WIP Added istanbul

* Cancel job if the exec has been canceled. Fixes #820

* WIP #820 Added test for stopping watching on cancel

* WIP #820 Increased the timeout for import torch

README.md

@@ -7,7 +7,13 @@
 **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)!
 
 # 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. Currently, it supports Convolutional Neural Networks, RNNs and LSTMs as well as the creation of custom layers. Additional features include:
+- Graphical architecture editor
+- Training/testing pipeline creation
+- Distributed pipeline execution
+- Real-time pipeline feedback
+- Collaborative editing
+- Automatic version control.
 
 ## Quick Start
 Simply run the following command to install deepforge with its dependencies:

config/config.webgme.js

@@ -20,6 +20,7 @@ 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');
 
 
 

package.json

@@ -9,10 +9,11 @@
     "local": "node ./bin/start-local.js",
     "worker": "node ./bin/start-worker.js",
     "test": "mkdir ./test-tmp; node ./node_modules/mocha/bin/mocha --recursive test",
+    "test-cover": "node node_modules/istanbul/lib/cli.js --hook-run-in-context cover node_modules/mocha/bin/_mocha -- -R spec test/**/*",
     "watch-test": "./node_modules/nodemon/bin/nodemon.js --exec 'node ./node_modules/mocha/bin/mocha --recursive test'",
     "build-nn": "node ./utils/nn-parser.js"
   },
-  "version": "0.15.0",
+  "version": "0.16.0",
   "dependencies": {
     "commander": "^2.9.0",
     "dotenv": "^2.0.0",
@@ -35,6 +36,7 @@
     "chai": "^3.0.0",
     "jszip": "^2.5.0",
     "mocha": "^2.2.5",
+    "istanbul": "^0.4.5",
     "mockery": "^1.7.0"
   }
 }

src/common/plugin/LocalExecutor.js

@@ -20,13 +20,13 @@ define([
                 var output = cntrs
                     .find(cntr => {
                         var metaNode = this.core.getMetaType(cntr),
-                            metaName = this.core.getAttribute(metaNode, 'name');
+                            metaName = this.getAttribute(metaNode, 'name');
                         return metaName === 'Outputs';
                     });
                 return this.core.loadChildren(output);
             })
             .then(dataNodes => {
-                hash = this.core.getAttribute(dataNodes[0], 'data');
+                hash = this.getAttribute(dataNodes[0], 'data');
                 return this.getOutputs(node);
             })
             .then(outputTuples => {
@@ -48,7 +48,7 @@ define([
         var hash,
             typeId = this.core.getPointerPath(node, 'type'),
             type,
-            artifactName = this.core.getAttribute(node, 'artifactName');
+            artifactName = this.getAttribute(node, 'artifactName');
 
         return this.core.loadByPath(this.rootNode, typeId)
             .then(_type => {
@@ -58,25 +58,20 @@ define([
             .then(saveDir => this.core.loadChildren(saveDir))
             .then(artifacts => {
                 return artifacts.find(artifact =>
-                    this.core.getAttribute(artifact, 'name') === artifactName &&
+                    this.getAttribute(artifact, 'name') === artifactName &&
                         this.isMetaTypeOf(artifact, type));
             })
             .then(matchingArtifact => {
-                hash = matchingArtifact && this.core.getAttribute(matchingArtifact, 'data');
+                hash = matchingArtifact && this.getAttribute(matchingArtifact, 'data');
                 // If no hash, just continue (the subsequent ops will receive 'nil')
                 if (!hash) {
                     return this.onOperationComplete(node);
                 } else {
                     return this.getOutputs(node)
                         .then(outputPairs => {
-                            var outputs = outputPairs.map(pair => pair[2]),
-                                paths;
-
-                            paths = outputs.map(output => this.core.getPath(output));
+                            var outputs = outputPairs.map(pair => pair[2]);
                             // Get the 'data' hash and store it in the output data ports
-                            this.logger.info(`Loading blob data (${hash}) to ${paths.map(p => `"${p}"`)}`);
-
-                            outputs.forEach(output => this.core.setAttribute(output, 'data', hash));
+                            outputs.forEach(output => this.setAttribute(output, 'data', hash));
 
