@realsee/dnalogel 2.1.0-alpha.13 → 2.1.0-alpha.15

package/libs/node_modules/glob/glob.js

@@ -0,0 +1,658 @@
+// Approach:
+//
+// 1. Get the minimatch set
+// 2. For each pattern in the set, PROCESS(pattern, false)
+// 3. Store matches per-set, then uniq them
+//
+// PROCESS(pattern, inGlobStar)
+// Get the first [n] items from pattern that are all strings
+// Join these together.  This is PREFIX.
+//   If there is no more remaining, then stat(PREFIX) and
+//   add to matches if it succeeds.  END.
+//
+// If inGlobStar and PREFIX is symlink and points to dir
+//   set ENTRIES = []
+// else readdir(PREFIX) as ENTRIES
+//   If fail, END
+//
+// with ENTRIES
+//   If pattern[n] is GLOBSTAR
+//     // handle the case where the globstar match is empty
+//     // by pruning it out, and testing the resulting pattern
+//     PROCESS(pattern[0..n] + pattern[n+1 .. $], false)
+//     // handle other cases.
+//     for ENTRY in ENTRIES (not dotfiles)
+//       // attach globstar + tail onto the entry
+//       // Mark that this entry is a globstar match
+//       PROCESS(pattern[0..n] + ENTRY + pattern[n .. $], true)
+//
+//   else // not globstar
+//     for ENTRY in ENTRIES (not dotfiles, unless pattern[n] is dot)
+//       Test ENTRY against pattern[n]
+//       If fails, continue
+//       If passes, PROCESS(pattern[0..n] + item + pattern[n+1 .. $])
+//
+// Caveat:
+//   Cache all stats and readdirs results to minimize syscall.  Since all
+//   we ever care about is existence and directory-ness, we can just keep
+//   `true` for files, and [children,...] for directories, or `false` for
+//   things that don't exist.
+module.exports = glob;
+var rp = require('fs.realpath');
+var minimatch = require('minimatch');
+var Minimatch = minimatch.Minimatch;
+var inherits = require('inherits');
+var EE = require('events').EventEmitter;
+var path = require('path');
+var assert = require('assert');
+var isAbsolute = require('path').isAbsolute;
+var globSync = require('./sync.js');
+var common = require('./common.js');
+var setopts = common.setopts;
+var ownProp = common.ownProp;
+var inflight = require('inflight');
+var util = require('util');
+var childrenIgnored = common.childrenIgnored;
+var isIgnored = common.isIgnored;
+var once = require('once');
+function glob(pattern, options, cb) {
+    if (typeof options === 'function')
+        cb = options, options = {};
+    if (!options)
+        options = {};
+    if (options.sync) {
+        if (cb)
+            throw new TypeError('callback provided to sync glob');
+        return globSync(pattern, options);
+    }
+    return new Glob(pattern, options, cb);
+}
+glob.sync = globSync;
+var GlobSync = glob.GlobSync = globSync.GlobSync;
+// old api surface
+glob.glob = glob;
+function extend(origin, add) {
+    if (add === null || typeof add !== 'object') {
+        return origin;
+    }
+    var keys = Object.keys(add);
+    var i = keys.length;
+    while (i--) {
+        origin[keys[i]] = add[keys[i]];
+    }
+    return origin;
+}
+glob.hasMagic = function (pattern, options_) {
+    var options = extend({}, options_);
+    options.noprocess = true;
+    var g = new Glob(pattern, options);
+    var set = g.minimatch.set;
+    if (!pattern)
+        return false;
+    if (set.length > 1)
+        return true;
+    for (var j = 0; j < set[0].length; j++) {
+        if (typeof set[0][j] !== 'string')
+            return true;
+    }
+    return false;
+};
+glob.Glob = Glob;
+inherits(Glob, EE);
+function Glob(pattern, options, cb) {
+    if (typeof options === 'function') {
+        cb = options;
+        options = null;
+    }
+    if (options && options.sync) {
+        if (cb)
+            throw new TypeError('callback provided to sync glob');
+        return new GlobSync(pattern, options);
+    }
+    if (!(this instanceof Glob))
+        return new Glob(pattern, options, cb);
+    setopts(this, pattern, options);
+    this._didRealPath = false;
+    // process each pattern in the minimatch set
+    var n = this.minimatch.set.length;
+    // The matches are stored as {<filename>: true,...} so that
+    // duplicates are automagically pruned.
