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Fix grouping by lineage. #87

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Fix grouping by lineage. #87

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15e068e
Fix grouping by lineage.
everaldorodrigo Mar 24, 2023
4c9b152
Fix grouping in prevalence.
everaldorodrigo Mar 27, 2023
f7fa3c3
Upgrade pandas.
everaldorodrigo Jun 28, 2023
9cee401
Filter by date min and max.
everaldorodrigo Jul 26, 2023
d2e2929
Merge branch 'master' into fix-lineages-min-max-date
everaldorodrigo Jul 26, 2023
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2 changes: 1 addition & 1 deletion requirements_web.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
# git+https://github.com/biothings/biothings.api@0.12.x#egg=biothings[web_extra]

biothings[web_extra]==0.12.2
pandas==1.4.3
pandas==1.5.3
pyjwt[crypto]==2.4.0
scipy==1.9.0
Jinja2==3.1.2
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4 changes: 2 additions & 2 deletions web/handlers/genomics/prevalence.py
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Original file line number Diff line number Diff line change
Expand Up @@ -264,7 +264,7 @@ def _get(self):
)
if query_window is not None:
df_response = df_response[df_response["date"] >= (dt.now() - timedelta(days = query_window))]
df_response = get_major_lineage_prevalence(df_response, "date", query_other_exclude, query_other_threshold, query_nday_threshold, query_ndays)
df_response = get_major_lineage_prevalence(df_response, "date", None, None, query_other_exclude, query_other_threshold, query_nday_threshold, query_ndays)
if not query_cumulative:
df_response = df_response.groupby("lineage").apply(compute_rolling_mean_all_lineages, "date", "lineage_count", "lineage_count_rolling", "lineage").reset_index()
df_response = df_response.groupby("date").apply(compute_total_count, "lineage_count_rolling", "total_count_rolling")
Expand All @@ -274,7 +274,7 @@ def _get(self):
df_response = df_response.fillna("None")
df_response = df_response[["date", "total_count", "lineage_count", "lineage", "prevalence", "prevalence_rolling"]]
else:
df_response = df_response.groupby("lineage").apply(expand_dates, df_response["date"].min(), df_response["date"].max(), "date", "lineage").reset_index()
df_response = df_response.groupby("lineage", group_keys=False).apply(expand_dates, df_response["date"].min(), df_response["date"].max(), "date", "lineage").reset_index()
df_response = df_response.groupby("date").apply(compute_total_count, "lineage_count", "total_count").reset_index()
df_response = df_response.groupby("lineage").agg({"total_count": "sum", "lineage_count": "sum"}).reset_index()
df_response.loc[:,"prevalence"] = df_response["lineage_count"]/df_response["total_count"]
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10 changes: 7 additions & 3 deletions web/handlers/genomics/util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,6 @@ def expand_dates(df, date_min, date_max, index_col, grp_col):
df
.set_index(index_col)
.reindex(idx, fill_value = 0)
.drop(grp_col, axis = 1)
.reset_index()
.rename(
columns = {
Expand Down Expand Up @@ -205,9 +204,14 @@ def classify_other_category(grp, keep_lineages):
})
return grp

def get_major_lineage_prevalence(df, index_col, keep_lineages = [], prevalence_threshold = 0.05, nday_threshold = 10, ndays = 180):
def get_major_lineage_prevalence(df, index_col, min_date = None, max_date = None, keep_lineages = [], prevalence_threshold = 0.05, nday_threshold = 10, ndays = 180):
date_limit = dt.today() - timedelta(days = ndays)
lineages_to_retain = df[(df["prevalence"] >= prevalence_threshold) & (df["date"] >= date_limit)]["lineage"].value_counts()
lineages_to_retain = df[
(df["prevalence"] >= prevalence_threshold)
& (df["date"] >= date_limit)
& ((min_date is None) | (df["date"] >= min_date))
& ((max_date is None) | (df["date"] <= max_date))
]["lineage"].value_counts()
num_unique_dates = df[df["date"] >= date_limit]["date"].unique().shape[0]
if num_unique_dates < nday_threshold:
nday_threshold = round((nday_threshold/ndays) * num_unique_dates)
Expand Down
8 changes: 6 additions & 2 deletions web/handlers/v2/genomics/prevalence_all_lineages_by_location.py
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@mindoftea mindoftea Jul 18, 2023

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In order to fix the issue with all lineages being reported under "other", we need to update the get_major_lineage_prevalence function to consider the min_date and max_date, if available

@everaldorodrigo everaldorodrigo Jul 26, 2023

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The function get_major_lineage_prevalence was updated to consider the min_date and max_date, if available.

Does this make sense, even if the ElasticSearch query is considering the min_date and max_date?

Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,8 @@ async def _get(self):
query_other_exclude.split(",") if query_other_exclude is not None else []
)
query_cumulative = self.args.cumulative
min_date = self.args.min_date
max_date = self.args.max_date
query = {
"size": 0,
"aggs": {
Expand All @@ -54,7 +56,7 @@ async def _get(self):
}
query_obj = parse_location_id_to_query(query_location)
date_range_filter = create_date_range_filter(
"date_collected", self.args.min_date, self.args.max_date
"date_collected", min_date, max_date
)
query_obj = parse_time_window_to_query(date_range_filter, query_obj=query_obj)
if query_obj:
Expand Down Expand Up @@ -98,6 +100,8 @@ async def _get(self):
df_response = get_major_lineage_prevalence(
df_response,
"date",
min_date,
max_date,
query_other_exclude,
query_other_threshold,
query_nday_threshold,
Expand Down Expand Up @@ -138,7 +142,7 @@ async def _get(self):
]
else:
df_response = (
df_response.groupby("lineage")
df_response.groupby("lineage", group_keys=False)
.apply(
expand_dates,
df_response["date"].min(),
Expand Down