taverna-prov/src/main/java/org/apache/taverna/prov/Saver.java - incubator-taverna-engine - Git at Google

 /*
 * Licensed to the Apache Software Foundation (ASF) under one
 * or more contributor license agreements. See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership. The ASF licenses this file
 * to you under the Apache License, Version 2.0 (the
 * "License"); you may not use this file except in compliance
 * with the License. You may obtain a copy of the License at
 *
 * http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing,
 * software distributed under the License is distributed on an
 * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
 * KIND, either express or implied. See the License for the
 * specific language governing permissions and limitations
 * under the License.
 */
 package org.apache.taverna.prov;

 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
 import java.net.ProtocolException;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.net.URL;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.security.DigestOutputStream;
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Comparator;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;

 import org.apache.taverna.invocation.InvocationContext;
 import org.apache.taverna.provenance.api.ProvenanceAccess;
 import org.apache.taverna.reference.ExternalReferenceSPI;
 import org.apache.taverna.reference.ReferenceService;
 import org.apache.taverna.reference.ReferenceSet;
 import org.apache.taverna.reference.ReferenceSetService;
 import org.apache.taverna.reference.T2Reference;
 import org.apache.taverna.reference.ValueCarryingExternalReference;
 import org.apache.taverna.spi.SPIRegistry;
 import org.apache.taverna.reference.config.DataManagementConfiguration;

 import org.apache.commons.beanutils.PropertyUtils;
 import org.apache.commons.codec.binary.Hex;
 import org.apache.commons.io.IOUtils;
 import org.apache.log4j.Logger;
 import org.apache.tika.Tika;
 import org.apache.tika.mime.MimeTypeException;
 import org.apache.tika.mime.MimeTypes;
 import org.openrdf.rio.RDFParserFactory;
 import org.openrdf.rio.RDFParserRegistry;
 import org.openrdf.rio.RDFWriterFactory;
 import org.openrdf.rio.RDFWriterRegistry;
 import org.apache.taverna.robundle.Bundle;

 import org.apache.taverna.databundle.DataBundles;

 public class Saver {

     private static final String APPLICATION_OCTET_STREAM = "application/octet-stream";

     private static Logger logger = Logger.getLogger(Saver.class);

     /**
      * @param saveProvAction
      */
     public Saver(ReferenceService referenceService, InvocationContext context,
             String runId, Map<String, T2Reference> chosenReferences) {
         this.setReferenceService(referenceService);
         this.setContext(context);
         this.setRunId(runId);
         this.setChosenReferences(chosenReferences);
         prepareSesame();
     }

     /**
      * Load
      */
     protected void prepareSesame() {
         RDFParserRegistry parserReg = RDFParserRegistry.getInstance();
         SPIRegistry<RDFParserFactory> parserSPI = new SPIRegistry<>(
                 RDFParserFactory.class);
         for (RDFParserFactory service : parserSPI.getInstances()) {
             parserReg.add(service);
         }

         RDFWriterRegistry writerReg = RDFWriterRegistry.getInstance();
         SPIRegistry<RDFWriterFactory> writerSPI = new SPIRegistry<>(
                 RDFWriterFactory.class);
         for (RDFWriterFactory service : writerSPI.getInstances()) {
             writerReg.add(service);
         }

     }

     private Map<Path, T2Reference> fileToId = new HashMap<>();

     private Map<Path, String> sha1sums = new HashMap<>();
     private Map<Path, String> sha512sums = new HashMap<>();

     private ReferenceService referenceService;

     private InvocationContext context;

     private String runId;

     private Map<String, T2Reference> chosenReferences;

     private Bundle bundle;

     private Map<T2Reference, String> mediaTypes = new HashMap<>();

