Windows compatibility, use bundle:// paths instead of file://

as bundle always uses / separator

Author: stain

src/main/java/org/commonwl/view/researchobject/ROBundleService.java

@@ -19,13 +19,33 @@
 
 package org.commonwl.view.researchobject;
 
+import static org.apache.commons.io.FileUtils.readFileToString;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.FilenameUtils;
 import org.apache.jena.query.QuerySolution;
 import org.apache.jena.query.ResultSet;
 import org.apache.taverna.robundle.Bundle;
 import org.apache.taverna.robundle.Bundles;
-import org.apache.taverna.robundle.manifest.*;
+import org.apache.taverna.robundle.manifest.Agent;
+import org.apache.taverna.robundle.manifest.Manifest;
+import org.apache.taverna.robundle.manifest.PathAnnotation;
+import org.apache.taverna.robundle.manifest.PathMetadata;
+import org.apache.taverna.robundle.manifest.Proxy;
 import org.commonwl.view.cwl.CWLTool;
 import org.commonwl.view.cwl.CWLValidationException;
 import org.commonwl.view.cwl.RDFService;
@@ -42,22 +62,6 @@
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Service;
 
-import java.io.File;
-import java.io.IOException;
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import static org.apache.commons.io.FileUtils.readFileToString;
-
 /**
  * Service handling Research Object Bundles
  */
@@ -197,8 +201,11 @@ public Bundle createBundle(Workflow workflow, GitDetails gitInfo) throws IOExcep
 
             // Git2prov history
             List<Path> history = new ArrayList<>();
-            history.add(Paths.get("http://git2prov.org/git2prov?giturl=" +
-                    gitInfo.getRepoUrl() + "&serialization=PROV-JSON"));
+            // FIXME: Below is a a hack to pretend the URI is a Path
+            String git2prov = "http://git2prov.org/git2prov?giturl=" + gitInfo.getRepoUrl()
+                    + "&serialization=PROV-JSON";
+            Path git2ProvPath = bundle.getRoot().relativize(bundle.getRoot().resolve(git2prov));
+            history.add(git2ProvPath);
             bundle.getManifest().setHistory(history);
 
         } catch (URISyntaxException ex) {
@@ -246,8 +253,9 @@ private void addFilesToBundle(GitDetails gitDetails, Bundle bundle, Path bundleP
                     try {
                         // Where to store the new file
                         Path bundleFilePath = bundlePath.resolve(file.getName());
-                        Path gitPath = Paths.get(gitDetails.getPath()).resolve(file.getName());
-
+                        Path gitFolder = Paths.get(gitDetails.getPath());
+                        Path gitPath = bundlePath.getRoot().resolve(gitFolder.resolve(file.getName()));
+                        
                         // Get direct URL permalink
                         URI rawURI = new URI("https://w3id.org/cwl/view/git/" + workflow.getLastCommit() +
                                 "/" + gitPath + "?format=raw");