                             this.onOperationComplete(node);
                         });
@@ -99,7 +94,7 @@ define([
 
                 if (containers.length > 1) {
                     saveDir = containers.find(c =>
-                        this.core.getAttribute(c, 'name').toLowerCase().indexOf('artifacts') > -1
+                        this.getAttribute(c, 'name').toLowerCase().indexOf('artifacts') > -1
                     ) || containers[0];
                 }
 
@@ -121,8 +116,8 @@ define([
             .then(artifacts => {
                 currNameHashPairs = artifacts
                     .map(node => [
-                        this.core.getAttribute(node, 'name'),
-                        this.core.getAttribute(node, 'data')
+                        this.getAttribute(node, 'name'),
+                        this.getAttribute(node, 'data')
                     ]);
                 return this.getInputs(node);
             })
@@ -142,9 +137,9 @@ define([
 
                 // Remove nodes that already exist
                 dataNodes = allDataNodes.filter(dataNode => {
-                    var hash = this.core.getAttribute(dataNode, 'data'),
+                    var hash = this.getAttribute(dataNode, 'data'),
                         name = this.core.getOwnAttribute(node, 'saveName') ||
-                            this.core.getAttribute(dataNode, 'name');
+                            this.getAttribute(dataNode, 'name');
 
                     return !(currNameHashPairs
                         .find(pair => pair[0] === name && pair[1] === hash));
@@ -156,10 +151,10 @@ define([
                         newName = this.core.getOwnAttribute(node, 'saveName');
                     if (newName) {
                         newNodes.forEach(node =>
-                            this.core.setAttribute(node, 'name', newName)
+                            this.setAttribute(node, 'name', newName)
                         );
                     }
-                    var hashes = dataNodes.map(n => this.core.getAttribute(n, 'data'));
+                    var hashes = dataNodes.map(n => this.getAttribute(n, 'data'));
                     this.logger.info(`saving hashes: ${hashes.map(h => `"${h}"`)}`);
                 } else if (allDataNodes.length === 0) {
                     this.logger.warn('No data nodes found!');

src/plugins/ExecuteJob/ExecuteJob.js

@@ -2,6 +2,7 @@
 /*jshint node:true, browser:true*/
 
 define([
+    'common/util/assert',
     'common/storage/constants',
     'text!./metadata.json',
     'executor/ExecutorClient',
@@ -15,6 +16,7 @@ define([
     'q',
     'underscore'
 ], function (
+    assert,
     STORAGE_CONSTANTS,
     pluginMetadata,
     ExecutorClient,
@@ -33,7 +35,9 @@ define([
     pluginMetadata = JSON.parse(pluginMetadata);
 
     var OUTPUT_INTERVAL = 1500,
-        STDOUT_FILE = 'job_stdout.txt';
+        STDOUT_FILE = 'job_stdout.txt',
+        CREATE_PREFIX = 'created_node_',
+        INDEX = 1;
 
     /**
      * Initializes a new instance of ExecuteJob.
@@ -53,7 +57,12 @@ define([
         this._oldMetadataByName = {};  // name -> id
         this.lastAppliedCmd = {};
         this.canceled = false;
+
         this.changes = {};
+        this.currentChanges = {};  // read-only changes being applied
+        this.creations = {};
+        this.deletions = [];
+        this.createIdToMetadataId = {};
         this.logManager = null;
     };
 
@@ -69,6 +78,18 @@ define([
     ExecuteJob.prototype = Object.create(PluginBase.prototype);
     ExecuteJob.prototype.constructor = ExecuteJob;
 
