v1.4.1

* WIP #1031 added container dependency info

* WIP #1031 updated quickstart

.codeclimate.yml

@@ -31,6 +31,8 @@ exclude_paths:
 - test/
 - src/common/lua.js
 - src/common/js-yaml.min.js
+- src/visualizers/widgets/Sidebar/lib/
 - src/visualizers/widgets/TextEditor/lib/
 - src/visualizers/widgets/PipelineIndex/styles/PipelineIndex.css
 - src/visualizers/widgets/LineGraph/lib/
+- src/visualizers/widgets/PipelineEditor/klay.js

.dockerignore

@@ -0,0 +1 @@
+/node_modules

.gitignore

@@ -35,3 +35,6 @@ test-tmp/
 blob-local-storage/
 src/seeds/nn/hash.txt
 src/seeds/pipeline/hash.txt
+
+notes/
+src/worker

.npmignore

@@ -0,0 +1,43 @@
+src/worker/tmp
+.env
+*.swp
+*.swo
+**.sass-cache
+# Logs
+logs
+*.log
+
+# Runtime data
+pids
+*.pid
+*.seed
+
+# Directory for instrumented libs generated by jscoverage/JSCover
+lib-cov
+
+# Coverage directory used by tools like istanbul
+coverage
+
+# Grunt intermediate storage (http://gruntjs.com/creating-plugins#storing-task-files)
+.grunt
+
+# node-waf configuration
+.lock-wscript
+
+# Compiled binary addons (http://nodejs.org/api/addons.html)
+build/Release
+
+# Dependency directory
+# https://www.npmjs.org/doc/misc/npm-faq.html#should-i-check-my-node_modules-folder-into-git
+node_modules
+tmp/
+test-tmp/
+blob-local-storage/
+src/seeds/nn/hash.txt
+src/seeds/pipeline/hash.txt
+
+# docs
+images/
+
+notes/
+src/worker

Dockerfile

@@ -0,0 +1,24 @@
+# Dockerfile for running the server itself
+FROM node:6.10.1
+MAINTAINER Brian Broll <brian.broll@gmail.com>
+
+RUN echo '{"allow_root": true}' > /root/.bowerrc && mkdir -p /root/.config/configstore/ && \
+    echo '{}' > /root/.config/configstore/bower-github.json
+
+RUN mkdir /deepforge
+ADD . /deepforge
+WORKDIR /deepforge
+
+RUN cd $(npm root -g)/npm \
+    && npm install fs-extra \
+    && sed -i -e s/graceful-fs/fs-extra/ -e s/fs.rename/fs.move/ ./lib/utils/rename.js
+
+RUN ln -s /deepforge/bin/deepforge /usr/local/bin
+
+EXPOSE 8888
+
+# Set up the data storage
+RUN deepforge config blob.dir /data/blob && \
+    deepforge config mongo.dir /data/db
+
+CMD ["deepforge", "start", "--server"]

Dockerfile.worker

@@ -0,0 +1,65 @@
+# This has torch and cuda support
+FROM kaixhin/cuda-torch
+MAINTAINER Brian Broll <brian.broll@gmail.com>
+
+# install nodejs v6
+RUN groupadd --gid 1000 node \
+  && useradd --uid 1000 --gid node --shell /bin/bash --create-home node
+
+# gpg keys listed at https://github.com/nodejs/node#release-team
+RUN set -ex \
+  && for key in \
+    9554F04D7259F04124DE6B476D5A82AC7E37093B \
+    94AE36675C464D64BAFA68DD7434390BDBE9B9C5 \
+    FD3A5288F042B6850C66B31F09FE44734EB7990E \
+    71DCFD284A79C3B38668286BC97EC7A07EDE3FC1 \
+    DD8F2338BAE7501E3DD5AC78C273792F7D83545D \
+    B9AE9905FFD7803F25714661B63B535A4C206CA9 \
+    C4F0DFFF4E8C1A8236409D08E73BC641CC11F4C8 \
+    56730D5401028683275BD23C23EFEFE93C4CFFFE \
+  ; do \
+    gpg --keyserver ha.pool.sks-keyservers.net --recv-keys "$key"; \
+  done
+
+ENV NPM_CONFIG_LOGLEVEL info
+ENV NODE_VERSION 6.10.1
+
+RUN curl -SLO "https://nodejs.org/dist/v$NODE_VERSION/node-v$NODE_VERSION-linux-x64.tar.xz" \
+  && curl -SLO "https://nodejs.org/dist/v$NODE_VERSION/SHASUMS256.txt.asc" \
+  && gpg --batch --decrypt --output SHASUMS256.txt SHASUMS256.txt.asc \
+  && grep " node-v$NODE_VERSION-linux-x64.tar.xz\$" SHASUMS256.txt | sha256sum -c - \
+  && tar -xJf "node-v$NODE_VERSION-linux-x64.tar.xz" -C /usr/local --strip-components=1 \
+  && rm "node-v$NODE_VERSION-linux-x64.tar.xz" SHASUMS256.txt.asc SHASUMS256.txt \
+  && ln -s /usr/local/bin/node /usr/local/bin/nodejs
+
+# install deepforge
+RUN echo '{"allow_root": true}' > /root/.bowerrc && mkdir -p /root/.config/configstore/ && \
+    echo '{}' > /root/.config/configstore/bower-github.json
+
+RUN mkdir /deepforge
+ADD . /deepforge
+WORKDIR /deepforge
+
+RUN cd $(npm root -g)/npm \
+    && npm install fs-extra \
+    && sed -i -e s/graceful-fs/fs-extra/ -e s/fs.rename/fs.move/ ./lib/utils/rename.js
+
+RUN ln -s /deepforge/bin/deepforge /usr/local/bin
+
+# configure the worker
+RUN deepforge config blob.dir /data/blob && \
+    deepforge config mongo.dir /data/db && \
+    deepforge config worker.cache.useBlob false && \
+    deepforge config worker.cache.dir /deepforge/worker-cache && \
+    deepforge config torch.dir /root/torch/ && \
+    git config --global user.email "deepforge-worker@deepforge.org" && \
+    git config --global user.name "deepforge-worker"
+
+# Update torch
+RUN apt-get update && apt-get install sudo wget && \
+    . /root/torch/install/bin/torch-activate && \
+    cd /root/torch/ && bash /root/torch/update.sh && \
+    deepforge update -t
+
+ENTRYPOINT ["deepforge", "start", "--worker"]
+CMD ["http://172.17.0.1:8888"]

README.md

@@ -1,34 +1,50 @@
 [![Release State](https://img.shields.io/badge/state-beta-yellow.svg)](https://img.shields.io/badge/state-beta-yellow.svg)
 [![License](https://img.shields.io/badge/license-Apache%202.0-blue.svg)](./LICENSE)
-[![Build Status](https://travis-ci.org/dfst/deepforge.svg?branch=master)](https://travis-ci.org/dfst/deepforge)
-[![Join the chat at https://gitter.im/dfst/deepforge](https://badges.gitter.im/dfst/deepforge.svg)](https://gitter.im/dfst/deepforge?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
-[![Stories in Ready](https://badge.waffle.io/dfst/deepforge.png?label=ready&title=Ready)](https://waffle.io/dfst/deepforge)
+[![Build Status](https://travis-ci.org/deepforge-dev/deepforge.svg?branch=master)](https://travis-ci.org/deepforge-dev/deepforge)
+[![Join the chat at https://gitter.im/deepforge-dev/deepforge](https://badges.gitter.im/deepforge-dev/deepforge.svg)](https://gitter.im/deepforge-dev/deepforge?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+[![Stories in Ready](https://badge.waffle.io/deepforge-dev/deepforge.png?label=ready&title=Ready)](https://waffle.io/deepforge-dev/deepforge)
 
-**Notice**: DeepForge is still a work in progress and is also lacking significant documentation! That being said, any contributions and/or feedback is greatly appreciated (and feel free to always ask any questions on the gitter)!
+Using DeepForge? [Let us know what you think!](https://goo.gl/forms/2pDdCPXoUvkQhVzQ2)
 
 # DeepForge
-DeepForge is an open-source visual development environment for deep learning. Currently, it supports Convolutional Neural Networks but we are planning on supporting additional deep learning classifiers such as RNNs and LSTMs. Additional features include real-time collaborative editing and version control.
+DeepForge is an open-source visual development environment for deep learning providing end-to-end support for creating deep learning models. This is achieved through providing the ability to design **architectures**, create training **pipelines**, and then execute these pipelines over a cluster. Using a notebook-esque api, users can get real-time feedback about the status of any of their **executions** including compare them side-by-side in real-time.
+
+![overview](images/overview.png "")
+
+Additional features include:
+- Graphical architecture editor
+- Training/testing pipeline creation
+- Distributed pipeline execution
+- Real-time pipeline feedback
+- Collaborative editing
+- Automatic version control.
+- Facilitates defining custom layers 
 
 ## Quick Start
-Simply run the following command to install deepforge with its dependencies:
-
+The easiest way to start deepforge is using [docker-compose](https://docs.docker.com/compose/). Using docker-compose, deepforge can be started with
 ```
-curl -o- https://raw.githubusercontent.com/dfst/deepforge/master/install.sh | bash
+wget https://raw.githubusercontent.com/deepforge-dev/deepforge/master/docker-compose.yml
+docker-compose up
 ```
 
-Or, if you already have NodeJS (v6) installed, simply run
+Finally, navigate to [http://localhost:8888](http://localhost:8888) to start using DeepForge! For more detailed instructions and other installation options, check out the [docs](http://deepforge.readthedocs.io/en/latest/deployment/overview.html).
 
-```
-npm install -g deepforge
-```
+## Additional Resources
+- [Intro to DeepForge Slides](https://docs.google.com/presentation/d/10_y5O3gHXSATfjHVLJg7dOdrz-tAXNWjlxhJ5SlA0ic/edit?usp=sharing)
+- [wiki](https://github.com/deepforge-dev/deepforge/wiki) containing overview, installation, configuration and developer information
+- [Starter Kit](https://github.com/deepforge-dev/examples/tree/master/starterkit) containing example pipelines demonstrating various deepforge features
+- [Examples](https://github.com/deepforge-dev/examples)
 
-Next, start deepforge with `deepforge start`!
-
-Finally, navigate to [http://localhost:8888](http://localhost:8888) to start using DeepForge! For more, detailed instructions, check out the [wiki](https://github.com/dfst/deepforge/wiki/Installation-Guide).
-
-Also, be sure to check out the other available features of the `deepforge` cli; it can be used to update, manage your torch installation, uninstall deepforge and run individual components!
+- [Datamodel Developer Slides](https://docs.google.com/presentation/d/1hd3IyUlzW_TIPnzCnE-1pdz00Pw8WaIxYiOW_Hyog-M/edit#slide=id.p)
 
 ## Interested in contributing?
-Contributions are welcome! Either fork the project and submit some PR's or shoot me an email about getting more involved!
+Contributions are welcome! There are a couple different ways to contribute to DeepForge:
+- Provide user feedback!
+    - on the [documentation](http://deepforge.readthedocs.io)
+    - on deepforge and its future development: https://goo.gl/forms/2pDdCPXoUvkQhVzQ2
+- Contribute to the project directly by submitting some PR's!
+
+If you have any questions, check out the [wiki](https://github.com/dfst/deepforge/wiki/) or drop me a line on the gitter!
+
 
 Sponsored by [Digital Reasoning](http://www.digitalreasoning.com/)

_config.yml

@@ -0,0 +1 @@
+theme: jekyll-theme-cayman

app.js

@@ -4,11 +4,17 @@
 var gmeConfig = require('./config'),
     webgme = require('webgme'),
     path = require('path'),
+    fs = require('fs'),
     rm_rf = require('rimraf'),
+    gracefulFs = require('graceful-fs'),
     myServer;
 
+process.chdir(__dirname);
 webgme.addToRequireJsPaths(gmeConfig);
 
+// Patch the 'fs' module to fix 'too many files open' error
+gracefulFs.gracefulify(fs);
+
 // Clear seed hash info
 ['nn', 'pipeline'].map(lib => path.join(__dirname, 'src', 'seeds', lib, 'hash.txt'))
     .forEach(file => rm_rf.sync(file));

bin/deepforge

@@ -1,6 +1,7 @@
 #!/usr/bin/env node
 
 var Command = require('commander').Command,
+    tcpPortUsed = require('tcp-port-used'),
     program = new Command(),
     childProcess = require('child_process'),
     rawSpawn = childProcess.spawn,
@@ -8,7 +9,8 @@ var Command = require('commander').Command,
     execSync = childProcess.execSync,
     path = require('path'),
     fs = require('fs'),
-    version = require('../package.json').version,
+    pkgJson = require('../package.json'),
+    version = pkgJson.version,
     exists = require('exists-file'),
     DEFAULT_CONFIG = require('./config.json'),
     merge = require('lodash.merge'),
@@ -117,32 +119,35 @@ var isLocalUri = function(protocol, uri) {
         uri.indexOf(protocol + '://127.0.0.1') === 0;
 };
 
-var checkMongo = function(args, notSilent) {
+var checkMongo = function(args, notSilent, mongoUri) {
     // check the webgme config
-    var gmeConfig = require('../config'),
-        mongoUri = gmeConfig.mongo.uri;
+    var gmeConfig = require('../config');
+
+    mongoUri = mongoUri || gmeConfig.mongo.uri;
 
     if (isLocalUri('mongodb', mongoUri)) {
+        var match = mongoUri.match(/:([0-9]+)/),
+            port = '80';
+
+        if (match) {
+            port = match[1];
+        }
+
         // Make sure mongo is running locally (using pgrep)
         try {
             execSync('pgrep mongod').toString();
             console.log('MongoDB is already running!');
         } catch (e) {  // no pIds
             console.log('Starting MongoDB...');
-            var match = mongoUri.match(/:([0-9]+)/),
-                port = '80';
-
-            if (match) {
-                port = match[1];
-            }
-
             startMongo(args, port, !notSilent);
         }
+        return tcpPortUsed.waitUntilUsed(+port, 100, 1000);
     } else if (notSilent) {
         console.log(`Cannot start remote mongo locally: ${mongoUri}`);
     } else {
         console.log(`Using remote mongo: ${mongoUri}`);
     }
+    return Q();
 };
 
 var startMongo = function(args, port, silent) {
@@ -208,28 +213,34 @@ var installTorch = function() {
         args = `clone https://github.com/torch/distro.git ${tgtDir} --recursive`.split(' ');
 
         return spawn('git', args)
-            .then(code => {
-                if (code !== 0) {
-                    if (code === 128) {
-                        console.error(`${tgtDir} is not empty. ` +
-                            'Please empty it or change the torch directory:\n' +
-                            '\n    deepforge config torch.dir NEW/TORCH/PATH\n');
+            .catch(result => {
+                var error = result.error || result.stderr ||
+                    `Torch install failed with exit code ${result.code}`;
 
-                    }
+                if (result.stderr.includes('unable to access')) {
+                    error = `Could not access the torch repository. Are you ` +
+                        `connected to the internet?\n`;
+                } else if (result.code === 128) {
+                    error = `${tgtDir} is not empty. ` +
+                        'Please empty it or change the torch directory:\n' +
+                        '\n    deepforge config torch.dir NEW/TORCH/PATH\n';
 
-                    throw `Torch install Failed with exit code ${code}`;
-                } else {  // continue installation
-                    process.chdir(tgtDir);
-                    return spawn('bash', ['install-deps'])
-                        .then(() => spawn('bash', ['install.sh'], true))
-                        .then(() => {
-                            storeConfig('torch.dir', tgtDir);
-                            console.log('Installed torch. Please close and ' +
-                                're-open your terminal to use DeepForge w/ ' +
-                                'torch support!');
-                            process.exit(0);
-                        });
                 }
+
+                console.error(error);
+                process.exit(result.code);
+            })
+            .then((code, stderr) => {
+                process.chdir(tgtDir);
+                return spawn('bash', ['install-deps'])
+                    .then(() => spawn('bash', ['install.sh'], true))
+                    .then(() => {
+                        storeConfig('torch.dir', tgtDir);
+                        console.log('Installed torch. Please close and ' +
+                            're-open your terminal to use DeepForge w/ ' +
+                            'torch support!');
+                        process.exit(0);
+                    });
             });
     } else {
         return Q();
@@ -242,21 +253,32 @@ var spawn = function(cmd, args, opts) {
         spawnOpts = typeof opts === 'object' ? opts : null,
         forwardStdin = opts === true,
         isOpen = true,
+        stderr = '',
         err;
 
     args = args || [];
     job = spawnOpts ? rawSpawn(cmd, args, spawnOpts) : rawSpawn(cmd, args);
     job.stdout.on('data', data => process.stdout.write(data));
-    job.stderr.on('data', data => process.stderr.write(data));
+    job.stderr.on('data', data => {
+        stderr += data;
+        process.stderr.write(data);
+    });
+
     job.on('close', code => {
         isOpen = false;
-        if (err) {
-            deferred.reject(err, code);
+        if (err || code !== 0) {
+            deferred.reject({
+                code: code,
+                stderr: stderr,
+                error: err
+            });
         } else {
             deferred.resolve(code);
         }
     });
-    job.on('error', e => err = e);
+    job.on('error', e => {
+        err = e;
+    });
 
     if (forwardStdin) {
         process.stdin.on('data', data => {
@@ -276,42 +298,49 @@ program.command('start')
     .option('-w, --worker [url]', 'start a worker and connect to given url. Defaults to local deepforge')
     .option('-m, --mongo', 'start MongoDB')
     .action(args => {
-        var main = path.join(__dirname, 'start-local.js');
+        var main = path.join(__dirname, 'start-local.js'),
+            current = Q();
 
         if (args.port) {
             process.env.PORT = args.port;
         }
 
+        if (args.mongo) {
+            current = current.then(() => checkMongo(args, true));
+        }
+
         if (args.server) {
-            checkMongo(args);
-            main = path.join(__dirname, '..', 'app.js');
-            spawn('node', [main]);
+            current = current
+                .then(() => checkMongo(args))
+                .then(() => {
+                    main = path.join(__dirname, '..', 'app.js');
+                    return spawn('node', [main]);
+                });
         }
 
         if (args.worker) {
             if (hasTorch()) {
-                installTorchExtras().then(() => {
-                    main = path.join(__dirname, 'start-worker.js');
-                    if (args.worker !== true) {
-                        spawn('node', [main, args.worker]);
-                    } else {
-                        spawn('node', [main]);
-                    }
-                });
+                current
+                    .then(() => installTorchExtras())
+                    .then(() => {
+                        main = path.join(__dirname, 'start-worker.js');
+                        if (args.worker !== true) {
+                            spawn('node', [main, args.worker]);
+                        } else {
+                            spawn('node', [main]);
+                        }
+                    });
             } else {
                 installTorch();
             }
         }
 
-        if (args.mongo) {
-            checkMongo(args, true);
-        }
-
         if (!args.server && !args.worker && !args.mongo) {
             // Starting everything
-            checkMongo(args);
+            current = current.then(() => checkMongo(args));
             if (hasTorch()) {
-                installTorchExtras().then(() => spawn('node', [main]));
+                current.then(() => installTorchExtras())
+                    .then(() => spawn('node', [main]));
             } else {
                 installTorch();
             }
@@ -334,7 +363,7 @@ program
         if (!args.torch || args.server) {
 
             if (args.git) {
-                pkg = 'dfst/deepforge';
+                pkg = pkgJson.repository.url;
             } else {
                 // Check the version
                 try {
@@ -447,12 +476,17 @@ program
         }
     });
 
+// extensions
+program
+    .command('extensions <command>', 'Manage deepforge extensions');
+
 module.exports = function(cmd) {
     var cmds = cmd.split(/\s+/).filter(w => !!w);
     cmds.unshift('./bin/deepforge');
     cmds.unshift('node');
     program.parse(cmds);
 };
+module.exports.checkMongo = checkMongo;
 
 if (require.main === module) {
     program.parse(process.argv);

bin/deepforge-extensions

@@ -0,0 +1,67 @@
+#!/usr/bin/env node
+
+var Command = require('commander').Command,
+    program = new Command(),
+    extender = require('../utils/extender');
+
+// Supported commands
+//  - add
+//  - remove
+//  - list
+//  - update
+program
+    .command('add <project>')
+    .description('Add an extension to deepforge')
+    .option('-n, --name <name>', 'Project name (if different from <project>)')
+    .action(project => {
+        console.log('loading extension from: ' + project);
+        extender.install(project)
+            .then(extConfig => 
+                console.log(`The ${extConfig.name} extension has been added to deepforge.`))
+            .fail(err => {
+                console.error('Could not install extension:\n');
+                console.error(err);
+                process.exit(1);
+            });
+    });
+
+program
+    .command('remove <name>').alias('rm')
+    .description('Remove an extension from deepforge')
+    .action(name => {
+        try {
+            extender.uninstall(name);
+            console.log(`${name} has been successfully removed!`);
+        } catch (e) {
+            console.error('Could not remove extension:');
+            console.error(e);
+            process.exit(1);
+        }
+    });
+
+program
+    .command('list').alias('ls')
+    .description('List installed deepforge extensions')
+    .action(() => {
+        var allExtConfigs = extender.getExtensionsConfig(),
+            types = Object.keys(allExtConfigs),
+            hasContents = false,
+            names;
+
+        for (var i = types.length; i--;) {
+            names = Object.keys(allExtConfigs[types[i]]);
+            if (names.length) {
+                hasContents = true;
+                console.log(types[i]);
+                for (var j = names.length; j--;) {
+                    console.log(`  ${names[j]}`);
+                }
+            }
+        }
+
+        if (!hasContents) {
+            console.log('No installed extensions');
+        }
+    });
+
+program.parse(process.argv);

bin/start-local.js

@@ -13,8 +13,8 @@ if (gmeConfig.blob.type === 'FS') {
 }
 
 process.env.NODE_ENV = 'local';
-execJob = spawn('npm', [
-    'start'
+execJob = spawn('node', [
+    path.join(__dirname, '..', 'app.js')
 ], env);
 execJob.stdout.pipe(process.stdout);
 execJob.stderr.pipe(process.stderr);

bin/start-worker.js

@@ -6,8 +6,7 @@ var path = require('path'),
     spawn = childProcess.spawn,
     rm_rf = require('rimraf'),
     projectConfig = require(__dirname + '/../config'),
-    executorSrc = path.join(__dirname, '..', 'node_modules', 'webgme', 'src',
-        'server', 'middleware', 'executor', 'worker'),
+    executorSrc = path.join(__dirname, '..', 'node_modules', '.bin', 'webgme-executor-worker'),
     id = Date.now(),
     workerRootPath = process.env.DEEPFORGE_WORKER_DIR || path.join(__dirname, '..', 'src', 'worker'),
     workerPath = path.join(workerRootPath, `worker_${id}`),
@@ -37,7 +36,6 @@ try {
 } catch (e) {
     // Create dir
     childProcess.spawnSync('ln', ['-s', `${__dirname}/../node_modules`, modules]);
-    return true;
 }
 
 // Check torch support
@@ -60,7 +58,7 @@ var startExecutor = function() {
 
     // Start the executor
     var execJob = spawn('node', [
-        'node_worker.js',
+        executorSrc,
         workerConfigPath,
         workerTmp
     ]);
@@ -74,20 +72,13 @@ var createConfigJson = function() {
 
     if (process.argv.length > 2) {
         address = process.argv[2];
+        if (!/^https?:\/\//.test(address)) {
+            address = 'http://' + address;
+        }
     }
 
     config[address] = {};
     fs.writeFile(workerConfigPath, JSON.stringify(config), startExecutor);
 };
 
-process.chdir(executorSrc);
-
-fs.mkdir(workerTmp, function() {
-    // npm install in this directory
-    var npmInstall = spawn('npm', ['install']);
-    npmInstall.stdout.pipe(process.stdout);
-    npmInstall.stderr.pipe(process.stderr);
-    npmInstall.on('close', function() {
-        createConfigJson();
-    });
-});
+fs.mkdir(workerTmp, createConfigJson);

config/components.json

@@ -2,13 +2,29 @@
     "AutoViz": {
         "preloadIds": [
             "ArchEditor",
+            "ArchIndex",
+            "PipelineIndex",
             "PipelineEditor",
             "OperationEditor",
             "ExecutionView"
-        ]
+        ],
+        "visualizerOverrides": {
+            "": "ForwardViz",
+            "MyArtifacts": "ArtifactIndex",
+            "MyArchitectures": "ArchIndex",
+            "MyExecutions": "ExecutionIndex",
+            "MyPipelines": "PipelineIndex"
+        }
+    },
+    "PipelineEditor": {
+        "itemName": "operation"
+    },
+    "ExecutionView": {
+        "itemName": "job"
     },
     "ArchEditor": {
         "hotkeys": "none",
+        "itemName": "layer",
         "LayerColors": {}
     },
     "BreadcrumbHeader": {
@@ -32,10 +48,6 @@
             "ImportTorch": {
                 "icon": "import_export",
                 "priority": -1
-            },
-            "GenerateExecFile": {
-                "icon": "play_for_work",
-                "priority": -1
             }
         }
     },
@@ -43,11 +55,11 @@
         "rootMenuClass": "deepforge-logo",
         "rootDisplayName": "DeepForge"
     },
-    "CHFLayout": {
+    "SidebarLayout": {
         "panels": [
             {
-                "id": "Header",
-                "panel": "BreadcrumbHeader/BreadcrumbHeaderPanel",
+                "id": "WorkerHeader",
+                "panel": "WorkerHeader/WorkerHeaderPanel",
                 "container": "header",
                 "DEBUG_ONLY": false
             },
@@ -63,6 +75,12 @@
                 "container": "center",
                 "DEBUG_ONLY": false
             },
+            {
+                "id": "Sidebar",
+                "panel": "Sidebar/SidebarPanel",
+                "container": "sidebar",
+                "DEBUG_ONLY": false
+            },
             {
                 "id": "ForgeActionButton",
                 "panel": "ForgeActionButton/ForgeActionButton",

config/config.base.js

@@ -8,6 +8,7 @@ require('dotenv').load({silent: true});
 
 // Add/overwrite any additional settings here
 config.server.port = +process.env.PORT || config.server.port;
+config.server.timeout = 0;
 config.mongo.uri = process.env.MONGO_URI || config.mongo.uri;
 config.blob.fsDir = process.env.DEEPFORGE_BLOB_DIR || config.blob.fsDir;
 

config/config.webgme.js

@@ -9,6 +9,7 @@ var config = require('webgme/config/config.default'),
 // The paths can be loaded from the webgme-setup.json
 config.plugin.basePaths.push(__dirname + '/../src/plugins');
 config.plugin.basePaths.push(__dirname + '/../node_modules/webgme-simple-nodes/src/plugins');
+config.visualization.layout.basePaths.push(__dirname + '/../src/layouts');
 config.visualization.layout.basePaths.push(__dirname + '/../node_modules/webgme-chflayout/src/layouts');
 config.visualization.decoratorPaths.push(__dirname + '/../src/decorators');
 config.visualization.decoratorPaths.push(__dirname + '/../node_modules/webgme-easydag/src/decorators');
@@ -20,6 +21,7 @@ config.seedProjects.basePaths.push(__dirname + '/../src/seeds/devPipelineTests')
 config.seedProjects.basePaths.push(__dirname + '/../src/seeds/project');
 config.seedProjects.basePaths.push(__dirname + '/../src/seeds/cifar10');
 config.seedProjects.basePaths.push(__dirname + '/../src/seeds/xor');
+config.seedProjects.basePaths.push(__dirname + '/../src/seeds/devProject');
 
 
 
@@ -31,6 +33,8 @@ config.visualization.panelPaths.push(__dirname + '/../src/visualizers/panels');
 
 
 config.rest.components['execution/logs'] = __dirname + '/../src/routers/JobLogsAPI/JobLogsAPI.js';
+config.rest.components['job/origins'] = __dirname + '/../src/routers/JobOriginAPI/JobOriginAPI.js';
+config.rest.components['execution/pulse'] = __dirname + '/../src/routers/ExecPulse/ExecPulse.js';
 
 // Visualizer descriptors
 config.visualization.visualizerDescriptors.push(__dirname + '/../src/visualizers/Visualizers.json');
@@ -55,7 +59,7 @@ config.requirejsPaths = {
   'widgets/FloatingActionButton': './node_modules/webgme-fab/src/visualizers/widgets/FloatingActionButton'
 };
 
-config.visualization.layout.default = 'CHFLayout';
+config.visualization.layout.default = 'SidebarLayout';
 config.mongo.uri = 'mongodb://127.0.0.1:27017/deepforge';
 validateConfig(config);
 module.exports = config;

docker-compose.yml

@@ -0,0 +1,22 @@
+--- 
+services: 
+  mongo: 
+    image: mongo
+    volumes: 
+      - "$HOME/.deepforge/data:/data/db"
+  server: 
+    environment: 
+      - "MONGO_URI=mongodb://mongo:27017/deepforge"
+    image: deepforge/server
+    ports: 
+      - "8888:8888"
+    volumes: 
+      - "$HOME/.deepforge/blob:/data/blob"
+    depends_on:
+      - mongo
+  worker: 
+    command: "http://server:8888"
+    image: deepforge/worker
+    depends_on:
+      - server
+version: "2"

docs/.gitignore

@@ -0,0 +1 @@
+_build

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = deepforge
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -0,0 +1,159 @@
+import sphinx_rtd_theme
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# deepforge documentation build configuration file, created by
+# sphinx-quickstart on Mon Mar 13 18:56:27 2017.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = []
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = 'DeepForge'
+copyright = '2017, Brian Broll'
+author = 'Brian Broll'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = ''
+# The full version, including alpha/beta/rc tags.
+release = ''
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'deepforgedoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'deepforge.tex', 'deepforge Documentation',
+     'Brian Broll', 'manual'),
+]
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'deepforge', 'deepforge Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'deepforge', 'deepforge Documentation',
+     author, 'deepforge', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+

docs/deployment/dockerized.rst

@@ -0,0 +1,45 @@
+Dockerized Installation
+-----------------------
+Each of the components are also available as docker containers. This page outlines the running of each of the main components as docker containers and connecting them as necessary.
+
+Database
+~~~~~~~~
+First, you can start the mongo container using:
+
+.. code-block:: bash
+
+    docker run -d -v /abs/path/to/data:/data/db mongo
+
+where :code:`/abs/path/to/data` is the path to the mongo data location on the host. If running the database in a container, you will need to get the ip address of the given container:
+
+.. code-block:: bash
+
+    docker inspect <container id>  | grep IPAddr
+
+The :code:`<container id>` is the value returned from the original :code:`docker run` command.
+
+When running mongo in a docker container, it is important to mount an external volume (using the :code:`-v` flag) to be used for the actual data (otherwise the data will be lost when the container is stopped).
+
+Server
+~~~~~~
+The DeepForge server can be started with
+
+.. code-block:: bash
+
+    docker run -d -v $HOME/.deepforge/blob:/data/blob \
+    -p 8888:8888 -e MONGO_URI=mongodb://172.17.0.2:27017/deepforge \
+    deepforge/server
+
+where :code:`172.17.0.2` is the ip address of the mongo container and :code:`$HOME/.deepforge/blob` is the path to use for binary DeepForge data on the host. Of course, if the mongo instance is locating at a different location, :code:`MONGO_URI` can be set to this address as well. Also, the first port (:code:`8888`) can be replaced with the desired port to expose on the host.
+
+Worker
+~~~~~~
+As workers may require GPU access, they will need to use the nvidia-docker plugin. Workers can be created using
+
+.. code-block:: bash
+
+    nvidia-docker run -d deepforge/worker http://172.17.0.1:8888
+
+where :code:`http://172.17.0.1:8888` is the location of the DeepForge server to which to connect.
+
+**Note**: The :code:`deepforge/worker` image is packaged with cuda 7.5. Depending upon your hardware and nvidia version, you may need to build your own docker image or run the worker natively.

