Add author information from Github commits to Research Objects

Mark Robinson · Mark Robinson · commit a77f4a40b2ab · 2017-02-26T19:09:48.000Z
diff --git a/src/main/java/org/commonwl/viewer/domain/HashableAgent.java b/src/main/java/org/commonwl/viewer/domain/HashableAgent.java
@@ -0,0 +1,68 @@
+package org.commonwl.viewer.domain;
+
+import org.apache.taverna.robundle.manifest.Agent;
+
+import java.net.URI;
+
+/**
+ * An implementation of Agent with added HashCode and Equals methods
+ * for use in sets
+ */
+public class HashableAgent extends Agent {
+
+    private String name;
+    private URI orcid;
+    private URI uri;
+
+    @Override
+    public String getName() {
+        return name;
+    }
+
+    @Override
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    @Override
+    public URI getOrcid() {
+        return orcid;
+    }
+
+    @Override
+    public void setOrcid(URI orcid) {
+        this.orcid = orcid;
+    }
+
+    @Override
+    public URI getUri() {
+        return uri;
+    }
+
+    @Override
+    public void setUri(URI uri) {
+        this.uri = uri;
+    }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass() || super.getClass() != o.getClass()) return false;
+
+        HashableAgent that = (HashableAgent) o;
+
+        if (name != null ? !name.equals(that.name) : that.name != null) return false;
+        if (orcid != null ? !orcid.equals(that.orcid) : that.orcid != null) return false;
+        return uri != null ? uri.equals(that.uri) : that.uri == null;
+
+    }
+
+    @Override
+    public int hashCode() {
+        int result = name != null ? name.hashCode() : 0;
+        result = 31 * result + (orcid != null ? orcid.hashCode() : 0);
+        result = 31 * result + (uri != null ? uri.hashCode() : 0);
+        return result;
+    }
+
+}
diff --git a/src/main/java/org/commonwl/viewer/domain/ROBundle.java b/src/main/java/org/commonwl/viewer/domain/ROBundle.java
@@ -19,8 +19,6 @@
 
 package org.commonwl.viewer.domain;
 
-import com.fasterxml.jackson.databind.JsonNode;
-import com.fasterxml.jackson.databind.ObjectMapper;
 import org.apache.commons.io.FilenameUtils;
 import org.apache.taverna.robundle.Bundle;
 import org.apache.taverna.robundle.Bundles;
@@ -29,18 +27,18 @@
 import org.apache.taverna.robundle.manifest.PathMetadata;
 import org.commonwl.viewer.services.GitHubService;
 import org.eclipse.egit.github.core.RepositoryContents;
-import org.eclipse.egit.github.core.User;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.yaml.snakeyaml.Yaml;
 
 import java.io.IOException;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 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;
 
@@ -56,6 +54,7 @@ public class ROBundle {
     private Bundle bundle;
     private GithubDetails githubInfo;
     private String commitSha;
+    private Set<HashableAgent> authors = new HashSet<HashableAgent>();
 
     // Pattern for extracting version from a cwl file
     private final String CWL_VERSION_REGEX = "cwlVersion:\\s*\"?(?:cwl:)?([^\\s\"]+)\"?";
@@ -85,25 +84,6 @@ public ROBundle(GitHubService githubService, GithubDetails githubInfo, String co
             cwlViewer.setUri(new URI(appURL));
             manifest.setCreatedBy(cwlViewer);
 
-            // Github author attribution
-            // TODO: way to add all the contributors somehow
-            // TODO: set the aggregates details according to the github information
-            User authorDetails = githubService.getUser(githubInfo.getOwner());
-
-            List<Agent> authorList = new ArrayList<>(1);
-            Agent author = new Agent(authorDetails.getName());
-            author.setUri(new URI(authorDetails.getHtmlUrl()));
-
-            // This tool supports putting your ORCID in the blog field of github as a URL
-            // eg http://orcid.org/0000-0000-0000-0000
-            String authorBlog = authorDetails.getBlog();
-            if (authorBlog != null && authorBlog.startsWith("http://orcid.org/")) {
-                author.setOrcid(new URI(authorBlog));
-            }
-
-            authorList.add(author);
-            manifest.setAuthoredBy(authorList);
-
             // Retrieval Info
             manifest.setRetrievedBy(cwlViewer);
             manifest.setRetrievedOn(manifest.getCreatedOn());
@@ -120,16 +100,18 @@ public ROBundle(GitHubService githubService, GithubDetails githubInfo, String co
 
         // Add the files from the Github repo to this workflow
         List<RepositoryContents> repoContents = githubService.getContents(githubInfo);
-        addFiles(repoContents, bundleFiles, manifest);
+        addFiles(repoContents, bundleFiles);
+
+        // Add combined authors
+        manifest.setAuthoredBy(new ArrayList<Agent>(authors));
     }
 
     /**
      * Add files to this bundle from a list of Github repository contents
      * @param repoContents The contents of the Github repository
      * @param path The path in the Research Object to add the files
      */
-    private void addFiles(List<RepositoryContents> repoContents, Path path,
-                          Manifest manifest) throws IOException {
+    private void addFiles(List<RepositoryContents> repoContents, Path path) throws IOException {
 
