meta-edc 1.5.0__py3-none-any.whl → 1.5.2__py3-none-any.whl

meta_analytics/dataframes/get_glucose_df.py

@@ -6,6 +6,8 @@ from edc_pdutils.dataframes import get_eos, get_subject_consent, get_subject_vis
 
 from meta_subject.models import Glucose, GlucoseFbg
 
+pd.set_option("future.no_silent_downcasting", True)
+
 
 def get_glucose_df(subject_identifiers: list[str] | None = None) -> pd.DataFrame:
     subject_visit_df = (
@@ -52,6 +54,9 @@ def get_glucose_df(subject_identifiers: list[str] | None = None) -> pd.DataFrame
         how="left",
     )
 
+    for col in [c for c in df_glucose_fbg.columns if "datetime" in c]:
+        df_glucose_fbg[col] = pd.to_datetime(df_glucose_fbg[col])
+
     if subject_identifiers:
         df_glucose = read_frame(
             Glucose.objects.filter(subject_visit__subject_identifier__in=subject_identifiers),
@@ -70,6 +75,9 @@ def get_glucose_df(subject_identifiers: list[str] | None = None) -> pd.DataFrame
     )
     df_glucose["source"] = "meta_subject.glucose"
 
+    for col in [c for c in df_glucose.columns if "datetime" in c]:
+        df_glucose[col] = pd.to_datetime(df_glucose[col])
+
     df_glucose = subject_visit_df[
         [
             "subject_identifier",
@@ -108,7 +116,6 @@ def get_glucose_df(subject_identifiers: list[str] | None = None) -> pd.DataFrame
         df_glucose_fbg[keep_cols],
         on="subject_visit_id",
         how="outer",
-        # indicator=True,
         suffixes=("", "_2"),
     )
 
@@ -127,9 +134,16 @@ def get_glucose_df(subject_identifiers: list[str] | None = None) -> pd.DataFrame
             f"ogtt_units{suffix}",
         ] = "mmol/L (millimoles/L)"
 
+    for col in [c for c in df.columns if "datetime" in c]:
+        df[col] = pd.to_datetime(df[col])
+
+    df[[col for col in df.columns if "datetime" in col]] = df[
+        [col for col in df.columns if "datetime" in col]
+    ].apply(lambda x: x.dt.tz_localize(None) if x.dtype == "datetime64[ns, UTC]" else x)
+
     # reconcile all to single column
     for col in ["fasted", "fbg_value", "ogtt_value", "fbg_datetime", "ogtt_datetime"]:
-        df.loc[(df[col].isna()) & (df[f"{col}_2"].notna()), col] = df[f"{col}_2"]
+        df[col] = df[col].fillna(df[f"{col}_2"])
 
     df_consent = get_subject_consent("meta_consent.subjectconsent")
     df_eos = get_eos("meta_prn.endofstudy")
@@ -143,10 +157,6 @@ def get_glucose_df(subject_identifiers: list[str] | None = None) -> pd.DataFrame
         how="left",
     )
 
-    df[[col for col in df.columns if "datetime" in col]] = df[
-        [col for col in df.columns if "datetime" in col]
-    ].apply(lambda x: x.dt.tz_localize(None) if x.dtype == "datetime64[ns, UTC]" else x)
-
     df["visit_days"] = df["baseline_datetime"].rsub(df["visit_datetime"]).dt.days
     df["fgb_days"] = df["baseline_datetime"].rsub(df["fbg_datetime"]).dt.days
     df["ogtt_days"] = df["baseline_datetime"].rsub(df["ogtt_datetime"]).dt.days

{meta_edc-1.5.0.dist-info → meta_edc-1.5.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: meta-edc
-Version: 1.5.0
+Version: 1.5.2
 Summary: META Trial EDC (https://www.isrctn.com/ISRCTN76157257)
 Keywords: django,clinicedc,META EDC,EDC,clinical trials,META Trial,ISRCTN76157257
 Author: Erik van Widenfelt, Jonathan Willitts
@@ -89,8 +89,8 @@ Assuming you are logged into the account ``myaccount``:
     mkdir ~/edc && \
     cd ~/edc && \
     uv venv && \
-    uv pip install -U meta-edc==1.4.1 && \
-    wget https://raw.githubusercontent.com/meta-trial/meta-edc/1.4.1/manage.py && \
+    uv pip install -U meta-edc==1.5.1 && \
+    wget https://raw.githubusercontent.com/meta-trial/meta-edc/1.5.1/manage.py && \
     uv pip freeze | grep meta-edc
 
