List of usage examples for java.lang String substring
public String substring(int beginIndex, int endIndex)
From source file:com.netscape.cmstools.CRMFPopClient.java
public static void main(String args[]) throws Exception { Options options = createOptions();/*from w w w. j ava 2s. com*/ CommandLine cmd = null; try { CommandLineParser parser = new PosixParser(); cmd = parser.parse(options, args); } catch (Exception e) { printError(e.getMessage()); System.exit(1); } if (cmd.hasOption("help")) { printHelp(); System.exit(0); } boolean verbose = cmd.hasOption("v"); String databaseDir = cmd.getOptionValue("d", "."); String tokenPassword = cmd.getOptionValue("p"); String tokenName = cmd.getOptionValue("h"); String algorithm = cmd.getOptionValue("a", "rsa"); int keySize = Integer.parseInt(cmd.getOptionValue("l", "2048")); String profileID = cmd.getOptionValue("f"); String subjectDN = cmd.getOptionValue("n"); boolean encodingEnabled = Boolean.parseBoolean(cmd.getOptionValue("k", "false")); // if transportCertFilename is not specified then assume no key archival String transportCertFilename = cmd.getOptionValue("b"); String popOption = cmd.getOptionValue("q", "POP_SUCCESS"); String curve = cmd.getOptionValue("c", "nistp256"); boolean sslECDH = Boolean.parseBoolean(cmd.getOptionValue("x", "false")); boolean temporary = Boolean.parseBoolean(cmd.getOptionValue("t", "true")); int sensitive = Integer.parseInt(cmd.getOptionValue("s", "-1")); int extractable = Integer.parseInt(cmd.getOptionValue("e", "-1")); boolean self_sign = cmd.hasOption("y"); // get the keywrap algorithm KeyWrapAlgorithm keyWrapAlgorithm = null; String kwAlg = KeyWrapAlgorithm.AES_KEY_WRAP_PAD.toString(); if (cmd.hasOption("w")) { kwAlg = cmd.getOptionValue("w"); } else { String alg = System.getenv("KEY_ARCHIVAL_KEYWRAP_ALGORITHM"); if (alg != null) { kwAlg = alg; } } String output = cmd.getOptionValue("o"); String hostPort = cmd.getOptionValue("m"); String username = cmd.getOptionValue("u"); String requestor = cmd.getOptionValue("r"); if (hostPort != null) { if (cmd.hasOption("w")) { printError("Any value specified for the key wrap parameter (-w) " + "will be overriden. CRMFPopClient will contact the " + "CA to determine the supported algorithm when " + "hostport is specified"); } } if (subjectDN == null) { printError("Missing subject DN"); System.exit(1); } if (tokenPassword == null) { printError("Missing token password"); System.exit(1); } if (algorithm.equals("rsa")) { if (cmd.hasOption("c")) { printError("Illegal parameter for RSA: -c"); System.exit(1); } if (cmd.hasOption("t")) { printError("Illegal parameter for RSA: -t"); System.exit(1); } if (cmd.hasOption("s")) { printError("Illegal parameter for RSA: -s"); System.exit(1); } if (cmd.hasOption("e")) { printError("Illegal parameter for RSA: -e"); System.exit(1); } if (cmd.hasOption("x")) { printError("Illegal parameter for RSA: -x"); System.exit(1); } } else if (algorithm.equals("ec")) { if (cmd.hasOption("l")) { printError("Illegal parameter for ECC: -l"); System.exit(1); } if (sensitive != 0 && sensitive != 1 && sensitive != -1) { printError("Illegal input parameters for -s: " + sensitive); System.exit(1); } if (extractable != 0 && extractable != 1 && extractable != -1) { printError("Illegal input parameters for -e: " + extractable); System.exit(1); } } else { printError("Invalid algorithm: " + algorithm); System.exit(1); } if (!popOption.equals("POP_SUCCESS") && !popOption.equals("POP_FAIL") && !popOption.equals("POP_NONE")) { printError("Invalid POP option: " + popOption); System.exit(1); } if (profileID == null) { if (algorithm.equals("rsa")) { profileID = "caEncUserCert"; } else if (algorithm.equals("ec")) { profileID = "caEncECUserCert"; } else { throw new Exception("Unknown algorithm: " + algorithm); } } try { if (verbose) System.out.println("Initializing security database: " + databaseDir); CryptoManager.initialize(databaseDir); CryptoManager manager = CryptoManager.getInstance(); CryptoToken token = CryptoUtil.getKeyStorageToken(tokenName); tokenName = token.getName(); manager.setThreadToken(token); Password password = new Password(tokenPassword.toCharArray()); try { token.login(password); } catch (Exception e) { throw new Exception("Unable to login: " + e, e); } CRMFPopClient client = new CRMFPopClient(); client.setVerbose(verbose); String encoded = null; X509Certificate transportCert = null; if (transportCertFilename != null) { if (verbose) System.out.println("archival option enabled"); if (verbose) System.out.println("Loading transport certificate"); encoded = new String(Files.readAllBytes(Paths.get(transportCertFilename))); byte[] transportCertData = Cert.parseCertificate(encoded); transportCert = manager.importCACertPackage(transportCertData); } else { if (verbose) System.out.println("archival option not enabled"); } if (verbose) System.out.println("Parsing subject DN"); Name subject = client.createName(subjectDN, encodingEnabled); if (subject == null) { subject = new Name(); subject.addCommonName("Me"); subject.addCountryName("US"); subject.addElement( new AVA(new OBJECT_IDENTIFIER("0.9.2342.19200300.100.1.1"), new PrintableString("MyUid"))); } if (verbose) System.out.println("Generating key pair"); KeyPair keyPair; if (algorithm.equals("rsa")) { keyPair = CryptoUtil.generateRSAKeyPair(token, keySize); } else if (algorithm.equals("ec")) { keyPair = client.generateECCKeyPair(token, curve, sslECDH, temporary, sensitive, extractable); } else { throw new Exception("Unknown algorithm: " + algorithm); } // print out keyid to be used in cmc decryptPOP PrivateKey privateKey = (PrivateKey) keyPair.getPrivate(); @SuppressWarnings("deprecation") byte id[] = privateKey.getUniqueID(); String kid = CryptoUtil.encodeKeyID(id); System.out.println("Keypair private key id: " + kid); if ((transportCert != null) && (hostPort != null)) { // check the CA for the required key wrap algorithm // if found, override whatever has been set by the command line // options for the key wrap algorithm ClientConfig config = new ClientConfig(); String host = hostPort.substring(0, hostPort.indexOf(':')); int port = Integer.parseInt(hostPort.substring(hostPort.indexOf(':') + 1)); config.setServerURL("http", host, port); PKIClient pkiclient = new PKIClient(config); kwAlg = getKeyWrapAlgotihm(pkiclient); } if (verbose && (transportCert != null)) System.out.println("Using key wrap algorithm: " + kwAlg); if (transportCert != null) { keyWrapAlgorithm = KeyWrapAlgorithm.fromString(kwAlg); } if (verbose) System.out.println("Creating certificate request"); CertRequest certRequest = client.createCertRequest(self_sign, token, transportCert, algorithm, keyPair, subject, keyWrapAlgorithm); ProofOfPossession pop = null; if (!popOption.equals("POP_NONE")) { if (verbose) System.out.println("Creating signer"); Signature signer = client.createSigner(token, algorithm, keyPair); if (popOption.equals("POP_SUCCESS")) { ByteArrayOutputStream bo = new ByteArrayOutputStream(); certRequest.encode(bo); signer.update(bo.toByteArray()); } else if (popOption.equals("POP_FAIL")) { byte[] data = { 0x1, 0x1, 0x1, 0x1, 0x1, 0x1, 0x1, 0x1 }; signer.update(data); } byte[] signature = signer.sign(); if (verbose) System.out.println("Creating POP"); pop = client.createPop(algorithm, signature); } if (verbose) System.out.println("Creating CRMF request"); String request = client.createCRMFRequest(certRequest, pop); StringWriter sw = new StringWriter(); try (PrintWriter out = new PrintWriter(sw)) { out.println(Cert.REQUEST_HEADER); out.print(request); out.println(Cert.REQUEST_FOOTER); } String csr = sw.toString(); if (hostPort != null) { System.out.println("Submitting CRMF request to " + hostPort); client.submitRequest(request, hostPort, username, profileID, requestor); } else if (output != null) { System.out.println("Storing CRMF request into " + output); try (FileWriter out = new FileWriter(output)) { out.write(csr); } } else { System.out.println(csr); } } catch (Exception e) { if (verbose) e.printStackTrace(); printError(e.getMessage()); System.exit(1); } }
