Merge pull request #158 from common-workflow-language/rdf-permalinks

Consistent RDF permalinks with content negotiation

Author: stain

pom.xml

@@ -93,6 +93,11 @@
             <artifactId>jena-osgi</artifactId>
             <version>3.3.0</version>
         </dependency>
+        <dependency>
+            <groupId>com.github.jsonld-java</groupId>
+            <artifactId>jsonld-java</artifactId>
+            <version>0.9.0</version>
+        </dependency>
         <dependency>
             <groupId>org.eclipse.jgit</groupId>
             <artifactId>org.eclipse.jgit</artifactId>

src/main/java/org/commonwl/view/GlobalControllerErrorHandling.java

@@ -0,0 +1,61 @@
+/*
+ * 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.commonwl.view;
+
+import org.commonwl.view.workflow.RepresentationNotFoundException;
+import org.commonwl.view.workflow.WorkflowNotFoundException;
+import org.springframework.http.HttpHeaders;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.ControllerAdvice;
+import org.springframework.web.bind.annotation.ExceptionHandler;
+
+/**
+ * Handles exception handling across the application
+ */
+@ControllerAdvice
+public class GlobalControllerErrorHandling {
+
+    /**
+     * Workflow can not be found
+     * @return A plain text error message
+     */
+    @ExceptionHandler(WorkflowNotFoundException.class)
+    public ResponseEntity<?> handleNotFound() {
+        final HttpHeaders headers = new HttpHeaders();
+        headers.setContentType(MediaType.TEXT_PLAIN);
+        return new ResponseEntity<>("Workflow could not be found", headers, HttpStatus.NOT_FOUND);
+    }
+
+    /**
+     * Workflow exists but representation is not found
+     * eg Generic git workflow asking for raw workflow URL
+     * @return A plain text error message
+     */
+    @ExceptionHandler(RepresentationNotFoundException.class)
+    public ResponseEntity<?> handleNoRepresentation() {
+        final HttpHeaders headers = new HttpHeaders();
+        headers.setContentType(MediaType.TEXT_PLAIN);
+        return new ResponseEntity<>("The workflow exists but the requested representation could not be found",
+                headers, HttpStatus.NOT_FOUND);
+    }
+
+}

src/main/java/org/commonwl/view/WebConfig.java

@@ -0,0 +1,52 @@
+/*
+ * 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.commonwl.view;
+
+import org.springframework.context.annotation.Configuration;
+import org.springframework.http.MediaType;
+import org.springframework.web.servlet.config.annotation.ContentNegotiationConfigurer;
+import org.springframework.web.servlet.config.annotation.WebMvcConfigurerAdapter;
+
+import static org.springframework.http.MediaType.parseMediaType;
+
+@Configuration
+public class WebConfig extends WebMvcConfigurerAdapter {
+
+    /**
+     * Allows the use of the format query parameter to be used
+     * instead of the Accept HTTP header
+     */
+    @Override
+    public void configureContentNegotiation(ContentNegotiationConfigurer configurer) {
+        configurer.favorParameter(true)
+            .mediaType("html", MediaType.TEXT_HTML)
+            .mediaType("json", MediaType.APPLICATION_JSON)
+            .mediaType("turtle", parseMediaType("text/turtle"))
+            .mediaType("jsonld", parseMediaType("application/ld+json"))
+            .mediaType("rdfxml", parseMediaType("application/rdf+xml"))
+            .mediaType("svg", parseMediaType("image/svg+xml"))
+            .mediaType("png", MediaType.IMAGE_PNG)
+            .mediaType("ro", parseMediaType("application/vnd.wf4ever.robundle+zip"))
+            .mediaType("zip", parseMediaType("application/zip"))
+            .mediaType("dot", parseMediaType("text/vnd+graphviz"))
+            .mediaType("yaml", parseMediaType("text/x-yaml"))
+            .mediaType("raw", MediaType.APPLICATION_OCTET_STREAM);
+    }
+}

