meta-edc 1.3.0__py3-none-any.whl → 1.4.1__py3-none-any.whl

meta_analytics/dataframes/constants.py

@@ -7,6 +7,7 @@ CASE_OGTT = 1
 EOS_DM_MET = "EOS - Patient developed diabetes"
 OGTT_THRESHOLD_MET = "OGTT >= 11.1"
 FBG_BEYOND_THRESHOLD = 20.0
+FBG_THRESHOLD_MET = f"FBG >= {FBG_BEYOND_THRESHOLD}"
 endpoint_columns = [
     "subject_identifier",
     "site_id",
@@ -30,6 +31,6 @@ endpoint_cases = {
     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_FBG_VERY_HIGH: f"FBG>={FBG_BEYOND_THRESHOLD}",
+    CASE_FBG_VERY_HIGH: FBG_THRESHOLD_MET,
     CASE_EOS: EOS_DM_MET,
 }

meta_analytics/dataframes/get_glucose_df.py

@@ -52,7 +52,16 @@ def get_glucose_df(subject_identifiers: list[str] | None = None) -> pd.DataFrame
         how="left",
     )
 
-    df_glucose = read_frame(Glucose.objects.all(), verbose=False).rename(
+    if subject_identifiers:
+        df_glucose = read_frame(
+            Glucose.objects.filter(subject_visit__subject_identifier__in=subject_identifiers),
+            verbose=False,
+        ).rename(columns={"subject_visit": "subject_visit_id", "fasting": "fasted"})
+    else:
+        df_glucose = read_frame(Glucose.objects.all(), verbose=False).rename(
+            columns={"subject_visit": "subject_visit_id", "fasting": "fasted"}
+        )
+    df_glucose = df_glucose.rename(
         columns={"subject_visit": "subject_visit_id", "fasting": "fasted"}
     )
     df_glucose["fasting_hrs"] = np.nan

meta_analytics/dataframes/glucose_endpoints/glucose_endpoints_by_date.py

@@ -6,7 +6,7 @@ from django.utils import timezone
 
 from ..constants import (
     CASE_EOS,
-    CASE_FBG_ONLY,
+    CASE_FBG_VERY_HIGH,
     CASE_FBGS_WITH_FIRST_OGTT,
     CASE_FBGS_WITH_SECOND_OGTT,
     CASE_OGTT,
@@ -76,6 +76,7 @@ class GlucoseEndpointsByDate:
             CASE_OGTT,
             CASE_FBGS_WITH_FIRST_OGTT,
             CASE_FBGS_WITH_SECOND_OGTT,
+            CASE_FBG_VERY_HIGH,
             CASE_EOS,
         ]
         self.endpoint_cases = {k: v for k, v in endpoint_cases.items() if k in self.case_list}
@@ -96,7 +97,7 @@ class GlucoseEndpointsByDate:
 
     def run(self):
         self.process_by_ogtt_only()
-        # self.process_by_fbg_only()
+        self.process_by_fbg_only()
         subject_identifiers_df = get_unique_subject_identifiers(self.df)
         for _, row in subject_identifiers_df.iterrows():
             subject_df = self.endpoint_cls(
@@ -111,10 +112,7 @@ class GlucoseEndpointsByDate:
         self.merge_with_final_endpoints()
 
     def process_by_fbg_only(self):
-        """Flag subjects that met endpoint by hitting the absurd FBG
-
-        Not used yet. Waiting for confirmation from Anu.
-        """
+        """Flag subjects that meta endpoint by hitting the absurd FBG"""
         subject_endpoint_df = self.working_df.loc[
             (self.working_df["fbg_value"] >= self.fbg_beyond_threshold)
             # & (self.working_df["fasted"] == YES)
@@ -129,8 +127,8 @@ class GlucoseEndpointsByDate:
         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_FBG_ONLY
+            subject_endpoint_df["endpoint_label"] = self.endpoint_cases[CASE_FBG_VERY_HIGH]
+            subject_endpoint_df["endpoint_type"] = CASE_FBG_VERY_HIGH
             subject_endpoint_df["interval_in_days"] = np.nan
 
