Current Dev State

static/js/ketcher2/node_modules/istanbul/lib/command/check-coverage.js

@@ -0,0 +1,195 @@
+/*
+ Copyright (c) 2012, Yahoo! Inc.  All rights reserved.
+ Copyrights licensed under the New BSD License. See the accompanying LICENSE file for terms.
+ */
+
+var nopt = require('nopt'),
+    path = require('path'),
+    fs = require('fs'),
+    Collector = require('../collector'),
+    formatOption = require('../util/help-formatter').formatOption,
+    util = require('util'),
+    utils = require('../object-utils'),
+    filesFor = require('../util/file-matcher').filesFor,
+    Command = require('./index'),
+    configuration = require('../config');
+
+function isAbsolute(file) {
+    if (path.isAbsolute) {
+        return path.isAbsolute(file);
+    }
+
+    return path.resolve(file) === path.normalize(file);
+}
+
+function CheckCoverageCommand() {
+    Command.call(this);
+}
+
+function removeFiles(covObj, root, files) {
+    var filesObj = {},
+        obj = {};
+
+    // Create lookup table.
+    files.forEach(function (file) {
+        filesObj[file] = true;
+    });
+
+    Object.keys(covObj).forEach(function (key) {
+        // Exclude keys will always be relative, but covObj keys can be absolute or relative
+        var excludeKey = isAbsolute(key) ? path.relative(root, key) : key;
+        // Also normalize for files that start with `./`, etc.
+        excludeKey = path.normalize(excludeKey);
+        if (filesObj[excludeKey] !== true) {
+            obj[key] = covObj[key];
+        }
+    });
+
+    return obj;
+}
+
+CheckCoverageCommand.TYPE = 'check-coverage';
+util.inherits(CheckCoverageCommand, Command);
+
+Command.mix(CheckCoverageCommand, {
+    synopsis: function () {
+        return "checks overall/per-file coverage against thresholds from coverage JSON files. Exits 1 if thresholds are not met, 0 otherwise";
+    },
+
+    usage: function () {
+        console.error('\nUsage: ' + this.toolName() + ' ' + this.type() + ' <options> [<include-pattern>]\n\nOptions are:\n\n' +
+            [
+                formatOption('--statements <threshold>', 'global statement coverage threshold'),
+                formatOption('--functions <threshold>', 'global function coverage threshold'),
+                formatOption('--branches <threshold>', 'global branch coverage threshold'),
+                formatOption('--lines <threshold>', 'global line coverage threshold')
+            ].join('\n\n') + '\n');
+
+        console.error('\n\n');
+
+        console.error('Thresholds, when specified as a positive number are taken to be the minimum percentage required.');
+        console.error('When a threshold is specified as a negative number it represents the maximum number of uncovered entities allowed.\n');
+        console.error('For example, --statements 90 implies minimum statement coverage is 90%.');
+        console.error('             --statements -10 implies that no more than 10 uncovered statements are allowed\n');
+        console.error('Per-file thresholds can be specified via a configuration file.\n');
+        console.error('<include-pattern> is a glob pattern that can be used to select one or more coverage files ' +
+            'for merge. This defaults to "**/coverage*.json"');
+
+        console.error('\n');
+    },
+
+    run: function (args, callback) {
+
+        var template = {
+                config: path,
+                root: path,
+                statements: Number,
+                lines: Number,
+                branches: Number,
+                functions: Number,
+                verbose: Boolean
+            },
+            opts = nopt(template, { v : '--verbose' }, args, 0),
+            // Translate to config opts.
+            config = configuration.loadFile(opts.config, {
+                verbose: opts.verbose,
+                check: {
+                    global: {
+                        statements: opts.statements,
+                        lines: opts.lines,
