Learning FHIR and trying to implement with MEAN stack which uses MongoDb as database, I would like to seek your help on my question.
When I get the POST request for a new resource docment, I will insert it into MongoDB. Since the MongoDB will add the _id (object id) to the resources as a unique id. When I retrieve the document, it will have the extra field _id. I think it will make the resources not compliance any more since the _id is not defined in the resources.
May I know how to handle this issue? Will this extra _id matter in the FHIR resource?
Best regards,
Autorun
So, I'm also using MongoDB - along with mongoose - to implement FHIR in nodejs.
I've just added a field called id in the schema definition for mongoose like this
import mongoose from 'mongoose';
import shortid from 'shortid';
class resource extends mongoose.Schema {
constructor(schema) {
super();
this.add({
// just added this to make MongoDB use shortid
_id: { type: String, default: shortid.generate },
id: { type: {} },
id_: { type: {} },
implicitRules: { type: String },
implicitRules_: { type: {} },
language: { type: String },
language_: { type: {} },
...schema
});
}
}
export default resource;
and then _id field takes its value from the id when create/update a resource
my code for upserting a patient resource
upsert(root, params, context, ast) {
const projection = this.getProjection(ast);
if (!params.data.id) {
params.data.id = shortid.generate();
}
params.data.resourceType = 'Patient';
const upserted = model
.findByIdAndUpdate(params.data.id, params.data, {
new: true,
upsert: true,
select: projection
})
.exec();
if (!upserted) {
throw new Error('Error upserting');
}
return upserted;
}
yes, the _id will not be conformant. You can't change it to 'id'?
Perhaps you can take a look at the Spark server, which also uses a MongoDB to store the resources. In the Spark.Store.Mongo namespace you will see some helper methods to convert a Mongo BSONdocument to a FHIR resource.
Related
Creating models in Mongoose is quite pointless since such models are already created with GraphQL and existing constructs (ie TypeScript interface).
How can we get GraphQL to use Mongoose's operations on models supplied from GraphQL without having to recreate models in Mongoose?
Also, it almost seems as if there should be a wrapper for GraphQL that just communicates with the database, avoiding having to write MyModel.findById etc
How does one do that?
Every example on the Internet that talks about GraphQL and Mongodb uses Mongoose.
You should look at GraphQL-to-MongoDB, or how I learned to stop worrying and love generated query APIs. It talks about a middleware package that leverages GraphQL's types to generate your GraphQL API and parses requests sent from clients into MongoDB queries. It more or less skips over Mongoose.
Disclaimer: this is my blog post.
The package generates GraphQL input types for your schema field args, and wraps around the resolve function to parse them into MongoDB queries.
Given a simple GraphQLType:
const PersonType = new GraphQLObjectType({
name: 'PersonType',
fields: () => ({
age: { type: GraphQLInt },
name: {
type: new GraphQLNonNull(new GraphQLObjectType({
name: 'NameType',
fields: () => ({
firstName: { type: GraphQLString },
lastName: { type: GraphQLString }
})
}))
}
})
});
For the most common use case, you'll build a field in the GraphQL schema with a getMongoDbQueryResolver and getGraphQLQueryArgs. The filter, projection, and options provided by the wrapper can be passed directly to the find function.
person: {
type: new GraphQLList(PersonType),
args: getGraphQLQueryArgs(PersonType),
resolve: getMongoDbQueryResolver(PersonType,
async (filter, projection, options, source, args, context) =>
await context.db.collection('person').find(filter, projection, options).toArray()
)
}
An example of a query you could send to such a field:
{
person (
filter: {
age: { GT: 18 },
name: {
firstName: { EQ: "John" }
}
},
sort: { age: DESC },
pagination: { limit: 50 }
) {
name {
lastName
}
age
}
}
There's also a wrapper and argument types generator for mutation fields.
My Mongoose schema:
// set up the schema
var CategorySubSchema = new Schema({
name: { type: String },
_category_main : { type: String, ref: 'CategoryMain' }
},
And my controller code:
CategorySub.create({
name : req.body.name,
_category_main : req.body.category_main
}, function(err, data){
An entry in my db:
{
"_id": "54dd163434d78ae58f6b1a69",
"name": "Snacks",
"_category_main": "54dcf4a71dfecb4d86ddcb87",
"__v": 0
},
So I used an underscore, because I was following an example. Does this mean anything to the database or is it just convention for references?