From source file:DIA_Umpire_Quant.DIA_Umpire_Quant.java
/** * @param args the command line arguments *///from www. j a va2 s . c o m public static void main(String[] args) throws FileNotFoundException, IOException, Exception { System.out.println( "================================================================================================="); System.out.println("DIA-Umpire quantitation with targeted re-extraction analysis (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length != 1) { System.out.println( "command format error, it should be like: java -jar -Xmx10G DIA_Umpire_Quant.jar diaumpire_quant.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_quant.log"); } catch (Exception e) { } try { Logger.getRootLogger().info("Version: " + UmpireInfo.GetInstance().Version); Logger.getRootLogger().info("Parameter file:" + args[0]); BufferedReader reader = new BufferedReader(new FileReader(args[0])); String line = ""; String WorkFolder = ""; int NoCPUs = 2; String UserMod = ""; String Combined_Prot = ""; String InternalLibID = ""; String ExternalLibPath = ""; String ExternalLibDecoyTag = "DECOY"; boolean DefaultProtFiltering = true; boolean DataSetLevelPepFDR = false; float ProbThreshold = 0.99f; float ExtProbThreshold = 0.99f; float Freq = 0f; int TopNPep = 6; int TopNFrag = 6; float MinFragMz = 200f; String FilterWeight = "GW"; float MinWeight = 0.9f; float RTWindow_Int = -1f; float RTWindow_Ext = -1f; TandemParam tandemPara = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); HashMap<String, File> AssignFiles = new HashMap<>(); boolean InternalLibSearch = false; boolean ExternalLibSearch = false; boolean ExportSaint = false; boolean SAINT_MS1 = false; boolean SAINT_MS2 = true; HashMap<String, String[]> BaitList = new HashMap<>(); HashMap<String, String> BaitName = new HashMap<>(); HashMap<String, String[]> ControlList = new HashMap<>(); HashMap<String, String> ControlName = new HashMap<>(); //<editor-fold defaultstate="collapsed" desc="Reading parameter file"> while ((line = reader.readLine()) != null) { line = line.trim(); Logger.getRootLogger().info(line); if (!"".equals(line) && !line.startsWith("#")) { //System.out.println(line); if (line.equals("==File list begin")) { do { line = reader.readLine(); line = line.trim(); if (line.equals("==File list end")) { continue; } else if (!"".equals(line)) { File newfile = new File(line); if (newfile.exists()) { AssignFiles.put(newfile.getAbsolutePath(), newfile); } else { Logger.getRootLogger().info("File: " + newfile + " does not exist."); } } } while (!line.equals("==File list end")); } if (line.split("=").length < 2) { continue; } String type = line.split("=")[0].trim(); String value = line.split("=")[1].trim(); switch (type) { case "TargetedExtraction": { InternalLibSearch = Boolean.parseBoolean(value); break; } case "InternalLibSearch": { InternalLibSearch = Boolean.parseBoolean(value); break; } case "ExternalLibSearch": { ExternalLibSearch = Boolean.parseBoolean(value); break; } case "Path": { WorkFolder = value; break; } case "path": { WorkFolder = value; break; } case "Thread": { NoCPUs = Integer.parseInt(value); break; } case "Fasta": { tandemPara.FastaPath = value; break; } case "Combined_Prot": { Combined_Prot = value; break; } case "DefaultProtFiltering": { DefaultProtFiltering = Boolean.parseBoolean(value); break; } case "DecoyPrefix": { if (!"".equals(value)) { tandemPara.DecoyPrefix = value; } break; } case "UserMod": { UserMod = value; break; } case "ProteinFDR": { tandemPara.ProtFDR = Float.parseFloat(value); break; } case "PeptideFDR": { tandemPara.PepFDR = Float.parseFloat(value); break; } case "DataSetLevelPepFDR": { DataSetLevelPepFDR = Boolean.parseBoolean(value); break; } case "InternalLibID": { InternalLibID = value; break; } case "ExternalLibPath": { ExternalLibPath = value; break; } case "ExtProbThreshold": { ExtProbThreshold = Float.parseFloat(value); break; } case "RTWindow_Int": { RTWindow_Int = Float.parseFloat(value); break; } case "RTWindow_Ext": { RTWindow_Ext = Float.parseFloat(value); break; } case "ExternalLibDecoyTag": { ExternalLibDecoyTag = value; if (ExternalLibDecoyTag.endsWith("_")) { ExternalLibDecoyTag = ExternalLibDecoyTag.substring(0, ExternalLibDecoyTag.length() - 1); } break; } case "ProbThreshold": { ProbThreshold = Float.parseFloat(value); break; } case "ReSearchProb": { //ReSearchProb = Float.parseFloat(value); break; } case "FilterWeight": { FilterWeight = value; break; } case "MinWeight": { MinWeight = Float.parseFloat(value); break; } case "TopNFrag": { TopNFrag = Integer.parseInt(value); break; } case "TopNPep": { TopNPep = Integer.parseInt(value); break; } case "Freq": { Freq = Float.parseFloat(value); break; } case "MinFragMz": { MinFragMz = Float.parseFloat(value); break; } //<editor-fold defaultstate="collapsed" desc="SaintOutput"> case "ExportSaintInput": { ExportSaint = Boolean.parseBoolean(value); break; } case "QuantitationType": { switch (value) { case "MS1": { SAINT_MS1 = true; SAINT_MS2 = false; break; } case "MS2": { SAINT_MS1 = false; SAINT_MS2 = true; break; } case "BOTH": { SAINT_MS1 = true; SAINT_MS2 = true; break; } } break; } // case "BaitInputFile": { // SaintBaitFile = value; // break; // } // case "PreyInputFile": { // SaintPreyFile = value; // break; // } // case "InterationInputFile": { // SaintInteractionFile = value; // break; // } default: { if (type.startsWith("BaitName_")) { BaitName.put(type.substring(9), value); } if (type.startsWith("BaitFile_")) { BaitList.put(type.substring(9), value.split("\t")); } if (type.startsWith("ControlName_")) { ControlName.put(type.substring(12), value); } if (type.startsWith("ControlFile_")) { ControlList.put(type.substring(12), value.split("\t")); } break; } //</editor-fold> } } } //</editor-fold> //Initialize PTM manager using compomics library PTMManager.GetInstance(); if (!UserMod.equals("")) { PTMManager.GetInstance().ImportUserMod(UserMod); } //Check if the fasta file can be found if (!new File(tandemPara.FastaPath).exists()) { Logger.getRootLogger().info("Fasta file :" + tandemPara.FastaPath + " cannot be found, the process will be terminated, please check."); System.exit(1); } //Check if the prot.xml