+    // Later, we do an Object.keys() on these.
+    // Keep them as a list so we can fill in when nonull is set.
+    this.matches = new Array(n);
+    if (typeof cb === 'function') {
+        cb = once(cb);
+        this.on('error', cb);
+        this.on('end', function (matches) {
+            cb(null, matches);
+        });
+    }
+    var self = this;
+    this._processing = 0;
+    this._emitQueue = [];
+    this._processQueue = [];
+    this.paused = false;
+    if (this.noprocess)
+        return this;
+    if (n === 0)
+        return done();
+    var sync = true;
+    for (var i = 0; i < n; i++) {
+        this._process(this.minimatch.set[i], i, false, done);
+    }
+    sync = false;
+    function done() {
+        --self._processing;
+        if (self._processing <= 0) {
+            if (sync) {
+                process.nextTick(function () {
+                    self._finish();
+                });
+            }
+            else {
+                self._finish();
+            }
+        }
+    }
+}
+Glob.prototype._finish = function () {
+    assert(this instanceof Glob);
+    if (this.aborted)
+        return;
+    if (this.realpath && !this._didRealpath)
+        return this._realpath();
+    common.finish(this);
+    this.emit('end', this.found);
+};
+Glob.prototype._realpath = function () {
+    if (this._didRealpath)
+        return;
+    this._didRealpath = true;
+    var n = this.matches.length;
+    if (n === 0)
+        return this._finish();
+    var self = this;
+    for (var i = 0; i < this.matches.length; i++)
+        this._realpathSet(i, next);
+    function next() {
+        if (--n === 0)
+            self._finish();
+    }
+};
+Glob.prototype._realpathSet = function (index, cb) {
+    var matchset = this.matches[index];
+    if (!matchset)
+        return cb();
+    var found = Object.keys(matchset);
+    var self = this;
+    var n = found.length;
+    if (n === 0)
+        return cb();
+    var set = this.matches[index] = Object.create(null);
+    found.forEach(function (p, i) {
+        // If there's a problem with the stat, then it means that
+        // one or more of the links in the realpath couldn't be
+        // resolved.  just return the abs value in that case.
+        p = self._makeAbs(p);
+        rp.realpath(p, self.realpathCache, function (er, real) {
+            if (!er)
+                set[real] = true;
+            else if (er.syscall === 'stat')
+                set[p] = true;
+            else
+                self.emit('error', er); // srsly wtf right here
+            if (--n === 0) {
+                self.matches[index] = set;
+                cb();
+            }
+        });
+    });
+};
+Glob.prototype._mark = function (p) {
+    return common.mark(this, p);
+};
+Glob.prototype._makeAbs = function (f) {
+    return common.makeAbs(this, f);
+};
+Glob.prototype.abort = function () {
+    this.aborted = true;
+    this.emit('abort');
+};
+Glob.prototype.pause = function () {
+    if (!this.paused) {
+        this.paused = true;
+        this.emit('pause');
+    }
+};
+Glob.prototype.resume = function () {
+    if (this.paused) {
+        this.emit('resume');
+        this.paused = false;
+        if (this._emitQueue.length) {
+            var eq = this._emitQueue.slice(0);
+            this._emitQueue.length = 0;
+            for (var i = 0; i < eq.length; i++) {
+                var e = eq[i];
+                this._emitMatch(e[0], e[1]);
+            }
+        }
+        if (this._processQueue.length) {
+            var pq = this._processQueue.slice(0);
+            this._processQueue.length = 0;
+            for (var i = 0; i < pq.length; i++) {
+                var p = pq[i];
+                this._processing--;
+                this._process(p[0], p[1], p[2], p[3]);
+            }
+        }
+    }
+};
+Glob.prototype._process = function (pattern, index, inGlobStar, cb) {
+    assert(this instanceof Glob);
+    assert(typeof cb === 'function');
+    if (this.aborted)
+        return;
+    this._processing++;
+    if (this.paused) {
+        this._processQueue.push([pattern, index, inGlobStar, cb]);
+        return;
+    }
+    //console.error('PROCESS %d', this._processing, pattern)
+    // Get the first [n] parts of pattern that are all strings.