         // Loop through repo contents and add them
         for (RepositoryContents repoContent : repoContents) {
@@ -147,7 +129,7 @@ private void addFiles(List<RepositoryContents> repoContents, Path path,
                 Files.createDirectory(subdirPath);
 
                 // Add the files in the subdirectory to this new folder
-                addFiles(subdirectory, subdirPath, manifest);
+                addFiles(subdirectory, subdirPath);
 
                 // Otherwise this is a file so add to the bundle
             } else if (repoContent.getType().equals("file")) {
@@ -162,7 +144,7 @@ private void addFiles(List<RepositoryContents> repoContents, Path path,
                 Bundles.setStringValue(newFilePort, fileContent);
 
                 // Manifest aggregation
-                PathMetadata aggregation = manifest.getAggregation(newFilePort);
+                PathMetadata aggregation = bundle.getManifest().getAggregation(newFilePort);
 
                 try {
                     // Special handling for cwl files
@@ -178,6 +160,11 @@ private void addFiles(List<RepositoryContents> repoContents, Path path,
                         }
                     }
 
+                    // Add authors from github commits to the file
+                    Set<HashableAgent> fileAuthors = githubService.getContributors(githubFile, commitSha);
+                    authors.addAll(fileAuthors);
+                    aggregation.setAuthoredBy(new ArrayList<Agent>(fileAuthors));
+
                     // Set retrievedFrom information for this file in the manifest
                     aggregation.setRetrievedFrom(new URI("https://github.com/" + githubFile.getOwner() + "/" +
                             githubFile.getRepoName() + "/blob/" + commitSha + "/" + githubFile.getPath()));
diff --git a/src/main/java/org/commonwl/viewer/services/GitHubService.java b/src/main/java/org/commonwl/viewer/services/GitHubService.java
@@ -21,22 +21,25 @@
 
 import org.apache.commons.io.IOUtils;
 import org.commonwl.viewer.domain.GithubDetails;
+import org.commonwl.viewer.domain.HashableAgent;
 import org.eclipse.egit.github.core.*;
-import org.eclipse.egit.github.core.RepositoryContents;
-import org.eclipse.egit.github.core.RepositoryId;
-import org.eclipse.egit.github.core.User;
 import org.eclipse.egit.github.core.client.GitHubClient;
 import org.eclipse.egit.github.core.service.CommitService;
 import org.eclipse.egit.github.core.service.ContentsService;
+import org.eclipse.egit.github.core.service.RepositoryService;
 import org.eclipse.egit.github.core.service.UserService;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Service;
 
 import java.io.IOException;
 import java.io.InputStream;
+import java.net.URI;
+import java.net.URISyntaxException;
 import java.net.URL;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
@@ -50,6 +53,7 @@ public class GitHubService {
     private final ContentsService contentsService;
     private final UserService userService;
     private final CommitService commitService;
+    private final RepositoryService repoService;
 
     // URL validation for directory links
     private final String GITHUB_DIR_REGEX = "^https:\\/\\/github\\.com\\/([A-Za-z0-9_.-]+)\\/([A-Za-z0-9_.-]+)\\/?(?:tree\\/([^/]+)\\/(.*))?$";
@@ -69,6 +73,7 @@ public GitHubService(@Value("${githubAPI.authentication}") String authSetting,
         this.contentsService = new ContentsService(client);
         this.userService = new UserService(client);
         this.commitService = new CommitService(client);
+        this.repoService = new RepositoryService(client);
     }
 
     /**
@@ -138,4 +143,37 @@ public String getCommitSha(GithubDetails githubInfo) throws IOException {
         RepositoryCommit currentCommit = commitService.getCommit(repo, githubInfo.getBranch());
         return currentCommit.getSha();
     }
+
+    /**
+     *
+     * Get the contributors to a specific file by their commits
+     * @param githubInfo The information to access the repository
+     * @return A list of unique contributors
+     * @throws IOException Any API errors which may have occurred
+     * @throws URISyntaxException Any error in the author's URI (should never occur)
+     */
+    public Set<HashableAgent> getContributors(GithubDetails githubInfo, String sha)
+            throws IOException, URISyntaxException {
+        RepositoryId repo = new RepositoryId(githubInfo.getOwner(), githubInfo.getRepoName());
+        Set<HashableAgent> authors = new HashSet<HashableAgent>();
+
+        for (RepositoryCommit commit : commitService.getCommits(repo, sha, githubInfo.getPath())) {
+            User author = commit.getAuthor();
+            CommitUser commitAuthor = commit.getCommit().getAuthor();
+
+            // If there is author information for this commit in some form
+            if (author != null || commitAuthor != null) {
+                // Create a new agent and add as much detail as possible
+                HashableAgent newAgent = new HashableAgent();
+                if (author != null) {
+                    newAgent.setUri(new URI(author.getHtmlUrl()));
+                }
+                if (commitAuthor != null) {
+                    newAgent.setName(commitAuthor.getName());
+                }
+                authors.add(newAgent);
+            }
+        }
+        return authors;
+    }
 }
