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Posted to commits@taverna.apache.org by st...@apache.org on 2015/03/06 23:34:11 UTC
[15/50] [abbrv] incubator-taverna-workbench git commit: Moved from
t2.lang
Moved from t2.lang
git-svn-id: https://taverna.googlecode.com/svn/taverna/utils/net.sf.taverna.t2.lang/branches/maintenance@16888 bf327186-88b3-11dd-a302-d386e5130c1c
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/commit/c7cfb2ef
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/tree/c7cfb2ef
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/diff/c7cfb2ef
Branch: refs/heads/master
Commit: c7cfb2efb53719b1d57a412d79c03eb360a33033
Parents: 52f2960
Author: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Wed Mar 19 16:51:06 2014 +0000
Committer: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Wed Mar 19 16:51:06 2014 +0000
----------------------------------------------------------------------
results/pom.xml | 54 ---
.../t2/lang/baclava/BaclavaDocumentHandler.java | 133 --------
.../taverna/t2/lang/results/ResultsUtils.java | 329 -------------------
3 files changed, 516 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/c7cfb2ef/results/pom.xml
----------------------------------------------------------------------
diff --git a/results/pom.xml b/results/pom.xml
deleted file mode 100644
index 4db22ee..0000000
--- a/results/pom.xml
+++ /dev/null
@@ -1,54 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <groupId>net.sf.taverna.t2.lang</groupId>
- <artifactId>results</artifactId>
- <parent>
- <groupId>net.sf.taverna.t2</groupId>
- <artifactId>lang</artifactId>
- <version>1.6-SNAPSHOT</version>
- </parent>
- <name>Common Results handling utilities</name>
- <description>Common utilities for handling results, in particular Baclava document handling and de-referencing T2References</description>
- <dependencies>
- <dependency>
- <groupId>uk.org.mygrid.taverna.baclava</groupId>
- <artifactId>baclava-core</artifactId>
- <version>${taverna.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.mygrid.taverna.baclava</groupId>
- <artifactId>baclava-core</artifactId>
- <version>${taverna.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>reference-api</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>workflowmodel-api</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.mygrid.resources.mimeutil</groupId>
- <artifactId>mime-util</artifactId>
- <version>2.1.2-7-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>uk.org.mygrid.resources.clapper</groupId>
- <artifactId>ocutil</artifactId>
- <version>2.5.1</version>
- </dependency>
- <dependency>
- <groupId>log4j</groupId>
- <artifactId>log4j</artifactId>
- </dependency>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <scope>test</scope>
- </dependency>
- </dependencies>
-</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/c7cfb2ef/results/src/main/java/net/sf/taverna/t2/lang/baclava/BaclavaDocumentHandler.java
----------------------------------------------------------------------
diff --git a/results/src/main/java/net/sf/taverna/t2/lang/baclava/BaclavaDocumentHandler.java b/results/src/main/java/net/sf/taverna/t2/lang/baclava/BaclavaDocumentHandler.java
deleted file mode 100644
index 62dbe65..0000000
--- a/results/src/main/java/net/sf/taverna/t2/lang/baclava/BaclavaDocumentHandler.java
+++ /dev/null
@@ -1,133 +0,0 @@
-package net.sf.taverna.t2.lang.baclava;
-
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.PrintWriter;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.Map;
-
-import net.sf.taverna.t2.invocation.InvocationContext;
-import net.sf.taverna.t2.lang.results.ResultsUtils;
-import net.sf.taverna.t2.reference.ReferenceService;
-import net.sf.taverna.t2.reference.T2Reference;
-
-import org.embl.ebi.escience.baclava.DataThing;
-import org.embl.ebi.escience.baclava.factory.DataThingFactory;
-import org.embl.ebi.escience.baclava.factory.DataThingXMLFactory;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.Namespace;
-import org.jdom.input.SAXBuilder;
-import org.jdom.output.Format;
-import org.jdom.output.XMLOutputter;
-
-/**
- * Handles the loading and saving of T2Reference data as Baclava documents
- *
- * @author Stuart Owen
- *
- */
-
-public class BaclavaDocumentHandler {
-
- private Map<String, T2Reference> chosenReferences;
-
- private static Namespace namespace = Namespace.getNamespace("b",
- "http://org.embl.ebi.escience/baclava/0.1alpha");
-
- protected ReferenceService referenceService;
-
- protected InvocationContext context;
-
- // private static Logger logger =
- // Logger.getLogger(BaclavaDocumentHandler.class);
-
-
- /**
- * Reads a baclava document from an InputStream and returns a map of DataThings mapped to the portName
- *
- * @throws IOException, JDOMException
- */
- public Map<String, DataThing> readData(InputStream inputStream)
- throws IOException, JDOMException {
-
- SAXBuilder builder = new SAXBuilder();
- Document inputDoc;
- inputDoc = builder.build(inputStream);
-
- return DataThingXMLFactory.parseDataDocument(inputDoc);
- }
-
- /**
- * Saves the result data to an XML Baclava file.