+    ExecuteJob.prototype.configure = function () {
+        var result = PluginBase.prototype.configure.apply(this, arguments);
+
+        this.logManager = new JobLogsClient({
+            logger: this.logger,
+            port: this.gmeConfig.server.port,
+            branchName: this.branchName,
+            projectId: this.projectId
+        });
+        return result;
+    };
+
     /**
      * Main function for the plugin to execute. This will perform the execution.
      * Notes:
@@ -81,19 +102,21 @@ define([
     ExecuteJob.prototype.main = function (callback) {
         // Check the activeNode to make sure it is a valid node
         var type = this.core.getMetaType(this.activeNode),
-            typeName = type && this.getAttribute(type, 'name');
+            typeName = type && this.getAttribute(type, 'name'),
+            execNode,
+            status;
 
         if (typeName !== 'Job') {
             return callback(`Cannot execute ${typeName} (expected Job)`, this.result);
         }
 
-        // Get the gmeConfig...
-        this.logManager = new JobLogsClient({
-            logger: this.logger,
-            port: this.gmeConfig.server.port,
-            branchName: this.branchName,
-            projectId: this.projectId
-        });
+        // Set the parent execution to 'running'
+        execNode = this.core.getParent(this.activeNode);
+        status = this.getAttribute(execNode, 'status');
+        if (status !== 'running') {
+            this.setAttribute(execNode, 'status', 'running');
+        }
+
         this._callback = callback;
         this.currentForkName = null;
         this.prepare()
@@ -117,12 +140,51 @@ define([
         });
     };
 
+    //////////////////////////// Safe Save ////////////////////////////
+    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 = this.core.getPath(node);
+        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] = {};
@@ -131,32 +193,53 @@ define([
     };
 
     ExecuteJob.prototype.getAttribute = function (node, attr) {
-        var nodeId = this.core.getPath(node),
-            base,
-            baseId;
+        var nodeId;
 
-        // Check the changes; fallback on actual node
-        if (this.changes[nodeId] && this.changes[nodeId][attr] !== undefined) {
-            // If deleted the attribute, get the default (inherited) value
-            if (this.changes[nodeId][attr] === null) {
-                base = this.core.getBase(node);
-                baseId = this.core.getPath(base);
-                return this.getAttribute(baseId, attr);
-            }
-            return this.changes[nodeId][attr];
+        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);
@@ -165,6 +248,12 @@ define([
         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,
@@ -175,6 +264,8 @@ define([
             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]]);
@@ -183,27 +274,165 @@ define([
                 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 => {
-            for (var i = nodes.length; i--;) {
-                id = this.core.getPath(nodes[i]);
-                this._applyNodeChanges(nodes[i], changesFor[id]);
+            // 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) {
         var name = this.getAttribute(this.activeNode, 'name');
+
         return this.updateForkName(name)
-            .then(() => this.applyChanges())
+            .then(() => this.applyModelChanges())
             .then(() => PluginBase.prototype.save.call(this, msg))
             .then(result => {
-                var msg;
+                this.logger.info(`Save finished w/ status: ${result.status}`);
                 if (result.status === STORAGE_CONSTANTS.FORKED) {
                     msg = `"${name}" execution has forked to "${result.forkName}"`;
                     this.currentForkName = result.forkName;
@@ -228,9 +457,37 @@ define([
                 this.rootNode = rootObject;
                 return this.core.loadByPath(rootObject,activeId);
             })
-            .then(activeObject => this.activeNode = activeObject);
+            .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);
+    };
+
+    //////////////////////////// END Safe Save ////////////////////////////
+
     ExecuteJob.prototype.getConnections = function (nodes) {
         var conns = [];
         for (var i = nodes.length; i--;) {
@@ -279,7 +536,8 @@ define([
             idsToDelete = [],
             type,
             base,
-            child;
+            child,
+            i;
 
         this.lastAppliedCmd[nodeId] = 0;
         this._oldMetadataByName[nodeId] = {};
@@ -287,7 +545,7 @@ define([
         return this.core.loadChildren(job)
             .then(jobChildren => {
                 // Remove any metadata nodes
-                for (var i = jobChildren.length; i--;) {
+                for (i = jobChildren.length; i--;) {
                     child = jobChildren[i];
                     if (this.isMetaTypeOf(child, this.META.Metadata)) {
                         id = this.core.getPath(child);
@@ -310,18 +568,22 @@ define([
                 }
 