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

@@ -52,6 +52,8 @@
 import java.io.File;
 import java.io.IOException;
 import java.io.StringWriter;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.*;
 
 import static org.apache.commons.io.FileUtils.readFileToString;
@@ -161,14 +163,14 @@ public List<WorkflowOverview> getWorkflowOverviewsFromPacked(File packedFile) th
      * @param packedWorkflowId The ID of the workflow object if the file is packed
      * @return The constructed workflow object
      */
-    public Workflow parseWorkflowNative(File workflowFile, String packedWorkflowId) throws IOException {
+    public Workflow parseWorkflowNative(Path workflowFile, String packedWorkflowId) throws IOException {
 
         // Check file size limit before parsing
-        long fileSizeBytes = workflowFile.length();
+        long fileSizeBytes = Files.size(workflowFile);
         if (fileSizeBytes <= singleFileSizeLimit) {
 
             // Parse file as yaml
-            JsonNode cwlFile = yamlStringToJson(readFileToString(workflowFile));
+            JsonNode cwlFile = yamlStringToJson(readFileToString(workflowFile.toFile()));
 
             // Check packed workflow occurs
             if (packedWorkflowId != null) {
@@ -199,7 +201,7 @@ public Workflow parseWorkflowNative(File workflowFile, String packedWorkflowId)
             // Use filename for label if there is no defined one
             String label = extractLabel(cwlFile);
             if (label == null) {
-                label = FilenameUtils.getName(workflowFile.getPath());
+                label = workflowFile.getFileName().toString();
             }
 
             // Construct the rest of the workflow model
@@ -221,7 +223,7 @@ public Workflow parseWorkflowNative(File workflowFile, String packedWorkflowId)
             return workflowModel;
 
         } else {
-            throw new IOException("File '" + workflowFile.getName() +  "' is over singleFileSizeLimit - " +
+            throw new IOException("File '" + workflowFile.getFileName() +  "' is over singleFileSizeLimit - " +
                     FileUtils.byteCountToDisplaySize(fileSizeBytes) + "/" +
                     FileUtils.byteCountToDisplaySize(singleFileSizeLimit));
         }
@@ -235,29 +237,32 @@ public Workflow parseWorkflowNative(File workflowFile, String packedWorkflowId)
      * @return The constructed workflow object
      */
     public Workflow parseWorkflowWithCwltool(Workflow basicModel,
-                                             File workflowFile) throws CWLValidationException {
+                                             Path workflowFile,
+                                             Path workTree) throws CWLValidationException {
         GitDetails gitDetails = basicModel.getRetrievedFrom();
         String latestCommit = basicModel.getLastCommit();
         String packedWorkflowID = gitDetails.getPackedId();
 
         // Get paths to workflow
-        String url = gitDetails.getUrl(latestCommit).replace("https://", "");
-        String localPath = workflowFile.toPath().toAbsolutePath().toString();
+        String url = basicModel.getPermalink();
+        String localPath = workflowFile.toAbsolutePath().toString();
         String gitPath = gitDetails.getPath();
         if (packedWorkflowID != null) {
             if (packedWorkflowID.charAt(0) != '#') {
                 localPath += "#";
-                url += "#";
                 gitPath += "#";
             }
             localPath += packedWorkflowID;
-            url += packedWorkflowID;
             gitPath += packedWorkflowID;
         }
 
         // Get RDF representation from cwltool
         if (!rdfService.graphExists(url)) {
             String rdf = cwlTool.getRDF(localPath);
+            rdf = rdf.replace("file://" + workTree.toAbsolutePath().toString(),
+                    "https://w3id.org/cwl/view/git/" + latestCommit);
+            // Workaround for common-workflow-language/cwltool#427
+            rdf = rdf.replace("<rdfs:>", "<http://www.w3.org/2000/01/rdf-schema#>");
 