+                        branches: opts.branches,
+                        functions: opts.functions
+                    }
+                }
+            }),
+            includePattern = '**/coverage*.json',
+            root,
+            collector = new Collector(),
+            errors = [];
+
+        if (opts.argv.remain.length > 0) {
+            includePattern = opts.argv.remain[0];
+        }
+
+        root = opts.root || process.cwd();
+        filesFor({
+            root: root,
+            includes: [ includePattern ]
+        }, function (err, files) {
+            if (err) { throw err; }
+            if (files.length === 0) {
+               return callback('ERROR: No coverage files found.');
+            }
+            files.forEach(function (file) {
+                var coverageObject = JSON.parse(fs.readFileSync(file, 'utf8'));
+                collector.add(coverageObject);
+            });
+            var thresholds = {
+                global: {
+                    statements: config.check.global.statements || 0,
+                    branches: config.check.global.branches || 0,
+                    lines: config.check.global.lines || 0,
+                    functions: config.check.global.functions || 0,
+                    excludes: config.check.global.excludes || []
+                },
+                each: {
+                    statements: config.check.each.statements || 0,
+                    branches: config.check.each.branches || 0,
+                    lines: config.check.each.lines || 0,
+                    functions: config.check.each.functions || 0,
+                    excludes: config.check.each.excludes || []
+                }
+            },
+                rawCoverage = collector.getFinalCoverage(),
+                globalResults = utils.summarizeCoverage(removeFiles(rawCoverage, root, thresholds.global.excludes)),
+                eachResults = removeFiles(rawCoverage, root, thresholds.each.excludes);
+
+            // Summarize per-file results and mutate original results.
+            Object.keys(eachResults).forEach(function (key) {
+                eachResults[key] = utils.summarizeFileCoverage(eachResults[key]);
+            });
+
+            if (config.verbose) {
+                console.log('Compare actuals against thresholds');
+                console.log(JSON.stringify({ global: globalResults, each: eachResults, thresholds: thresholds }, undefined, 4));
+            }
+
+            function check(name, thresholds, actuals) {
+                [
+                    "statements",
+                    "branches",
+                    "lines",
+                    "functions"
+                ].forEach(function (key) {
+                    var actual = actuals[key].pct,
+                        actualUncovered = actuals[key].total - actuals[key].covered,
+                        threshold = thresholds[key];
+
+                    if (threshold < 0) {
+                        if (threshold * -1 < actualUncovered) {
+                            errors.push('ERROR: Uncovered count for ' + key + ' (' + actualUncovered +
+                                ') exceeds ' + name + ' threshold (' + -1 * threshold + ')');
+                        }
+                    } else {
+                        if (actual < threshold) {
+                            errors.push('ERROR: Coverage for ' + key + ' (' + actual +
+                                '%) does not meet ' + name + ' threshold (' + threshold + '%)');
+                        }
+                    }
+                });
+            }
+
+            check("global", thresholds.global, globalResults);
+
+            Object.keys(eachResults).forEach(function (key) {
+                check("per-file" + " (" + key + ") ", thresholds.each, eachResults[key]);
+            });
+
+            return callback(errors.length === 0 ? null : errors.join("\n"));
+        });
+    }
+});
+
+module.exports = CheckCoverageCommand;
+
+

