mirror of
https://github.com/atlanticbiomedical/biomedjs.git
synced 2025-07-02 00:47:26 -04:00
Added node-modules
This commit is contained in:
4
node_modules/mongoose/lib/drivers/SPEC.md
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vendored
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4
node_modules/mongoose/lib/drivers/SPEC.md
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@ -0,0 +1,4 @@
|
||||
|
||||
# Driver Spec
|
||||
|
||||
TODO
|
8
node_modules/mongoose/lib/drivers/node-mongodb-native/binary.js
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vendored
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8
node_modules/mongoose/lib/drivers/node-mongodb-native/binary.js
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vendored
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|
||||
|
||||
/*!
|
||||
* Module dependencies.
|
||||
*/
|
||||
|
||||
var Binary = require('mongodb').BSONPure.Binary;
|
||||
|
||||
module.exports = exports = Binary;
|
211
node_modules/mongoose/lib/drivers/node-mongodb-native/collection.js
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vendored
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211
node_modules/mongoose/lib/drivers/node-mongodb-native/collection.js
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vendored
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@ -0,0 +1,211 @@
|
||||
|
||||
/*!
|
||||
* Module dependencies.
|
||||
*/
|
||||
|
||||
var MongooseCollection = require('../../collection')
|
||||
, Collection = require('mongodb').Collection
|
||||
, STATES = require('../../connectionstate')
|
||||
, utils = require('../../utils')
|
||||
|
||||
/**
|
||||
* A [node-mongodb-native](https://github.com/mongodb/node-mongodb-native) collection implementation.
|
||||
*
|
||||
* All methods methods from the [node-mongodb-native](https://github.com/mongodb/node-mongodb-native) driver are copied and wrapped in queue management.
|
||||
*
|
||||
* @inherits Collection
|
||||
* @api private
|
||||
*/
|
||||
|
||||
function NativeCollection () {
|
||||
this.collection = null;
|
||||
MongooseCollection.apply(this, arguments);
|
||||
}
|
||||
|
||||
/*!
|
||||
* Inherit from abstract Collection.
|
||||
*/
|
||||
|
||||
NativeCollection.prototype.__proto__ = MongooseCollection.prototype;
|
||||
|
||||
/**
|
||||
* Called when the connection opens.
|
||||
*
|
||||
* @api private
|
||||
*/
|
||||
|
||||
NativeCollection.prototype.onOpen = function () {
|
||||
var self = this;
|
||||
|
||||
// always get a new collection in case the user changed host:port
|
||||
// of parent db instance when re-opening the connection.
|
||||
|
||||
if (!self.opts.capped.size) {
|
||||
// non-capped
|
||||
return self.conn.db.collection(self.name, callback);
|
||||
}
|
||||
|
||||
// capped
|
||||
return self.conn.db.collection(self.name, function (err, c) {
|
||||
if (err) return callback(err);
|
||||
|
||||
// discover if this collection exists and if it is capped
|
||||
c.options(function (err, exists) {
|
||||
if (err) return callback(err);
|
||||
|
||||
if (exists) {
|
||||
if (exists.capped) {
|
||||
callback(null, c);
|
||||
} else {
|
||||
var msg = 'A non-capped collection exists with the name: '+ self.name +'\n\n'
|
||||
+ ' To use this collection as a capped collection, please '
|
||||
+ 'first convert it.\n'
|
||||
+ ' http://www.mongodb.org/display/DOCS/Capped+Collections#CappedCollections-Convertingacollectiontocapped'
|
||||
err = new Error(msg);
|
||||
callback(err);
|
||||
}
|
||||
} else {
|
||||
// create
|
||||
var opts = utils.clone(self.opts.capped);
|
||||
opts.capped = true;
|
||||
self.conn.db.createCollection(self.name, opts, callback);
|
||||
}
|
||||
});
|
||||
});
|
||||
|
||||
function callback (err, collection) {
|
||||
if (err) {
|
||||
// likely a strict mode error
|
||||
self.conn.emit('error', err);
|
||||
} else {
|
||||
self.collection = collection;
|
||||
MongooseCollection.prototype.onOpen.call(self);
|
||||
}
|
||||
};
|
||||
};
|
||||
|
||||
/**
|
||||
* Called when the connection closes
|
||||
*
|
||||
* @api private
|
||||
*/
|
||||
|
||||
NativeCollection.prototype.onClose = function () {
|
||||
MongooseCollection.prototype.onClose.call(this);
|
||||
};
|
||||
|
||||
/*!