docs/deployment/native.rst

@@ -0,0 +1,130 @@
+Native Installation
+===================
+
+Dependencies
+------------
+First, install `NodeJS <https://nodejs.org/en/>`_ (v6) and `MongoDB <https://www.mongodb.org/>`_. You may also need to install git if you haven't already.
+
+Next, you can install DeepForge using npm:
+
+.. code-block:: bash
+
+    npm install -g deepforge
+
+Now, you can check that it installed correctly:
+
+.. code-block:: bash
+
+    deepforge --version
+
+DeepForge can now be started with:
+
+.. code-block:: bash
+
+    deepforge start
+
+However, the first time DeepForge is started, it will make sure that the deep learning framework is installed (if it isn't found on the host system). This may require you to start DeepForge a couple times; the first time it starts it will install Torch7 and require a terminal restart to update a couple environment variables (like `PATH`). The second time it starts it will install additional torch packages but will not require a terminal restart. Finally, DeepForge will start with all the required dependencies.
+
+Database
+~~~~~~~~
+Download and install MongoDB from the `website <https://www.mongodb.org/>`_. If you are planning on running MongoDB locally on the same machine as DeepForge, simply start `mongod` and continue to setting up DeepForge.
+
+If you are planning on running MongoDB remotely, set the environment variable "MONGO_URI" to the URI of the Mongo instance that DeepForge will be using:
+
+.. code-block:: bash
+
+    MONGO_URI="mongodb://pathToMyMongo.com:27017/myCollection" deepforge start
+
+Server
+~~~~~~
+The DeepForge server is included with the deepforge cli and can be started simply with 
+
+.. code-block:: bash
+
+    deepforge start --server
+
+By default, DeepForge will start on `http://localhost:8888`. However, the port can be specified with the `--port` option. For example:
+
+.. code-block:: bash
+
+    deepforge start --server --port 3000
+
+Worker
+~~~~~~
+The DeepForge worker can be started with
+
+.. code-block:: bash
+
+    deepforge start --worker
+
+The worker will install dependencies the first time it is run (including torch, if it is not already installed). 
+
+To connect to a remote deepforge instance, add the url of the DeepForge server:
+
+.. code-block:: bash
+
+    deepforge start --worker http://myaddress.com:1234
+
+Updating
+~~~~~~~~
+DeepForge can be updated with the command line interface rather simply:
+
+.. code-block:: bash
+
+    deepforge update
+
+By default, this will update both DeepForge and the local torch installation. To only update DeepForge, add the `--server` flag:
+
+.. code-block:: bash
+
+    deepforge update --server
+
+For more update options, check out `deepforge update --help`!
+
+Manual Installation (Development)
+---------------------------------
+Installing DeepForge for development is essentially cloning the repository and then using `npm` (node package manager) to run the various start, test, etc, commands (including starting the individual components). The deepforge cli can still be used but must be referenced from `./bin/deepforge`. That is, `deepforge start` becomes `./bin/deepforge start` (from the project root).
+
+DeepForge Server
+~~~~~~~~~~~~~~~~
+First, clone the repository:
+
+.. code-block:: bash
+
+    git clone https://github.com/dfst/deepforge.git
+
+Then install the project dependencies:
+
+.. code-block:: bash
+
+    npm install
+
+To run all components locally start with 
+
+.. code-block:: bash
+
+    ./bin/deepforge start
+
+and navigate to `http://localhost:8888` to start using DeepForge!
+
+Alternatively, if jobs are going to be executed on an external worker, run `./bin/deepforge start -s` locally and navigate to `http://localhost:8888`.
+
+DeepForge Worker
+~~~~~~~~~~~~~~~~
+If you are using `./bin/deepforge start -s` you will need to set up a DeepForge worker (`./bin/deepforge start` starts a local worker for you!). DeepForge workers are slave machines connected to DeepForge which execute the provided jobs. This allows the jobs to access the GPU, etc, and provides a number of benefits over trying to perform deep learning tasks in the browser.
+
+Once DeepForge is installed on the worker, start it with
+
+.. code-block:: bash
+
+    ./bin/deepforge start -w
+
+Note: If you are running the worker on a different machine, put the address of the DeepForge server as an argument to the command. For example:
+
+.. code-block:: bash
+
+    ./bin/deepforge start -w http://myaddress.com:1234
+
+Updating
+~~~~~~~~
+Updating can be done the same as any other git project; that is, by running `git pull` from the project root. Sometimes, the dependencies need to be updated so it is recommended to run `npm install` following `git pull`.

docs/deployment/overview.rst

@@ -0,0 +1,26 @@
+Overview
+========
+
+DeepForge Component Overview
+----------------------------
+DeepForge is composed of four main elements:
+
+- *Server*: Main component hosting all the project information and is connected to by the clients
+- *Database*: MongoDB database containing DeepForge, job queue for the workers, etc
+- *Worker*: Slave machine performing the actual machine learning computation
+- *Client*: The connected browsers working on DeepForge projects.
+
+Of course, only the *Server*, *Database* (MongoDB) and *Worker* need to be installed. If you are not going to execute any machine learning pipelines, installing the *Worker* can be skipped.
+
+Component Dependencies
+----------------------
+The following dependencies are required for each component:
+
+- *Server* (NodeJS v6.2.1)
+- *Database* (MongoDB v3.0.7)
+- *Worker*: NodeJS v6.2.1 (used for job management logic) and `Torch <http://torch.ch/docs/getting-started.html#>`_ (this will be installed automatically by the cli when needed)
+- *Client*: We recommend using Google Chrome and are not supporting other browsers (for now). In other words, other browsers can be used at your own risk.
+
+Configuration
+-------------
+After installing DeepForge, it can be helpful to check out `configuring DeepForge <getting_started/configuration.rst>`_

docs/fundamentals/custom_data_types.rst

@@ -0,0 +1,13 @@
+Custom Data Types
+=================
+
+As operation inputs and outputs are strongly typed, DeepForge supports the creation of custom data types to promote flexibility when designing complex pipelines and operations. DeepForge data types can be either primitive types or custom classes. Custom DeepForge primitive types are relatively straight-forward; they can inherit from other types and must implement a serialization and deserialization methods (which may be as simple as :code:`torch.save` and :code:`torch.load`). Custom classes are also relatively simple to define but actually contain their own methods along with serialization and deserialization functions.
+
+New data types can be defined from the operation editor from the dialog for selecting input or output data for the operation. After defining a new class, this class is available from within any of the operations in the DeepForge project.
+
+.. figure:: model_data_editor.png
+    :align: center
+    :scale: 55 %
+
+    Editing the serialization and deserialization for the "model" type
+

docs/fundamentals/custom_layers.rst

@@ -0,0 +1,87 @@
+Custom Layers
+=============
+
+DeepForge supports the creation of custom neural network layers using Torch7 and the easy usage of these layers in the visual architecture editor. Before creating custom layers, it is recommended to read about `creating custom layers in Torch7 <http://torch.ch/docs/developer-docs.html>`_.
+
+A new custom layer can be created from the "add layer dialog" in the architecture editor. When creating a layer, DeepForge provides a code editor for creating custom neural network layers prepopulated with a basic template for defining the custom layer.
+
+After defining the layer in the layer editor, DeepForge will provide this layer in the architecture editor and expose any configurable attributes for the layer. These attributes are parsed from the layer definition.
+
+Best Practices
+--------------
+Here are a couple best practices to keep in mind when defining custom neural network layers:
+
+-  Use type assertions for layer, boolean attributes
+
+-  Return :code:`self` when defining setter functions
+
+**Type assertions** should be used when defining layer attributes (ie, constructor arguments or arguments to a setter function). For example, consider the following layer definition for :code:`RecurrentAttention` which accepts an :code:`action` layer argument to its constructor.
+
+.. code-block:: lua
+
+    local RecurrentAttention, parent = torch.class("nn.RecurrentAttention", "nn.AbstractSequencer")
+
+    function RecurrentAttention:__init(rnn, action, nStep, hiddenSize)
+       parent.__init(self)
+       assert(torch.isTypeOf(action, 'nn.Module'))
+       assert(torch.type(nStep) == 'number')
+       assert(torch.type(hiddenSize) == 'table')
+       assert(torch.type(hiddenSize[1]) == 'number', "Does not support table hidden layers" )
+       
+       self.rnn = rnn
+       -- we can decorate the module with a Recursor to make it AbstractRecurrent
+       self.rnn = (not torch.isTypeOf(rnn, 'nn.AbstractRecurrent')) and nn.Recursor(rnn) or rnn
+       
+       -- samples an x,y actions for each example
+       self.action =  (not torch.isTypeOf(action, 'nn.AbstractRecurrent')) and nn.Recursor(action) or action 
+       self.hiddenSize = hiddenSize
+       self.nStep = nStep
+       
+       self.modules = {self.rnn, self.action}
+       
+       self.output = {} -- rnn output
+       self.actions = {} -- action output
+       
+       self.forwardActions = false
+       
+       self.gradHidden = {}
+    end
+
+In this example, :code:`assert(torch.isTypeOf(action, 'nn.Module'))` enforces that the :code:`action` variable is another neural network layer. After defining the layer, DeepForge will parse the layer definition and create a visual representation for use in the architecture editor. As this assertion enforces that :code:`action` is a neural network layer, DeepForge will update itself accordingly; in this case, editing the attribute will allow the user to hierarchically create nested neural network architectures to be passed as the :code:`action` argument to the constructor.
+
+.. figure:: recurrent_attention.png
+    :align: center
+    :scale: 85 %
+
+    RecurrentAttention has attributes for each of the constructor arguments
+
+An example of the generated visual model for the :code:`RecurrentAttention` is provided above. This layer has attributes for each of the constructor arguments defined in its definition. Clicking on the :code:`<none>` value for the :code:`action` attribute will then allow the user to provide layer inputs as shown below.
+
+.. figure:: action_layer.png
+    :align: center
+    :scale: 55 %
+
+    Creating layer inputs for the "action" variable
+
+The second best practice is to make sure to **return self in any setter functions**. An example of this can be found in the setters in the :code:`SpatialMaxPooling` layer shown below:
+
+.. code-block:: lua
+
+    function SpatialMaxPooling:ceil()
+      self.ceil_mode = true
+      return self
+    end
+
+    function SpatialMaxPooling:floor()
+      self.ceil_mode = false
+      return self
+    end
+
+Returning :code:`self` in setter functions is a good convention when defining neural network layers in Torch7 as it promotes simple and legible code such as
+
+.. code-block:: lua
+
+    net:add(nn.SpatialMaxPooling(5, 5, 2, 2):ceil())
+
+where :code:`net` is a container like a :code:`Sequential` layer. DeepForge enforces this convention and, if it finds a setter function (which also returns :code:`self`) in the layer definition will expose the internal variable (in this case :code:`ceil_mode`) to the user in the visual editor.
+

docs/fundamentals/custom_operations.rst

@@ -0,0 +1,69 @@
+Custom Operations
+=================
+
+In this document we will outline the basics of custom operations including the operation editor and operation feedback utilities.
+
+The Basics
+----------
+Operations are used in pipelines and have named, typed inputs and outputs. When creating a pipeline, if you don't currently find an operation for the given task, you can easily create your own by selecting the `New Operation...` operation from the add operation dialog. This will create a new operation definition and open it in the operation editor. The operation editor has two main parts, the interface editor and the implementation editor.
+
+.. figure:: operation_editor.png
+    :align: center
+    :scale: 45 %
+
+    Editing the "train" operation provided in the "First Steps" section
+
+The interface editor is provided on the left and presents the interface as a diagram showing the input data and output data as objects flowing into or out of the given operation. Selecting the operation node in the operation interface editor will expand the node and allow the user to add or edit attributes for the given operation. These attributes are exposed when using this operation in a pipeline and can be set at design time - that is, these are set when creating the given pipeline. The interface diagram may also contain light blue nodes flowing into the operation. These nodes represent "references" that the operation accepts as input before running. When using the operation, references will appear alongside the attributes but will allow the user to select from a list of all possible targets when clicked.
+
+.. figure:: operation_interface.png
+    :align: center
+    :scale: 85 %
+
+    The train operation accepts training data, an architecture and criterion and returns a trained model
+
+On the right of the operation editor is the implementation editor. The implementation editor is a code editor specially tailored for programming the implementations of operations in DeepForge. This includes some autocomplete support for common globals in this context like the :code:`deepforge` and :code:`torch` globals. It also is synchronized with the interface editor and will provide input to the interface editor about unused variables, etc. These errors will present themselves as error or warning highlights on the data in the interface editor. A section of the implementation is shown below:
+
+.. code:: lua
+
+	trainer = nn.StochasticGradient(net, criterion)
+	trainer.learningRate = attributes.learningRate
+	trainer.maxIteration = attributes.maxIterations
+
+	print('training for ' .. tostring(attributes.maxIterations) .. ' iterations (max)')
+	print('learning rate is ' .. tostring(attributes.learningRate))
+	print(trainer)
+
+	-- Adding the error graph
+	graph = deepforge.Graph('Training Error') -- creating graph feedback
+	errLine = graph:line('error')
+	trainer.hookIteration = function(t, iter, currentErr)
+	   errLine:add(iter, currentErr) -- reporting the current error (will update in real time in DeepForge)
+	end
+
+	trainer:train(trainset)
+
+	return {
+	   net = net
+	}
+
+The "train" operation uses the :code:`StochasticGradient` functionality from the :code:`nn` package to perform stochastic gradient descent. This operation sets all the parameters using values provided to the operation as either attributes or references. In the implementation, attributes are provided by the :code:`attributes` variable and provides access to the user defined attributes from within the implementation. References are treated similarly to operation inputs and are defined in variables of the same name. This can be seen with the :code:`net` and :code:`criterion` variables in the first line. Finally, operations return a table of their named outputs; in this example, it returns a single output named :code:`net`, that is, the trained neural network.
+
+After defining the interface and implementation, we can now use the "train" operation in our pipelines! An example is shown below.
+
+.. figure:: train_operation.png
+    :align: center
+    :scale: 85 %
+
+    Using the custom "train" operation in a pipeline
+
+Operation feedback
+------------------
+Operations in DeepForge can generate metadata about its execution. This metadata is generated during the execution and provided back to the user in real-time. An example of this includes providing real-time plotting feedback of the loss function of a model while training. When implementing an operation in DeepForge, this metadata can be created using the :code:`deepforge` global.
+
+.. figure:: graph_example.png
+    :align: center
+    :scale: 75 %
+
+    An example graph of the loss function while training a neural network
+
+Detailed information about the available operation metadata types can be found in the `reference <reference/feedback_mechanisms.rst>`_.

docs/getting_started/getting_started.rst

@@ -0,0 +1,32 @@
+Getting Started
+===============
+
+.. _Torch: http://torch.ch
+
+What is DeepForge?
+------------------
+Deep learning is a very promising, yet complex, area of machine learning. This complexity can both create a barrier to entry for those wanting to get involved in deep learning as well as slow the development of those already comfortable in deep learning.
+
+DeepForge is a development environment for deep learning focused on alleviating these problems. Leveraging the flexibility of Torch_, DeepForge is able to reduce the complexity of using deep learning while still providing advanced features such as defining custom layers.
+
+Design Goals
+------------
+As mentioned above, DeepForge focuses on two main goals:
+
+1. **Improving the efficiency** of experienced data scientists/researchers in deep learning
+2. **Lowering the barrier to entry** for newcomers to deep learning
+
+It is important to highlight that although one of the goals is focused on lowering the barrier to entry, DeepForge is intended to be more than simply an educational tool; that is, it is important not to compromise on flexibility and effectiveness as a research/industry tool in order to provide an easier experience for beginners (that's what forks are for!).
+
+Overview and Features
+---------------------
+DeepForge provides a collaborative, distributed development environment for deep learning. The development environment is a hybrid visual and textual programming environment. Higher levels of abstraction, such as creating architectures, use visual environments to capture the overall structure of the task while lower levels of abstraction, such as defining custom layers, utilize text environments to maintain the flexibility provided by torch.
+
+Concepts and Terminology
+~~~~~~~~~~~~~~~~~~~~~~~~
+- *Architecture* - neural network architecture composed of torch defined layers
+- *Operation* - essentially a function written in torch (such as `SGD`)
+- *Pipeline* - directed acyclic graph composed of operations
+  - eg, a training pipeline may retrieve and normalize data, train an architecture and return the trained model
+- *Execution* - when a pipeline is run, an "execution" is created and reports the status of each operation as it is run (distributed over a number of worker machines)
+- *Artifact* - an artifact represents some data (either user uploaded or created during an execution)

docs/getting_started/hello_cifar.rst

@@ -0,0 +1,63 @@
+First Steps
+===========
+DeepForge provides an example project for creating a classifier using the `CIFAR10 <https://www.kaggle.com/c/cifar-10>`_ dataset.
+
+When first opening DeepForge in your browser (at `http://localhost:8888` if following the instructions from the `quick start <getting_started/installation.rst>`_), you will be prompted with a list of projects to open and provided the option to create a new project. For this example, let's click "Create new..." and name our project "hello_cifar".
+
+.. figure:: create_project.png
+    :align: center
+    :scale: 65 %
+
+    Creating our "hello_cifar" example project
+
+Clicking "Create" will bring us to a prompt for the "seed" for our project. Select "cifar10" from the dropdown and click "Create". This will now create our new project based on the cifar10 example provided with DeepForge.
+
+.. figure:: set_seed.png
+    :align: center
+    :scale: 75 %
+
+    Selecting the "cifar10" example seed
+
+In this example, we have three main pipelines: :code:`download-normalize`, :code:`train` and :code:`test`. :code:`download-normalize` downloads and prepares our data. The :code:`train` pipeline trains a neural network model on the cifar10 dataset and the :code:`test` pipeline tests our trained model on our test set from the cifar10 dataset.
+
+.. figure:: pipelines.png
+    :align: center
+    :scale: 65 %
+
+    Three main pipelines in the cifar10 example project
+
+First, we will have to retrieve and prepare the data by running the :code:`download-normalize` pipeline. This can be done by opening the given pipeline then selecting the `Execute Pipeline` option from the action button in the lower right. As soon as that pipeline finishes, we can now use this data to train a neural network.
+
+Next, we can open the :code:`train` pipeline. Before we execute the pipeline we have to set the input training data that we will be using. This is done by selecting the :code:`Input` operation then clicking the value for the :code:`artifact` field. This will provide all the possible options for the input data; for this example, we will want to select the "trainingdata" artifact. After setting the input, we can click on the :code:`train` operation to inspect the hyperparameters we are using and the architecture we are training. Selecting the :code:`Output` operation will allow you to change the name of the resulting artifact of this operation (in this case, a trained model). Finally, we can execute this pipeline like before to train the model.
+
+.. figure:: select_train_data.png
+    :align: center
+    :scale: 65 %
+
+    Selecting the training data for the input to the training pipeline
+
+As this operation trains, we can view the status by viewing the running execution. The easiest way to view the running execution is by clicking the given execution from the execution tray in the bottom left when viewing the originating pipeline.
+
+.. figure:: training_execution.png
+    :align: center
+    :scale: 65 %
+
+    Viewing the execution of the training pipeline
+
+Once the model has been trained, we can test the given model using the :code:`test` pipeline. In this pipeline, we have a few more inputs to set: "testing data", "model to test" and the "human-readable class labels". If you aren't clear which operation provides which input, you can simply hover over it's connected port on the :code:`test` operation. This will provide a tooltip with the full name of the input.
+
+.. figure:: test_pipeline.png
+    :align: center
+    :scale: 65 %
+
+    Viewing the execution of the testing pipeline
+
+After setting the inputs for the :code:`test` pipeline (using the trained model and data from the first two pipelines), we can simply execute this pipeline to test our model. After executing the :code:`test` pipeline, we can view the execution and open the :code:`test` job to view the stdout for the given job. In the :code:`test` operation, this will allow us to view the printed accuracies of the model over each class.
+
+.. figure:: test_results.png
+    :align: center
+    :scale: 65 %
+
+    Viewing the results of the testing operation
+
+And that's it! We have just trained and tested our first neural network model using DeepForge. Although there are still a lot more advanced features that can be used, this should at least familiarize us with some of the core concepts in DeepForge.

docs/getting_started/quick_start.rst

@@ -0,0 +1,19 @@
+Quick Start
+===========
+The easiest way to get started quickly with DeepForge is using docker-compose. First, install `docker <https://docs.docker.com/engine/installation/>`_ and `docker-compose <https://docs.docker.com/compose/install/>`_.
+
+Next, download the docker-compose file for DeepForge:
+
+.. code-block:: bash
+
+    wget https://raw.githubusercontent.com/deepforge-dev/deepforge/master/docker-compose.yml
+
+Then start DeepForge using docker-compose:
+
+.. code-block:: bash
+
+    docker-compose up
+
+and now DeepForge can be used by opening a browser to `http://localhost:8888 <http://localhost:8888>`_!
+
+For detailed instructions about deployment installations, check out our `deployment installation instructions <getting_started/configuration.rst>`_

docs/index.rst

@@ -0,0 +1,40 @@
+.. DeepForge documentation master file, created by
+   sphinx-quickstart on Mon Mar 13 18:56:27 2017.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to DeepForge's documentation!
+=====================================
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Getting Started
+
+   getting_started/getting_started.rst
+   getting_started/quick_start.rst
+   getting_started/hello_cifar.rst
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Fundamentals
+
+   fundamentals/custom_operations.rst
+   fundamentals/custom_layers.rst
+   fundamentals/custom_data_types.rst
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Deployment
+
+   deployment/overview.rst
+   deployment/native.rst
+   deployment/dockerized.rst
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Reference
+
+   reference/cli.rst
+   reference/configuration.rst
+   reference/operation_feedback.rst
+   reference/extensions.rst

docs/reference/cli.rst

@@ -0,0 +1,91 @@
+Command Line Interface
+======================
+
+This document outlines the functionality of the deepforge command line interface (provided after installing deepforge with :code:`npm install -g deepforge`).
+
+- Installation Configuration
+- Starting DeepForge or Components
+- Installing and Upgrading Torch
+- Update or Uninstall DeepForge
+- Managing Extensions
+
+Installation Configuration
+--------------------------
+Installation configuration including the installation location of Torch7 and data storage locations. These can be edited using the :code:`deepforge config` command as shown in the following examples:
+
+Printing all the configuration settings:
+
+.. code-block:: bash
+
+    deepforge config
+
+
+Printing the value of a configuration setting:
+
+.. code-block:: bash
+
+    deepforge config torch.dir
+
+
+Setting a configuration option, such as :code:`torch.dir` can be done with:
+
+.. code-block:: bash
+
+    deepforge config torch.dir /some/new/directory
+
+
+For more information about the configuration settings, check out the `configuration <configuration.rst>`_ page.
+
+
+Starting DeepForge Components
+-----------------------------
+DeepForge components, such as the server or the workers, can be started with the :code:`deepforge start` command. By default, this command will start all the necessary components to run including the server, a mongo database (if applicable) and a worker.
+
+The server can be started by itself using
+
+.. code-block:: bash
+
+    deepforge start --server
+
+
+The worker can be started by itself using
+
+.. code-block:: bash
+
+    deepforge start --worker http://154.95.87.1:7543
+
+
+where `http://154.95.87.1:7543` is the url of the deepforge server.
+
+Installing and Upgrading Torch7
+-------------------------------
+Torch7 is lazily installed when starting a worker (if torch isn't already installed) with the rnn package. This installation can be manually updated as described in the update and installation section.
+
+Update/Uninstall DeepForge
+--------------------------
+DeepForge can be updated or uninstalled using
+
+.. code-block:: bash
+
+    deepforge update
+
+
+The torch installation can be updated using
+
+.. code-block:: bash
+
+    deepforge update --torch
+
+
+DeepForge can be uninstalled using :code:`deepforge uninstall`
+
+Managing Extensions
+-------------------
+DeepForge extensions can be installed and removed using the :code:`deepforge extensions` subcommand. Extensions can be added, removed and listed as shown below
+
+.. code-block:: bash
+
+    deepforge extensions add https://github.com/example/some-extension
+    deepforge extensions remove some-extension
+    deepforge extensions list
+

docs/reference/configuration.rst

@@ -0,0 +1,77 @@
+Configuration
+=============
+
+Configuration of deepforge is done through the `deepforge config` command from the command line interface. To see all config options, simply run `deepforge config` with no additional arguments. This will print a JSON representation of the configuration settings similar to:
+
+.. code-block:: bash
+
+    Current config:
+    {
+      "torch": {
+        "dir": "/home/irishninja/.deepforge/torch"
+      },
+      "blob": {
+        "dir": "/home/irishninja/.deepforge/blob"
+      },
+      "worker": {
+        "cache": {
+          "useBlob": true,
+          "dir": "~/.deepforge/worker/cache"
+        },
+        "dir": "~/.deepforge/worker"
+      },
+      "mongo": {
+        "dir": "~/.deepforge/data"
+      }
+    }
+
+Setting an attribute, say `worker.cache.dir`, is done as follows
+
+.. code-block:: bash
+
+    deepforge config worker.cache.dir /tmp
+
+Environment Variables
+---------------------
+Most settings have a corresponding environment variable which can be used to override the value set in the cli's configuration. This allows the values to be temporarily set for a single run. For example, starting a worker with a different cache than set in `worker.cache.dir` can be done with:
+
+.. code-block:: bash
+
+    DEEPFORGE_WORKER_CACHE=/tmp deepforge start -w
+
+The complete list of the environment variable overrides for the configuration options can be found `here <https://github.com/deepforge-dev/deepforge/blob/master/bin/envConfig.json>`_.
+
+Settings
+--------
+
+torch.dir
+~~~~~~~~~
+The path to the local installation of torch to be used by the deepforge worker. This is used when installing, upgrading and removing the local torch installation
+
+blob.dir
+~~~~~~~~
+The path to the blob (large file storage containing models, datasets, etc) to be used by the deepforge server.
+
+This can be overridden with the `DEEPFORGE_BLOB_DIR` environment variable.
+
+worker.dir
+~~~~~~~~~~
+The path to the directory used for worker executions. The workers will run the executions from this directory.
+
+This can be overridden with the `DEEPFORGE_WORKER_DIR` environment variable.
+
+mongo.dir
+~~~~~~~~~
+The path to use for the `--dbpath` option of mongo if starting mongo using the command line interface. That is, if the MONGO_URI is set to a local uri and the cli is starting the deepforge server, the cli will check to verify that an instance of mongo is running locally. If not, it will start it on the given port and use this setting for the `--dbpath` setting of mongod.
+
+worker.cache.dir
+~~~~~~~~~~~~~~~~
+The path to the worker cache directory.
+
+This can be overridden with the `DEEPFORGE_WORKER_CACHE` environment variable.
+
+worker.cache.useBlob
+~~~~~~~~~~~~~~~~~~~~
+When running the worker on the same machine as the server, this allows the worker to use the blob as a cache and simply create symbolic links to the data (eg, training data, models) to prevent having to even perform a copy of the data on the given machine.
+
+This can be overridden with the `DEEPFORGE_WORKER_USE_BLOB` environment variable.

docs/reference/operation_feedback.rst

@@ -0,0 +1,53 @@
+Operation Feedback
+==================
+
+DeepForge provides the `deepforge` global object in operation implementations for providing feedback during the execution. The various types of metadata are provided and discussed below.
+
+Graphs
+------
+Real-time graphs can be created using the graph constructor:
+
+.. code-block:: lua
+
+    local graph = deepforge.Graph('My Graph')  -- created a new graph called "My Graph"
+
+After creating a graph, lines can be added similarly.
+
+.. code-block:: lua
+
+    local line1 = graph:line('first line')  -- created a new line called "first line"
+    local line2 = graph:line('second line')  -- created a second line called "second line"
+
+Finally, points can be added to the lines by calling the `:add` method on the line and passing the x and y values for the given point.
+
+.. code-block:: lua
+
+    line1:add(1, 3)  -- adding point (1, 3) to line1
+    line2:add(1, 4)  -- adding point (1, 4) to line2
+
+    line1:add(2, 5)  -- adding point (2, 5) to line1
+    line2:add(2, 6)  -- adding point (2, 6) to line2
+
+Graphs can then label their axis as follows:
+
+.. code-block:: lua
+
+    graph:xlabel('x axis')  -- label the x axis "x axis"
+    graph:ylabel('y axis')  -- label the y axis "y axis"
+
+
+Images
+------
+Images can be created using:
+
+.. code-block:: lua
+
+    local image = deepforge.Image('My Example Image', imageTensor)
+
+The first argument is the title of the image and the second argument is the tensor for the image (optional). Both the title and the tensor can be updated during execution as follows.
+
+.. code-block:: lua
+
+    image:title('My New Title')  -- updating the image title
+    image:update(newTensor)  -- updating the displayed image
+

install.sh

@@ -42,10 +42,10 @@ detect_profile() {
 detect_profile
 
 set_node_version() {
-    # Install nodejs v6.2.0
-    echo "Installing NodeJS v6.2.0"
-    nvm install v6.2.0
-    nvm alias default v6.2.0
+    # Install nodejs v6.2.1
+    echo "Installing NodeJS v6.2.1"
+    nvm install v6.2.1
+    nvm alias default v6.2.1
 