static/js/ketcher2/node_modules/istanbul/lib/command/common/run-with-cover.js

@@ -0,0 +1,261 @@
+/*
+ Copyright (c) 2012, Yahoo! Inc.  All rights reserved.
+ Copyrights licensed under the New BSD License. See the accompanying LICENSE file for terms.
+ */
+var Module = require('module'),
+    path = require('path'),
+    fs = require('fs'),
+    nopt = require('nopt'),
+    which = require('which'),
+    mkdirp = require('mkdirp'),
+    existsSync = fs.existsSync || path.existsSync,
+    inputError = require('../../util/input-error'),
+    matcherFor = require('../../util/file-matcher').matcherFor,
+    Instrumenter = require('../../instrumenter'),
+    Collector = require('../../collector'),
+    formatOption = require('../../util/help-formatter').formatOption,
+    hook = require('../../hook'),
+    Reporter = require('../../reporter'),
+    resolve = require('resolve'),
+    configuration = require('../../config');
+
+function usage(arg0, command) {
+
+    console.error('\nUsage: ' + arg0 + ' ' + command + ' [<options>] <executable-js-file-or-command> [-- <arguments-to-jsfile>]\n\nOptions are:\n\n'
+        + [
+            formatOption('--config <path-to-config>', 'the configuration file to use, defaults to .istanbul.yml'),
+            formatOption('--root <path> ', 'the root path to look for files to instrument, defaults to .'),
+            formatOption('-x <exclude-pattern> [-x <exclude-pattern>]', 'one or more glob patterns e.g. "**/vendor/**"'),
+            formatOption('-i <include-pattern> [-i <include-pattern>]', 'one or more glob patterns e.g. "**/*.js"'),
+            formatOption('--[no-]default-excludes', 'apply default excludes [ **/node_modules/**, **/test/**, **/tests/** ], defaults to true'),
+            formatOption('--hook-run-in-context', 'hook vm.runInThisContext in addition to require (supports RequireJS), defaults to false'),
+            formatOption('--post-require-hook <file> | <module>', 'JS module that exports a function for post-require processing'),
+            formatOption('--report <format> [--report <format>] ', 'report format, defaults to lcov (= lcov.info + HTML)'),
+            formatOption('--dir <report-dir>', 'report directory, defaults to ./coverage'),
+            formatOption('--print <type>', 'type of report to print to console, one of summary (default), detail, both or none'),
+            formatOption('--verbose, -v', 'verbose mode'),
+            formatOption('--[no-]preserve-comments', 'remove / preserve comments in the output, defaults to false'),
+            formatOption('--include-all-sources', 'instrument all unused sources after running tests, defaults to false'),
+            formatOption('--[no-]include-pid', 'include PID in output coverage filename')
+        ].join('\n\n') + '\n');
+    console.error('\n');
+}
+
+function run(args, commandName, enableHooks, callback) {
+
+    var template = {
+            config: path,
+            root: path,
+            x: [ Array, String ],
+            report: [Array, String ],
+            dir: path,
+            verbose: Boolean,
+            yui: Boolean,
+            'default-excludes': Boolean,
+            print: String,
+            'self-test': Boolean,
+            'hook-run-in-context': Boolean,
+            'post-require-hook': String,
+            'preserve-comments': Boolean,
+            'include-all-sources': Boolean,
+            'preload-sources': Boolean,
+            i: [ Array, String ],
+            'include-pid': Boolean
+        },
+        opts = nopt(template, { v : '--verbose' }, args, 0),
+        overrides = {
+            verbose: opts.verbose,
+            instrumentation: {
+                root: opts.root,
+                'default-excludes': opts['default-excludes'],
+                excludes: opts.x,
+                'include-all-sources': opts['include-all-sources'],
+                'preload-sources': opts['preload-sources'],
+                'include-pid': opts['include-pid']
+            },
+            reporting: {
+                reports: opts.report,
+                print: opts.print,
+                dir: opts.dir
+            },
+            hooks: {
+                'hook-run-in-context': opts['hook-run-in-context'],
+                'post-require-hook': opts['post-require-hook'],
+                'handle-sigint': opts['handle-sigint']
+            }
+        },
+        config = configuration.loadFile(opts.config, overrides),
+        verbose = config.verbose,
+        cmdAndArgs = opts.argv.remain,
+        preserveComments = opts['preserve-comments'],
+        includePid = opts['include-pid'],
+        cmd,
+        cmdArgs,
+        reportingDir,
+        reporter = new Reporter(config),
+        runFn,
+        excludes;
+
+    if (cmdAndArgs.length === 0) {
+        return callback(inputError.create('Need a filename argument for the ' + commandName + ' command!'));
+    }
+
+    cmd = cmdAndArgs.shift();
+    cmdArgs = cmdAndArgs;
+
+    if (!existsSync(cmd)) {
+        try {
+            cmd = which.sync(cmd);
+        } catch (ex) {
+            return callback(inputError.create('Unable to resolve file [' + cmd + ']'));
+        }
+    } else {
+        cmd = path.resolve(cmd);
+    }
+
+    runFn = function () {
+        process.argv = ["node", cmd].concat(cmdArgs);
+        if (verbose) {
+            console.log('Running: ' + process.argv.join(' '));
+        }
+        process.env.running_under_istanbul=1;
+        Module.runMain(cmd, null, true);
+    };
+
+    excludes = config.instrumentation.excludes(true);
+
+    if (enableHooks) {
+        reportingDir = path.resolve(config.reporting.dir());
+        mkdirp.sync(reportingDir); //ensure we fail early if we cannot do this
+        reporter.dir = reportingDir;
+        reporter.addAll(config.reporting.reports());
+        if (config.reporting.print() !== 'none') {
+            switch (config.reporting.print()) {
+            case 'detail':
+                reporter.add('text');
+                break;
+            case 'both':
+                reporter.add('text');
+                reporter.add('text-summary');
+                break;
+            default:
+                reporter.add('text-summary');