- *
- * @throws IOException
- */
- public void saveData(File file) throws IOException {
- // Build the string containing the XML document from the result map
- Document doc = getDataDocument();
- XMLOutputter xo = new XMLOutputter(Format.getPrettyFormat());
- PrintWriter out = new PrintWriter(new FileWriter(file));
- xo.output(doc, out);
- }
-
- /**
- * Returns a org.jdom.Document from a map of port named to DataThingS
- * containing the port's results.
- */
- public Document getDataDocument() {
- Element rootElement = new Element("dataThingMap", namespace);
- Document theDocument = new Document(rootElement);
- // Build the DataThing map from the chosenReferences
- // First convert map of references to objects into a map of real result
- // objects
- for (String portName : getChosenReferences().keySet()) {
- DataThing thing = DataThingFactory.bake(getObjectForName(portName));
- Element dataThingElement = new Element("dataThing", namespace);
- dataThingElement.setAttribute("key", portName);
- dataThingElement.addContent(thing.getElement());
- rootElement.addContent(dataThingElement);
- }
- return theDocument;
- }
-
- /**
- * @param referenceService
- * the referenceService to set
- */
- public void setReferenceService(ReferenceService referenceService) {
- this.referenceService = referenceService;
- }
-
- /**
- * Sets the InvocationContext to be used to get the Reference Service to be
- * used dereference the reference.
- */
- public void setInvocationContext(InvocationContext context) {
- this.context = context;
- }
-
- protected Object getObjectForName(String name) {
- Object result = null;
- if (getChosenReferences().containsKey(name)) {
- result = ResultsUtils.convertReferenceToObject(
- getChosenReferences().get(name), referenceService, context);
- }
- if (result == null) {
- result = "null";
- }
- return result;
- }
-
- private Map<String, T2Reference> getChosenReferences() {
- return chosenReferences;
- }
-
- public void setChosenReferences(Map<String, T2Reference> chosenReferences) {
- this.chosenReferences = chosenReferences;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/c7cfb2ef/results/src/main/java/net/sf/taverna/t2/lang/results/ResultsUtils.java
----------------------------------------------------------------------
diff --git a/results/src/main/java/net/sf/taverna/t2/lang/results/ResultsUtils.java b/results/src/main/java/net/sf/taverna/t2/lang/results/ResultsUtils.java
deleted file mode 100644
index c99a646..0000000
--- a/results/src/main/java/net/sf/taverna/t2/lang/results/ResultsUtils.java
+++ /dev/null
@@ -1,329 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.lang.results;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-import java.util.Set;
-
-import javax.swing.tree.DefaultMutableTreeNode;
-
-import net.sf.taverna.t2.invocation.InvocationContext;
-import net.sf.taverna.t2.reference.ErrorDocument;
-import net.sf.taverna.t2.reference.ErrorDocumentService;
-import net.sf.taverna.t2.reference.ExternalReferenceSPI;
-import net.sf.taverna.t2.reference.IdentifiedList;
-import net.sf.taverna.t2.reference.ListService;
-import net.sf.taverna.t2.reference.ReferenceService;
-import net.sf.taverna.t2.reference.ReferenceServiceException;
-import net.sf.taverna.t2.reference.ReferenceSet;
-import net.sf.taverna.t2.reference.ReferencedDataNature;
-import net.sf.taverna.t2.reference.StackTraceElementBean;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.reference.T2ReferenceType;
-import net.sf.taverna.t2.reference.ValueCarryingExternalReference;
-
-import org.apache.log4j.Logger;
-import org.clapper.util.misc.MIMETypeUtil;
-
-import eu.medsea.mimeutil.MimeType;
-import eu.medsea.mimeutil.MimeUtil2;
-
-/**
- * Convenience methods for displaying and storing workflow run results. For
- * example, converting result error documents into various representations (e.g.
- * StringS or JTreeS), getting MIME type of result objects, etc.
- *
- * @author Alex Nenadic
- *
- */
-public class ResultsUtils {
-
- private static Logger logger = Logger.getLogger(ResultsUtils.class);
-
- /**
- * Converts a T2Reference pointing to results to
- * a list of (lists of ...) dereferenced result object.