file can be found if (!new File(Combined_Prot).exists()) { Logger.getRootLogger().info("ProtXML file: " + Combined_Prot + " cannot be found, the export protein summary table will be empty."); } LCMSID protID = null; //Parse prot.xml and generate protein master list given an FDR if (Combined_Prot != null && !Combined_Prot.equals("")) { protID = LCMSID.ReadLCMSIDSerialization(Combined_Prot); if (!"".equals(Combined_Prot) && protID == null) { protID = new LCMSID(Combined_Prot, tandemPara.DecoyPrefix, tandemPara.FastaPath); ProtXMLParser protxmlparser = new ProtXMLParser(protID, Combined_Prot, 0f); //Use DIA-Umpire default protein FDR calculation if (DefaultProtFiltering) { protID.RemoveLowLocalPWProtein(0.8f); protID.RemoveLowMaxIniProbProtein(0.9f); protID.FilterByProteinDecoyFDRUsingMaxIniProb(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } //Get protein FDR calculation without other filtering else { protID.FilterByProteinDecoyFDRUsingLocalPW(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } protID.LoadSequence(); protID.WriteLCMSIDSerialization(Combined_Prot); } Logger.getRootLogger().info("Protein No.:" + protID.ProteinList.size()); } HashMap<String, HashMap<String, FragmentPeak>> IDSummaryFragments = new HashMap<>(); //Generate DIA file list ArrayList<DIAPack> FileList = new ArrayList<>(); File folder = new File(WorkFolder); if (!folder.exists()) { Logger.getRootLogger().info("The path : " + WorkFolder + " cannot be found."); System.exit(1); } for (final File fileEntry : folder.listFiles()) { if (fileEntry.isFile() && (fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry.getAbsolutePath(), fileEntry); } if (fileEntry.isDirectory()) { for (final File fileEntry2 : fileEntry.listFiles()) { if (fileEntry2.isFile() && (fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry2.getAbsolutePath(), fileEntry2); } } } } Logger.getRootLogger().info("No. of files assigned :" + AssignFiles.size()); for (File fileEntry : AssignFiles.values()) { Logger.getRootLogger().info(fileEntry.getAbsolutePath()); String mzXMLFile = fileEntry.getAbsolutePath(); if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) { DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs); FileList.add(DiaFile); HashMap<String, FragmentPeak> FragMap = new HashMap<>(); IDSummaryFragments.put(FilenameUtils.getBaseName(mzXMLFile), FragMap); Logger.getRootLogger().info( "================================================================================================="); Logger.getRootLogger().info("Processing " + mzXMLFile); if (!DiaFile.LoadDIASetting()) { Logger.getRootLogger().info("Loading DIA setting failed, job is incomplete"); System.exit(1); } if (!DiaFile.LoadParams()) { Logger.getRootLogger().info("Loading parameters failed, job is incomplete"); System.exit(1); } } } LCMSID combinePepID = null; if (DataSetLevelPepFDR) { combinePepID = LCMSID.ReadLCMSIDSerialization(WorkFolder + "combinePepID.SerFS"); if (combinePepID == null) { FDR_DataSetLevel fdr = new FDR_DataSetLevel(); fdr.GeneratePepIonList(FileList, tandemPara, WorkFolder + "combinePepID.SerFS"); combinePepID = fdr.combineID; combinePepID.WriteLCMSIDSerialization(WorkFolder + "combinePepID.SerFS"); } } //process each DIA file for quantification based on untargeted identifications for (DIAPack DiaFile : FileList) { long time = System.currentTimeMillis(); Logger.getRootLogger().info("Loading identification results " + DiaFile.Filename + "...."); //If the LCMSID serialization is found if (!DiaFile.ReadSerializedLCMSID()) { DiaFile.ParsePepXML(tandemPara, combinePepID); DiaFile.BuildStructure(); if (!DiaFile.MS1FeatureMap.ReadPeakCluster()) { Logger.getRootLogger().info("Loading peak and structure failed, job is incomplete"); System.exit(1); } DiaFile.MS1FeatureMap.ClearMonoisotopicPeakOfCluster(); //Generate mapping between index of precursor feature and pseudo MS/MS scan index DiaFile.GenerateClusterScanNomapping(); //Doing quantification DiaFile.AssignQuant(); DiaFile.ClearStructure(); } DiaFile.IDsummary.ReduceMemoryUsage(); time = System.currentTimeMillis() - time; Logger.getRootLogger().info(DiaFile.Filename + " processed time:" + String.format("%d hour, %d min, %d sec", TimeUnit.MILLISECONDS.toHours(time), TimeUnit.MILLISECONDS.toMinutes(time) - TimeUnit.HOURS.toMinutes(TimeUnit.MILLISECONDS.toHours(time)), TimeUnit.MILLISECONDS.toSeconds(time) - TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes(time)))); } //<editor-fold defaultstate="collapsed" desc="Targete re-extraction using internal library"> Logger.getRootLogger().info( "================================================================================================="); if (InternalLibSearch && FileList.size() > 1) { Logger.getRootLogger().info("Module C: Targeted extraction using internal library"); FragmentLibManager libManager = FragmentLibManager.ReadFragmentLibSerialization(WorkFolder, InternalLibID); if (libManager == null) { Logger.getRootLogger().info("Building internal spectral library"); libManager = new FragmentLibManager(InternalLibID); ArrayList<LCMSID> LCMSIDList = new ArrayList<>(); for (DIAPack dia : FileList) { LCMSIDList.add(dia.IDsummary); } libManager.ImportFragLibTopFrag(LCMSIDList, Freq, TopNFrag); libManager.WriteFragmentLibSerialization(WorkFolder); } libManager.ReduceMemoryUsage(); Logger.getRootLogger() .info("Building retention time prediction model and generate candidate peptide list"); for (int i = 0; i < FileList.size(); i++) { FileList.get(i).IDsummary.ClearMappedPep(); } for (int i = 0; i < FileList.size(); i++) { for (int j = i + 1; j < FileList.size(); j++) { RTAlignedPepIonMapping alignment = new RTAlignedPepIonMapping(WorkFolder, FileList.get(i).GetParameter(), FileList.get(i).IDsummary, FileList.get(j).IDsummary); alignment.GenerateModel(); alignment.GenerateMappedPepIon(); } FileList.get(i).ExportID(); FileList.get(i).IDsummary = null; } Logger.getRootLogger().info("Targeted matching........"); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); } if (!diafile.IDsummary.GetMappedPepIonList().isEmpty()) { diafile.UseMappedIon = true; diafile.FilterMappedIonByProb = false; diafile.BuildStructure(); diafile.MS1FeatureMap.ReadPeakCluster(); diafile.MS1FeatureMap.ClearMonoisotopicPeakOfCluster(); diafile.GenerateMassCalibrationRTMap(); diafile.TargetedExtractionQuant(false, libManager, 1.1f, RTWindow_Int); diafile.MS1FeatureMap.ClearAllPeaks(); diafile.IDsummary.ReduceMemoryUsage(); diafile.IDsummary.RemoveLowProbMappedIon(ProbThreshold); diafile.ExportID(); Logger.getRootLogger().info("Peptide ions: " + diafile.IDsummary.GetPepIonList().size() + " Mapped ions: " + diafile.IDsummary.GetMappedPepIonList().size()); diafile.ClearStructure(); } diafile.IDsummary = null; System.gc(); } Logger.getRootLogger().info( "================================================================================================="); } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Targeted re-extraction using external library"> //External library search if (ExternalLibSearch) { Logger.getRootLogger().info("Module C: Targeted extraction using external library"); //Read