+                break;
+            }
+        }
+
+        excludes.push(path.relative(process.cwd(), path.join(reportingDir, '**', '*')));
+        matcherFor({
+            root: config.instrumentation.root() || process.cwd(),
+            includes: opts.i || config.instrumentation.extensions().map(function (ext) {
+                return '**/*' + ext;
+            }),
+            excludes: excludes
+        },
+            function (err, matchFn) {
+                if (err) { return callback(err); }
+
+                var coverageVar = '$$cov_' + new Date().getTime() + '$$',
+                    instrumenter = new Instrumenter({ coverageVariable: coverageVar , preserveComments: preserveComments}),
+                    transformer = instrumenter.instrumentSync.bind(instrumenter),
+                    hookOpts = { verbose: verbose, extensions: config.instrumentation.extensions() },
+                    postRequireHook = config.hooks.postRequireHook(),
+                    postLoadHookFile;
+
+                if (postRequireHook) {
+                    postLoadHookFile = path.resolve(postRequireHook);
+                } else if (opts.yui) { //EXPERIMENTAL code: do not rely on this in anyway until the docs say it is allowed
+                    postLoadHookFile = path.resolve(__dirname, '../../util/yui-load-hook');
+                }
+
+                if (postRequireHook) {
+                    if (!existsSync(postLoadHookFile)) { //assume it is a module name and resolve it
+                        try {
+                            postLoadHookFile = resolve.sync(postRequireHook, { basedir: process.cwd() });
+                        } catch (ex) {
+                            if (verbose) { console.error('Unable to resolve [' + postRequireHook + '] as a node module'); }
+                            callback(ex);
+                            return;
+                        }
+                    }
+                }
+                if (postLoadHookFile) {
+                    if (verbose) { console.error('Use post-load-hook: ' + postLoadHookFile); }
+                    hookOpts.postLoadHook = require(postLoadHookFile)(matchFn, transformer, verbose);
+                }
+
+                if (opts['self-test']) {
+                    hook.unloadRequireCache(matchFn);
+                }
+                // runInThisContext is used by RequireJS [issue #23]
+                if (config.hooks.hookRunInContext()) {
+                    hook.hookRunInThisContext(matchFn, transformer, hookOpts);
+                }
+                hook.hookRequire(matchFn, transformer, hookOpts);
+
+                //initialize the global variable to stop mocha from complaining about leaks
+                global[coverageVar] = {};
+
+                // enable passing --handle-sigint to write reports on SIGINT.
+                // This allows a user to manually kill a process while
+                // still getting the istanbul report.
+                if (config.hooks.handleSigint()) {
+                    process.once('SIGINT', process.exit);
+                }
+
+                process.once('exit', function () {
+                    var pidExt = includePid ? ('-' + process.pid) : '',
+                        file = path.resolve(reportingDir, 'coverage' + pidExt + '.json'),
+                        collector,
+                        cov;
+                    if (typeof global[coverageVar] === 'undefined' || Object.keys(global[coverageVar]).length === 0) {
+                        console.error('No coverage information was collected, exit without writing coverage information');
+                        return;
+                    } else {
+                        cov = global[coverageVar];
+                    }
+                    //important: there is no event loop at this point
+                    //everything that happens in this exit handler MUST be synchronous
+                    if (config.instrumentation.includeAllSources()) {
+                        // Files that are not touched by code ran by the test runner is manually instrumented, to
+                        // illustrate the missing coverage.
+                        matchFn.files.forEach(function (file) {
+                            if (!cov[file]) {
+                                transformer(fs.readFileSync(file, 'utf-8'), file);
+
+                                // When instrumenting the code, istanbul will give each FunctionDeclaration a value of 1 in coverState.s,
+                                // presumably to compensate for function hoisting. We need to reset this, as the function was not hoisted,
+                                // as it was never loaded.
+                                Object.keys(instrumenter.coverState.s).forEach(function (key) {
+                                    instrumenter.coverState.s[key] = 0;
+                                });
+
+                                cov[file] = instrumenter.coverState;
+                            }
+                        });
+                    }
+                    mkdirp.sync(reportingDir); //yes, do this again since some test runners could clean the dir initially created
+                    if (config.reporting.print() !== 'none') {
+                        console.error('=============================================================================');
+                        console.error('Writing coverage object [' + file + ']');
+                    }
+                    fs.writeFileSync(file, JSON.stringify(cov), 'utf8');
+                    collector = new Collector();
+                    collector.add(cov);
+                    if (config.reporting.print() !== 'none') {
+                        console.error('Writing coverage reports at [' + reportingDir + ']');
+                        console.error('=============================================================================');
+                    }
+                    reporter.write(collector, true, callback);
+                });
+                runFn();
+            });
+    } else {
+        runFn();
+    }
+}
+
+module.exports = {
+    run: run,
+    usage: usage
+};