- * @param context
- * @param referenceService
- */
- public static Object convertReferenceToObject(T2Reference reference, ReferenceService referenceService, InvocationContext context) {
-
- if (reference.getReferenceType() == T2ReferenceType.ReferenceSet){
-
- ReferenceSet rs = referenceService.getReferenceSetService().getReferenceSet(reference);
- if (rs == null) {
- throw new ReferenceServiceException("Could not find ReferenceSet " + reference);
- }
- // Check that there are references in the set
- if (rs.getExternalReferences().isEmpty()) {
- throw new ReferenceServiceException(
- "Can't render an empty reference set to a POJO");
- }
-
- ReferencedDataNature dataNature = ReferencedDataNature.UNKNOWN;
- for (ExternalReferenceSPI ers : rs.getExternalReferences()) {
- ReferencedDataNature erDataNature = ers.getDataNature();
- if (!erDataNature.equals(ReferencedDataNature.UNKNOWN)) {
- dataNature = erDataNature;
- break;
- }
- }
-
- // Dereference the object
- Object dataValue;
- try{
- if (dataNature.equals(ReferencedDataNature.TEXT)) {
- dataValue = referenceService.renderIdentifier(reference, String.class, context);
- } else {
- dataValue = referenceService.renderIdentifier(reference, byte[].class, context);
- }
- }
- catch(ReferenceServiceException rse){
- String message = "Problem rendering T2Reference in convertReferencesToObjects().";
- logger.error("BaclavaDocumentHandler Error: "+ message, rse);
- throw rse;
- }
- return dataValue;
- }
- else if (reference.getReferenceType() == T2ReferenceType.ErrorDocument){
- // Dereference the ErrorDocument and convert it to some string representation
- ErrorDocument errorDocument = (ErrorDocument)referenceService.resolveIdentifier(reference, null, context);
- String errorString = ResultsUtils.buildErrorDocumentString(errorDocument, context);
- return errorString;
- }
- else { // it is an IdentifiedList<T2Reference> - go recursively
- IdentifiedList<T2Reference> identifiedList = referenceService.getListService().getList(reference);
- List<Object> list = new ArrayList<Object>();
-
- for (int j=0; j<identifiedList.size(); j++){
- T2Reference ref = identifiedList.get(j);
- list.add(convertReferenceToObject(ref,referenceService,context));
- }
- return list;
- }
- }
-
- /**
- * Creates a string representation of the ErrorDocument.
- */
- public static String buildErrorDocumentString(ErrorDocument errDocument,
- InvocationContext context) {
-
- String errDocumentString = "";
-
- String message = errDocument.getMessage();
- if (message != null && !message.isEmpty()) {
- errDocumentString = message + "\n";
- }
-
- String exceptionMessage = errDocument.getExceptionMessage();
- if (exceptionMessage != null && !exceptionMessage.equals("")) {
- errDocumentString += exceptionMessage + "\n";
- List<StackTraceElementBean> stackTrace = errDocument
- .getStackTraceStrings();
- if (stackTrace.size() > 0) {
- for (StackTraceElementBean stackTraceElement : stackTrace) {
- errDocumentString += getStackTraceElementString(stackTraceElement)
- + "\n";
- }
- }
-
- }
-
- Set<T2Reference> errorReferences = errDocument.getErrorReferences();
- if (!errorReferences.isEmpty()) {
- errDocumentString += "Set of ErrorDocuments to follow." + "\n";
- }
- int errorCounter = 1;
- int listCounter = 0;
- for (T2Reference reference : errorReferences) {
- if (reference.getReferenceType().equals(
- T2ReferenceType.ErrorDocument)) {
- ErrorDocumentService errorDocumentService = context
- .getReferenceService().getErrorDocumentService();
- ErrorDocument causeErrorDocument = errorDocumentService
- .getError(reference);
- if (listCounter == 0) {
- errDocumentString += "ErrorDocument " + (errorCounter++)
- + "\n";
- } else {
- errDocumentString += "ErrorDocument " + listCounter + "."
