meta-edc 0.3.23__tar.gz → 0.3.25__tar.gz

{meta_edc-0.3.23 → meta_edc-0.3.25}/CHANGES

@@ -1,6 +1,23 @@
 Changes
 -------
 
+0.3.25
+------
+- refactor GlucoseEndpointsByDate
+- add Endpoints report for ALL endpoints, not just those still
+  on study
+- improve navigation between endpoint reports and glucose summary
+
+
+0.3.24
+------
+- add glucose summary
+- simplify DM referral baseline form
+
+0.3.23
+------
+- add report for missing OGTT at screening
+
 0.3.21
 ------
 - bump edc 0.6.0, django-crypto-fields 0.4.2, Django 5.1

{meta_edc-0.3.23 → meta_edc-0.3.25}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: meta-edc
-Version: 0.3.23
+Version: 0.3.25
 Summary: META Trial EDC (http://www.isrctn.com/ISRCTN76157257)
 Home-page: https://github.com/meta-trial/meta-edc
 Author: Erik van Widenfelt
@@ -19,7 +19,7 @@ Requires-Python: >=3.12
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: AUTHORS
-Requires-Dist: edc==0.6.1
+Requires-Dist: edc==0.6.3
 Requires-Dist: edc-microscopy
 Requires-Dist: beautifulsoup4
 Requires-Dist: edc-analytics

{meta_edc-0.3.23 → meta_edc-0.3.25}/meta_analytics/dataframes/glucose_endpoints/constants.py

@@ -1,8 +1,10 @@
-OGTT_THRESHOLD_MET = "OGTT >= 11.1"
-EOS_DM_MET = "EOS - Patient developed diabetes"
-CASE_OGTT = 1
 CASE_EOS = 7
+CASE_FBGS_WITH_FIRST_OGTT = 2
+CASE_FBGS_WITH_SECOND_OGTT = 3
 CASE_FBG_ONLY = 4
+CASE_OGTT = 1
+EOS_DM_MET = "EOS - Patient developed diabetes"
+OGTT_THRESHOLD_MET = "OGTT >= 11.1"
 
 endpoint_columns = [
     "subject_identifier",
@@ -24,8 +26,8 @@ endpoint_columns = [
 
 endpoint_cases = {
     CASE_OGTT: OGTT_THRESHOLD_MET,
-    2: "FBG >= 7 x 2, first OGTT<=11.1",
-    3: "FBG >= 7 x 2, second OGTT<=11.1",
-    4: "FBG >= 7 x 2, OGTT not considered",
+    CASE_FBGS_WITH_FIRST_OGTT: "FBG >= 7 x 2, first OGTT<=11.1",
+    CASE_FBGS_WITH_SECOND_OGTT: "FBG >= 7 x 2, second OGTT<=11.1",
+    CASE_FBG_ONLY: "FBG >= 7 x 2, OGTT not considered",
     CASE_EOS: EOS_DM_MET,
 }

meta_edc-0.3.25/meta_analytics/dataframes/glucose_endpoints/glucose_endpoints_by_date.py

