Merge branch 'master' into ui-tweaks

Author: stain

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

@@ -19,6 +19,9 @@
 
 package org.commonwl.view;
 
+import java.util.Collections;
+
+import org.commonwl.view.workflow.MultipleWorkflowsException;
 import org.commonwl.view.workflow.RepresentationNotFoundException;
 import org.commonwl.view.workflow.WorkflowNotFoundException;
 import org.springframework.http.HttpHeaders;
@@ -29,7 +32,12 @@
 import org.springframework.web.bind.annotation.ExceptionHandler;
 
 /**
- * Handles exception handling across the application
+ * Handles exception handling across the application.
+ * <p>
+ * Because of Spring Boot's content negotiation these handlers are needed when
+ * the error is returned with an otherwise "non acceptable" content type (e.g.
+ * Accept: image/svg+xml but we have to say 404 Not Found)
+ *
  */
 @ControllerAdvice
 public class GlobalControllerErrorHandling {
@@ -42,20 +50,34 @@ public class GlobalControllerErrorHandling {
     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);
+        return new ResponseEntity<>("Workflow or git commit could not be found", headers, HttpStatus.NOT_FOUND);
+    }
+
+    /**
+     * More than one workflow (or workflow parts) found
+     *
+     * @return A text/uri-list of potential representations
+     */
+    @ExceptionHandler(MultipleWorkflowsException.class)
+    public ResponseEntity<?> handleMultipleWorkflows(MultipleWorkflowsException ex) {
+        final HttpHeaders headers = new HttpHeaders();
+        headers.setContentType(MediaType.parseMediaType("text/uri-list"));
+        return new ResponseEntity<>(ex.toString(), headers, HttpStatus.MULTIPLE_CHOICES);
     }
 
     /**
-     * Workflow exists but representation is not found
-     * eg Generic git workflow asking for raw workflow URL
+     * 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.setVary(Collections.singletonList("Accept"));
         headers.setContentType(MediaType.TEXT_PLAIN);
         return new ResponseEntity<>("The workflow exists but the requested representation could not be found",
-                headers, HttpStatus.NOT_FOUND);
+                headers, HttpStatus.NOT_ACCEPTABLE);
     }
 
 }

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

@@ -21,6 +21,8 @@
 
 import static org.springframework.http.MediaType.parseMediaType;
 
+import org.commonwl.view.workflow.Workflow;
+import org.commonwl.view.workflow.WorkflowPermalinkController;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.http.MediaType;
 import org.springframework.web.servlet.config.annotation.ContentNegotiationConfigurer;
@@ -31,39 +33,52 @@
 public class WebConfig extends WebMvcConfigurerAdapter {
 
     /**
-     * Ordered list of formats as presented on Workflow page - must match the
-     * .mediaType() strings below.
+     * Ordered list of formats as presented on Workflow page and supported for
+     * content negotiation.
+     * 
+     * @see Workflow#getPermalink(Format)
+     * @see WorkflowPermalinkController
      *
      */
-    public static enum formats {
-        html, json, turtle, jsonld, rdfxml, svg, png, dot, zip, ro, yaml, raw
+    public static enum Format {
+        // Browser
+        html(MediaType.TEXT_HTML),
+        // API
+        json(MediaType.APPLICATION_JSON),
+        // RDF
+        turtle("text/turtle"), jsonld("application/ld+json"), rdfxml("application/rdf+xml"),
+        // Images
+        svg("image/svg+xml"), png(MediaType.IMAGE_PNG), dot("text/vnd+graphviz"),
+        // Archives
+        zip("application/zip"), ro("application/vnd.wf4ever.robundle+zip"),
+        // raw redirects
+        yaml("text/x-yaml"), raw(MediaType.APPLICATION_OCTET_STREAM);
+
+        private final MediaType mediaType;
+
+        Format(MediaType mediaType) {
+            this.mediaType = mediaType;
+        }
+
+        Format(String mediaType) {
+            this.mediaType = parseMediaType(mediaType);
+        }
+
+        public MediaType mediaType() {
+            return mediaType;
+        }
     }
 