static/js/ketcher2/node_modules/istanbul/lib/command/cover.js

@@ -0,0 +1,33 @@
+/*
+ Copyright (c) 2012, Yahoo! Inc.  All rights reserved.
+ Copyrights licensed under the New BSD License. See the accompanying LICENSE file for terms.
+ */
+
+var runWithCover = require('./common/run-with-cover'),
+    util = require('util'),
+    Command = require('./index');
+
+function CoverCommand() {
+    Command.call(this);
+}
+
+CoverCommand.TYPE = 'cover';
+util.inherits(CoverCommand, Command);
+
+Command.mix(CoverCommand, {
+    synopsis: function () {
+        return "transparently adds coverage information to a node command. Saves coverage.json and reports at the end of execution";
+    },
+
+    usage: function () {
+        runWithCover.usage(this.toolName(), this.type());
+    },
+
+    run: function (args, callback) {
+        runWithCover.run(args, this.type(), true, callback);
+    }
+});
+
+
+module.exports = CoverCommand;
+

static/js/ketcher2/node_modules/istanbul/lib/command/help.js

@@ -0,0 +1,102 @@
+/*
+ Copyright (c) 2012, Yahoo! Inc.  All rights reserved.
+ Copyrights licensed under the New BSD License. See the accompanying LICENSE file for terms.
+ */
+
+var Command = require('./index.js'),
+    util = require('util'),
+    formatOption = require('../util/help-formatter').formatOption,
+    VERSION = require('../../index').VERSION,
+    configuration = require('../config'),
+    yaml = require('js-yaml'),
+    formatPara = require('../util/help-formatter').formatPara;
+
+function showConfigHelp(toolName) {
+
+    console.error('\nConfiguring ' + toolName);
+    console.error('====================');
+    console.error('\n' +
+        formatPara(toolName + ' can be configured globally using a .istanbul.yml YAML file ' +
+            'at the root of your source tree. Every command also accepts a --config=<config-file> argument to ' +
+            'customize its location per command. The alternate config file can be in YAML, JSON or node.js ' +
+            '(exporting the config object).'));
+    console.error('\n' +
+        formatPara('The config file currently has four sections for instrumentation, reporting, hooks, ' +
+            'and checking. Note that certain commands (like `cover`) use information from multiple sections.'));
+    console.error('\n' +
+        formatPara('Keys in the config file usually correspond to command line parameters with the same name. ' +
+            'The verbose option for every command shows you the exact configuration used. See the api ' +
+            'docs for an explanation of each key.'));
+
+    console.error('\n' +
+        formatPara('You only need to specify the keys that you want to override. Your overrides will be merged ' +
+            'with the default config.'));
+    console.error('\nThe default configuration is as follows:\n');
+    console.error(yaml.safeDump(configuration.defaultConfig(), { indent: 4, flowLevel: 3 }));
+    console.error('\n' +
+        formatPara('The `watermarks` section does not have a command line equivalent. It allows you to set up ' +
+            'low and high watermark percentages for reporting. These are honored by all reporters that colorize ' +
+            'their output based on low/ medium/ high coverage.'));
+    console.error('\n' +
+        formatPara('The `reportConfig` section allows you to configure each report format independently ' +
+            'and has no command-line equivalent either.'));
+    console.error('\n' +
+        formatPara('The `check` section configures minimum threshold enforcement for coverage results. ' +
+            '`global` applies to all files together and `each` on a per-file basis. A list of files can ' +
+            'be excluded from enforcement relative to root via the `exclude` property.'));
+    console.error('');
+}
+
+function HelpCommand() {
+    Command.call(this);
+}
+
+HelpCommand.TYPE = 'help';
+util.inherits(HelpCommand, Command);
+
+Command.mix(HelpCommand, {
+    synopsis: function () {
+        return "shows help";
+    },
+
+    usage: function () {
+
+        console.error('\nUsage: ' + this.toolName() + ' ' + this.type() + ' config | <command>\n');
+        console.error('`config` provides help with istanbul configuration\n');
+        console.error('Available commands are:\n');
+
+        var commandObj;
+        Command.getCommandList().forEach(function (cmd) {
+            commandObj = Command.create(cmd);
+            console.error(formatOption(cmd, commandObj.synopsis()));
+            console.error("\n");
+        });
+        console.error("Command names can be abbreviated as long as the abbreviation is unambiguous");
+        console.error(this.toolName() + ' version:' + VERSION);
+        console.error("\n");
+    },
+    run: function (args, callback) {
+        var command;
+        if (args.length === 0) {
+            this.usage();
+        } else {
+            if (args[0] === 'config') {
+                showConfigHelp(this.toolName());
+            } else {
+                try {
+                    command = Command.create(args[0]);
+                    command.usage('istanbul', Command.resolveCommandName(args[0]));
+                } catch (ex) {
+                    console.error('Invalid command: ' + args[0]);
+                    this.usage();
+                }
+            }
+        }
+        return callback();
+    }
+});
+
+
+module.exports = HelpCommand;
+
+

static/js/ketcher2/node_modules/istanbul/lib/command/index.js

@@ -0,0 +1,33 @@
+/*
+ Copyright (c) 2012, Yahoo! Inc.  All rights reserved.
+ Copyrights licensed under the New BSD License. See the accompanying LICENSE file for terms.
+ */
+
+var Factory = require('../util/factory'),
+    factory = new Factory('command', __dirname, true);
+
+function Command() {}
+// add register, create, mix, loadAll, getCommandList, resolveCommandName to the Command object
+factory.bindClassMethods(Command);
+
+Command.prototype = {
+    toolName: function () {
+        return require('../util/meta').NAME;
+    },
+
+    type: function () {
+        return this.constructor.TYPE;
+    },
+    synopsis: /* istanbul ignore next: base method */ function () {
+        return "the developer has not written a one-line summary of the " + this.type() + " command";
+    },
+    usage: /* istanbul ignore next: base method */ function () {
+        console.error("the developer has not provided a usage for the " + this.type() + " command");
+    },
+    run: /* istanbul ignore next: abstract method */ function (args, callback) {
+        return callback(new Error("run: must be overridden for the " + this.type() + " command"));
+    }
+};
+
+module.exports = Command;
+