                 // make the deletion ids relative to the job node
-                idsToDelete = idsToDelete.map(id => id.replace(nodeId, ''));
-                return Q.all(idsToDelete.map(id => this.core.loadByPath(job, id)));
-            })
-            .then(nodes => nodes.forEach(node => this.core.deleteNode(node)));
+                this.logger.debug(`About to delete ${idsToDelete.length}: ${idsToDelete.join(', ')}`);
+                for (i = idsToDelete.length; i--;) {
+                    this.deleteNode(idsToDelete[i]);
+                }
+            });
     };
 
     ExecuteJob.prototype.clearOldMetadata = function (job) {
         var nodeId = this.core.getPath(job),
-            nodeIds = Object.keys(this._markForDeletion[nodeId]);
+            nodeIds = Object.keys(this._markForDeletion[nodeId]),
+            node;
 
+        this.logger.debug(`About to delete ${nodeIds.length}: ${nodeIds.join(', ')}`);
         for (var i = nodeIds.length; i--;) {
-            this.core.deleteNode(this._markForDeletion[nodeId][nodeIds[i]]);
+            node = this._markForDeletion[nodeId][nodeIds[i]];
+            this.deleteNode(this.core.getPath(node));
         }
         delete this.lastAppliedCmd[nodeId];
         delete this._markForDeletion[nodeId];
@@ -472,20 +734,32 @@ define([
                 })
                 .then(mds => {
                     // Record the large files
-                    var inputData = {};
+                    var inputData = {},
+                        runsh = '# Bash script to download data files and run job\n' +
+                        'if [ -z "$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];
+                            hash = files.inputAssets[input],
+                            dataPath = 'inputs/' + input + '/data',
+                            url = this.blobClient.getRelativeDownloadURL(hash);
 
-                        inputData['inputs/' + input + '/data'] = {
+                        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)
@@ -865,8 +1139,8 @@ define([
     };
 
     ExecuteJob.prototype.createAttributeFile = function (node, files) {
-        var skip = ['code'],
-            numRegex = /^\d+\.?\d*((e|e-)\d+)?$/,
+        var skip = ['code', 'stdout', 'execFiles', 'jobId', 'secret'],
+            numOrBool = /^(-?\d+\.?\d*((e|e-)\d+)?|(true|false))$/,
             table;
 
         this.logger.info('Creating attributes file...');
@@ -874,7 +1148,7 @@ define([
             .filter(attr => skip.indexOf(attr) === -1)
             .map(name => {
                 var value = this.getAttribute(node, name);
-                if (!numRegex.test(value)) {
+                if (!numOrBool.test(value)) {
                     value = `"${value}"`;
                 }
                 return [name, value];
@@ -920,6 +1194,11 @@ define([
         });
     };
 
+    ExecuteJob.prototype.isExecutionCanceled = function () {
+        var execNode = this.core.getParent(this.activeNode);
+        return this.getAttribute(execNode, 'status') === 'canceled';
+    };
+
     ExecuteJob.prototype.watchOperation = function (executor, hash, op, job) {
         var jobId = this.core.getPath(job),
             opId = this.core.getPath(op),
@@ -928,7 +1207,7 @@ define([
             name = this.getAttribute(job, 'name');
 
         // If canceled, stop the operation
-        if (this.canceled) {
+        if (this.canceled || this.isExecutionCanceled()) {
             secret = this.getAttribute(job, 'secret');
             if (secret) {
                 executor.cancelJob(hash, secret);
@@ -954,6 +1233,7 @@ define([
                                 last = stdout.lastIndexOf('\n'),
                                 result,
                                 lastLine,
+                                next = Q(),
                                 msg;
 