     /**
-     * Allows the use of the format query parameter to be used
-     * instead of the Accept HTTP header
+     * 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)
-                // Browser
-                .mediaType("html", MediaType.TEXT_HTML)
-                // API
-            .mediaType("json", MediaType.APPLICATION_JSON)
-                // RDF
-            .mediaType("turtle", parseMediaType("text/turtle"))
-            .mediaType("jsonld", parseMediaType("application/ld+json"))
-            .mediaType("rdfxml", parseMediaType("application/rdf+xml"))
-                // Images
-            .mediaType("svg", parseMediaType("image/svg+xml"))
-            .mediaType("png", MediaType.IMAGE_PNG)
-                .mediaType("dot", parseMediaType("text/vnd+graphviz"))
-                // Archives
-                .mediaType("zip", parseMediaType("application/zip"))
-            .mediaType("ro", parseMediaType("application/vnd.wf4ever.robundle+zip"))
-                // raw redirects
-            .mediaType("yaml", parseMediaType("text/x-yaml"))
-            .mediaType("raw", MediaType.APPLICATION_OCTET_STREAM);
+        ContentNegotiationConfigurer c = configurer.favorParameter(true);
+        for (Format f : Format.values()) {
+            c = c.mediaType(f.name(), f.mediaType());
+        }
     }
 
     @Override

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

@@ -19,11 +19,20 @@
 
 package org.commonwl.view.cwl;
 
-import com.fasterxml.jackson.databind.JsonNode;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.databind.node.ArrayNode;
-import com.fasterxml.jackson.databind.node.ObjectNode;
-import com.fasterxml.jackson.databind.node.TextNode;
+import static org.apache.commons.io.FileUtils.readFileToString;
+
+import java.io.ByteArrayInputStream;
+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.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.FilenameUtils;
 import org.apache.jena.iri.IRI;
@@ -48,15 +57,11 @@
 import org.springframework.stereotype.Service;
 import org.yaml.snakeyaml.Yaml;
 
-import java.io.ByteArrayInputStream;
-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;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+import com.fasterxml.jackson.databind.node.TextNode;
 
 /**
  * Provides CWL parsing for workflows to gather an overview
@@ -244,8 +249,10 @@ public Workflow parseWorkflowWithCwltool(Workflow basicModel,
         String packedWorkflowID = gitDetails.getPackedId();
 
         // Get paths to workflow
-        String url = basicModel.getPermalink();
-        String localPath = workflowFile.toAbsolutePath().toString();
+        String url = basicModel.getIdentifier();
+        String workflowFileURI = workflowFile.toAbsolutePath().toUri().toString();
+        String workTreeUri = workTree.toAbsolutePath().toUri().toString();
+		String localPath = workflowFileURI;
         String gitPath = gitDetails.getPath();
         if (packedWorkflowID != null) {
             if (packedWorkflowID.charAt(0) != '#') {
@@ -259,8 +266,10 @@ public Workflow parseWorkflowWithCwltool(Workflow basicModel,
         // 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);
+            // Replace /tmp/123123 with permalink base 
+            // NOTE: We do not just replace workflowFileURI, all referenced files will also get rewritten
+			rdf = rdf.replace(workTreeUri,
+                    "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#>");
 

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

@@ -46,6 +46,7 @@
 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.WebConfig.Format;
 import org.commonwl.view.cwl.CWLTool;
 import org.commonwl.view.cwl.CWLValidationException;
 import org.commonwl.view.cwl.RDFService;
@@ -137,7 +138,7 @@ public Bundle createBundle(Workflow workflow, GitDetails gitInfo) throws IOExcep
             // TODO: Make this importedBy/On/From
             manifest.setRetrievedBy(appAgent);
             manifest.setRetrievedOn(manifest.getCreatedOn());
-            manifest.setRetrievedFrom(new URI(workflow.getPermalink("ro")));
+            manifest.setRetrievedFrom(new URI(workflow.getPermalink(Format.ro)));
 
             // Make a directory in the RO bundle to store the files
             Path bundleRoot = bundle.getRoot();
@@ -164,12 +165,12 @@ public Bundle createBundle(Workflow workflow, GitDetails gitInfo) throws IOExcep
             File png = graphVizService.getGraph(workflow.getID() + ".png", workflow.getVisualisationDot(), "png");
             Files.copy(png.toPath(), bundleRoot.resolve("visualisation.png"));
             PathMetadata pngAggr = bundle.getManifest().getAggregation(bundleRoot.resolve("visualisation.png"));
-            pngAggr.setRetrievedFrom(new URI(workflow.getPermalink("png")));
+            pngAggr.setRetrievedFrom(new URI(workflow.getPermalink(Format.png)));
 