     # Install npm@2
     npm install npm@2 -g

package.json

@@ -1,33 +1,44 @@
 {
   "name": "deepforge",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/deepforge-dev/deepforge.git"
+  },
   "bin": {
     "deepforge": "./bin/deepforge"
   },
   "scripts": {
-    "start": "node app.js",
+    "start": "./bin/deepforge start",
+    "postinstall": "node utils/reinstall-extensions.js",
     "start-dev": "NODE_ENV=dev node app.js",
     "local": "node ./bin/start-local.js",
     "worker": "node ./bin/start-worker.js",
-    "test": "mkdir ./test-tmp; node ./node_modules/mocha/bin/mocha --recursive test",
-    "watch-test": "./node_modules/nodemon/bin/nodemon.js --exec 'node ./node_modules/mocha/bin/mocha --recursive test'",
+    "test": "mkdir ./test-tmp; mocha --recursive test",
+    "watch-test": "nodemon --exec 'mocha --recursive test'",
     "build-nn": "node ./utils/nn-parser.js"
   },
-  "version": "0.16.0",
+  "version": "1.4.1",
   "dependencies": {
     "commander": "^2.9.0",
     "dotenv": "^2.0.0",
     "exists-file": "^2.1.0",
     "express": "^4.14.0",
+    "graceful-fs": "^4.1.10",
     "lodash.difference": "^4.1.2",
     "lodash.merge": "^4.5.1",
+    "lodash.template": "^4.4.0",
+    "mongodb": "^2.2.10",
     "nodemon": "^1.9.2",
+    "npm": "^4.0.5",
     "q": "1.4.1",
     "rimraf": "^2.4.0",
-    "webgme": "^2.0.0",
-    "webgme-autoviz": "dfst/webgme-autoviz",
+    "tcp-port-used": "^0.1.2",
+    "webgme": "^2.7.1",
+    "webgme-autoviz": "^2.2.0",
     "webgme-breadcrumbheader": "^2.1.1",
     "webgme-chflayout": "^2.0.0",
     "webgme-easydag": "dfst/webgme-easydag",
+    "webgme-executor-worker": "^1.0.1",
     "webgme-fab": "dfst/webgme-fab",
     "webgme-simple-nodes": "^2.1.0"
   },

src/common/Constants.js

@@ -1,31 +1,58 @@
 /* globals define */
-define({
-    LINE_OFFSET: 'lineOffset',
+(function(root, factory){
+    if(typeof define === 'function' && define.amd) {
+        define([], function(){
+            return factory();
+        });
+    } else if(typeof module === 'object' && module.exports) {
+        module.exports = factory();
+    } else {
+        root.CONSTANTS = factory();
+    }
+}(this, function() {
+    return {
+        CONTAINED_LAYER_SET: 'addLayers',
+        CONTAINED_LAYER_INDEX: 'index',
 
-    // DeepForge metadata creation in dist execution
-    START_CMD: 'deepforge-cmd',
+        LINE_OFFSET: 'lineOffset',
+        DISPLAY_COLOR: 'displayColor',
 
-    IMAGE: {  // all prefixed w/ 'IMG' for simple upload detection
-        PREFIX: 'IMG',
-        BASIC: 'IMG-B',
-        CREATE: 'IMG-C',
-        UPDATE: 'IMG-U',
-        NAME: 'IMAGE-N'  // No upload required
-    },
+        // DeepForge metadata creation in dist execution
+        START_CMD: 'deepforge-cmd',
 
-    GRAPH_CREATE: 'GRAPH',
-    GRAPH_PLOT: 'PLOT',
-    GRAPH_CREATE_LINE: 'LINE',
+        IMAGE: {  // all prefixed w/ 'IMG' for simple upload detection
+            PREFIX: 'IMG',
+            BASIC: 'IMG-B',
+            CREATE: 'IMG-C',
+            UPDATE: 'IMG-U',
+            NAME: 'IMAGE-N'  // No upload required
+        },
 
-    // Code Generation Constants
-    CTOR_ARGS_ATTR: 'ctor_arg_order',
+        GRAPH_CREATE: 'GRAPH',
+        GRAPH_PLOT: 'PLOT',
+        GRAPH_CREATE_LINE: 'LINE',
+        GRAPH_LABEL_AXIS: {
+            X: 'X',
+            Y: 'Y'
+        },
 
-    // Operation types
-    OP: {
-        INPUT: 'Input',
-        OUTPUT: 'Output'
-    },
+        // Code Generation Constants
+        CTOR_ARGS_ATTR: 'ctor_arg_order',
 
-    // Job stdout update
-    STDOUT_UPDATE: 'stdout_update'
-});
+        // Operation types
+        OP: {
+            INPUT: 'Input',
+            OUTPUT: 'Output'
+        },
+
+        // Heartbeat constants (ExecPulse router)
+        PULSE: {
+            DEAD: 0,
+            ALIVE: 1,
+            DOESNT_EXIST: 2
+        },
+
+        // Job stdout update
+        STDOUT_UPDATE: 'stdout_update'
+    };
+}));

src/common/LayerParser.js

@@ -265,6 +265,7 @@
     var findTorchClass = function(ast){ 
         var torchClassArgs,  // args for `torch.class(...)`
             name = '',
+            alias,
             baseType,
             params,
             setters = {},
@@ -283,6 +284,7 @@
                     name = torchClassArgs[0];
                     if(name !== ''){
                         name = name.replace('nn.', '');
+                        alias = func.names[0] || name;
                         if (torchClassArgs.length > 1) {
                             baseType = torchClassArgs[1].replace('nn.', '');
                         }
@@ -302,7 +304,7 @@
                 attrName;
 
             // Record the setter functions
-            if (isSetterMethod(curr, parent, name)) {
+            if (isSetterMethod(curr, parent, alias)) {
                 firstLine = curr.block.stats[0];
                 // just use the attribute attrName for now...
                 attrName = getSettingAttrName(firstLine);
@@ -316,7 +318,7 @@
                 } else {
                     setters[attrName] = schema;
                 }
-            } else if (isInitFn(curr, name)) {  // Record the defaults
+            } else if (isInitFn(curr, alias)) {  // Record the defaults
                 paramDefs = getAttrsAndVals(curr);
                 attrDefs = getClassAttrDefs(curr);
                 types = inferParamTypes(curr, paramDefs);

src/common/api/APIClient.js

@@ -0,0 +1,75 @@
+/*globals define*/
+define([
+    'q',
+    'superagent'
+], function(
+    Q,
+    superagent
+) {
+    'use strict';
+
+    // Wrap the ability to read, update, and delete logs using the JobLogsAPI
+    var APIClient = function(params) {
+        params = params || {};
+
+        this.logger = this.logger || params.logger.fork('APIClient');
+
+        // Get the server url
+        this.token = params.token;
+        this.origin = this._getServerUrl(params);
+        this.relativeUrl = this.relativeUrl || '';
+        this.url = this.origin + this.relativeUrl;
+
+        this.logger.debug(`Setting url to ${this.url}`);
+
+        this.branch = params.branchName;
+        this.project = params.projectId;
+        this._modifiedJobs = [];
+
+        this.logger.debug(`Using <project>:<branch>: "${this.project}"/"${this.branch}"`);
+        this.logger.info('ctor finished');
+    };
+
+    APIClient.prototype._getServerUrl = function(params) {
+        if (typeof window !== 'undefined') {
+            return window.location.origin;
+        }
+
+        // If not in browser, set using the params
+        var server = params.server || '127.0.0.1',
+            port = params.port || '80',
+            protocol = params.httpsecure ? 'https' : 'http';  // default is http
+
+        return params.origin || `${protocol}://${server}:${port}`;
+    };
+
+    APIClient.prototype.getUrl = function() {
+        return this.url;
+    };
+
+    APIClient.prototype._request = function(method, jobId, content) {
+        var deferred = Q.defer(),
+            req = superagent[method](this.getUrl(jobId));
+
+        this.logger.debug(`sending ${method} request to ${this.getUrl(jobId)}`);
+        if (this.token) {
+            req.set('Authorization', 'Bearer ' + this.token);
+        }
+
+        if (content) {
+            req = req.send(content);
+        }
+
+        req.end((err, res) => {
+            if (err || res.status > 399) {
+                return deferred.reject(res || err);
+            }
+
+            return deferred.resolve(res);
+        });
+
+        return deferred.promise;
+    };
+
+    return APIClient;
+});

src/common/api/ExecPulseClient.js

@@ -0,0 +1,44 @@
+/* globals define */
+define([
+    './APIClient'
+], function(
+    APIClient
+) {
+    'use strict';
+
+    var ExecPulseClient = function(params) {
+        this.relativeUrl = '/execution/pulse/';
+        this.logger = params.logger.fork('ExecPulseClient');
+        APIClient.call(this, params);
+    };
+
+    ExecPulseClient.prototype = Object.create(APIClient.prototype);
+
+    ExecPulseClient.prototype.getUrl = function(hash) {
+        return this.url + hash;
+    };
+
+    // - update the heartbeat
+    // - check the heartbeat
+    // - delete the heartbeat
+    ExecPulseClient.prototype.update = function(hash) {
+        return this._request('post', hash)
+            .catch(err => {
+                throw err.text || err;
+            });
+    };
+
+    ExecPulseClient.prototype.check = function(hash) {
+        return this._request('get', hash)
+            .then(res => JSON.parse(res.text))
+            .catch(err => {
+                throw err.text || err;
+            });
+    };
+
+    ExecPulseClient.prototype.clear = function(hash) {
+        return this._request('delete', hash);
+    };
+
+    return ExecPulseClient;
+});

src/common/api/JobLogsClient.js

@@ -1,51 +1,38 @@
 /* globals define */
 define([
+    './APIClient',
     'q',
     'superagent'
 ], function(
+    APIClient,
     Q,
     superagent
 ) {
     'use strict';
 
     // Wrap the ability to read, update, and delete logs using the JobLogsAPI
+    var METADATA_FIELDS = [
+        'lineCount'
+    ];
     var JobLogsClient = function(params) {
         params = params || {};
 
-        this.logger = params.logger.fork('JobLogsClient');
-
-        // Get the server url
-        this.token = params.token;
-        this.origin = this._getServerUrl(params);
         this.relativeUrl = '/execution/logs';
-        this.url = this.origin + this.relativeUrl;
-
-        this.logger.debug(`Setting url to ${this.url}`);
+        this.logger = params.logger.fork('JobLogsClient');
+        APIClient.call(this, params);
 
         // Get the project, branch name
         if (!(params.branchName && params.projectId)) {
             throw Error('"branchName" and "projectId" required');
         }
-        this.branch = params.branchName;
-        this.project = params.projectId;
+
         this._modifiedJobs = [];
 
         this.logger.debug(`Using <project>:<branch>: "${this.project}"/"${this.branch}"`);
         this.logger.info('ctor finished');
     };
 
-    JobLogsClient.prototype._getServerUrl = function(params) {
-        if (typeof window !== 'undefined') {
-            return window.location.origin;
-        }
-
-        // If not in browser, set using the params
-        var server = params.server || '127.0.0.1',
-            port = params.port || '80',
-            protocol = params.httpsecure ? 'https' : 'http';  // default is http
-
-        return params.origin || `${protocol}://${server}:${port}`;
-    };
+    JobLogsClient.prototype = Object.create(APIClient.prototype);
 
     // This method could be optimized - it could make a log of requests
     JobLogsClient.prototype.fork = function(forkName) {
@@ -79,53 +66,54 @@ define([
     };
 
     JobLogsClient.prototype.getUrl = function(jobId) {
+        var url = this.url;
+            
+        if (typeof jobId !== 'string') {
+            url = this.url + jobId.route;
+            jobId = jobId.jobId;
+        }
+
         return [
-            this.url,
+            url,
             encodeURIComponent(this.project),
             encodeURIComponent(this.branch),
             encodeURIComponent(jobId)
         ].join('/');
     };
 
-    JobLogsClient.prototype._logRequest = function(method, jobId, content) {
-        var deferred = Q.defer(),
-            req = superagent[method](this.getUrl(jobId));
-
-        this.logger.info(`sending ${method} request to ${this.getUrl(jobId)}`);
-        if (this.token) {
-            req.set('Authorization', 'Bearer ' + this.token);
-        }
-
-        if (content) {
-            req = req.send(content);
-        }
-
-        req.end((err, res) => {
-            if (err || res.status > 399) {
-                return deferred.reject(err || res.status);
-            }
-
-            return deferred.resolve(res);
-        });
-
-        return deferred.promise;
+    var hasRequiredFields = function(md) {
+        return METADATA_FIELDS.reduce((passing, nextField) => {
+            return passing && md.hasOwnProperty(nextField);
+        }, true);
     };
 
-    JobLogsClient.prototype.appendTo = function(jobId, text) {
+    JobLogsClient.prototype.appendTo = function(jobId, text, metadata) {
         this._modifiedJobs.push(jobId);
         this.logger.info(`Appending logs to ${jobId}`);
-        return this._logRequest('patch', jobId, {patch: text});
+
+        if (metadata && !hasRequiredFields(metadata)) {
+            throw Error(`Required metadata fields: ${METADATA_FIELDS.join(', ')}`);
+        }
+        metadata = metadata || {};
+        metadata.patch = text;
+        return this._request('patch', jobId, metadata);
     };
 
     JobLogsClient.prototype.getLog = function(jobId) {
         this.logger.info(`Getting logs for ${jobId}`);
-        return this._logRequest('get', jobId)
+        return this._request('get', jobId)
             .then(res => res.text);
     };
 
     JobLogsClient.prototype.deleteLog = function(jobId) {
         this.logger.info(`Deleting logs for ${jobId}`);
-        return this._logRequest('delete', jobId);
+        return this._request('delete', jobId);
+    };
+
+    JobLogsClient.prototype.getMetadata = function(jobId) {
+        this.logger.info(`Getting line count for ${jobId}`);
+        return this._request('get', {jobId: jobId, route: '/metadata'})
+            .then(res => JSON.parse(res.text));
     };
 
     return JobLogsClient;

src/common/api/JobOriginClient.js

@@ -0,0 +1,60 @@
+/* globals define */
+define([
+    './APIClient'
+], function(
+    APIClient
+) {
+    'use strict';
+
+    var JobOriginClient = function(params) {
+        this.relativeUrl = '/job/origins/';
+        this.logger = params.logger.fork('JobOriginClient');
+        APIClient.call(this, params);
+    };
+
+    JobOriginClient.prototype = Object.create(APIClient.prototype);
+
+    // - Record the origin
+    // - Look up the origin
+    // - Delete record
+    JobOriginClient.prototype.getUrl = function(hash) {
+        return this.url + hash;
+    };
+
+    JobOriginClient.prototype.record = function(hash, info) {
+        var jobInfo = {
+            hash: hash,
+            nodeId: info.nodeId,
+            job: info.job,
+            project: info.project || this.project,
+            branch: info.branch || this.branch,
+            execution: info.execution
+        };
+
+        return this._request('post', hash, jobInfo)
+            .catch(err => {
+                throw err.text || err;
+            });
+    };
+
+    JobOriginClient.prototype.getOrigin = function(hash) {
+        return this._request('get', hash)
+            .then(res => JSON.parse(res.text))
+            .catch(res => {
+                if (res.status && res.status === 404) {
+                    return null;
+                }
+                throw res;
+            });
+    };
+
+    JobOriginClient.prototype.fork = function(hash, forkName) {
+        return this._request('patch', hash, {branch: forkName});
+    };
+
+    JobOriginClient.prototype.deleteRecord = function(hash) {
+        return this._request('delete', hash);
+    };
+
+    return JobOriginClient;
+});

src/common/globals.js

@@ -57,7 +57,7 @@ define([
     };
 
     var createNamedNode = function(baseId, parentId, isMeta) {
-        var newId = client.createChild({parentId, baseId}),
+        var newId = client.createNode({parentId, baseId}),
             baseNode = client.getNode(baseId),
             basename = 'New' + baseNode.getAttribute('name'),
             newName = getUniqueName(parentId, basename);
@@ -72,7 +72,7 @@ define([
             client.setRegistry(newId, 'isAbstract', false);
         }
 
-        client.setAttributes(newId, 'name', newName);
+        client.setAttribute(newId, 'name', newName);
         return newId;
     };
 
@@ -83,7 +83,9 @@ define([
             exists = {},
             i = 2;
 
-        children.forEach(child => exists[child.getAttribute('name')] = true);
+        children
+            .filter(child => child !== null)
+            .forEach(child => exists[child.getAttribute('name')] = true);
 
         while (exists[name]) {
             name = basename + '_' + i;
@@ -191,7 +193,7 @@ define([
                 .getId();
 
         // Look up the parent container
-        DeepForge.places[placeName]().then(parentId => {
+        return DeepForge.places[placeName]().then(parentId => {
 
             client.startTransaction(msg);
             newId = createNamedNode(baseId, parentId, !!metasheetName);
@@ -265,14 +267,12 @@ define([
         }
 
         dataBaseId = dataBase.getId();
-        dataTypes = metanodes.filter(n => client.isTypeOf(n.getId(), dataBaseId))
+        dataTypes = metanodes.filter(n => n.isTypeOf(dataBaseId))
             .filter(n => !n.getRegistry('isAbstract'))
             .map(node => node.getAttribute('name'));
 
-        //this.logger.info(`Found ${dataTypes.length} data types`);
-
-        // Add the target type to the pluginMetadata... hacky :/
-        var metadata = WebGMEGlobal.allPluginsMetadata[UPLOAD_PLUGIN], 
+        // Add the target type to the pluginMetadata...
+        var metadata = WebGMEGlobal.allPluginsMetadata[UPLOAD_PLUGIN],
             config = metadata.configStructure
                 .find(opt => opt.name === DATA_TYPE_CONFIG.name);
 
@@ -297,7 +297,8 @@ define([
     };
 
     DeepForge.last = {};
-    DeepForge.create  = {};
+    DeepForge.create = {};
+    DeepForge.register = {};
     instances.forEach(type => {
         DeepForge.create[type] = function() {
             return createNew.call(null, type);
@@ -308,6 +309,10 @@ define([
         DeepForge.create[type] = function() {
             return createNew.call(null, type, type);
         };
+        DeepForge.register[type] = function(id) {
+            // Add the given element to the metasheet!
+            return addToMetaSheet(id, type);
+        };
     });
 
     DeepForge.create.Layer = createCustomLayer;

src/common/lua.js

@@ -2565,7 +2565,7 @@ function LuaContext(){
             case 'number':
                 return c;
             case 'string':
-                return parseInt(s) || dummy0;
+                return parseInt(c) || dummy0;
             default:
                 if (c == dummy0){
                     return c;

src/common/plugin/LocalExecutor.js

@@ -148,11 +148,14 @@ define([
                 // get the input node
                 if (dataNodes.length !== 0) {
                     var newNodes = this.core.copyNodes(dataNodes, parentNode),
-                        newName = this.core.getOwnAttribute(node, 'saveName');
+                        newName = this.core.getOwnAttribute(node, 'saveName'),
+                        createdAt = Date.now();
+
                     if (newName) {
-                        newNodes.forEach(node =>
-                            this.setAttribute(node, 'name', newName)
-                        );
+                        newNodes.forEach(node => {
+                            this.setAttribute(node, 'name', newName);
+                            this.setAttribute(node, 'createdAt', createdAt);
+                        });
                     }
                     var hashes = dataNodes.map(n => this.getAttribute(n, 'data'));
                     this.logger.info(`saving hashes: ${hashes.map(h => `"${h}"`)}`);

src/common/plugin/Operation.js

@@ -0,0 +1,35 @@
+/*globals define */
+// This is a mixin containing helpers for working with operation nodes
+define([],function() {
+
+    var OperationOps = function() {
+    };
+
+    OperationOps.prototype.getOutputs = function (node) {
+        return this.getOperationData(node, this.META.Outputs);
+    };
+
+    OperationOps.prototype.getInputs = function (node) {
+        return this.getOperationData(node, this.META.Inputs);
+    };
+
+    OperationOps.prototype.getOperationData = function (node, metaType) {
+        // Load the children and the output's children
+        return this.core.loadChildren(node)
+            .then(containers => {
+                var outputs = containers.find(c => this.core.isTypeOf(c, metaType));
+                return outputs ? this.core.loadChildren(outputs) : [];
+            })
+            .then(outputs => {
+                var bases = outputs.map(node => this.core.getMetaType(node));
+                // return [[arg1, Type1, node1], [arg2, Type2, node2]]
+                return outputs.map((node, i) => [
+                    this.getAttribute(node, 'name'),
+                    this.getAttribute(bases[i], 'name'),
+                    node
+                ]);
+            });
+    };
+
+    return OperationOps;
+});

src/common/plugin/PtrCodeGen.js

@@ -6,27 +6,64 @@ define([
     PluginUtils,
     Q
 ) {
+
+    var CodeGen = {
+        Operation: {
+            pluginId: 'GenerateJob',
+            namespace: 'pipeline'
+        }
+    };
+
     var PtrCodeGen = function() {
     };
 
+    PtrCodeGen.prototype.getCodeGenPluginIdFor = function(node) {
+        var base = this.core.getBase(node),
+            name = this.core.getAttribute(node, 'name'),
+            namespace = this.core.getNamespace(node),
+            pluginId;
+
+        //this.logger.debug(`loaded pointer target of ${ptrId}: ${ptrNode}`);
+        pluginId = (this.core.getOwnRegistry(node, 'validPlugins') || '').split(' ').shift();
+        //this.logger.info(`generating code for ${this.core.getAttribute(ptrNode, 'name')} using ${pluginId}`);
+
+        if (this.core.isMetaNode(node) && CodeGen[name]) {
+            pluginId = CodeGen[name].pluginId || CodeGen[name];
+            namespace = CodeGen[name].namespace;
+        }
+
+        if (pluginId) {
+            return {
+                namespace: namespace,
+                pluginId: pluginId
+            };
+        } else if (base) {
+            return this.getCodeGenPluginIdFor(base);
+        } else {
+            return null;
+        }
+    };
+
     PtrCodeGen.prototype.getPtrCodeHash = function(ptrId) {
         return this.core.loadByPath(this.rootNode, ptrId)
             .then(ptrNode => {
                 // Look up the plugin to use
-                var metanode = this.core.getMetaType(ptrNode),
-                    pluginId;
+                var genInfo = this.getCodeGenPluginIdFor(ptrNode);
 
-                this.logger.debug(`loaded pointer target of ${ptrId}: ${ptrNode}`);
-                pluginId = this.core.getRegistry(ptrNode, 'validPlugins').split(' ').shift();
-                this.logger.info(`generating code for ${this.core.getAttribute(ptrNode, 'name')} using ${pluginId}`);
+                if (genInfo.pluginId) {
+                    var context = {
+                        namespace: genInfo.namespace,
+                        activeNode: this.core.getPath(ptrNode)
+                    };
 
-                var context = {
-                    namespace: this.core.getNamespace(metanode),
-                    activeNode: this.core.getPath(ptrNode)
-                };
-
-                // Load and run the plugin
-                return this.executePlugin(pluginId, context);
+                    // Load and run the plugin
+                    return this.executePlugin(genInfo.pluginId, context);
+                } else {
+                    var metanode = this.core.getMetaType(ptrNode),
+                        type = this.core.getAttribute(metanode, 'name');
+                    this.logger.warn(`Could not find plugin for ${type}. Will try to proceed anyway`);
+                    return null;
+                }
             })
             .then(hashes => hashes[0]);  // Grab the first asset for now
     };
@@ -56,12 +93,13 @@ define([
         return PluginUtils.loadNodesAtCommitHash(
             this.project,
             this.core,
-            this.commitHash,
+            this.currentHash,
             this.logger,
             opts
         ).then(config => {
             plugin.initialize(logger, this.blobClient, this.gmeConfig);
             config.core = this.core;
+            config.project = this.project;
             plugin.configure(config);
             return plugin;
         });

src/common/viz/Buttons.js

@@ -1,8 +1,10 @@
 /*globals define, WebGMEGlobal*/
 define([
+    'deepforge/globals',
     'widgets/EasyDAG/Buttons',
     'widgets/EasyDAG/Icons'
 ], function(
+    DeepForge,
     EasyDAGButtons,
     Icons
 ) {
@@ -57,9 +59,79 @@ define([
         return n && n.getBaseId();
     };
 
+    var CloneAndEdit = function(params) {
+        GoToBase.call(this, params);
+    };
+
+    CloneAndEdit.prototype = Object.create(GoToBase.prototype);
+    CloneAndEdit.prototype.BTN_CLASS = 'clone-and-edit';
+
+    CloneAndEdit.prototype._render = function() {
+        var lineRadius = GoToBase.SIZE - GoToBase.BORDER,
+            btnColor = '#a5d6a7';
+
+        if (this.disabled) {
+            btnColor = '#e0e0e0';
+        }
+
+        this.$el
+            .append('circle')
+            .attr('r', GoToBase.SIZE)
+            .attr('fill', btnColor);
+
+        // Show the 'code' icon
+        Icons.addIcon('code', this.$el, {
+            radius: lineRadius
+        });
+    };
+
+    CloneAndEdit.prototype._onClick = function(item) {
+        var node = client.getNode(item.id),
+            baseId = node && node.getBaseId(),
+            base = baseId && client.getNode(baseId),
+            typeId = base && base.getBaseId(),
+            type = typeId && client.getNode(typeId),
+            ctrName,
+            typeName,
+            name,
+            newId;
+
+        // Clone the given node's base and change to it
+        if (type) {
+            typeName = type.getAttribute('name');
+            ctrName = `My${typeName}s`;
+            if (DeepForge.places[ctrName]) {
+                DeepForge.places[ctrName]().then(ctrId => {
+                    type = base.getAttribute('name');
+                    client.startTransaction(`Creating new ${typeName} from ${item.name}`);
+                    newId = client.copyNode(baseId, ctrId);
+                    name = node.getAttribute('name');
+                    client.setAttribute(newId, 'name', 'Copy of ' + name);
+                    DeepForge.register[typeName](newId);
+
+                    client.completeTransaction();
+                    WebGMEGlobal.State.registerActiveObject(newId);
+                });
+            }
+        } else {
+            this._logger.warn('Could not find the base node!');
+        }
+    };
+
+    var Insert = function(params) {
+        EasyDAGButtons.ButtonBase.call(this, params);
+    };
+
+    Insert.prototype = Object.create(EasyDAGButtons.Add.prototype);
+    Insert.prototype._onClick = function(item) {
+        this.onInsertButtonClicked(item);
+    };
+
     return {
         DeleteOne: EasyDAGButtons.DeleteOne,
-        GoToBase: GoToBase
+        GoToBase: GoToBase,
+        CloneAndEdit: CloneAndEdit,
+        Insert: Insert
     };
 });
 

src/common/viz/Execute.js

@@ -3,21 +3,31 @@
 define([
     'q',
     'executor/ExecutorClient',
+    'deepforge/api/ExecPulseClient',
+    'deepforge/api/JobOriginClient',
+    'deepforge/Constants',
     'panel/FloatingActionButton/styles/Materialize'
 ], function(
     Q,
     ExecutorClient,
+    ExecPulseClient,
+    JobOriginClient,
+    CONSTANTS,
     Materialize
 ) {
 
     var Execute = function(client, logger) {
         this.client = this.client || client;
         this.logger = this.logger || logger;
+        this.pulseClient = new ExecPulseClient({
+            logger: this.logger
+        });
         this._executor = new ExecutorClient({
             logger: this.logger.fork('ExecutorClient'),
             serverPort: WebGMEGlobal.gmeConfig.server.port,
             httpsecure: window.location.protocol === 'https:'
         });
+        this.originManager = new JobOriginClient({logger: this.logger});
     };
 
     Execute.prototype.executeJob = function(node) {
@@ -102,6 +112,21 @@ define([
             .fail(err => this.logger.error(`Job cancel failed: ${err}`));
     };
 
+    Execute.prototype._setJobStopped = function(jobId, silent) {
+        if (!silent) {
+            var name = this.client.getNode(jobId).getAttribute('name');
+            this.client.startTransaction(`Stopping "${name}" job`);
+        }
+
+        this.client.delAttribute(jobId, 'jobId');
+        this.client.delAttribute(jobId, 'secret');
+        this.client.setAttribute(jobId, 'status', 'canceled');
+
+        if (!silent) {
+            this.client.completeTransaction();
+        }
+    };
+
     Execute.prototype.stopJob = function(job, silent) {
         var jobId;
 
@@ -109,18 +134,7 @@ define([
         jobId = job.getId();
 
         this.silentStopJob(job);
-
-        if (!silent) {
-            this.client.startTransaction(`Stopping "${name}" job`);
-        }
-
-        this.client.delAttributes(jobId, 'jobId');
-        this.client.delAttributes(jobId, 'secret');
-        this.client.setAttributes(jobId, 'status', 'canceled');
-
-        if (!silent) {
-            this.client.completeTransaction();
-        }
+        this._setJobStopped(jobId, silent);
     };
 
 
@@ -165,14 +179,17 @@ define([
     };
 
     Execute.prototype._stopExecution = function(execNode, inTransaction) {
-        var msg = `Canceling ${execNode.getAttribute('name')} execution`;
+        var msg = `Canceling ${execNode.getAttribute('name')} execution`,
+            jobIds;
 
         if (!inTransaction) {
             this.client.startTransaction(msg);
         }
 
-        this._silentStopExecution(execNode);
-        this.client.setAttributes(execNode.getId(), 'status', 'canceled');
+        jobIds = this._silentStopExecution(execNode);
+
+        this.client.setAttribute(execNode.getId(), 'status', 'canceled');
+        jobIds.forEach(jobId => this._setJobStopped(jobId, true));
 
         if (!inTransaction) {
             this.client.completeTransaction();
@@ -180,11 +197,88 @@ define([
     };
 
     Execute.prototype._silentStopExecution = function(execNode) {
-        var jobIds = execNode.getChildrenIds();
+        var runningJobIds = execNode.getChildrenIds()
+            .map(id => this.client.getNode(id))
+            .filter(job => this.isRunning(job));  // get running jobs
 
-        jobIds.map(id => this.client.getNode(id))
-            .filter(job => this.isRunning(job))  // get running jobs
-            .forEach(job => this.silentStopJob(job));  // stop them
+        runningJobIds.forEach(job => this.silentStopJob(job));  // stop them
+
+        return runningJobIds;
+    };
+
+    // Resuming Executions
+    Execute.prototype.checkJobExecution= function (job) {
+        var pipelineId = job.getParentId(),
+            pipeline = this.client.getNode(pipelineId);
+
+        // First check the parent execution. If it doesn't exist, then check the job
+        return this.checkPipelineExecution(pipeline)
+            .then(tryToStartJob => {
+                if (tryToStartJob) {
+                    return this._checkJobExecution(job);
+                }
+            });
+    };
+
+    Execute.prototype._checkJobExecution = function (job) {
+        var jobId = job.getAttribute('jobId'),
+            status = job.getAttribute('status');
+
+        if (status === 'running' && jobId) {
+            return this.pulseClient.check(jobId)
+                .then(status => {
+                    if (status !== CONSTANTS.PULSE.DOESNT_EXIST) {
+                        return this._onOriginBranch(jobId).then(onBranch => {
+                            if (onBranch) {
+                                this.runExecutionPlugin('ExecuteJob', {
+                                    node: job
+                                });
+                            }
+                        });
+                    } else {
+                        this.logger.warn(`Could not restart job: ${job.getId()}`);
+                    }
+                });
+        }
+        return Q();
+    };
+
+    Execute.prototype._onOriginBranch = function (hash) {
+        return this.originManager.getOrigin(hash)
+            .then(origin => {
+                var currentBranch = this.client.getActiveBranchName();
+                if (origin && origin.branch) {
+                    return origin.branch === currentBranch;
+                }
+                return false;
+            });
+    };
+
+    Execute.prototype.checkPipelineExecution = function (pipeline) {
+        var runId = pipeline.getAttribute('runId'),
+            status = pipeline.getAttribute('status'),
+            tryToStartJob = true;
+
+        if (status === 'running' && runId) {
+            return this.pulseClient.check(runId)
+                .then(status => {
+                    if (status === CONSTANTS.PULSE.DEAD) {
+                        // Check the origin branch
+                        return this._onOriginBranch(runId).then(onBranch => {
+                            if (onBranch) {
+                                this.runExecutionPlugin('ExecutePipeline', {
+                                    node: pipeline
+                                });
+                            }
+                        });
+                    }
+                    // only try to start if the pulse info doesn't exist
+                    tryToStartJob = status === CONSTANTS.PULSE.DOESNT_EXIST;
+                    return tryToStartJob;
+                });
+        } else {
+            return Q().then(() => tryToStartJob);
+        }
     };
 
     return Execute;

src/common/viz/NodePrompter.js

@@ -4,9 +4,11 @@
 // adding a "plus" button for creating new objects in line
 
 define([
+    'deepforge/Constants',
     'q',
     'css!./NodePrompter.css'
 ], function(
+    Constants,
     Q
 ) {
 