exteranl library FragmentLibManager ExlibManager = FragmentLibManager.ReadFragmentLibSerialization(WorkFolder, FilenameUtils.getBaseName(ExternalLibPath)); if (ExlibManager == null) { ExlibManager = new FragmentLibManager(FilenameUtils.getBaseName(ExternalLibPath)); //Import traML file ExlibManager.ImportFragLibByTraML(ExternalLibPath, ExternalLibDecoyTag); //Check if there are decoy spectra ExlibManager.CheckDecoys(); //ExlibManager.ImportFragLibBySPTXT(ExternalLibPath); ExlibManager.WriteFragmentLibSerialization(WorkFolder); } Logger.getRootLogger() .info("No. of peptide ions in external lib:" + ExlibManager.PeptideFragmentLib.size()); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); } //Generate RT mapping RTMappingExtLib RTmap = new RTMappingExtLib(diafile.IDsummary, ExlibManager, diafile.GetParameter()); RTmap.GenerateModel(); RTmap.GenerateMappedPepIon(); diafile.BuildStructure(); diafile.MS1FeatureMap.ReadPeakCluster(); diafile.GenerateMassCalibrationRTMap(); //Perform targeted re-extraction diafile.TargetedExtractionQuant(false, ExlibManager, ProbThreshold, RTWindow_Ext); diafile.MS1FeatureMap.ClearAllPeaks(); diafile.IDsummary.ReduceMemoryUsage(); //Remove target IDs below the defined probability threshold diafile.IDsummary.RemoveLowProbMappedIon(ExtProbThreshold); diafile.ExportID(); diafile.ClearStructure(); Logger.getRootLogger().info("Peptide ions: " + diafile.IDsummary.GetPepIonList().size() + " Mapped ions: " + diafile.IDsummary.GetMappedPepIonList().size()); } } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Peptide and fragment selection"> Logger.getRootLogger().info("Peptide and fragment selection across the whole dataset"); ArrayList<LCMSID> SummaryList = new ArrayList<>(); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); diafile.IDsummary.ClearAssignPeakCluster(); //diafile.IDsummary.ClearPSMs(); } if (protID != null) { //Generate protein list according to mapping of peptide ions for each DIA file to the master protein list diafile.IDsummary.GenerateProteinByRefIDByPepSeq(protID, true); diafile.IDsummary.ReMapProPep(); } if ("GW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByGroupWeight(); } else if ("PepW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByWeight(); } SummaryList.add(diafile.IDsummary); } FragmentSelection fragselection = new FragmentSelection(SummaryList); fragselection.freqPercent = Freq; fragselection.MinFragMZ = MinFragMz; fragselection.GeneratePepFragScoreMap(); fragselection.GenerateTopFragMap(TopNFrag); fragselection.GenerateProtPepScoreMap(MinWeight); fragselection.GenerateTopPepMap(TopNPep); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Writing general reports"> ExportTable export = new ExportTable(WorkFolder, SummaryList, IDSummaryFragments, protID, fragselection); export.Export(TopNPep, TopNFrag, Freq); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="//<editor-fold defaultstate="collapsed" desc="Generate SAINT input files"> if (ExportSaint && protID != null) { HashMap<String, DIAPack> Filemap = new HashMap<>(); for (DIAPack DIAfile : FileList) { Filemap.put(DIAfile.GetBaseName(), DIAfile); } FileWriter baitfile = new FileWriter(WorkFolder + "SAINT_Bait_" + DateTimeTag.GetTag() + ".txt"); FileWriter preyfile = new FileWriter(WorkFolder + "SAINT_Prey_" + DateTimeTag.GetTag() + ".txt"); FileWriter interactionfileMS1 = null; FileWriter interactionfileMS2 = null; if (SAINT_MS1) { interactionfileMS1 = new FileWriter( WorkFolder + "SAINT_Interaction_MS1_" + DateTimeTag.GetTag() + ".txt"); } if (SAINT_MS2) { interactionfileMS2 = new FileWriter( WorkFolder + "SAINT_Interaction_MS2_" + DateTimeTag.GetTag() + ".txt"); } HashMap<String, String> PreyID = new HashMap<>(); for (String samplekey : ControlName.keySet()) { String name = ControlName.get(samplekey); for (String file : ControlList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "C\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } for (String samplekey : BaitName.keySet()) { String name = BaitName.get(samplekey); for (String file : BaitList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "T\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } baitfile.close(); if (SAINT_MS1) { interactionfileMS1.close(); } if (SAINT_MS2) { interactionfileMS2.close(); } for (String AccNo : PreyID.keySet()) { preyfile.write(AccNo + "\t" + PreyID.get(AccNo) + "\n"); } preyfile.close(); } //</editor-fold> Logger.getRootLogger().info("Job done"); Logger.getRootLogger().info( "================================================================================================="); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }
From source file:com.adobe.aem.demo.communities.Loader.java
public static void main(String[] args) { String hostname = null;//ww w . j a va 2 s. co m String port = null; String altport = null; String csvfile = null; String location = null; String language = "en"; String analytics = null; String adminPassword = "admin"; String[] url = new String[10]; // Handling 10 levels maximum for nested comments boolean reset = false; boolean configure = false; int urlLevel = 0; int row = 0; HashMap<String, ArrayList<String>> learningpaths = new HashMap<String, ArrayList<String>>(); // Command line options for this tool Options options = new Options(); options.addOption("h", true, "Hostname"); options.addOption("p", true, "Port"); options.addOption("a", true, "Alternate Port"); options.addOption("f", true, "CSV file"); options.addOption("r", false, "Reset"); options.addOption("u", true, "Admin Password"); options.addOption("c", false, "Configure"); options.addOption("s", true, "Analytics Endpoint"); options.addOption("t", false, "Analytics Tracking"); CommandLineParser parser = new BasicParser(); try { CommandLine cmd = parser.parse(options, args); if (cmd.hasOption("h")) { hostname = cmd.getOptionValue("h"); } if (cmd.hasOption("p")) { port = cmd.getOptionValue("p"); } if (cmd.hasOption("a")) { altport = cmd.getOptionValue("a"); } if (cmd.hasOption("f")) { csvfile = cmd.getOptionValue("f"); } if (cmd.hasOption("u")) { adminPassword = cmd.getOptionValue("u"); } if (cmd.hasOption("t")) { if (cmd.hasOption("s")) { analytics = cmd.getOptionValue("s"); } } if (cmd.hasOption("r")) { reset = true; } if (cmd.hasOption("c")) { configure = true; } if (csvfile == null || port == null || hostname == null) { System.out.println( "Request parameters: -h hostname -p port -a alternateport -u adminPassword -f path_to_CSV_file -r (true|false, delete content before import) -c (true|false, post additional properties)"); System.exit(-1); } } catch (ParseException ex) { logger.error(ex.getMessage()); } String componentType = null; try { logger.debug("AEM Demo Loader: Processing file " + csvfile); // Reading the CSV file, line by line Reader in = new FileReader(csvfile); Iterable<CSVRecord> records = CSVFormat.EXCEL.parse(in); for (CSVRecord record : records) { row = row + 1; logger.info("Row: " + row + ", new record: " + record.get(0)); // Let's see if we deal with a comment if (record.get(0).startsWith("#")) { // We can ignore the comment line and move on continue; } // Let's