Merge branch 'master' into permalinks-packed

Author: stain

Dockerfile

@@ -44,5 +44,5 @@ RUN mvn clean package -DskipTests && cp target/cwlviewer-*.jar /usr/lib/cwlviewe
 WORKDIR /tmp
 
 EXPOSE 8080
-
+ENV LC_ALL C.UTF-8
 CMD ["/usr/bin/java", "-jar", "/usr/lib/cwlviewer.jar"]

NOTICE.md

@@ -1,8 +1,8 @@
 # CWL Viewer
 https://github.com/common-workflow-language/cwlviewer/
 
-* Copyright (c) 2016-2017 Mark Robinson http://orcid.org/0000-0002-8184-7507
-* Copyright (c) 2016-2017 The University of Manchester
+* Copyright (c) 2016-2017 Mark Robinson https://orcid.org/0000-0002-8184-7507
+* Copyright (c) 2016-2018 The University of Manchester
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
@@ -32,8 +32,7 @@ This logo may be used only for attribution within the CWL Viewer project.
 img/BioExcel_logo_cropped.svg
 http://bioexcel.eu/
 
-Distributed under a Creative Commons Attribution 4.0 license.
-https://creativecommons.org/licenses/by/4.0/
+Distributed under a [Creative Commons Attribution 4.0 license](https://creativecommons.org/licenses/by/4.0/)
 
 -----------
 

README.md

@@ -90,6 +90,8 @@ $ mvn spring-boot:run
 
 Alternatively, you can run the application from your IDE as a simple Java application by importing the Maven project.
 
+You need to install [Graphviz](http://www.graphviz.org/) for all unit tests to pass.
+
 You can create an executable JAR file by using:
 
     mvn clean install

pom.xml

@@ -103,6 +103,12 @@
             <artifactId>org.eclipse.jgit</artifactId>
             <version>4.8.0.201706111038-r</version>
         </dependency>
+        <dependency>
+            <groupId>org.mockito</groupId>
+            <artifactId>mockito-all</artifactId>
+            <version>1.10.19</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 
     <build>

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

@@ -26,6 +26,7 @@
 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.CorsRegistry;
 import org.springframework.web.servlet.config.annotation.WebMvcConfigurerAdapter;
 
 @Configuration
@@ -79,4 +80,9 @@ public void configureContentNegotiation(ContentNegotiationConfigurer configurer)
             c = c.mediaType(f.name(), f.mediaType());
         }
     }
-}
+
+    @Override
+    public void addCorsMappings(CorsRegistry registry) {
+	registry.addMapping("/**").exposedHeaders("Location");  // .setMaxAge(Long.MAX_VALUE)
+    }
+}

src/main/java/org/commonwl/view/git/GitService.java

@@ -23,6 +23,7 @@
 import org.commonwl.view.researchobject.HashableAgent;
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.errors.GitAPIException;
+import org.eclipse.jgit.api.errors.RefNotFoundException;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.PersonIdent;
 import org.eclipse.jgit.revwalk.RevCommit;
@@ -32,6 +33,7 @@
 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;
@@ -67,7 +69,7 @@ public GitService(@Value("${gitStorage}") Path gitStorage,
      * Gets a repository, cloning into a local directory or
      * @param gitDetails The details of the Git repository
      * @param reuseDir Whether the cached repository can be used
-     * @returns The git object for the repository
+     * @return The git object for the repository
      */
     public Git getRepository(GitDetails gitDetails, boolean reuseDir)
             throws GitAPIException, IOException {
@@ -84,34 +86,45 @@ public Git getRepository(GitDetails gitDetails, boolean reuseDir)
             } else {
                 // Create a folder and clone repository into it
                 Files.createDirectory(repoDir);
-                repo = Git.cloneRepository()
-                        .setCloneSubmodules(cloneSubmodules)
-                        .setURI(gitDetails.getRepoUrl())
-                        .setDirectory(repoDir.toFile())
-                        .setCloneAllBranches(true)
-                        .call();
+                repo = cloneRepo(gitDetails.getRepoUrl(), repoDir.toFile());
             }
         } else {
             // Another thread is already using the existing folder
             // Must create another temporary one
-            repo = Git.cloneRepository()
-                    .setCloneSubmodules(cloneSubmodules)
-                    .setURI(gitDetails.getRepoUrl())
-                    .setDirectory(createTempDir())
-                    .setCloneAllBranches(true)
-                    .call();
+            repo = cloneRepo(gitDetails.getRepoUrl(), createTempDir());
         }
 
         // Checkout the specific branch or commit ID
         if (repo != null) {
             // Create a new local branch if it does not exist and not a commit ID
             String branchOrCommitId = gitDetails.getBranch();
-            if (!ObjectId.isId(branchOrCommitId)) {
+            final boolean isId = ObjectId.isId(branchOrCommitId);
+            if (!isId) {
                 branchOrCommitId = "refs/remotes/origin/" + branchOrCommitId;
             }
-            repo.checkout()
-                    .setName(branchOrCommitId)
-                    .call();
+            try {
+                repo.checkout()
+                        .setName(branchOrCommitId)
+                        .call();
+            }
+            catch (Exception ex) {
+                // Maybe it was a tag
+                if (!isId && ex instanceof RefNotFoundException) {
+                    final String tag = gitDetails.getBranch();
+                    try {
+                        repo.checkout()
+                                .setName(tag)
+                                .call();
+                    }
+                    catch (Exception ex2) {
+                        // Throw the first exception, to keep the same behavior as before.
+                        throw ex;
+                    }
+                }
+                else {
+                    throw ex;
+                }
+            }
         }
 
         return repo;
@@ -184,4 +197,19 @@ public GitDetails transferPathToBranch(GitDetails githubInfo) {
         }
     }
 
+    /**
+     * Clones a Git repository
+     * @param repoUrl the url of the Git repository
+     * @param directory the directory to clone the repo into
+     * @return a Git instance
+     * @throws GitAPIException if any error occurs cloning the repo
+     */
+    protected Git cloneRepo(String repoUrl, File directory) throws GitAPIException {
+        return Git.cloneRepository()
+                .setCloneSubmodules(cloneSubmodules)
+                .setURI(repoUrl)
+                .setDirectory(directory)
+                .setCloneAllBranches(true)
+                .call();
+    }
 }

src/main/resources/static/css/main-20170616.css renamed to src/main/resources/static/css/main-20180518.css

@@ -328,3 +328,20 @@ td.run, td.doc {
 #format-html { 
 	display: none;
 }
+/**
+ * Workaround (not really) for
+ * https://github.com/common-workflow-language/cwlviewer/issues/166
+ */
+#format-json { 
+	display: none;
+}
+
+/**
+ * Light email-obfuscation 
+ */
+.obf-hide {
+  display: none;
+}
+.obf-at::before { 
+  content: "@" 
+ }