|
||||
* Copy the collection methods and make them subject to queues
|
||||
*/
|
||||
|
||||
for (var i in Collection.prototype) {
|
||||
(function(i){
|
||||
NativeCollection.prototype[i] = function () {
|
||||
if (this.buffer) {
|
||||
this.addQueue(i, arguments);
|
||||
return;
|
||||
}
|
||||
|
||||
var collection = this.collection
|
||||
, args = arguments
|
||||
, self = this
|
||||
, debug = self.conn.base.options.debug;
|
||||
|
||||
if (debug) {
|
||||
if ('function' === typeof debug) {
|
||||
debug.apply(debug
|
||||
, [self.name, i].concat(utils.args(args, 0, args.length-1)));
|
||||
} else {
|
||||
console.error('\x1B[0;36mMongoose:\x1B[0m %s.%s(%s) %s %s %s'
|
||||
, self.name
|
||||
, i
|
||||
, print(args[0])
|
||||
, print(args[1])
|
||||
, print(args[2])
|
||||
, print(args[3]))
|
||||
}
|
||||
}
|
||||
|
||||
collection[i].apply(collection, args);
|
||||
};
|
||||
})(i);
|
||||
}
|
||||
|
||||
/*!
|
||||
* Debug print helper
|
||||
*/
|
||||
|
||||
function print (arg) {
|
||||
var type = typeof arg;
|
||||
if ('function' === type || 'undefined' === type) return '';
|
||||
return format(arg);
|
||||
}
|
||||
|
||||
/*!
|
||||
* Debug print helper
|
||||
*/
|
||||
|
||||
function format (obj, sub) {
|
||||
var x = utils.clone(obj);
|
||||
if (x) {
|
||||
if ('Binary' === x.constructor.name) {
|
||||
x = '[object Buffer]';
|
||||
} else if ('ObjectID' === x.constructor.name) {
|
||||
var representation = 'ObjectId("' + x.toHexString() + '")';
|
||||
x = { inspect: function() { return representation; } };
|
||||
} else if ('Date' === x.constructor.name) {
|
||||
var representation = 'new Date("' + x.toUTCString() + '")';
|
||||
x = { inspect: function() { return representation; } };
|
||||
} else if ('Object' === x.constructor.name) {
|
||||
var keys = Object.keys(x)
|
||||
, i = keys.length
|
||||
, key
|
||||
while (i--) {
|
||||
key = keys[i];
|
||||
if (x[key]) {
|
||||
if ('Binary' === x[key].constructor.name) {
|
||||
x[key] = '[object Buffer]';
|
||||
} else if ('Object' === x[key].constructor.name) {
|
||||
x[key] = format(x[key], true);
|
||||
} else if ('ObjectID' === x[key].constructor.name) {
|
||||
;(function(x){
|
||||
var representation = 'ObjectId("' + x[key].toHexString() + '")';
|
||||
x[key] = { inspect: function() { return representation; } };
|
||||
})(x)
|
||||
} else if ('Date' === x[key].constructor.name) {
|
||||
;(function(x){
|
||||
var representation = 'new Date("' + x[key].toUTCString() + '")';
|
||||
x[key] = { inspect: function() { return representation; } };
|
||||
})(x)
|
||||
} else if (Array.isArray(x[key])) {
|
||||
x[key] = x[key].map(function (o) {
|
||||
return format(o, true)
|
||||
});
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
if (sub) return x;
|
||||
}
|
||||
|
||||
return require('util')
|
||||
.inspect(x, false, 10, true)
|
||||
.replace(/\n/g, '')
|
||||
.replace(/\s{2,}/g, ' ')
|
||||
}
|
||||
|
||||
/**
|
||||
* Retreives information about this collections indexes.
|
||||
*
|
||||
* @param {Function} callback
|
||||
* @method getIndexes
|
||||
* @api public
|
||||
*/
|
||||
|
||||
NativeCollection.prototype.getIndexes = NativeCollection.prototype.indexInformation;
|
||||
|
||||
/*!