Also, instead of passing the entire JSON object in the request - req.body.category_main, why not just pass and id and change my schema to this?:
var CategorySubSchema = new Schema({
name: { type: String },
category_main_id : { type: String }
},
In short, Yes.
The below schema definition is an example of Manual references.
var CategorySubSchema = new Schema({
name: { type: String },
category_main_id : { type: String }
}
where,
you save the _id field of one document in another document as a
reference. Then your application can run a second query to return the
related data. These references are simple and sufficient for most use
cases.
In this case, we need to write explicit application code to fetch the referred document and resolve the reference. Since the driver that we use wouldn't know about the collection in which the referred document is present nor the database in which the referred document is present.
When you define the schema as below, this is an example of storing the details of the referred document .(Database references)
var CategorySubSchema = new Schema({
name: { type: String },
_category_main : { type: String, ref: 'CategoryMain' }
}
They include the name of the collection, and in some cases the
database name, in addition to the value from the _id field.
These details allow various drivers to resolve the references by themselves, since the name of the collection and the database(optional) of the referred document would be contained in the document itself, rather than we writing explicit application code to resolve the references.
So I used an underscore, because I was following an example. Does this mean anything to the database or is it just convention for
references?
Using underscore in the _id field is a valid naming convention, but mongoDb doesn't explicitly mention about the naming convention of other fields which are used to resolve references. You could just use any other field name as long as it conforms to this.
sailsjs: I am trying to define a model. I would like to add a property vendorID. The type would be the monogdb objectID from the vendor collection.
Something like for a store model:
module.exports ={
attributes :{
vendorId : { type: <Monog ObjectId>}, <-- this would be a FK to the vendor Collection
storeName: {type: 'string'}
....
}
Waterline docu says:
The following attribute types are currently available:
string
text
integer
float
date
time
datetime
boolean
binary
array
json
So what do I pick?
Thanks
You should look into SailsJS associations. With waterline you shouldn't need to deal directly with id types. Just create an attribute that points to another collection via the model or collection properties.
Here's a simple example from the Sails/Waterline docs.
//Pet.js - A Pet may only have a single user
module.exports = {
attributes: {
name:'STRING',
color:'STRING',
owner:{
model:'user'
}
}
}
//User.js - A user may have multiple pets
module.exports = {
attributes: {
name:'STRING',
age:'INTEGER',
pets:{
collection: 'pet',
via: 'owner'
}
}
}
The _id is created automatically for you by Waterline you don't have to do this.
I'm using MongoDB as a log keeper for my app to then sync mobile clients. I have this models set up in NodeJS:
var UserArticle = new Schema({
date: { type: Number, default: Math.round((new Date()).getTime() / 1000) }, //Timestamp!
user: [{type: Schema.ObjectId, ref: "User"}],
article: [{type: Schema.ObjectId, ref: "Article"}],
place: Number,
read: Number,
starred: Number,
source: String
});
mongoose.model("UserArticle",UserArticle);
var Log = new Schema({
user: [{type: Schema.ObjectId, ref: "User"}],
action: Number, // O => Insert, 1 => Update, 2 => Delete
uarticle: [{type: Schema.ObjectId, ref: "UserArticle"}],
timestamp: { type: Number, default: Math.round((new Date()).getTime() / 1000) }
});
mongoose.model("Log",Log);
When I want to retrive the log I use the follwing code:
var log = mongoose.model('Log');
log
.where("user", req.session.user)
.desc("timestamp")
.populate("uarticle")
.populate("uarticle.article")
.run(function (err, articles) {
if (err) {
console.log(err);
res.send(500);
return;
}
res.json(articles);
As you can see, I want mongoose to populate the "uarticle" field from the Log collection and, then, I want to populate the "article" field of the UserArticle ("uarticle").
But, using this code, Mongoose only populates "uarticle" using the UserArticle Model, but not the article field inside of uarticle.
Is it possible to accomplish it using Mongoose and populate() or I should do something else?
Thank you,
From what I've checked in the documentation and from what I hear from you, this cannot be achieved, but you can populate the "uarticle.article" documents yourself in the callback function.
However I want to point out another aspect which I consider more important. You have documents in collection A which reference collection B, and in collection B's documents you have another reference to documents in collection C.
You are either doing this wrong (I'm referring to the database structure), or you should be using a relational database such as MySQL here. MongoDB's power relies in the fact you can embed more information in documents, thus having to make lesser queries (having your data in a single collection). While referencing something is ok, having a reference and then another reference doesn't seem like you're taking the full advantage of MongoDB here.