see if we need to terminate this process if (record.get(0).equals(KILL)) { System.exit(1); } // Let's see if we need to create a new Community site if (record.get(0).equals(SITE)) { // Building the form entity to be posted MultipartEntityBuilder builder = MultipartEntityBuilder.create(); builder.setCharset(MIME.UTF8_CHARSET); builder.addTextBody(":operation", "social:createSite", ContentType.create("text/plain", MIME.UTF8_CHARSET)); builder.addTextBody("_charset_", "UTF-8", ContentType.create("text/plain", MIME.UTF8_CHARSET)); String urlName = null; for (int i = 2; i < record.size() - 1; i = i + 2) { if (record.get(i) != null && record.get(i + 1) != null && record.get(i).length() > 0) { String name = record.get(i).trim(); String value = record.get(i + 1).trim(); if (value.equals("TRUE")) { value = "true"; } if (value.equals("FALSE")) { value = "false"; } if (name.equals("urlName")) { urlName = value; } if (name.equals(LANGUAGE)) { language = value; } if (name.equals(BANNER)) { File attachment = new File( csvfile.substring(0, csvfile.indexOf(".csv")) + File.separator + value); builder.addBinaryBody(BANNER, attachment, ContentType.MULTIPART_FORM_DATA, attachment.getName()); } else if (name.equals(THUMBNAIL)) { File attachment = new File( csvfile.substring(0, csvfile.indexOf(".csv")) + File.separator + value); builder.addBinaryBody(THUMBNAIL, attachment, ContentType.MULTIPART_FORM_DATA, attachment.getName()); } else { builder.addTextBody(name, value, ContentType.create("text/plain", MIME.UTF8_CHARSET)); } } } // Site creation String siteId = doPost(hostname, port, "/content.social.json", "admin", adminPassword, builder.build(), "response/siteId"); // Site publishing, if there's a publish instance to publish to if (!port.equals(altport)) { List<NameValuePair> nameValuePairs = new ArrayList<NameValuePair>(); nameValuePairs.add(new BasicNameValuePair("id", "nobot")); nameValuePairs.add(new BasicNameValuePair(":operation", "social:publishSite")); nameValuePairs .add(new BasicNameValuePair("path", "/content/sites/" + urlName + "/" + language)); doPost(hostname, port, "/communities/sites.html", "admin", adminPassword, new UrlEncodedFormEntity(nameValuePairs), null); // Wait for site to be available on Publish doWait(hostname, altport, "admin", adminPassword, (siteId != null ? siteId : urlName) + "-groupadministrators"); } continue; } // Let's see if we need to create a new Tag if (record.get(0).equals(TAG)) { // Building the form entity to be posted MultipartEntityBuilder builder = MultipartEntityBuilder.create(); builder.setCharset(MIME.UTF8_CHARSET); builder.addTextBody("_charset_", "UTF-8", ContentType.create("text/plain", MIME.UTF8_CHARSET)); for (int i = 1; i < record.size() - 1; i = i + 2) { if (record.get(i) != null && record.get(i + 1) != null && record.get(i).length() > 0 && record.get(i + 1).length() > 0) { String name = record.get(i).trim(); String value = record.get(i + 1).trim(); builder.addTextBody(name, value, ContentType.create("text/plain", MIME.UTF8_CHARSET)); } } // Tag creation doPost(hostname, port, "/bin/tagcommand", "admin", adminPassword, builder.build(), null); continue; } // Let's see if we need to create a new Community site template, and if we can do it (script run against author instance) if (record.get(0).equals(SITETEMPLATE)) { // Building the form entity to be posted MultipartEntityBuilder builder = MultipartEntityBuilder.create(); builder.setCharset(MIME.UTF8_CHARSET); builder.addTextBody(":operation", "social:createSiteTemplate", ContentType.create("text/plain", MIME.UTF8_CHARSET)); builder.addTextBody("_charset_", "UTF-8", ContentType.create("text/plain", MIME.UTF8_CHARSET)); for (int i = 2; i < record.size() - 1; i = i + 2) { if (record.get(i) != null && record.get(i + 1) != null && record.get(i).length() > 0) { String name = record.get(i).trim(); String value = record.get(i + 1).trim(); builder.addTextBody(name, value, ContentType.create("text/plain", MIME.UTF8_CHARSET)); } } // Site template creation doPost(hostname, port, "/content.social.json", "admin", adminPassword, builder.build(), null); continue; } // Let's see if we need to create a new Community group if (record.get(0).equals(GROUP)) { // Building the form entity to be posted MultipartEntityBuilder builder = MultipartEntityBuilder.create(); builder.setCharset(MIME.UTF8_CHARSET); builder.addTextBody(":operation", "social:createCommunityGroup", ContentType.create("text/plain", MIME.UTF8_CHARSET)); builder.addTextBody("_charset_", "UTF-8", ContentType.create("text/plain", MIME.UTF8_CHARSET)); for (int i = 3; i < record.size() - 1; i = i + 2) { if (record.get(i) != null && record.get(i + 1) != null && record.get(i).length() > 0) { String name = record.get(i).trim(); String value = record.get(i + 1).trim(); if (value.equals("TRUE")) { value = "true"; } if (value.equals("FALSE")) { value = "false"; } if (name.equals(IMAGE)) { File attachment = new File( csvfile.substring(0, csvfile.indexOf(".csv")) + File.separator + value); builder.addBinaryBody(IMAGE, attachment, ContentType.MULTIPART_FORM_DATA, attachment.getName()); } else { builder.addTextBody(name, value, ContentType.create("text/plain", MIME.UTF8_CHARSET)); } } } // Group creation String memberGroupId = doPost(hostname, port, record.get(1), getUserName(record.get(2)), getPassword(record.get(2), adminPassword), builder.build(), "response/memberGroupId"); // Wait for group to be available on Publish, if available logger.debug("Waiting for completion of Community Group creation"); doWait(hostname, port, "admin", adminPassword, memberGroupId); continue; } // Let's see if it's simple Sling Delete request if (record.get(0).equals(SLINGDELETE)) { doDelete(hostname, port, record.get(1), "admin", adminPassword); continue; } // Let's see if we need to add users to an AEM Group if ((record.get(0).equals(GROUPMEMBERS) || record.get(0).equals(SITEMEMBERS)) && record.get(GROUP_INDEX_NAME) != null) { // Checking if we have a member group for this site String groupName = record.get(GROUP_INDEX_NAME); if (record.get(0).equals(SITEMEMBERS)) { // Let's fetch the siteId for this Community Site Url String siteConfig = doGet(hostname, port, groupName, "admin", adminPassword, null); try { String siteId = new JSONObject(siteConfig).getString("siteId"); if (siteId != null) groupName = "community-" + siteId + "-members"; logger.debug("Member group name is " + groupName); } catch (Exception e) { logger.error(e.getMessage()); } } // Pause until the group can found doWait(hostname, port, "admin", adminPassword, groupName); List<NameValuePair> nameValuePairs = new ArrayList<NameValuePair>(); nameValuePairs.add(new BasicNameValuePair("filter", "[{\"operation\":\"like\",\"rep:principalName\":\"" + groupName + "\"}]")); nameValuePairs.add(new BasicNameValuePair("type", "groups")); String groupList = doGet(hostname, port, "/libs/social/console/content/content/userlist.social.0.10.json", "admin", adminPassword, nameValuePairs); logger.debug("List of groups" + groupList); if (groupList.indexOf(groupName) > 0) { logger.debug("Group was found on " + port); try { JSONArray jsonArray = new