Current Dev State

static/js/ketcher2/node_modules/orchestrator/LICENSE

@@ -0,0 +1,20 @@
+Copyright (c) 2013 [Richardson & Sons, LLC](http://richardsonandsons.com/)
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

static/js/ketcher2/node_modules/orchestrator/README.md

@@ -0,0 +1,286 @@
+[![Build Status](https://secure.travis-ci.org/robrich/orchestrator.svg?branch=master)](https://travis-ci.org/robrich/orchestrator)
+[![Dependency Status](https://david-dm.org/robrich/orchestrator.svg)](https://david-dm.org/robrich/orchestrator)
+
+Orchestrator
+============
+
+A module for sequencing and executing tasks and dependencies in maximum concurrency
+
+Usage
+-----
+
+### 1. Get a reference:
+
+```javascript
+var Orchestrator = require('orchestrator');
+var orchestrator = new Orchestrator();
+```
+
+### 2. Load it up with stuff to do:
+
+```javascript
+orchestrator.add('thing1', function(){
+  // do stuff
+});
+orchestrator.add('thing2', function(){
+  // do stuff
+});
+```
+
+### 3. Run the tasks:
+
+```javascript
+orchestrator.start('thing1', 'thing2', function (err) {
+  // all done
+});
+```
+
+API
+---
+
+### orchestrator.add(name[, deps][, function]);
+
+Define a task
+
+```javascript
+orchestrator.add('thing1', function(){
+  // do stuff
+});
+```
+
+#### name
+Type: `String`
+
+The name of the task.
+
+#### deps
+Type: `Array`
+
+An array of task names to be executed and completed before your task will run.
+
+```javascript
+orchestrator.add('mytask', ['array', 'of', 'task', 'names'], function() {
+  // Do stuff
+});
+```
+
+**Note:** Are your tasks running before the dependencies are complete?  Make sure your dependency tasks
+are correctly using the async run hints: take in a callback or return a promise or event stream.
+
+#### fn
+Type: `function`
+
+The function that performs the task's operations.  For asynchronous tasks, you need to provide a hint when the task is complete:
+
+- Take in a callback
+- Return a stream or a promise
+
+#### examples:
+
+**Accept a callback:**
+
+```javascript
+orchestrator.add('thing2', function(callback){
+  // do stuff
+  callback(err);
+});
+```
+
+**Return a promise:**
+
+```javascript
+var Q = require('q');
+
+orchestrator.add('thing3', function(){
+  var deferred = Q.defer();
+
+  // do async stuff
+  setTimeout(function () {
+    deferred.resolve();
+  }, 1);
+
+  return deferred.promise;
+});
+```
+
+**Return a stream:** (task is marked complete when stream ends)
+
+```javascript
+var map = require('map-stream');
+
+orchestrator.add('thing4', function(){
+  var stream = map(function (args, cb) {
+    cb(null, args);
+  });
+  // do stream stuff
+  return stream;
+});
+```
+
+**Note:** By default, tasks run with maximum concurrency -- e.g. it launches all the tasks at once and waits for nothing.
+If you want to create a series where tasks run in a particular order, you need to do two things:
+
+- give it a hint to tell it when the task is done,
+- and give it a hint that a task depends on completion of another.
+
+For these examples, let's presume you have two tasks, "one" and "two" that you specifically want to run in this order:
+
+1. In task "one" you add a hint to tell it when the task is done.  Either take in a callback and call it when you're
+done or return a promise or stream that the engine should wait to resolve or end respectively.
+
+2. In task "two" you add a hint telling the engine that it depends on completion of the first task.
+
+So this example would look like this:
+
+```javascript
+var Orchestrator = require('orchestrator');
+var orchestrator = new Orchestrator();
+
+// takes in a callback so the engine knows when it'll be done
+orchestrator.add('one', function (cb) {
+    // do stuff -- async or otherwise
+    cb(err); // if err is not null or undefined, the orchestration will stop, and note that it failed
