Fixed bug with git not adding deleted files.

services/git-bridge/src/main/java/uk/ac/ic/wlgitbridge/bridge/WLBridgedProject.java

@@ -49,6 +49,9 @@ public class WLBridgedProject {
             for (WritableRepositoryContents contents : writableRepositories) {
                 contents.write();
                 Git git = new Git(repository);
+                for (String missing : git.status().call().getMissing()) {
+                    git.rm().setCached(true).addFilepattern(missing).call();
+                }
                 git.add().addFilepattern(".").call();
                 git.commit().setAuthor(new PersonIdent(contents.getUserName(), contents.getUserEmail(), contents.getWhen(), TimeZone.getDefault()))
                             .setMessage(contents.getCommitMessage())

services/git-bridge/src/main/java/uk/ac/ic/wlgitbridge/test/util/FileUtil.java

@@ -34,8 +34,8 @@ public class FileUtil {
     }
 
     public static boolean gitDirectoriesAreEqual(Path dir1, Path dir2) {
-        Set<String> dir1Contents = getAllFilesRecursivelyInDirectoryApartFrom(dir1, dir1.resolve(".git"));
+        Set<String> dir1Contents = getAllRecursivelyInDirectoryApartFrom(dir1, dir1.resolve(".git"));
-        Set<String> dir2Contents = getAllFilesRecursivelyInDirectoryApartFrom(dir2, dir2.resolve(".git"));
+        Set<String> dir2Contents = getAllRecursivelyInDirectoryApartFrom(dir2, dir2.resolve(".git"));
         boolean filesEqual = dir1Contents.equals(dir2Contents);
         if (!filesEqual) {
             System.out.println("Not equal: (" + dir1Contents + ", " + dir2Contents + ")");
@@ -72,20 +72,31 @@ public class FileUtil {
         }
     }
 
-    public static Set<String> getAllFilesRecursivelyInDirectoryApartFrom(Path dir, Path excluded) {
+    public static Set<String> getAllRecursivelyInDirectoryApartFrom(Path dir, Path excluded) {
+        return getAllRecursivelyInDirectoryApartFrom(dir, excluded, true);
+    }
+
+    public static Set<String> getOnlyFilesRecursivelyInDirectoryApartFrom(Path dir, Path excluded) {
+        return getAllRecursivelyInDirectoryApartFrom(dir, excluded, false);
+    }
+
+    private static Set<String> getAllRecursivelyInDirectoryApartFrom(Path dir, Path excluded, boolean directories) {
         if (!dir.toFile().isDirectory()) {
             throw new IllegalArgumentException("need a directory");
         }
-        return getAllFilesRecursively(dir, dir, excluded);
+        return getAllFilesRecursively(dir, dir, excluded, directories);
     }
 
-    static Set<String> getAllFilesRecursively(Path baseDir, Path dir, Path excluded) {
+    static Set<String> getAllFilesRecursively(Path baseDir, Path dir, Path excluded, boolean directories) {
         Set<String> files = new HashSet<String>();
         for (File file : dir.toFile().listFiles()) {
             if (!file.equals(excluded.toFile())) {
-                files.add(baseDir.relativize(file.toPath()).toString());
+                boolean isDirectory = file.isDirectory();
-                if (file.isDirectory()) {
+                if (directories || !isDirectory) {
-                    files.addAll(getAllFilesRecursively(baseDir, file.toPath(), excluded));
+                    files.add(baseDir.relativize(file.toPath()).toString());
+                }
+                if (isDirectory) {
+                    files.addAll(getAllFilesRecursively(baseDir, file.toPath(), excluded, directories));
                 }
             }
         }

services/git-bridge/src/main/java/uk/ac/ic/wlgitbridge/writelatex/filestore/GitDirectoryContents.java

@@ -36,6 +36,7 @@ public class GitDirectoryContents implements WritableRepositoryContents {
     public void write() throws IOException, FailedConnectionException {
         WLFileStore.deleteInDirectoryApartFrom(gitDirectory, ".git");
         for (FileNode fileNode : fileNodes) {
+            System.out.println("Writing: " + fileNode.getFilePath());
             fileNode.writeToDisk(gitDirectory);
         }
     }

services/git-bridge/src/main/java/uk/ac/ic/wlgitbridge/writelatex/filestore/store/WLFileStore.java