             // Create a workflow model from RDF representation
             Model model = ModelFactory.createDefaultModel();
@@ -270,7 +275,7 @@ public Workflow parseWorkflowWithCwltool(Workflow basicModel,
         // Base workflow details
         String label = FilenameUtils.getName(url);
         String doc = null;
-        ResultSet labelAndDoc = rdfService.getLabelAndDoc(gitPath, url);
+        ResultSet labelAndDoc = rdfService.getLabelAndDoc(url);
         if (labelAndDoc.hasNext()) {
             QuerySolution labelAndDocSoln = labelAndDoc.nextSolution();
             if (labelAndDocSoln.contains("label")) {
@@ -283,7 +288,7 @@ public Workflow parseWorkflowWithCwltool(Workflow basicModel,
 
         // Inputs
         Map<String, CWLElement> wfInputs = new HashMap<>();
-        ResultSet inputs = rdfService.getInputs(gitPath, url);
+        ResultSet inputs = rdfService.getInputs(url);
         while (inputs.hasNext()) {
             QuerySolution input = inputs.nextSolution();
             String inputName = rdfService.stepNameFromURI(gitPath, input.get("name").toString());
@@ -316,7 +321,7 @@ public Workflow parseWorkflowWithCwltool(Workflow basicModel,
 
         // Outputs
         Map<String, CWLElement> wfOutputs = new HashMap<>();
-        ResultSet outputs = rdfService.getOutputs(gitPath, url);
+        ResultSet outputs = rdfService.getOutputs(url);
         while (outputs.hasNext()) {
             QuerySolution output = outputs.nextSolution();
             CWLElement wfOutput = new CWLElement();
@@ -355,7 +360,7 @@ public Workflow parseWorkflowWithCwltool(Workflow basicModel,
 
         // Steps
         Map<String, CWLStep> wfSteps = new HashMap<>();
-        ResultSet steps = rdfService.getSteps(gitPath, url);
+        ResultSet steps = rdfService.getSteps(url);
         while (steps.hasNext()) {
             QuerySolution step = steps.nextSolution();
             String uri = rdfService.stepNameFromURI(gitPath, step.get("step").toString());
@@ -376,9 +381,7 @@ public Workflow parseWorkflowWithCwltool(Workflow basicModel,
                 // Add new step
                 CWLStep wfStep = new CWLStep();
 
-                IRI wfStepUri = iriFactory.construct(step.get("wf").asResource().getURI());
-                IRI workflowPath = wfStepUri.resolve("./");
-
+                IRI workflowPath = iriFactory.construct(url).resolve("./");
                 IRI runPath = iriFactory.construct(step.get("run").asResource().getURI());
                 wfStep.setRun(workflowPath.relativize(runPath).toString());
                 wfStep.setRunType(rdfService.strToRuntype(step.get("runtype").toString()));
@@ -409,7 +412,7 @@ public Workflow parseWorkflowWithCwltool(Workflow basicModel,
         }
 
         // Docker link
-        ResultSet dockerResult = rdfService.getDockerLink(gitPath, url);
+        ResultSet dockerResult = rdfService.getDockerLink(url);
         String dockerLink = null;
         if (dockerResult.hasNext()) {
             QuerySolution docker = dockerResult.nextSolution();

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

@@ -19,10 +19,6 @@
 
 package org.commonwl.view.cwl;
 
-import java.io.IOException;
-import java.nio.file.Path;
-import java.util.Date;
-
 import org.apache.jena.query.QueryException;
 import org.commonwl.view.git.GitDetails;
 import org.commonwl.view.git.GitSemaphore;
@@ -40,6 +36,10 @@
 import org.springframework.scheduling.annotation.EnableAsync;
 import org.springframework.stereotype.Component;
 
+import java.io.IOException;
+import java.nio.file.Path;
+import java.util.Date;
+
 /**
  * Replace existing workflow with the one given by cwltool
  */
@@ -85,7 +85,8 @@ public void createWorkflowFromQueued(QueuedWorkflow queuedWorkflow)
             Path workflowFile = localPath.resolve(gitInfo.getPath()).normalize().toAbsolutePath();
             Workflow newWorkflow = cwlService.parseWorkflowWithCwltool(
                     tempWorkflow,
-                    workflowFile.toFile());
+                    workflowFile,
+                    localPath);
 
             // Success
             newWorkflow.setRetrievedFrom(tempWorkflow.getRetrievedFrom());