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Add min and max date filters to lineage-mutations. #92

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Add min and max date filters to lineage-mutations. #92

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16 changes: 14 additions & 2 deletions web/handlers/v2/genomics/lineage_mutations.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,12 @@
import pandas as pd

from web.handlers.genomics.base import BaseHandler
from web.handlers.genomics.util import create_nested_mutation_query, get_total_hits
from web.handlers.genomics.util import (
create_date_range_filter,
create_nested_mutation_query,
get_total_hits,
parse_time_window_to_query,
)


class LineageMutationsHandler(BaseHandler):
Expand All @@ -28,6 +33,8 @@ class LineageMutationsHandler(BaseHandler):
"pangolin_lineage": {"type": str, "required": True},
"frequency": {"type": float, "default": 0.8, "min": 0, "max": 1},
"gene": {"type": str, "default": None},
"min_date": {"type": str, "default": None, "date_format": "%Y-%m-%d"},
"max_date": {"type": str, "default": None, "date_format": "%Y-%m-%d"},
}

async def _get(self):
Expand All @@ -38,6 +45,11 @@ async def _get(self):
genes = gene.lower().split(",")
else:
genes = []

date_range_filter = create_date_range_filter(
"date_collected", self.args.min_date, self.args.max_date
)

dict_response = {}
# Query structure: Lineage 1 OR Lineage 2 OR Lineage 3 AND Mutation 1 AND Mutation 2, Lineage 4 AND Mutation 2, Lineage 5 ....
for query_lineage in pangolin_lineage.split(","):
Expand Down Expand Up @@ -66,7 +78,7 @@ async def _get(self):
query["query"] = create_nested_mutation_query(
lineages=query_pangolin_lineage, mutations=query_mutations
)
# print(query)
parse_time_window_to_query(date_range_filter, query["query"])
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@mindoftea mindoftea Jul 17, 2023

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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?

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@everaldorodrigo everaldorodrigo Jul 19, 2023

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Looking into the range filter created here:

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?

resp = await self.asynchronous_fetch(query)
path_to_results = ["aggregations", "mutations", "mutations", "buckets"]
buckets = resp
Expand Down