+});
+
+// identifies a dependent task must be complete before this one begins
+orchestrator.add('two', ['one'], function () {
+    // task 'one' is done now
+});
+
+orchestrator.start('one', 'two');
+```
+
+### orchestrator.hasTask(name);
+
+Have you defined a task with this name?
+
+#### name
+Type: `String`
+
+The task name to query
+
+### orchestrator.start(tasks...[, cb]);
+
+Start running the tasks
+
+#### tasks
+Type: `String` or `Array` of `String`s
+
+Tasks to be executed. You may pass any number of tasks as individual arguments.
+
+#### cb
+Type: `function`: `function (err) {`
+
+Callback to call after run completed.
+
+Passes single argument: `err`: did the orchestration succeed?
+
+**Note:** Tasks run concurrently and therefore may not complete in order.
+**Note:** Orchestrator uses `sequencify` to resolve dependencies before running, and therefore may not start in order.
+Listen to orchestration events to watch task running.
+
+```javascript
+orchestrator.start('thing1', 'thing2', 'thing3', 'thing4', function (err) {
+  // all done
+});
+```
+```javascript
+orchestrator.start(['thing1','thing2'], ['thing3','thing4']);
+```
+
+**FRAGILE:** Orchestrator catches exceptions on sync runs to pass to your callback
+but doesn't hook to process.uncaughtException so it can't pass those exceptions
+to your callback
+
+**FRAGILE:** Orchestrator will ensure each task and each dependency is run once during an orchestration run
+even if you specify it to run more than once. (e.g. `orchestrator.start('thing1', 'thing1')`
+will only run 'thing1' once.) If you need it to run a task multiple times, wait for
+the orchestration to end (start's callback) then call start again.
+(e.g. `orchestrator.start('thing1', function () {orchestrator.start('thing1');})`.)
+Alternatively create a second orchestrator instance.
+
+### orchestrator.stop()
+
+Stop an orchestration run currently in process
+
+**Note:** It will call the `start()` callback with an `err` noting the orchestration was aborted
+
+### orchestrator.on(event, cb);
+
+Listen to orchestrator internals
+
+#### event
+Type: `String`
+
+Event name to listen to:
+- start: from start() method, shows you the task sequence
+- stop: from stop() method, the queue finished successfully
+- err: from stop() method, the queue was aborted due to a task error
+- task_start: from _runTask() method, task was started
+- task_stop: from _runTask() method, task completed successfully
+- task_err: from _runTask() method, task errored
+- task_not_found: from start() method, you're trying to start a task that doesn't exist
+- task_recursion: from start() method, there are recursive dependencies in your task list
+
+#### cb
+Type: `function`: `function (e) {`
+
+Passes single argument: `e`: event details
+
+```javascript
+orchestrator.on('task_start', function (e) {
+  // e.message is the log message
+  // e.task is the task name if the message applies to a task else `undefined`
+  // e.err is the error if event is 'err' else `undefined`
+});
+// for task_end and task_err:
+orchestrator.on('task_stop', function (e) {
+  // e is the same object from task_start
+  // e.message is updated to show how the task ended
+  // e.duration is the task run duration (in seconds)
+});
+```
+
+**Note:** fires either *stop or *err but not both.
+
+### orchestrator.onAll(cb);
+
+Listen to all orchestrator events from one callback
+
+#### cb
+Type: `function`: `function (e) {`
+
+Passes single argument: `e`: event details
+
+```javascript
+orchestrator.onAll(function (e) {
+  // e is the original event args
+  // e.src is event name
+});
+```
+
+LICENSE
+-------
+
+(MIT License)
+
+Copyright (c) 2013-2015 [Richardson & Sons, LLC](http://richardsonandsons.com/)
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