|
||||
* Module exports.
|
||||
*/
|
||||
|
||||
module.exports = NativeCollection;
|
303
node_modules/mongoose/lib/drivers/node-mongodb-native/connection.js
generated
vendored
Normal file
303
node_modules/mongoose/lib/drivers/node-mongodb-native/connection.js
generated
vendored
Normal file
@ -0,0 +1,303 @@
|
||||
/*!
|
||||
* Module dependencies.
|
||||
*/
|
||||
|
||||
var MongooseConnection = require('../../connection')
|
||||
, mongo = require('mongodb')
|
||||
, Db = mongo.Db
|
||||
, Server = mongo.Server
|
||||
, Mongos = mongo.Mongos
|
||||
, STATES = require('../../connectionstate')
|
||||
, ReplSetServers = mongo.ReplSetServers;
|
||||
|
||||
/**
|
||||
* A [node-mongodb-native](https://github.com/mongodb/node-mongodb-native) connection implementation.
|
||||
*
|
||||
* @inherits Connection
|
||||
* @api private
|
||||
*/
|
||||
|
||||
function NativeConnection() {
|
||||
MongooseConnection.apply(this, arguments);
|
||||
this._listening = false;
|
||||
};
|
||||
|
||||
/*!
|
||||
* Inherits from Connection.
|
||||
*/
|
||||
|
||||
NativeConnection.prototype.__proto__ = MongooseConnection.prototype;
|
||||
|
||||
/**
|
||||
* Opens the connection to MongoDB.
|
||||
*
|
||||
* @param {Function} fn
|
||||
* @return {Connection} this
|
||||
* @api private
|
||||
*/
|
||||
|
||||
NativeConnection.prototype.doOpen = function (fn) {
|
||||
if (this.db) {
|
||||
mute(this);
|
||||
}
|
||||
|
||||
var server = new Server(this.host, this.port, this.options.server);
|
||||
this.db = new Db(this.name, server, this.options.db);
|
||||
|
||||
var self = this;
|
||||
this.db.open(function (err) {
|
||||
if (err) return fn(err);
|
||||
listen(self);
|
||||
fn();
|
||||
});
|
||||
|
||||
return this;
|
||||
};
|
||||
|
||||
/*!
|
||||
* Register listeners for important events and bubble appropriately.
|
||||
*/
|
||||
|
||||
function listen (conn) {
|
||||
if (conn._listening) return;
|
||||
conn._listening = true;
|
||||
|
||||
conn.db.on('close', function(){
|
||||
if (conn._closeCalled) return;
|
||||
|
||||
// the driver never emits an `open` event. auto_reconnect still
|
||||
// emits a `close` event but since we never get another
|
||||
// `open` we can't emit close
|
||||
if (conn.db.serverConfig.autoReconnect) {
|
||||
conn.readyState = STATES.disconnected;
|
||||
conn.emit('close');
|
||||
return;
|
||||
}
|
||||
conn.onClose();
|
||||
});
|
||||
conn.db.on('error', function(err){
|
||||
conn.emit('error', err);
|
||||
});
|
||||
conn.db.on('timeout', function(err){
|
||||
var error = new Error(err && err.err || 'connection timeout');
|
||||
conn.emit('error', error);
|
||||
});
|
||||
conn.db.on('open', function (err, db) {
|
||||
if (STATES.disconnected === conn.readyState && db && db.databaseName) {
|
||||
conn.readyState = STATES.connected;
|
||||
conn.emit('reconnected')
|
||||
}
|
||||
})
|
||||
}
|
||||
|
||||
/*!
|
||||
* Remove listeners registered in `listen`
|
||||
*/
|
||||
|
||||
function mute (conn) {
|
||||
if (!conn.db) throw new Error('missing db');
|
||||
conn.db.removeAllListeners("close");
|
||||
conn.db.removeAllListeners("error");
|
||||
conn.db.removeAllListeners("timeout");
|
||||
conn.db.removeAllListeners("open");
|
||||
conn.db.removeAllListeners("fullsetup");
|
||||
conn._listening = false;
|
||||
}
|
||||
|
||||
/**
|
||||
* Opens a connection to a MongoDB ReplicaSet.
