoded R " + "object output " + rData.getName() + " [ RStringVector ]."); List<String> hipNamesVal = ((RStringVector) rData).getValue(); log.info("[ DATA OUTPUT ] Retrieved DeployR-encoded R " + "object " + rData.getName() + " value=" + hipNamesVal); } else { log.info("Unexpected DeployR-encoded R object returned, " + "object name=" + rData.getName() + ", encoding=" + rData.getClass()); } } /* * Retrieve the working directory files (artifact) * was generated by the execution. */ List<RProjectFile> wdFiles = exec.about().artifacts; for (RProjectFile wdFile : wdFiles) { log.info("[ DATA OUTPUT ] Retrieved working directory " + "file output " + wdFile.about().filename + " [ RProjectFile ]."); InputStream fis = null; try { fis = wdFile.download(); } catch (Exception ex) { log.warn("Working directory binary file download " + ex); } finally { IOUtils.closeQuietly(fis); } } /* * Retrieve R graphics device plots (results) called * unnamedplot*.png that was generated by the execution. */ List<RProjectResult> results = exec.about().results; for (RProjectResult result : results) { log.info("[ DATA OUTPUT ] Retrieved graphics device " + "plot output " + result.about().filename + " [ RProjectResult ]."); InputStream fis = null; try { fis = result.download(); } catch (Exception ex) { log.warn("Graphics device plot download " + ex); } finally { IOUtils.closeQuietly(fis); } } } catch (Exception ex) { log.warn("Unexpected runtime exception=" + ex); } finally { try { if (rProject != null) { /* * Close rProject before application exits. */ rProject.close(); } } catch (Exception fex) { } try { if (rClient != null) { /* * Release rClient connection before application exits. */ rClient.release(); } } catch (Exception fex) { } } }