     /**
      * @return the bundle
      */
     public Bundle getBundle() {
         return bundle;
     }

     public void saveData(Path bundlePath) throws FileNotFoundException,
             IOException {
         Bundle bundle = DataBundles.createBundle();
         // String folderName = bundlePath.getFileName().toString();
         // if (folderName.endsWith(".")) {
         // bundlePath = bundlePath.resolveSibling(folderName.substring(0,
         // folderName.length() - 1));
         // }
         setBundle(bundle);
         saveToFolder(bundle.getRoot(), getChosenReferences(),
                 getReferenceService());
         DataBundles.closeAndSaveBundle(bundle, bundlePath);
     }

     private void setBundle(Bundle bundle) {
         this.bundle = bundle;
     }

     protected static Tika tika = new Tika();

     public Path saveReference(T2Reference t2Ref, Path file) throws IOException {
         ReferenceSetService refSet = getReferenceService()
                 .getReferenceSetService();
         ReferenceSet referenceSet = refSet.getReferenceSet(t2Ref);
         List<ExternalReferenceSPI> externalReferences = new ArrayList<ExternalReferenceSPI>(
                 referenceSet.getExternalReferences());
         Collections.sort(externalReferences,
                 new Comparator<ExternalReferenceSPI>() {
                     public int compare(ExternalReferenceSPI o1,
                             ExternalReferenceSPI o2) {
                         return (int) (o1.getResolutionCost() - o2
                                 .getResolutionCost());
                     }
                 });
         String mimeType = findMimeType(externalReferences);
         getMediaTypes().put(t2Ref, mimeType);

         Path targetFile = writeIfLocal(externalReferences, file, mimeType);
         if (targetFile == null) {
             URI uri = referenceAsURI(externalReferences);
             if (uri != null) {
                 targetFile = DataBundles.setReference(file, uri);
             }
         }

         if (targetFile != null) {
             getFileToId().put(targetFile, t2Ref);
         } else {
             logger.warn("Could not write out reference " + t2Ref);
         }

         return targetFile;

     }

     private Path writeIfLocal(List<ExternalReferenceSPI> externalReferences,
             Path file, String mimeType) throws IOException {

         ValueCarryingExternalReference<?> valRef = null;
         for (ExternalReferenceSPI ref : externalReferences) {
             if (ref instanceof ValueCarryingExternalReference) {
                 valRef = (ValueCarryingExternalReference<?>) ref;
                 break;
             }
         }

         if (valRef == null) {
             return null;
         }

         String fileExtension;
         try {
             fileExtension = MimeTypes.getDefaultMimeTypes().forName(mimeType)
                     .getExtension();
         } catch (MimeTypeException e1) {
             fileExtension = "";
         }
         Path targetFile = file.resolveSibling(file.getFileName()
                 + fileExtension);

         MessageDigest sha = null;
         MessageDigest sha512 = null;
         OutputStream output = Files.newOutputStream(targetFile);
         try {
             try {
                 sha = MessageDigest.getInstance("SHA");
                 output = new DigestOutputStream(output, sha);

                 sha512 = MessageDigest.getInstance("SHA-512");
                 output = new DigestOutputStream(output, sha512);
             } catch (NoSuchAlgorithmException e) {
                 logger.info("Could not find digest", e);
             }

             IOUtils.copyLarge(valRef.openStream(getContext()), output);
         } finally {
             output.close();
         }

         if (sha != null) {
             getSha1sums().put(targetFile.toRealPath(), hexOfDigest(sha));
         }
         if (sha512 != null) {
             sha512.digest();
             getSha512sums().put(targetFile.toRealPath(), hexOfDigest(sha512));
         }

         return targetFile;
     }

     private URI referenceAsURI(List<ExternalReferenceSPI> externalReferences) {
         for (ExternalReferenceSPI ref : externalReferences) {
             String className = ref.getClass().getName();
             if (className
                     .equals("net.sf.taverna.t2.reference.impl.external.http.HttpReference")) {
                 URL url = (URL) getProperty(ref, "httpUrl");
                 try {
                     return url.toURI();
                 } catch (URISyntaxException e) {
                     logger.warn("Can't convert HttpReference to URI: " + url, e);
                     continue;
                 }
             } else if (className
                     .equals("net.sf.taverna.t2.reference.impl.external.file.FileReference")) {
                 File file = (File) getProperty(ref, "file");
                 return file.toURI();
             } else if (className
                     .equals("de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshReference")) {
                 String host = (String) getProperty(ref, "host");
                 int port = (int) getProperty(ref, "port");
                 String path = (String) getProperty(ref, "fullPath");
                 try {
                     return new URI("sftp", null, host, port, path, null, null);
                 } catch (URISyntaxException e) {
                     logger.warn("Can't convert SshReference to URI: sftp://"
                             + host + ":" + port + path, e);
                     continue;
                 }
             }
         }
         return null;
     }

