Iron out duplicate fields in a collection and update marker fields

ConsolidatingDuplicateVariants-MongoDB.js

function reorderProperties(obj) {
    var sortedObj = {};
    Object.keySet(obj).sort().forEach(key => {
        sortedObj[key] = obj[key];
    });
    return sortedObj;
};

db.SimpleVariants.updateMany({}, { $unset: { "qualifiers": 1, "coordinates.hg19.qualifiers": 2, "coordinates.rcrs.qualifiers": 3 } });

//make sure keys are all ordered so equivalency checks work as expected.
db.SimpleVariants.find({}).forEach((variant) => {
    Object.keys(variant.coordinates).forEach(referenceSet => {
        variant.coordinates[referenceSet] = reorderProperties(variant.coordinates[referenceSet]);
    });
    db.SimpleVariants.replaceOne({ _id: variant._id }, variant);
});

// Point all curations at a single equivalent variant
db.SimpleVariants.aggregate([
    { $group: { _id: "$coordinates", count: { $sum: 1 } } },
    { $match: { count: { $gt: 1 } } }
]).forEach(dup => {
    var allMatches = db.SimpleVariants.find({ "coordinates": dup._id });
    var allIds = allMatches.map((it) => {
        return it._id;
    });
    db.Curations.updateMany({ variant: { $in: allIds.slice(1) } }, { $set: { variant: allIds[0] } });
});

// remove orphaned variants
db.SimpleVariants.deleteMany({ _id: { $nin: db.Curations.distinct("variant") } })

//update transient variant details so they match
db.SimpleVariants.find({}).forEach((variant) => {
    db.Curations.updateMany({ variant: variant._id }, { $set: { "transientVariantDetails": variant } })
});

//reset preferred curations and latest for
db.Curations.updateMany({}, { $set: { "preferredForContexts": [], "contextsClassificationIsLatestForVariant":[]} });
db.Curations.distinct("variant", {}).forEach(variantId => {
    db.Curations.distinct("context", {variant:variantId}).forEach(variantContext => {
        //update latest
        db.Curations.find({variant:variantId, conclusion:{$exists: true}, "revoked":{$exists:false}, context:{$elemMatch: {$eq: variantContext}}}).sort({ "updated.when":-1 }).limit(1).forEach((latestCuration)=> {
            //set this as the latest.
            db.Curations.updateOne({_id:latestCuration._id},{$push:{"contextsClassificationIsLatestForVariant":variantContext}});
            
            //for each context find the earliest with the same conclusion and make that preferrred
            db.Curations.find({variant:variantId, conclusion:latestCuration.conclusion, "revoked":{$exists:false}, context:{$elemMatch: {$eq: variantContext}}}).sort({ "updated.when":1 }).limit(1).forEach((preferredCuration)=> {
                db.Curations.updateOne({_id:preferredCuration._id},{$push:{"preferredForContexts":variantContext}});    
            });
        });
    });
});