                             // parse deepforge commands
@@ -967,13 +1247,15 @@ define([
 
                             if (output) {
                                 // Send notification to all clients watching the branch
-                                this.logManager.appendTo(jobId, output)
+                                next = next
+                                    .then(() => this.logManager.appendTo(jobId, output))
                                     .then(() => this.notifyStdoutUpdate(jobId));
                             }
                             if (result.hasMetadata) {
                                 msg = `Updated graph/image output for ${name}`;
-                                return this.save(msg);
+                                next = next.then(() => this.save(msg));
                             }
+                            return next;
                         });
                 }
             })
@@ -1186,14 +1468,12 @@ define([
         // Check if the graph already exists
         graph = this._getExistingMetadata(jobId, 'Graph', name);
         if (!graph) {
-            graph = this.core.createNode({
-                base: this.META.Graph,
-                parent: job
-            });
+            graph = this.createNode('Graph', job);
 
             if (name) {
                 this.setAttribute(graph, 'name', name);
             }
+            this.createIdToMetadataId[graph] = id;
         }
 
         this._metadata[id] = graph;
@@ -1201,25 +1481,25 @@ define([
 
     ExecuteJob.prototype[CONSTANTS.GRAPH_PLOT] = function (job, id, x, y) {
         var jobId = this.core.getPath(job),
-            nonNum = /[^\d\.]*/g,
-            graph,
+            nonNum = /[^\d-\.]*/g,
+            line,
             points;
             
 
         id = jobId + '/' + id;
         this.logger.info(`Adding point ${x}, ${y} to ${id}`);
-        graph = this._metadata[id];
-        if (!graph) {
-            this.logger.warn(`Can't add point to non-existent graph: ${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(graph, 'points');
+        points = this.getAttribute(line, 'points');
         points += `${x},${y};`;
-        this.setAttribute(graph, 'points', points);
+        this.setAttribute(line, 'points', points);
     };
 
     ExecuteJob.prototype[CONSTANTS.GRAPH_CREATE_LINE] = function (job, graphId, id) {
@@ -1230,12 +1510,10 @@ define([
 
         // Create a 'line' node in the given Graph metadata node
         name = name.replace(/\s+$/, '');
-        line = this.core.createNode({
-            base: this.META.Line,
-            parent: graph
-        });
+        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] =
@@ -1265,11 +1543,9 @@ define([
             imageNode = this._getExistingMetadata(jobId, 'Image', name);
             if (!imageNode) {
                 this.logger.info(`Creating image ${id} named ${name}`);
-                imageNode = this.core.createNode({
-                    base: this.META.Image,
-                    parent: job
-                });
+                imageNode = this.createNode('Image', job);
                 this.setAttribute(imageNode, 'name', name);
+                this.createIdToMetadataId[imageNode] = id;
             }
             this._metadata[id] = imageNode;
         }

src/plugins/ExecutePipeline/ExecutePipeline.js

@@ -37,6 +37,10 @@ define([
 
         this._currentSave = Q();
         this.changes = {};
+        this.currentChanges = {};  // read-only changes being applied
+        this.creations = {};
+        this.deletions = [];
+        this.createIdToMetadataId = {};
         this.initRun();
     };
 
@@ -149,7 +153,7 @@ define([
         // before continuing
         this._currentSave = this._currentSave
             .then(() => this.updateForkName(this.pipelineName))
-            .then(() => this.applyChanges())
+            .then(() => this.applyModelChanges())
             .then(() => CreateExecution.prototype.save.call(this, msg))
             .then(result => {
                 var msg;
@@ -185,6 +189,10 @@ 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);

src/routers/JobLogsAPI/JobLogManager.js

@@ -12,7 +12,7 @@ var JobLogManager = function(logger, config) {
 };
 