@@ -271,12 +273,14 @@ define([
     };
 
     var Container = function(svg, node) {  // used for positioning
+        var colorAttr = node.attributes[Constants.DISPLAY_COLOR];
         this.$el = svg.append('g');
         this.x = 0;
         this.y = 0;
         this.node = node;
         this.decorator = new node.Decorator({
             node: node,
+            color: colorAttr && colorAttr.value,
             parentEl: this.$el
         });
     };

src/common/viz/PipelineControl.js

@@ -65,7 +65,7 @@ define([
 
     PipelineControl.prototype.createNode = function(baseId) {
         var parentId = this._currentNodeId,
-            newNodeId = this._client.createChild({parentId, baseId});
+            newNodeId = this._client.createNode({parentId, baseId});
 
         return newNodeId;
     };
@@ -103,6 +103,10 @@ define([
                 delete desc.attributes.code;
             }
 
+            // Handle the display color
+            desc.displayColor = desc.attributes[CONSTANTS.DISPLAY_COLOR].value;
+            delete desc.attributes[CONSTANTS.DISPLAY_COLOR];
+
         } else if (desc.isConnection) {
             // Set src, dst to siblings and add srcPort, dstPort
             desc.srcPort = desc.src;

src/common/viz/RenameablePanel.js

@@ -49,7 +49,7 @@ define([
 
                 if (!/^\s*$/.test(newValue)) {
                     this._client.startTransaction(msg);
-                    this._client.setAttributes(nodeId, 'name', newValue);
+                    this._client.setAttribute(nodeId, 'name', newValue);
                     this._client.completeTransaction();
                 }
             }

src/common/viz/panels/ThumbnailControl.js

@@ -0,0 +1,41 @@
+/* globals define */
+define([
+    'panels/EasyDAG/EasyDAGControl'
+], function(
+    EasyDAGControl
+) {
+    var ThumbnailControl = function() {
+        EasyDAGControl.apply(this, arguments);
+    };
+
+    ThumbnailControl.prototype = Object.create(EasyDAGControl.prototype);
+
+    ThumbnailControl.prototype._initWidgetEventHandlers = function () {
+        EasyDAGControl.prototype._initWidgetEventHandlers.call(this);
+        this._widget.updateThumbnail = this.updateThumbnail.bind(this);
+    };
+
+    ThumbnailControl.prototype.updateThumbnail = function (svg) {
+        var node = this._client.getNode(this._currentNodeId),
+            name,
+            attrs,
+            currentThumbnail,
+            attrName = 'thumbnail',
+            msg;
+
+        if (node) {  // may have been deleted
+            name = node.getAttribute('name');
+            attrs = node.getValidAttributeNames();
+            currentThumbnail = node.getAttribute(attrName);
+            msg = `Updating pipeline thumbnail for "${name}"`;
+
+            if (attrs.indexOf(attrName) > -1 && currentThumbnail !== svg) {
+                this._client.startTransaction(msg);
+                this._client.setAttribute(this._currentNodeId, attrName, svg);
+                this._client.completeTransaction();
+            }
+        }
+    };
+
+    return ThumbnailControl;
+});

src/common/viz/widgets/Thumbnail.js

@@ -0,0 +1,84 @@
+/* globals define, $, _ */
+define([
+    'widgets/EasyDAG/EasyDAGWidget'
+], function(
+    EasyDAGWidget
+) {
+
+    var ThumbnailWidget = function() {
+        EasyDAGWidget.apply(this, arguments);
+    };
+
+    ThumbnailWidget.prototype = Object.create(EasyDAGWidget.prototype);
+
+    ThumbnailWidget.prototype.addNode = function() {
+        var result = EasyDAGWidget.prototype.addNode.apply(this, arguments);
+
+        this.refreshThumbnail();
+        return result;
+    };
+
+    ThumbnailWidget.prototype.removeNode = function() {
+        var result = EasyDAGWidget.prototype.removeNode.apply(this, arguments);
+
+        this.refreshThumbnail();
+        return result;
+    };
+
+    ThumbnailWidget.prototype._removeConnection = function() {
+        var result = EasyDAGWidget.prototype._removeConnection.apply(this, arguments);
+
+        this.refreshThumbnail();
+        return result;
+    };
+
+    ThumbnailWidget.prototype.addConnection = function() {
+        var result = EasyDAGWidget.prototype.addConnection.apply(this, arguments);
+
+        this.refreshThumbnail();
+        return result;
+    };
+
+    ////////////////////////// Thumbnail updates //////////////////////////
+    ThumbnailWidget.prototype.getSvgDistanceDim = function(dim) {
+        var maxValue = this._getMaxAlongAxis(dim),
+            nodes,
+            minValue;
+
+        nodes = this.graph.nodes().map(id => this.graph.node(id));
+        minValue = nodes.length ? Math.min.apply(null, nodes.map(node => node[dim] || 0)) : 0;
+        return maxValue-minValue;
+    };
+
+    ThumbnailWidget.prototype.getSvgWidth = function() {
+        return this.getSvgDistanceDim('x');
+    };
+
+    ThumbnailWidget.prototype.getSvgHeight = function() {
+        return this.height - 25;
+    };
+
+    ThumbnailWidget.prototype.getViewBox = function() {
+        var maxX = this.getSvgWidth('x'),
+            maxY = this.getSvgHeight('y');
+
+        return `0 0 ${maxX} ${maxY}`;
+    };
+
+    ThumbnailWidget.prototype.refreshThumbnail = _.debounce(function() {
+        // Get the svg...
+        var svg = document.createElement('svg'),
+            group = this.$svg.node(),
+            child;
+
+        svg.setAttribute('viewBox', this.getViewBox());
+        for (var i = 0; i < group.children.length; i++) {
+            child = $(group.children[i]);
+            svg.appendChild(child.clone()[0]);
+        }
+
+        this.updateThumbnail(svg.outerHTML);
+    }, 1000);
+
+    return ThumbnailWidget;
+});

src/decorators/ArtifactOpDecorator/EasyDAG/ArtifactOpDecorator.EasyDAGWidget.js

@@ -40,10 +40,40 @@ define([
     ArtifactOpDecorator.prototype.DECORATOR_ID = DECORATOR_ID;
 
     ArtifactOpDecorator.prototype.getTargetFilterFnFor = function() {
+        var currentNode,
+            pId,
+            peerIds,
+            currentDataId,
+            targetTypeIds = [];
+
+        // Get all connections from this node's data
+        if (this._node.outputs[0]) {
+            currentNode = this.client.getNode(this._node.id);
+            pId = currentNode.getParentId();
+            peerIds = this.client.getNode(pId).getChildrenIds();
+            currentDataId = this._node.outputs[0].id;
+
+            targetTypeIds = peerIds.map(id => this.client.getNode(id))
+                .filter(node => {
+                    var ptr = node.getPointer('src');
+                    return ptr.to === currentDataId;
+                })
+
+                // Get the target data types
+                .map(node => this.client.getNode(node.getPointer('dst').to).getMetaTypeId());
+        }
+
         return id => {
             var node = this.client.getNode(id),
-                isMetaTgt = node.getId() === node.getMetaTypeId();
-            return isMetaTgt === this.castOpts.metaTgt;
+                isMetaTgt = node.getId() === node.getMetaTypeId(),
+                isValidType = true;
+
+            // make sure it is a type of the target types
+            isValidType = targetTypeIds.reduce((passing, typeId) => {
+                return passing && node.isTypeOf(typeId);
+            }, true);
+
+            return isValidType && isMetaTgt === this.castOpts.metaTgt;
         };
     };
 
@@ -57,13 +87,13 @@ define([
             this.client.startTransaction(`Removing output of ${this.name}`);
             this.client.delPointer(this._node.id, name);
             if (outputId) {
-                this.client.delAttributes(outputId, 'data');
+                this.client.delAttribute(outputId, 'data');
             }
             this.client.completeTransaction();
         } else if (name === this.castOpts.ptr) {  // set the casted value
             this.client.startTransaction(`Setting output of ${this.name} to ${to}`);
             this.castOutputType(to);
-            this.client.makePointer(this._node.id, name, to);
+            this.client.setPointer(this._node.id, name, to);
             this.client.completeTransaction();
         } else {
             DecoratorBase.prototype.savePointer.call(this, name, to);

src/decorators/ContainerLayerDecorator/ContainerLayerDecorator.js

@@ -0,0 +1,39 @@
+/*globals define, _*/
+/*jshint browser: true, camelcase: false*/
+
+define([
+    'js/Decorators/DecoratorBase',
+    './EasyDAG/ContainerLayerDecorator.EasyDAGWidget'
+], function (
+    DecoratorBase,
+    ContainerLayerDecoratorEasyDAGWidget
+) {
+
+    'use strict';
+
+    var ContainerLayerDecorator,
+        __parent__ = DecoratorBase,
+        __parent_proto__ = DecoratorBase.prototype,
+        DECORATOR_ID = 'ContainerLayerDecorator';
+
+    ContainerLayerDecorator = function (params) {
+        var opts = _.extend({loggerName: this.DECORATORID}, params);
+
+        __parent__.apply(this, [opts]);
+
+        this.logger.debug('ContainerLayerDecorator ctor');
+    };
+
+    _.extend(ContainerLayerDecorator.prototype, __parent_proto__);
+    ContainerLayerDecorator.prototype.DECORATORID = DECORATOR_ID;
+
+    /*********************** OVERRIDE DecoratorBase MEMBERS **************************/
+
+    ContainerLayerDecorator.prototype.initializeSupportedWidgetMap = function () {
+        this.supportedWidgetMap = {
+            EasyDAG: ContainerLayerDecoratorEasyDAGWidget
+        };
+    };
+
+    return ContainerLayerDecorator;
+});

src/decorators/ContainerLayerDecorator/EasyDAG/ContainerLayerDecorator.EasyDAGWidget.css

@@ -0,0 +1,25 @@
+.condense .nested-layers {
+  display: none;
+}
+
+.nested-layers .hover-box {
+  stroke: black;
+  stroke-dasharray: 4, 4;
+  stroke-opacity: 0;
+}
+
+.nested-layers .unhovered .button {
+  opacity: 0;
+}
+
+.nested-layers .hovered .button {
+  opacity: 1;
+}
+
+.nested-layers .unhovered .hover-box {
+  stroke-opacity: 0;
+}
+
+.nested-layers .hovered .hover-box {
+  stroke-opacity: 0;
+}

src/decorators/ContainerLayerDecorator/EasyDAG/ContainerLayerDecorator.EasyDAGWidget.js

@@ -0,0 +1,428 @@
+/*globals define, _, */
+/*jshint browser: true, camelcase: false*/
+
+define([
+    'decorators/LayerDecorator/EasyDAG/LayerDecorator.EasyDAGWidget',
+    'js/Constants',
+    'deepforge/Constants',
+    './NestedLayer',
+    'widgets/EasyDAG/Buttons',
+    'css!./ContainerLayerDecorator.EasyDAGWidget.css'
+], function (
+    LayerDecorator,
+    GME_CONSTANTS,
+    CONSTANTS,
+    NestedLayer,
+    Buttons
+) {
+
+    'use strict';
+
+    var ContainerLayerDecorator,
+        ZOOM = 0.8,
+        DECORATOR_ID = 'ContainerLayerDecorator';
+
+    // Container layer nodes need to be able to nest the containedLayers
+    // in order inside of themselves when expanded
+    ContainerLayerDecorator = function (options) {
+        this.nestedLayers = {};
+        LayerDecorator.call(this, options);
+        this.$nested = this.$el.append('g')
+            .attr('class', 'nested-layers');
+
+        // If clicked, deselect the given nested layer
+        this.$el.on('click', () => {
+            if (this.expanded) {
+                Object.keys(this.nestedLayers).forEach(id => {
+                    this.nestedLayers[id].widget.onBackgroundClick();
+                });
+            }
+        });
+        this.onNestedRefresh = _.debounce(this.updateExpand.bind(this), 50);
+
+        // Add event handlers
+        NestedLayer.prototype.addLayerBefore = function(layerId) {
+            var decorator = this._parent,
+                index = decorator._node.containedLayers.indexOf(this.id);
+            return decorator.addLayerAt(layerId, index - 1);
+        };
+
+        NestedLayer.prototype.addLayerAfter = function(layerId) {
+            var decorator = this._parent,
+                index = decorator._node.containedLayers.indexOf(this.id);
+            return decorator.addLayerAt(layerId, index + 1);
+        };
+
+        NestedLayer.prototype.isLast = function() {
+            var index = this._parent._node.containedLayers.length - 1;
+            return this._parent._node.containedLayers[index] === this.id;
+        };
+
+        NestedLayer.prototype.isFirst = function() {
+            return this._parent._node.containedLayers[0] === this.id;
+        };
+
+        NestedLayer.prototype.moveLayerForward = function() {
+            return this.moveLayer(true);
+        };
+
+        NestedLayer.prototype.moveLayerBackward = function() {
+            return this.moveLayer();
+        };
+
+        NestedLayer.prototype.moveLayer = function(forward) {
+            var decorator = this._parent,
+                index = decorator._node.containedLayers.indexOf(this.id),
+                client = decorator.client,
+                msg;
+
+            decorator._node.containedLayers.splice(index, 1);
+            if (forward) {
+                index = Math.max(0, index - 1);
+            } else {
+                index++;
+            }
+
+            decorator._node.containedLayers.splice(index, 0, this.id);
+
+            msg = `Swapping nested layers at ${index} and ${forward ? index-1 : index+1}`;
+            client.startTransaction(msg);
+            decorator._updateNestedIndices();
+            client.completeTransaction();
+        };
+
+        NestedLayer.prototype.onLastNodeRemoved = function() {
+            var decorator = this._parent,
+                index = decorator._node.containedLayers.indexOf(this.id),
+                msg = `Removing nested layer of ${decorator._node.name} at position ${index}`;
+
+            decorator.client.startTransaction(msg);
+            decorator.client.deleteNode(this.id);
+            decorator.client.completeTransaction();
+        };
+        this.updateNestedTerritory();
+    };
+
+    _.extend(ContainerLayerDecorator.prototype, LayerDecorator.prototype);
+
+    ContainerLayerDecorator.prototype.DECORATOR_ID = DECORATOR_ID;
+
+    ContainerLayerDecorator.prototype._updateNestedIndices = function() {
+        this._node.containedLayers.forEach((layerId, index) => {
+            // Set the layer's member registry to it's index
+            this.client.setMemberRegistry(
+                this._node.id,
+                layerId,
+                CONSTANTS.CONTAINED_LAYER_SET,
+                CONSTANTS.CONTAINED_LAYER_INDEX,
+                index
+            );
+        });
+    };
+
+    ContainerLayerDecorator.prototype.addLayerAt = function(baseId, index) {
+        var client = this.client,
+            parentId = this._node.id,
+            archNode,
+            newId,
+            msg;
+
+        // Get the index of the given layer
+        index = Math.max(index, 0);
+
+        archNode = client.getAllMetaNodes()
+            .find(node => node.getAttribute('name') === 'Architecture');
+
+        // Create a new Architecture node in the given node
+        msg = `Adding layer to ${this._node.name} at position ${index}`;
+        client.startTransaction(msg);
+
+        newId = client.createNode({
+            parentId: parentId,
+            baseId: archNode.getId()
+        });
+        // Create the selected layer
+        client.createNode({
+            parentId: newId,
+            baseId: baseId
+        });
+        client.addMember(parentId, newId, CONSTANTS.CONTAINED_LAYER_SET);
+        this._node.containedLayers.splice(index, 0, newId);
+        this._updateNestedIndices();
+
+        client.completeTransaction();
+    };
+
+    ContainerLayerDecorator.prototype.condense = function() {
+        // hide the nested layers
+        this.$el.attr('class', 'centering-offset condense');
+        this.removeCreateNestedBtn();
+        return LayerDecorator.prototype.condense.apply(this, arguments);
+    };
+
+    ContainerLayerDecorator.prototype.updateNestedTerritory = function() {
+        // Add the nested layers and update
+        if (!this._nestedTerritoryUI) {
+            this._nestedTerritoryUI = this.client.addUI(this, this._containedEvents.bind(this));
+        }
+        this._territory = {};
+        this._node.containedLayers.forEach(id => this._territory[id] = {children: 0});
+        this.client.updateTerritory(this._nestedTerritoryUI, this._territory);
+    };
+
+    ContainerLayerDecorator.prototype._containedEvents = function(events) {
+        for (var i = events.length; i--;) {
+            switch (events[i].etype) {
+            case GME_CONSTANTS.TERRITORY_EVENT_LOAD:
+                if (!this.nestedLayers[events[i].eid]) {
+                    this.createNestedWidget(events[i].eid);
+                }
+                break;
+
+            case GME_CONSTANTS.TERRITORY_EVENT_UNLOAD:
+                this.removeNestedWidget(events[i].eid);
+                break;
+            }
+        }
+        if (events.length > 1) {  // if more than just 'complete' event
+            this.updateExpand();
+        }
+    };
+
+    ContainerLayerDecorator.prototype.update = function(node) {
+        var attrsUpdated = false,
+            attrs = this._attributes;
+
+        this._node = node;
+        // Update the attributes
+        this.setAttributes();
+        attrsUpdated = !_.isEqual(attrs, this._attributes);
+
+        // Check for a new nested layer
+        var hasNewLayers = this._node.containedLayers
+            .filter(id => !this.nestedLayers[id])
+            .length > 0;
+
+        if (hasNewLayers) {
+            this.updateNestedTerritory();
+        } else {
+            // Update the order of the nested layers
+            if (this._selected) {
+                this.expand();
+            } else {
+                this.condense();
+            }
+        }
+        // Only reset fieldsWidth if the attribute has gotten larger
+        if (attrsUpdated) {
+            this.fieldsWidth = null;
+        }
+    };
+
+    ContainerLayerDecorator.prototype.updateExpand = function() {
+        if (this.expanded) {
+            this.expand();
+        }
+    };
+
+    ContainerLayerDecorator.prototype.createNestedWidget = function(id) {
+        if (!this.$nested) {
+            this.$nested = this.$el.append('g')
+                .attr('class', 'nested-layers');
+        }
+
+        this.nestedLayers[id] = new NestedLayer({
+            $container: this.$nested,
+            parent: this,
+            client: this.client,
+            logger: this.logger,
+            onRefresh: this.onNestedRefresh,
+            id: id
+        });
+        return this.nestedLayers[id];
+    };
+
+    ContainerLayerDecorator.prototype.removeNestedWidget = function(id) {
+        this.nestedLayers[id].destroy();
+        delete this.nestedLayers[id];
+        this.updateExpand();
+    };
+
+    ContainerLayerDecorator.prototype._renderInfo = function(top, width) {
+        var isAnUpdate = this.expanded,
+            y = top;
+
+        // Add the attribute fields
+        this.clearFields();
+        this.$attributes = this.$el.append('g')
+            .attr('fill', '#222222');
+
+        if (!isAnUpdate) {
+            this.$attributes.attr('opacity', 0);
+        }
+
+        y = this.createAttributeFields(y, width);
+        y = this.createPointerFields(y, width);
+
+        if (y !== top) {
+            y += this.ROW_HEIGHT/2;
+        }
+        return y;
+    };
+
+    ContainerLayerDecorator.prototype.expand = function() {
+        // This should be rendered with the attributes
+        var height,
+            width,
+
+            // Attributes
+            initialY = 25,
+            isAnUpdate = this.expanded,
+            NAME_MARGIN = 15,
+            nestedMargin = 15,  // minimum
+            margin = 5,
+            y = margin + initialY,
+            x = margin,
+            i;
+
+        // Shift name down
+        this.$name.attr('y', 20);
+
+        // Add the nested children
+        var ids = this._node.containedLayers.filter(id => this.nestedLayers[id]),
+            totalNestedWidth = 0,
+            maxNestedHeight = 0,
+            fieldWidth,
+            widget;
+
+        if (ids.length === 0) {
+            maxNestedHeight = CreateNestedBtn.SIZE * 2;
+        } else {
+            for (i = 0; i < ids.length; i++) {
+                widget = this.nestedLayers[ids[i]].widget;
+                totalNestedWidth += widget.getSvgWidth() * ZOOM;
+                maxNestedHeight = Math.max(widget.getSvgHeight() * ZOOM, maxNestedHeight);
+
+                // Update the buttons (in case of reorder)
+                this.nestedLayers[ids[i]].refreshButtons();
+            }
+        }
+
+        fieldWidth = this.fieldsWidth + 3 * NAME_MARGIN;
+        width = Math.max(
+            this.nameWidth + 2 * NAME_MARGIN,
+            this.size.width,
+            fieldWidth,
+            totalNestedWidth + (ids.length + 1) * nestedMargin
+        );
+
+        // Render attributes
+        y = this._renderInfo(y, fieldWidth);
+        y += nestedMargin;
+
+        // Update width, height
+        height = y + maxNestedHeight + nestedMargin;
+
+        // Equally space the nested widgets
+        nestedMargin = (width - totalNestedWidth)/(ids.length + 1);
+        x = nestedMargin - width/2;
+        for (i = 0; i < ids.length; i++) {
+            this.nestedLayers[ids[i]].$el
+                .attr('transform', `translate(${x}, ${y}) scale(${ZOOM})`);
+            x += this.nestedLayers[ids[i]].widget.getSvgWidth() * ZOOM + nestedMargin;
+        }
+
+        this.removeCreateNestedBtn();
+
+        if (ids.length === 0) {
+            // Add the 'create nested layer' button if no nested layers
+            this.$createNestedBtn = new CreateNestedBtn({
+                context: this,
+                $pEl: this.$el,
+                y: y + CreateNestedBtn.SIZE
+            });
+        }
+
+        this.$body
+            .transition()
+            .attr('x', -width/2)
+            .attr('y', 0)
+            .attr('rx', 0)
+            .attr('ry', 0)
+            .attr('width', width)
+            .attr('height', height)
+            .each('end', () => {
+                if (!isAnUpdate) {
+                    this.$attributes.attr('opacity', 1);
+                    this.$el.attr('class', 'centering-offset expand');
+                }
+            });
+
+        if (this.height !== height || this.width !== width) {
+            this.height = height;
+            this.width = width;
+            this.expanded = true;
+            this.$el
+                .attr('transform', `translate(${this.width/2}, 0)`);
+
+            this.onResize();
+        }
+    };
+
+    ContainerLayerDecorator.prototype.removeCreateNestedBtn = function() {
+        if (this.$createNestedBtn) {
+            this.$createNestedBtn.remove();
+            this.$createNestedBtn = null;
+        }
+    };
+
+    ContainerLayerDecorator.prototype.destroyNested = function() {
+        Object.keys(this.nestedLayers).forEach(id => this.nestedLayers[id].destroy());
+        this.nestedLayers = {};
+
+        if (this.$nested) {
+            this.$nested.remove();
+            this.$nested = this.$el.append('g')
+                .attr('class', 'nested-layers');
+        }
+    };
+
+    ContainerLayerDecorator.prototype.destroy = function() {
+        LayerDecorator.prototype.destroy.call(this);
+        if (this._nestedTerritoryUI) {
+            this.client.removeUI(this._nestedTerritoryUI);
+            this._nestedTerritoryUI = null;
+        }
+        this.destroyNested();
+    };
+
+    var CreateNestedBtn = function(params) {
+        params.title = 'Add nested layer';
+        Buttons.Add.call(this, params);
+    };
+
+    CreateNestedBtn.SIZE = Buttons.Add.SIZE;
+    CreateNestedBtn.prototype = Object.create(Buttons.Add.prototype);
+
+    CreateNestedBtn.prototype._onClick = function() {
+        // Call addLayerAfter and prompt for a layer
+        this.promptLayer()
+            .then(layerId => this.addLayerAt(layerId, 0));
+    };
+
+    ContainerLayerDecorator.prototype.expandAll = function() {
+        this.expand();
+        // For each of the nested layers, expand all their nodes
+        Object.keys(this.nestedLayers)
+            .forEach(id => this.nestedLayers[id].widget.expandAllNodes());
+    };
+
+    ContainerLayerDecorator.prototype.condenseAll = function() {
+        this.condense();
+        // For each of the nested layers, expand all their nodes
+        Object.keys(this.nestedLayers)
+            .forEach(id => this.nestedLayers[id].widget.expandAllNodes(true));
+    };
+
+    return ContainerLayerDecorator;
+});

src/decorators/ContainerLayerDecorator/EasyDAG/NestedLayer.js

@@ -0,0 +1,175 @@
+/*globals define, _ */
+define([
+    'panels/ArchEditor/ArchEditorControl',
+    'widgets/ArchEditor/ArchEditorWidget',
+    'widgets/EasyDAG/Buttons'
+], function(
+    ArchEditor,
+    ArchEditorWidget,
+    Buttons
+) {
+    var nop = () => {};
+    var NestedLayer = function(opts) {
+        this.$el = opts.$container.append('g')
+            .attr('class', 'nested-layer');
+
+        this.id = opts.id;
+        this._parent = opts.parent;
+        this.logger = opts.logger;
+
+        this.refreshButtons = _.debounce(this.updateButtons.bind(this), 100);
+        this.$outline = this.$el.append('rect')  // for hover detection
+            .attr('fill-opacity', 0)
+            .attr('x', 0)
+            .attr('y', 0);
+
+        this.$content = this.$el.append('g');
+        this.initHover();
+
+        this.widget = new ArchEditorWidget({
+            logger: this.logger.fork('ArchWidget'),
+            autoCenter: false,
+            svg: this.$content
+        });
+        this.widget.setTitle =
+        this.widget.updateEmptyMsg = nop;
+        this.onRefresh = opts.onRefresh;
+        this.widget.refreshExtras = this.onWidgetRefresh.bind(this);
+
+        this.control = new ArchEditor({
+            logger: this.logger.fork('ArchControl'),
+            client: opts.client,
+            embedded: true,
+            widget: this.widget
+        });
+        this.control._onUnload = id => {
+            ArchEditor.prototype._onUnload.call(this.control, id);
+            // If it was the last node, remove it
+            var node = this.control._client.getNode(this.id);
+            if (node.getChildrenIds().length === 0) {
+                this.onLastNodeRemoved();
+            }
+        };
+
+        // hack :(
+        this.control.$btnModelHierarchyUp = {
+            show: nop,
+            hide: nop
+        };
+        this.widget.active = true;
+        this.control.selectedObjectChanged(this.id);
+    };
+
+    NestedLayer.prototype.initHover = function() {
+        this.$hover = this.$el.append('g')
+            .attr('class', 'hover-items');
+
+
+
+        this.$el.on('mouseenter', this.onHover.bind(this));
+        this.$el.on('mouseleave', this.onUnhover.bind(this));
+
+        // Buttons
+        this.$leftBtn = new Buttons.Add({
+            hide: true,
+            icon: this.isFirst() ? 'plus' : 'chevron-left',
+            $pEl: this.$hover
+        });
+
+        this.$rightBtn = new Buttons.Add({
+            hide: true,
+            icon: this.isLast() ? 'plus' : 'chevron-right',
+            $pEl: this.$hover
+        });
+
+        this.$deleteBtn = new Buttons.DeleteOne({
+            hide: true,
+            title: 'Delete',
+            $pEl: this.$hover
+        });
+
+        this.$leftBtn._onClick = this.clickLeft.bind(this);
+        this.$rightBtn._onClick = this.clickRight.bind(this);
+        this.$deleteBtn._onClick = () => this.onLastNodeRemoved();
+
+        this.$leftHint = this.$leftBtn.$el.append('title');
+        this.$rightHint = this.$rightBtn.$el.append('title');
+        this.refreshButtons();
+    };
+
+    NestedLayer.prototype.updateButtons = function() {
+        this.$leftBtn.icon = this.isFirst() ? 'plus' : 'chevron-left';
+        this.$rightBtn.icon = this.isLast() ? 'plus' : 'chevron-right';
+
+        this.$leftHint.text(this.isFirst() ?
+            'Add nested layer' :
+            'Move nested layer left'
+        );
+        this.$rightHint.text(this.isLast() ?
+            'Add nested layer' :
+            'Move nested layer right'
+        );
+
+        this.$leftBtn.render();
+        this.$rightBtn.render();
+    };
+
+    NestedLayer.prototype.clickLeft = function() {
+        if (this.isFirst()) {
+            this.promptLayer()
+                .then(layerId => this.addLayerBefore(layerId));
+        } else {
+            this.moveLayerForward();
+        }
+        this.onUnhover();
+    };
+
+    NestedLayer.prototype.promptLayer = function() {
+        var nodes = this.widget.getValidInitialNodes();
+
+        return this.widget.promptLayer(nodes)
+            .then(selected => selected.node.id);
+    };
+
+    NestedLayer.prototype.clickRight = function() {
+        if (this.isLast()) {
+            this.promptLayer()
+                .then(layerId => this.addLayerAfter(layerId));
+        } else {
+            this.moveLayerBackward();
+        }
+        this.onUnhover();
+    };
+
+    NestedLayer.prototype.onHover = function() {
+        this.refreshButtons();
+        this.$hover.attr('class', 'hover-items hovered');
+    };
+
+    NestedLayer.prototype.onUnhover = function() {
+        this.$hover.attr('class', 'hover-items unhovered');
+    };
+
+    NestedLayer.prototype.onWidgetRefresh = function() {
+        var width = this.widget.getSvgWidth(),
+            height = this.widget.getSvgHeight();
+
+        this.$outline
+            .attr('width', width)
+            .attr('height', height);
+
+        this.$leftBtn.$el.attr('transform', `translate(0, ${height/2})`);
+        this.$rightBtn.$el
+            .attr('transform', `translate(${width}, ${height/2})`);
+
+        this.onRefresh();
+    };
+
+    NestedLayer.prototype.destroy = function() {
+        this.control.destroy();
+        this.widget.destroy();
+        this.$el.remove();
+    };
+
+    return NestedLayer;
+});

src/decorators/DcOpDecorator/EasyDAG/DcOpDecorator.EasyDAGWidget.js

@@ -47,11 +47,11 @@ define([
             // create the outputId node
             outputId = this._createOutputNode(baseId);
         } else {
-            this.client.makePointer(outputId, CONSTANTS.POINTER_BASE, baseId);
+            this.client.setPointer(outputId, CONSTANTS.POINTER_BASE, baseId);
         }
         // Copy the data content to the output node
         hash = target.getAttribute('data');
-        this.client.setAttributes(outputId, 'data', hash);
+        this.client.setAttribute(outputId, 'data', hash);
     };
 