|
||||
*
|
||||
* See description of [doOpen](#NativeConnection-doOpen) for server options. In this case `options.replset` is also passed to ReplSetServers.
|
||||
*
|
||||
* @param {Function} fn
|
||||
* @api private
|
||||
* @return {Connection} this
|
||||
*/
|
||||
|
||||
NativeConnection.prototype.doOpenSet = function (fn) {
|
||||
if (this.db) {
|
||||
mute(this);
|
||||
}
|
||||
|
||||
var servers = []
|
||||
, self = this;
|
||||
|
||||
this.hosts.forEach(function (server) {
|
||||
var host = server.host || server.ipc;
|
||||
var port = server.port || 27017;
|
||||
servers.push(new Server(host, port, self.options.server));
|
||||
})
|
||||
|
||||
var server = this.options.mongos
|
||||
? new Mongos(servers, this.options.mongos)
|
||||
: new ReplSetServers(servers, this.options.replset);
|
||||
this.db = new Db(this.name, server, this.options.db);
|
||||
|
||||
this.db.on('fullsetup', function () {
|
||||
self.emit('fullsetup')
|
||||
});
|
||||
|
||||
this.db.open(function (err) {
|
||||
if (err) return fn(err);
|
||||
fn();
|
||||
listen(self);
|
||||
});
|
||||
|
||||
return this;
|
||||
};
|
||||
|
||||
/**
|
||||
* Closes the connection
|
||||
*
|
||||
* @param {Function} fn
|
||||
* @return {Connection} this
|
||||
* @api private
|
||||
*/
|
||||
|
||||
NativeConnection.prototype.doClose = function (fn) {
|
||||
this.db.close();
|
||||
if (fn) fn();
|
||||
return this;
|
||||
}
|
||||
|
||||
/**
|
||||
* Prepares default connection options for the node-mongodb-native driver.
|
||||
*
|
||||
* _NOTE: `passed` options take precedence over connection string options._
|
||||
*
|
||||
* @param {Object} passed options that were passed directly during connection
|
||||
* @param {Object} [connStrOptions] options that were passed in the connection string
|
||||
* @api private
|
||||
*/
|
||||
|
||||
NativeConnection.prototype.parseOptions = function (passed, connStrOpts) {
|
||||
var o = passed || {};
|
||||
o.db || (o.db = {});
|
||||
o.auth || (o.auth = {});
|
||||
o.server || (o.server = {});
|
||||
o.replset || (o.replset = {});
|
||||
o.server.socketOptions || (o.server.socketOptions = {});
|
||||
o.replset.socketOptions || (o.replset.socketOptions = {});
|
||||
|
||||
var opts = connStrOpts || {};
|
||||
Object.keys(opts).forEach(function (name) {
|
||||
switch (name) {
|
||||
case 'poolSize':
|
||||
if ('undefined' == typeof o.server.poolSize) {
|
||||
o.server.poolSize = o.replset.poolSize = opts[name];
|
||||
}
|
||||
break;
|
||||
case 'slaveOk':
|
||||
if ('undefined' == typeof o.server.slave_ok) {
|
||||
o.server.slave_ok = opts[name];
|
||||
}
|
||||
break;
|
||||
case 'autoReconnect':
|
||||
if ('undefined' == typeof o.server.auto_reconnect) {
|
||||
o.server.auto_reconnect = opts[name];
|
||||
}
|
||||
break;
|
||||
case 'ssl':
|
||||
case 'socketTimeoutMS':
|
||||
case 'connectTimeoutMS':
|
||||
if ('undefined' == typeof o.server.socketOptions[name]) {
|
||||
o.server.socketOptions[name] = o.replset.socketOptions[name] = opts[name];
|
||||
}
|
||||
break;
|
||||
case 'authdb':
|
||||
if ('undefined' == typeof o.auth.authdb) {
|
||||
o.auth.authdb = opts[name];
|
||||
}
|
||||
break;
|
||||
case 'authSource':
|
||||
if ('undefined' == typeof o.auth.authSource) {
|
||||
o.auth.authSource = opts[name];
|
||||
}
|
||||
break;
|
||||
case 'retries':
|
