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Dashboard filter - use data for country if available #37

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Merged
tedinburgh merged 1 commit into from
Nov 5, 2025
Merged

Dashboard filter - use data for country if available #37

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9 changes: 6 additions & 3 deletions vertex/getREDCapData.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ def get_records(redcap_url, redcap_api_key, data_access_groups=None, user_assign
}
response = requests.post(redcap_url, data=conex)
logger.debug("HTTP Status: " + str(response.status_code))
df = pd.read_csv(io.StringIO(response.text), keep_default_na=False)
df = pd.read_csv(io.StringIO(response.text), dtype={"subjid": "str"}, keep_default_na=False)
if data_access_groups is not None:
ind = df["redcap_data_access_group"].isin(data_access_groups)
df = df.loc[ind].reset_index(drop=True)
Expand Down Expand Up @@ -70,7 +70,7 @@ def get_records(redcap_url, redcap_api_key, data_access_groups=None, user_assign
}
try:
response = requests.post(redcap_url, data=conex)
df_new = pd.read_csv(io.StringIO(response.text), keep_default_na=False)
df_new = pd.read_csv(io.StringIO(response.text), dtype={"subjid": "str"}, keep_default_na=False)
df_new["redcap_data_access_group"] = dag
df_list.append(df_new)
logger.debug(f"Data access group ID: {dag}, HTTP Status: {response.status_code}")
Expand Down Expand Up @@ -721,7 +721,10 @@ def get_redcap_data(redcap_url, redcap_api_key, data_access_groups=None, user_as
df_map, new_dictionary, quality_report = get_df_map(data, new_dictionary)
df_forms_dict = get_df_forms(data, new_dictionary)

if country_mapping is None:
if "demog_country" in dictionary["field_name"].values:
countries = pd.read_csv("assets/countries.csv", encoding="latin-1")
df_map["country_iso"] = df_map["demog_country"].replace(dict(zip(countries["Country"], countries["Code"])))
elif country_mapping is None:
dag = data[["subjid", "redcap_data_access_group"]].drop_duplicates()
dag = dag.rename(columns={"redcap_data_access_group": "site"})
dag["country_iso"] = dag["site"].apply(lambda x: x.split("-")[1])
Expand Down
4 changes: 3 additions & 1 deletion vertex/layout/filters.py
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Original file line number Diff line number Diff line change
Expand Up @@ -322,7 +322,9 @@ def get_filter_options(df_map):

outcome_options = [{"label": v, "value": v} for v in df_map["filters_outcome"].dropna().unique()]

country_options = [{"label": c, "value": c} for c in sorted(df_map["filters_country"].dropna().unique())]
countries = pd.read_csv("assets/countries.csv", encoding="latin-1")
country_dict = dict(zip(countries["Code"], countries["Country"]))
country_options = [{"label": country_dict.get(c, None), "value": c} for c in df_map["filters_country"].dropna().unique()]

sex_options = [{"label": c, "value": c} for c in sorted(df_map["filters_sex"].dropna().unique())]

Expand Down
2 changes: 1 addition & 1 deletion vertex/map.py
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Expand Up @@ -151,6 +151,6 @@ def filter_df_map(df_map, sex_value, age_value, country_value, admdate_value, ad
& ((df_map["filters_admdate"] >= admdate_min) | df_map["filters_admdate"].isna())
& ((df_map["filters_admdate"] <= admdate_max) | df_map["filters_admdate"].isna())
& (df_map["filters_outcome"].isin(outcome_value))
& (df_map["filters_country"].isin(country_value))
& (df_map["filters_country"].isin(country_value) | df_map["filters_country"].isna())
]
return df_map_filtered.reset_index(drop=True)