+    var n = 0;
+    while (typeof pattern[n] === 'string') {
+        n++;
+    }
+    // now n is the index of the first one that is *not* a string.
+    // see if there's anything else
+    var prefix;
+    switch (n) {
+        // if not, then this is rather simple
+        case pattern.length:
+            this._processSimple(pattern.join('/'), index, cb);
+            return;
+        case 0:
+            // pattern *starts* with some non-trivial item.
+            // going to readdir(cwd), but not include the prefix in matches.
+            prefix = null;
+            break;
+        default:
+            // pattern has some string bits in the front.
+            // whatever it starts with, whether that's 'absolute' like /foo/bar,
+            // or 'relative' like '../baz'
+            prefix = pattern.slice(0, n).join('/');
+            break;
+    }
+    var remain = pattern.slice(n);
+    // get the list of entries.
+    var read;
+    if (prefix === null)
+        read = '.';
+    else if (isAbsolute(prefix) ||
+        isAbsolute(pattern.map(function (p) {
+            return typeof p === 'string' ? p : '[*]';
+        }).join('/'))) {
+        if (!prefix || !isAbsolute(prefix))
+            prefix = '/' + prefix;
+        read = prefix;
+    }
+    else
+        read = prefix;
+    var abs = this._makeAbs(read);
+    //if ignored, skip _processing
+    if (childrenIgnored(this, read))
+        return cb();
+    var isGlobStar = remain[0] === minimatch.GLOBSTAR;
+    if (isGlobStar)
+        this._processGlobStar(prefix, read, abs, remain, index, inGlobStar, cb);
+    else
+        this._processReaddir(prefix, read, abs, remain, index, inGlobStar, cb);
+};
+Glob.prototype._processReaddir = function (prefix, read, abs, remain, index, inGlobStar, cb) {
+    var self = this;
+    this._readdir(abs, inGlobStar, function (er, entries) {
+        return self._processReaddir2(prefix, read, abs, remain, index, inGlobStar, entries, cb);
+    });
+};
+Glob.prototype._processReaddir2 = function (prefix, read, abs, remain, index, inGlobStar, entries, cb) {
+    // if the abs isn't a dir, then nothing can match!
+    if (!entries)
+        return cb();
+    // It will only match dot entries if it starts with a dot, or if
+    // dot is set.  Stuff like @(.foo|.bar) isn't allowed.
+    var pn = remain[0];
+    var negate = !!this.minimatch.negate;
+    var rawGlob = pn._glob;
+    var dotOk = this.dot || rawGlob.charAt(0) === '.';
+    var matchedEntries = [];
+    for (var i = 0; i < entries.length; i++) {
+        var e = entries[i];
+        if (e.charAt(0) !== '.' || dotOk) {
+            var m;
+            if (negate && !prefix) {
+                m = !e.match(pn);
+            }
+            else {
+                m = e.match(pn);
+            }
+            if (m)
+                matchedEntries.push(e);
+        }
+    }
+    //console.error('prd2', prefix, entries, remain[0]._glob, matchedEntries)
+    var len = matchedEntries.length;
+    // If there are no matched entries, then nothing matches.
+    if (len === 0)
+        return cb();
+    // if this is the last remaining pattern bit, then no need for
+    // an additional stat *unless* the user has specified mark or
+    // stat explicitly.  We know they exist, since readdir returned
+    // them.