             # add back the others rows for these subjects
@@ -356,14 +354,19 @@ class GlucoseEndpointsByDate:
         model_cls = django_apps.get_model(model)
         if self.subject_identifiers:
             model_cls.objects.filter(subject_identifier__in=self.subject_identifiers).delete()
-            df = (
-                self.endpoint_only_df[
-                    self.endpoint_only_df["subject_identifier"].isin(self.subject_identifiers)
-                ]
-                .copy()
-                .sort_values(by=["subject_identifier"])
-                .reset_index(drop=True)
-            )
+            if self.endpoint_only_df.empty:
+                df = pd.DataFrame()
+            else:
+                df = (
+                    self.endpoint_only_df[
+                        self.endpoint_only_df["subject_identifier"].isin(
+                            self.subject_identifiers
+                        )
+                    ]
+                    .copy()
+                    .sort_values(by=["subject_identifier"])
+                    .reset_index(drop=True)
+                )
         else:
             model_cls.objects.all().delete()
         created = 0

{meta_edc-1.3.0.dist-info → meta_edc-1.4.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: meta-edc
-Version: 1.3.0
+Version: 1.4.1
 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
@@ -15,12 +15,12 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Requires-Dist: clinicedc>=2.1.0
-Requires-Dist: edc-he>=1.4.0
-Requires-Dist: edc-microscopy>=1.4.0
+Requires-Dist: clinicedc>=2.2.2
+Requires-Dist: edc-he>=1.5.2
+Requires-Dist: edc-microscopy>=1.4.2
 Requires-Dist: edc-mnsi>=1.4.0
-Requires-Dist: edc-phq9>=1.3.0
-Requires-Dist: edc-qol>=1.3.0
+Requires-Dist: edc-phq9>=1.3.1
+Requires-Dist: edc-qol>=1.4.0
 Requires-Python: >=3.12, <3.14
 Description-Content-Type: text/x-rst
 
@@ -88,8 +88,8 @@ Assuming you are logged into the account ``myaccount``:
     mkdir ~/edc && \
     cd ~/edc && \
     uv venv && \
-    uv pip install -U meta-edc==1.2.9 && \
-    wget https://raw.githubusercontent.com/meta-trial/meta-edc/1.2.9/manage.py && \
+    uv pip install -U meta-edc==1.4.0 && \
+    wget https://raw.githubusercontent.com/meta-trial/meta-edc/1.4.0/manage.py && \
     uv pip freeze | grep meta-edc
 
 Copy your ``.env`` file to ``~/.etc``.
@@ -139,7 +139,7 @@ From the above example:
 
     cd ~/edc && \
     uv venv --clear && \
-    uv pip install -U meta-edc==1.2.9 && \
+    uv pip install -U meta-edc==1.4.0 && \
     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-1.3.0.dist-info → meta_edc-1.4.1.dist-info}/RECORD

