group in mongo excluding null values

You need an extra $match pipeline step that will filter the incoming documents based on the embedded field "$productAttribute.colour" existing and not null:

db.productMetadata.aggregate([
    { $match: {
        "productAttribute.colour": { 
            $exists: true, 
            $ne: null 
        }
    } },
    { $group: {
        _id: {
           color: "$productAttribute.colour",
           gender: "$productAttribute.gender"
        },
        count: { $sum: 1 }
    } }        
]);

this example includes two different Collections. For this we use aggregate function. I am also using Mongoose

  1. I am joining the cusmtomfield with customfiellabels with $lookup
  2. Flat the array with $unwind
  3. $match to exclude the name that have INACTIVE in the text (I'm using REGEX)
  4. $project to rename the Fields to show properly on the client

    . async getAllMasterDataCustomFields(req) {

        let response = {};
        try {
    
          response = await customfieldsModel.aggregate([
            {
              $lookup: {
                from: 'customfieldlabels',
                localField: 'cfId',
                foreignField: 'cfId',
                as: 'info'
              }
            },
            { '$unwind': { 'path': '$info', 'preserveNullAndEmptyArrays': true } },
            { '$match': { 'childs.name': { $not: /INACTIVE/ }}},
            {
              $project: {
                'cfId': 1,
                'label': '$info.label',
                'type': '$info.type',
                'childs': 1
              }
            }]).exec();
    
        } catch (e) {
          logger.log('error', `Error while getting response ${e.meesage}`);
        }
    
        return response;
      }
    

    .