     protected Object getProperty(ExternalReferenceSPI ref, String propertyName) {
         try {
             return PropertyUtils.getSimpleProperty(ref, propertyName);
         } catch (Exception ex) {
             throw new IllegalArgumentException("Can't look up " + propertyName
                     + " in bean " + ref, ex);
         }
     }

     private String findMimeType(List<ExternalReferenceSPI> externalReferences)
             throws IOException, ProtocolException {
         String mimeType = null;
         for (ExternalReferenceSPI externalReference : externalReferences) {
             String className = externalReference.getClass().getName();
             if (className
                     .equals("net.sf.taverna.t2.reference.impl.external.http.HttpReference")) {
                 URL url = (URL) getProperty(externalReference, "httpUrl");
                 mimeType = tika.detect(url);
             } else if (className
                     .equals("net.sf.taverna.t2.reference.impl.external.file.FileReference")) {
                 File file = (File) getProperty(externalReference, "file");
                 mimeType = tika.detect(file);
             } else if (className
                     .equals("de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshReference")) {
                 String filename = (String) getProperty(externalReference,
                         "fileName");
                 try (InputStream instream = externalReference
                         .openStream(context)) {
                     mimeType = tika.detect(instream, filename);
                 }
             } else if (className
                     .equals("net.sf.taverna.t2.reference.impl.external.object.VMObjectReference")) {
                 mimeType = "application/x-java-serialized-object";
             } else {
                 try (InputStream instream = externalReference
                         .openStream(context)) {
                     mimeType = tika.detect(instream);
                 }
             }
             if (mimeType != null && !mimeType.equals(APPLICATION_OCTET_STREAM)) {
                 break;
             }
         }
         if (mimeType == null || mimeType.isEmpty()) {
             return APPLICATION_OCTET_STREAM;
         }
         return mimeType;
     }

     protected void saveToFolder(Path folder,
             Map<String, T2Reference> chosenReferences,
             ReferenceService referenceService) throws IOException,
             FileNotFoundException {
         logger.info("Saving provenance and outputs to " + folder.toRealPath());
         Files.createDirectories(folder);
         String connectorType = DataManagementConfiguration.getInstance()
                 .getConnectorType();
         ProvenanceAccess provenanceAccess = new ProvenanceAccess(connectorType,
                 getContext());
         W3ProvenanceExport export = new W3ProvenanceExport(provenanceAccess,
                 getRunId(), this);
         export.setFileToT2Reference(getFileToId());
         export.setBundle(bundle);

         try {
             logger.debug("Saving provenance");
             export.exportAsW3Prov();
             logger.info("Saved provenance");
         } catch (Exception e) {
             logger.error("Failed to save the provenance graph", e);
         }
     }

     private String hexOfDigest(MessageDigest sha) {
         return new String(Hex.encodeHex(sha.digest()));
     }

     public ReferenceService getReferenceService() {
         return referenceService;
     }

     public void setReferenceService(ReferenceService referenceService) {
         this.referenceService = referenceService;
     }

     public InvocationContext getContext() {
         return context;
     }

     public void setContext(InvocationContext context) {
         this.context = context;
     }

     public String getRunId() {
         return runId;
     }

     public void setRunId(String runId) {
         this.runId = runId;
     }

     public Map<String, T2Reference> getChosenReferences() {
         return chosenReferences;
     }

     public void setChosenReferences(Map<String, T2Reference> chosenReferences) {
         this.chosenReferences = chosenReferences;
     }

     public Map<Path, T2Reference> getFileToId() {
         return fileToId;
     }

     public void setFileToId(Map<Path, T2Reference> fileToId) {
         this.fileToId = fileToId;
     }

     public Map<Path, String> getSha1sums() {
         return sha1sums;
     }

     public Map<T2Reference, String> getMediaTypes() {
         return mediaTypes;
     }

     public Map<Path, String> getSha512sums() {
         return sha512sums;
     }

     public void setMediaTypes(Map<T2Reference, String> mediaTypes) {
         this.mediaTypes = mediaTypes;
     }