||||
case 'reconnectWait':
|
||||
case 'rs_name':
|
||||
if ('undefined' == typeof o.replset[name]) {
|
||||
o.replset[name] = opts[name];
|
||||
}
|
||||
break;
|
||||
case 'replicaSet':
|
||||
if ('undefined' == typeof o.replset.rs_name) {
|
||||
o.replset.rs_name = opts[name];
|
||||
}
|
||||
break;
|
||||
case 'readSecondary':
|
||||
if ('undefined' == typeof o.replset.read_secondary) {
|
||||
o.replset.read_secondary = opts[name];
|
||||
}
|
||||
break;
|
||||
case 'nativeParser':
|
||||
if ('undefined' == typeof o.db.native_parser) {
|
||||
o.db.native_parser = opts[name];
|
||||
}
|
||||
break;
|
||||
case 'w':
|
||||
case 'safe':
|
||||
case 'fsync':
|
||||
case 'journal':
|
||||
case 'wtimeoutMS':
|
||||
if ('undefined' == typeof o.db[name]) {
|
||||
o.db[name] = opts[name];
|
||||
}
|
||||
break;
|
||||
case 'readPreference':
|
||||
if ('undefined' == typeof o.db.read_preference) {
|
||||
o.db.read_preference = opts[name];
|
||||
}
|
||||
break;
|
||||
case 'readPreferenceTags':
|
||||
if ('undefined' == typeof o.db.read_preference_tags) {
|
||||
o.db.read_preference_tags = opts[name];
|
||||
}
|
||||
break;
|
||||
}
|
||||
})
|
||||
|
||||
if (!('auto_reconnect' in o.server)) {
|
||||
o.server.auto_reconnect = true;
|
||||
}
|
||||
|
||||
if (!o.db.read_preference) {
|
||||
// read from primaries by default
|
||||
o.db.read_preference = 'primary';
|
||||
}
|
||||
|
||||
// mongoose creates its own ObjectIds
|
||||
o.db.forceServerObjectId = false;
|
||||
|
||||
// default safe using new nomenclature
|
||||
if (!('journal' in o.db || 'j' in o.db ||
|
||||
'fsync' in o.db || 'safe' in o.db || 'w' in o.db)) {
|
||||
o.db.w = 1;
|
||||
}
|
||||
|
||||
validate(o);
|
||||
return o;
|
||||
}
|
||||
|
||||
/*!
|
||||
* Validates the driver db options.
|
||||
*
|
||||
* @param {Object} o
|
||||
*/
|
||||
|
||||
function validate (o) {
|
||||
if (-1 === o.db.w || 0 === o.db.w) {
|
||||
if (o.db.journal || o.db.fsync || o.db.safe) {
|
||||
throw new Error(
|
||||
'Invalid writeConcern: '
|
||||
+ 'w set to -1 or 0 cannot be combined with safe|fsync|journal');
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/*!
|
||||
* Module exports.
|
||||
*/
|
||||
|
||||
module.exports = NativeConnection;
|
29
node_modules/mongoose/lib/drivers/node-mongodb-native/objectid.js
generated
vendored
Normal file
29
node_modules/mongoose/lib/drivers/node-mongodb-native/objectid.js
generated
vendored
Normal file
@ -0,0 +1,29 @@
|
||||
|
||||
/*!
|
||||
* [node-mongodb-native](https://github.com/mongodb/node-mongodb-native) ObjectId
|
||||
* @constructor NodeMongoDbObjectId
|
||||
* @see ObjectId
|
||||
*/
|
||||
|
||||
var ObjectId = require('mongodb').BSONPure.ObjectID;
|
||||
|
||||
/*!
|
||||
* ignore
|
||||
*/
|
||||
|
||||
var ObjectIdToString = ObjectId.toString.bind(ObjectId);
|
||||
module.exports = exports = ObjectId;
|
||||
|
||||
ObjectId.fromString = function(str){
|
||||
// patch native driver bug in V0.9.6.4
|
||||
if (!('string' === typeof str && 24 === str.length)) {
|
||||
throw new Error("Invalid ObjectId");
|
||||
}
|
||||
|
||||
return ObjectId.createFromHexString(str);
|
||||
};
|
||||
|
||||
ObjectId.toString = function(oid){
|
||||
if (!arguments.length) return ObjectIdToString();
|
||||
return oid.toHexString();
|
||||
};
|
Reference in New Issue
Block a user