Merge pull request #175 from common-workflow-language/permalinks-ui

stain · web-flow · commit 9929cfa54f25 · 2017-09-01T14:12:16.000+01:00
Show permalinks in HTML
diff --git a/src/main/java/org/commonwl/view/WebConfig.java b/src/main/java/org/commonwl/view/WebConfig.java
@@ -19,33 +19,48 @@
 
 package org.commonwl.view;
 
+import static org.springframework.http.MediaType.parseMediaType;
+
 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 {
 
+    /**
+     * Ordered list of formats as presented on Workflow page - must match the
+     * .mediaType() strings below.
+     *
+     */
+    public static enum formats {
+        html, json, turtle, jsonld, rdfxml, svg, png, dot, zip, ro, yaml, raw
+    }
+
     /**
      * 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)
+                // 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"))
-            .mediaType("zip", parseMediaType("application/zip"))
-            .mediaType("dot", parseMediaType("text/vnd+graphviz"))
+                // raw redirects
             .mediaType("yaml", parseMediaType("text/x-yaml"))
             .mediaType("raw", MediaType.APPLICATION_OCTET_STREAM);
     }
diff --git a/src/main/java/org/commonwl/view/researchobject/ROBundleService.java b/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) {
@@ -246,11 +253,13 @@ 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());
+                        String relativePath = gitFolder.resolve(file.getName()).toString();
+                        Path gitPath = bundlePath.getRoot().resolve(relativePath); // would start with /
+                        
                         // Get direct URL permalink
                         URI rawURI = new URI("https://w3id.org/cwl/view/git/" + workflow.getLastCommit() +
-                                "/" + gitPath + "?format=raw");
+                                gitPath + "?format=raw");
 
                         // Variable to store file contents and aggregation
                         String fileContent = null;
diff --git a/src/main/java/org/commonwl/view/workflow/Workflow.java b/src/main/java/org/commonwl/view/workflow/Workflow.java
@@ -19,8 +19,9 @@
 
 package org.commonwl.view.workflow;
 
-import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
-import com.fasterxml.jackson.annotation.JsonInclude;
+import java.util.Date;
+import java.util.Map;
+
 import org.commonwl.view.cwl.CWLElement;
 import org.commonwl.view.cwl.CWLStep;
 import org.commonwl.view.git.GitDetails;
@@ -29,8 +30,8 @@
 import org.springframework.data.mongodb.core.mapping.Document;
 import org.springframework.format.annotation.DateTimeFormat;
 
-import java.util.Date;
-import java.util.Map;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonInclude;
 
 /**
  * Representation of a workflow
@@ -223,4 +224,8 @@ public String getPermalink() {
         return getPermalink(null);
     }
 
+    public boolean isPacked() {
+        return retrievedFrom.getPackedId() != null;
+    }
+
 }
diff --git a/src/main/java/org/commonwl/view/workflow/WorkflowController.java b/src/main/java/org/commonwl/view/workflow/WorkflowController.java
@@ -19,7 +19,16 @@
 
 package org.commonwl.view.workflow;
 
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+import javax.validation.Valid;
+
 import org.apache.commons.lang.StringUtils;
+import org.commonwl.view.WebConfig;
 import org.commonwl.view.cwl.CWLToolStatus;
 import org.commonwl.view.git.GitDetails;
 import org.commonwl.view.graphviz.GraphVizService;
@@ -36,18 +45,15 @@
 import org.springframework.ui.Model;
 import org.springframework.validation.BeanPropertyBindingResult;
 import org.springframework.validation.BindingResult;
-import org.springframework.web.bind.annotation.*;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.PostMapping;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.ResponseBody;
 import org.springframework.web.servlet.HandlerMapping;
 import org.springframework.web.servlet.ModelAndView;
 import org.springframework.web.servlet.mvc.support.RedirectAttributes;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-import javax.validation.Valid;
-import java.io.File;
-import java.io.IOException;
-import java.util.List;
-
 @Controller
 public class WorkflowController {
 
@@ -58,15 +64,19 @@ public class WorkflowController {
     private final GraphVizService graphVizService;
 
     /**
-     * Autowired constructor to initialise objects used by the controller
-     * @param workflowFormValidator Validator to validate the workflow form
-     * @param workflowService Builds new Workflow objects
-     * @param graphVizService Generates and stores imagess
+     * Autowired constructor to initialise objects used by the controller.
+     * 
+     * @param workflowFormValidator
+     *            Validator to validate the workflow form
+     * @param workflowService
+     *            Builds new Workflow objects
+     * @param graphVizService
+     *            Generates and stores images
      */
     @Autowired
     public WorkflowController(WorkflowFormValidator workflowFormValidator,
                               WorkflowService workflowService,
-                              GraphVizService graphVizService) {
+            GraphVizService graphVizService) {
         this.workflowFormValidator = workflowFormValidator;
         this.workflowService = workflowService;
         this.graphVizService = graphVizService;
@@ -532,7 +542,8 @@ private ModelAndView getWorkflow(GitDetails gitDetails, RedirectAttributes redir
             }
             return new ModelAndView("loading", "queued", queued);
         } else {
-            return new ModelAndView("workflow", "workflow", workflowModel);
+            return new ModelAndView("workflow", "workflow", workflowModel).addObject("formats",
+                    WebConfig.formats.values());
         }
     }
 }
diff --git a/src/main/resources/static/css/main-20170616.css b/src/main/resources/static/css/main-20170616.css
@@ -287,3 +287,42 @@ polygon.hover {
     font-style: italic;
     margin-bottom: 30px;
 }
+
+@media screen {
+	.permalink {
+		overflow: hidden;
+		text-overflow: ellipsis;
+	}
+}
+
+.help {
+	color: #9af;
+}
+
+@media print {
+	.help {
+		display: none !important;
+	}
+}
+
+#permalink {
+	font-size: smaller;
+	font-family: Consolas, Inconsolata, monospace;
+
+    overflow: hidden;
+    white-space: nowrap;
+}
+
+/**
+ * Already showing HTML
+ */
+#format-html { 
+	display: none;
+}
+/**
+ * Workaround (not really) for
+ * https://github.com/common-workflow-language/cwlviewer/issues/166
+ */
+#format-json { 
+	display: none;
+}
diff --git a/src/main/resources/static/img/workflow-compile.svg b/src/main/resources/static/img/workflow-compile.svg
diff --git a/src/main/resources/templates/workflow.html b/src/main/resources/templates/workflow.html