@@ -82,15 +82,15 @@ meta_analytics/README.rst,sha256=TRjju_9l-FoV6YU9qBwlktJDjiK3yfvrSvMo7Rd4mc8,422
 meta_analytics/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 meta_analytics/constants.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 meta_analytics/dataframes/__init__.py,sha256=naGZtYGJ8BW03XslsFPZe9VZ2fWuU9ew84BB_iBLWxo,1266
-meta_analytics/dataframes/constants.py,sha256=AyEbvPGjZ4IVIukutRk5puzcGYLvzDtct7uvdOIqDYE,899
+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=vr0NqJ9N93d24W1UagL6PRBcMWpsXuL_GORJnmLdKfM,5477
+meta_analytics/dataframes/get_glucose_df.py,sha256=eGzA7dxh3igGZdNKvMfiH7maRl2IAngWiQp9Dx8FZHU,5884
 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
 meta_analytics/dataframes/glucose_endpoints/__init__.py,sha256=C78zm7_ebYdAQBaldn7LpKlRHvK2ufdT7nFBGZdAMFw,163
 meta_analytics/dataframes/glucose_endpoints/endpoint_by_date.py,sha256=bgbvvkeDbId_F4FWWtzHHq5TZf-YZEIJjR_p7Kjzmcw,7361
-meta_analytics/dataframes/glucose_endpoints/glucose_endpoints_by_date.py,sha256=nxzfoBZGQbUSChBdRaTV6Jkm-Fu1WA75prAt6VtaNQE,16369
+meta_analytics/dataframes/glucose_endpoints/glucose_endpoints_by_date.py,sha256=VBEHtAcfMOOJKmf3BRg-h4qjYwJxoUvFqjza9LRm-DA,16536
 meta_analytics/dataframes/screening/__init__.py,sha256=1SegmpN-ceginLsJUADqJzfhLVpAgBmMb53gnKRQsPw,176
 meta_analytics/dataframes/screening/get_glucose_tested_only_df.py,sha256=jW8eCT2Nu2nBLwcxVg6ftnBk1SbCejSpiURORmi3Aso,648
 meta_analytics/dataframes/screening/get_screening_df.py,sha256=OU-cLE3FH7cvHoXJxR6RiMS4VcWfOGzP7whlRZ7N3Qg,6153
@@ -480,7 +480,7 @@ meta_reports/admin/dbviews/unattended_three_in_row_admin.py,sha256=eTOK8nbUDXGk4
 meta_reports/admin/dbviews/unattended_two_in_row_admin.py,sha256=xaJJYYkKCyMFd2TvNWUEKU97libnJBjTHuxmJoatD4I,1062
 meta_reports/admin/endpoints_admin.py,sha256=AX_EQEINoknVkSnr8ciLTuHd6Oa2v-gp4Ninmhhp-p4,530
 meta_reports/admin/endpoints_all_admin.py,sha256=KVw25W033Fo88x5HQtlp4Ko-vrudICQWiAVefny8Dz8,475
-meta_reports/admin/last_imp_refill_admin.py,sha256=NqG7UAeTMZheOwzzrgBWKOjEnEr45YubwriyIDnlxj0,6553
+meta_reports/admin/last_imp_refill_admin.py,sha256=J_SuoFRTDBu6Mu0qHTWW82EblZb5VimrxCuaAyUMBvw,6493
 meta_reports/admin/list_filters.py,sha256=9OMjrCLG6W-ticvT3HAnSGhJYr4lr-Qxs5aEJMVX2mE,898
 meta_reports/admin/modeladmin_mixins.py,sha256=ntX259X7xMDqWJ4NzRHeQC0hTqrRoyMxi8GPuOWlhjg,3446
 meta_reports/admin_site.py,sha256=xoA18u9f341iLxuuhUeSEwaP-r2j6NFO2iRnagL2KR8,169
@@ -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-1.3.0.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-meta_edc-1.3.0.dist-info/WHEEL,sha256=DpNsHFUm_gffZe1FgzmqwuqiuPC6Y-uBCzibcJcdupM,78
-meta_edc-1.3.0.dist-info/METADATA,sha256=ECeSXe43ycOYmUCAsWI-OJHcUUtucdCrYHGyxbAbqwE,5131
-meta_edc-1.3.0.dist-info/RECORD,,
+meta_edc-1.4.1.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+meta_edc-1.4.1.dist-info/WHEEL,sha256=w4ZtLaDgMAZW2MMZZwtH8zENekoQYBCeullI-zsXJQk,78
+meta_edc-1.4.1.dist-info/METADATA,sha256=aat3YZPqv-YJUOu8NjiF13qhD7kaMXEklAOFAZdAlhs,5131
+meta_edc-1.4.1.dist-info/RECORD,,

{meta_edc-1.3.0.dist-info → meta_edc-1.4.1.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: uv 0.9.8
+Generator: uv 0.9.9
 Root-Is-Purelib: true
 Tag: py3-none-any

meta_reports/admin/last_imp_refill_admin.py

@@ -8,7 +8,6 @@ from django.utils.safestring import mark_safe
 from edc_model_admin.dashboard import ModelAdminDashboardMixin
 from edc_model_admin.list_filters import PastDateListFilter
 from edc_model_admin.mixins import TemplatesModelAdminMixin
-from edc_pdutils.actions import export_to_csv
 from edc_qareports.modeladmin_mixins import QaReportModelAdminMixin
 from edc_sites.admin import SiteModelAdminMixin
 from edc_sites.admin.list_filters import SiteListFilter
@@ -87,7 +86,7 @@ class LastImpRefillAdmin(
         render_to_string("meta_reports/last_imp_refill/changelist_note.html")
     )  # nosec B308, B703
 
-    actions = (update_report, export_to_csv)
+    actions = (update_report,)
 
     list_display = (
         "dashboard",