static/js/ketcher2/node_modules/orchestrator/index.js

@@ -0,0 +1,304 @@
+/*jshint node:true */
+
+"use strict";
+
+var util = require('util');
+var events = require('events');
+var EventEmitter = events.EventEmitter;
+var runTask = require('./lib/runTask');
+
+var Orchestrator = function () {
+	EventEmitter.call(this);
+	this.doneCallback = undefined; // call this when all tasks in the queue are done
+	this.seq = []; // the order to run the tasks
+	this.tasks = {}; // task objects: name, dep (list of names of dependencies), fn (the task to run)
+	this.isRunning = false; // is the orchestrator running tasks? .start() to start, .stop() to stop
+};
+util.inherits(Orchestrator, EventEmitter);
+
+	Orchestrator.prototype.reset = function () {
+		if (this.isRunning) {
+			this.stop(null);
+		}
+		this.tasks = {};
+		this.seq = [];
+		this.isRunning = false;
+		this.doneCallback = undefined;
+		return this;
+	};
+	Orchestrator.prototype.add = function (name, dep, fn) {
+		if (!fn && typeof dep === 'function') {
+			fn = dep;
+			dep = undefined;
+		}
+		dep = dep || [];
+		fn = fn || function () {}; // no-op
+		if (!name) {
+			throw new Error('Task requires a name');
+		}
+		// validate name is a string, dep is an array of strings, and fn is a function
+		if (typeof name !== 'string') {
+			throw new Error('Task requires a name that is a string');
+		}
+		if (typeof fn !== 'function') {
+			throw new Error('Task '+name+' requires a function that is a function');
+		}
+		if (!Array.isArray(dep)) {
+			throw new Error('Task '+name+' can\'t support dependencies that is not an array of strings');
+		}
+		dep.forEach(function (item) {
+			if (typeof item !== 'string') {
+				throw new Error('Task '+name+' dependency '+item+' is not a string');
+			}
+		});
+		this.tasks[name] = {
+			fn: fn,
+			dep: dep,
+			name: name
+		};
+		return this;
+	};
+	Orchestrator.prototype.task = function (name, dep, fn) {
+		if (dep || fn) {
+			// alias for add, return nothing rather than this
+			this.add(name, dep, fn);
+		} else {
+			return this.tasks[name];
+		}
+	};
+	Orchestrator.prototype.hasTask = function (name) {
+		return !!this.tasks[name];
+	};
+	// tasks and optionally a callback
+	Orchestrator.prototype.start = function() {
+		var args, arg, names = [], lastTask, i, seq = [];
+		args = Array.prototype.slice.call(arguments, 0);
+		if (args.length) {
+			lastTask = args[args.length-1];
+			if (typeof lastTask === 'function') {
+				this.doneCallback = lastTask;
+				args.pop();
+			}
+			for (i = 0; i < args.length; i++) {
+				arg = args[i];
+				if (typeof arg === 'string') {
+					names.push(arg);
+				} else if (Array.isArray(arg)) {
+					names = names.concat(arg); // FRAGILE: ASSUME: it's an array of strings
+				} else {
+					throw new Error('pass strings or arrays of strings');
+				}
+			}
+		}
+		if (this.isRunning) {
+			// reset specified tasks (and dependencies) as not run
+			this._resetSpecificTasks(names);
+		} else {
+			// reset all tasks as not run
+			this._resetAllTasks();
+		}
+		if (this.isRunning) {
+			// if you call start() again while a previous run is still in play
+			// prepend the new tasks to the existing task queue
+			names = names.concat(this.seq);
+		}
+		if (names.length < 1) {
+			// run all tasks
+			for (i in this.tasks) {
+				if (this.tasks.hasOwnProperty(i)) {
+					names.push(this.tasks[i].name);
+				}
+			}
+		}
+		seq = [];
+		try {
+			this.sequence(this.tasks, names, seq, []);
+		} catch (err) {
+			// Is this a known error?
+			if (err) {
+				if (err.missingTask) {
+					this.emit('task_not_found', {message: err.message, task:err.missingTask, err: err});
+				}
+				if (err.recursiveTasks) {
+					this.emit('task_recursion', {message: err.message, recursiveTasks:err.recursiveTasks, err: err});
+				}
+			}
+			this.stop(err);
+			return this;
+		}
+		this.seq = seq;
+		this.emit('start', {message:'seq: '+this.seq.join(',')});
+		if (!this.isRunning) {
+			this.isRunning = true;
+		}
+		this._runStep();
+		return this;
+	};
+	Orchestrator.prototype.stop = function (err, successfulFinish) {
+		this.isRunning = false;
+		if (err) {
+			this.emit('err', {message:'orchestration failed', err:err});
+		} else if (successfulFinish) {
+			this.emit('stop', {message:'orchestration succeeded'});
