Extractor Modules / Taverna Extractor / Diff of /src/net/timbusproject/extractors/TavernaExtractor.java

Diff of /src/net/timbusproject/extractors/TavernaExtractor.java [9d46ed] .. [f9a9cc]

Switch to unified view


...

package net.timbusproject.extractors;

import java.awt.Dimension;
import java.awt.Point;

import java.io.*;





import java.net.URL;
import java.nio.file.Files;
import java.nio.file.InvalidPathException;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
...
import javax.xml.xpath.XPathConstants;
import javax.xml.xpath.XPathExpression;
import javax.xml.xpath.XPathExpressionException;
import javax.xml.xpath.XPathFactory;

import edu.emory.mathcs.backport.java.util.Arrays;
import net.sf.taverna.t2.activities.beanshell.BeanshellActivity;
import net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean;
import net.sf.taverna.t2.activities.dataflow.DataflowActivity;
import net.sf.taverna.t2.activities.externaltool.ExternalToolActivity;
import net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean;
...
            npe.printStackTrace();
            LOGGER.error("ERROR reading workflow from [" + inputFileName + "]." + npe.getMessage());
            return;
        }


        // current classpath
        String classpath = System.getProperty("java.class.path");
        String[] classpathEntries = classpath.split(File.pathSeparator);
        List<String> cleanClasspathEntries = cleanedClasspath(Arrays.asList(classpathEntries));

        factory = IArchimateFactory.eINSTANCE;

        IArchimateModel model = factory.createArchimateModel();
        model.setDefaults();
        model.setName("Converted Taverna Workflow " + inputFileName);
...
        infrastructureFolder = model.getFolder(FolderType.TECHNOLOGY);
        motivationFolder = model.getFolder(FolderType.MOTIVATION);
        applicationFolder = model.getFolder(FolderType.APPLICATION);
        relationsFolder = model.getFolder(FolderType.RELATIONS);

        // LAYERED VIEWS
        layeredView = factory.createArchimateDiagramModel();
        layeredView.setName("Layered View");
        layeredView.setViewpoint(IViewpoint.LAYERED_VIEWPOINT);
        diagramFolder.getElements().add(layeredView);

...
                beanshellScriptDep.getProperties().add(jarLocation);

                // do proper checking whether the file exists !
                Path pathToDep = Paths.get(fileName);
                if (Files.exists(pathToDep)) {


                    String license = licenseCheck.extract(pathToDep.toAbsolutePath().toString());

                    if (license.equals("Unknown license")) {
                        LOGGER.debug("\t Unknown license for dependency [" + item + "].");
                    }

...
        return inputsNumber;
    }

    private boolean isDotAvailable() {


        if (dotLocation != null && !dotLocation.isEmpty()) {

            try {
                Paths.get(dotLocation);
            }catch(InvalidPathException ipe){
                return false;
            }
            return true;
        }
        return false;
    }

...
                }
            }
        }
    }


    private List<String> cleanedClasspath(List<String> classpathEntries){

        List<String> cleanedClasspathEntries = new ArrayList<String>();

        for(String entry : classpathEntries)
            if(entry.contains("taverna-2."))
                cleanedClasspathEntries.add(entry);


        return cleanedClasspathEntries;
    }

    private URL getJarLocationOfClass(Class clazz) {
        return clazz.getProtectionDomain().getCodeSource().getLocation();
    }