@@ -0,0 +1,480 @@
+import numpy as np
+import pandas as pd
+from django.apps import apps as django_apps
+from edc_constants.constants import NO, YES
+from edc_pdutils.dataframes import get_crf, get_eos, get_subject_consent
+from edc_utils import get_utcnow
+
+from .constants import (
+    CASE_EOS,
+    CASE_FBG_ONLY,
+    CASE_FBGS_WITH_FIRST_OGTT,
+    CASE_FBGS_WITH_SECOND_OGTT,
+    CASE_OGTT,
+    endpoint_cases,
+    endpoint_columns,
+)
+from .endpoint_by_date import EndpointByDate
+from .utils import (
+    get_empty_endpoint_df,
+    get_test_string,
+    get_unique_subject_identifiers,
+    get_unique_visit_codes,
+)
+
+
+def normalize_date_columns(df: pd.DataFrame, cols: list[str] = None) -> pd.DataFrame:
+    """Normalize date columns by flooring"""
+    for col in cols:
+        if not df[col].empty:
+            df[col] = df[col].dt.floor("d")
+        else:
+            df[col] = pd.NaT
+    return df
+
+
+def calculate_fasting_hrs(df: pd.DataFrame):
+    df.loc[(df["fasting"] == NO), "fasting_duration_delta"] = pd.NaT
+    if df.empty:
+        df["fasting_hrs"] = np.nan
+    else:
+        df["fasting_hrs"] = df["fasting_duration_delta"].dt.total_seconds() / 3600
+    return df
+
+
+class GlucoseEndpointsByDate:
+
+    fbg_threshhold = 7.0
+    ogtt_threshhold = 11.1
+    endpoint_cls = EndpointByDate
+    keep_cols = [
+        "fasting",
+        "fasting_hrs",
+        "fbg_value",
+        "fbg_units",
+        "fbg_datetime",
+        "ogtt_value",
+        "ogtt_units",
+        "ogtt_datetime",
+        "source",
+        "report_datetime",
+        "subject_visit_id",
+        "subject_identifier",
+        "visit_code",
+        "visit_datetime",
+        "site",
+        "baseline_datetime",
+    ]
+
+    def __init__(
+        self, subject_identifiers: list[str] | None = None, case_list: list[int] | None = None
+    ):
+        self._glucose_fbg_df = pd.DataFrame()
+        self._glucose_fbg_ogtt_df = pd.DataFrame()
+        self.endpoint_only_df = pd.DataFrame()
+
+        self.subject_identifiers = subject_identifiers or []
+        self.case_list = case_list or [
+            CASE_OGTT,
+            CASE_FBGS_WITH_FIRST_OGTT,
+            CASE_FBGS_WITH_SECOND_OGTT,
+            CASE_EOS,
+        ]
+        self.endpoint_cases = {k: v for k, v in endpoint_cases.items() if k in self.case_list}
+
+        # merge two model DFs
+        self.df = pd.merge(
+            self.glucose_fbg_ogtt_df,
+            self.glucose_fbg_df,
+            on=["subject_visit_id", "fbg_datetime", "fbg_value"],
+            how="outer",
+            indicator=True,
+            suffixes=("", "2"),
+        )
+        self.df = self.df.reset_index(drop=True)
+
+        # pivot right_only cols
+        cols = {
+            "fasting": None,
+            "fasting_hrs": np.nan,
+            "fbg_units": None,
+            "source": None,
+            "report_datetime": pd.NaT,
+        }
+        for col, null_value in cols.items():
+            self.df.loc[self.df["_merge"] == "right_only", col] = self.df[f"{col}2"]
+        cols = [col for col in self.df.columns if col.endswith("2")]
+        cols.append("_merge")
+        self.df = self.df.drop(columns=cols)
+        self.df = self.df.reset_index(drop=True)
+
+        self.merge_with_consent()
+        self.merge_with_eos()
+        self.add_calculated_days_from_baseline_to_event_columns()
+
+        # label rows by type of glu tests (ones with value)
+        self.df["test"] = self.df.apply(get_test_string, axis=1)
+        self.df = self.df.reset_index(drop=True)
+
+        self.visit_codes_df = get_unique_visit_codes(self.df)
+        self.subject_identifiers_df = get_unique_subject_identifiers(self.df)
+
+        self.df = self.df.sort_values(by=["subject_identifier", "fbg_datetime"])
+        self.df = self.df.reset_index(drop=True)
+
+        self.working_df = self.df.copy()
+        self.working_df["endpoint"] = 0
+        self.endpoint_df = get_empty_endpoint_df()
+
+    def run(self):
+        self.pre_check_endpoint()
+        for index, row in self.subject_identifiers_df.iterrows():
+            subject_df = self.get_subject_df(row["subject_identifier"])
+            subject_df = self.check_endpoint_by_fbg_for_subject(
+                subject_df, case_list=[CASE_FBGS_WITH_FIRST_OGTT, CASE_FBGS_WITH_SECOND_OGTT]
+            )
+            if len(subject_df.loc[subject_df["endpoint"] == 1]) == 1:
+                self.append_subject_to_endpoint_df(subject_df)
+                self.remove_subject_from_working_df(row)
+
+        if CASE_FBG_ONLY in self.endpoint_cases:
+            for index, row in self.subject_identifiers_df.iterrows():
+                subject_df = self.get_subject_df(row["subject_identifier"])
+                subject_df = self.check_endpoint_by_fbg_for_subject(
+                    subject_df, case_list=[CASE_FBG_ONLY]
+                )
+                if len(subject_df.loc[subject_df["endpoint"] == 1]) == 1:
+                    self.append_subject_to_endpoint_df(subject_df)
+                    self.remove_subject_from_working_df(row)
+
+        self.post_check_endpoint()
+        self.merge_with_final_endpoints()
+
+    @property
+    def glucose_fbg_df(self) -> pd.DataFrame:
+        """Returns a prepared Dataframe of CRF
+        meta_subject.glucosefbg.
+
+        Note: meta_subject.glucosefbg has only FBG measures.
+        """
+        if self._glucose_fbg_df.empty:
+            df = get_crf(
+                model="meta_subject.glucosefbg",
+                subject_identifiers=self.subject_identifiers,
+                subject_visit_model="meta_subject.subjectvisit",
+            )
+            df["source"] = "meta_subject.glucosefbg"
+            df.rename(columns={"fbg_fasting": "fasting"}, inplace=True)
+            df.loc[(df["fasting"] == "fasting"), "fasting"] = YES
+            df.loc[(df["fasting"] == "non_fasting"), "fasting"] = NO
+            df = calculate_fasting_hrs(df)
+            df = df[[col for col in self.keep_cols if not col.startswith("ogtt")]]
+            df = df.reset_index(drop=True)
+            df = normalize_date_columns(
+                df, cols=["fbg_datetime", "report_datetime", "visit_datetime"]
+            )
+            self._glucose_fbg_df = df
+        return self._glucose_fbg_df
+
+    @property
+    def glucose_fbg_ogtt_df(self):
+        """Returns a prepared Dataframe of CRF meta_subject.glucose.
+
+        Note: meta_subject.glucose has FBG and OGTT measures.
+        """
+        if self._glucose_fbg_ogtt_df.empty:
+            df = get_crf(
+                model="meta_subject.glucose",
+                subject_identifiers=self.subject_identifiers,
+                subject_visit_model="meta_subject.subjectvisit",
+            )
+            df["source"] = "meta_subject.glucose"
+            df = calculate_fasting_hrs(df)
+            df = df[self.keep_cols]
+            df = df.reset_index(drop=True)
+            df = normalize_date_columns(
+                df, cols=["fbg_datetime", "ogtt_datetime", "report_datetime", "visit_datetime"]
+            )
+            self._glucose_fbg_ogtt_df = df
+        return self._glucose_fbg_ogtt_df
+
+    def merge_with_consent(self):
+        """Merge in consent DF."""
+        df_consent = get_subject_consent("meta_consent.subjectconsent")
+        self.df = pd.merge(self.df, df_consent, on="subject_identifier", how="left")
+        self.df = self.df.sort_values(by=["subject_identifier", "fbg_datetime"])
+        self.df = self.df.reset_index(drop=True)
+
+    def merge_with_eos(self):
+        """Merge in EoS DF.
+
+        Drops patients who were taken off study by late exclusion.
+        """
+        df_eos = get_eos("meta_prn.endofstudy")
+        df_eos = df_eos[
+            df_eos["offstudy_reason"]
+            != (
+                "Patient fulfilled late exclusion criteria (due to abnormal blood "
+                "values or raised blood pressure at enrolment"
+            )
+        ]
+        self.df = pd.merge(self.df, df_eos, on="subject_identifier", how="left")
+        self.df = self.df.sort_values(by=["subject_identifier", "fbg_datetime"])
+        self.df = self.df.reset_index(drop=True)
+
+    def add_calculated_days_from_baseline_to_event_columns(self):
+        """Add columns that calculate number of days from
+        baseline to visit, fbg, and ogtt.
+        """
+        self.df["visit_days"] = np.nan
+        self.df["fbg_days"] = np.nan
+        self.df["ogtt_days"] = np.nan
+        self.df["test"] = np.nan
+        self.df["visit_days"] = (
+            self.df["visit_datetime"] - self.df["baseline_datetime"]
+        ).dt.days
+        if not self.df["fbg_datetime"].empty:
+            self.df["fbg_days"] = (
+                self.df["fbg_datetime"] - self.df["baseline_datetime"]
+            ).dt.days
+        if not self.df["ogtt_datetime"].empty:
+            self.df["ogtt_days"] = (
+                self.df["ogtt_datetime"] - self.df["baseline_datetime"]
+            ).dt.days
+        self.df["visit_days"] = pd.to_numeric(self.df["visit_days"], downcast="integer")
+        self.df["fbg_days"] = pd.to_numeric(self.df["fbg_days"], downcast="integer")
+        self.df["ogtt_days"] = pd.to_numeric(self.df["ogtt_days"], downcast="integer")
+        self.df = self.df.reset_index(drop=True)
+
+    def pre_check_endpoint(self):
+        """Flag subjects that met endpoint by hitting the OGTT
+        threshold.
+
+        Add them to the endpoint_df and remove them from the
+        working_df.
+
+        Subject must have fasted at the timepoint.
+
+        The OGTT must have an FBG measure at the same timepoint.
+        The value of the FBG is not considered.
+
+        Most of these where taken off study for the OGTT. We are
+        using the OGTT as the reason/date instead of the offstudy
+        reason/date.
+
