RO Bundle generation tests from local test resources

MarkRobbo · MarkRobbo · commit cc0ea0908597 · 2017-08-01T16:55:36.000+01:00
diff --git a/src/main/java/org/commonwl/view/git/GitService.java b/src/main/java/org/commonwl/view/git/GitService.java
@@ -20,8 +20,11 @@
 package org.commonwl.view.git;
 
 import org.apache.commons.codec.digest.DigestUtils;
+import org.commonwl.view.researchobject.HashableAgent;
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.errors.GitAPIException;
+import org.eclipse.jgit.lib.PersonIdent;
+import org.eclipse.jgit.revwalk.RevCommit;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -30,7 +33,11 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.net.URI;
+import java.net.URISyntaxException;
 import java.nio.file.Path;
+import java.util.HashSet;
+import java.util.Set;
 
 /**
  * Handles Git related functionality
@@ -111,5 +118,38 @@ public String getCurrentCommitID(Git repo) throws IOException {
         return repo.getRepository().findRef("HEAD").getObjectId().getName();
     }
 
+    /**
+     * Gets a set of authors for a path in a given repository
+     * @param repo The git repository
+     * @param path The path to get commits for
+     * @return An iterable of commits
+     * @throws GitAPIException Any API errors which may occur
+     * @throws URISyntaxException Error constructing mailto link
+     */
+    public Set<HashableAgent> getAuthors(Git repo, String path) throws GitAPIException, URISyntaxException {
+        Iterable<RevCommit> logs = repo.log().addPath(path).call();
+        Set<HashableAgent> fileAuthors = new HashSet<>();
+        for (RevCommit rev : logs) {
+            // Use author first with backup of committer
+            PersonIdent author = rev.getAuthorIdent();
+            if (author == null) {
+                author = rev.getCommitterIdent();
+            }
+            // Create a new agent and add as much detail as possible
+            if (author != null) {
+                HashableAgent newAgent = new HashableAgent();
+                String name = author.getName();
+                if (name != null && name.length() > 0) {
+                    newAgent.setName(author.getName());
+                }
+                String email = author.getEmailAddress();
+                if (email != null && email.length() > 0) {
+                    newAgent.setUri(new URI("mailto:" + author.getEmailAddress()));
+                }
+                fileAuthors.add(newAgent);
+            }
+        }
+        return fileAuthors;
+    }
 
 }
diff --git a/src/main/java/org/commonwl/view/researchobject/HashableAgent.java b/src/main/java/org/commonwl/view/researchobject/HashableAgent.java
@@ -33,6 +33,14 @@ public class HashableAgent extends Agent {
     private URI orcid;
     private URI uri;
 
+    public HashableAgent() {}
+
+    public HashableAgent(String name, URI orcid, URI uri) {
+        this.name = name;
+        this.orcid = orcid;
+        this.uri = uri;
+    }
+
     @Override
     public String getName() {
         return name;
diff --git a/src/main/java/org/commonwl/view/researchobject/ROBundleService.java b/src/main/java/org/commonwl/view/researchobject/ROBundleService.java
@@ -33,8 +33,6 @@
 import org.commonwl.view.workflow.Workflow;
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.errors.GitAPIException;
-import org.eclipse.jgit.lib.PersonIdent;
-import org.eclipse.jgit.revwalk.RevCommit;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -288,30 +286,8 @@ private void addFilesToBundle(GitDetails gitDetails, Bundle bundle, Path bundleP
 
                         // Add authors from git commits to the file
                         try {
-                            Set<HashableAgent> fileAuthors = new HashSet<>();
-                            Iterable<RevCommit> logs = gitRepo.log()
-                                    .addPath(Paths.get(gitDetails.getPath()).resolve(file.getName()).toString())
-                                    .call();
-                            for (RevCommit rev : logs) {
-                                // Use author first with backup of committer
-                                PersonIdent author = rev.getAuthorIdent();
-                                if (author == null) {
-                                    author = rev.getCommitterIdent();
-                                }
-                                // Create a new agent and add as much detail as possible
-                                if (author != null) {
-                                    HashableAgent newAgent = new HashableAgent();
-                                    String name = author.getName();
-                                    if (name != null && name.length() > 0) {
-                                        newAgent.setName(author.getName());
-                                    }
-                                    String email = author.getEmailAddress();
-                                    if (email != null && email.length() > 0) {
-                                        newAgent.setUri(new URI("mailto:" + author.getEmailAddress()));
-                                    }
-                                    fileAuthors.add(newAgent);
-                                }
-                            }
+                            Set<HashableAgent> fileAuthors = gitService.getAuthors(gitRepo,
+                                    Paths.get(gitDetails.getPath()).resolve(file.getName()).toString());
                             authors.addAll(fileAuthors);
                             aggregation.setAuthoredBy(new ArrayList<>(fileAuthors));
                         } catch (GitAPIException ex) {
diff --git a/src/main/java/org/commonwl/view/workflow/WorkflowController.java b/src/main/java/org/commonwl/view/workflow/WorkflowController.java
@@ -108,7 +108,7 @@ public String searchWorkflows(Model model,
     @PostMapping("/workflows")
     public ModelAndView newWorkflowFromGithubURL(@Valid WorkflowForm workflowForm, BindingResult bindingResult) {
 