+		} else {
+			// ASSUME
+			err = 'orchestration aborted';
+			this.emit('err', {message:'orchestration aborted', err: err});
+		}
+		if (this.doneCallback) {
+			// Avoid calling it multiple times
+			this.doneCallback(err);
+		} else if (err && !this.listeners('err').length) {
+			// No one is listening for the error so speak louder
+			throw err;
+		}
+	};
+	Orchestrator.prototype.sequence = require('sequencify');
+	Orchestrator.prototype.allDone = function () {
+		var i, task, allDone = true; // nothing disputed it yet
+		for (i = 0; i < this.seq.length; i++) {
+			task = this.tasks[this.seq[i]];
+			if (!task.done) {
+				allDone = false;
+				break;
+			}
+		}
+		return allDone;
+	};
+	Orchestrator.prototype._resetTask = function(task) {
+		if (task) {
+			if (task.done) {
+				task.done = false;
+			}
+			delete task.start;
+			delete task.stop;
+			delete task.duration;
+			delete task.hrDuration;
+			delete task.args;
+		}
+	};
+	Orchestrator.prototype._resetAllTasks = function() {
+		var task;
+		for (task in this.tasks) {
+			if (this.tasks.hasOwnProperty(task)) {
+				this._resetTask(this.tasks[task]);
+			}
+		}
+	};
+	Orchestrator.prototype._resetSpecificTasks = function (names) {
+		var i, name, t;
+
+		if (names && names.length) {
+			for (i = 0; i < names.length; i++) {
+				name = names[i];
+				t = this.tasks[name];
+				if (t) {
+					this._resetTask(t);
+					if (t.dep && t.dep.length) {
+						this._resetSpecificTasks(t.dep); // recurse
+					}
+				//} else {
+					// FRAGILE: ignore that the task doesn't exist
+				}
+			}
+		}
+	};
+	Orchestrator.prototype._runStep = function () {
+		var i, task;
+		if (!this.isRunning) {
+			return; // user aborted, ASSUME: stop called previously
+		}
+		for (i = 0; i < this.seq.length; i++) {
+			task = this.tasks[this.seq[i]];
+			if (!task.done && !task.running && this._readyToRunTask(task)) {
+				this._runTask(task);
+			}
+			if (!this.isRunning) {
+				return; // task failed or user aborted, ASSUME: stop called previously
+			}
+		}
+		if (this.allDone()) {
+			this.stop(null, true);
+		}
+	};
+	Orchestrator.prototype._readyToRunTask = function (task) {
+		var ready = true, // no one disproved it yet
+			i, name, t;
+		if (task.dep.length) {
+			for (i = 0; i < task.dep.length; i++) {
+				name = task.dep[i];
+				t = this.tasks[name];
+				if (!t) {
+					// FRAGILE: this should never happen
+					this.stop("can't run "+task.name+" because it depends on "+name+" which doesn't exist");
+					ready = false;
+					break;
+				}
+				if (!t.done) {
+					ready = false;
+					break;
+				}
+			}
+		}
+		return ready;
+	};
+	Orchestrator.prototype._stopTask = function (task, meta) {
+		task.duration = meta.duration;
+		task.hrDuration = meta.hrDuration;
+		task.running = false;
+		task.done = true;
+	};
+	Orchestrator.prototype._emitTaskDone = function (task, message, err) {
+		if (!task.args) {
+			task.args = {task:task.name};
+		}
+		task.args.duration = task.duration;
+		task.args.hrDuration = task.hrDuration;
+		task.args.message = task.name+' '+message;
+		var evt = 'stop';
+		if (err) {
+			task.args.err = err;
+			evt = 'err';
+		}
+		// 'task_stop' or 'task_err'
+		this.emit('task_'+evt, task.args);
+	};
+	Orchestrator.prototype._runTask = function (task) {
+		var that = this;
+
+		task.args = {task:task.name, message:task.name+' started'};
+		this.emit('task_start', task.args);
+		task.running = true;
+
+		runTask(task.fn.bind(this), function (err, meta) {
+			that._stopTask.call(that, task, meta);
+			that._emitTaskDone.call(that, task, meta.runMethod, err);
+			if (err) {
+				return that.stop.call(that, err);
+			}
+			that._runStep.call(that);
+		});
+	};
+
+// FRAGILE: ASSUME: this list is an exhaustive list of events emitted
+var events = ['start','stop','err','task_start','task_stop','task_err','task_not_found','task_recursion'];
+
+var listenToEvent = function (target, event, callback) {
+	target.on(event, function (e) {
+		e.src = event;
+		callback(e);
+	});
+};
+
+	Orchestrator.prototype.onAll = function (callback) {
+		var i;
+		if (typeof callback !== 'function') {
+			throw new Error('No callback specified');
+		}
+
+		for (i = 0; i < events.length; i++) {
+			listenToEvent(this, events[i], callback);
+		}
+	};
+
+module.exports = Orchestrator;