+        See `merge_with_final_endpoints` where we pick the date of
+        the first OGTT.
+        """
+        subject_endpoint_df = self.working_df.loc[
+            (self.working_df["ogtt_value"] >= self.ogtt_threshhold)
+            & (self.working_df["fasting"] == YES)
+            & (self.working_df["fbg_value"].notna())
+        ].copy()
+        if not subject_endpoint_df.empty:
+            # flag the selected endpoint rows as endpoints
+            subject_endpoint_df["endpoint"] = 1
+            subject_endpoint_df["endpoint_label"] = self.endpoint_cases[CASE_OGTT]
+            subject_endpoint_df["endpoint_type"] = CASE_OGTT
+            subject_endpoint_df["interval_in_days"] = np.nan
+
+            # add back the others rows for these subjects
+            subjects_df = self.working_df.loc[
+                (
+                    self.working_df["subject_identifier"].isin(
+                        subject_endpoint_df["subject_identifier"]
+                    )
+                    & ~(
+                        self.working_df["fbg_datetime"].isin(
+                            subject_endpoint_df["fbg_datetime"]
+                        )
+                    )
+                )
+            ].copy()
+            subjects_df = subjects_df.reset_index(drop=True)
+            subjects_df["endpoint"] = np.nan
+            subjects_df["endpoint_label"] = None
+            subjects_df["endpoint_type"] = None
+            subjects_df["interval_in_days"] = np.nan
+            subjects_df = pd.concat([subjects_df, subject_endpoint_df])
+            subjects_df = subjects_df.reset_index(drop=True)
+
+            self.append_subject_to_endpoint_df(subjects_df[endpoint_columns])
+            self.remove_subjects_from_working_df(subjects_df)
+
+    def append_subject_to_endpoint_df(self, subject_df: pd.DataFrame) -> None:
+        """Appends all rows of a subject, or subjects, to the
+        Endpoints DF.
+        """
+        if self.endpoint_df.empty:
+            self.endpoint_df = subject_df.copy()
+        else:
+            self.endpoint_df = pd.concat([self.endpoint_df, subject_df])
+            self.endpoint_df = self.endpoint_df.sort_values(
+                by=["subject_identifier", "visit_code"]
+            )
+            self.endpoint_df = self.endpoint_df.reset_index(drop=True)
+
+    def remove_subject_from_working_df(self, row: pd.Series) -> None:
+        """Removes one subject from the working DF given a Series with
+        value `subject_identifier`.
+        """
+        self.working_df = self.working_df.drop(
+            index=self.working_df[
+                self.working_df["subject_identifier"] == row["subject_identifier"]
+            ].index
+        )
+        self.working_df = self.working_df.reset_index(drop=True)
+
+    def remove_subjects_from_working_df(self, rows: pd.DataFrame) -> None:
+        """Removes subjects from the working DF given a DF with
+        column `subject_identifier`.
+        """
+        self.working_df = self.working_df.drop(
+            index=self.working_df.loc[
+                self.working_df["subject_identifier"].isin(rows["subject_identifier"])
+            ].index
+        )
+        self.working_df = self.working_df.reset_index(drop=True)
+
+    def get_subject_df(self, subject_identifier: str) -> pd.DataFrame:
+        subject_df = self.working_df.loc[
+            self.working_df["subject_identifier"] == subject_identifier
+        ].copy()
+        subject_df["interval_in_days"] = np.nan
+        subject_df["endpoint_type"] = None
+        subject_df["endpoint_label"] = None
+        subject_df["endpoint"] = 0
+        subject_df = subject_df.sort_values(["subject_identifier", "fbg_datetime"])
+        subject_df = subject_df.reset_index(drop=True)
+        subject_df = subject_df[endpoint_columns]
+        subject_df = subject_df.merge(
+            self.visit_codes_df,
+            on="visit_code",
+            how="outer",
+            indicator=False,
+            suffixes=["", "2"],
+        )
+        subject_df["subject_identifier"] = subject_identifier
+        subject_df = subject_df.drop(columns=["count"])
+        subject_df = subject_df.reset_index(drop=True)
+        return subject_df
+
+    def check_endpoint_by_fbg_for_subject(
+        self, subject_df: pd.DataFrame, case_list: list[int] | None = None
+    ) -> pd.DataFrame:
+        case_list = case_list or [2, 3]
+        endpoint = self.endpoint_cls(
+            subject_df=subject_df,
+            fbg_threshhold=self.fbg_threshhold,
+            ogtt_threshhold=self.ogtt_threshhold,
+            case_list=case_list,
+        )
+        return endpoint.subject_df
+
+    def post_check_endpoint(self):
+        df_eos = self.working_df.loc[
+            self.working_df["offstudy_reason"] == "Patient developed diabetes"
+        ].copy()
+        df_eos["endpoint"] = 1
+        df_eos["endpoint_label"] = self.endpoint_cases[CASE_EOS]