    public void treatProcessors(List<? extends Processor> processors) {

	a/src/net/timbusproject/extractors/TavernaExtractor.java		b/src/net/timbusproject/extractors/TavernaExtractor.java
	...		...
18		18
19	package net.timbusproject.extractors;	19	package net.timbusproject.extractors;
20		20
21	import java.awt.Dimension;	21	import java.awt.Dimension;
22	import java.awt.Point;	22	import java.awt.Point;
23	import java.io.BufferedReader;
24	import java.io.File;	23	import java.io.*;
25	import java.io.FileWriter;
26	import java.io.IOException;
27	import java.io.InputStream;
28	import java.io.InputStreamReader;
29	import java.io.StringWriter;
30	import java.net.URL;	24	import java.net.URL;
31	import java.nio.file.Files;	25	import java.nio.file.Files;
		26	import java.nio.file.InvalidPathException;
32	import java.nio.file.Path;	27	import java.nio.file.Path;
33	import java.nio.file.Paths;	28	import java.nio.file.Paths;
34	import java.util.ArrayList;	29	import java.util.ArrayList;
35	import java.util.Collections;	30	import java.util.Collections;
36	import java.util.HashMap;	31	import java.util.HashMap;
	...		...
47	import javax.xml.xpath.XPathConstants;	42	import javax.xml.xpath.XPathConstants;
48	import javax.xml.xpath.XPathExpression;	43	import javax.xml.xpath.XPathExpression;
49	import javax.xml.xpath.XPathExpressionException;	44	import javax.xml.xpath.XPathExpressionException;
50	import javax.xml.xpath.XPathFactory;	45	import javax.xml.xpath.XPathFactory;
51		46
		47	import edu.emory.mathcs.backport.java.util.Arrays;
52	import net.sf.taverna.t2.activities.beanshell.BeanshellActivity;	48	import net.sf.taverna.t2.activities.beanshell.BeanshellActivity;
53	import net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean;	49	import net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean;
54	import net.sf.taverna.t2.activities.dataflow.DataflowActivity;	50	import net.sf.taverna.t2.activities.dataflow.DataflowActivity;
55	import net.sf.taverna.t2.activities.externaltool.ExternalToolActivity;	51	import net.sf.taverna.t2.activities.externaltool.ExternalToolActivity;
56	import net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean;	52	import net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean;
	...		...
338	npe.printStackTrace();	334	npe.printStackTrace();
339	LOGGER.error("ERROR reading workflow from [" + inputFileName + "]." + npe.getMessage());	335	LOGGER.error("ERROR reading workflow from [" + inputFileName + "]." + npe.getMessage());
340	return;	336	return;
341	}	337	}
342		338
		339
		340	// current classpath
		341	String classpath = System.getProperty("java.class.path");
		342	String[] classpathEntries = classpath.split(File.pathSeparator);
		343	List<String> cleanClasspathEntries = cleanedClasspath(Arrays.asList(classpathEntries));
		344
343	factory = IArchimateFactory.eINSTANCE;	345	factory = IArchimateFactory.eINSTANCE;
344		346
345	IArchimateModel model = factory.createArchimateModel();	347	IArchimateModel model = factory.createArchimateModel();
346	model.setDefaults();	348	model.setDefaults();
347	model.setName("Converted Taverna Workflow " + inputFileName);	349	model.setName("Converted Taverna Workflow " + inputFileName);
	...		...
352	infrastructureFolder = model.getFolder(FolderType.TECHNOLOGY);	354	infrastructureFolder = model.getFolder(FolderType.TECHNOLOGY);
353	motivationFolder = model.getFolder(FolderType.MOTIVATION);	355	motivationFolder = model.getFolder(FolderType.MOTIVATION);
354	applicationFolder = model.getFolder(FolderType.APPLICATION);	356	applicationFolder = model.getFolder(FolderType.APPLICATION);
355	relationsFolder = model.getFolder(FolderType.RELATIONS);	357	relationsFolder = model.getFolder(FolderType.RELATIONS);
356		358
357	// LAYERD VIEWS	359	// LAYERED VIEWS
358	layeredView = factory.createArchimateDiagramModel();	360	layeredView = factory.createArchimateDiagramModel();
359	layeredView.setName("Layered View");	361	layeredView.setName("Layered View");
360	layeredView.setViewpoint(IViewpoint.LAYERED_VIEWPOINT);	362	layeredView.setViewpoint(IViewpoint.LAYERED_VIEWPOINT);
361	diagramFolder.getElements().add(layeredView);	363	diagramFolder.getElements().add(layeredView);
362		364
	...		...
969	beanshellScriptDep.getProperties().add(jarLocation);	971	beanshellScriptDep.getProperties().add(jarLocation);
970		972
971	// do proper checking whether the file exists !	973	// do proper checking whether the file exists !
972	Path pathToDep = Paths.get(fileName);	974	Path pathToDep = Paths.get(fileName);
973	if (Files.exists(pathToDep)) {	975	if (Files.exists(pathToDep)) {
974	String license = null;
975
976	license = licenseCheck.extract(pathToDep.toAbsolutePath().toString());	976	String license = licenseCheck.extract(pathToDep.toAbsolutePath().toString());
977		977
978	if (license.equals("Unknown license")) {	978	if (license.equals("Unknown license")) {
979	LOGGER.debug("\t Unknown license for dependency [" + item + "].");	979	LOGGER.debug("\t Unknown license for dependency [" + item + "].");
980	}	980	}
981		981
	...		...
1786	return inputsNumber;	1786	return inputsNumber;
1787	}	1787	}
1788		1788
1789	private boolean isDotAvailable() {	1789	private boolean isDotAvailable() {
1790		1790
1791	// TODO improve checking if DOT is available on system.
1792	if (dotLocation != null && !dotLocation.isEmpty()) {	1791	if (dotLocation != null && !dotLocation.isEmpty()) {
		1792
		1793	try {
		1794	Paths.get(dotLocation);
		1795	}catch(InvalidPathException ipe){
		1796	return false;
		1797	}
1793	return true;	1798	return true;
1794	}	1799	}
1795	return false;	1800	return false;
1796	}	1801	}
1797		1802
	...		...
1878	}	1883	}
1879	}	1884	}
1880	}	1885	}
1881	}	1886	}
1882		1887
		1888
		1889	private List<String> cleanedClasspath(List<String> classpathEntries){
		1890
		1891	List<String> cleanedClasspathEntries = new ArrayList<String>();
		1892
		1893	for(String entry : classpathEntries)
		1894	if(entry.contains("taverna-2."))
		1895	cleanedClasspathEntries.add(entry);
		1896
		1897
		1898	return cleanedClasspathEntries;
		1899	}
		1900
1883	private URL getJarLocationOfClass(Class clazz) {	1901	private URL getJarLocationOfClass(Class clazz) {
1884	return clazz.getProtectionDomain().getCodeSource().getLocation();	1902	return clazz.getProtectionDomain().getCodeSource().getLocation();
1885	}	1903	}
1886		1904
1887	public void treatProcessors(List<? extends Processor> processors) {	1905	public void treatProcessors(List<? extends Processor> processors) {