Add validation rules to MostRecentDateHandler

config_web/genomics.py

@@ -43,6 +43,14 @@
         r"/{pre}/{ver}/location-lookup",
         "web.handlers.v2.genomics.LocationDetailsHandler",
     ),
+    (
+        r"/{pre}/{ver}/most-recent-collection-date-by-location",
+        "web.handlers.v2.genomics.MostRecentCollectionDateHandler",
+    ),
+    (
+        r"/{pre}/{ver}/most-recent-submission-date-by-location",
+        "web.handlers.v2.genomics.MostRecentSubmissionDateHandler",
+    ),
 ]
 
 APP_LIST_SWITCHED_TO_V2 = [

web/handlers/v2/genomics/__init__.py

@@ -3,6 +3,8 @@
 from .lineage_mutations import LineageMutationsHandler
 from .location import LocationHandler
 from .prevalence_by_aa_position import PrevalenceByAAPositionHandler
+from .most_recent_date import MostRecentCollectionDateHandler, MostRecentSubmissionDateHandler
+from .prevalence_by_aa_position import PrevalenceByAAPositionHandler
 from .location_details import LocationDetailsHandler
 from .mutation_details import MutationDetailsHandler
 from .mutations import MutationHandler

web/handlers/v2/genomics/most_recent_date.py

@@ -0,0 +1,70 @@
+import pandas as pd
+
+from web.handlers.genomics.base import BaseHandler
+from web.handlers.genomics.util import create_nested_mutation_query
+
+
+class MostRecentDateHandler(BaseHandler):
+    field = "date_collected"
+    name = "most-recent-date"
+    kwargs = dict(BaseHandler.kwargs)
+    kwargs["GET"] = {
+        "pangolin_lineage": {"type": str, "default": None},
+        "mutations": {"type": str, "default": None},
+        "location_id": {"type": str, "default": None},
+    }
+
+    async def _get(self):
+        query_pangolin_lineage = self.args.pangolin_lineage
+        query_location = self.args.location_id
+        query_mutations = self.args.mutations
+        query_mutations = query_mutations.split(",") if query_mutations is not None else []
+        query = {
+            "size": 0,
+            "query": {},
+            "aggs": {"date_collected": {"terms": {"field": self.field, "size": 10000}}},
+        }
+        query_pangolin_lineage = (
+            query_pangolin_lineage.split(",") if query_pangolin_lineage is not None else []
+        )
+        query_obj = create_nested_mutation_query(
+            lineages=query_pangolin_lineage, mutations=query_mutations, location_id=query_location
+        )
+        query["query"] = query_obj
+        resp = await self.asynchronous_fetch(query)
+        # print(resp)
+        path_to_results = ["aggregations", "date_collected", "buckets"]
+        buckets = resp
+        for i in path_to_results:
+            buckets = buckets[i]
+        if len(buckets) == 0:
+            return {"success": True, "results": []}
+        flattened_response = []
+        for i in buckets:
+            if len(i["key"].split("-")) == 1 or "XX" in i["key"]:
+                continue
+            flattened_response.append({"date": i["key"], "date_count": i["doc_count"]})
+        df_response = (
+            pd.DataFrame(flattened_response)
+            .assign(
+                date=lambda x: pd.to_datetime(x["date"], format="%Y-%m-%d"),
+                date_count=lambda x: x["date_count"].astype(int),
+            )
+            .sort_values("date")
+        )
+        df_response = df_response.iloc[-1]
+        df_response.loc["date"] = df_response["date"].strftime("%Y-%m-%d")
+        df_response.loc["date_count"] = int(df_response["date_count"])
+        dict_response = df_response.to_dict()
+        resp = {"success": True, "results": dict_response}
+        return resp
+
+
+class MostRecentCollectionDateHandler(MostRecentDateHandler):
+    field = "date_collected"
+    name = "most-recent-collection-date-by-location"
+
+
+class MostRecentSubmissionDateHandler(MostRecentDateHandler):
+    field = "date_submitted"
+    name = "most-recent-submission-date-by-location"