+        df_eos["endpoint_type"] = CASE_EOS
+        df_eos["interval_in_days"] = np.nan
+        df_eos = df_eos.reset_index(drop=True)
+        self.append_subject_to_endpoint_df(df_eos[endpoint_columns])
+        self.working_df = self.working_df.drop(
+            index=self.working_df.loc[
+                self.working_df["subject_identifier"].isin(df_eos["subject_identifier"])
+            ].index
+        )
+
+    def merge_with_final_endpoints(self):
+        """Merge endpoint_df with original df"""
+        if self.endpoint_df.empty:
+            self.df = self.df[~(self.df["subject_identifier"].isin(self.subject_identifiers))]
+        else:
+            self.endpoint_df["test"] = self.endpoint_df.apply(get_test_string, axis=1)
+            self.endpoint_df.loc[self.endpoint_df["endpoint"] == 1, "days_to_endpoint"] = (
+                self.endpoint_df["fbg_datetime"] - self.endpoint_df["baseline_datetime"]
+            ).dt.days
+
+            # Create DF of subjects taken offstudy (EOS) where endpoint==1.
+            # Keep the last record for the subject by fbg_datetime.
+            df1 = self.endpoint_df.copy()
+            df1 = df1[
+                (df1["endpoint_type"].isin([CASE_EOS, CASE_OGTT])) & (df1["endpoint"] == 1)
+            ]
+            df1 = df1.sort_values(["subject_identifier", "fbg_datetime"])
+            df1 = df1.reset_index(drop=True)
+            df1 = df1.set_index(["subject_identifier"])
+            df1 = df1[~df1.index.duplicated(keep="last")]
+            df1 = df1.reset_index(drop=False)
+
+            # Create DF of subjects still on-study where endpoint==1.
+            # Keep the first record for the subject by fbg_datetime.
+            df2 = self.endpoint_df.copy()
+            df2 = df2[
+                ~(df2["endpoint_type"].isin([CASE_EOS, CASE_OGTT])) & (df2["endpoint"] == 1)
+            ]
+            df2 = df2.sort_values(["subject_identifier", "fbg_datetime"])
+            df2 = df2.reset_index(drop=True)
+            df2 = df2.set_index(["subject_identifier"])
+            df2 = df2[~df2.index.duplicated(keep="first")]
+            df2 = df2.reset_index(drop=False)
+
+            # create new DF with ONE row per subject for those that reached
+            # the endpoint (endpoint=1) by merging two DFs above.
+            self.endpoint_only_df = pd.concat([df1, df2])
+            self.endpoint_only_df = self.endpoint_only_df.reset_index(drop=True)
+
+            self.df = pd.merge(
+                self.df,
+                self.endpoint_only_df[["subject_identifier", "visit_code", "endpoint"]],
+                on=["subject_identifier", "visit_code"],
+                how="left",
+                suffixes=("", "_y"),
+            )
+        self.df = self.df.sort_values(by=["subject_identifier", "fbg_datetime"])
+        self.df = self.df.reset_index(drop=True)
+
+    def to_model(self, model: str | None = None, subject_identifiers: list[str] | None = None):
+        """Write endpoint_only_df to the Endpoints model"""
+        df = self.endpoint_only_df
+        model = model or "meta_reports.endpoints"
+        now = get_utcnow()
+        model_cls = django_apps.get_model(model)
+        if subject_identifiers:
+            model_cls.objects.filter(subject_identifier__in=subject_identifiers).delete()
+        else:
+            model_cls.objects.all().delete()
+        created = 0
+        if not df.empty:
+            data = [
+                model_cls(
+                    subject_identifier=row["subject_identifier"],
+                    site_id=row["site"],
+                    baseline_datetime=(
+                        None if pd.isna(row["baseline_datetime"]) else row["baseline_datetime"]
+                    ),
+                    visit_code=None if pd.isna(row["visit_code"]) else row["visit_code"],
+                    fbg_value=(None if pd.isna(row["fbg_value"]) else row["fbg_value"]),
+                    ogtt_value=None if pd.isna(row["ogtt_value"]) else row["ogtt_value"],
+                    fbg_datetime=(
+                        None if pd.isna(row["fbg_datetime"]) else row["fbg_datetime"]
+                    ),
+                    fasting=(None if pd.isna(row["fasting"]) else row["fasting"]),
+                    endpoint_label=(
+                        None if pd.isna(row["endpoint_label"]) else row["endpoint_label"]
+                    ),
+                    offstudy_datetime=(
+                        None if pd.isna(row["offstudy_datetime"]) else row["offstudy_datetime"]
+                    ),
+                    offstudy_reason=(
+                        None if pd.isna(row["offstudy_reason"]) else row["offstudy_reason"]
+                    ),
+                    report_model=model,
+                    created=now,
+                )
+                for _, row in df.iterrows()
+            ]
+            created = len(model_cls.objects.bulk_create(data))
+        return created