@@ -58,6 +58,7 @@ public class WLFileStore implements PersistentStoreSource {
                 if (file.isDirectory()) {
                     deleteInDirectory(file);
                 }
+                System.out.println("deleting: " + file.getAbsolutePath());
                 file.delete();
             }
         }

services/git-bridge/src/test/java/uk/ac/ic/wlgitbridge/WLGitBridgeIntegrationTest.java

@@ -36,6 +36,10 @@ public class WLGitBridgeIntegrationTest {
                     put("base", new SnapshotAPIStateBuilder(getResourceAsStream("/canPullAModifiedTexFile/base/state.json")).build());
                     put("withModifiedTexFile", new SnapshotAPIStateBuilder(getResourceAsStream("/canPullAModifiedTexFile/withModifiedTexFile/state.json")).build());
                 }});
+                put("canPullADeletedTexFile", new HashMap<String, SnapshotAPIState>() {{
+                    put("base", new SnapshotAPIStateBuilder(getResourceAsStream("/canPullADeletedTexFile/base/state.json")).build());
+                    put("withDeletedTexFile", new SnapshotAPIStateBuilder(getResourceAsStream("/canPullADeletedTexFile/withDeletedTexFile/state.json")).build());
+                }});
             }};
 
     @Rule
@@ -111,6 +115,29 @@ public class WLGitBridgeIntegrationTest {
         assertTrue(FileUtil.gitDirectoriesAreEqual(getResource("/canPullAModifiedTexFile/withModifiedTexFile/testproj"), git.toPath()));
     }
 
+    @Test
+    public void canPullADeletedTexFile() throws IOException, GitAPIException {
+        MockSnapshotServer server = new MockSnapshotServer(3860, getResource("/canPullADeletedTexFile").toFile());
+        server.start();
+        server.setState(states.get("canPullADeletedTexFile").get("base"));
+        WLGitBridgeApplication wlgb = new WLGitBridgeApplication(new String[] {
+                makeConfigFile(33860, 3860)
+        });
+        wlgb.run();
+        folder.create();
+        File git = folder.newFolder();
+        Git base = Git.cloneRepository()
+                .setURI("http://127.0.0.1:33860/testproj.git")
+                .setDirectory(git)
+                .call();
+        assertTrue(FileUtil.gitDirectoriesAreEqual(getResource("/canPullADeletedTexFile/base/testproj"), git.toPath()));
+        server.setState(states.get("canPullADeletedTexFile").get("withDeletedTexFile"));
+        base.pull().call();
+        base.close();
+        wlgb.stop();
+        assertTrue(FileUtil.gitDirectoriesAreEqual(getResource("/canPullADeletedTexFile/withDeletedTexFile/testproj"), git.toPath()));
+    }
+
     private String makeConfigFile(int port, int apiPort) throws IOException {
         File wlgb = folder.newFolder();
         File config = folder.newFile();

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/WLGitBridgeIntegrationTest/canPullADeletedTexFile/base/state.json

@@ -0,0 +1,46 @@
+[
+	{
+		"project": "testproj",
+		"getDoc": {
+			"versionID": 1,
+			"createdAt": "2014-11-30T18:40:58Z",
+			"email": "jdleesmiller+1@gmail.com",
+			"name": "John+1"
+		},
+		"getSavedVers": [
+        	{
+        		"versionID": 1,
+        		"comment": "added more info on doc GET and error details",
+        		"email": "jdleesmiller+1@gmail.com",
+        		"name": "John+1",
+        		"createdAt": "2014-11-30T18:47:01Z"
+        	}
+		],
+		"getForVers": [
+			{
+				"versionID": 1,
+				"srcs": [
+                    {
+                    	"content": "content\n",
+                    	"path": "main.tex"
+                    },
+                    {
+                    	"content": "This text is from another file.",
+                    	"path": "test.tex"
+                    }
+	            ],
+	            "atts": [
+	            	{
+	            		"url": "http://127.0.0.1:3860/base/testproj/overleaf-white-410.png",
+	            		"path": "overleaf-white-410.png"
+	            	}
+	            ]
+	        }
+		],
+		"push": "success",
+		"postback": {
+			"type": "success",
+			"versionID": 2
+		}
+	}
+]