static/js/ketcher2/node_modules/istanbul/lib/command/instrument.js

@@ -0,0 +1,265 @@
+/*
+ Copyright (c) 2012, Yahoo! Inc.  All rights reserved.
+ Copyrights licensed under the New BSD License. See the accompanying LICENSE file for terms.
+ */
+
+var path = require('path'),
+    mkdirp = require('mkdirp'),
+    once = require('once'),
+    async = require('async'),
+    fs = require('fs'),
+    filesFor = require('../util/file-matcher').filesFor,
+    nopt = require('nopt'),
+    Instrumenter = require('../instrumenter'),
+    inputError = require('../util/input-error'),
+    formatOption = require('../util/help-formatter').formatOption,
+    util = require('util'),
+    Command = require('./index'),
+    Collector = require('../collector'),
+    configuration = require('../config'),
+    verbose;
+
+
+/*
+ * Chunk file size to use when reading non JavaScript files in memory
+ * and copying them over when using complete-copy flag.
+ */
+var READ_FILE_CHUNK_SIZE = 64 * 1024;
+
+function BaselineCollector(instrumenter) {
+    this.instrumenter = instrumenter;
+    this.collector = new Collector();
+    this.instrument = instrumenter.instrument.bind(this.instrumenter);
+
+    var origInstrumentSync = instrumenter.instrumentSync;
+    this.instrumentSync = function () {
+        var args = Array.prototype.slice.call(arguments),
+            ret = origInstrumentSync.apply(this.instrumenter, args),
+            baseline = this.instrumenter.lastFileCoverage(),
+            coverage = {};
+        coverage[baseline.path] = baseline;
+        this.collector.add(coverage);
+        return ret;
+    };
+    //monkey patch the instrumenter to call our version instead
+    instrumenter.instrumentSync = this.instrumentSync.bind(this);
+}
+
+BaselineCollector.prototype = {
+    getCoverage: function () {
+        return this.collector.getFinalCoverage();
+    }
+};
+
+
+function processFiles(instrumenter, inputDir, outputDir, relativeNames, extensions) {
+    var processor = function (name, callback) {
+            var inputFile = path.resolve(inputDir, name),
+                outputFile = path.resolve(outputDir, name),
+                inputFileExtenstion = path.extname(inputFile),
+                isJavaScriptFile = extensions.indexOf(inputFileExtenstion) > -1,
+                oDir = path.dirname(outputFile),
+                readStream, writeStream;
+
+            callback = once(callback);
+            mkdirp.sync(oDir);
+
+            if (fs.statSync(inputFile).isDirectory()) {
+                return callback(null, name);
+            }
+
+            if (isJavaScriptFile) {
+                fs.readFile(inputFile, 'utf8', function (err, data) {
+                    if (err) { return callback(err, name); }
+                    instrumenter.instrument(data, inputFile, function (iErr, instrumented) {
+                        if (iErr) { return callback(iErr, name); }
+                        fs.writeFile(outputFile, instrumented, 'utf8', function (err) {
+                            return callback(err, name);
+                        });
+                    });
+                });
+            }
+            else {
+                // non JavaScript file, copy it as is
+                readStream = fs.createReadStream(inputFile, {'bufferSize': READ_FILE_CHUNK_SIZE});
+                writeStream = fs.createWriteStream(outputFile);
+
+                readStream.on('error', callback);
+                writeStream.on('error', callback);
+
+                readStream.pipe(writeStream);
+                readStream.on('end', function() {
+                    callback(null, name);
+                });
+            }
+        },
+        q = async.queue(processor, 10),
+        errors = [],
+        count = 0,
+        startTime = new Date().getTime();
+
+    q.push(relativeNames, function (err, name) {
+        var inputFile, outputFile;
+        if (err) {
+            errors.push({ file: name, error: err.message || err.toString() });
+            inputFile = path.resolve(inputDir, name);
+            outputFile = path.resolve(outputDir, name);
+            fs.writeFileSync(outputFile, fs.readFileSync(inputFile));
+        }
+        if (verbose) {
+            console.log('Processed: ' + name);
+        } else {
+            if (count % 100 === 0) { process.stdout.write('.'); }
+        }
+        count += 1;
+    });
+
+    q.drain = function () {
+        var endTime = new Date().getTime();
+        console.log('\nProcessed [' + count + '] files in ' + Math.floor((endTime - startTime) / 1000) + ' secs');
+        if (errors.length > 0) {
+            console.log('The following ' + errors.length + ' file(s) had errors and were copied as-is');
+            console.log(errors);
+        }
+    };
+}
+
+
+function InstrumentCommand() {
+    Command.call(this);
+}
+
+InstrumentCommand.TYPE = 'instrument';
+util.inherits(InstrumentCommand, Command);
+
+Command.mix(InstrumentCommand, {
+    synopsis: function synopsis() {
+        return "instruments a file or a directory tree and writes the instrumented code to the desired output location";
+    },
+
+    usage: function () {
+        console.error('\nUsage: ' + this.toolName() + ' ' + this.type() + ' <options> <file-or-directory>\n\nOptions are:\n\n' +
+            [
+                formatOption('--config <path-to-config>', 'the configuration file to use, defaults to .istanbul.yml'),
+                formatOption('--output <file-or-dir>', 'The output file or directory. This is required when the input is a directory, ' +
