MongoDB嵌套对象聚合计数

Question

我有一个高度嵌套的 mongoDB 对象集，我想计算与给定条件匹配的子文档的数量编辑:(在每个文档中)。例如:

{"_id":{"chr":"20","pos":"14371","ref":"A","alt":"G"},
"studies":[
    {
        "study_id":"Study1",
        "samples":[
            {
                "sample_id":"NA00001",
                "formatdata":[
                    {"GT":"1|0","GQ":48,"DP":8,"HQ":[51,51]}
                ]
            },
            {
                "sample_id":"NA00002",
                "formatdata":[
                    {"GT":"0|0","GQ":48,"DP":8,"HQ":[51,51]}
                ]
            }
        ]
    }
]
}
{"_id":{"chr":"20","pos":"14372","ref":"T","alt":"AA"},
"studies":[
    {
        "study_id":"Study3",
        "samples":[
            {
                "sample_id":"SAMPLE1",
                "formatdata":[
                    {"GT":"1|0","GQ":48,"DP":8,"HQ":[51,51]}
                ]
            },
            {
                "sample_id":"SAMPLE2",
                "formatdata":[
                    {"GT":"1|0","GQ":48,"DP":8,"HQ":[51,51]}
                ]
            }
        ]
    }
]
}
{"_id":{"chr":"20","pos":"14373","ref":"C","alt":"A"},
"studies":[
    {
        "study_id":"Study3",
        "samples":[
            {
                "sample_id":"SAMPLE3",
                "formatdata":[
                    {"GT":"0|0","GQ":48,"DP":8,"HQ":[51,51]}
                ]
            },
            {
                "sample_id":"SAMPLE7",
                "formatdata":[
                    {"GT":"0|0","GQ":48,"DP":8,"HQ":[51,51]}
                ]
            }
        ]
    }
]
}

我想知道有多少子文档包含 GT:"1|0"，在这种情况下，第一个文档中为 1，第二个文档中为 2，第三个文档中为 0。我已经尝试过展开和聚合函数，但我显然没有做正确的事情。当我尝试按“GT”字段计算子文档时，mongo 提示:

db.collection.aggregate([{$group: {"$studies.samples.formatdata.GT":1,_id:0}}])

因为我的组名不能包含“.”，但如果我把它们排除在外:

db.collection.aggregate([{$group: {"$GT":1,_id:0}}])

它提示是因为“$GT 不能是运算符(operator)名称”

有什么想法吗？

Answer 1

您需要处理$unwind使用数组时，您需要执行此操作 3 次:

 db.collection.aggregate([

     // Un-wind the array's to access filtering 
     { "$unwind": "$studies" },
     { "$unwind": "$studies.samples" },
     { "$unwind": "$studies.samples.formdata" },

     // Group results to obtain the matched count per key
     { "$group": {
         "_id": "$studies.samples.formdata.GT",
         "count": { "$sum": 1 }
     }}
 ])

理想情况下，您希望过滤输入。可能使用 $match 执行此操作在处理 $unwind 之前和之后都使用 $regex匹配点的数据以“1”开头的文档。

 db.collection.aggregate([

     // Match first to exclude documents where this is not present in any array member
     { "$match": { "studies.samples.formdata.GT": /^1/ } },

     // Un-wind the array's to access filtering 
     { "$unwind": "$studies" },
     { "$unwind": "$studies.samples" },
     { "$unwind": "$studies.samples.formdata" },

     // Match to filter
     { "$match": { "studies.samples.formdata.GT": /^1/ } },

     // Group results to obtain the matched count per key
     { "$group": {
         "_id": {
              "_id": "$_id",
              "key": "$studies.samples.formdata.GT"
         },
         "count": { "$sum": 1 }
     }}
 ])

请注意，在所有情况下，以“美元 $”为前缀的条目都是指文档属性的“变量”。这些是使用右侧输入的“值”。左侧的“keys”必须指定为纯字符串键。没有变量可以用来命名键。