static/js/ketcher2/node_modules/orchestrator/lib/runTask.js

@@ -0,0 +1,66 @@
+/*jshint node:true */
+
+"use strict";
+
+var eos = require('end-of-stream');
+var consume = require('stream-consume');
+
+module.exports = function (task, done) {
+	var that = this, finish, cb, isDone = false, start, r;
+
+	finish = function (err, runMethod) {
+		var hrDuration = process.hrtime(start);
+
+		if (isDone && !err) {
+			err = new Error('task completion callback called too many times');
+		}
+		isDone = true;
+
+		var duration = hrDuration[0] + (hrDuration[1] / 1e9); // seconds
+
+		done.call(that, err, {
+			duration: duration, // seconds
+			hrDuration: hrDuration, // [seconds,nanoseconds]
+			runMethod: runMethod
+		});
+	};
+
+	cb = function (err) {
+		finish(err, 'callback');
+	};
+
+	try {
+		start = process.hrtime();
+		r = task(cb);
+	} catch (err) {
+		return finish(err, 'catch');
+	}
+
+	if (r && typeof r.then === 'function') {
+		// wait for promise to resolve
+		// FRAGILE: ASSUME: Promises/A+, see http://promises-aplus.github.io/promises-spec/
+		r.then(function () {
+			finish(null, 'promise');
+		}, function(err) {
+			finish(err, 'promise');
+		});
+
+	} else if (r && typeof r.pipe === 'function') {
+		// wait for stream to end
+
+		eos(r, { error: true, readable: r.readable, writable: r.writable && !r.readable }, function(err){
+			finish(err, 'stream');
+		});
+
+		// Ensure that the stream completes
+        consume(r);
+
+	} else if (task.length === 0) {
+		// synchronous, function took in args.length parameters, and the callback was extra
+		finish(null, 'sync');
+
+	//} else {
+		// FRAGILE: ASSUME: callback
+
+	}
+};

static/js/ketcher2/node_modules/orchestrator/package.json

@@ -0,0 +1,69 @@
+{
+  "_from": "orchestrator@^0.3.0",
+  "_id": "orchestrator@0.3.8",
+  "_inBundle": false,
+  "_integrity": "sha1-FOfp4nZPcxX7rBhOUGx6pt+UrX4=",
+  "_location": "/orchestrator",
+  "_phantomChildren": {},
+  "_requested": {
+    "type": "range",
+    "registry": true,
+    "raw": "orchestrator@^0.3.0",
+    "name": "orchestrator",
+    "escapedName": "orchestrator",
+    "rawSpec": "^0.3.0",
+    "saveSpec": null,
+    "fetchSpec": "^0.3.0"
+  },
+  "_requiredBy": [
+    "/gulp"
+  ],
+  "_resolved": "https://registry.npmjs.org/orchestrator/-/orchestrator-0.3.8.tgz",
+  "_shasum": "14e7e9e2764f7315fbac184e506c7aa6df94ad7e",
+  "_spec": "orchestrator@^0.3.0",
+  "_where": "/home/manfred/enviPath/ketcher2/ketcher/node_modules/gulp",
+  "author": {
+    "name": "Rob Richardson",
+    "url": "http://robrich.org/"
+  },
+  "bugs": {
+    "url": "https://github.com/robrich/orchestrator/issues"
+  },
+  "bundleDependencies": false,
+  "dependencies": {
+    "end-of-stream": "~0.1.5",
+    "sequencify": "~0.0.7",
+    "stream-consume": "~0.1.0"
+  },
+  "deprecated": false,
+  "description": "A module for sequencing and executing tasks and dependencies in maximum concurrency",
+  "devDependencies": {
+    "event-stream": "~3.3.4",
+    "gulp-uglify": "^2.0.0",
+    "jshint": "^2.9.4",
+    "map-stream": "~0.0.6",
+    "merge-stream": "~1.0.0",
+    "mocha": "~3.1.2",
+    "q": "~1.4.1",
+    "should": "~11.1.1",
+    "vinyl-fs": "~2.4.4"
+  },
+  "homepage": "https://github.com/robrich/orchestrator",
+  "keywords": [
+    "async",
+    "task",
+    "parallel",
+    "compose"
+  ],
+  "license": "MIT",
+  "main": "./index.js",
+  "name": "orchestrator",
+  "repository": {
+    "type": "git",
+    "url": "git://github.com/robrich/orchestrator.git"
+  },
+  "scripts": {
+    "test": "mocha"
+  },
+  "version": "0.3.8"
+}