Fix resolution of relative URIs

Author: MarkRobbo

src/main/java/org/commonwl/view/cwl/CWLService.java

@@ -185,7 +185,7 @@ public Workflow parseWorkflowWithCwltool(GitDetails gitDetails,
                                              File workflowFile,
                                              String packedWorkflowID) throws CWLValidationException {
 
-        // Get RDF representation from cwltool
+        // Get paths to workflow
         String url = gitDetails.getUrl().replace("https://", "");
         String localPath = workflowFile.toPath().toAbsolutePath().toString();
         String gitPath = gitDetails.getPath();
@@ -200,6 +200,7 @@ public Workflow parseWorkflowWithCwltool(GitDetails gitDetails,
             gitPath += packedWorkflowID;
         }
 
+        // Get RDF representation from cwltool
         if (!rdfService.graphExists(url)) {
             String rdf = cwlTool.getRDF(localPath);
 
@@ -368,7 +369,7 @@ public Workflow parseWorkflowWithCwltool(GitDetails gitDetails,
                 // Add new step
                 CWLStep wfStep = new CWLStep();
 
-                Path workflowPath = Paths.get(FilenameUtils.getPath(url));
+                Path workflowPath = Paths.get(step.get("wf").toString()).getParent();
                 Path runPath = Paths.get(step.get("run").toString());
                 wfStep.setRun(workflowPath.relativize(runPath).toString());
                 wfStep.setRunType(rdfService.strToRuntype(step.get("runtype").toString()));

src/main/java/org/commonwl/view/cwl/RDFService.java

@@ -204,7 +204,7 @@ public ResultSet getOutputs(String path, String workflowURI) {
     public ResultSet getSteps(String path, String workflowURI) {
         ParameterizedSparqlString stepQuery = new ParameterizedSparqlString();
         stepQuery.setCommandText(queryCtx +
-                "SELECT ?step ?run ?runtype ?label ?doc ?stepinput ?default ?src\n" +
+                "SELECT ?wf ?step ?run ?runtype ?label ?doc ?stepinput ?default ?src\n" +
                 "WHERE {\n" +
                 "  GRAPH ?graphName {" +
                 "    ?wf Workflow:steps ?step .\n" +
@@ -232,7 +232,7 @@ public ResultSet getSteps(String path, String workflowURI) {
     public ResultSet getStepLinks(String path, String workflowURI) {
         ParameterizedSparqlString linkQuery = new ParameterizedSparqlString();
         linkQuery.setCommandText(queryCtx +
-                "SELECT ?src ?dest ?default\n" +
+                "SELECT ?wf ?src ?dest ?default\n" +
                 "WHERE {\n" +
                 "  GRAPH ?graphName {" +
                 "    ?wf Workflow:steps ?step .\n" +

src/main/java/org/commonwl/view/graphviz/RDFDotWriter.java

@@ -19,7 +19,6 @@
 
 package org.commonwl.view.graphviz;
 
-import org.apache.commons.io.FilenameUtils;
 import org.apache.jena.query.QuerySolution;
 import org.apache.jena.query.ResultSet;
 import org.commonwl.view.cwl.CWLProcess;
@@ -175,7 +174,7 @@ private void writeStepLinks(String workflowUri) throws IOException {
                 if (stepLink.get("default").isLiteral()) {
                     label = rdfService.formatDefault(stepLink.get("default").toString());
                 } else if (stepLink.get("default").isURIResource()) {
-                    Path workflowPath = Paths.get(FilenameUtils.getPath(workflowUri));
+                    Path workflowPath = Paths.get(stepLink.get("wf").toString()).getParent();
                     Path resourcePath = Paths.get(stepLink.get("default").toString());
                     label = workflowPath.relativize(resourcePath).toString();
                 } else {