Frontend modules

.gitignore

@@ -9,6 +9,7 @@ docs
 logo
 logs
 db
+dev
 project/project
 project/target
 conf/generated.keystore
@@ -30,6 +31,8 @@ experiments
 dev.bat
 dev.sh
 node_modules
-client-graph.js
 client-html.html
 csv
+
+.vscode
+generated

CONTRIBUTING.md

@@ -0,0 +1,33 @@
+# Contributing
+There are many different ways to contribute to the Breadboard project. We welcome issues, code, documentation
+and examples. 
+
+## Development
+
+### Environment setup
+Breadboard works with Java 7+. Make sure the Java SDK is installed before beginning development.
+
+- `cd frontend`
+- `npm install`
+
+### Running
+#### Backend development
+If modifications will be made to files in the **frontend** directory, use the frontend development instructions instead
+- Start the play framework server using `sbt "run -Dconfig.file=conf/application-prod.conf"`
+
+#### Frontend development
+This uses a slightly different configuration to allow hot module replacement via webpack on frontend files.
+- Start the webpack server using `cd frontend && npm start`
+- Start the play framework server using `sbt "run -Dconfig.file=conf/application-dev.conf"`
+
+
+From a terminal run . This will start a dev server which will
+automatically rebuild the frontend files whenever a file changes.
+
+
+## Production
+
+### Compile jars
+- `cd frontend && npm run build` to build frontend assets if this code has changed
+- `sh create_prod_dist.sh` to compile distributable files
+- In many cases, only copying the compiled **breadboard.jar** file is enough to update existing Breadboard applications.

README.md

@@ -27,3 +27,6 @@ breadboard is built using:
 * [CodeMirror](https://codemirror.net/)
 
 Also [Apache Commons](https://commons.apache.org/), [imgscalr](https://github.com/thebuzzmedia/imgscalr), [JUNG](http://jung.sourceforge.net/), [jQuery](https://jquery.com/), [Modernizr](https://modernizr.com/), [Underscore](http://underscorejs.org/), and [Bootstrap](http://getbootstrap.com/).
+
+### Contributing
+See the [contributing guide](CONTRIBUTING.md)

app/Global.java

@@ -35,13 +35,15 @@ public void onStart(Application app) {
     SqlRow versionTableCount = Ebean.createSqlQuery(sql).findUnique();
     String count = versionTableCount.getString("table_count");
 
+    // If the breadboard_version table doesn't exist we're < v2.3
     if (count.equals("0")) {
 
       // Create the breadboard_version table
       sql = "create table breadboard_version ( version varchar(255) ); ";
       Ebean.createSqlUpdate(sql).execute();
       // Update the version
-      sql = "insert into breadboard_version values ('v2.3.1'); ";
+      String version = play.Play.application().configuration().getString("application.version");
+      sql = "insert into breadboard_version values ('" + version + "'); ";
       Ebean.createSqlUpdate(sql).execute();
 
       // Create the languages table
@@ -155,25 +157,24 @@ public void onStart(Application app) {
       // TODO: Add message telling user what was done
       // TODO: Load v2.3 version notes as message from file system
 
+      // Upgrade to version 2.4.0
+      version2Point4Upgrade();
+    } else {
+      // The breadboard_version table exists, let's check if we're v2.3 or v2.4
+      sql = "select version from breadboard_version limit 1;";
+      SqlRow versionString = Ebean.createSqlQuery(sql).findUnique();
+      String version = versionString != null ? versionString.getString("version") : "";
+      if (version.equals("v2.3.0") || version.equals("v2.3.1")) {
+        // Add v2.4.0 fields
+        version2Point4Upgrade();
+      } // Otherwise, no upgrade needed
     }
+  }
 
-    //InitialData.insert(app);
-    boolean isWin = System.getProperty("os.name").toUpperCase().indexOf("WIN") >= 0;
-    String cwd = System.getProperty("user.dir");
-    // TODO: If omitted, this should default to PROD
-    String mode = play.Play.application().configuration().getString("application.mode");
-    if(mode.toUpperCase().equals("DEV")) {
-      // Try to start the assets server
-      try {
-        ProcessBuilder pb = new ProcessBuilder("node", cwd + "/frontend/webpack/webpack.server.js");
-        pb.directory(new File(cwd + "/frontend"));
-        pb.inheritIO();
-        process = pb.start();
-      } catch (Exception e) {
-        e.printStackTrace();
-      }
-    }
-    // TODO: We could build the production resources when the framework starts instead of having to build them manually
+  private void version2Point4Upgrade() {
+    // Changes to support Experiment fileMode
+    String sql = "alter table experiments add column if not exists file_mode bit default 0;";
+    Ebean.createSqlUpdate(sql).execute();
   }
 