{meta_edc-0.3.23 → meta_edc-0.3.25}/meta_analytics/dataframes/glucose_endpoints/utils.py

@@ -49,18 +49,17 @@ def get_empty_endpoint_df() -> pd.DataFrame:
     return endpoint_df
 
 
-def get_unique_visit_codes(source_df: pd.DataFrame) -> pd.DataFrame:
-    codes = source_df[source_df["visit_code"] % 1 == 0]["visit_code"].value_counts().to_frame()
-    codes = codes.reset_index()
-    codes["visit_code"] = codes["visit_code"].astype(float)
-    codes = codes.sort_values(["visit_code"])
-    # visit_codes = visit_codes[visit_codes["visit_code"] > self.after_visit_code]
-    codes = codes.reset_index(drop=True)
-    return codes
+def get_unique_visit_codes(df: pd.DataFrame) -> pd.DataFrame:
+    stats_df = df[df["visit_code"] % 1 == 0]["visit_code"].value_counts().to_frame()
+    stats_df = stats_df.reset_index()
+    stats_df["visit_code"] = stats_df["visit_code"].astype(float)
+    stats_df = stats_df.sort_values(["visit_code"])
+    stats_df = stats_df.reset_index(drop=True)
+    return stats_df
 
 
-def get_unique_subject_identifiers(source_df) -> pd.DataFrame:
-    df = pd.DataFrame(source_df["subject_identifier"].unique(), columns=["subject_identifier"])
-    df = df.sort_values(["subject_identifier"])
-    df = df.reset_index()
-    return df
+def get_unique_subject_identifiers(df: pd.DataFrame) -> pd.DataFrame:
+    values_df = pd.DataFrame(df["subject_identifier"].unique(), columns=["subject_identifier"])
+    values_df = values_df.sort_values(["subject_identifier"])
+    values_df = values_df.reset_index()
+    return values_df

{meta_edc-0.3.23 → meta_edc-0.3.25}/meta_edc/__init__.py

@@ -2,6 +2,9 @@ import os
 import sys
 from importlib.metadata import PackageNotFoundError, version
 
+# celery_app loads settings before Django, so ensure
+# it will load the correct settings module coming from
+# systemd service
 if "meta_edc.celery.live:app" in sys.argv:
     from .celery.live import app as celery_app
 elif "meta_edc.celery.uat:app" in sys.argv:

meta_edc-0.3.25/meta_edc/celery/__init__.py

@@ -0,0 +1,2 @@
+# do not import modules
+# see conditional import at root __init__

{meta_edc-0.3.23 → meta_edc-0.3.25}/meta_edc.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: meta-edc
-Version: 0.3.23
+Version: 0.3.25
 Summary: META Trial EDC (http://www.isrctn.com/ISRCTN76157257)
 Home-page: https://github.com/meta-trial/meta-edc
 Author: Erik van Widenfelt
@@ -19,7 +19,7 @@ Requires-Python: >=3.12
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: AUTHORS
-Requires-Dist: edc==0.6.1
+Requires-Dist: edc==0.6.3
 Requires-Dist: edc-microscopy
 Requires-Dist: beautifulsoup4
 Requires-Dist: edc-analytics