 Copy your ``.env`` file to ``~/.etc``.
@@ -140,7 +140,7 @@ From the above example:
 
     cd ~/edc && \
     uv venv --clear && \
-    uv pip install -U meta-edc==1.4.1 && \
+    uv pip install -U meta-edc==1.5.1 && \
     wget -O manage.py https://raw.githubusercontent.com/meta-trial/meta-edc/1.1.10/manage.py && \
     uv pip freeze | grep meta-edc && \
     python manage.py check

{meta_edc-1.5.0.dist-info → meta_edc-1.5.2.dist-info}/RECORD

@@ -84,7 +84,7 @@ meta_analytics/constants.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 meta_analytics/dataframes/__init__.py,sha256=naGZtYGJ8BW03XslsFPZe9VZ2fWuU9ew84BB_iBLWxo,1266
 meta_analytics/dataframes/constants.py,sha256=oA0a9N7RzYstXuZXWclUjrbsWvNQbv1F4P9lFGlNRRg,937
 meta_analytics/dataframes/get_eos_df.py,sha256=N_7A_Io3KCGj8mrMjUfYP7w6gi7_2Dx2RSG6orQTWp4,1226
-meta_analytics/dataframes/get_glucose_df.py,sha256=eGzA7dxh3igGZdNKvMfiH7maRl2IAngWiQp9Dx8FZHU,5884
+meta_analytics/dataframes/get_glucose_df.py,sha256=4WOu5rmVxB3E-Gflwlinl0qfzeNPTzvIitOGY7hwegg,6244
 meta_analytics/dataframes/get_glucose_fbg_df.py,sha256=yAshgtc_R6Q41p5iA9n7a_W0llp1JRsnj3NGQE6kVRk,898
 meta_analytics/dataframes/get_glucose_fbg_ogtt_df.py,sha256=BfMU1sNj1a4dVOy7yKGESARpb3SNTFxLA-BVB5oZ14Q,657
 meta_analytics/dataframes/get_last_imp_visits_df.py,sha256=N5tL6gANDr_g5AuNVv_cEN4U-QktLxJUAJaUIW2MiWs,3818
@@ -1158,7 +1158,7 @@ meta_visit_schedule/visit_schedules/phase_three/schedule.py,sha256=LU1HRaV6o1UeK
 meta_visit_schedule/visit_schedules/phase_three/schedule_dm_referral.py,sha256=q12p5wXc2D7lSiJVBnoSQw8Q3vL6uDx1t3PuDJO-Z-U,1735
 meta_visit_schedule/visit_schedules/phase_three/schedule_pregnancy.py,sha256=bEpbpCX3vfZmnsqudr0z8PU5kiaX4ws1sO5Im98Mo28,1106
 meta_visit_schedule/visit_schedules/phase_three/visit_schedule.py,sha256=ak4qazeKlpIlvpqrK9hDDO0fwWuWyvb4Ec-JU31IJxc,654
-meta_edc-1.5.0.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-meta_edc-1.5.0.dist-info/WHEEL,sha256=ZHijuPszqKbNczrBXkSuoxdxocbxgFghqnequ9ZQlVk,79
-meta_edc-1.5.0.dist-info/METADATA,sha256=gfx4FujUAmAv6WqApfCMhDVLqRmytRrBd4Zjp2G3RFQ,5162
-meta_edc-1.5.0.dist-info/RECORD,,
+meta_edc-1.5.2.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+meta_edc-1.5.2.dist-info/WHEEL,sha256=ZHijuPszqKbNczrBXkSuoxdxocbxgFghqnequ9ZQlVk,79
+meta_edc-1.5.2.dist-info/METADATA,sha256=obgIfLrCBL7boOhiRrCm9fAFpOVHsWanM3Z7GzmVSkg,5162
+meta_edc-1.5.2.dist-info/RECORD,,