
...

        //setup
        TavernaExtractor.setTavernaHomeLib(TavernaExtractor.getTavernaHome().resolve("lib"));
        TavernaExtractor.setTavernaHomeRepo(TavernaExtractor.getTavernaHome().resolve("repository"));

        //validateDirectories(TavernaExtractor.getTavernaHome(), TavernaExtractor.getTavernaHomeLib(), TavernaExtractor.getTavernaHomeRepo());

        LOGGER.info( "TavernaHome is set to [" + TavernaExtractor.getTavernaHome() + "].");
        LOGGER.info( "TavernaHomeLib is set to [" + TavernaExtractor.getTavernaHomeLib() + "].");
        LOGGER.info( "TavernaHomeRepo is set to [" + TavernaExtractor.getTavernaHomeRepo() + "].");
        LOGGER.info( "Workflow input file is [" + TavernaExtractor.getInputFileName() + "].");
...
            if (file.exists()) {
                    workflowURL = file.toURI().toURL();
            }

            LOGGER.info( "Reading workflow from " + workflowURL);
            System.out.println("Reading workflow from " + workflowURL);
            dataflow = openDataflow(workflowURL);
        } catch (NullPointerException npe) {
            npe.printStackTrace();
            LOGGER.error( "ERROR reading workflow from [" + inputFileName + "]." + npe.getMessage());
            return;
...
                }
            }
        }
    }

    // TODO valdiate dirs of remote machine
    private void validateDirectories(Path... dirs) throws IOException{

        for(Path path : dirs) {
            if (path == null || Files.notExists(path) || !Files.isDirectory(path) || !Files.isReadable(path)) {
                throw new IOException("Directory '" + path + "' does not exists or is invalid.");

	a/src/main/java/net/timbusproject/extractors/modules/tavernaextractor/TavernaExtractor.java		b/src/main/java/net/timbusproject/extractors/modules/tavernaextractor/TavernaExtractor.java
	...		...
263		263
264	//setup	264	//setup
265	TavernaExtractor.setTavernaHomeLib(TavernaExtractor.getTavernaHome().resolve("lib"));	265	TavernaExtractor.setTavernaHomeLib(TavernaExtractor.getTavernaHome().resolve("lib"));
266	TavernaExtractor.setTavernaHomeRepo(TavernaExtractor.getTavernaHome().resolve("repository"));	266	TavernaExtractor.setTavernaHomeRepo(TavernaExtractor.getTavernaHome().resolve("repository"));
267		267
268	validateDirectories(TavernaExtractor.getTavernaHome(), TavernaExtractor.getTavernaHomeLib(), TavernaExtractor.getTavernaHomeRepo());	268	//validateDirectories(TavernaExtractor.getTavernaHome(), TavernaExtractor.getTavernaHomeLib(), TavernaExtractor.getTavernaHomeRepo());
269		269
270	LOGGER.info( "TavernaHome is set to [" + TavernaExtractor.getTavernaHome() + "].");	270	LOGGER.info( "TavernaHome is set to [" + TavernaExtractor.getTavernaHome() + "].");
271	LOGGER.info( "TavernaHomeLib is set to [" + TavernaExtractor.getTavernaHomeLib() + "].");	271	LOGGER.info( "TavernaHomeLib is set to [" + TavernaExtractor.getTavernaHomeLib() + "].");
272	LOGGER.info( "TavernaHomeRepo is set to [" + TavernaExtractor.getTavernaHomeRepo() + "].");	272	LOGGER.info( "TavernaHomeRepo is set to [" + TavernaExtractor.getTavernaHomeRepo() + "].");
273	LOGGER.info( "Workflow input file is [" + TavernaExtractor.getInputFileName() + "].");	273	LOGGER.info( "Workflow input file is [" + TavernaExtractor.getInputFileName() + "].");
	...		...
322	if (file.exists()) {	322	if (file.exists()) {
323	workflowURL = file.toURI().toURL();	323	workflowURL = file.toURI().toURL();
324	}	324	}
325		325
326	LOGGER.info( "Reading workflow from " + workflowURL);	326	LOGGER.info( "Reading workflow from " + workflowURL);
		327	System.out.println("Reading workflow from " + workflowURL);
327	dataflow = openDataflow(workflowURL);	328	dataflow = openDataflow(workflowURL);
328	} catch (NullPointerException npe) {	329	} catch (NullPointerException npe) {
329	npe.printStackTrace();	330	npe.printStackTrace();
330	LOGGER.error( "ERROR reading workflow from [" + inputFileName + "]." + npe.getMessage());	331	LOGGER.error( "ERROR reading workflow from [" + inputFileName + "]." + npe.getMessage());
331	return;	332	return;
	...		...
1943	}	1944	}
1944	}	1945	}
1945	}	1946	}
1946	}	1947	}
1947		1948
		1949	// TODO valdiate dirs of remote machine
1948	private void validateDirectories(Path... dirs) throws IOException{	1950	private void validateDirectories(Path... dirs) throws IOException{
1949		1951
1950	for(Path path : dirs) {	1952	for(Path path : dirs) {
1951	if (path == null \|\| Files.notExists(path) \|\| !Files.isDirectory(path) \|\| !Files.isReadable(path)) {	1953	if (path == null \|\| Files.notExists(path) \|\| !Files.isDirectory(path) \|\| !Files.isReadable(path)) {
1952	throw new IOException("Directory '" + path + "' does not exists or is invalid.");	1954	throw new IOException("Directory '" + path + "' does not exists or is invalid.");