     DcOpDecorator.prototype._createOutputNode = function(baseId) {
@@ -69,7 +69,7 @@ define([
             return metaType.getAttribute('name') === 'Outputs';
         });
 
-        return this.client.createChild({
+        return this.client.createNode({
             baseId: baseId,
             parentId: outputCntrId
         });

src/decorators/LayerDecorator/EasyDAG/LayerDecorator.EasyDAGWidget.js

@@ -77,11 +77,11 @@ define([
         // Create a nested "architecture" node and set the ptr target to it
         baseId = base.getId();
         this.client.startTransaction(msg);
-        tgtId = this.client.createChild({
+        tgtId = this.client.createNode({
             parentId: this._node.id,
             baseId: baseId
         });
-        this.client.setAttributes(tgtId, 'name', `${ptr} (${this._node.name})`);
+        this.client.setAttribute(tgtId, 'name', `${ptr} (${this._node.name})`);
         this.savePointer(ptr, tgtId);
         this.client.completeTransaction();
         WebGMEGlobal.State.registerActiveObject(tgtId);
@@ -95,7 +95,7 @@ define([
             // If the target is contained in the current node, delete it!
             if (currentId.indexOf(this._node.id) === 0) {
                 this.client.startTransaction(`Removing layer for ${ptr} of ${name}`);
-                this.client.delMoreNodes([currentId]);
+                this.client.deleteNode(currentId);
                 this.client.completeTransaction();
                 this.logger.info(`Removed ${ptr} and deleted target (${currentId})`);
             } else {

src/decorators/OpIntDecorator/EasyDAG/OpIntDecorator.EasyDAGWidget.js

@@ -34,7 +34,13 @@ define([
             this.enableTooltip(this._node.baseName, 'dark');
         }
         DecoratorBase.prototype.initialize.call(this);
-        this.$name.on('dblclick', this.editName.bind(this));
+        this.$name.on('click', () => {
+            // Operations must already be selected. Otherwise, they will animate
+            // after the edit name box is created and it will be placed incorrectly
+            if (this.expanded || !this.isOperation()) {
+                this.editName();
+            }
+        });
     };
 
     OpIntDecorator.prototype.AttributeField = AttributeField;
@@ -102,8 +108,8 @@ define([
             msg = `Deleting "${name}" attribute from "${opName}" operation`;
 
         this.client.startTransaction(msg);
-        this.client.removeAttributeSchema(this._node.id, name);
-        this.client.delAttributes(this._node.id, name);
+        this.client.delAttributeMeta(this._node.id, name);
+        this.client.delAttribute(this._node.id, name);
         this.client.completeTransaction();
     };
 
@@ -129,14 +135,14 @@ define([
 
         if (name !== desc.name) {  // Renaming attribute
             if (name) {
-                this.client.removeAttributeSchema(this._node.id, name);
-                this.client.delAttributes(this._node.id, name);
+                this.client.delAttributeMeta(this._node.id, name);
+                this.client.delAttribute(this._node.id, name);
             }
             name = desc.name;
         }
 
-        this.client.setAttributeSchema(this._node.id, name, schema);
-        this.client.setAttributes(this._node.id, name, desc.defaultValue);
+        this.client.setAttributeMeta(this._node.id, name, schema);
+        this.client.setAttribute(this._node.id, name, desc.defaultValue);
         this.client.completeTransaction();
     };
 

src/decorators/OperationDecorator/EasyDAG/OperationDecorator.EasyDAGWidget.js

@@ -2,9 +2,11 @@
 /*jshint browser: true, camelcase: false*/
 
 define([
+    'deepforge/Constants',
     'decorators/EllipseDecorator/EasyDAG/EllipseDecorator.EasyDAGWidget',
     'css!./OperationDecorator.EasyDAGWidget.css'
 ], function (
+    CONSTANTS,
     DecoratorBase
 ) {
 
@@ -13,6 +15,7 @@ define([
     var OperationDecorator,
         NAME_MARGIN = 25,
         DECORATOR_ID = 'OperationDecorator',
+        OPERATION_COLORS = {},
         PORT_TOOLTIP_OPTS = {
             tipJoint: 'left',
             removeElementsOnHide: true,
@@ -24,8 +27,10 @@ define([
     //     - highlight ports
     //     - unhighlight ports
     //     - report the location of specific ports
+    OPERATION_COLORS[CONSTANTS.OP.OUTPUT] = '#b0bec5';
+    OPERATION_COLORS[CONSTANTS.OP.INPUT] = '#b0bec5';
     OperationDecorator = function (options) {
-        options.color = options.color || '#78909c';
+        options.color = OPERATION_COLORS[options.node.name] || options.color || '#78909c';
         DecoratorBase.call(this, options);
 
         this.id = this._node.id;
@@ -73,14 +78,15 @@ define([
 
     OperationDecorator.prototype.showPorts = function(ids, areInputs) {
         var allPorts = areInputs ? this._node.inputs : this._node.outputs,
-            ports = ids ? allPorts.filter(port => ids.indexOf(port.id) > -1) : allPorts,
             x = -this.width/2,
-            dx = this.width/(ports.length+1),
+            dx = this.width/(allPorts.length+1),
             y = areInputs ? 0 : this.height;  // (this.height/2);
 
-        ports.forEach(port => {
+        allPorts.forEach(port => {
             x += dx;
-            this.renderPort(port, x, y, areInputs);
+            if (!ids || ids.indexOf(port.id) > -1) {
+                this.renderPort(port, x, y, areInputs);
+            }
         });
     };
 
@@ -117,7 +123,7 @@ define([
         tooltip = new Opentip(portIcon[0][0], PORT_TOOLTIP_OPTS);
         tooltip.setContent(port.name);
         portIcon.on('mouseenter', () => tooltip.show());
-        portIcon.on('mouseout', () => tooltip.hide());
+        portIcon.on('mouseleave', () => tooltip.hide());
         this.$portTooltips[port.id] = tooltip;
     };
 

src/layouts/SidebarLayout/SidebarLayout.css

@@ -0,0 +1,12 @@
+.ui-layout-center .layout-center {
+    left: 40px;
+    height: 100%;
+    width: 100%;
+    position: absolute;
+}
+
+.ui-layout-sidebar {
+    top: 64px;
+    width: 40px;
+    bottom: 27px;
+}

src/layouts/SidebarLayout/SidebarLayout.js

@@ -0,0 +1,57 @@
+/*globals define, */
+define([
+    'layout/CHFLayout/CHFLayout/CHFLayout',
+    'text!./templates/SidebarLayout.html',
+    'css!./SidebarLayout.css'
+], function(
+    CHFLayout,
+    SidebarTemplate
+) {
+    'use strict';
+    
+    var SidebarLayout = function(params) {
+        params = params || {};
+        params.template = SidebarTemplate;
+        CHFLayout.call(this, params);
+    };
+
+    SidebarLayout.prototype = Object.create(CHFLayout.prototype);
+
+    SidebarLayout.prototype.getComponentId = function () {
+        return 'SidebarLayout';
+    };
+
+    /**
+     * Initialize the html page. This example is using the jQuery Layout plugin.
+     *
+     * @return {undefined}
+     */
+    SidebarLayout.prototype.init = function() {
+        CHFLayout.prototype.init.apply(this, arguments);
+        this._sidebarPanel = this._body.find('div.ui-layout-sidebar');
+        this._centerPanel = this._body.find('div.layout-center');
+    };
+
+    /**
+     * Add a panel to a given container. This is defined in the corresponding
+     * layout config JSON file.
+     *
+     * @param {Panel} panel
+     * @param {String} container
+     * @return {undefined}
+     */
+    SidebarLayout.prototype.addToContainer = function(panel, container) {
+        if (container === 'sidebar') {
+            this._sidebarPanel.append(panel.$pEl);
+        } else {
+            CHFLayout.prototype.addToContainer.apply(this, arguments);
+        }
+    };
+
+    SidebarLayout.prototype._onCenterResize = function() {
+        var width = this._centerPanel.width() - this._sidebarPanel.width();
+        this._canvas.setSize(width, this._centerPanel.height());
+    };
+
+    return SidebarLayout;
+});

src/layouts/SidebarLayout/templates/SidebarLayout.html

@@ -0,0 +1,7 @@
+<div class="ui-layout-center" style="position: relative;">
+    <div class="layout-center"></div>
+    <div class="float"></div>
+</div>
+<div class="ui-layout-sidebar"></div>
+<div class="ui-layout-north"></div>
+<div class="ui-layout-south"></div>

src/plugins/CheckLibraries/CheckLibraries.js

@@ -92,7 +92,7 @@ define([
 
                     this.logger.info(`${tuple[0]} version info:\n${projVersion} ` +
                         `(project)\n${latest} (latest)`);
-                    return latest !== projVersion;
+                    return projVersion < latest;
                 });
 
                 return Q.all(tuples.map(tuple => this.uploadSeed.apply(this, tuple)));

src/plugins/CreateExecution/CreateExecution.js

@@ -173,7 +173,10 @@ define([
             name,
             i = 2;
 
-        basename = basename.replace(/[^\da-zA-Z_]/g, '_');
+        basename = basename
+            .replace(/^\s*/, '')
+            .replace(/\s*$/, '')
+            .replace(/[^\da-zA-Z_]/g, '_');
         name = basename;
 
         // Get a unique name wrt the tags and the other executions

src/plugins/CreateTorchMeta/schemas/nn.json

@@ -65,7 +65,14 @@
       "affine"
     ],
     "setters": {},
-    "defaults": {},
+    "types": {
+      "eps": "number",
+      "momentum": "number"
+    },
+    "defaults": {
+      "momentum": 0.1,
+      "eps": 0.00001
+    },
     "type": "Misc"
   },
   {
@@ -82,6 +89,35 @@
     "defaults": {},
     "type": "Misc"
   },
+  {
+    "name": "Bottle",
+    "baseType": "Container",
+    "params": [
+      "module",
+      "nInputDim",
+      "nOutputDim"
+    ],
+    "setters": {},
+    "types": {
+      "nInputDim": "number",
+      "module": "nn.Module"
+    },
+    "defaults": {
+      "nInputDim": 2
+    },
+    "type": "Container"
+  },
+  {
+    "name": "CAdd",
+    "baseType": "Module",
+    "params": [
+      "params"
+    ],
+    "setters": {},
+    "types": {},
+    "defaults": {},
+    "type": "Misc"
+  },
   {
     "name": "CAddTable",
     "baseType": "Module",
@@ -102,6 +138,24 @@
     "defaults": {},
     "type": "Misc"
   },
+  {
+    "name": "CMaxTable",
+    "baseType": "Module",
+    "params": [],
+    "setters": {},
+    "types": {},
+    "defaults": {},
+    "type": "Misc"
+  },
+  {
+    "name": "CMinTable",
+    "baseType": "Module",
+    "params": [],
+    "setters": {},
+    "types": {},
+    "defaults": {},
+    "type": "Misc"
+  },
   {
     "name": "CMul",
     "baseType": "Module",
@@ -175,7 +229,7 @@
     "setters": {},
     "types": {},
     "defaults": {},
-    "type": "Containers"
+    "type": "Simple"
   },
   {
     "name": "ConcatTable",
@@ -184,7 +238,7 @@
     "setters": {},
     "types": {},
     "defaults": {},
-    "type": "Misc"
+    "type": "Container"
   },
   {
     "name": "Contiguous",
@@ -296,13 +350,16 @@
     "params": [
       "p",
       "v1",
-      "inplace"
+      "inplace",
+      "stochasticInference"
     ],
     "setters": {},
     "types": {
-      "p": "number"
+      "p": "number",
+      "stochasticInference": "boolean"
     },
     "defaults": {
+      "stochasticInference": false,
       "p": 0.5
     },
     "type": "Simple"
@@ -357,8 +414,11 @@
   {
     "name": "GradientReversal",
     "baseType": "Module",
-    "params": [],
+    "params": [
+      "lambda"
+    ],
     "setters": {},
+    "types": {},
     "defaults": {},
     "type": "Misc"
   },
@@ -382,7 +442,8 @@
     "baseType": "Module",
     "params": [
       "min_value",
-      "max_value"
+      "max_value",
+      "inplace"
     ],
     "setters": {},
     "types": {
@@ -508,9 +569,7 @@
   {
     "name": "Log",
     "baseType": "Module",
-    "params": [
-      "inputSize"
-    ],
+    "params": [],
     "setters": {},
     "types": {},
     "defaults": {},
@@ -865,7 +924,7 @@
     "setters": {},
     "types": {},
     "defaults": {},
-    "type": "Misc"
+    "type": "Container"
   },
   {
     "name": "ParallelCriterion",
@@ -885,7 +944,7 @@
     "setters": {},
     "types": {},
     "defaults": {},
-    "type": "Misc"
+    "type": "Container"
   },
   {
     "name": "PartialLinear",
@@ -900,6 +959,17 @@
     "defaults": {},
     "type": "Misc"
   },
+  {
+    "name": "PixelShuffle",
+    "baseType": "Module",
+    "params": [
+      "upscaleFactor"
+    ],
+    "setters": {},
+    "types": {},
+    "defaults": {},
+    "type": "Misc"
+  },
   {
     "name": "Power",
     "baseType": "Module",
@@ -939,6 +1009,17 @@
     "defaults": {},
     "type": "Transfer"
   },
+  {
+    "name": "ReLU6",
+    "baseType": "Module",
+    "params": [
+      "inplace"
+    ],
+    "setters": {},
+    "types": {},
+    "defaults": {},
+    "type": "Transfer"
+  },
   {
     "name": "Replicate",
     "baseType": "Module",
@@ -1156,6 +1237,18 @@
     "defaults": {},
     "type": "Convolution"
   },
+  {
+    "name": "SpatialClassNLLCriterion",
+    "baseType": "Criterion",
+    "params": [
+      "weights",
+      "sizeAverage"
+    ],
+    "setters": {},
+    "types": {},
+    "defaults": {},
+    "type": "Criterion"
+  },
   {
     "name": "SpatialContrastiveNormalization",
     "baseType": "Module",
@@ -1279,6 +1372,56 @@
     },
     "type": "Convolution"
   },
+  {
+    "name": "SpatialDilatedConvolution",
+    "baseType": "SpatialConvolution",
+    "params": [
+      "nInputPlane",
+      "nOutputPlane",
+      "kW",
+      "kH",
+      "dW",
+      "dH",
+      "padW",
+      "padH",
+      "dilationW",
+      "dilationH"
+    ],
+    "setters": {},
+    "types": {
+      "dilationW": "number",
+      "dilationH": "number"
+    },
+    "defaults": {
+      "dilationH": 1,
+      "dilationW": 1
+    },
+    "type": "Convolution"
+  },
+  {
+    "name": "SpatialDilatedMaxPooling",
+    "baseType": "SpatialMaxPooling",
+    "params": [
+      "kW",
+      "kH",
+      "dW",
+      "dH",
+      "padW",
+      "padH",
+      "dilationW",
+      "dilationH"
+    ],
+    "setters": {},
+    "types": {
+      "dilationW": "number",
+      "dilationH": "number"
+    },
+    "defaults": {
+      "dilationH": 1,
+      "dilationW": 1
+    },
+    "type": "Misc"
+  },
   {
     "name": "SpatialDivisiveNormalization",
     "baseType": "Module",
@@ -1301,13 +1444,16 @@
     "name": "SpatialDropout",
     "baseType": "Module",
     "params": [
-      "p"
+      "p",
+      "stochasticInference"
     ],
     "setters": {},
     "types": {
-      "p": "number"
+      "p": "number",
+      "stochasticInference": "boolean"
     },
     "defaults": {
+      "stochasticInference": false,
       "p": 0.5
     },
     "type": "Convolution"
@@ -1387,6 +1533,14 @@
     "defaults": {},
     "type": "Convolution"
   },
+  {
+    "name": "SpatialLogSoftMax",
+    "baseType": "Module",
+    "params": [],
+    "setters": {},
+    "defaults": {},
+    "type": "Misc"
+  },
   {
     "name": "SpatialMaxPooling",
     "baseType": "Module",
@@ -1497,6 +1651,17 @@
     },
     "type": "Convolution"
   },
+  {
+    "name": "SpatialUpSamplingBilinear",
+    "baseType": "Module",
+    "params": [
+      "params"
+    ],
+    "setters": {},
+    "types": {},
+    "defaults": {},
+    "type": "Misc"
+  },
   {
     "name": "SpatialUpSamplingNearest",
     "baseType": "Module",
@@ -1627,6 +1792,22 @@
     "defaults": {},
     "type": "Convolution"
   },
+  {
+    "name": "TemporalDynamicKMaxPooling",
+    "baseType": "Module",
+    "params": [
+      "minK",
+      "factor"
+    ],
+    "setters": {},
+    "types": {
+      "factor": "number"
+    },
+    "defaults": {
+      "factor": 0
+    },
+    "type": "Misc"
+  },
   {
     "name": "TemporalMaxPooling",
     "baseType": "Module",
@@ -1764,16 +1945,81 @@
     "type": "Convolution"
   },
   {
-    "name": "VolumetricDropout",
-    "baseType": "Module",
+    "name": "VolumetricDilatedConvolution",
+    "baseType": "VolumetricConvolution",
     "params": [
-      "p"
+      "nInputPlane",
+      "nOutputPlane",
+      "kT",
+      "kW",
+      "kH",
+      "dT",
+      "dW",
+      "dH",
+      "padT",
+      "padW",
+      "padH",
+      "dilationT",
+      "dilationW",
+      "dilationH"
     ],
     "setters": {},
     "types": {
-      "p": "number"
+      "dilationT": "number",
+      "dilationW": "number",
+      "dilationH": "number"
     },
     "defaults": {
+      "dilationH": 1,
+      "dilationW": 1,
+      "dilationT": 1
+    },
+    "type": "Misc"
+  },
+  {
+    "name": "VolumetricDilatedMaxPooling",
+    "baseType": "VolumetricMaxPooling",
+    "params": [
+      "kT",
+      "kW",
+      "kH",
+      "dT",
+      "dW",
+      "dH",
+      "padT",
+      "padW",
+      "padH",
+      "dilationT",
+      "dilationW",
+      "dilationH"
+    ],
+    "setters": {},
+    "types": {
+      "dilationT": "number",
+      "dilationW": "number",
+      "dilationH": "number"
+    },
+    "defaults": {
+      "dilationH": 1,
+      "dilationW": 1,
+      "dilationT": 1
+    },
+    "type": "Misc"
+  },
+  {
+    "name": "VolumetricDropout",
+    "baseType": "Module",
+    "params": [
+      "p",
+      "stochasticInference"
+    ],
+    "setters": {},
+    "types": {
+      "p": "number",
+      "stochasticInference": "boolean"
+    },
+    "defaults": {
+      "stochasticInference": false,
       "p": 0.5
     },
     "type": "Convolution"
@@ -1864,6 +2110,22 @@
     "defaults": {},
     "type": "Convolution"
   },
+  {
+    "name": "VolumetricReplicationPadding",
+    "baseType": "Module",
+    "params": [
+      "pleft",
+      "pright",
+      "ptop",
+      "pbottom",
+      "pfront",
+      "pback"
+    ],
+    "setters": {},
+    "types": {},
+    "defaults": {},
+    "type": "Misc"
+  },
   {
     "name": "WeightedEuclidean",
     "baseType": "Module",
@@ -1887,4 +2149,4 @@
     "defaults": {},
     "type": "Criterion"
   }
-]
+]

src/plugins/ExecuteJob/ExecuteJob.Metadata.js

@@ -0,0 +1,146 @@
+/*globals define*/
+define([
+    'deepforge/Constants'
+], function(
+    CONSTANTS
+) {
+
+    var ExecuteJob = function() {
+    };
+
+    ExecuteJob.prototype[CONSTANTS.GRAPH_CREATE] = function (job, id) {
+        var graph,
+            name = Array.prototype.slice.call(arguments, 2).join(' '),
+            jobId = this.core.getPath(job);
+
+        id = jobId + '/' + id;
+        this.logger.info(`Creating graph ${id} named ${name}`);
+
+        // Check if the graph already exists
+        graph = this._getExistingMetadata(jobId, 'Graph', name);
+        if (!graph) {
+            graph = this.createNode('Graph', job);
+
+            if (name) {
+                this.setAttribute(graph, 'name', name);
+            }
+            this.createIdToMetadataId[graph] = id;
+        }
+
+        this._metadata[id] = graph;
+    };
+
+    ExecuteJob.prototype[CONSTANTS.GRAPH_LABEL_AXIS.X] = function (job, id) {
+        var name = Array.prototype.slice.call(arguments, 2).join(' '),
+            jobId = this.core.getPath(job),
+            graph;
+
+        id = jobId + '/' + id;
+        this.logger.info(`Labeling the x-axis of ${id}: ${name}`);
+
+        graph = this._metadata[id];
+        this.setAttribute(graph, 'xlabel', name);
+    };
+
+    ExecuteJob.prototype[CONSTANTS.GRAPH_LABEL_AXIS.Y] = function (job, id) {
+        var name = Array.prototype.slice.call(arguments, 2).join(' '),
+            jobId = this.core.getPath(job),
+            graph;
+
+        id = jobId + '/' + id;
+        this.logger.info(`Labeling the y-axis of ${id}: ${name}`);
+
+        graph = this._metadata[id];
+        this.setAttribute(graph, 'ylabel', name);
+    };
+
+    ExecuteJob.prototype[CONSTANTS.GRAPH_PLOT] = function (job, id, x, y) {
+        var jobId = this.core.getPath(job),
+            nonNum = /[^\d-\.]*/g,
+            line,
+            points;
+            
+
+        id = jobId + '/' + id;
+        this.logger.info(`Adding point ${x}, ${y} to ${id}`);
+        line = this._metadata[id];
+        if (!line) {
+            this.logger.warn(`Can't add point to non-existent line: ${id}`);
+            return;
+        }
+
+        // Clean the points by removing and special characters
+        x = x.replace(nonNum, '');
+        y = y.replace(nonNum, '');
+        points = this.getAttribute(line, 'points');
+        points += `${x},${y};`;
+        this.setAttribute(line, 'points', points);
+    };
+
+    ExecuteJob.prototype[CONSTANTS.GRAPH_CREATE_LINE] = function (job, graphId, id) {
+        var jobId = this.core.getPath(job),
+            graph = this._metadata[jobId + '/' + graphId],
+            name = Array.prototype.slice.call(arguments, 3).join(' '),
+            line;
+
+        // Create a 'line' node in the given Graph metadata node
+        name = name.replace(/\s+$/, '');
+        line = this.createNode('Line', graph);
+        this.setAttribute(line, 'name', name);
+        this._metadata[jobId + '/' + id] = line;
+        this.createIdToMetadataId[line] = jobId + '/' + id;
+    };
+
+    ExecuteJob.prototype[CONSTANTS.IMAGE.BASIC] =
+    ExecuteJob.prototype[CONSTANTS.IMAGE.UPDATE] =
+    ExecuteJob.prototype[CONSTANTS.IMAGE.CREATE] = function (job, hash, imgId) {
+        var name = Array.prototype.slice.call(arguments, 3).join(' '),
+            imageNode = this._getImageNode(job, imgId, name);
+
+        this.setAttribute(imageNode, 'data', hash);
+    };
+
+    ExecuteJob.prototype[CONSTANTS.IMAGE.NAME] = function (job, imgId) {
+        var name = Array.prototype.slice.call(arguments, 2).join(' '),
+            imageNode = this._getImageNode(job, imgId, name);
+
+        this.setAttribute(imageNode, 'name', name);
+    };
+
+    ExecuteJob.prototype._getImageNode = function (job, imgId, name) {
+        var jobId = this.core.getPath(job),
+            id = jobId + '/IMAGE/' + imgId,
+            imageNode = this._metadata[id];  // Look for the metadata imageNode
+
+        if (!imageNode) {
+
+            // Check if the imageNode already exists
+            imageNode = this._getExistingMetadata(jobId, 'Image', name);
+            if (!imageNode) {
+                this.logger.info(`Creating image ${id} named ${name}`);
+                imageNode = this.createNode('Image', job);
+                this.setAttribute(imageNode, 'name', name);
+                this.createIdToMetadataId[imageNode] = id;
+            }
+            this._metadata[id] = imageNode;
+        }
+        return imageNode;
+    };
+
+    ExecuteJob.prototype._getExistingMetadata = function (jobId, type, name) {
+        var oldMetadata = this._oldMetadataByName[jobId] && this._oldMetadataByName[jobId][type],
+            node,
+            id;
+
+        if (oldMetadata && oldMetadata[name]) {
+            id = oldMetadata[name];
+            node = this._markForDeletion[jobId][id];
+            delete this._markForDeletion[jobId][id];
+            this.createdMetadataIds[jobId].push(id);  // used for resuming jobs
+        }
+
+        return node || null;
+    };
+
+    return ExecuteJob;
+});

