Add min and max date filters to lineage-mutations.

[everaldorodrigo]

No description provided.

[mindoftea]

The current behavior looks like the date range filter isn't operating. I think the problem might be that we need to change this line to update the query with the new time window being calculated -- something like query["query"] = parse_time_window... maybe?

[everaldorodrigo]

Looking into the range filter created here:

• outbreak.api/web/handlers/genomics/util.py

  Line 302 in 0fa9506

  def create_date_range_filter(field_name, min_date=None, max_date=None):

When making the request to the endpoint below for test purposes:

• /genomics/lineage-mutations?pangolin_lineage=BA.2&frequency=0&gene=ORF1a,ORF1b,S,ORF7b&min_date=2022-01-12&max_date=2022-10-22

The query created is below. The date range was added date_collected.

{
    "size": 0,
    "query": {
        "bool": {
            "should": [
                {
                    "bool": {
                        "must": [
                            {
                                "term": {
                                    "pangolin_lineage": "BA.2"
                                }
                            },
                            {
                                "range": {
                                    "date_collected": {
                                        "lte": "2022-10-22",
                                        "gte": "2022-01-12"
                                    }
                                }
                            }
                        ]
                    }
                }
            ]
        }
    },
    "aggs": {
        "mutations": {
            "nested": {
                "path": "mutations"
            },
            "aggs": {
                "mutations": {
                    "terms": {
                        "field": "mutations.mutation",
                        "size": 10000
                    },
                    "aggs": {
                        "genomes": {
                            "reverse_nested": {}
                        }
                    }
                }
            }
        }
    }
}

The query dict is mutable and passed by reference when calling the function below:

parse_time_window_to_query(date_range_filter, query["query"])

Does it make sense?