Perhaps you would like to share your situation and the database structure so we could help you out more.
You can use the mongoose-deep-populate plugin to do this. Usage:
User.find({}, function (err, users) {
User.deepPopulate(users, 'uarticle.article', function (err, users) {
// now each user document includes uarticle and each uarticle includes article
})
})
Disclaimer: I'm the author of the plugin.
I faced the same problem,but after hours of efforts i find the solution.It can be without using any external plugin:)
applicantListToExport: function (query, callback) {
this
.find(query).select({'advtId': 0})
.populate({
path: 'influId',
model: 'influencer',
select: { '_id': 1,'user':1},
populate: {
path: 'userid',
model: 'User'
}
})
.populate('campaignId',{'campaignTitle':1})
.exec(callback);
}
Mongoose v5.5.5 seems to allow populate on a populated document.
You can even provide an array of multiple fields to populate on the populated document
var batch = await mstsBatchModel.findOne({_id: req.body.batchId})
.populate({path: 'loggedInUser', select: 'fname lname', model: 'userModel'})
.populate({path: 'invoiceIdArray', model: 'invoiceModel',
populate: [
{path: 'updatedBy', select: 'fname lname', model: 'userModel'},
{path: 'createdBy', select: 'fname lname', model: 'userModel'},
{path: 'aircraftId', select: 'tailNum', model: 'aircraftModel'}
]});
how about something like:
populate_deep = function(type, instance, complete, seen)
{
if (!seen)
seen = {};
if (seen[instance._id])
{
complete();
return;
}
seen[instance._id] = true;
// use meta util to get all "references" from the schema
var refs = meta.get_references(meta.schema(type));
if (!refs)
{
complete();
return;
}
var opts = [];
for (var i=0; i<refs.length; i++)
opts.push({path: refs[i].name, model: refs[i].ref});
mongoose.model(type).populate(instance, opts, function(err,o){
utils.forEach(refs, function (ref, next) {
if (ref.is_array)
utils.forEach(o[ref.name], function (v, lnext) {
populate_deep(ref.ref_type, v, lnext, seen);
}, next);
else
populate_deep(ref.ref_type, o[ref.name], next, seen);
}, complete);
});
}
meta utils is rough... want the src?
or you can simply pass an obj to the populate as:
const myFilterObj = {};
const populateObj = {
path: "parentFileds",
populate: {
path: "childFileds",
select: "childFiledsToSelect"
},
select: "parentFiledsToSelect"
};
Model.find(myFilterObj)
.populate(populateObj).exec((err, data) => console.log(data) );
I am using mongoose (node), what is the best way to output id instead of _id?
Given you're using Mongoose, you can use 'virtuals', which are essentially fake fields that Mongoose creates. They're not stored in the DB, they just get populated at run time:
// Duplicate the ID field.
Schema.virtual('id').get(function(){
return this._id.toHexString();
});
// Ensure virtual fields are serialised.
Schema.set('toJSON', {
virtuals: true
});
Any time toJSON is called on the Model you create from this Schema, it will include an 'id' field that matches the _id field Mongo generates. Likewise you can set the behaviour for toObject in the same way.
See:
http://mongoosejs.com/docs/api.html
http://mongoosejs.com/docs/guide.html#toJSON
http://mongoosejs.com/docs/guide.html#toObject
You can abstract this into a BaseSchema all your models then extend/invoke to keep the logic in one place. I wrote the above while creating an Ember/Node/Mongoose app, since Ember really prefers to have an 'id' field to work with.
As of Mongoose v4.0 part of this functionality is supported out of the box. It's no longer required to manually add a virtual id field as explained by #Pascal Zajac.
Mongoose assigns each of your schemas an id virtual getter by default
which returns the documents _id field cast to a string, or in the case
of ObjectIds, its hexString. If you don't want an id getter added to
your schema, you may disable it passing this option at schema
construction time. Source
However, to export this field to JSON, it's still required to enable serialization of virtual fields:
Schema.set('toJSON', {
virtuals: true
});
I used this :
schema.set('toJSON', {
virtuals: true,
versionKey:false,
transform: function (doc, ret) { delete ret._id }
});
I think it would be great if they automatically suppress _id when virtuals is true.