   @Override

app/actors/FileWatcherActor.java

@@ -0,0 +1,106 @@
+package actors;
+
+import actors.FileWatcherActorProtocol.FileWatch;
+import akka.actor.UntypedActor;
+import models.Admin;
+import models.FileWatcher;
+import org.apache.commons.io.FileUtils;
+import play.Logger;
+
+import java.io.IOException;
+import java.nio.file.*;
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
+import java.util.Date;
+
+import static java.nio.file.StandardWatchEventKinds.ENTRY_CREATE;
+import static java.nio.file.StandardWatchEventKinds.ENTRY_DELETE;
+import static java.nio.file.StandardWatchEventKinds.ENTRY_MODIFY;
+
+public class FileWatcherActor extends UntypedActor {
+  private static DateFormat dateFormat;
+
+  public FileWatcherActor() {
+    dateFormat = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
+  }
+
+
+  @Override
+  public void onReceive(Object message) {
+    if (message instanceof FileWatch) {
+      FileWatcher fileWatcher = ((FileWatch) message).fileWatcher;
+
+      // If fileMode for the selected experiment is false, do nothing
+      /* TODO: if there are multiple admins listening, they could each be watching different experiments which is weird in the context of a single file watcher */
+      // if ( fileWatcher.getAdminListeners().isEmpty() || fileWatcher.getAdminListeners().get(0).getUser().selectedExperiment == null || (! fileWatcher.getAdminListeners().get(0).getUser().selectedExperiment.getFileMode()) ) {
+      //  return;
+      //}
+      fileWatcher.incrementUpdateIteration();
+      Long updateIteration = fileWatcher.getUpdateIteration();
+      if (updateIteration % 100 == 0) {
+        Logger.debug(dateFormat.format(new Date()) + " - FileWatch:" + updateIteration);
+      }
+
+      WatchKey watchKey;
+      boolean changed = false;
+      watchKey = fileWatcher.getWatcher().poll();
+      if (watchKey == null) {
+        return;
+      }
+
+      Path dir = fileWatcher.getWatchKeys().get(watchKey);
+      if (dir == null) {
+        Logger.error("Event triggered from watchKey not registered properly.");
+        return;
+      }
+
+      for (WatchEvent<?> event: watchKey.pollEvents()) {
+        WatchEvent<Path> ev = (WatchEvent<Path>) event;
+        Path name = ev.context();
+        Path child = dir.resolve(name);
+        Logger.debug(child.toString());
+        String selectedExperimentDirectory = (fileWatcher.getAdminListeners().get(0).getUser().selectedExperiment == null) ? "" : fileWatcher.getAdminListeners().get(0).getUser().selectedExperiment.getDirectoryName();
+        boolean selectedExperimentChanged = child.toString().contains(selectedExperimentDirectory);
+
+        if (ev.kind() == ENTRY_CREATE && child.toFile().isDirectory()) {
+          // new directory, need to watch it
+          try {
+            fileWatcher.registerRecursive(child);
+          } catch (IOException ioe) {
+            Logger.error("Unable to watch directory " + child.toFile().getPath() + " check the permissions.");
+          }
+          Logger.debug("DIRECTORY ENTRY_CREATE");
+        } else if ((ev.kind() == ENTRY_CREATE || ev.kind() == ENTRY_MODIFY) && child.toFile().isFile() && selectedExperimentChanged) {
+          // A file was modified or created in the selected experiment directory, update the admin
+          changed = true;
+          if (child.toFile().getParent().endsWith("/Steps")) {
+            // Step was modified or created, send to ScriptEngine
+            try {
+              String stepContents = FileUtils.readFileToString(child.toFile());
+              fileWatcher.loadStep(stepContents, fileWatcher.getAdminListeners().get(0).getOut(), child.getFileName().toString());
+            } catch (IOException ioe) {
+              Logger.error("Unable to read contents of Step " + child.getFileName().toString() + " check your permissions.");
+            }
+          }
+          Logger.debug("FILE ENTRY_MODIFY || ENTRY_CREATE");
+        } else if (ev.kind() == ENTRY_DELETE) {
+          Logger.debug("ENTRY_DELETE");
+        }
+      }
+
+      if (changed) {
+        // Something was changed, let's update all admin listeners
+        for(Admin a : fileWatcher.getAdminListeners()) {
+          a.update();
+        }
+      }
+
+      boolean valid = watchKey.reset();
+      if (!valid) {
+        fileWatcher.getWatchKeys().remove(watchKey);
+        Logger.debug("Watched directory was deleted.");
+      }
+    }
+  }
+}
+