JSONObject(groupList).getJSONArray("items"); if (jsonArray.length() == 1) { JSONObject jsonObject = jsonArray.getJSONObject(0); String groupPath = jsonObject.getString("path"); logger.debug("Group path is " + groupPath); // Constructing a multi-part POST for group membership MultipartEntityBuilder builder = MultipartEntityBuilder.create(); builder.setCharset(MIME.UTF8_CHARSET); builder.setMode(HttpMultipartMode.BROWSER_COMPATIBLE); List<NameValuePair> groupNameValuePairs = buildNVP(record, 2); for (NameValuePair nameValuePair : groupNameValuePairs) { builder.addTextBody(nameValuePair.getName(), nameValuePair.getValue(), ContentType.create("text/plain", MIME.UTF8_CHARSET)); } // Adding the list of group members doPost(hostname, port, groupPath + ".rw.userprops.html", "admin", adminPassword, builder.build(), null); } else { logger.info("We have more than one match for a group with this name!"); } } catch (Exception e) { logger.error(e.getMessage()); } } continue; } // Let's see if it's user related if (record.get(0).equals(USERS)) { //First we need to get the path to the user node String json = doGet(hostname, port, "/libs/granite/security/currentuser.json", getUserName(record.get(1)), getPassword(record.get(1), adminPassword), null); if (json != null) { try { // Fetching the home property String home = new JSONObject(json).getString("home"); if (record.get(2).equals(PREFERENCES)) { home = home + "/preferences"; } else { home = home + "/profile"; } logger.debug(home); // Now we can post all the preferences or the profile List<NameValuePair> nameValuePairs = buildNVP(record, 3); doPost(hostname, port, home, "admin", adminPassword, new UrlEncodedFormEntity(nameValuePairs), null); } catch (Exception e) { logger.error(e.getMessage()); } } continue; } // Let's see if we deal with a new block of content or just a new entry if (record.get(0).equals(CALENDAR) || record.get(0).equals(SLINGPOST) || record.get(0).equals(RATINGS) || record.get(0).equals(BLOG) || record.get(0).equals(JOURNAL) || record.get(0).equals(COMMENTS) || record.get(0).equals(REVIEWS) || record.get(0).equals(FILES) || record.get(0).equals(SUMMARY) || record.get(0).equals(ACTIVITIES) || record.get(0).equals(JOIN) || record.get(0).equals(FOLLOW) || record.get(0).equals(MESSAGE) || record.get(0).equals(ASSET) || record.get(0).equals(AVATAR) || record.get(0).equals(RESOURCE) || record.get(0).equals(LEARNING) || record.get(0).equals(QNA) || record.get(0).equals(FORUM)) { // New block of content, we need to reset the processing to first Level componentType = record.get(0); url[0] = record.get(1); urlLevel = 0; if (!componentType.equals(SLINGPOST) && reset) { int pos = record.get(1).indexOf("/jcr:content"); if (pos > 0) doDelete(hostname, port, "/content/usergenerated" + record.get(1).substring(0, pos), "admin", adminPassword); } // If the Configure command line flag is set, we try to configure the component with all options enabled if (componentType.equals(SLINGPOST) || configure) { String configurePath = getConfigurePath(record.get(1)); List<NameValuePair> nameValuePairs = buildNVP(record, 2); if (nameValuePairs.size() > 2) // Only do this when really have configuration settings doPost(hostname, port, configurePath, "admin", adminPassword, new UrlEncodedFormEntity(nameValuePairs), null); } // We're done with this line, moving on to the next line in the CSV file continue; } // Let's see if we need to indent the list, if it's a reply or a reply to a reply if (record.get(1).length() != 1) continue; // We need a valid level indicator if (Integer.parseInt(record.get(1)) > urlLevel) { url[++urlLevel] = location; logger.debug("Incremented urlLevel to: " + urlLevel + ", with a new location:" + location); } else if (Integer.parseInt(record.get(1)) < urlLevel) { urlLevel = Integer.parseInt(record.get(1)); logger.debug("Decremented urlLevel to: " + urlLevel); } // Get the credentials or fall back to password String password = getPassword(record.get(0), adminPassword); String userName = getUserName(record.get(0)); // Adding the generic properties for all POST requests List<NameValuePair> nameValuePairs = new ArrayList<NameValuePair>(); if (!componentType.equals(RESOURCE)) nameValuePairs.add(new BasicNameValuePair("id", "nobot")); nameValuePairs.add(new BasicNameValuePair("_charset_", "UTF-8")); // Setting some specific fields depending on the content type if (componentType.equals(COMMENTS)) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:createComment")); nameValuePairs.add(new BasicNameValuePair("message", record.get(2))); } // Creates a forum post (or reply) if (componentType.equals(FORUM)) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:createForumPost")); nameValuePairs.add(new BasicNameValuePair("subject", record.get(2))); nameValuePairs.add(new BasicNameValuePair("message", record.get(3))); } // Follows a user (followedId) for the user posting the request if (componentType.equals(FOLLOW)) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:follow")); nameValuePairs.add(new BasicNameValuePair("userId", "/social/authors/" + userName)); nameValuePairs.add(new BasicNameValuePair("followedId", "/social/authors/" + record.get(2))); } // Uploading Avatar picture if (componentType.equals(AVATAR)) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:changeAvatar")); } // Joins a user (posting the request) to a Community Group (path) if (componentType.equals(JOIN)) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:joinCommunityGroup")); int pos = url[0].indexOf("/configuration.social.json"); if (pos > 0) nameValuePairs.add(new BasicNameValuePair("path", url[0].substring(0, pos) + ".html")); else continue; // Invalid record } // Creates a new private message if (componentType.equals(MESSAGE)) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:createMessage")); nameValuePairs.add(new BasicNameValuePair("sendMail", "Sending...")); nameValuePairs.add(new BasicNameValuePair("content", record.get(4))); nameValuePairs.add(new BasicNameValuePair("subject", record.get(3))); nameValuePairs.add(new BasicNameValuePair("serviceSelector", "/bin/community")); nameValuePairs.add(new BasicNameValuePair("to", "/social/authors/" + record.get(2))); nameValuePairs.add(new BasicNameValuePair("userId", "/social/authors/" + record.get(2))); nameValuePairs.add(new BasicNameValuePair(":redirect", "//messaging.html")); nameValuePairs.add(new BasicNameValuePair(":formid", "generic_form")); nameValuePairs.add(new BasicNameValuePair(":formstart", "/content/sites/communities/messaging/compose/jcr:content/content/primary/start")); } // Creates a file or a folder if (componentType.equals(FILES)) { // Top level is always assumed to be a folder, second level files, and third and subsequent levels comments on files if (urlLevel == 0) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:createFileLibraryFolder")); nameValuePairs.add(new BasicNameValuePair("name", record.get(2))); nameValuePairs.add(new BasicNameValuePair("message", record.get(3))); } else if (urlLevel == 1) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:createComment")); } } // Creates a question, a reply