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/WLGitBridgeIntegrationTest/canPullADeletedTexFile/base/testproj/main.tex

@@ -0,0 +1 @@
+content

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/WLGitBridgeIntegrationTest/canPullADeletedTexFile/base/testproj/overleaf-white-410.png

@@ -0,0 +1,12 @@
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html;charset=ISO-8859-1"/>
+<title>Error 404 </title>
+</head>
+<body>
+<h2>HTTP ERROR: 404</h2>
+<p>Problem accessing /state/testproj1/overleaf-white-410.png. Reason:
+<pre>    Not Found</pre></p>
+<hr /><i><small>Powered by Jetty://</small></i>
+</body>
+</html>

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/WLGitBridgeIntegrationTest/canPullADeletedTexFile/base/testproj/test.tex

@@ -0,0 +1 @@
+This text is from another file.

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/WLGitBridgeIntegrationTest/canPullADeletedTexFile/withDeletedTexFile/state.json

@@ -0,0 +1,68 @@
+[
+	{
+		"project": "testproj",
+		"getDoc": {
+			"versionID": 2,
+			"createdAt": "2014-11-30T18:40:58Z",
+			"email": "jdleesmiller+1@gmail.com",
+			"name": "John+1"
+		},
+		"getSavedVers": [
+        	{
+        		"versionID": 2,
+        		"comment": "i deleted test.tex",
+        		"email": "jdleesmiller+1@gmail.com",
+        		"name": "John+1",
+        		"createdAt": "2014-11-30T18:48:01Z"
+        	},
+        	{
+        		"versionID": 1,
+        		"comment": "added more info on doc GET and error details",
+        		"email": "jdleesmiller+1@gmail.com",
+        		"name": "John+1",
+        		"createdAt": "2014-11-30T18:47:01Z"
+        	}
+		],
+		"getForVers": [
+			{
+				"versionID": 2,
+				"srcs": [
+                    {
+                    	"content": "content\nadded more stuff\n",
+                    	"path": "main.tex"
+                    }
+	            ],
+	            "atts": [
+	            	{
+	            		"url": "http://127.0.0.1:3860/withDeletedTexFile/testproj/overleaf-white-410.png",
+	            		"path": "overleaf-white-410.png"
+	            	}
+	            ]
+	        },
+			{
+				"versionID": 1,
+				"srcs": [
+                    {
+                    	"content": "content\n",
+                    	"path": "main.tex"
+                    },
+                    {
+                    	"content": "This text is from another file.",
+                    	"path": "test.tex"
+                    }
+	            ],
+	            "atts": [
+	            	{
+	            		"url": "http://127.0.0.1:3860/base/testproj/overleaf-white-410.png",
+	            		"path": "overleaf-white-410.png"
+	            	}
+	            ]
+	        }
+		],
+		"push": "success",
+		"postback": {
+			"type": "success",
+			"versionID": 2
+		}
+	}
+]

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/WLGitBridgeIntegrationTest/canPullADeletedTexFile/withDeletedTexFile/testproj/main.tex

@@ -0,0 +1,2 @@
+content
+added more stuff

services/git-bridge/src/test/resources/uk/ac/ic/wlgitbridge/WLGitBridgeIntegrationTest/canPullADeletedTexFile/withDeletedTexFile/testproj/overleaf-white-410.png

@@ -0,0 +1,12 @@
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html;charset=ISO-8859-1"/>
+<title>Error 404 </title>
+</head>
+<body>
+<h2>HTTP ERROR: 404</h2>
+<p>Problem accessing /state/testproj1/overleaf-white-410.png. Reason:
+<pre>    Not Found</pre></p>
+<hr /><i><small>Powered by Jetty://</small></i>
+</body>
+</html>