I found this question through another question which was KeystoneJS specific but was marked as duplicate. If anyone here might be looking for a Keystone answer, this is how I did my deep populate query in Keystone.
Mongoose two level population using KeystoneJs [duplicate]
exports.getStoreWithId = function (req, res) {
Store.model
.find()
.populate({
path: 'productTags productCategories',
populate: {
path: 'tags',
},
})
.where('updateId', req.params.id)
.exec(function (err, item) {
if (err) return res.apiError('database error', err);
// possibly more than one
res.apiResponse({
store: item,
});
});
};