or mark a reply as the best answer if (componentType.equals(QNA)) { if (urlLevel == 0) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:createQnaPost")); nameValuePairs.add(new BasicNameValuePair("subject", record.get(2))); nameValuePairs.add(new BasicNameValuePair("message", record.get(3))); } else if (urlLevel == 1) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:createQnaPost")); nameValuePairs.add(new BasicNameValuePair("message", record.get(3))); } else if (urlLevel == 2) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:selectAnswer")); } } // Creates an article or a comment if (componentType.equals(JOURNAL) || componentType.equals(BLOG)) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:createJournalComment")); nameValuePairs.add(new BasicNameValuePair("subject", record.get(2))); StringBuffer message = new StringBuffer("<p>" + record.get(3) + "</p>"); //We might have more paragraphs to add to the blog or journal article for (int i = 6; i < record.size(); i++) { if (record.get(i).length() > 0) { message.append("<p>" + record.get(i) + "</p>"); } } //We might have some tags to add to the blog or journal article if (record.get(5).length() > 0) { nameValuePairs.add(new BasicNameValuePair("tags", record.get(5))); } nameValuePairs.add(new BasicNameValuePair("message", message.toString())); } // Creates a review or a comment if (componentType.equals(REVIEWS)) { nameValuePairs.add(new BasicNameValuePair("message", record.get(2))); // This might be a top level review, or a comment on a review or another comment if (urlLevel == 0) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:createReview")); nameValuePairs.add(new BasicNameValuePair("ratings", record.get(3))); if (record.size() > 4 && record.get(4).length() > 0) { // If we are dealing with a non-existent resource, then the design drives the behavior nameValuePairs.add(new BasicNameValuePair("scf:resourceType", "social/reviews/components/hbs/reviews")); nameValuePairs.add(new BasicNameValuePair("scf:included", record.get(4))); } } else { nameValuePairs.add(new BasicNameValuePair(":operation", "social:createComment")); } } // Creates a rating if (componentType.equals(RATINGS)) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:postTallyResponse")); nameValuePairs.add(new BasicNameValuePair("tallyType", "Rating")); nameValuePairs.add(new BasicNameValuePair("response", record.get(2))); } // Creates a DAM asset if (componentType.equals(ASSET) && record.get(ASSET_INDEX_NAME).length() > 0) { nameValuePairs.add(new BasicNameValuePair("fileName", record.get(ASSET_INDEX_NAME))); } // Creates an enablement resource if (componentType.equals(RESOURCE)) { nameValuePairs.add(new BasicNameValuePair(":operation", "se:createResource")); List<NameValuePair> otherNameValuePairs = buildNVP(record, RESOURCE_INDEX_PROPERTIES); nameValuePairs.addAll(otherNameValuePairs); // Adding the site nameValuePairs.add(new BasicNameValuePair("site", "/content/sites/" + record.get(RESOURCE_INDEX_SITE) + "/resources/en")); // Building the cover image fragment if (record.get(RESOURCE_INDEX_THUMBNAIL).length() > 0) { nameValuePairs.add(new BasicNameValuePair("cover-image", doThumbnail(hostname, port, adminPassword, csvfile, record.get(RESOURCE_INDEX_THUMBNAIL)))); } else { nameValuePairs.add(new BasicNameValuePair("cover-image", "")); } // Building the asset fragment String coverPath = "/content/dam/" + record.get(RESOURCE_INDEX_SITE) + "/resource-assets/" + record.get(2) + "/jcr:content/renditions/cq5dam.thumbnail.319.319.png"; String coverSource = "dam"; String assets = "[{\"cover-img-path\":\"" + coverPath + "\",\"thumbnail-source\":\"" + coverSource + "\",\"asset-category\":\"enablementAsset:dam\",\"resource-asset-name\":null,\"state\":\"A\",\"asset-path\":\"/content/dam/" + record.get(RESOURCE_INDEX_SITE) + "/resource-assets/" + record.get(2) + "\"}]"; nameValuePairs.add(new BasicNameValuePair("assets", assets)); logger.debug("assets:" + assets); } // Creates a learning path if (componentType.equals(LEARNING)) { nameValuePairs.add(new BasicNameValuePair(":operation", "se:editLearningPath")); List<NameValuePair> otherNameValuePairs = buildNVP(record, RESOURCE_INDEX_PROPERTIES); nameValuePairs.addAll(otherNameValuePairs); // Adding the site nameValuePairs.add(new BasicNameValuePair("site", "/content/sites/" + record.get(RESOURCE_INDEX_SITE) + "/resources/en")); // Building the cover image fragment if (record.get(RESOURCE_INDEX_THUMBNAIL).length() > 0) { nameValuePairs.add(new BasicNameValuePair("card-image", doThumbnail(hostname, port, adminPassword, csvfile, record.get(RESOURCE_INDEX_THUMBNAIL)))); } // Building the learning path fragment StringBuffer assets = new StringBuffer("[\""); if (learningpaths.get(record.get(2)) != null) { ArrayList<String> paths = learningpaths.get(record.get(2)); int i = 0; for (String path : paths) { assets.append("{\\\"type\\\":\\\"linked-resource\\\",\\\"path\\\":\\\""); assets.append(path); assets.append("\\\"}"); if (i++ < paths.size() - 1) { assets.append("\",\""); } } } else { logger.debug("No asset for this learning path"); } assets.append("\"]"); nameValuePairs.add(new BasicNameValuePair("learningpath-items", assets.toString())); logger.debug("Learning path:" + assets.toString()); } // Creates a calendar event if (componentType.equals(CALENDAR)) { nameValuePairs.add(new BasicNameValuePair(":operation", "social:createEvent")); try { JSONObject event = new JSONObject(); // Building the JSON fragment for a new calendar event event.accumulate("subject", record.get(2)); event.accumulate("message", record.get(3)); event.accumulate("location", record.get(4)); event.accumulate("tags", ""); event.accumulate("undefined", "update"); String startDate = record.get(5); startDate = startDate.replaceAll("YYYY", Integer.toString(Calendar.getInstance().get(Calendar.YEAR))); startDate = startDate.replaceAll("MM", Integer.toString(1 + Calendar.getInstance().get(Calendar.MONTH))); event.accumulate("start", startDate); String endDate = record.get(6); endDate = endDate.replaceAll("YYYY", Integer.toString(Calendar.getInstance().get(Calendar.YEAR))); endDate = endDate.replaceAll("MM", Integer.toString(1 + Calendar.getInstance().get(Calendar.MONTH))); event.accumulate("end", endDate); nameValuePairs.add(new BasicNameValuePair("event", event.toString())); } catch (Exception ex) { logger.error(ex.getMessage()); } } // Constructing a multi-part POST request MultipartEntityBuilder builder = MultipartEntityBuilder.create(); builder.setCharset(MIME.UTF8_CHARSET); builder.setMode(HttpMultipartMode.BROWSER_COMPATIBLE); for (NameValuePair nameValuePair : nameValuePairs) { builder.addTextBody(nameValuePair.getName(), nameValuePair.getValue(), ContentType.create("text/plain", MIME.UTF8_CHARSET)); } // See if we have attachments for this new post - or some other actions require a form nonetheless if ((componentType.equals(ASSET) || componentType.equals(AVATAR) || componentType.equals(FORUM) || (componentType.equals(JOURNAL)) || componentType.equals(BLOG)) && record.size() > 4 && record.get(ASSET_INDEX_NAME).length() > 0) { File attachment = new