+    if (remain.length === 1 && !this.mark && !this.stat) {
+        if (!this.matches[index])
+            this.matches[index] = Object.create(null);
+        for (var i = 0; i < len; i++) {
+            var e = matchedEntries[i];
+            if (prefix) {
+                if (prefix !== '/')
+                    e = prefix + '/' + e;
+                else
+                    e = prefix + e;
+            }
+            if (e.charAt(0) === '/' && !this.nomount) {
+                e = path.join(this.root, e);
+            }
+            this._emitMatch(index, e);
+        }
+        // This was the last one, and no stats were needed
+        return cb();
+    }
+    // now test all matched entries as stand-ins for that part
+    // of the pattern.
+    remain.shift();
+    for (var i = 0; i < len; i++) {
+        var e = matchedEntries[i];
+        var newPattern;
+        if (prefix) {
+            if (prefix !== '/')
+                e = prefix + '/' + e;
+            else
+                e = prefix + e;
+        }
+        this._process([e].concat(remain), index, inGlobStar, cb);
+    }
+    cb();
+};
+Glob.prototype._emitMatch = function (index, e) {
+    if (this.aborted)
+        return;
+    if (isIgnored(this, e))
+        return;
+    if (this.paused) {
+        this._emitQueue.push([index, e]);
+        return;
+    }
+    var abs = isAbsolute(e) ? e : this._makeAbs(e);
+    if (this.mark)
+        e = this._mark(e);
+    if (this.absolute)
+        e = abs;
+    if (this.matches[index][e])
+        return;
+    if (this.nodir) {
+        var c = this.cache[abs];
+        if (c === 'DIR' || Array.isArray(c))
+            return;
+    }
+    this.matches[index][e] = true;
+    var st = this.statCache[abs];
+    if (st)
+        this.emit('stat', e, st);
+    this.emit('match', e);
+};
+Glob.prototype._readdirInGlobStar = function (abs, cb) {
+    if (this.aborted)
+        return;
+    // follow all symlinked directories forever
+    // just proceed as if this is a non-globstar situation
+    if (this.follow)
+        return this._readdir(abs, false, cb);
+    var lstatkey = 'lstat\0' + abs;
+    var self = this;
+    var lstatcb = inflight(lstatkey, lstatcb_);
+    if (lstatcb)
+        self.fs.lstat(abs, lstatcb);
+    function lstatcb_(er, lstat) {
+        if (er && er.code === 'ENOENT')
+            return cb();
+        var isSym = lstat && lstat.isSymbolicLink();
+        self.symlinks[abs] = isSym;
+        // If it's not a symlink or a dir, then it's definitely a regular file.
+        // don't bother doing a readdir in that case.
+        if (!isSym && lstat && !lstat.isDirectory()) {
+            self.cache[abs] = 'FILE';
+            cb();
+        }
+        else
+            self._readdir(abs, false, cb);
+    }
+};
+Glob.prototype._readdir = function (abs, inGlobStar, cb) {
+    if (this.aborted)
+        return;
+    cb = inflight('readdir\0' + abs + '\0' + inGlobStar, cb);
+    if (!cb)
+        return;
+    //console.error('RD %j %j', +inGlobStar, abs)
+    if (inGlobStar && !ownProp(this.symlinks, abs))
+        return this._readdirInGlobStar(abs, cb);
+    if (ownProp(this.cache, abs)) {
+        var c = this.cache[abs];
+        if (!c || c === 'FILE')
+            return cb();
+        if (Array.isArray(c))
+            return cb(null, c);
+    }
+    var self = this;
+    self.fs.readdir(abs, readdirCb(this, abs, cb));
+};
+function readdirCb(self, abs, cb) {
+    return function (er, entries) {
+        if (er)
+            self._readdirError(abs, er, cb);
+        else
+            self._readdirEntries(abs, entries, cb);
+    };
+}
+Glob.prototype._readdirEntries = function (abs, entries, cb) {
+    if (this.aborted)
+        return;
+    // if we haven't asked to stat everything, then just
+    // assume that everything in there exists, so we can avoid
+    // having to stat it a second time.