+                    'defaults to standard output when input is a file'),
+                formatOption('-x <exclude-pattern> [-x <exclude-pattern>]', 'one or more glob patterns (e.g. "**/vendor/**" to ignore all files ' +
+                    'under a vendor directory). Also see the --default-excludes option'),
+                formatOption('--variable <global-coverage-variable-name>', 'change the variable name of the global coverage variable from the ' +
+                    'default value of `__coverage__` to something else'),
+                formatOption('--embed-source', 'embed source code into the coverage object, defaults to false'),
+                formatOption('--[no-]compact', 'produce [non]compact output, defaults to compact'),
+                formatOption('--[no-]preserve-comments', 'remove / preserve comments in the output, defaults to false'),
+                formatOption('--[no-]complete-copy', 'also copy non-javascript files to the ouput directory as is, defaults to false'),
+                formatOption('--save-baseline', 'produce a baseline coverage.json file out of all files instrumented'),
+                formatOption('--baseline-file <file>', 'filename of baseline file, defaults to coverage/coverage-baseline.json'),
+                formatOption('--es-modules', 'source code uses es import/export module syntax')
+            ].join('\n\n') + '\n');
+        console.error('\n');
+    },
+
+    run: function (args, callback) {
+
+        var template = {
+                config: path,
+                output: path,
+                x: [Array, String],
+                variable: String,
+                compact: Boolean,
+                'complete-copy': Boolean,
+                verbose: Boolean,
+                'save-baseline': Boolean,
+                'baseline-file': path,
+                'embed-source': Boolean,
+                'preserve-comments': Boolean,
+                'es-modules': Boolean
+            },
+            opts = nopt(template, { v : '--verbose' }, args, 0),
+            overrides = {
+                verbose: opts.verbose,
+                instrumentation: {
+                    variable: opts.variable,
+                    compact: opts.compact,
+                    'embed-source': opts['embed-source'],
+                    'preserve-comments': opts['preserve-comments'],
+                    excludes: opts.x,
+                    'complete-copy': opts['complete-copy'],
+                    'save-baseline': opts['save-baseline'],
+                    'baseline-file': opts['baseline-file'],
+                    'es-modules': opts['es-modules']
+                }
+            },
+            config = configuration.loadFile(opts.config, overrides),
+            iOpts = config.instrumentation,
+            cmdArgs = opts.argv.remain,
+            file,
+            stats,
+            stream,
+            includes,
+            instrumenter,
+            needBaseline = iOpts.saveBaseline(),
+            baselineFile = path.resolve(iOpts.baselineFile()),
+            output = opts.output;
+
+        verbose = config.verbose;
+        if (cmdArgs.length !== 1) {
+            return callback(inputError.create('Need exactly one filename/ dirname argument for the instrument command!'));
+        }
+
+        if (iOpts.completeCopy()) {
+            includes = ['**/*'];
+        }
+        else {
+            includes = iOpts.extensions().map(function(ext) {
+                return '**/*' + ext;
+            });
+        }
+
+        instrumenter = new Instrumenter({
+            coverageVariable: iOpts.variable(),
+            embedSource: iOpts.embedSource(),
+            noCompact: !iOpts.compact(),
+            preserveComments: iOpts.preserveComments(),
+            esModules: iOpts.esModules()
+        });
+
+        if (needBaseline) {
+            mkdirp.sync(path.dirname(baselineFile));
+            instrumenter = new BaselineCollector(instrumenter);
+            process.on('exit', function () {
+                console.log('Saving baseline coverage at: ' + baselineFile);
+                fs.writeFileSync(baselineFile, JSON.stringify(instrumenter.getCoverage()), 'utf8');
+            });
+        }
+
+        file = path.resolve(cmdArgs[0]);
+        stats = fs.statSync(file);
+        if (stats.isDirectory()) {
+            if (!output) { return callback(inputError.create('Need an output directory [-o <dir>] when input is a directory!')); }
+            if (output === file) { return callback(inputError.create('Cannot instrument into the same directory/ file as input!')); }
+            mkdirp.sync(output);
+            filesFor({
+                root: file,
+                includes: includes,
+                excludes: opts.x || iOpts.excludes(false), // backwards-compat, *sigh*
+                relative: true
+            }, function (err, files) {
+                if (err) { return callback(err); }
+                processFiles(instrumenter, file, output, files, iOpts.extensions());
+            });
+        } else {
+            if (output) {
+                stream = fs.createWriteStream(output);
+            } else {
+                stream = process.stdout;
+            }
+            stream.write(instrumenter.instrumentSync(fs.readFileSync(file, 'utf8'), file));
+            if (stream !== process.stdout) {
+                stream.end();
+            }
+        }
+    }
+});
+
+module.exports = InstrumentCommand;
+