 }
	/*
	* Licensed to the Apache Software Foundation (ASF) under one
	* or more contributor license agreements. See the NOTICE file
	* distributed with this work for additional information
	* regarding copyright ownership. The ASF licenses this file
	* to you under the Apache License, Version 2.0 (the
	* "License"); you may not use this file except in compliance
	* with the License. You may obtain a copy of the License at
	*
	* http://www.apache.org/licenses/LICENSE-2.0
	*
	* Unless required by applicable law or agreed to in writing,
	* software distributed under the License is distributed on an
	* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
	* KIND, either express or implied. See the License for the
	* specific language governing permissions and limitations
	* under the License.
	*/
	package org.apache.taverna.prov;

	import java.io.File;
	import java.io.FileNotFoundException;
	import java.io.IOException;
	import java.io.InputStream;
	import java.io.OutputStream;
	import java.net.ProtocolException;
	import java.net.URI;
	import java.net.URISyntaxException;
	import java.net.URL;
	import java.nio.file.Files;
	import java.nio.file.Path;
	import java.security.DigestOutputStream;
	import java.security.MessageDigest;
	import java.security.NoSuchAlgorithmException;
	import java.util.ArrayList;
	import java.util.Collections;
	import java.util.Comparator;
	import java.util.HashMap;
	import java.util.List;
	import java.util.Map;

	import org.apache.taverna.invocation.InvocationContext;
	import org.apache.taverna.provenance.api.ProvenanceAccess;
	import org.apache.taverna.reference.ExternalReferenceSPI;
	import org.apache.taverna.reference.ReferenceService;
	import org.apache.taverna.reference.ReferenceSet;
	import org.apache.taverna.reference.ReferenceSetService;
	import org.apache.taverna.reference.T2Reference;
	import org.apache.taverna.reference.ValueCarryingExternalReference;
	import org.apache.taverna.spi.SPIRegistry;
	import org.apache.taverna.reference.config.DataManagementConfiguration;

	import org.apache.commons.beanutils.PropertyUtils;
	import org.apache.commons.codec.binary.Hex;
	import org.apache.commons.io.IOUtils;
	import org.apache.log4j.Logger;
	import org.apache.tika.Tika;
	import org.apache.tika.mime.MimeTypeException;
	import org.apache.tika.mime.MimeTypes;
	import org.openrdf.rio.RDFParserFactory;
	import org.openrdf.rio.RDFParserRegistry;
	import org.openrdf.rio.RDFWriterFactory;
	import org.openrdf.rio.RDFWriterRegistry;
	import org.apache.taverna.robundle.Bundle;

	import org.apache.taverna.databundle.DataBundles;

	public class Saver {

	private static final String APPLICATION_OCTET_STREAM = "application/octet-stream";

	private static Logger logger = Logger.getLogger(Saver.class);

	/**
	* @param saveProvAction
	*/
	public Saver(ReferenceService referenceService, InvocationContext context,
	String runId, Map<String, T2Reference> chosenReferences) {
	this.setReferenceService(referenceService);
	this.setContext(context);
	this.setRunId(runId);
	this.setChosenReferences(chosenReferences);
	prepareSesame();
	}

	/**
	* Load
	*/
	protected void prepareSesame() {
	RDFParserRegistry parserReg = RDFParserRegistry.getInstance();
	SPIRegistry<RDFParserFactory> parserSPI = new SPIRegistry<>(
	RDFParserFactory.class);
	for (RDFParserFactory service : parserSPI.getInstances()) {
	parserReg.add(service);
	}

	RDFWriterRegistry writerReg = RDFWriterRegistry.getInstance();
	SPIRegistry<RDFWriterFactory> writerSPI = new SPIRegistry<>(
	RDFWriterFactory.class);
	for (RDFWriterFactory service : writerSPI.getInstances()) {
	writerReg.add(service);
	}

	}

	private Map<Path, T2Reference> fileToId = new HashMap<>();

	private Map<Path, String> sha1sums = new HashMap<>();
	private Map<Path, String> sha512sums = new HashMap<>();

	private ReferenceService referenceService;

	private InvocationContext context;

	private String runId;

	private Map<String, T2Reference> chosenReferences;

	private Bundle bundle;

	private Map<T2Reference, String> mediaTypes = new HashMap<>();