app/actors/FileWatcherActorProtocol.java

@@ -0,0 +1,13 @@
+package actors;
+
+import models.FileWatcher;
+
+public class FileWatcherActorProtocol {
+  public static class FileWatch {
+    final FileWatcher fileWatcher;
+    public FileWatch(FileWatcher fileWatcher) {
+      this.fileWatcher = fileWatcher;
+    }
+  }
+}
+

app/controllers/Application.java

@@ -1,16 +1,13 @@
 package controllers;
 
 import models.*;
-import org.apache.commons.io.FileUtils;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.node.ObjectNode;
 import org.mindrot.jbcrypt.BCrypt;
 import play.Logger;
 import play.data.Form;
 import play.libs.Json;
 import play.mvc.*;
-import play.mvc.Http.MultipartFormData;
-import play.mvc.Http.MultipartFormData.FilePart;
 import views.html.*;
 import java.io.*;
 import java.text.SimpleDateFormat;
@@ -84,7 +81,7 @@ public static Result authenticate() {
       User user = User.findByEmail(email);
 
       if (user != null) {
-        Logger.info("authenticate: uid = " + uid);
+        Logger.debug("authenticate: uid = " + uid);
         user.uid = uid;
         user.update();
         result = Json.newObject();
@@ -103,9 +100,10 @@ public static Result logout() {
     return unauthorized();
   }
 
-  public static Result index() {
-      final File file = play.Play.application().getFile("assets/templates/breadboard.html");
-      return ok(file, true);
+  public static Result index () {
+      // final File file = play.Play.application().getFile("assets/templates/breadboard.html");
+      String assetsRoot = play.Play.application().configuration().getString("breadboard.assetsRoot", "/assets");
+      return ok(main.render(assetsRoot));
   }
 
   @Security.Authenticated(Secured.class)
@@ -115,82 +113,9 @@ public static Result getState() {
     result.put("juid", session("juid"));
     result.put("email", session("email"));
     result.put("connectSocket", play.Play.application().configuration().getString("breadboard.wsUrl"));
-    result.put("imageUploadRoute", routes.Application.uploadImage().toString());
     return ok(result);
   }
 
-  @Security.Authenticated(Secured.class)
-  public static Result uploadImage() {
-    MultipartFormData body = request().body().asMultipartFormData();
-    FilePart picture = body.getFile("picture");
-    if (picture != null) {
-      String fileName = picture.getFilename();
-      String contentType = picture.getContentType();
-      File file = picture.getFile();
-
-      Map<String, String[]> values = body.asFormUrlEncoded();
-
-      try {
-        String experimentId = values.get("experimentId")[0];
-        Long eid = Long.parseLong(experimentId);
-        Experiment experiment = Experiment.findById(eid);
-        Image image = new Image();
-        image.fileName = fileName;
-        image.file = FileUtils.readFileToByteArray(file);
-        image.contentType = contentType;
-        experiment.images.add(image);
-        experiment.save();
-      } catch (NullPointerException npe) {
-        Logger.error("IOException in uploadImage(): " + npe.getMessage());
-        return ok("Error uploading");
-      } catch (NumberFormatException nfe) {
-        Logger.error("IOException in uploadImage(): " + nfe.getMessage());
-        return ok("Error uploading");
-      } catch (IOException ioe) {
-        Logger.error("IOException in uploadImage(): " + ioe.getMessage());
-        return ok("Error uploading");
-      }
-
-
-      //TODO: For web deployment consider storing images to filesystem
-      //Integer nextId = (Integer)Ebean.nextId(Image.class);
-      //String uniqueFileName = nextId.toString() + "_" + fileName;
-      //Logger.info("uniquefileName = " + uniqueFileName);
-      //String uploadPath = "";
-
-
-      return ok("File uploaded");
-    } else {
-      return ok("Error uploading");
-    }
-  }
-
-  public static Result getImage(Long imageId) {
-    Image image = Image.findById(imageId);
-
-    if (image != null) {
-      if (image.contentType != null && image.file != null) {
-        response().setContentType(image.contentType);
-        return ok(image.file);
-      }
-    }
-
-    return notFound();
-  }
-
-  public static Result getImageThumb(Long imageId) {
-    Image image = Image.findById(imageId);
-
-    if (image != null) {
-      if (image.contentType != null && image.thumbFile != null && image.thumbFile.length > 0) {
-        response().setContentType(image.contentType);
-        return ok(image.thumbFile);
-      }
-    }
-
-    return notFound();
-  }
-
   @Security.Authenticated(Secured.class)
   public static Result saveUserSettings() {
     Form<UserSettings> userSettingsForm = Form.form(UserSettings.class);