static/js/ketcher2/node_modules/istanbul/lib/command/report.js

@@ -0,0 +1,123 @@
+/*
+ Copyright (c) 2012, Yahoo! Inc.  All rights reserved.
+ Copyrights licensed under the New BSD License. See the accompanying LICENSE file for terms.
+ */
+
+var nopt = require('nopt'),
+    Report = require('../report'),
+    Reporter = require('../reporter'),
+    path = require('path'),
+    fs = require('fs'),
+    Collector = require('../collector'),
+    helpFormatter = require('../util/help-formatter'),
+    formatOption = helpFormatter.formatOption,
+    formatPara = helpFormatter.formatPara,
+    filesFor = require('../util/file-matcher').filesFor,
+    util = require('util'),
+    Command = require('./index'),
+    configuration = require('../config');
+
+function ReportCommand() {
+    Command.call(this);
+}
+
+ReportCommand.TYPE = 'report';
+util.inherits(ReportCommand, Command);
+
+function printDeprecationMessage(pat, fmt) {
+    console.error('**********************************************************************');
+    console.error('DEPRECATION WARNING! You are probably using the old format of the report command');
+    console.error('This will stop working soon, see `istanbul help report` for the new command format');
+    console.error('Assuming you meant: istanbul report --include=' + pat + ' ' + fmt);
+    console.error('**********************************************************************');
+}
+
+Command.mix(ReportCommand, {
+    synopsis: function () {
+        return "writes reports for coverage JSON objects produced in a previous run";
+    },
+
+    usage: function () {
+        console.error('\nUsage: ' + this.toolName() + ' ' + this.type() + ' <options> [ <format> ... ]\n\nOptions are:\n\n' +
+            [
+                formatOption('--config <path-to-config>', 'the configuration file to use, defaults to .istanbul.yml'),
+                formatOption('--root <input-directory>', 'The input root directory for finding coverage files'),
+                formatOption('--dir <report-directory>', 'The output directory where files will be written. This defaults to ./coverage/'),
+                formatOption('--include <glob>', 'The glob pattern to select one or more coverage files, defaults to **/coverage*.json'),
+                formatOption('--verbose, -v', 'verbose mode')
+            ].join('\n\n'));
+
+        console.error('\n');
+        console.error('<format> is one of ');
+        Report.getReportList().forEach(function (name) {
+           console.error(formatOption(name, Report.create(name).synopsis()));
+        });
+        console.error("");
+        console.error(formatPara([
+            'Default format is lcov unless otherwise specified in the config file.',
+            'In addition you can tweak the file names for various reports using the config file.',
+            'Type `istanbul help config` to see what can be tweaked.'
+        ].join(' ')));
+        console.error('\n');
+    },
+
+    run: function (args, callback) {
+
+        var template = {
+                config: path,
+                root: path,
+                dir: path,
+                include: String,
+                verbose: Boolean
+            },
+            opts = nopt(template, { v : '--verbose' }, args, 0),
+            includePattern = opts.include || '**/coverage*.json',
+            root,
+            collector = new Collector(),
+            config = configuration.loadFile(opts.config, {
+                verbose: opts.verbose,
+                reporting: {
+                    dir: opts.dir
+                }
+            }),
+            formats = opts.argv.remain,
+            reporter = new Reporter(config);
+
+        // Start: backward compatible processing
+        if (formats.length === 2 &&
+                Report.getReportList().indexOf(formats[1]) < 0) {
+            includePattern = formats[1];
+            formats = [ formats[0] ];
+            printDeprecationMessage(includePattern, formats[0]);
+        }
+        // End: backward compatible processing
+
+        if (formats.length === 0) {
+            formats = config.reporting.reports();
+        }
+        if (formats.length === 0) {
+            formats = [ 'lcov' ];
+        }
+        reporter.addAll(formats);
+
+        root = opts.root || process.cwd();
+        filesFor({
+            root: root,
+            includes: [ includePattern ]
+        }, function (err, files) {
+            if (err) { throw err; }
+            files.forEach(function (file) {
+                var coverageObject =  JSON.parse(fs.readFileSync(file, 'utf8'));
+                collector.add(coverageObject);
+            });
+            reporter.write(collector, false, function (err) {
+                console.log('Done');
+                return callback(err);
+            });
+        });
+    }
+});
+
+module.exports = ReportCommand;
+
+

static/js/ketcher2/node_modules/istanbul/lib/command/test.js

@@ -0,0 +1,31 @@
+/*
+ Copyright (c) 2012, Yahoo! Inc.  All rights reserved.
+ Copyrights licensed under the New BSD License. See the accompanying LICENSE file for terms.
+ */
+
+var runWithCover = require('./common/run-with-cover'),
+    util = require('util'),
+    Command = require('./index');
+
+function TestCommand() {
+    Command.call(this);
+}
+
+TestCommand.TYPE = 'test';
+util.inherits(TestCommand, Command);
+
+Command.mix(TestCommand, {
+    synopsis: function () {
+        return "cover a node command only when npm_config_coverage is set. Use in an `npm test` script for conditional coverage";
+    },
+
+    usage: function () {
+        runWithCover.usage(this.toolName(), this.type());
+    },
+
+    run: function (args, callback) {
+        runWithCover.run(args, this.type(), !!process.env.npm_config_coverage, callback);
+    }
+});
+
+module.exports = TestCommand;