+    if (!this.mark && !this.stat) {
+        for (var i = 0; i < entries.length; i++) {
+            var e = entries[i];
+            if (abs === '/')
+                e = abs + e;
+            else
+                e = abs + '/' + e;
+            this.cache[e] = true;
+        }
+    }
+    this.cache[abs] = entries;
+    return cb(null, entries);
+};
+Glob.prototype._readdirError = function (f, er, cb) {
+    if (this.aborted)
+        return;
+    // handle errors, and cache the information
+    switch (er.code) {
+        case 'ENOTSUP': // https://github.com/isaacs/node-glob/issues/205
+        case 'ENOTDIR': // totally normal. means it *does* exist.
+            var abs = this._makeAbs(f);
+            this.cache[abs] = 'FILE';
+            if (abs === this.cwdAbs) {
+                var error = new Error(er.code + ' invalid cwd ' + this.cwd);
+                error.path = this.cwd;
+                error.code = er.code;
+                this.emit('error', error);
+                this.abort();
+            }
+            break;
+        case 'ENOENT': // not terribly unusual
+        case 'ELOOP':
+        case 'ENAMETOOLONG':
+        case 'UNKNOWN':
+            this.cache[this._makeAbs(f)] = false;
+            break;
+        default: // some unusual error.  Treat as failure.
+            this.cache[this._makeAbs(f)] = false;
+            if (this.strict) {
+                this.emit('error', er);
+                // If the error is handled, then we abort
+                // if not, we threw out of here
+                this.abort();
+            }
+            if (!this.silent)
+                console.error('glob error', er);
+            break;
+    }
+    return cb();
+};
+Glob.prototype._processGlobStar = function (prefix, read, abs, remain, index, inGlobStar, cb) {
+    var self = this;
+    this._readdir(abs, inGlobStar, function (er, entries) {
+        self._processGlobStar2(prefix, read, abs, remain, index, inGlobStar, entries, cb);
+    });
+};
+Glob.prototype._processGlobStar2 = function (prefix, read, abs, remain, index, inGlobStar, entries, cb) {
+    //console.error('pgs2', prefix, remain[0], entries)
+    // no entries means not a dir, so it can never have matches
+    // foo.txt/** doesn't match foo.txt
+    if (!entries)
+        return cb();
+    // test without the globstar, and with every child both below
+    // and replacing the globstar.
+    var remainWithoutGlobStar = remain.slice(1);
+    var gspref = prefix ? [prefix] : [];
+    var noGlobStar = gspref.concat(remainWithoutGlobStar);
+    // the noGlobStar pattern exits the inGlobStar state
+    this._process(noGlobStar, index, false, cb);
+    var isSym = this.symlinks[abs];
+    var len = entries.length;
+    // If it's a symlink, and we're in a globstar, then stop
+    if (isSym && inGlobStar)
+        return cb();
+    for (var i = 0; i < len; i++) {
+        var e = entries[i];
+        if (e.charAt(0) === '.' && !this.dot)
+            continue;
+        // these two cases enter the inGlobStar state
+        var instead = gspref.concat(entries[i], remainWithoutGlobStar);
+        this._process(instead, index, true, cb);
+        var below = gspref.concat(entries[i], remain);
+        this._process(below, index, true, cb);
+    }
+    cb();
+};
+Glob.prototype._processSimple = function (prefix, index, cb) {
+    // XXX review this.  Shouldn't it be doing the mounting etc
+    // before doing stat?  kinda weird?