 JobLogManager.prototype._getFilePath = function(jInfo) {
-    this.logger.info(`getting file path for ${jInfo.job} in ${jInfo.project} on ${jInfo.branch}`);
+    this.logger.debug(`getting file path for ${jInfo.job} in ${jInfo.project} on ${jInfo.branch}`);
     var jobId = jInfo.job.replace(/\//g, '_'),
         filename = `${jobId}.txt`;
 
@@ -123,7 +123,7 @@ JobLogManager.prototype.appendTo = function(jobInfo, logs) {
 JobLogManager.prototype.getLog = function(jobInfo) {
     var filename = this._getFilePath(jobInfo);
 
-    this.logger.info(`Getting log content to ${filename}`);
+    this.logger.info(`Getting log content from ${filename}`);
     return this.exists(jobInfo)
         .then(exists => {
             if (exists) {

test/plugins/ExecuteJob/ExecuteJob.spec.js

@@ -10,12 +10,14 @@ describe('ExecuteJob', function () {
         PluginCliManager = testFixture.WebGME.PluginCliManager,
         projectName = 'testProject',
         pluginName = 'ExecuteJob',
+        manager = new PluginCliManager(null, logger, gmeConfig),
         project,
         gmeAuth,
         storage,
         commitHash;
 
     before(function (done) {
+        this.timeout(10000);
         testFixture.clearDBAndGetGMEAuth(gmeConfig, projectName)
             .then(function (gmeAuth_) {
                 gmeAuth = gmeAuth_;
@@ -25,7 +27,7 @@ describe('ExecuteJob', function () {
             })
             .then(function () {
                 var importParam = {
-                    projectSeed: testFixture.path.join(testFixture.SEED_DIR, 'EmptyProject.webgmex'),
+                    projectSeed: testFixture.path.join(testFixture.DF_SEED_DIR, 'devProject', 'devProject.webgmex'),
                     projectName: projectName,
                     branchName: 'master',
                     logger: logger,
@@ -51,9 +53,7 @@ describe('ExecuteJob', function () {
     });
 