-        // Run validator which checks the github URL is valid
+        // Run validator which checks the git URL is valid
         GitDetails gitInfo = workflowFormValidator.validateAndParse(workflowForm, bindingResult);
 
         if (bindingResult.hasErrors() || gitInfo == null) {
diff --git a/src/test/java/org/commonwl/view/git/GitDetailsTest.java b/src/test/java/org/commonwl/view/git/GitDetailsTest.java
@@ -17,10 +17,8 @@
  * under the License.
  */
 
-package org.commonwl.view.github;
+package org.commonwl.view.git;
 
-import org.commonwl.view.git.GitDetails;
-import org.commonwl.view.git.GitType;
 import org.junit.Test;
 
 import static org.commonwl.view.git.GitDetails.normaliseUrl;
diff --git a/src/test/java/org/commonwl/view/researchobject/ROBundleServiceTest.java b/src/test/java/org/commonwl/view/researchobject/ROBundleServiceTest.java
@@ -30,6 +30,7 @@
 import org.commonwl.view.graphviz.GraphVizService;
 import org.commonwl.view.workflow.Workflow;
 import org.eclipse.jgit.api.Git;
+import org.eclipse.jgit.lib.Repository;
 import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
@@ -39,7 +40,9 @@
 import java.io.File;
 import java.net.URI;
 import java.nio.file.Path;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 
 import static org.junit.Assert.*;
 import static org.mockito.Matchers.anyObject;
@@ -52,7 +55,11 @@ public class ROBundleServiceTest {
 
     @Before
     public void setUp() throws Exception {
-        gitRepo = Git.open(new File("src/test/resources/lobstr-draft3"));
+        Repository mockRepo = Mockito.mock(Repository.class);
+        when(mockRepo.getWorkTree()).thenReturn(new File("src/test/resources/cwl/"));
+
+        gitRepo = Mockito.mock(Git.class);
+        when(gitRepo.getRepository()).thenReturn(mockRepo);
     }
 
     /**
@@ -62,7 +69,7 @@ public void setUp() throws Exception {
     public TemporaryFolder roBundleFolder = new TemporaryFolder();
 
     /**
-     * Generate a Research Object bundle from lobstr-v1 and check it
+     * Generate a Research Object bundle from lobstr and check it
      */
     @Test
     public void generateAndSaveROBundle() throws Exception {
@@ -71,6 +78,11 @@ public void generateAndSaveROBundle() throws Exception {
         GitService mockGitService = Mockito.mock(GitService.class);
         when(mockGitService.getRepository(anyObject())).thenReturn(gitRepo);
 
+        Set<HashableAgent> authors = new HashSet<>();
+        authors.add(new HashableAgent("Mark Robinson", null, new URI("mailto:mark@example.com")));
+        when(mockGitService.getAuthors(anyObject(), anyObject()))
+                .thenReturn(authors);
+
         // Mock Graphviz service
         GraphVizService mockGraphvizService = Mockito.mock(GraphVizService.class);
         when(mockGraphvizService.getGraph(anyString(), anyString(), anyString()))
@@ -93,7 +105,7 @@ public void generateAndSaveROBundle() throws Exception {
 
         // RO details
         GitDetails lobSTRv1RODetails = new GitDetails("https://github.com/common-workflow-language/workflows.git",
-                "933bf2a1a1cce32d88f88f136275535da9df0954", "workflows/lobSTR");
+                "933bf2a1a1cce32d88f88f136275535da9df0954", "lobstr-draft3/");
 