File(csvfile.substring(0, csvfile.indexOf(".csv")) + File.separator + record.get(ASSET_INDEX_NAME)); ContentType ct = ContentType.MULTIPART_FORM_DATA; if (record.get(ASSET_INDEX_NAME).indexOf(".mp4") > 0) { ct = ContentType.create("video/mp4", MIME.UTF8_CHARSET); } else if (record.get(ASSET_INDEX_NAME).indexOf(".jpg") > 0 || record.get(ASSET_INDEX_NAME).indexOf(".jpeg") > 0) { ct = ContentType.create("image/jpeg", MIME.UTF8_CHARSET); } else if (record.get(ASSET_INDEX_NAME).indexOf(".png") > 0) { ct = ContentType.create("image/png", MIME.UTF8_CHARSET); } else if (record.get(ASSET_INDEX_NAME).indexOf(".pdf") > 0) { ct = ContentType.create("application/pdf", MIME.UTF8_CHARSET); } else if (record.get(ASSET_INDEX_NAME).indexOf(".zip") > 0) { ct = ContentType.create("application/zip", MIME.UTF8_CHARSET); } builder.addBinaryBody("file", attachment, ct, attachment.getName()); logger.debug("Adding file to payload with name: " + attachment.getName() + " and type: " + ct.getMimeType()); } // If it's a resource or a learning path, we need the path to the resource for subsequent publishing String jsonElement = "location"; if (componentType.equals(RESOURCE)) { jsonElement = "changes/argument"; } if (componentType.equals(LEARNING)) { jsonElement = "path"; } if (componentType.equals(ASSET)) { jsonElement = null; } // This call generally returns the path to the content fragment that was just created location = Loader.doPost(hostname, port, url[urlLevel], userName, password, builder.build(), jsonElement); // If we are loading a DAM asset, we are waiting for all renditions to be generated before proceeding if (componentType.equals(ASSET)) { int pathIndex = url[urlLevel].lastIndexOf(".createasset.html"); if (pathIndex > 0) doWaitPath(hostname, port, adminPassword, url[urlLevel].substring(0, pathIndex) + "/" + record.get(ASSET_INDEX_NAME) + "/jcr:content/renditions", "nt:file"); } // Let's see if it needs to be added to a learning path if (componentType.equals(RESOURCE) && record.get(RESOURCE_INDEX_PATH).length() > 0 && location != null) { // Adding the location to a list of a resources for this particular Learning Path if (learningpaths.get(record.get(RESOURCE_INDEX_PATH)) == null) learningpaths.put(record.get(RESOURCE_INDEX_PATH), new ArrayList<String>()); logger.debug("Adding resource to Learning path: " + record.get(RESOURCE_INDEX_PATH)); ArrayList<String> locations = learningpaths.get(record.get(RESOURCE_INDEX_PATH)); locations.add(location); learningpaths.put(record.get(RESOURCE_INDEX_PATH), locations); } // If it's a Learning Path, we publish it when possible if (componentType.equals(LEARNING) && !port.equals(altport) && location != null) { // Publishing the learning path List<NameValuePair> publishNameValuePairs = new ArrayList<NameValuePair>(); publishNameValuePairs.add(new BasicNameValuePair(":operation", "se:publishEnablementContent")); publishNameValuePairs.add(new BasicNameValuePair("replication-action", "activate")); logger.debug("Publishing a learning path from: " + location); Loader.doPost(hostname, port, location, userName, password, new UrlEncodedFormEntity(publishNameValuePairs), null); // Waiting for the learning path to be published Loader.doWait(hostname, altport, "admin", adminPassword, location.substring(1 + location.lastIndexOf("/")) // Only search for groups with the learning path in it ); // Decorate the resources within the learning path with comments and ratings, randomly generated ArrayList<String> paths = learningpaths.get(record.get(2)); for (String path : paths) { doDecorate(hostname, altport, path, record, analytics); } } // If it's an Enablement Resource, a lot of things need to happen... // Step 1. If it's a SCORM resource, we wait for the SCORM metadata workflow to be complete before proceeding // Step 2. We publish the resource // Step 3. We set a new first published date on the resource (3 weeks earlier) so that reporting data is more meaningful // Step 4. We wait for the resource to be available on publish (checking that associated groups are available) // Step 5. We retrieve the json for the resource on publish to retrieve the Social endpoints // Step 6. We post ratings and comments for each of the enrollees on publish if (componentType.equals(RESOURCE) && !port.equals(altport) && location != null) { // Wait for the data to be fully copied doWaitPath(hostname, port, adminPassword, location + "/assets/asset", "nt:file"); // If we are dealing with a SCORM asset, we wait a little bit before publishing the resource to that the SCORM workflow is completed if (record.get(2).indexOf(".zip") > 0) { doSleep(10000, "SCORM Resource, waiting for workflow to complete"); } // Publishing the resource List<NameValuePair> publishNameValuePairs = new ArrayList<NameValuePair>(); publishNameValuePairs.add(new BasicNameValuePair(":operation", "se:publishEnablementContent")); publishNameValuePairs.add(new BasicNameValuePair("replication-action", "activate")); logger.debug("Publishing a resource from: " + location); Loader.doPost(hostname, port, location, userName, password, new UrlEncodedFormEntity(publishNameValuePairs), null); // Waiting for the resource to be published Loader.doWait(hostname, altport, "admin", adminPassword, location.substring(1 + location.lastIndexOf("/")) // Only search for groups with the resource path in it ); // Setting the first published timestamp so that reporting always comes with 3 weeks of data after building a new demo instance DateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss"); Calendar cal = Calendar.getInstance(); cal.add(Calendar.DATE, REPORTINGDAYS); List<NameValuePair> publishDateNameValuePairs = new ArrayList<NameValuePair>(); publishDateNameValuePairs .add(new BasicNameValuePair("date-first-published", dateFormat.format(cal.getTime()))); logger.debug("Setting the publish date for a resource from: " + location); doPost(hostname, port, location, userName, password, new UrlEncodedFormEntity(publishDateNameValuePairs), null); // Adding comments and ratings for this resource doDecorate(hostname, altport, location, record, analytics); } } } catch (IOException e) { logger.error(e.getMessage()); } }
From source file:Main.java
private static String removeLastChar(String str) { return str.substring(0, str.length() - 1); }
From source file:Main.java
public static String removeCharAt(String s, int pos) { return s.substring(0, pos) + s.substring(pos + 1); }
From source file:Main.java
private static String capitalizeFirstLetter(String in) { return in.substring(0, 1).toUpperCase() + in.substring(1); }
From source file:Main.java
public static String replaceCharAt(String s, int pos, char c) { return s.substring(0, pos) + c + s.substring(pos + 1); }
From source file:Main.java
License:asdf
public static String removeCharAt(int pos, String text) { return text.substring(0, pos) + text.substring(pos + 1, text.length()); }
From source file:Main.java
private static String delQuot(String s) { return s.substring(s.indexOf('"') + 1, s.lastIndexOf('"')); }
From source file:Main.java
public static String capitalize(String s) { return s.substring(0, 1).toUpperCase() + s.substring(1); }