     it('should verify activeNode is "Job"', function (done) {
-        var manager = new PluginCliManager(null, logger, gmeConfig),
-            pluginConfig = {
-            },
+        var pluginConfig = {},
             context = {
                 project: project,
                 commitHash: commitHash,
@@ -68,4 +68,285 @@ describe('ExecuteJob', function () {
             done();
         });
     });
+
+    ////////// Helper Functions //////////
+    var plugin,
+        node,
+        preparePlugin = function(done) {
+            var context = {
+                project: project,
+                commitHash: commitHash,
+                branchName: 'test',
+                activeNode: '/K/R/p'  // hello world job
+            };
+
+            return manager.initializePlugin(pluginName)
+                .then(plugin_ => {
+                    plugin = plugin_;
+                    return manager.configurePlugin(plugin, {}, context);
+                })
+                .then(() => node = plugin.activeNode)
+                .nodeify(done);
+        };
+
+    ////////// END Helper Functions //////////
+
+    // Race condition checks w/ saving...
+    describe('get/set', function() {
+        beforeEach(preparePlugin);
+
+        it('should get correct attribute after set', function() {
+            plugin.setAttribute(node, 'status', 'queued');
+            var attrValue = plugin.getAttribute(node, 'status');
+            expect(attrValue).to.equal('queued');
+        });
+
+        it('should get correct attribute before updating nodes', function(done) {
+            // Run setAttribute on some node
+            plugin.setAttribute(node, 'status', 'queued');
+
+            // Check that the value is correct before applying node changes
+            var updateNodes = plugin.updateNodes;
+            plugin.updateNodes = function() {
+                var attrValue = plugin.getAttribute(node, 'status');
+                expect(attrValue).to.equal('queued');
+                return updateNodes.apply(this, arguments);
+            };
+            plugin.save().nodeify(done);
+        });
+
+        it('should get correct attribute (from new node) before updating nodes', function(done) {
+            // Run setAttribute on some node
+            var graphTmp = plugin.createNode('pipeline.Graph', node),
+                newVal = 'testGraph',
+                id = 'testId';
+
+            // Get the 
+            plugin.setAttribute(graphTmp, 'name', newVal);
+            plugin._metadata[id] = graphTmp;
+            plugin.createIdToMetadataId[graphTmp] = id;
+
+            // Check that the value is correct before applying node changes
+            var updateNodes = plugin.updateNodes;
+            plugin.updateNodes = function() {
+                var graph = plugin._metadata[id],
+                    attrValue = plugin.getAttribute(graph, 'name');
+
+                expect(attrValue).to.equal(newVal);
+                return updateNodes.apply(this, arguments);
+            };
+            plugin.save().nodeify(done);
+        });
+
+        it('should get correct attribute after save', function(done) {
+            // Run setAttribute on some node
+            plugin.setAttribute(node, 'status', 'queued');
+
+            // Check that the value is correct before applying node changes
+            plugin.save()
+                .then(() => {
+                    var attrValue = plugin.getAttribute(node, 'status');
+                    expect(attrValue).to.equal('queued');
+                })
+                .nodeify(done);
+        });
+
+        it('should get correct attribute while applying node changes', function(done) {
+            // Run setAttribute on some node
+            plugin.setAttribute(node, 'status', 'queued');
+
+            // Check that the value is correct before applying node changes
+            var oldApplyChanges = plugin._applyNodeChanges;
+            plugin._applyNodeChanges = function() {
+                var attrValue = plugin.getAttribute(node, 'status');
+                expect(attrValue).to.equal('queued');
+                return oldApplyChanges.apply(this, arguments);
+            };
+            plugin.save().nodeify(done);
+        });
+    });
+
+    describe('createNode', function() {
+        beforeEach(preparePlugin);
+
+        it('should update _metadata after applying changes', function(done) {
+            // Run setAttribute on some node
+            var graphTmp = plugin.createNode('pipeline.Graph', node),
+                id = 'testId';
+
+            plugin._metadata[id] = graphTmp;
+            plugin.createIdToMetadataId[graphTmp] = id;
+
+            // Check that the value is correct before applying node changes
+            var applyModelChanges = plugin.applyModelChanges;
+            plugin.applyModelChanges = function() {
+                return applyModelChanges.apply(this, arguments)
+                    .then(() => {
+                        var graph = plugin._metadata[id];
+                        expect(graph).to.not.equal(graphTmp);
+                    });
+            };
+            plugin.save().nodeify(done);
+        });
+
+        it('should update _metadata in updateNodes', function(done) {
+            var id = 'testId';
+
+            plugin._metadata[id] = node;
+            node.old = true;
+            plugin.updateNodes()
+                    .then(() => {
+                        var graph = plugin._metadata[id];
+                        expect(graph.old).to.not.equal(true);
+                    })
+                    .nodeify(done);
+        });
+
+        // Check that it gets the correct value from a newly created node after
+        // it has been saved/created