src/plugins/ExecuteJob/ExecuteJob.SafeSave.js

@@ -0,0 +1,377 @@
+/*globals define*/
+define([
+    'plugin/PluginBase',
+    'common/storage/constants',
+    'q',
+    'common/util/assert'
+], function(
+    PluginBase,
+    STORAGE_CONSTANTS,
+    Q,
+    assert
+) {
+
+    var CREATE_PREFIX = 'created_node_',
+        INDEX = 1;
+
+    var ExecuteJob = function() {
+        this.forkNameBase = null;
+        this.runningJobHashes = [];
+        this._currentSave = Q();
+    };
+
+    ExecuteJob.prototype.getCreateId = function () {
+        return CREATE_PREFIX + (++INDEX);
+    };
+
+    ExecuteJob.prototype.isCreateId = function (id) {
+        return (typeof id === 'string') && (id.indexOf(CREATE_PREFIX) === 0);
+    };
+
+    ExecuteJob.prototype.createNode = function (baseType, parent) {
+        var id = this.getCreateId(),
+            parentId = this.isCreateId(parent) ? parent : this.core.getPath(parent);
+
+        this.logger.info(`Creating ${id} of type ${baseType} in ${parentId}`);
+        assert(this.META[baseType], `Cannot create node w/ unrecognized type: ${baseType}`);
+        this.creations[id] = {
+            base: baseType,
+            parent: parentId
+        };
+        return id;
+    };
+
+    ExecuteJob.prototype.deleteNode = function (nodeId) {
+        this.deletions.push(nodeId);
+    };
+
+    ExecuteJob.prototype.delAttribute = function (node, attr) {
+        return this.setAttribute(node, attr, null);
+    };
+
+    ExecuteJob.prototype.setAttribute = function (node, attr, value) {
+        var nodeId;
+
+        if (this.isCreateId(node)) {
+            nodeId = node;
+        } else {
+            nodeId = this.core.getPath(node);
+            assert(typeof nodeId === 'string', `Cannot set attribute of ${nodeId}`);
+        }
+
+        if (value !== null) {
+            this.logger.info(`Setting ${attr} of ${nodeId} to ${value}`);
+        } else {
+            this.logger.info(`Deleting ${attr} of ${nodeId}`);
+        }
+
+        if (!this.changes[nodeId]) {
+            this.changes[nodeId] = {};
+        }
+        this.changes[nodeId][attr] = value;
+    };
+
+    ExecuteJob.prototype.getAttribute = function (node, attr) {
+        var nodeId;
+
+        assert(this.deletions.indexOf(nodeId) === -1,
+            `Cannot get ${attr} from deleted node ${nodeId}`);
+
+        // Check if it was newly created
+        if (this.isCreateId(node)) {
+            nodeId = node;
+            assert(this.creations[nodeId], `Creation node not updated: ${nodeId}`);
+            node = this.META[this.creations[nodeId].base];
+        } else {
+            nodeId = this.core.getPath(node);
+        }
+
+        // Check the most recent changes, then the currentChanges, then the model
+        var value = this._getValueFrom(nodeId, attr, node, this.changes) ||
+            this._getValueFrom(nodeId, attr, node, this.currentChanges);
+
+        if (value) {
+            return value;
+        }
+
+        return this.core.getAttribute(node, attr);
+    };
+
+    ExecuteJob.prototype._getValueFrom = function (nodeId, attr, node, changes) {
+        var base;
+        if (changes[nodeId] && changes[nodeId][attr] !== undefined) {
+            // If deleted the attribute, get the default (inherited) value
+            if (changes[nodeId][attr] === null) {
+                base = this.isCreateId(nodeId) ? node : this.core.getBase(node);
+                return this.getAttribute(base, attr);
+            }
+            return changes[nodeId][attr];
+        }
+    };
+
+    ExecuteJob.prototype._applyNodeChanges = function (node, changes) {
+        var attr,
+            value;
+
+        this.logger.info(`About to apply changes for ${this.core.getPath(node)}`);
+        for (var i = changes.length; i--;) {
+            attr = changes[i][0];
+            value = changes[i][1];
+            if (value !== null) {
+                this.logger.info(`Setting ${attr} to ${value} (${this.core.getPath(node)})`);
+                this.core.setAttribute(node, attr, value);
+            } else {
+                this.core.delAttribute(node, attr);
+            }
+        }
+        return node;
+    };
+
+    ExecuteJob.prototype.applyModelChanges = function () {
+        return this.applyCreations()
+            .then(() => this.applyChanges())
+            .then(() => this.applyDeletions());
+    };
+
+    ExecuteJob.prototype.applyChanges = function () {
+        var nodeIds = Object.keys(this.changes),
+            attrs,
+            value,
+            changes,
+            promises = [],
+            changesFor = {},
+            id,
+            promise;
+
+        this.logger.info('Collecting changes to apply in commit');
+
+        for (var i = nodeIds.length; i--;) {
+            changes = [];
+            attrs = Object.keys(this.changes[nodeIds[i]]);
+            for (var a = attrs.length; a--;) {
+                value = this.changes[nodeIds[i]][attrs[a]];
+                changes.push([attrs[a], value]);
+            }
+            changesFor[nodeIds[i]] = changes;
+
+            assert(changes, `changes are invalid for ${nodeIds[i]}: ${changes}`);
+            assert(!this.isCreateId(nodeIds[i]),
+                `Creation id not resolved to actual id: ${nodeIds[i]}`);
+            promise = this.core.loadByPath(this.rootNode, nodeIds[i]);
+            promises.push(promise);
+        }
+
+        this.currentChanges = this.changes;
+        this.changes = {};
+        // Need to differentiate between read/write changes.
+        this.logger.info(`About to apply changes for ${promises.length} nodes`);
+        return Q.all(promises)
+            .then(nodes => {
+                for (var i = nodes.length; i--;) {
+                    id = this.core.getPath(nodes[i]);
+                    assert(nodes[i], `node is ${nodes[i]} (${nodeIds[i]})`);
+                    this._applyNodeChanges(nodes[i], changesFor[id]);
+                }
+
+                // Local model is now up-to-date. No longer need currentChanges
+                this.currentChanges = {};
+            });
+    };
+
+    ExecuteJob.prototype.applyCreations = function () {
+        var nodeIds = Object.keys(this.creations),
+            tiers = this.createCreationTiers(nodeIds),
+            creations = this.creations,
+            newIds = {},
+            promise = Q(),
+            tier;
+
+        this.logger.info('Applying node creations');
+        for (var i = 0; i < tiers.length; i++) {
+            tier = tiers[i];
+            // Chain the promises, loading each tier sequentially
+            promise = promise.then(this.applyCreationTier.bind(this, creations, newIds, tier));
+        }
+
+        this.creations = {};
+        return promise;
+    };
+
+    ExecuteJob.prototype.applyCreationTier = function (creations, newIds, tier) {
+        var promises = [],
+            parentId,
+            node;
+
+        for (var j = tier.length; j--;) {
+            node = creations[tier[j]];
+            assert(node, `Could not find create info for ${tier[j]}`);
+            parentId = newIds[node.parent] || node.parent;
+            promises.push(this.applyCreation(tier[j], node.base, parentId));
+        }
+        return Q.all(promises).then(nodes => {
+            // Record the newIds so they can be used to resolve creation ids
+            // in subsequent tiers
+            for (var i = tier.length; i--;) {
+                newIds[tier[i]] = this.core.getPath(nodes[i]);
+            }
+        });
+    };
+
+    // Figure out the dependencies between nodes to create.
+    // eg, if newId1 is to be created in newId2, then newId2 will
+    // be in an earlier tier than newId1. Essentially a topo-sort
+    // on a tree structure
+    ExecuteJob.prototype.createCreationTiers = function (nodeIds) {
+        var tiers = [],
+            prevTier = {},
+            tier = {},
+            id,
+            prevLen,
+            i;
+
+        // Create first tier (created inside existing nodes)
+        for (i = nodeIds.length; i--;) {
+            id = nodeIds[i];
+            if (!this.isCreateId(this.creations[id].parent)) {
+                tier[id] = true;
+                nodeIds.splice(i, 1);
+            }
+        }
+        prevTier = tier;
+        tiers.push(Object.keys(tier));
+
+        // Now, each tier consists of the nodes to be created inside a
+        // node from the previous tier
+        while (nodeIds.length) {
+            prevLen = nodeIds.length;
+            tier = {};
+            for (i = nodeIds.length; i--;) {
+                id = nodeIds[i];
+                if (prevTier[this.creations[id].parent]) {
+                    tier[id] = true;
+                    nodeIds.splice(i, 1);
+                }
+            }
+            prevTier = tier;
+            tiers.push(Object.keys(tier));
+            // Every iteration should find at least one node
+            assert(prevLen > nodeIds.length,
+                `Created empty create tier! Remaining: ${nodeIds.join(', ')}`);
+        }
+
+        return tiers;
+    };
+
+    ExecuteJob.prototype.applyCreation = function (tmpId, baseType, parentId) {
+        var base = this.META[baseType],
+            nodeId,
+            id;
+
+        this.logger.info(`Applying creation of ${tmpId} (${baseType}) in ${parentId}`);
+
+        assert(!this.isCreateId(parentId),
+            `Did not resolve parent id: ${parentId} for ${tmpId}`);
+        assert(base, `Invalid base type: ${baseType}`);
+        return this.core.loadByPath(this.rootNode, parentId)
+            .then(parent => this.core.createNode({base, parent}))
+            .then(node => {  // Update the _metadata records
+                id = this.createIdToMetadataId[tmpId];
+                delete this.createIdToMetadataId[tmpId];
+                this._metadata[id] = node;
+
+                // Update creations
+                nodeId = this.core.getPath(node);
+                if (this.changes[tmpId]) {
+                    assert(!this.changes[nodeId],
+                        `Newly created node cannot already have changes! (${nodeId})`);
+                    this.changes[nodeId] = this.changes[tmpId];
+                    delete this.changes[tmpId];
+                }
+                return node;
+            });
+    };
+
+    ExecuteJob.prototype.applyDeletions = function () {
+        var deletions = this.deletions;
+
+        this.deletions = [];
+        return Q.all(deletions.map(id => this.core.loadByPath(this.rootNode, id)))
+            .then(nodes => {
+                for (var i = nodes.length; i--;) {
+                    this.core.deleteNode(nodes[i]);
+                }
+            });
+    };
+
+    // Override 'save' to notify the user on fork
+    ExecuteJob.prototype.save = function (msg) {
+        this._currentSave = this._currentSave
+            .then(() => this.updateForkName(this.forkNameBase))
+            .then(() => this.applyModelChanges())
+            .then(() => PluginBase.prototype.save.call(this, msg))
+            .then(result => {
+                this.logger.info(`Save finished w/ status: ${result.status}`);
+                if (result.status === STORAGE_CONSTANTS.FORKED) {
+                    return this.onSaveForked(result.forkName);
+                } else if (result.status === STORAGE_CONSTANTS.MERGED) {
+                    this.logger.debug('Merged changes. About to update plugin nodes');
+                    return this.updateNodes();
+                }
+            });
+
+        return this._currentSave;
+    };
+
+    ExecuteJob.prototype.onSaveForked = function (forkName) {
+        var name = this.getAttribute(this.activeNode, 'name'),
+            msg = `"${name}" execution has forked to "${forkName}"`;
+        this.currentForkName = forkName;
+
+        this.logManager.fork(forkName);
+        this.runningJobHashes.forEach(jobId => this.originManager.fork(jobId, forkName));
+        this.sendNotification(msg);
+    };
+
+    ExecuteJob.prototype.updateNodes = function (hash) {
+        var activeId = this.core.getPath(this.activeNode);
+
+        hash = hash || this.currentHash;
+        return Q.ninvoke(this.project, 'loadObject', hash)
+            .then(commitObject => {
+                return this.core.loadRoot(commitObject.root);
+            })
+            .then(rootObject => {
+                this.rootNode = rootObject;
+                return this.core.loadByPath(rootObject,activeId);
+            })
+            .then(activeObject => this.activeNode = activeObject)
+            .then(() => {
+                var metaNames = Object.keys(this.META);
+
+                return Q.all(metaNames.map(name => this.updateMetaNode(name)));
+            })
+            .then(() => {
+                var mdNodes,
+                    mdIds;
+
+                mdIds = Object.keys(this._metadata)
+                    .filter(id => !this.isCreateId(this._metadata[id]));
+
+                mdNodes = mdIds.map(id => this.core.getPath(this._metadata[id]))
+                    .map(nodeId => this.core.loadByPath(this.rootNode, nodeId));
+
+                return Q.all(mdNodes).then(nodes => {
+                    for (var i = nodes.length; i--;) {
+                        this._metadata[mdIds[i]] = nodes[i];
+                    }
+                });
+            });
+    };
+
+    ExecuteJob.prototype.updateMetaNode = function (name) {
+        var id = this.core.getPath(this.META[name]);
+        return this.core.loadByPath(this.rootNode, id).then(node => this.META[name] = node);
+    };
+
+    return ExecuteJob;
+});

src/plugins/ExecutePipeline/ExecutePipeline.js

@@ -4,17 +4,17 @@
 define([
     'plugin/CreateExecution/CreateExecution/CreateExecution',
     'plugin/ExecuteJob/ExecuteJob/ExecuteJob',
-    'deepforge/JobLogsClient',
     'common/storage/constants',
     'common/core/constants',
+    'deepforge/Constants',
     'q',
     'text!./metadata.json',
     'underscore'
 ], function (
     CreateExecution,
     ExecuteJob,
-    JobLogsClient,
     STORAGE_CONSTANTS,
+    GME_CONSTANTS,
     CONSTANTS,
     Q,
     pluginMetadata,
@@ -33,10 +33,11 @@ define([
     var ExecutePipeline = function () {
         // Call base class' constructor.
         CreateExecution.call(this);
+        ExecuteJob.call(this);
         this.pluginMetadata = pluginMetadata;
 
-        this._currentSave = Q();
         this.changes = {};
+        this.currentChanges = {};  // read-only changes being applied
         this.creations = {};
         this.deletions = [];
         this.createIdToMetadataId = {};
@@ -100,7 +101,8 @@ define([
      * @param {function(string, plugin.PluginResult)} callback - the result callback
      */
     ExecutePipeline.prototype.main = function (callback) {
-        var startPromise;
+        var startPromise,
+            runId;
 
         this.initRun();
         if (this.core.isTypeOf(this.activeNode, this.META.Pipeline)) {
@@ -117,58 +119,135 @@ define([
             return callback('Current node is not a Pipeline or Execution!', this.result);
         }
 
-        // Get the gmeConfig...
-        this.logManager = new JobLogsClient({
-            logger: this.logger,
-            port: this.gmeConfig.server.port,
-            branchName: this.branchName,
-            projectId: this.projectId
-        });
         this._callback = callback;
         this.currentForkName = null;
 
         startPromise
-        .then(() => this.core.loadSubTree(this.activeNode))
-        .then(subtree => {
-            var children = subtree
-                .filter(n => this.core.getParent(n) === this.activeNode);
+            .then(() => this.core.loadSubTree(this.activeNode))
+            .then(subtree => {
+                var children;
 
-            this.pipelineName = this.getAttribute(this.activeNode, 'name');
-            this.logger.debug(`Loaded subtree of ${this.pipelineName}. About to build cache`);
-            this.buildCache(subtree);
-            this.logger.debug('Parsing execution for job inter-dependencies');
-            this.parsePipeline(children);  // record deps, etc
+                children = subtree
+                    .filter(n => this.core.getParent(n) === this.activeNode);
 
-            this.logger.debug('Clearing old results');
-            return this.clearResults();
-        })
-        .then(() => this.executePipeline())
-        .fail(e => this.logger.error(e));
+                this.pipelineName = this.getAttribute(this.activeNode, 'name');
+                this.forkNameBase = this.pipelineName;
+                this.logger.debug(`Loaded subtree of ${this.pipelineName}. About to build cache`);
+                this.buildCache(subtree);
+                this.logger.debug('Parsing execution for job inter-dependencies');
+                this.parsePipeline(children);  // record deps, etc
+
+                // Detect if resuming execution
+                runId = this.getAttribute(this.activeNode, 'runId');
+                return this.isResuming().then(resuming => {
+                    if (resuming) {
+                        this.currentRunId = runId;
+                        this.startExecHeartBeat();
+                        return this.resumePipeline();
+                    }
+                    return this.startPipeline();
+                });
+
+            })
+            .fail(e => this.logger.error(e));
     };
 
-    // Override 'save' to prevent race conditions while saving
-    ExecutePipeline.prototype.save = function (msg) {
-        // When 'save'  is called, it should still finish any current save op
-        // before continuing
-        this._currentSave = this._currentSave
-            .then(() => this.updateForkName(this.pipelineName))
-            .then(() => this.applyModelChanges())
-            .then(() => CreateExecution.prototype.save.call(this, msg))
-            .then(result => {
-                var msg;
-                if (result.status === STORAGE_CONSTANTS.FORKED) {
-                    this.currentForkName = result.forkName;
-                    this.logManager.fork(result.forkName);
-                    msg = `"${this.pipelineName}" execution has forked to "${result.forkName}"`;
-                    this.sendNotification(msg);
-                } else if (result.status === STORAGE_CONSTANTS.MERGED) {
-                    this.logger.debug('Merged changes. About to update plugin nodes');
-                    return this.updateNodes();
+    ExecutePipeline.prototype.isResuming = function () {
+        var currentlyRunning = this.getAttribute(this.activeNode, 'status') === 'running',
+            runId = this.getAttribute(this.activeNode, 'runId');
+
+        if (runId && currentlyRunning) {
+            // Verify that it is on the correct branch
+            return this.originManager.getOrigin(runId)
+                .then(origin => {
+                    if (origin && origin.branch === this.branchName) {
+                        return this.pulseClient.check(runId)
+                            // If it is dead (not unknown!), then resume
+                            .then(status => status === CONSTANTS.PULSE.DEAD);
+                    } else {
+                        return false;
+                    }
+                });
+        }
+        return Q().then(() => false);
+    };
+
+    ExecutePipeline.prototype.resumePipeline = function () {
+        var nodes = Object.keys(this.nodes).map(id => this.nodes[id]),
+            allJobs = nodes.filter(node => this.core.isTypeOf(node, this.META.Job)),
+            name = this.getAttribute(this.activeNode, 'name'),
+            status,
+            jobs = {
+                success: [],
+                failed: [],
+                running: [],
+                pending: []
+            };
+
+        this.logger.info(`Resuming pipeline execution: ${this.currentRunId}`);
+
+        // Get all completed jobs' operations and update records for these
+        for (var i = allJobs.length; i--;) {
+            status = this.getAttribute(allJobs[i], 'status');
+            if (!jobs[status]) {
+                jobs[status] = [];
+            }
+
+            // If any running jobs are missing jobIds, set them to pending
+            if (status === 'running' && !this.canResumeJob(allJobs[i])) {
+                jobs.pending.push(allJobs[i]);
+            } else {
+                jobs[status].push(allJobs[i]);
+            }
+        }
+
+        // Remove finished jobs from incomingCounts
+        jobs.success.concat(jobs.failed, jobs.running)
+            .map(job => this.core.getPath(job))
+            .forEach(id => delete this.incomingCounts[id]);
+
+        return Q.all(allJobs.map(job => this.recordOldMetadata(job, true)))
+            .then(() => Q.all(jobs.success.map(job => this.getOperation(job))))
+            .then(ops => ops.forEach(op => this.updateJobCompletionRecords(op)))
+            .then(() => this.save(`Resuming pipeline execution: ${name}`))
+            .then(() => {
+                
+                if (jobs.running.length) {  // Resume all running jobs
+                    return Q.all(jobs.running.map(job => this.resumeJob(job)));
+                } else if (this.completedCount === this.totalCount) {
+                    return this.onPipelineComplete();
+                } else {
+                    // If none are running, try to start the next ones
+                    return this.executeReadyOperations();
                 }
+            })
+            .fail(err => this._callback(err));
+    };
 
-            });
+    ExecutePipeline.prototype.startPipeline = function () {
+        var rand = Math.floor(Math.random()*10000),
+            commit = this.commitHash.replace('#', '');
 
-        return this._currentSave;
+        this.logger.debug('Clearing old results');
+        this.currentRunId = `Pipeline_${commit}_${Date.now()}_${rand}`;
+
+        // Record the execution origin
+        this.originManager.record(this.currentRunId, {
+            nodeId: this.core.getPath(this.activeNode),
+            job: 'N/A',
+            execution: this.getAttribute(this.activeNode, 'name')
+        });
+
+        this.startExecHeartBeat();
+        return this.clearResults()
+            .then(() => this.executePipeline())
+            .fail(e => this.logger.error(e));
+    };
+
+    ExecutePipeline.prototype.onSaveForked = function (forkName) {
+        // Update the origin on fork
+        this.originManager.fork(this.currentRunId, forkName);
+        return ExecuteJob.prototype.onSaveForked.call(this, forkName);
     };
 
     ExecutePipeline.prototype.updateNodes = function (hash) {
@@ -188,6 +267,10 @@ define([
         });
     };
 
+    ExecutePipeline.prototype.isExecutionCanceled = function () {
+        return this.getAttribute(this.activeNode, 'status') === 'canceled';
+    };
+
     ExecutePipeline.prototype.isInputData = function (node) {
         var prnt = this.core.getParent(node);
         return this.core.isTypeOf(prnt, this.META.Inputs);
@@ -215,6 +298,7 @@ define([
         this.logger.info('Setting all jobs status to "pending"');
         this.logger.debug(`Making a commit from ${this.currentHash}`);
         this.setAttribute(this.activeNode, 'startTime', Date.now());
+        this.setAttribute(this.activeNode, 'runId', this.currentRunId);
         this.core.delAttribute(this.activeNode, 'endTime');
         return this.save(`Initializing ${this.pipelineName} for execution`);
     };
@@ -292,10 +376,10 @@ define([
     };
 
     ExecutePipeline.prototype.getSiblingIdContaining = function (nodeId) {
-        var parentId = this.core.getPath(this.activeNode) + CONSTANTS.PATH_SEP,
+        var parentId = this.core.getPath(this.activeNode) + GME_CONSTANTS.PATH_SEP,
             relid = nodeId.replace(parentId, '');
 
-        return parentId + relid.split(CONSTANTS.PATH_SEP).shift();
+        return parentId + relid.split(GME_CONSTANTS.PATH_SEP).shift();
     };
 
     ExecutePipeline.prototype.executePipeline = function() {
@@ -353,7 +437,8 @@ define([
             msg += 'finished!';
         }
 
-        this.isDeleted().then(isDeleted => {
+        return this.isDeleted().then(isDeleted => {
+            this.stopExecHeartBeat();
             if (!isDeleted) {
 
                 this.logger.debug(`Pipeline "${name}" complete!`);
@@ -436,10 +521,9 @@ define([
 
     ExecutePipeline.prototype.onOperationComplete = function (opNode) {
         var name = this.getAttribute(opNode, 'name'),
-            nextPortIds = this.getOperationOutputIds(opNode),
             jNode = this.core.getParent(opNode),
-            resultPorts,
             jobId = this.core.getPath(jNode),
+            counts,
             hasReadyOps;
 
         // Set the operation to 'success'!
@@ -449,38 +533,14 @@ define([
         this.logger.info(`Setting ${jobId} status to "success"`);
         this.logger.info(`There are now ${this.runningJobs} running jobs`);
         this.logger.debug(`Making a commit from ${this.currentHash}`);
+
+        counts = this.updateJobCompletionRecords(opNode);
+
         this.save(`Operation "${name}" in ${this.pipelineName} completed successfully`)
             .then(() => {
 
-                // Transport the data from the outputs to any connected inputs
-                //   - Get all the connections from each outputId
-                //   - Get the corresponding dst outputs
-                //   - Use these new ids for checking 'hasReadyOps'
-                resultPorts = nextPortIds.map(id => this.inputPortsFor[id])
-                    .reduce((l1, l2) => l1.concat(l2), []);
+                hasReadyOps = counts.indexOf(0) > -1;
 
-                resultPorts
-                    .map((id, i) => [this.nodes[id], this.nodes[nextPortIds[i]]])
-                    .forEach(pair => {  // [ resultPort, nextPort ]
-                        var result = pair[0],
-                            next = pair[1],
-                            hash = this.getAttribute(result, 'data');
-                        
-                        this.logger.info(`forwarding data (${hash}) from ${this.core.getPath(result)} ` +
-                            `to ${this.core.getPath(next)}`);
-                        this.setAttribute(next, 'data', hash);
-                        this.logger.info(`Setting ${jobId} data to ${hash}`);
-                    });
-
-                // For all the nextPortIds, decrement the corresponding operation's incoming counts
-                hasReadyOps = nextPortIds.map(id => this.getSiblingIdContaining(id))
-                    .reduce((l1, l2) => l1.concat(l2), [])
-
-                    // decrement the incoming counts for each operation id
-                    .map(opId => --this.incomingCounts[opId])
-                    .indexOf(0) > -1;
-
-                this.completedCount++;
                 this.logger.debug(`Operation "${name}" completed. ` + 
                     `${this.totalCount - this.completedCount} remaining.`);
                 if (hasReadyOps) {
@@ -491,9 +551,47 @@ define([
             });
     };
 
+    ExecutePipeline.prototype.updateJobCompletionRecords = function (opNode) {
+        var nextPortIds = this.getOperationOutputIds(opNode),
+            resultPorts,
+            counts;
+
+        // Transport the data from the outputs to any connected inputs
+        //   - Get all the connections from each outputId
+        //   - Get the corresponding dst outputs
+        //   - Use these new ids for checking 'hasReadyOps'
+
+        resultPorts = nextPortIds.map(id => this.inputPortsFor[id])  // dst -> src port
+            .reduce((l1, l2) => l1.concat(l2), []);
+
+        resultPorts
+            .map((id, i) => [this.nodes[id], this.nodes[nextPortIds[i]]])
+            .forEach(pair => {  // [ resultPort, nextPort ]
+                var result = pair[0],
+                    next = pair[1],
+                    hash = this.getAttribute(result, 'data');
+                
+                this.logger.info(`forwarding data (${hash}) from ${this.core.getPath(result)} ` +
+                    `to ${this.core.getPath(next)}`);
+                this.setAttribute(next, 'data', hash);
+                //this.logger.info(`Setting ${jobId} data to ${hash}`);
+            });
+
+        // For all the nextPortIds, decrement the corresponding operation's incoming counts
+        counts = nextPortIds.map(id => this.getSiblingIdContaining(id))
+            .reduce((l1, l2) => l1.concat(l2), [])
+
+            // decrement the incoming counts for each operation id
+            .map(opId => --this.incomingCounts[opId]);
+
+        this.completedCount++;
+        return counts;
+    };
+
     ExecutePipeline.prototype.getOperationOutputIds = function(node) {
         var jobId = this.getSiblingIdContaining(this.core.getPath(node));
 
+        // Map the job to it's output ports
         return this.outputsOf[jobId] || [];
     };
 