+    var self = this;
+    this._stat(prefix, function (er, exists) {
+        self._processSimple2(prefix, index, er, exists, cb);
+    });
+};
+Glob.prototype._processSimple2 = function (prefix, index, er, exists, cb) {
+    //console.error('ps2', prefix, exists)
+    if (!this.matches[index])
+        this.matches[index] = Object.create(null);
+    // If it doesn't exist, then just mark the lack of results
+    if (!exists)
+        return cb();
+    if (prefix && isAbsolute(prefix) && !this.nomount) {
+        var trail = /[\/\\]$/.test(prefix);
+        if (prefix.charAt(0) === '/') {
+            prefix = path.join(this.root, prefix);
+        }
+        else {
+            prefix = path.resolve(this.root, prefix);
+            if (trail)
+                prefix += '/';
+        }
+    }
+    if (process.platform === 'win32')
+        prefix = prefix.replace(/\\/g, '/');
+    // Mark this as a match
+    this._emitMatch(index, prefix);
+    cb();
+};
+// Returns either 'DIR', 'FILE', or false
+Glob.prototype._stat = function (f, cb) {
+    var abs = this._makeAbs(f);
+    var needDir = f.slice(-1) === '/';
+    if (f.length > this.maxLength)
+        return cb();
+    if (!this.stat && ownProp(this.cache, abs)) {
+        var c = this.cache[abs];
+        if (Array.isArray(c))
+            c = 'DIR';
+        // It exists, but maybe not how we need it
+        if (!needDir || c === 'DIR')
+            return cb(null, c);
+        if (needDir && c === 'FILE')
+            return cb();
+        // otherwise we have to stat, because maybe c=true
+        // if we know it exists, but not what it is.
+    }
+    var exists;
+    var stat = this.statCache[abs];
+    if (stat !== undefined) {
+        if (stat === false)
+            return cb(null, stat);
+        else {
+            var type = stat.isDirectory() ? 'DIR' : 'FILE';
+            if (needDir && type === 'FILE')
+                return cb();
+            else
+                return cb(null, type, stat);
+        }
+    }
+    var self = this;
+    var statcb = inflight('stat\0' + abs, lstatcb_);
+    if (statcb)
+        self.fs.lstat(abs, statcb);
+    function lstatcb_(er, lstat) {
+        if (lstat && lstat.isSymbolicLink()) {
+            // If it's a symlink, then treat it as the target, unless
+            // the target does not exist, then treat it as a file.
+            return self.fs.stat(abs, function (er, stat) {
+                if (er)
+                    self._stat2(f, abs, null, lstat, cb);
+                else
+                    self._stat2(f, abs, er, stat, cb);
+            });
+        }
+        else {
+            self._stat2(f, abs, er, lstat, cb);
+        }
+    }
+};
+Glob.prototype._stat2 = function (f, abs, er, stat, cb) {
+    if (er && (er.code === 'ENOENT' || er.code === 'ENOTDIR')) {
+        this.statCache[abs] = false;
+        return cb();
+    }
+    var needDir = f.slice(-1) === '/';
+    this.statCache[abs] = stat;
+    if (abs.slice(-1) === '/' && stat && !stat.isDirectory())
+        return cb(null, false, stat);
+    var c = true;
+    if (stat)
+        c = stat.isDirectory() ? 'DIR' : 'FILE';
+    this.cache[abs] = this.cache[abs] || c;
+    if (needDir && c === 'FILE')
+        return cb();
+    return cb(null, c, stat);
+};

package/libs/node_modules/glob/sync.d.ts

@@ -0,0 +1,23 @@
+export = globSync;
+declare function globSync(pattern: any, options: any, ...args: any[]): any;
+declare namespace globSync {
+    export { GlobSync };
+}
+declare function GlobSync(pattern: any, options: any, ...args: any[]): GlobSync;
+declare class GlobSync {
+    constructor(pattern: any, options: any, ...args: any[]);
+    matches: any[];
+    _finish(): void;
+    _process(pattern: any, index: any, inGlobStar: any): void;
+    _processReaddir(prefix: any, read: any, abs: any, remain: any, index: any, inGlobStar: any): void;
+    _emitMatch(index: any, e: any): void;
+    _readdirInGlobStar(abs: any): any;
+    _readdir(abs: any, inGlobStar: any): any;
+    _readdirEntries(abs: any, entries: any): any;
+    _readdirError(f: any, er: any): void;
+    _processGlobStar(prefix: any, read: any, abs: any, remain: any, index: any, inGlobStar: any): void;
+    _processSimple(prefix: any, index: any): void;
+    _stat(f: any): any;
+    _mark(p: any): any;
+    _makeAbs(f: any): any;
+}