I create a toClient() method on my models where I do this. It's also a good place to rename/remove other attributes you don't want to send to the client:
Schema.method('toClient', function() {
var obj = this.toObject();
//Rename fields
obj.id = obj._id;
delete obj._id;
return obj;
});
Here is an alternative version of the answer provided by #user3087827. If you find that schema.options.toJSON is undefined then you can use:
schema.set('toJSON', {
transform: function (doc, ret, options) {
ret.id = ret._id;
delete ret._id;
delete ret.__v;
}
});
//Transform
Schema.options.toJSON.transform = function (doc, ret, options) {
// remove the _id of every document before returning the result
ret.id = ret._id;
delete ret._id;
delete ret.__v;
}
there is a "Schema.options.toObject.transform" property to do the reverse or you could just setup as a virtual id.
If you want to use id instead of _id globally then you can set toJSON config on mongoose object(starting from v5.3):
mongoose.set('toJSON', {
virtuals: true,
transform: (doc, converted) => {
delete converted._id;
}
});
Overwrite default method toJSON by new one:
schema.method('toJSON', function () {
const { __v, _id, ...object } = this.toObject();
object.id = _id;
return object;
});
There is also normalize-mongoose a simple package that removes _id and __v for you.
From something like this:
import mongoose from 'mongoose';
import normalize from 'normalize-mongoose';
const personSchema = mongoose.Schema({ name: String });
personSchema.plugin(normalize);
const Person = mongoose.model('Person', personSchema);
const someone = new Person({ name: 'Abraham' });
const result = someone.toJSON();
console.log(result);
So let's say you have something like this:
{
"_id": "5dff03d3218b91425b9d6fab",
"name": "Abraham",
"__v": 0
}
You will get this output:
{
"id": "5dff03d3218b91425b9d6fab",
"name": "Abraham"
}
I created an easy to use plugin for this purpose that I apply for all my projects and to all schema's globally. It converts _id to id and strips the __v parameter as well.
So it converts:
{
"_id": "400e8324a71d4410b9dc3980b5f8cdea",
"__v": 2,
"name": "Item A"
}
To a simpler and cleaner:
{
"id": "400e8324a71d4410b9dc3980b5f8cdea",
"name": "Item A"
}
Usage as a global plugin:
const mongoose = require('mongoose');
mongoose.plugin(require('meanie-mongoose-to-json'));
Or for a specific schema:
const mongoose = require('mongoose');
const Schema = mongoose.Schema;
const MySchema = new Schema({});
MySchema.plugin(require('meanie-mongoose-to-json'));
Hope this helps someone.
You can also use the aggregate function when searching for items to return. $project will allow you to create fields, which you can do and assign it to _id.
<model>.aggregate([{$project: {_id: 0, id: '$_id'}], (err, res) => {
//
})
If you are using lodash to pick the elements you want, this will work for you.
UserSchema.virtual('id').get(function(){
return this._id.toHexString();
});
UserSchema.set('toObject', { virtuals: true })
UserSchema.methods.toJSON = function() {
return _.pick(
this.toObject(),
['id','email','firstName','lastName','username']
);
Override toJSONmethod for specific model schema.
https://mongoosejs.com/docs/api.html#schema_Schema-method
YourSchema.methods.toJSON = function () {
return {
id: this._id,
some_field: this.some_field,
created_at: this.createdAt
}
}
Create a base schema
import { Schema } from "mongoose";
export class BaseSchema extends Schema {
constructor(sche: any) {
super(sche);
this.set('toJSON', {
virtuals: true,
transform: (doc, converted) => {
delete converted._id;
}
});
}
}
Now in your mongoose model, use BaseSchema instead of Schema
import mongoose, { Document} from 'mongoose';
import { BaseSchema } from '../../helpers/mongoose';
const UserSchema = new BaseSchema({
name: String,
age: Number,
});
export interface IUser {
name: String,
age: Number,
}
interface IPlanModel extends IUser, Document { }
export const PlanDoc = mongoose.model<IPlanModel>('User', UserSchema);
Typescript implementation of #Pascal Zajac answer
There's another driver that does that http://alexeypetrushin.github.com/mongo-lite set convertId option to true. See "Defaults & Setting" section for more details.
Mongoose assigns each of your schemas an id virtual getter by default which returns the document's _id field cast to a string, or in the case of ObjectIds, its hexString.
https://mongoosejs.com/docs/guide.html
You can also use pre 'save' hook:
TouSchema.pre('save', function () {
if (this.isNew) {
this._doc.id = this._id;
}
}
JSON.parse(JSON.stringify(doc.toJSON()))