- + (errorCounter++) + "\n";
- }
- errDocumentString += buildErrorDocumentString(
- causeErrorDocument, context)
- + "\n";
- } else if (reference.getReferenceType().equals(
- T2ReferenceType.IdentifiedList)) {
- List<ErrorDocument> errorDocuments = getErrorDocuments(
- reference, context.getReferenceService());
- errDocumentString += "ErrorDocument list " + (++listCounter)
- + "\n";
- for (ErrorDocument causeErrorDocument : errorDocuments) {
- errDocumentString += buildErrorDocumentString(
- causeErrorDocument, context)
- + "\n";
- }
- }
- }
-
- return errDocumentString;
- }
-
- public static void buildErrorDocumentTree(DefaultMutableTreeNode node,
- ErrorDocument errorDocument, ReferenceService referenceService) {
- DefaultMutableTreeNode child = new DefaultMutableTreeNode(errorDocument);
- String exceptionMessage = errorDocument.getExceptionMessage();
- if (exceptionMessage != null && !exceptionMessage.equals("")) {
- DefaultMutableTreeNode exceptionMessageNode = new DefaultMutableTreeNode(
- exceptionMessage);
- child.add(exceptionMessageNode);
- List<StackTraceElementBean> stackTrace = errorDocument
- .getStackTraceStrings();
- if (stackTrace.size() > 0) {
- for (StackTraceElementBean stackTraceElement : stackTrace) {
- exceptionMessageNode.add(new DefaultMutableTreeNode(
- getStackTraceElementString(stackTraceElement)));
- }
- }
-
- }
- node.add(child);
-
- Set<T2Reference> errorReferences = errorDocument.getErrorReferences();
- for (T2Reference reference : errorReferences) {
- if (reference.getReferenceType().equals(
- T2ReferenceType.ErrorDocument)) {
- ErrorDocumentService errorDocumentService = referenceService
- .getErrorDocumentService();
- ErrorDocument causeErrorDocument = errorDocumentService
- .getError(reference);
- if (errorReferences.size() == 1) {
- buildErrorDocumentTree(node, causeErrorDocument, referenceService);
- } else {
- buildErrorDocumentTree(child, causeErrorDocument, referenceService);
- }
- } else if (reference.getReferenceType().equals(
- T2ReferenceType.IdentifiedList)) {
- List<ErrorDocument> errorDocuments = getErrorDocuments(
- reference, referenceService);
- if (errorDocuments.size() == 1) {
- buildErrorDocumentTree(node, errorDocuments.get(0), referenceService);
- } else {
- for (ErrorDocument errorDocument2 : errorDocuments) {
- buildErrorDocumentTree(child, errorDocument2, referenceService);
- }
- }
- }
- }
- }
-
- private static String getStackTraceElementString(
- StackTraceElementBean stackTraceElement) {
- StringBuilder sb = new StringBuilder();
- sb.append(stackTraceElement.getClassName());
- sb.append('.');
- sb.append(stackTraceElement.getMethodName());
- if (stackTraceElement.getFileName() == null) {
- sb.append("(unknown file)");
- } else {
- sb.append('(');
- sb.append(stackTraceElement.getFileName());
- sb.append(':');
- sb.append(stackTraceElement.getLineNumber());
- sb.append(')');
- }
- return sb.toString();
- }
-
- public static List<ErrorDocument> getErrorDocuments(T2Reference reference,
- ReferenceService referenceService) {
- List<ErrorDocument> errorDocuments = new ArrayList<ErrorDocument>();
- if (reference.getReferenceType().equals(T2ReferenceType.ErrorDocument)) {
- ErrorDocumentService errorDocumentService = referenceService
- .getErrorDocumentService();
- errorDocuments.add(errorDocumentService.getError(reference));
- } else if (reference.getReferenceType().equals(
- T2ReferenceType.IdentifiedList)) {
- ListService listService = referenceService.getListService();
- IdentifiedList<T2Reference> list = listService.getList(reference);
- for (T2Reference listReference : list) {
- errorDocuments
- .addAll(getErrorDocuments(listReference, referenceService));
- }
- }
- return errorDocuments;
- }
-
- @SuppressWarnings("unchecked")
- public static List<MimeType> getMimeTypes(
- ExternalReferenceSPI externalReference, InvocationContext context) {
- List<MimeType> mimeList = new ArrayList<MimeType>();
- MimeUtil2 mimeUtil = new MimeUtil2();
- mimeUtil
- .registerMimeDetector("eu.medsea.mimeutil.detector.ExtensionMimeDetector");
- mimeUtil
- .registerMimeDetector("eu.medsea.mimeutil.detector.MagicMimeMimeDetector");
- mimeUtil
- .registerMimeDetector("eu.medsea.mimeutil.detector.WindowsRegistryMimeDetector");
- mimeUtil
- .registerMimeDetector("eu.medsea.mimeutil.detector.ExtraMimeTypes");
- InputStream inputStream = externalReference.openStream(context);
- try {
- byte[] bytes = new byte[2048]; // need to read this much if we want to detect SVG using the hack below
- inputStream.read(bytes);
- Collection mimeTypes2 = mimeUtil.getMimeTypes(bytes);
- mimeList.addAll(mimeTypes2);
-
- // Hack for SVG that seems not to be recognised
- String bytesString = new String(bytes, "UTF-8");
- if (bytesString.contains("http://www.w3.org/2000/svg")){
- MimeType svgMimeType = new MimeType("image/svg+xml");
- if (!mimeList.contains(svgMimeType)){
- mimeList.add(svgMimeType);
- }
- }
-
- } catch (IOException e) {
- logger.error("Failed to read from stream to determine mimetype", e);
- } finally {
- try {
- inputStream.close();
- } catch (IOException e) {
- logger.error(
- "Failed to close stream after determining mimetype", e);
- }
- }
-
- return mimeList;
- }
-
- public static String getExtension(String mimeType) {
-
- String mimeTypeForFileExtension = MIMETypeUtil
- .fileExtensionForMIMEType(mimeType);
- return mimeTypeForFileExtension;
- }
-}