src/plugins/Export/Export.js

@@ -0,0 +1,925 @@
+/*globals define */
+/*jshint node:true, browser:true*/
+
+define([
+    'text!./metadata.json',
+    'text!./deepforge.ejs',
+    './format',
+    'plugin/PluginBase',
+    'deepforge/plugin/PtrCodeGen',
+    'deepforge/Constants',
+    'blob/BlobConfig',
+    'underscore',
+    'q'
+], function (
+    pluginMetadata,
+    DeepForgeBaseCode,
+    FORMATS,
+    PluginBase,
+    PtrCodeGen,
+    CONSTANTS,
+    BlobConfig,
+    _,
+    Q
+) {
+    'use strict';
+
+    pluginMetadata = JSON.parse(pluginMetadata);
+    var HEADER_LENGTH = 60,
+        SKIP_ATTRS = {
+            lineOffset: true,
+            code: true
+        },
+        RESERVED = /^(and|break|do|else|elseifend|false|for|function|if|in|local|nil|not|orrepeat|return|then|true|until|while|print)$/,
+        DeepForgeTpl = _.template(DeepForgeBaseCode);
+
+    /**
+     * Initializes a new instance of Export.
+     * @class
+     * @augments {PluginBase}
+     * @classdesc This class represents the plugin Export.
+     * @constructor
+     */
+    var Export = function () {
+        // Call base class' constructor.
+        PluginBase.call(this);
+        this.initRecords();
+    };
+
+    /**
+     * Metadata associated with the plugin. Contains id, name, version, description, icon, configStructue etc.
+     * This is also available at the instance at this.pluginMetadata.
+     * @type {object}
+     */
+    Export.metadata = pluginMetadata;
+
+    // Prototypical inheritance from PluginBase.
+    Export.prototype = Object.create(PluginBase.prototype);
+    Export.prototype.constructor = Export;
+
+    Export.prototype.initRecords = function() {
+        this.pluginMetadata = pluginMetadata;
+
+        this._srcIdFor = {};  // input path -> output data node path
+
+        this._nameFor = {};  // input path -> opname
+        this._outputNames = {};
+        this._baseNameFor = {};
+        this._dataNameFor = {};  
+        this._instanceNames = {};
+        this._opBaseNames = {};
+        this._fnNameFor = {};
+        this._functions = {};  // function definitions for the operations
+
+        // topo sort stuff
+        this._nextOps = {};
+        this._incomingCnts = {};
+
+        this._operations = {};
+        this.activeNodeId = null;
+        this.activeNodeDepth = null;
+
+        this.isInputOp = {};
+        this._portCache = {};
+        this.inputNode = {};
+        this.outputDataToOpId = {};
+        this.isOutputOp = {};
+    };
+
+    /**
+     * Main function for the plugin to execute. This will perform the execution.
+     * Notes:
+     * - Always log with the provided logger.[error,warning,info,debug].
+     * - Do NOT put any user interaction logic UI, etc. inside this method.
+     * - callback always has to be called even if error happened.
+     *
+     * @param {function(string, plugin.PluginResult)} callback - the result callback
+     */
+    Export.prototype.main = function (callback) {
+        this.initRecords();
+
+        // Get all the children and call generate exec file
+        this.activeNodeId = this.core.getPath(this.activeNode);
+        this.activeNodeDepth = this.activeNodeId.split('/').length + 1;
+
+        if (this.isMetaTypeOf(this.activeNode, this.META.Execution)) {
+            this.activeNodeDepth++;
+        }
+
+        return this.core.loadChildren(this.activeNode)
+            .then(nodes => this.generateOutputFiles(nodes))
+            .catch(err => callback(err))
+            .then(hash => {
+                this.result.addArtifact(hash);
+                this.result.setSuccess(true);
+                callback(null, this.result);
+            })
+            .fail(err => callback(err));
+    };
+
+    Export.prototype.getCurrentConfig = function () {
+        var config = PluginBase.prototype.getCurrentConfig.call(this);
+        config.staticInputs = config.staticInputs || [];
+        return config;
+    };
+
+    Export.prototype.getExporterFor = function (name) {
+        var Exporter = function() {},
+            format = FORMATS[name],
+            exporter;
+
+        Exporter.prototype = this;
+        exporter = new Exporter();
+
+        if (typeof format === 'function') {
+            exporter.main = format;
+        } else {
+            _.extend(exporter, format);
+        }
+        return exporter;
+    };
+
+    Export.prototype.generateOutputFiles = function (children) {
+        var name = this.core.getAttribute(this.activeNode, 'name');
+
+        return this.createCodeSections(children)
+            .then(sections => {
+                // Get the selected format
+                var config = this.getCurrentConfig(),
+                    format = config.format || 'Basic CLI',
+                    exporter,
+                    staticInputs,
+                    files;
+
+                this.logger.info(`About to retrieve ${config.format} exporter`);
+                exporter = this.getExporterFor(format);
+
+                staticInputs = config.staticInputs.map(id => {
+                    var opId = id.split('/').splice(0, this.activeNodeDepth).join('/'),
+                        port = this._portCache[id];
+
+                    return {
+                        portId: id,
+                        id: opId,
+                        hash: this.core.getAttribute(port, 'data'),
+                        name: this._nameFor[opId]
+                    };
+                });
+
+                this.logger.info('Invoking exporter "main" function...');
+                try {
+                    files = exporter.main(sections, staticInputs, config.extensionConfig);
+                } catch (e) {
+                    this.logger.error(`Exporter failed: ${e.toString()}`);
+                    throw e;
+                }
+                // If it returns a string, just put a single file
+                if (typeof files === 'string') {
+                    return this.blobClient.putFile(`${name}.lua`, files);
+                } else {  // filename -> content
+                    var artifact = this.blobClient.createArtifact(name),
+                        objects = {};
+
+                    Object.keys(files).forEach(key => {
+                        if (BlobConfig.hashRegex.test(files[key])) {
+                            objects[key] = files[key];
+                            delete files[key];
+                        }
+                    });
+
+                    return artifact.addFiles(files)
+                        .then(() => artifact.addObjectHashes(objects))
+                        .then(() => artifact.save());
+                }
+            });
+    };
+
+    Export.prototype.createCodeSections = function (children) {
+        // Convert opNodes' jobs to the nested operations
+        var opNodes,
+            nodes;
+
+        return this.unpackJobs(children)
+            .then(_nodes => {
+                nodes = _nodes;
+                opNodes = nodes
+                    .filter(node => this.isMetaTypeOf(node, this.META.Operation));
+
+                // Sort the connections to come first
+                nodes
+                    .map(node => [
+                        node,
+                        this.isMetaTypeOf(node, this.META.Transporter) ? -1 : 1
+                    ])
+                    .sort((a, b) => a[1] < b[1] ? -1 : 1);
+
+                return Q.all(nodes.map(node => this.registerNode(node)));
+            })
+            .then(() => Q.all(opNodes
+                .filter(n => {
+                    var id = this.core.getPath(n);
+                    return !this.isInputOp[id];
+                })
+                .map(node => this.createOperation(node)))
+            )
+            .then(operations => {
+                var opDict = {},
+                    firstOpIds;
+
+                firstOpIds = opNodes.map(n => this.core.getPath(n))
+                    .filter(id => !this._incomingCnts[id]);
+
+                operations.forEach(op => opDict[op.id] = op);
+
+                // Toposort!
+                return this.sortOperations(opDict, firstOpIds);
+            })
+            .then(operations => this.generateCodeSections(operations))
+            .fail(err => this.logger.error(err));
+    };
+
+    Export.prototype.unpackJobs = function (nodes) {
+        return Q.all(
+            nodes.map(node => {
+                if (!this.isMetaTypeOf(node, this.META.Job)) {
+                    return node;
+                }
+                return this.core.loadChildren(node)
+                    .then(children =>
+                        children.find(c => this.isMetaTypeOf(c, this.META.Operation))
+                    );
+            })
+        );
+    };
+
+    Export.prototype.sortOperations = function (operationDict, opIds) {
+        var nextIds = [],
+            sorted = opIds,
+            dstIds,
+            id;
+
+        if (!opIds.length) {
+            return [];
+        }
+
+        // Decrement all next ops
+        dstIds = opIds.map(id => this._nextOps[id])
+            .reduce((l1, l2) => l1.concat(l2), []);
+
+        for (var i = dstIds.length; i--;) {
+            id = dstIds[i];
+            if (--this._incomingCnts[id] === 0) {
+                nextIds.push(id);
+            }
+        }
+
+        // append
+        return sorted
+            .map(id => operationDict[id])
+            .filter(op => !!op)
+            .concat(this.sortOperations(operationDict, nextIds));
+    };
+
+    Export.prototype.generateCodeSections = function(sortedOps) {
+        // Create the code sections:
+        //  - operation definitions
+        //  - pipeline definition
+        //  - main
+        var code = {},
+            baseIds = [],
+            outputOps = [],
+            mainOps = [];
+
+        // Define the operation functions...
+        code.operations = {};
+        for (var i = 0; i < sortedOps.length; i++) {
+            if (this.isInputOp[sortedOps[i].id]) {
+                continue;
+            }
+            if (!this.isOutputOp[sortedOps[i].id]) {
+                if (!baseIds.includes(sortedOps[i].baseId)) {  // new definition
+                    code.operations[sortedOps[i].basename] = this.defineOperationFn(sortedOps[i]);
+                    baseIds.push(sortedOps[i].baseId);
+                }
+                mainOps.push(sortedOps[i]);
+            } else {
+                outputOps.push(sortedOps[i]);
+            }
+        }
+
+        // Define the pipeline function
+        code.pipelines = this.definePipelineFn(mainOps, outputOps);
+
+        // Define the serializers/deserializers
+        this.addCodeSerializers(code);
+
+        // Define the main input names
+        code.pipelineName = Object.keys(code.pipelines)[0];
+        code.pipelineInputNames = Object.keys(this.isInputOp).map(id => this._nameFor[id]);
+
+        // Add custom class definitions
+        this.addCustomClasses(code);
+
+        // Add custom layer definitions
+        this.addCustomLayers(code);
+
+        return code;
+    };
+
+    // expose this utility function to format extensions
+    var indent = Export.prototype.indent = function(text, spaces) {
+        spaces = spaces || 3;
+        return text.replace(/^/mg, new Array(spaces+1).join(' '));
+    };
+
+    Export.prototype.defineOperationFn = function(operation) {
+        var lines = [],
+            args = operation.inputNames || [];
+
+        // Create the function definition
+        args.unshift('attributes');
+        // Add the refs to the end
+        args = args.concat(operation.refNames);
+
+        args = args.join(', ');
+
+        lines.push(`local function ${operation.basename}(${args})`);
+        lines.push(indent(operation.code));
+        lines.push('end');
+
+        return lines.join('\n');
+    };
+
+    Export.prototype.definePipelineFn = function(sortedOps, outputOps) {
+        var inputArgs = Object.keys(this.isInputOp).map(id => this._nameFor[id]),
+            name = this.core.getAttribute(this.activeNode, 'name'),
+            safename = getUniqueName(name, this._opBaseNames),
+            results = [],
+            result = {},
+            returnStat,
+            fnbody;
+
+        // Call each function in order, with the respective attributes, etc
+        fnbody = sortedOps.map(op => this.getOpInvocation(op)).join('\n');
+
+        // Create the return statement
+        results.push('\n\nresults = {}');
+        outputOps.map(op => this.getOutputPair(op))
+            .forEach(pair => results.push(`results['${pair[0]}'] = ${pair[1]}`));
+        results.push('return results');
+        returnStat = results.join('\n');
+
+        // Merge the fnbody, return statement and the function def
+        result[safename] = `local function ${safename} (${inputArgs.join(', ')})\n` +
+            `${indent(fnbody + returnStat)}\nend`;
+
+        return result;
+    };
+
+    Export.prototype.getOutputPair = function(operation) {
+        var input = operation.inputValues[0].slice(),
+            value;
+
+        // Get the src operation name and data value name
+        input[0] += '_results';
+        value = input.join('.');
+        return [this._nameFor[operation.id], value];
+    };
+
+    Export.prototype.addCodeSerializers = function(sections) {
+        var loadNodes = {},
+            saveNodes = {};
+
+        // Add the serializer fn names for each input
+        sections.serializerFor = {};
+        sections.deserializerFor = {};
+
+        Object.keys(this.isOutputOp).map(id => {
+            var name = this._nameFor[id];
+            sections.serializerFor[name] = `__save['${name}']`;
+        });
+
+        // Add the serializer definitions
+        Object.keys(this.isInputOp).forEach(id => {
+            var node = this.inputNode[id],
+                name = this._nameFor[id];
+
+            loadNodes[id] = node;
+            sections.deserializerFor[name] = `__load['${this._nameFor[id]}']`;
+        });
+
+        sections.deserializers = this.createTorchFnDict(
+            '__load',
+            loadNodes,
+            'deserialize',
+            'path'
+        );
+
+        // Add the deserializer definitions
+        Object.keys(this.outputDataToOpId).forEach(dataId => {
+            var opId = this.outputDataToOpId[dataId];
+            // The key is used for the output name resolution. The
+            // value is used for the serialization fn look-up. So,
+            // the key is the output operation id and the value is
+            // the data port connected to the output operation
+            saveNodes[opId] = this._portCache[this._srcIdFor[dataId]];
+        });
+
+        sections.serializers = this.createTorchFnDict(
+            '__save',
+            saveNodes,
+            'serialize',
+            'path, data'
+        );
+
+        // Add a saveOutputs method for convenience
+        sections.serializeOutputsDef = [
+            'local function __saveOutputs(data)',
+            indent(Object.keys(this.isOutputOp).map(id => {
+                var name = this._nameFor[id];
+                return [
+                    `print('saving ${name}...')`,
+                    `${sections.serializerFor[name]}('${name}', data['${name}'])`
+                ].join('\n');
+
+            }).join('\n')),
+            'end'
+        ].join('\n');
+
+        sections.serializeOutputs = '__saveOutputs(outputs)';
+    };
+
+    Export.prototype.createTorchFnDict = function(name, nodeDict, attr, args) {
+        return [
+            `local ${name} = {}`,
+            Object.keys(nodeDict).map(id => {
+                var node = nodeDict[id];
+                return [
+                    `${name}['${this._nameFor[id]}'] = function(${args})`,
+                    indent(this.core.getAttribute(node, attr)),
+                    'end'
+                ].join('\n');
+            }).join('\n')
+        ].join('\n');
+    };
+
+    Export.prototype.addCustomClasses = function(sections) {
+        var metaDict = this.core.getAllMetaNodes(this.rootNode),
+            isClass,
+            metanodes,
+            classNodes,
+            inheritanceLvl = {};
+
+        this.logger.info('Creating custom layer file...');
+        metanodes = Object.keys(metaDict).map(id => metaDict[id]);
+        isClass = this.getTypeDictFor('Complex', metanodes);
+
+        // Store the dependencies for each class
+        sections.classDependencies = {};
+
+        classNodes = metanodes.filter(node => {
+            var base = this.core.getBase(node),
+                baseId,
+                deps = [],
+                name,
+                count = 1;
+
+            // Count the sets back to a class node
+            while (base) {
+                deps.push(this.core.getAttribute(base, 'name'));
+                baseId = this.core.getPath(base);
+                if (isClass[baseId]) {
+                    inheritanceLvl[this.core.getPath(node)] = count;
+                    name = this.core.getAttribute(node, 'name');
+                    sections.classDependencies[name] = deps;
+                    return true;
+                }
+                base = this.core.getBase(base);
+                count++;
+            }
+
+            return false;
+        });
+
+        // Get the code definitions for each
+        sections.classes = {};
+        classNodes
+            .sort((a, b) => {
+                var aId = this.core.getPath(a),
+                    bId = this.core.getPath(b);
+
+                return inheritanceLvl[aId] > inheritanceLvl[bId];
+            })
+            .forEach(node => {
+                var name = this.core.getAttribute(node, 'name'),
+                    code = this.core.getAttribute(node, 'code');
+
+                sections.classes[name] = code;
+            });
+
+        // order classes by dependency
+        sections.orderedClasses = Object.keys(sections.classes)
+            .sort((a, b) => {
+                // if a depends on b, switch them (return 1)
+                if (sections.classDependencies[a].includes(b)) {
+                    return 1;
+                }
+                return -1;
+            });
+    };
+
+    Export.prototype.addCustomLayers = function(sections) {
+        var metaDict = this.core.getAllMetaNodes(this.rootNode),
+            isCustomLayer,
+            metanodes,
+            customLayers;
+
+        this.logger.info('Creating custom layer file...');
+        metanodes = Object.keys(metaDict).map(id => metaDict[id]);
+        isCustomLayer = this.getTypeDictFor('CustomLayer', metanodes);
+
+        customLayers = metanodes.filter(node =>
+            this.core.getMixinPaths(node).some(id => isCustomLayer[id]));
+
+        // Get the code definitions for each
+        sections.layers = {};
+        customLayers
+            .map(layer => [
+                this.core.getAttribute(layer, 'name'),
+                this.core.getAttribute(layer, 'code')
+            ])
+            .forEach(pair => sections.layers[pair[0]] = pair[1]);
+    };
+
+
+    Export.prototype.getTypeDictFor = function (name, metanodes) {
+        var isType = {};
+        // Get all the custom layers
+        for (var i = metanodes.length; i--;) {
+            if (this.core.getAttribute(metanodes[i], 'name') === name) {
+                isType[this.core.getPath(metanodes[i])] = true;
+            }
+        }
+        return isType;
+    };
+
+    var toAttrString = function(attr) {
+        if (/^\d+\.?\d*$/.test(attr) || /^(true|false|nil)$/.test(attr)) {
+            return attr;
+        }
+        return `"${attr}"`;
+    };
+
+    Export.prototype.getOpInvocation = function(op) {
+        var lines = [],
+            attrs,
+            refInits = [],
+            args;
+
+        attrs = '{' +
+            Object.keys(op.attributes).map(key => `${key}=${toAttrString(op.attributes[key])}`)
+            .join(',') +
+        '}';
+
+        lines.push(`local ${op.name}_attrs = ${attrs}`);
+        args = (op.inputValues || [])
+            .map(val => val instanceof Array ? `${val[0]}_results.${val[1]}` : val);
+
+        args.unshift(op.name + '_attrs');
+            
+        // Create the ref init functions
+        refInits = op.refs.map((code, index) => {
+            return [
+                `local function create_${op.refNames[index]}()`,
+                indent(code),
+                'end'
+            ].join('\n');
+        });
+        lines = lines.concat(refInits);
+        args = args.concat(op.refNames.map(name => `create_${name}()`));
+        args = args.join(', ');
+        lines.push(`local ${op.name}_results = ${op.basename}(${args})`);
+
+        return lines.join('\n');
+    };
+
+    Export.prototype.getOutputName = function(node) {
+        var basename = this.core.getAttribute(node, 'saveName');
+
+        return getUniqueName(basename, this._outputNames, true);
+    };
+
+    Export.prototype.getVariableName = function (/*node*/) {
+        var c = Object.keys(this.isInputOp).length;
+
+        if (c !== 1) {
+            return `input${c}`;
+        }
+
+        return 'input';
+    };
+
+    Export.prototype.registerNode = function (node) {
+        if (this.isMetaTypeOf(node, this.META.Operation)) {
+            return this.registerOperation(node);
+        } else if (this.isMetaTypeOf(node, this.META.Transporter)) {
+            return this.registerTransporter(node);
+        }
+    };
+
+    var getUniqueName = function(namebase, takenDict, unsafeAllowed) {
+        var name,
+            i = 2,
+            isUnsafe = function(name) {
+                return !unsafeAllowed && RESERVED.test(name);
+            };
+
+        if (!unsafeAllowed) {
+            namebase = namebase.replace(/[^A-Za-z\d]/g, '_');
+        }
+        name = namebase;
+        // Get a unique operation name
+        while (takenDict[name] || isUnsafe(name)) {
+            name = namebase + '_' + i;
+            i++;
+        }
+        takenDict[name] = true;
+
+        return name;
+    };
+
+    Export.prototype.registerOperation = function (node) {
+        var name = this.core.getAttribute(node, 'name'),
+            id = this.core.getPath(node),
+            base = this.core.getBase(node),
+            baseId = this.core.getPath(base),
+            baseName = this.core.getAttribute(base, 'name');
+
+        // If it is an Input/Output operation, assign it a variable name
+        if (baseName === CONSTANTS.OP.INPUT) {
+            this.isInputOp[id] = node;
+            name = this.getVariableName(node);
+        } else if (baseName === CONSTANTS.OP.OUTPUT) {
+            this.isOutputOp[id] = node;
+            name = this.getOutputName(node);
+        } else {
+            // get a unique operation instance name
+            name = getUniqueName(name, this._instanceNames);
+        }
+
+        this._nameFor[id] = name;
+
+        // get a unique operation base name
+        if (!this._fnNameFor[baseId]) {
+            name = this.core.getAttribute(base, 'name');
+            name = getUniqueName(name, this._opBaseNames);
+            this._fnNameFor[baseId] = name;
+        }
+
+        // For operations, register all output data node names by path
+        return this.core.loadChildren(node)
+            .then(cntrs => {
+                var outputs = cntrs.find(n => this.isMetaTypeOf(n, this.META.Outputs)),
+                    inputs = cntrs.find(n => this.isMetaTypeOf(n, this.META.Inputs));
+
+                return Q.all([inputs, outputs].map(cntr => this.core.loadChildren(cntr)));
+            })
+            .then(data => {
+                var inputs = data[0],
+                    outputs = data[1];
+
+                // Get the input type
+                outputs.forEach(output => {
+                    var dataId = this.core.getPath(output);
+
+                    name = this.core.getAttribute(output, 'name');
+                    this._dataNameFor[dataId] = name;
+
+                    this._portCache[dataId] = output;
+                });
+                inputs.forEach(input => 
+                    this._portCache[this.core.getPath(input)] = input
+                );
+
+                // Extra recording for input/output nodes in the pipeline
+                if (this.isInputOp[id]) {
+                    this.inputNode[id] = outputs[0];
+                } else if (this.isOutputOp[id]) {
+                    this.outputDataToOpId[this.core.getPath(inputs[0])] = id;
+                }
+            });
+    };
+
+    Export.prototype.registerTransporter = function (node) {
+        var outputData = this.core.getPointerPath(node, 'src'),
+            inputData = this.core.getPointerPath(node, 'dst'),
+            srcOpId = this.getOpIdFor(outputData),
+            dstOpId = this.getOpIdFor(inputData);
+
+        this._srcIdFor[inputData] = outputData;
+
+        // Store the next operation ids for the op id
+        if (!this._nextOps[srcOpId]) {
+            this._nextOps[srcOpId] = [];
+        }
+        this._nextOps[srcOpId].push(dstOpId);
+
+        // Increment the incoming counts for each dst op
+        this._incomingCnts[dstOpId] = this._incomingCnts[dstOpId] || 0;
+        this._incomingCnts[dstOpId]++;
+    };
+
+    Export.prototype.getOpIdFor = function (dataId) {
+        var ids = dataId.split('/'),
+            depth = ids.length;
+
+        ids.splice(this.activeNodeDepth - depth);
+        return ids.join('/');
+    };
+
+    // For each operation...
+    //   - unpack the inputs from prev ops
+    //   - add the attributes table (if used)
+    //     - check for '\<attributes\>' in code
+    //   - add the references
+    //     - generate the code
+    //     - replace the `return <thing>` w/ `<ref-name> = <thing>`
+    Export.prototype.createOperation = function (node) {
+        var id = this.core.getPath(node),
+            baseId = this.core.getPath(this.core.getBase(node)),
+            attrNames = this.core.getValidAttributeNames(node),
+            operation = {};
+
+        operation.name = this._nameFor[id];
+        operation.basename = this._fnNameFor[baseId];
+        operation.baseId = baseId;
+        operation.id = id;
+        operation.code = this.core.getAttribute(node, 'code');
+        operation.attributes = {};
+        for (var i = attrNames.length; i--;) {
+            if (!SKIP_ATTRS[attrNames[i]]) {
+                operation.attributes[attrNames[i]] = this.core.getAttribute(node, attrNames[i]);
+            }
+        }
+
+        // Get all the input names (and sources)
+        return this.core.loadChildren(node)
+            .then(containers => {
+                var inputs;
+
+                inputs = containers
+                    .find(cntr => this.isMetaTypeOf(cntr, this.META.Inputs));
+
+                this.logger.info(`${operation.name} has ${containers.length} cntrs`);
+                return this.core.loadChildren(inputs);
+            })
+            .then(data => {
+                // Get the input names and sources
+                var inputNames = data.map(d => this.core.getAttribute(d, 'name')),
+                    ids = data.map(d => this.core.getPath(d)),
+                    srcIds = ids.map(id => this._srcIdFor[id]);
+
+                operation.inputNames = inputNames || [];
+                operation.inputValues = inputNames.map((name, i) => {
+                    var id = srcIds[i],
+                        srcDataName = this._dataNameFor[id],
+                        srcOpId = this.getOpIdFor(id),
+                        srcOpName = this._nameFor[srcOpId];
+
+                    if (this.isInputOp[srcOpId]) {
+                        return this._nameFor[srcOpId];
+                    } else {
+                        return [srcOpName, srcDataName];
+                    }
+                });
+
+                return operation;
+
+            })
+            .then(operation => {
+
+                // For each reference, run the plugin and retrieve the generated code
+                operation.refNames = [];
+
+                if (!this.isInputOp[operation.id]) {
+                    operation.refNames = this.core.getPointerNames(node)
+                        .filter(name => name !== 'base');
+                }
+
+                var refs = operation.refNames
+                    .map(ref => [ref, this.core.getPointerPath(node, ref)]);
+
+                return Q.all(
+                    refs.map(pair => this.genPtrSnippet.apply(this, pair))
+                );
+            })
+            .then(codeFiles => {
+                operation.refs = codeFiles;
+                return operation;
+            });
+    };
+
+    Export.prototype.genPtrSnippet = function (ptrName, pId) {
+        return this.getPtrCodeHash(pId)
+            .then(hash => this.blobClient.getObjectAsString(hash));
+    };
+
+    Export.prototype.createHeader = function (title, length) {
+        var len;
+        title = ` ${title} `;
+        length = length || HEADER_LENGTH;
+
+        len = Math.max(
+            Math.floor((length - title.length)/2),
+            2
+        );
+
+        return [
+            '',
+            title,
+            ''
+        ].join(new Array(len+1).join('-')) + '\n';
+
+    };
+
+    Export.prototype.genOperationCode = function (operation) {
+        var header = this.createHeader(`"${operation.name}" Operation`),
+            codeParts = [],
+            body = [];
+
+        codeParts.push(header);
+        codeParts.push(`local ${operation.name}_results`);
+        codeParts.push('do');
+
+        if (operation.inputs.length) {
+            body.push(operation.inputs.join('\n'));
+        }
+
+        if (operation.refs.length) {
+            body.push(operation.refs.join('\n'));
+        }
+
+        body.push(operation.code);
+
+        codeParts.push(indent(body.join('\n')));
+        codeParts.push('end');
+        codeParts.push('');
+
+        operation.code = codeParts.join('\n');
+        return operation;
+    };
+
+    _.extend(Export.prototype, PtrCodeGen.prototype);
+
+    // Extra utilities for export types
+    Export.prototype.INIT_CLASSES_FN = '__init_classes';
+    Export.prototype.INIT_LAYERS_FN = '__init_layers';
+    Export.prototype.getAllDefinitions = function (sections) {
+        var code = [],
+            classes,
+            initClassFn,
+            initLayerFn;
+
+        classes = sections.orderedClasses
+            // Create fns from the classes
+            .map(name => this.indent(sections.classes[name])).join('\n');
+
+        initClassFn = [
+            `local function ${this.INIT_CLASSES_FN}()`,
+            this.indent(classes),
+            'end'
+        ].join('\n');
+
+        code = code.concat(initClassFn);
+
+        // wrap the layers in a function
+        initLayerFn = [
+            `local function ${this.INIT_LAYERS_FN}()`,
+            this.indent(_.values(sections.layers).join('\n\n')),
+            'end'
+        ].join('\n');
+        code = code.concat(initLayerFn);
+
+        // Add operation fn definitions
+        code = code.concat(_.values(sections.operations));
+        code = code.concat(_.values(sections.pipelines));
+
+        // define deserializers, serializers
+        code.push(sections.deserializers);
+        code.push(sections.serializers);
+
+        code.push(this.getDeepforgeObject());
+        code.push('deepforge.initialize()');
+
+        code.push(sections.serializeOutputsDef);
+        return code.join('\n\n');
+    };
+
+    Export.prototype.getDeepforgeObject = function (content) {
+        content = content || {};
+        content.initCode = content.initCode || `${this.INIT_CLASSES_FN}()\n${'   '}${this.INIT_LAYERS_FN}()`;
+        return DeepForgeTpl(content);
+    };
+
+    return Export;
+});

src/plugins/Export/deepforge.ejs

@@ -0,0 +1,47 @@
+-- Instantiate the deepforge object
+deepforge = {}
+
+function deepforge.initialize()
+    require 'nn'
+    require 'rnn'
+    <%= initCode %>
+end
+
+-- Graph support
+torch.class('deepforge.Graph')
+
+function deepforge.Graph:__init(name)
+    -- nop
+end
+
+torch.class('deepforge._Line')
+
+function deepforge._Line:__init(graphId, name, opts)
+   -- nop
+end
+
+function deepforge._Line:add(x, y)
+   -- nop
+end
+
+function deepforge.Graph:line(name, opts)
+    return deepforge._Line(self.id, name, opts)
+end
+
+-- Image support
+function deepforge.image(name, tensor)
+   -- nop
+end
+
+torch.class('deepforge.Image')
+function deepforge.Image:__init(name, tensor)
+   -- nop
+end
+
+function deepforge.Image:update(tensor)
+   -- nop
+end
+
+function deepforge.Image:title(name)
+   -- nop
+end

src/plugins/Export/format.js

@@ -0,0 +1,13 @@
+
+/* globals define*/
+// The supported export formats and metadata
+define([
+    './formats/cli/cli'
+], function(
+    Format0
+) {
+
+    return {
+        'Basic CLI': Format0
+    };
+});

src/plugins/Export/format.js.ejs

@@ -0,0 +1,21 @@
+<% // Add default format
+formats.unshift({ name: 'cli', main: 'cli.js', displayName: 'Basic CLI' })
+%>
+/* globals define*/
+// The supported export formats and metadata
+define([
+<%= formats.map(function(format) {
+    return '    \'./formats/' + format.name + '/' +
+        path.basename(format.main.replace(/\.js$/, '')) + '\''
+    })
+    .join(',\n') %>
+], function(
+<%= formats.map(function(f, index) { return '    Format' + index; }).join(',\n') %>
+) {
+
+    return {
+<%= formats.map(function(f, index) {
+        return '        \'' + f.displayName + '\': Format' + index;
+    }).join(',\n') %>
+    };
+});

src/plugins/Export/formats/cli/cli.js

@@ -0,0 +1,103 @@
+/*globals define*/
+// Simple torch cli for the given pipeline
+define([
+], function(
+) {
+
+    var TOBOOLEAN = 
+`local function toboolean(str)
+    if str == 'true' then
+        return true
+    elseif str == 'false' then
+        return false
+    end
+end`;
+
+    var CliExporter = {};
+
+    CliExporter.deserializersFromString = function(sections) {
+        var hasBool = false;
+
+        // Add serializers given cli string input
+        Object.keys(this.isInputOp).forEach(id => {
+            var node = this.inputNode[id],
+                base = this.core.getBase(node),
+                type = this.core.getAttribute(base, 'name'),
+                name = this._nameFor[id];
+
+            if (type === 'boolean') {
+                hasBool = true;
+                sections.deserializerFor[name] = 'toboolean';
+            } else if (type === 'number') {
+                sections.deserializerFor[name] = 'tonumber';
+            } else if (type === 'string') {
+                sections.deserializerFor[name] = 'tostring';
+            }
+        });
+
+        if (hasBool) {
+            sections.deserializers += '\n' + TOBOOLEAN;
+        }
+
+        return sections;
+    };
+
+    CliExporter.main = function (sections, staticInputs) {
+        var code = [];
+
+        // Update deserializers for cli input
+        this.deserializersFromString(sections);
+
+        // Define all the operations, pipelines, etc
+        // 'getAllDefinitions' is provided as part of the public api
+        code.push(this.getAllDefinitions(sections));
+
+        // Command line specific stuff
+        var files = {},
+            main,
+            args,
+            staticNames = staticInputs.map(input => input.name),
+            varDefs,
+            index = 1;
+
+        // Create some names for the inputs
+        args = sections.pipelineInputNames.map(name => `${sections.deserializerFor[name]}(${name})`);
+
+        main = `local outputs = ${sections.pipelineName}(${args.join(', ')})`;
+
+        // Grab the args from the cli
+        code.push(sections.pipelineInputNames.map((name, index) => {
+            return `local ${name} = arg[${index + 1}]`;
+        }).join('\n'));
+
+        // Add the hash for each of the static inputs and reference them
+        staticInputs.forEach(input => {
+            files[`res/${input.name}`] = input.hash;
+        });
+
+        varDefs = staticNames.map(name => {
+            return `local ${name} = './res/${name}'`;
+        });
+
+        // Grab the remaining args from the cli
+        varDefs = varDefs.concat(sections.pipelineInputNames.map(name => {
+            if (!staticNames.includes(name)) {
+                return `local ${name} = arg[${index++}]`;
+            }
+        }));
+
+        // Add the main fn
+        code.push(varDefs.join('\n'));
+        code.push(main);
+
+        // Save outputs to disk
+        code.push(sections.serializeOutputs);
+
+        files['init.lua'] = code.join('\n\n');
+
+        // if no extra assets, just return the main file
+        return staticInputs.length ? files : files['init.lua'];
+    };
+
+    return CliExporter;
+});

src/plugins/Export/metadata.json

@@ -0,0 +1,14 @@
+{
+  "id": "Export",
+  "name": "Export",
+  "version": "1.0.0",
+  "description": "",
+  "icon": {
+    "class": "glyphicon glyphicon-cog",
+    "src": ""
+  },
+  "disableServerSideExecution": false,
+  "disableBrowserSideExecution": false,
+  "writeAccessRequired": false,
+  "configStructure": []
+}

src/plugins/Export/toboolean.lua

@@ -0,0 +1,7 @@
+local function toboolean(str)
+    if str == 'true' then
+        return true
+    elseif str == 'false' then
+        return false
+    end
+end

src/plugins/GenerateArchitecture/GenerateArchitecture.js

@@ -6,13 +6,15 @@ define([
     'SimpleNodes/Constants',
     'deepforge/layer-args',
     'deepforge/utils',
+    'deepforge/Constants',
     'underscore',
     'text!./metadata.json'
 ], function (
     PluginBase,
-    Constants,
+    SimpleNodeConstants,
     createLayerDict,
     utils,
+    Constants,
     _,
     metadata
 ) {
@@ -47,6 +49,11 @@ define([
         this.LayerDict = createLayerDict(this.core, this.META);
         this.uniqueId = 2;
         this.varnames = {net: true};
+        this.definitions = [
+            'require \'nn\'',
+            'require \'rnn\''
+        ];
+
         return PluginBase.prototype.main.apply(this, arguments);
     };
 
@@ -65,15 +72,10 @@ define([
     };
 
     GenerateArchitecture.prototype.createOutputFiles = function (tree) {
-        var layers = tree[Constants.CHILDREN],
+        var layers = tree[SimpleNodeConstants.CHILDREN],
             result = {},
             code = '';
 
-        this.definitions = [
-            'require \'nn\'',
-            'require \'rnn\''
-        ];
-
         // Add an index to each layer
         layers.forEach((l, index) => l[INDEX] = index);
 
@@ -125,12 +127,61 @@ define([
     };
 
     GenerateArchitecture.prototype.createLayer = function (layer) {
-        var args = this.createArgString(layer);
-        return `nn.${layer.name}${args}`;
+        var args = this.createArgString(layer),
+            def = `nn.${layer.name}${args}`,
+            type = layer.base.base.name,
+            memberIds,
+            node,
+            name,
+            children,
+            id;
+
+        // Check if it is a container and has the 'addLayers' set
+        // If so, it should sort them by their registry 'index' and add
+        // each nested architecture's code to the given container
+        if (type === 'Container') {
+            // Get the members of the 'addLayers' set
+            memberIds = {};
+            id = layer[SimpleNodeConstants.NODE_PATH];
+            node = this._nodeCache[id];
+            this.core.getMemberPaths(node, Constants.CONTAINED_LAYER_SET)
+                .forEach(id => memberIds[id] = true);
+
+            // Get the (sorted) children
+            children = layer[SimpleNodeConstants.CHILDREN]
+                .map(child => {  // get (child, index) tuples
+                    var index = null;
+
+                    id = child[SimpleNodeConstants.NODE_PATH];
+                    if (memberIds[id]) {
+                        index = this.core.getMemberRegistry(node,
+                            Constants.CONTAINED_LAYER_SET, id, Constants.CONTAINED_LAYER_INDEX);
+                    }
+                    return [child, index];
+                })
+                .filter(pair => pair[1] !== null)  // remove non-members
+                .sort((a, b) => a[1] < b[1] ? -1 : 1)  // sort by 'index'
+                .map(pair => pair[0]);
+
+
+            var addedLayerDefs = '',
+                firstLayer;
+
+            for (var i = 0; i < children.length; i++) {
+                id = children[i][SimpleNodeConstants.NODE_PATH];
+                // Get the children!
+                firstLayer = children[i][SimpleNodeConstants.CHILDREN][0];
+                name = this.getVarName(utils.abbr(layer.name + '_' + i));
+                addedLayerDefs += this.createSequential(firstLayer, name).code;
+                def += `:add(${name})`;
+            }
+            this.hoist(addedLayerDefs);
+        }
+        return def;
     };
 
     GenerateArchitecture.prototype.createSequential = function (layer, name) {
-        var next = layer[Constants.NEXT][0],
+        var next = layer[SimpleNodeConstants.NEXT][0],
             args,
             snippet,
             snippets,
@@ -142,7 +193,7 @@ define([
 
         while (layer) {
             // if there is only one successor, just add the given layer
-            if (layer[Constants.PREV].length > 1) {  // sequential layers are over
+            if (layer[SimpleNodeConstants.PREV].length > 1) {  // sequential layers are over
                 next = layer;  // the given layer will be added by the caller
                 break;
             } else {  // add the given layer
@@ -151,11 +202,11 @@ define([
 
             }
 
-            while (layer && layer[Constants.NEXT].length > 1) {  // concat/parallel
+            while (layer && layer[SimpleNodeConstants.NEXT].length > 1) {  // concat/parallel
                 // if there is a fork, recurse and add a concat layer
 
-                this.logger.debug(`detected fork of size ${layer[Constants.NEXT].length}`);
-                snippets = layer[Constants.NEXT].map(nlayer =>
+                this.logger.debug(`detected fork of size ${layer[SimpleNodeConstants.NEXT].length}`);
+                snippets = layer[SimpleNodeConstants.NEXT].map(nlayer =>
                     this.createSequential(nlayer, this.getVarName('net')));
                 code += '\n' + snippets.map(snippet => snippet.code).join('\n');
 
@@ -183,7 +234,7 @@ define([
                                 `concat_${layer[INDEX]}:add(${snippet.name})`)
                             .join('\n') + `\n\n${name}:add(concat_${layer[INDEX]})`;
                         