+        it('should get changed attribute', function(done) {
+            // Run setAttribute on some node
+            var graphTmp = plugin.createNode('pipeline.Graph', node),
+                id = 'testId';
+
+            plugin._metadata[id] = node;
+            plugin.createIdToMetadataId[graphTmp] = id;
+
+            plugin.setAttribute(graphTmp, 'name', 'firstName');
+
+            // Check that the value is correct before applying node changes
+            plugin.save()
+                .then(() => {
+                    var graph = plugin._metadata[id],
+                        val = plugin.getAttribute(graph, 'name');
+                    expect(val).to.equal('firstName');
+                })
+                .nodeify(done);
+        });
+
+        it('should get inherited attribute', function(done) {
+            // Run setAttribute on some node
+            var graphTmp = plugin.createNode('pipeline.Graph', node),
+                id = 'testId',
+                val;
+
+            // Check that the value is correct before applying node changes
+            plugin._metadata[id] = node;
+            plugin.createIdToMetadataId[graphTmp] = id;
+
+            val = plugin.getAttribute(graphTmp, 'name');
+            expect(val).to.equal('Graph');
+
+            plugin.save()
+                .then(() => {
+                    var graph = plugin._metadata[id];
+
+                    val = plugin.getAttribute(graph, 'name');
+
+                    expect(val).to.equal('Graph');
+                })
+                .nodeify(done);
+        });
+    });
+
+    // Canceling
+    describe('cancel', function() {
+        beforeEach(preparePlugin);
+
+        it('should stop the job if the execution is canceled', function(done) {
+            var job = node,
+                hash = 'abc123',
+                exec = {
+                    cancelJob: jobHash => expect(jobHash).equal(hash)
+                };
+
+            plugin.setAttribute(node, 'secret', 'abc');
+            plugin.isExecutionCanceled = () => true;
+            plugin.onOperationCanceled = () => done();
+            plugin.watchOperation(exec, hash, job, job);
+        });
+
+        it('should stop the job if a job is canceled', function(done) {
+            var job = node,
+                hash = 'abc123',
+                exec = {
+                    cancelJob: jobHash => expect(jobHash).equal(hash)
+                };
+
+            plugin.setAttribute(job, 'secret', 'abc');
+            plugin.canceled = true;
+            plugin.onOperationCanceled = () => done();
+            plugin.watchOperation(exec, hash, job, job);
+        });
+
+        it('should set exec to running', function(done) {
+            var job = node,
+                execNode = plugin.core.getParent(job);
+
+            // Set the execution to canceled
+            plugin.setAttribute(execNode, 'status', 'canceled');
+            plugin.prepare = () => {
+                var status = plugin.getAttribute(execNode, 'status');
+                expect(status).to.not.equal('canceled');
+                return {then: () => done()};
+            };
+            plugin.main();
+        });
+    });
+
+    describe('exec files', function() {
+        describe('attribute file', function() {
+            var boolString = /['"](true|false)['"]/g;
+
+            beforeEach(preparePlugin);
+
+            it('should not quote true (s) boolean values', function() {
+                var files = {},
+                    content,
+                    matches;
+
+                plugin.setAttribute(node, 'debug', 'true');
+                plugin.createAttributeFile(node, files);
+                content = files['attributes.lua'];
+                matches = content.match(boolString);
+                expect(matches).to.equal(null);
+            });
+
+            it('should not quote true boolean values', function() {
+                var files = {},
+                    content,
+                    matches;
+
+                plugin.setAttribute(node, 'debug', true);
+                plugin.createAttributeFile(node, files);
+                content = files['attributes.lua'];
+                matches = content.match(boolString);
+                expect(matches).to.equal(null);
+            });
+
+            it('should not quote false (s) boolean values', function() {
+                var files = {},
+                    content,
+                    matches;
+
+                plugin.setAttribute(node, 'debug', 'false');
+                plugin.createAttributeFile(node, files);
+                content = files['attributes.lua'];
+                matches = content.match(boolString);
+                expect(matches).to.equal(null);
+            });
+
+            it('should not quote false boolean values', function() {
+                var files = {},
+                    content,
+                    matches;
+
+                plugin.setAttribute(node, 'debug', false);
+                plugin.createAttributeFile(node, files);
+                content = files['attributes.lua'];
+                matches = content.match(boolString);
+                expect(matches).to.equal(null);
+            });
+        });
+    });
 });

test/plugins/ImportTorch/ImportTorch.spec.js

@@ -14,7 +14,7 @@ var testFixture = require('../../globals'),
     ];
 
 describe('ImportTorch', function () {
-    this.timeout(5000);
+    this.timeout(7500);
     var gmeConfig = testFixture.getGmeConfig(),
         Q = testFixture.Q,
         GraphChecker = testFixture.requirejs('deepforge/GraphChecker'),

webgme-setup.json

@@ -280,6 +280,9 @@
       },
       "xor": {
         "src": "src/seeds/xor"
+      },
+      "devProject": {
+        "src": "src/seeds/devProject"
       }
     },
     "routers": {