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a/src/main/java/net/timbusproject/extractors/modules/tavernaextractor/Main.java |
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b/src/main/java/net/timbusproject/extractors/modules/tavernaextractor/Main.java |
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package net.timbusproject.extractors.modules.tavernaextractor;
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package net.timbusproject.extractors.modules.tavernaextractor;
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import java.io.BufferedReader;
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import java.io.BufferedReader;
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import java.io.File;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.IOException;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.InputStream;
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import java.io.InputStreamReader;
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import java.io.InputStreamReader;
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import java.nio.file.Path;
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import java.nio.file.Path;
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import java.nio.file.Paths;
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import java.nio.file.Paths;
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if (parse.hasOption("i") && parse.hasOption("o")) {
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if (parse.hasOption("i") && parse.hasOption("o")) {
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String archimateOutputPath = parse.getOptionValue("o");
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String archimateOutputPath = parse.getOptionValue("o");
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String inputFileName = parse.getOptionValue("i");
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String inputFileName = parse.getOptionValue("i");
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// setup the extractor
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TavernaExtractor extractor = null;
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if (parse.hasOption("v"))
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if (parse.hasOption("v"))
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verbose = true;
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verbose = true;
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// setup the extractor
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extractor = new TavernaExtractor(verbose);
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TavernaExtractor extractor = new TavernaExtractor(verbose);
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TavernaExtractor.setTavernaHome(Main.getTavernaHome(tavernaHome));
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extractor.setTavernaHome(Main.getTavernaHome(tavernaHome));
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TavernaExtractor.setArchimateOutputPath(Paths.get(archimateOutputPath));
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extractor.setArchimateOutputPath(Paths.get(archimateOutputPath));
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TavernaExtractor.setInputFileName(Paths.get(inputFileName));
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extractor.setInputFileName(Paths.get(inputFileName));
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TavernaExtractor.setDotLocation(Paths.get(dotExeLocation));
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extractor.setDotLocation(Paths.get(dotExeLocation));
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extractor.process(false); //false = local execution
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extractor.process(false); //false = local execution
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}
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}
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// List all provenance entries OR Running DROID identification
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// List all provenance entries OR Running DROID identification
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if (parse.hasOption("p")) {
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if (parse.hasOption("p")) {
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System.out.println("Your input '" + input + "' was not a valid number. Process stopped.");
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System.out.println("Your input '" + input + "' was not a valid number. Process stopped.");
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}
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}
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}
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}
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}
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}
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// Generate report out of DROID profile file
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// if (parse.hasOption("cr")) {
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//
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// String droidProfileFile = parse.getOptionValue("cr");
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//
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// if (droidProfileFile != null) {
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//
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// ProvenanceAccessClient pac;
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// if (tavernaT2DatabasePath != null && !tavernaT2DatabasePath.isEmpty()) {
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// pac = new ProvenanceAccessClient(tavernaT2DatabasePath);
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// } else {
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// pac = new ProvenanceAccessClient();
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// }
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// pac.generateReport(new File(droidProfileFile));
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// }
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// }
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// Extend DSO with PRONOM information
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// Extend DSO with PRONOM information
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if (parse.hasOption("ont") && parse.hasOption("r")) {
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if (parse.hasOption("ont") && parse.hasOption("r")) {
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LOGGER.debug("Start extending ontology ...");
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LOGGER.debug("Start extending ontology ...");
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System.out.println("Start extending ontology ...");
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System.out.println("Start extending ontology ...");
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} catch (ParseException exp) {
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} catch (ParseException exp) {
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helpFormater.printHelp("TavernaExtractor", createOptions());
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helpFormater.printHelp("TavernaExtractor", createOptions());
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LOGGER.error("ERROR: Wrong usage:" + exp.getMessage());
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LOGGER.error("ERROR: Wrong usage:" + exp.getMessage());
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exp.printStackTrace();
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exp.printStackTrace();
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return;
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}
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}
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} catch (Exception e) {
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} catch (Exception e) {
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LOGGER.error(e.getMessage());
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LOGGER.error(e.getMessage());
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// also print the error stack trace
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// also print the error stack trace
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if(verbose)
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if(verbose)
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OptionBuilder.withDescription("Specifies the taverna t2flow (input) file.");
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OptionBuilder.withDescription("Specifies the taverna t2flow (input) file.");
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OptionBuilder.hasArg();
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OptionBuilder.hasArg();
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OptionBuilder.withLongOpt("input-file");
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OptionBuilder.withLongOpt("input-file");
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options.addOption(OptionBuilder.create("i"));
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options.addOption(OptionBuilder.create("i"));
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//TODO : rename
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OptionBuilder.withDescription("Fetching processed files from workflow");
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OptionBuilder.withDescription("Fetching provenance information from a workflow execution");
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OptionBuilder.withArgName("\\path\\to\\copy\\provenance-trace");
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OptionBuilder.hasArg();
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OptionBuilder.hasArg();
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OptionBuilder.withLongOpt("provenance");
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OptionBuilder.withLongOpt("provenance");
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options.addOption(OptionBuilder.create("p"));
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options.addOption(OptionBuilder.create("p"));
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// OptionBuilder.withDescription("Generate CSV Report out of DROID profile.");
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// OptionBuilder.hasArg();
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// OptionBuilder.withLongOpt("create-report");
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// options.addOption(OptionBuilder.create("cr"));
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OptionBuilder.withDescription("The ontology file");
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OptionBuilder.withDescription("Ontology file");
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OptionBuilder.withArgName("\\path\\to\\myOntology.owl");
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OptionBuilder.withArgName("\\path\\to\\myOntology.owl");
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OptionBuilder.hasArg();
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OptionBuilder.hasArg();
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OptionBuilder.withLongOpt("ontology-file");
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OptionBuilder.withLongOpt("ontology-file");
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options.addOption(OptionBuilder.create("ont"));
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options.addOption(OptionBuilder.create("ont"));
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OptionBuilder.withDescription("output file");
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OptionBuilder.withDescription("DROID report file");
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OptionBuilder.withArgName("\\path\\to\\myDroidCSVreportFile.droid.csv");
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OptionBuilder.withArgName("\\path\\to\\myDroidCSVreportFile.droid.csv");
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OptionBuilder.hasArg();
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OptionBuilder.hasArg();
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OptionBuilder.withLongOpt("reportFile");
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OptionBuilder.withLongOpt("reportFile");
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options.addOption(OptionBuilder.create("r"));
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options.addOption(OptionBuilder.create("r"));
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}
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}
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private static Properties loadProperties() {
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private static Properties loadProperties() {
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Properties prop = new Properties();
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Properties prop = new Properties();
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InputStream input = null;
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try {
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try {
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input = Main.class.getClassLoader().getResourceAsStream("TavernaExtractor.properties");
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InputStream input = Main.class.getClassLoader().getResourceAsStream("TavernaExtractor.properties");
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prop.load(input);
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prop.load(input);
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LOGGER.debug("Load properties successfully.");
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LOGGER.debug("Load properties successfully.");
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} catch (IOException io) {
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} catch (IOException io) {
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LOGGER.error(io.getMessage());
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LOGGER.error(io.getMessage());
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io.printStackTrace();
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io.printStackTrace();
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