-                        next = layer[Constants.NEXT][0];
+                        next = layer[SimpleNodeConstants.NEXT][0];
                     } else {
                         next = null;  // no next layers
                     }
@@ -203,7 +254,7 @@ define([
             }
 
             layer = next;
-            next = layer && layer[Constants.NEXT][0];
+            next = layer && layer[SimpleNodeConstants.NEXT][0];
         }
 
         return {
@@ -218,14 +269,14 @@ define([
         var content = layer[arg];
 
         if (typeof content === 'object') {  // layer as arg
-            if (content[Constants.CHILDREN].length) {
+            if (content[SimpleNodeConstants.CHILDREN].length) {
                 // Generate the code for the children of layer[arg]
                 var name = this.getVarName(utils.abbr(arg)),
                     layers;
 
                 this.logger.debug(`Adding layer arg for ${arg} (${layer.name})`);
                 try {
-                    layers = this.genRawArchCode(layer[arg][Constants.CHILDREN], name);
+                    layers = this.genRawArchCode(layer[arg][SimpleNodeConstants.CHILDREN], name);
                 } catch (e) {
                     this.logger.error(`Layer arg creation failed: ${e}`);
                     return null;
@@ -244,7 +295,7 @@ define([
     GenerateArchitecture.prototype.createArgString = function (layer) {
         var setters = this.LayerDict[layer.name].setters,
             setterNames = Object.keys(this.LayerDict[layer.name].setters),
-            base = layer[Constants.BASE],
+            base = layer[SimpleNodeConstants.BASE],
             desc,
             fn,
             layerCode,

src/plugins/GenerateExecFile/GenerateExecFile.js

@@ -1,344 +0,0 @@
-/*globals define, _*/
-/*jshint node:true, browser:true*/
-
-/**
- * Generated by PluginGenerator 1.7.0 from webgme on Sat Jun 04 2016 18:01:54 GMT-0500 (CDT).
- * A plugin that inherits from the PluginBase. To see source code documentation about available
- * properties and methods visit %host%/docs/source/PluginBase.html.
- */
-
-define([
-    'text!./metadata.json',
-    'plugin/PluginBase',
-    'deepforge/plugin/PtrCodeGen',
-    'q'
-], function (
-    pluginMetadata,
-    PluginBase,
-    PtrCodeGen,
-    Q
-) {
-    'use strict';
-
-    pluginMetadata = JSON.parse(pluginMetadata);
-    var HEADER_LENGTH = 60;
-
-    /**
-     * Initializes a new instance of GenerateExecFile.
-     * @class
-     * @augments {PluginBase}
-     * @classdesc This class represents the plugin GenerateExecFile.
-     * @constructor
-     */
-    var GenerateExecFile = function () {
-        // Call base class' constructor.
-        PluginBase.call(this);
-        this.pluginMetadata = pluginMetadata;
-
-        this._srcIdFor = {};  // input path -> output data node path
-
-        this._nameFor = {};  // input path -> opname
-        this._dataNameFor = {};  
-        this._opNames = {};
-
-        // topo sort stuff
-        this._nextOps = {};
-        this._incomingCnts = {};
-
-        this._operations = {};
-        this.activeNodeId = null;
-        this.activeNodeDepth = null;
-    };
-
-    /**
-     * Metadata associated with the plugin. Contains id, name, version, description, icon, configStructue etc.
-     * This is also available at the instance at this.pluginMetadata.
-     * @type {object}
-     */
-    GenerateExecFile.metadata = pluginMetadata;
-
-    // Prototypical inheritance from PluginBase.
-    GenerateExecFile.prototype = Object.create(PluginBase.prototype);
-    GenerateExecFile.prototype.constructor = GenerateExecFile;
-
-    /**
-     * Main function for the plugin to execute. This will perform the execution.
-     * Notes:
-     * - Always log with the provided logger.[error,warning,info,debug].
-     * - Do NOT put any user interaction logic UI, etc. inside this method.
-     * - callback always has to be called even if error happened.
-     *
-     * @param {function(string, plugin.PluginResult)} callback - the result callback
-     */
-    GenerateExecFile.prototype.main = function (callback) {
-        // Get all the children and call generate exec file
-        this.activeNodeId = this.core.getPath(this.activeNode);
-        this.activeNodeDepth = this.activeNodeId.split('/').length + 1;
-
-        if (this.isMetaTypeOf(this.activeNode, this.META.Execution)) {
-            this.activeNodeDepth++;
-        }
-
-        return this.core.loadChildren(this.activeNode)
-            .then(nodes => this.createExecFile(nodes))
-            .then(code => this.blobClient.putFile('init.lua', code))
-            .then(hash => {
-                this.result.addArtifact(hash);
-                this.result.setSuccess(true);
-                callback(null, this.result);
-            })
-            .fail(err => callback(err));
-    };
-
-    GenerateExecFile.prototype.createExecFile = function (children) {
-        // Convert opNodes' jobs to the nested operations
-        var opNodes,
-            nodes;
-
-        return this.unpackJobs(children)
-            .then(_nodes => {
-                nodes = _nodes;
-                opNodes = nodes
-                    .filter(node => this.isMetaTypeOf(node, this.META.Operation));
-                return Q.all(nodes.map(node => this.registerNameAndData(node)));
-            })
-            .then(() => Q.all(opNodes.map(node => this.createOperation(node))))
-            .then(operations => {
-                var nextIds = opNodes.map(n => this.core.getPath(n))
-                        .filter(id => !this._incomingCnts[id]);
-
-                operations.forEach(op => this._operations[op.id] = op);
-
-                // Toposort and concat!
-                return this.combineOpNodes(nextIds);
-            })
-            .fail(err => this.logger.error(err));
-    };
-
-    GenerateExecFile.prototype.unpackJobs = function (nodes) {
-        return Q.all(
-            nodes.map(node => {
-                if (!this.isMetaTypeOf(node, this.META.Job)) {
-                    return node;
-                }
-                return this.core.loadChildren(node)
-                    .then(children =>
-                        children.find(c => this.isMetaTypeOf(c, this.META.Operation))
-                    );
-            })
-        );
-    };
-
-    GenerateExecFile.prototype.combineOpNodes = function (opIds) {
-        var nextIds = [],
-            dstIds,
-            code,
-            id;
-
-        // Combine all nodes with incoming cnts of 0
-        code = opIds.map(id => this._operations[id].code).join('\n');
-
-        // Decrement all next ops
-        dstIds = opIds.map(id => this._nextOps[id])
-            .reduce((l1, l2) => l1.concat(l2), []);
-        for (var i = dstIds.length; i--;) {
-            id = dstIds[i];
-            if (--this._incomingCnts[id] === 0) {
-                nextIds.push(id);
-            }
-        }
-
-        // append
-        return [
-            code,
-            nextIds.length ? this.combineOpNodes(nextIds) : ''
-        ].join('\n');
-    };
-
-    GenerateExecFile.prototype.registerNameAndData = function (node) {
-        var name = this.core.getAttribute(node, 'name'),
-            id = this.core.getPath(node),
-            basename = name,
-            i = 2;
-
-        if (this.isMetaTypeOf(node, this.META.Operation)) {
-
-            // Get a unique operation name
-            while (this._opNames[name]) {
-                name = basename + '_' + i;
-                i++;
-            }
-
-            // register the unique name
-            this._opNames[name] = true;
-            this._nameFor[id] = name;
-
-            // For operations, register all output data node names by path
-            return this.core.loadChildren(node)
-                .then(cntrs => {
-                    var cntr = cntrs.find(n => this.isMetaTypeOf(n, this.META.Outputs));
-                    return this.core.loadChildren(cntr);
-                })
-                .then(outputs => {
-                    outputs.forEach(output => {
-                        var dataId = this.core.getPath(output);
-
-                        name = this.core.getAttribute(output, 'name');
-                        this._dataNameFor[dataId] = name;
-                    });
-                });
-
-        // For each input data node, register the associated output id
-        } else if (this.isMetaTypeOf(node, this.META.Transporter)) {
-            var outputData = this.core.getPointerPath(node, 'src'),
-                inputData = this.core.getPointerPath(node, 'dst'),
-                srcOpId = this.getOpIdFor(outputData),
-                dstOpId = this.getOpIdFor(inputData);
-
-            this._srcIdFor[inputData] = outputData;
-
-            // Store the next operation ids for the op id
-            if (!this._nextOps[srcOpId]) {
-                this._nextOps[srcOpId] = [];
-            }
-            this._nextOps[srcOpId].push(dstOpId);
-
-            // Increment the incoming counts for each dst op
-            this._incomingCnts[dstOpId] = this._incomingCnts[dstOpId] || 0;
-            this._incomingCnts[dstOpId]++;
-        }
-    };
-
-    GenerateExecFile.prototype.getOpIdFor = function (dataId) {
-        var ids = dataId.split('/'),
-            depth = ids.length;
-
-        ids.splice(this.activeNodeDepth - depth);
-        return ids.join('/');
-    };
-
-    // For each operation...
-    //   - unpack the inputs from prev ops
-    //   - add the attributes table (if used)
-    //     - check for '\<attributes\>' in code
-    //   - add the references
-    //     - generate the code
-    //     - replace the `return <thing>` w/ `<ref-name> = <thing>`
-    GenerateExecFile.prototype.createOperation = function (node) {
-        var id = this.core.getPath(node),
-            operation = {};
-
-        operation.name = this._nameFor[id];
-        operation.id = id;
-        operation.code = this.core.getAttribute(node, 'code');
-
-        // Update the 'code' attribute
-        // Change the last return statement to assign the results to a table
-        operation.code = this.assignResultToVar(operation.code,
-            `${operation.name}_results`);
-
-        // Get all the input names (and sources)
-        return this.core.loadChildren(node)
-            .then(containers => {
-                var inputs;
-
-                inputs = containers
-                    .find(cntr => this.isMetaTypeOf(cntr, this.META.Inputs));
-
-                this.logger.info(`${name} has ${containers.length} cntrs`);
-                return this.core.loadChildren(inputs);
-            })
-            .then(data => {
-                // Get the input names and sources
-                var inputNames = data.map(d => this.core.getAttribute(d, 'name')),
-                    ids = data.map(d => this.core.getPath(d)),
-                    srcIds = ids.map(id => this._srcIdFor[id]);
-
-                operation.inputs = inputNames.map((name, i) => {
-                    var id = srcIds[i],
-                        srcDataName = this._dataNameFor[id],
-                        srcOpId = this.getOpIdFor(id),
-                        srcOpName = this._nameFor[srcOpId];
-
-                    return `local ${name} = ${srcOpName}_results.${srcDataName}`;
-                });
-
-                return operation;
-
-            })
-            .then(operation => {
-
-                // For each reference, run the plugin and retrieve the generated code
-                operation.refNames = this.core.getPointerNames(node)
-                    .filter(name => name !== 'base');
-
-                var refs = operation.refNames
-                    .map(ref => [ref, this.core.getPointerPath(node, ref)]);
-
-                return Q.all(
-                    refs.map(pair => this.genPtrSnippet.apply(this, pair))
-                );
-            })
-            .then(codeFiles => {
-                operation.refs = codeFiles;
-                this.genOperationCode(operation);
-                return operation;
-            });
-    };
-
-    GenerateExecFile.prototype.genPtrSnippet = function (ptrName, pId) {
-        return this.getPtrCodeHash(pId)
-            .then(hash => this.blobClient.getObjectAsString(hash))
-            .then(code => this.createHeader(`creating ${ptrName}`, 40) + '\n' +
-                this.assignResultToVar(code, ptrName));
-    };
-
-    GenerateExecFile.prototype.createHeader = function (title, length) {
-        var len;
-        title = ` ${title} `;
-        length = length || HEADER_LENGTH;
-
-        len = Math.max(
-            Math.floor((length - title.length)/2),
-            2
-        );
-
-        return [
-            '',
-            title,
-            ''
-        ].join(new Array(len+1).join('-')) + '\n';
-
-    };
-
-    GenerateExecFile.prototype.genOperationCode = function (operation) {
-        var header = this.createHeader(`"${operation.name}" Operation`),
-            codeParts = [];
-
-        codeParts.push(header);
-
-        if (operation.inputs.length) {
-            codeParts.push(operation.inputs.join('\n'));
-        }
-
-        if (operation.refs.length) {
-            codeParts.push(operation.refs.join('\n'));
-        }
-
-        codeParts.push(operation.code);
-        codeParts.push('');
-        operation.code = codeParts.join('\n');
-        return operation;
-    };
-
-    GenerateExecFile.prototype.assignResultToVar = function (code, name) {
-        var i = code.lastIndexOf('return');
-        return code.substring(0, i) +
-            code.substring(i)
-                .replace('return', `local ${name} = `);
-    };
-
-    _.extend(GenerateExecFile.prototype, PtrCodeGen.prototype);
-
-    return GenerateExecFile;
-});

src/plugins/GenerateJob/GenerateJob.js

@@ -0,0 +1,568 @@
+/*globals define*/
+/*jshint node:true, browser:true*/
+
+define([
+    './templates/index',
+    'q',
+    'underscore',
+    'deepforge/Constants',
+    'deepforge/plugin/Operation',
+    'deepforge/plugin/PtrCodeGen',
+    'text!./metadata.json',
+    'plugin/PluginBase'
+], function (
+    Templates,
+    Q,
+    _,
+    CONSTANTS,
+    OperationHelpers,
+    PtrCodeGen,
+    pluginMetadata,
+    PluginBase
+) {
+    'use strict';
+
+    pluginMetadata = JSON.parse(pluginMetadata);
+    var OUTPUT_INTERVAL = 1500,
+        STDOUT_FILE = 'job_stdout.txt',
+        SKIP_ATTRIBUTES = [
+            'code',
+            'stdout',
+            'execFiles',
+            'jobId',
+            'secret',
+            CONSTANTS.LINE_OFFSET,
+            CONSTANTS.DISPLAY_COLOR
+        ];
+
+    /**
+     * Initializes a new instance of GenerateJob.
+     * @class
+     * @augments {PluginBase}
+     * @classdesc This class represents the plugin GenerateJob.
+     * @constructor
+     */
+    var GenerateJob = function () {
+        // Call base class' constructor.
+        PluginBase.call(this);
+        this.pluginMetadata = pluginMetadata;
+    };
+
+    /**
+     * Metadata associated with the plugin. Contains id, name, version, description, icon, configStructue etc.
+     * This is also available at the instance at this.pluginMetadata.
+     * @type {object}
+     */
+    GenerateJob.metadata = pluginMetadata;
+
+    // Prototypical inheritance from PluginBase.
+    GenerateJob.prototype = Object.create(PluginBase.prototype);
+    GenerateJob.prototype.constructor = GenerateJob;
+
+    /**
+     * Main function for the plugin to execute. This will perform the execution.
+     * Notes:
+     * - Always log with the provided logger.[error,warning,info,debug].
+     * - Do NOT put any user interaction logic UI, etc. inside this method.
+     * - callback always has to be called even if error happened.
+     *
+     * @param {function(string, plugin.PluginResult)} callback - the result callback
+     */
+    GenerateJob.prototype.main = function (callback) {
+        var files,
+            artifactName,
+            artifact,
+            data = {},
+            inputs,
+            name,
+            opId;
+
+        name = this.getAttribute(this.activeNode, 'name');
+        opId = this.core.getPath(this.activeNode);
+
+        return this.createOperationFiles(this.activeNode)
+            .then(results => {
+                this.logger.info('Created operation files!');
+                files = results;
+                artifactName = `${name}_${opId.replace(/\//g, '_')}-execution-files`;
+                artifact = this.blobClient.createArtifact(artifactName);
+
+                // Add the input assets
+                //   - get the metadata (name)
+                //   - add the given inputs
+                inputs = Object.keys(files.inputAssets);
+
+                return Q.all(
+                    inputs.map(input => {  // Get the metadata for each input
+                        var hash = files.inputAssets[input];
+
+                        // data asset for "input"
+                        return this.blobClient.getMetadata(hash)
+                            .fail(() => {
+                                throw Error(`BLOB_FETCH_FAILED:${input}`);
+                            });
+                    })
+                );
+            })
+            .then(mds => {
+                // Record the large files
+                var inputData = {},
+                    runsh = '# Bash script to download data files and run job\n' +
+                    'if [ -z "$DEEPFORGE_URL" ]; then\n  echo "Please set DEEPFORGE_URL and' +
+                    ' re-run:"\n  echo ""  \n  echo "  DEEPFORGE_URL=http://my.' +
+                    'deepforge.server.com:8080 bash run.sh"\n  echo ""\n exit 1\nfi\n';
+
+                mds.forEach((metadata, i) => {
+                    // add the hashes for each input
+                    var input = inputs[i], 
+                        hash = files.inputAssets[input],
+                        dataPath = 'inputs/' + input + '/data',
+                        url = this.blobClient.getRelativeDownloadURL(hash);
+
+                    inputData[dataPath] = {
+                        req: hash,
+                        cache: metadata.content
+                    };
+
+                    // Add to the run.sh file
+                    runsh += `wget $DEEPFORGE_URL${url} -O ${dataPath}\n`;
+                });
+
+                delete files.inputAssets;
+                files['input-data.json'] = JSON.stringify(inputData, null, 2);
+                runsh += 'th init.lua';
+                files['run.sh'] = runsh;
+
+                // Add pointer assets
+                Object.keys(files.ptrAssets)
+                    .forEach(path => data[path] = files.ptrAssets[path]);
+
+                // Add the executor config
+                return this.getOutputs(this.activeNode);
+            })
+            .then(outputArgs => {
+                var config,
+                    outputs,
+                    fileList,
+                    ptrFiles = Object.keys(files.ptrAssets),
+                    file;
+
+                delete files.ptrAssets;
+                fileList = Object.keys(files).concat(ptrFiles);
+
+                outputs = outputArgs.map(pair => pair[0])
+                    .map(name => {
+                        return {
+                            name: name,
+                            resultPatterns: [`outputs/${name}`]
+                        };
+                    });
+
+                outputs.push(
+                    {
+                        name: 'stdout',
+                        resultPatterns: [STDOUT_FILE]
+                    },
+                    {
+                        name: name + '-all-files',
+                        resultPatterns: fileList
+                    }
+                );
+
+                config = {
+                    cmd: 'node',
+                    args: ['start.js'],
+                    outputInterval: OUTPUT_INTERVAL,
+                    resultArtifacts: outputs
+                };
+                files['executor_config.json'] = JSON.stringify(config, null, 4);
+
+                // Save the artifact
+                // Remove empty hashes
+                for (file in data) {
+                    if (!data[file]) {
+                        this.logger.warn(`Empty data hash has been found for file "${file}". Removing it...`);
+                        delete data[file];
+                    }
+                }
+                return artifact.addObjectHashes(data);
+            })
+            .then(() => {
+                this.logger.info(`Added ptr/input data hashes for "${artifactName}"`);
+                return artifact.addFiles(files);
+            })
+            .then(() => {
+                this.logger.info(`Added execution files for "${artifactName}"`);
+                return artifact.save();
+            })
+            .then(hash => {
+                this.result.setSuccess(true);
+                this.result.addArtifact(hash);
+                callback(null, this.result);
+            })
+            .fail(err => {
+                this.result.setSuccess(false);
+                callback(err, this.result);
+            });
+    }; 
+
+    GenerateJob.prototype.createOperationFiles = function (node) {
+        var files = {};
+        // For each operation, generate the output files:
+        //   inputs/<arg-name>/init.lua  (respective data deserializer)
+        //   pointers/<name>/init.lua  (result of running the main plugin on pointer target - may need a rename)
+        //   outputs/<name>/  (make dirs for each of the outputs)
+        //   outputs/init.lua  (serializers for data outputs)
+        //
+        //   attributes.lua (returns lua table of operation attributes)
+        //   init.lua (main file -> calls main and serializes outputs)
+        //   <name>.lua (entry point -> calls main operation code)
+
+        // add the given files
+        this.logger.info('About to create dist execution files');
+        files['start.js'] = _.template(Templates.START)(CONSTANTS);
+        return this.createEntryFile(node, files)
+            .then(() => this.createClasses(node, files))
+            .then(() => this.createCustomLayers(node, files))
+            .then(() => this.createInputs(node, files))
+            .then(() => this.createOutputs(node, files))
+            .then(() => this.createMainFile(node, files))
+            .then(() => {
+                this.createAttributeFile(node, files);
+                return Q.ninvoke(this, 'createPointers', node, files);
+            })
+            .fail(err => {
+                this.logger.error(err);
+                throw err;
+            });
+    };
+
+    GenerateJob.prototype.createEntryFile = function (node, files) {
+        this.logger.info('Creating entry files...');
+        return this.getOutputs(node)
+            .then(outputs => {
+                var name = this.getAttribute(node, 'name'),
+                    content = {};
+
+                // inputs and outputs
+                content.name = name;
+                content.outputs = outputs;
+
+                files['init.lua'] = _.template(Templates.ENTRY)(content);
+
+                // Create the deepforge file
+                files['deepforge.lua'] = _.template(Templates.DEEPFORGE)(CONSTANTS);
+            });
+    };
+
+    GenerateJob.prototype.createClasses = function (node, files) {
+        var metaDict = this.core.getAllMetaNodes(this.rootNode),
+            isClass,
+            metanodes,
+            classNodes,
+            inheritanceLvl = {},
+            code;
+
+        this.logger.info('Creating custom layer file...');
+        metanodes = Object.keys(metaDict).map(id => metaDict[id]);
+        isClass = this.getTypeDictFor('Complex', metanodes);
+
+        classNodes = metanodes.filter(node => {
+            var base = this.core.getBase(node),
+                baseId,
+                count = 1;
+
+            // Count the sets back to a class node
+            while (base) {
+                baseId = this.core.getPath(base);
+                if (isClass[baseId]) {
+                    inheritanceLvl[this.core.getPath(node)] = count;
+                    return true;
+                }
+                base = this.core.getBase(base);
+                count++;
+            }
+
+            return false;
+        });
+
+        // Get the code definitions for each
+        // Sort by levels of inheritance...
+        code = classNodes.sort((a, b) => {
+            var aId = this.core.getPath(a),
+                bId = this.core.getPath(b);
+
+            return inheritanceLvl[aId] > inheritanceLvl[bId];
+        }).map(node =>
+            `require './${this.getAttribute(node, 'name')}.lua'`
+        ).join('\n');
+
+        // Create the class files
+        classNodes.forEach(node => {
+            var name = this.getAttribute(node, 'name');
+            files[`classes/${name}.lua`] = this.getAttribute(node, 'code');
+        });
+
+        // Create the custom layers file
+        files['classes/init.lua'] = code;
+    };
+
+    GenerateJob.prototype.getTypeDictFor = function (name, metanodes) {
+        var isType = {};
+        // Get all the custom layers
+        for (var i = metanodes.length; i--;) {
+            if (this.getAttribute(metanodes[i], 'name') === name) {
+                isType[this.core.getPath(metanodes[i])] = true;
+            }
+        }
+        return isType;
+    };
+
+    GenerateJob.prototype.createCustomLayers = function (node, files) {
+        var metaDict = this.core.getAllMetaNodes(this.rootNode),
+            isCustomLayer,
+            metanodes,
+            customLayers,
+            code;
+
+        this.logger.info('Creating custom layer file...');
+        metanodes = Object.keys(metaDict).map(id => metaDict[id]);
+        isCustomLayer = this.getTypeDictFor('CustomLayer', metanodes);
+
+        customLayers = metanodes.filter(node =>
+            this.core.getMixinPaths(node).some(id => isCustomLayer[id]));
+
+        // Get the code definitions for each
+        code = 'require \'nn\'\n\n' + customLayers
+            .map(node => this.getAttribute(node, 'code')).join('\n');
+
+        // Create the custom layers file
+        files['custom-layers.lua'] = code;
+    };
+
+    GenerateJob.prototype.getConnectionContainer = function () {
+        var container = this.core.getParent(this.activeNode);
+
+        if (this.isMetaTypeOf(container, this.META.Job)) {
+            container = this.core.getParent(container);
+        }
+
+        return container;
+    };
+
+    GenerateJob.prototype.getInputPortsFor = function (nodeId) {
+        var container = this.getConnectionContainer();
+
+        // Get the connections to this node
+        return this.core.loadChildren(container)
+            .then(children => {
+                return children.filter(child =>
+                    this.core.getPointerPath(child, 'dst') === nodeId)
+                    .map(conn => this.core.getPointerPath(conn, 'src'))[0];
+            });
+    };
+
+    GenerateJob.prototype.createInputs = function (node, files) {
+        var tplContents,
+            inputs;
+
+        this.logger.info('Retrieving inputs and deserialize fns...');
+        return this.getInputs(node)
+            .then(allInputs => {
+                // For each input, match the connection with the input name
+                //   [ name, type ] => [ name, type, node ]
+                //
+                // For each input,
+                //  - create the deserializer
+                //  - put it in inputs/<name>/init.lua
+                //  - copy the data asset to /inputs/<name>/init.lua
+                inputs = allInputs
+                    .filter(pair => !!this.getAttribute(pair[2], 'data'));  // remove empty inputs
+
+                files.inputAssets = {};  // data assets
+                return Q.all(inputs.map(pair => {
+                    var name = pair[0],
+                        node = pair[2],
+                        nodeId = this.core.getPath(node);
+
+                    // Get the deserialize function. First, try to get it from
+                    // the source method (this guarantees that the correct
+                    // deserialize method is used despite any auto-upcasting
+                    return this.getInputPortsFor(nodeId)
+                        .then(fromNodeId => this.core.loadByPath(this.rootNode, fromNodeId || nodeId))
+                        .then(fromNode => {
+                            var deserFn,
+                                base,
+                                className;
+
+                            deserFn = this.getAttribute(fromNode, 'deserialize');
+
+                            if (this.isMetaTypeOf(node, this.META.Complex)) {
+                                // Complex objects are expected to define their own
+                                // (static) deserialize factory method
+                                base = this.core.getMetaType(node);
+                                className = this.getAttribute(base, 'name');
+                                deserFn = `return ${className}.deserialize(path)`;
+                            }
+
+                            return {
+                                name: name,
+                                code: deserFn
+                            };
+                        });
+                }));
+            })
+            .then(_tplContents => {
+                tplContents = _tplContents;
+                var hashes = inputs.map(pair => {
+                    var hash = this.getAttribute(pair[2], 'data');
+                    files.inputAssets[pair[0]] = hash;
+                    return {
+                        hash: hash,
+                        name: pair[0]
+                    };
+                });
+
+                return Q.all(hashes.map(pair => 
+                    this.blobClient.getMetadata(pair.hash)
+                        .fail(() => {
+                            throw Error(`BLOB_FETCH_FAILED:${pair.name}`);
+                        })));
+            })
+            .then(metadatas => {
+                // Create the deserializer
+                tplContents.forEach((ctnt, i) => {
+                    // Get the name of the given asset
+                    ctnt.filename = metadatas[i].name;
+                    files['inputs/' + ctnt.name + '/init.lua'] = _.template(Templates.DESERIALIZE)(ctnt);
+                });
+                return files;
+            });
+    };
+
+    GenerateJob.prototype.createOutputs = function (node, files) {
+        // For each of the output types, grab their serialization functions and
+        // create the `outputs/init.lua` file
+        this.logger.info('Creating outputs/init.lua...');
+        return this.getOutputs(node)
+            .then(outputs => {
+                var outputTypes = outputs
+                // Get the serialize functions for each
+                    .map(tuple => {
+                        var node = tuple[2],
+                            serFn = this.getAttribute(node, 'serialize');
+
+                        if (this.isMetaTypeOf(node, this.META.Complex)) {
+                            // Complex objects are expected to define their own
+                            // serialize methods
+                            serFn = 'if data ~= nil then data:serialize(path) end';
+                        }
+
+                        return [tuple[1], serFn];
+                    });
+
+                files['outputs/init.lua'] = _.template(Templates.SERIALIZE)({types: outputTypes});
+            });
+    };
+
+    GenerateJob.prototype.createMainFile = function (node, files) {
+        this.logger.info('Creating main file...');
+        return this.getInputs(node)
+            .then(inputs => {
+                var name = this.getAttribute(node, 'name'),
+                    code = this.getAttribute(node, 'code'),
+                    pointers = this.core.getPointerNames(node).filter(ptr => ptr !== 'base'),
+                    content = {
+                        name: name
+                    };
+
+                // Get input data arguments
+                content.inputs = inputs
+                    .map(pair => [pair[0], !this.getAttribute(pair[2], 'data')]);  // remove empty inputs
+
+                // Defined variables for each pointers
+                content.pointers = pointers
+                    .map(id => [id, this.core.getPointerPath(node, id) === null]);
+
+                // Add remaining code
+                content.code = code;
+
+                files['main.lua'] = _.template(Templates.MAIN)(content);
+
+                // Set the line offset
+                var lineOffset = this.getLineOffset(files['main.lua'], code);
+                this.setAttribute(node, CONSTANTS.LINE_OFFSET, lineOffset);
+            });
+    };
+
+    GenerateJob.prototype.getLineOffset = function (main, snippet) {
+        var i = main.indexOf(snippet),
+            lines = main.substring(0, i).match(/\n/g);
+
+        return lines ? lines.length : 0;
+    };
+
+    GenerateJob.prototype.createAttributeFile = function (node, files) {
+        var numOrBool = /^(-?\d+\.?\d*((e|e-)\d+)?|(true|false))$/,
+            table;
+
+        this.logger.info('Creating attributes file...');
+        table = '{\n\t' + this.core.getAttributeNames(node)
+            .filter(attr => SKIP_ATTRIBUTES.indexOf(attr) === -1)
+            .map(name => {
+                var value = this.getAttribute(node, name);
+                if (!numOrBool.test(value)) {
+                    value = `"${value}"`;
+                }
+                return [`['${name}']`, value];
+            })
+            .map(pair => pair.join(' = '))
+            .join(',\n\t') + '\n}';
+
+        files['attributes.lua'] = `-- attributes of ${this.getAttribute(node, 'name')}\nreturn ${table}`;
+    };
+
+    GenerateJob.prototype.createPointers = function (node, files, cb) {
+        var pointers,
+            nIds;
+
+        this.logger.info('Creating pointers file...');
+        pointers = this.core.getPointerNames(node)
+            .filter(name => name !== 'base')
+            .filter(id => this.core.getPointerPath(node, id) !== null);
+
+        nIds = pointers.map(p => this.core.getPointerPath(node, p));
+        files.ptrAssets = {};
+        Q.all(
+            nIds.map(nId => this.getPtrCodeHash(nId))
+        )
+        .then(resultHashes => {
+            var name = this.getAttribute(node, 'name');
+            this.logger.info(`Pointer generation for ${name} FINISHED!`);
+            resultHashes.forEach((hash, index) => {
+                files.ptrAssets[`pointers/${pointers[index]}/init.lua`] = hash;
+            });
+            return cb(null, files);
+        })
+        .fail(e => {
+            this.logger.error(`Could not generate pointer files for ${this.getAttribute(node, 'name')}: ${e.toString()}`);
+            return cb(e);
+        });
+    };
+
+    GenerateJob.prototype.getAttribute = function (node, attr) {
+        return this.core.getAttribute(node, attr);
+    };
+
+    GenerateJob.prototype.setAttribute = function (node, attr, value) {
+        return this.core.setAttribute(node, attr, value);
+    };
+
+    _.extend(
+        GenerateJob.prototype,
+        OperationHelpers.prototype,
+        PtrCodeGen.prototype
+    );
+
+    return GenerateJob;
+});

src/plugins/GenerateJob/metadata.json

@@ -1,6 +1,6 @@
 {
-  "id": "GenerateExecFile",
-  "name": "Generate Execution File",
+  "id": "GenerateJob",
+  "name": "GenerateJob",
   "version": "0.1.0",
   "description": "",
   "icon": {
@@ -11,4 +11,4 @@
   "disableBrowserSideExecution": false,
   "writeAccessRequired": false,
   "configStructure": []
-}
+}