	/**
	* @return the bundle
	*/
	public Bundle getBundle() {
	return bundle;
	}

	public void saveData(Path bundlePath) throws FileNotFoundException,
	IOException {
	Bundle bundle = DataBundles.createBundle();
	// String folderName = bundlePath.getFileName().toString();
	// if (folderName.endsWith(".")) {
	// bundlePath = bundlePath.resolveSibling(folderName.substring(0,
	// folderName.length() - 1));
	// }
	setBundle(bundle);
	saveToFolder(bundle.getRoot(), getChosenReferences(),
	getReferenceService());
	DataBundles.closeAndSaveBundle(bundle, bundlePath);
	}

	private void setBundle(Bundle bundle) {
	this.bundle = bundle;
	}

	protected static Tika tika = new Tika();

	public Path saveReference(T2Reference t2Ref, Path file) throws IOException {
	ReferenceSetService refSet = getReferenceService()
	.getReferenceSetService();
	ReferenceSet referenceSet = refSet.getReferenceSet(t2Ref);
	List<ExternalReferenceSPI> externalReferences = new ArrayList<ExternalReferenceSPI>(
	referenceSet.getExternalReferences());
	Collections.sort(externalReferences,
	new Comparator<ExternalReferenceSPI>() {
	public int compare(ExternalReferenceSPI o1,
	ExternalReferenceSPI o2) {
	return (int) (o1.getResolutionCost() - o2
	.getResolutionCost());
	}
	});
	String mimeType = findMimeType(externalReferences);
	getMediaTypes().put(t2Ref, mimeType);

	Path targetFile = writeIfLocal(externalReferences, file, mimeType);
	if (targetFile == null) {
	URI uri = referenceAsURI(externalReferences);
	if (uri != null) {
	targetFile = DataBundles.setReference(file, uri);
	}
	}

	if (targetFile != null) {
	getFileToId().put(targetFile, t2Ref);
	} else {
	logger.warn("Could not write out reference " + t2Ref);
	}

	return targetFile;

	}

	private Path writeIfLocal(List<ExternalReferenceSPI> externalReferences,
	Path file, String mimeType) throws IOException {

	ValueCarryingExternalReference<?> valRef = null;
	for (ExternalReferenceSPI ref : externalReferences) {
	if (ref instanceof ValueCarryingExternalReference) {
	valRef = (ValueCarryingExternalReference<?>) ref;
	break;
	}
	}

	if (valRef == null) {
	return null;
	}

	String fileExtension;
	try {
	fileExtension = MimeTypes.getDefaultMimeTypes().forName(mimeType)
	.getExtension();
	} catch (MimeTypeException e1) {
	fileExtension = "";
	}
	Path targetFile = file.resolveSibling(file.getFileName()
	+ fileExtension);

	MessageDigest sha = null;
	MessageDigest sha512 = null;
	OutputStream output = Files.newOutputStream(targetFile);
	try {
	try {
	sha = MessageDigest.getInstance("SHA");
	output = new DigestOutputStream(output, sha);

	sha512 = MessageDigest.getInstance("SHA-512");
	output = new DigestOutputStream(output, sha512);
	} catch (NoSuchAlgorithmException e) {
	logger.info("Could not find digest", e);
	}

	IOUtils.copyLarge(valRef.openStream(getContext()), output);
	} finally {
	output.close();
	}

	if (sha != null) {
	getSha1sums().put(targetFile.toRealPath(), hexOfDigest(sha));
	}
	if (sha512 != null) {
	sha512.digest();
	getSha512sums().put(targetFile.toRealPath(), hexOfDigest(sha512));
	}

	return targetFile;
	}

	private URI referenceAsURI(List<ExternalReferenceSPI> externalReferences) {
	for (ExternalReferenceSPI ref : externalReferences) {
	String className = ref.getClass().getName();
	if (className
	.equals("net.sf.taverna.t2.reference.impl.external.http.HttpReference")) {
	URL url = (URL) getProperty(ref, "httpUrl");
	try {
	return url.toURI();
	} catch (URISyntaxException e) {
	logger.warn("Can't convert HttpReference to URI: " + url, e);
	continue;
	}
	} else if (className
	.equals("net.sf.taverna.t2.reference.impl.external.file.FileReference")) {
	File file = (File) getProperty(ref, "file");
	return file.toURI();
	} else if (className
	.equals("de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshReference")) {
	String host = (String) getProperty(ref, "host");
	int port = (int) getProperty(ref, "port");
	String path = (String) getProperty(ref, "fullPath");
	try {
	return new URI("sftp", null, host, port, path, null, null);
	} catch (URISyntaxException e) {
	logger.warn("Can't convert SshReference to URI: sftp://"
	+ host + ":" + port + path, e);
	continue;
	}
	}
	}
	return null;
	}

