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a/src/main/java/net/timbusproject/extractors/modules/tavernaextractor/TavernaExtractor.java |
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b/src/main/java/net/timbusproject/extractors/modules/tavernaextractor/TavernaExtractor.java |
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... |
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File tavernaFile = null;
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File tavernaFile = null;
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public void process(boolean remote) throws EditException, OpenDataflowException, InvalidOptionException,
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public void process(boolean remote) throws EditException, OpenDataflowException, InvalidOptionException,
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InvalidDataflowException, TokenOrderException, ReadInputException, DatabaseConfigurationException,
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InvalidDataflowException, TokenOrderException, ReadInputException, DatabaseConfigurationException,
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CMException, IOException, DeserializationException, IterationTypeMismatchException {
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CMException, IOException, DeserializationException, IterationTypeMismatchException, TavernaExtractorException {
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LOGGER.info( "Start Taverna Extractor ...");
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LOGGER.info( "Start Taverna Extractor ...");
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//setup
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//setup
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TavernaExtractor.setTavernaHomeLib(TavernaExtractor.getTavernaHome().resolve("lib"));
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TavernaExtractor.setTavernaHomeLib(TavernaExtractor.getTavernaHome().resolve("lib"));
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TavernaExtractor.setTavernaHomeRepo(TavernaExtractor.getTavernaHome().resolve("repository"));
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TavernaExtractor.setTavernaHomeRepo(TavernaExtractor.getTavernaHome().resolve("repository"));
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if(remote)
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validateRemoteDirectories(TavernaExtractor.getTavernaHome(), TavernaExtractor.getTavernaHomeLib(), TavernaExtractor.getTavernaHomeRepo());
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else
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//validateDirectories(TavernaExtractor.getTavernaHome(), TavernaExtractor.getTavernaHomeLib(), TavernaExtractor.getTavernaHomeRepo());
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validateDirectories(TavernaExtractor.getTavernaHome(), TavernaExtractor.getTavernaHomeLib(), TavernaExtractor.getTavernaHomeRepo());
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LOGGER.info( "TavernaHome is set to [" + TavernaExtractor.getTavernaHome() + "].");
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LOGGER.info( "TavernaHome is set to [" + TavernaExtractor.getTavernaHome() + "].");
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LOGGER.info( "TavernaHomeLib is set to [" + TavernaExtractor.getTavernaHomeLib() + "].");
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LOGGER.info( "TavernaHomeLib is set to [" + TavernaExtractor.getTavernaHomeLib() + "].");
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LOGGER.info( "TavernaHomeRepo is set to [" + TavernaExtractor.getTavernaHomeRepo() + "].");
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LOGGER.info( "TavernaHomeRepo is set to [" + TavernaExtractor.getTavernaHomeRepo() + "].");
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LOGGER.info( "Workflow input file is [" + TavernaExtractor.getInputFileName() + "].");
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LOGGER.info( "Workflow input file is [" + TavernaExtractor.getInputFileName() + "].");
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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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}
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}
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}
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// TODO valdiate dirs of remote machine
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private void validateDirectories(Path... dirs) throws IOException{
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private void validateDirectories(Path... dirs) throws TavernaExtractorException{
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for(Path path : dirs) {
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for(Path path : dirs) {
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if (path == null || Files.notExists(path) || !Files.isDirectory(path) || !Files.isReadable(path)) {
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if (path == null || Files.notExists(path) || !Files.isDirectory(path) || !Files.isReadable(path)) {
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throw new IOException("Directory '" + path + "' does not exists or is invalid.");
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throw new TavernaExtractorException("Directory '" + path + "' does not exists or is invalid.");
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}
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}
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}
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}
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private void validateRemoteDirectories(Path... dirs) throws TavernaExtractorException{
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try {
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for(Path path : dirs)
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sshManager.directoryExists(sshManager.createSession(15000), path);
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}
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catch(SSHManagerException sshME){
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throw new TavernaExtractorException(sshME.getLocalizedMessage());
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}
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}
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}
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}
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private List<String> cleanedClasspath(List<String> classpathEntries){
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private List<String> cleanedClasspath(List<String> classpathEntries){
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