             File svg = graphVizService.getGraph(workflow.getID() + ".svg", workflow.getVisualisationDot(), "svg");
             Files.copy(svg.toPath(), bundleRoot.resolve("visualisation.svg"));
             PathMetadata svgAggr = bundle.getManifest().getAggregation(bundleRoot.resolve("visualisation.svg"));
-            svgAggr.setRetrievedFrom(new URI(workflow.getPermalink("svg")));
+            svgAggr.setRetrievedFrom(new URI(workflow.getPermalink(Format.svg)));
 
             // Add annotation files
             GitDetails wfDetails = workflow.getRetrievedFrom();
@@ -192,7 +193,7 @@ public Bundle createBundle(Workflow workflow, GitDetails gitInfo) throws IOExcep
             } catch (CWLValidationException ex) {
                 logger.error("Could not pack workflow when creating Research Object", ex.getMessage());
             }
-            String rdfUrl = workflow.getPermalink();
+            String rdfUrl = workflow.getIdentifier();
             if (rdfService.graphExists(rdfUrl)) {
                 addAggregation(bundle, manifestAnnotations, "workflow.ttl",
                         new String(rdfService.getModel(rdfUrl, "TURTLE")));
@@ -314,7 +315,7 @@ private void addFilesToBundle(GitDetails gitDetails, Bundle bundle, Path bundleP
                                 // Attempt to get authors from cwl description - takes priority
                                 ResultSet descAuthors = rdfService.getAuthors(bundlePath
                                         .resolve(file.getName()).toString().substring(10),
-                                        workflow.getPermalink());
+                                        workflow.getIdentifier());
                                 if (descAuthors.hasNext()) {
                                     QuerySolution authorSoln = descAuthors.nextSolution();
                                     HashableAgent newAuthor = new HashableAgent();

src/main/java/org/commonwl/view/workflow/MultipleWorkflowsException.java

@@ -0,0 +1,104 @@
+/*
+ * 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.workflow;
+
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.commonwl.view.WebConfig.Format;
+import org.springframework.http.HttpStatus;
+import org.springframework.web.bind.annotation.ResponseStatus;
+
+/**
+ * Exception thrown when multiple workflows exist for the request
+ */
+@ResponseStatus(value = HttpStatus.MULTIPLE_CHOICES)
+public class MultipleWorkflowsException extends RuntimeException {
+
+    private final Collection<Workflow> matches;
+
+    public MultipleWorkflowsException(Workflow match) {
+        this(Collections.singleton(match));
+    }
+
+    public MultipleWorkflowsException(Collection<Workflow> matches) {
+        if (matches.isEmpty()) {
+            throw new IllegalArgumentException("MultipleWorkflowsException, but empty list of workflows");
+        }
+        this.matches = matches;
+    }
+
+    // Always CRLF in text/uri-list
+    private final String CRLF = "\r\n";
+
+    public String getRawPermalink() {
+        // all raw URIs should be the same without ?part=
+        return matches.stream().findAny().get().getPermalink(Format.raw);
+    }
+
+    /**
+     * Generate a text/uri-list of potential representations/redirects
+     * 
+     * @see https://www.iana.org/assignments/media-types/text/uri-list
+     */
+    @Override
+    public String toString() {
+        StringBuffer sb = new StringBuffer();
+        sb.append("## Multiple workflow representations found");
+        sb.append(CRLF);
+        sb.append("# ");
+        sb.append(CRLF);
+
+        sb.append("# ");
+        sb.append(Format.raw.mediaType());
+        sb.append(CRLF);
+        sb.append(getRawPermalink());
+        sb.append(CRLF);
+
+        Set<String> seen = new HashSet<>();
+        // For each workflow, link to each remaining format
+        for (Workflow w : matches) {
+            if (!seen.add(w.getIdentifier())) {
+                // Skip permalink duplicates
+                continue;
+            }
+            sb.append("#");
+            sb.append(CRLF);
+            sb.append("# ");
+            sb.append(w.getIdentifier());
+            sb.append(CRLF);
+            for (Format f : Format.values()) {
+                if (f == Format.raw) {
+                    // Already did that one above
+                    continue;
+                }
+                sb.append("#   ");
+                sb.append(f.mediaType());
+                sb.append(CRLF);
+                sb.append(w.getPermalink(f));
+                sb.append(CRLF);
+            }
+        }
+        return sb.toString();
+    }
+
+}