	protected Object getProperty(ExternalReferenceSPI ref, String propertyName) {
	try {
	return PropertyUtils.getSimpleProperty(ref, propertyName);
	} catch (Exception ex) {
	throw new IllegalArgumentException("Can't look up " + propertyName
	+ " in bean " + ref, ex);
	}
	}

	private String findMimeType(List<ExternalReferenceSPI> externalReferences)
	throws IOException, ProtocolException {
	String mimeType = null;
	for (ExternalReferenceSPI externalReference : externalReferences) {
	String className = externalReference.getClass().getName();
	if (className
	.equals("net.sf.taverna.t2.reference.impl.external.http.HttpReference")) {
	URL url = (URL) getProperty(externalReference, "httpUrl");
	mimeType = tika.detect(url);
	} else if (className
	.equals("net.sf.taverna.t2.reference.impl.external.file.FileReference")) {
	File file = (File) getProperty(externalReference, "file");
	mimeType = tika.detect(file);
	} else if (className
	.equals("de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshReference")) {
	String filename = (String) getProperty(externalReference,
	"fileName");
	try (InputStream instream = externalReference
	.openStream(context)) {
	mimeType = tika.detect(instream, filename);
	}
	} else if (className
	.equals("net.sf.taverna.t2.reference.impl.external.object.VMObjectReference")) {
	mimeType = "application/x-java-serialized-object";
	} else {
	try (InputStream instream = externalReference
	.openStream(context)) {
	mimeType = tika.detect(instream);
	}
	}
	if (mimeType != null && !mimeType.equals(APPLICATION_OCTET_STREAM)) {
	break;
	}
	}
	if (mimeType == null \|\| mimeType.isEmpty()) {
	return APPLICATION_OCTET_STREAM;
	}
	return mimeType;
	}

	protected void saveToFolder(Path folder,
	Map<String, T2Reference> chosenReferences,
	ReferenceService referenceService) throws IOException,
	FileNotFoundException {
	logger.info("Saving provenance and outputs to " + folder.toRealPath());
	Files.createDirectories(folder);
	String connectorType = DataManagementConfiguration.getInstance()
	.getConnectorType();
	ProvenanceAccess provenanceAccess = new ProvenanceAccess(connectorType,
	getContext());
	W3ProvenanceExport export = new W3ProvenanceExport(provenanceAccess,
	getRunId(), this);
	export.setFileToT2Reference(getFileToId());
	export.setBundle(bundle);

	try {
	logger.debug("Saving provenance");
	export.exportAsW3Prov();
	logger.info("Saved provenance");
	} catch (Exception e) {
	logger.error("Failed to save the provenance graph", e);
	}
	}

	private String hexOfDigest(MessageDigest sha) {
	return new String(Hex.encodeHex(sha.digest()));
	}

	public ReferenceService getReferenceService() {
	return referenceService;
	}

	public void setReferenceService(ReferenceService referenceService) {
	this.referenceService = referenceService;
	}

	public InvocationContext getContext() {
	return context;
	}

	public void setContext(InvocationContext context) {
	this.context = context;
	}

	public String getRunId() {
	return runId;
	}

	public void setRunId(String runId) {
	this.runId = runId;
	}

	public Map<String, T2Reference> getChosenReferences() {
	return chosenReferences;
	}

	public void setChosenReferences(Map<String, T2Reference> chosenReferences) {
	this.chosenReferences = chosenReferences;
	}

	public Map<Path, T2Reference> getFileToId() {
	return fileToId;
	}

	public void setFileToId(Map<Path, T2Reference> fileToId) {
	this.fileToId = fileToId;
	}

	public Map<Path, String> getSha1sums() {
	return sha1sums;
	}

	public Map<T2Reference, String> getMediaTypes() {
	return mediaTypes;
	}

	public Map<Path, String> getSha512sums() {
	return sha512sums;
	}

	public void setMediaTypes(Map<T2Reference, String> mediaTypes) {
	this.mediaTypes = mediaTypes;
	}

	}