         // Create new RO bundle
         ROBundleService bundleService = new ROBundleService(roBundleFolder.getRoot().toPath(),
@@ -115,12 +127,13 @@ public void generateAndSaveROBundle() throws Exception {
         // Check cwl aggregation information
         PathMetadata cwlAggregate = manifest.getAggregation(
                 bundleRoot.resolve("lobSTR-workflow.cwl"));
-        assertEquals("https://raw.githubusercontent.com/common-workflow-language/workflows/933bf2a1a1cce32d88f88f136275535da9df0954/workflows/lobSTR/lobSTR-workflow.cwl",
+        assertEquals("https://raw.githubusercontent.com/common-workflow-language/workflows/933bf2a1a1cce32d88f88f136275535da9df0954/lobstr-draft3/lobSTR-workflow.cwl",
                 cwlAggregate.getRetrievedFrom().toString());
         assertEquals("Mark Robinson", cwlAggregate.getAuthoredBy().get(0).getName());
+        assertEquals("mailto:mark@example.com", cwlAggregate.getAuthoredBy().get(0).getUri().toString());
         assertNull(cwlAggregate.getAuthoredBy().get(0).getOrcid());
         assertEquals("text/x-yaml", cwlAggregate.getMediatype());
-        assertEquals("https://w3id.org/cwl/v1.0", cwlAggregate.getConformsTo().toString());
+        assertEquals("https://w3id.org/cwl/draft-3", cwlAggregate.getConformsTo().toString());
 
         // Check visualisations exist as aggregates
         PathMetadata pngAggregate = manifest.getAggregation(bundleRoot.resolve("visualisation.png"));
@@ -137,7 +150,7 @@ public void generateAndSaveROBundle() throws Exception {
         // Check git2prov link is in the history
         List<Path> history = manifest.getHistory();
         assertEquals(1, history.size());
-        assertEquals("http:/git2prov.org/git2prov?giturl=https:/github.com/common-workflow-language/workflows&serialization=PROV-JSON",
+        assertEquals("http:/git2prov.org/git2prov?giturl=https:/github.com/common-workflow-language/workflows.git&serialization=PROV-JSON",
                 history.get(0).toString());
 
         // Save and check it exists in the temporary folder
@@ -162,6 +175,11 @@ public void filesOverLimit() throws Exception {
         GitService mockGitService = Mockito.mock(GitService.class);
         when(mockGitService.getRepository(anyObject())).thenReturn(gitRepo);
 
+        Set<HashableAgent> authors = new HashSet<>();
+        authors.add(new HashableAgent("Mark Robinson", null, new URI("mailto:mark@example.com")));
+        when(mockGitService.getAuthors(anyObject(), anyObject()))
+                .thenReturn(authors);
+
         // Mock Graphviz service
         GraphVizService mockGraphvizService = Mockito.mock(GraphVizService.class);
         when(mockGraphvizService.getGraph(anyString(), anyString(), anyString()))
@@ -184,7 +202,7 @@ public void filesOverLimit() throws Exception {
 
         // RO details
         GitDetails lobSTRv1RODetails = new GitDetails("https://github.com/common-workflow-language/workflows.git",
-                "933bf2a1a1cce32d88f88f136275535da9df0954", "workflows/lobSTR");
+                "933bf2a1a1cce32d88f88f136275535da9df0954", "lobstr-draft3/lobSTR-workflow.cwl");
 
         // Create new RO bundle
         ROBundleService bundleService = new ROBundleService(roBundleFolder.getRoot().toPath(),
@@ -198,9 +216,7 @@ public void filesOverLimit() throws Exception {
         assertEquals(14, manifest.getAggregates().size());
 
         PathMetadata urlAggregate = manifest.getAggregation(
-                new URI("https://raw.githubusercontent.com/common-workflow-language/workflows/" +
-                        "933bf2a1a1cce32d88f88f136275535da9df0954/workflows/lobSTR/models/" +
-                        "illumina_v3.pcrfree.stepmodel"));
+                new URI("https://raw.githubusercontent.com/common-workflow-language/workflows/933bf2a1a1cce32d88f88f136275535da9df0954/lobstr-draft3/lobSTR-workflow.cwl/models/illumina_v3.pcrfree.stepmodel"));
         assertEquals("Mark Robinson", urlAggregate.getAuthoredBy().get(0).getName());
 
     }
diff --git a/src/test/java/org/commonwl/view/workflow/WorkflowServiceTest.java b/src/test/java/org/commonwl/view/workflow/WorkflowServiceTest.java
@@ -94,7 +94,7 @@ public void getWorkflowCacheHasExpired() throws Exception {
                 Mockito.mock(CWLToolRunner.class), -1);
 
         // Will use check cache algorithm, find expired,
-        // check github and find commit IDs do not match,
+        // check git and find commit IDs do not match,
         // and thus create a new workflow + matching RO bundle
         Workflow workflow = testWorkflowService.getWorkflow(githubInfo);
 
