meta-edc 1.2.6__py3-none-any.whl → 1.2.8__py3-none-any.whl

meta_analytics/dataframes/constants.py

@@ -2,10 +2,11 @@ CASE_EOS = 7
 CASE_FBGS_WITH_FIRST_OGTT = 2
 CASE_FBGS_WITH_SECOND_OGTT = 3
 CASE_FBG_ONLY = 4
+CASE_FBG_VERY_HIGH = 5
 CASE_OGTT = 1
 EOS_DM_MET = "EOS - Patient developed diabetes"
 OGTT_THRESHOLD_MET = "OGTT >= 11.1"
-
+FBG_BEYOND_THRESHOLD = 20.0
 endpoint_columns = [
     "subject_identifier",
     "site_id",
@@ -29,5 +30,6 @@ 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_EOS: EOS_DM_MET,
 }

meta_analytics/dataframes/get_glucose_df.py

@@ -7,13 +7,23 @@ from edc_pdutils.dataframes import get_eos, get_subject_consent, get_subject_vis
 from meta_subject.models import Glucose, GlucoseFbg
 
 
-def get_glucose_df() -> pd.DataFrame:
+def get_glucose_df(subject_identifiers: list[str] | None = None) -> pd.DataFrame:
     subject_visit_df = (
-        get_subject_visit("meta_subject.subjectvisit")
+        get_subject_visit("meta_subject.subjectvisit", subject_identifiers)
         .rename(columns={"id": "subject_visit_id"})
         .query("appt_timing!=@MISSED_APPT")
     )
-    df_glucose_fbg = read_frame(GlucoseFbg.objects.all(), verbose=False).rename(
+    if subject_identifiers:
+        df_glucose_fbg = read_frame(
+            GlucoseFbg.objects.filter(
+                subject_visit__subject_identifier__in=subject_identifiers
+            ),
+            verbose=False,
+        )
+    else:
+        df_glucose_fbg = read_frame(GlucoseFbg.objects.all(), verbose=False)
+
+    df_glucose_fbg = df_glucose_fbg.rename(
         columns={"fasting": "fasted", "subject_visit": "subject_visit_id"},
     )
     df_glucose_fbg["fasting_hrs"] = np.nan

meta_analytics/dataframes/glucose_endpoints/endpoint_by_date.py

@@ -67,9 +67,11 @@ class CaseData:
             self.previous_fasted = self.df.loc[self.index - 1, "fasted"]
 
     def case_two(self) -> bool:
-        """ "FBG >= 7 x 2, first OGTT<=11.1"""
+        """FBG >= 7 x 2, first OGTT<=11.1"""
         return bool(
-            self.fbg_value >= self.fbg_threshold
+            pd.notna(self.next_fbg_datetime)
+            and pd.notna(self.fbg_datetime)
+            and self.fbg_value >= self.fbg_threshold
             and self.next_fbg_value >= self.fbg_threshold
             and 0.0 < self.ogtt_value < self.ogtt_threshold
             and self.fasted == YES
@@ -78,9 +80,11 @@ class CaseData:
         )
 
     def case_three(self) -> bool:
-        """ "FBG >= 7 x 2, second OGTT<=11.1"""
+        """FBG >= 7 x 2, second OGTT<=11.1"""
         return bool(
-            self.fbg_value >= self.fbg_threshold
+            pd.notna(self.next_fbg_datetime)
+            and pd.notna(self.fbg_datetime)
+            and self.fbg_value >= self.fbg_threshold
             and self.next_fbg_value >= self.fbg_threshold
             and 0.0 < self.next_ogtt_value < self.ogtt_threshold
             and self.fasted == YES
@@ -91,7 +95,9 @@ class CaseData:
     def case_two_reversed(self) -> bool:
         """Same as case 2, but with the previous FBG reading."""
         return bool(
-            self.fbg_value >= self.fbg_threshold
+            pd.notna(self.next_fbg_datetime)
+            and pd.notna(self.fbg_datetime)
+            and self.fbg_value >= self.fbg_threshold
             and self.previous_fbg_value >= self.fbg_threshold
             and 0.0 < self.previous_ogtt_value < self.ogtt_threshold
             and self.fasted == YES
@@ -99,6 +105,19 @@ class CaseData:
             and (self.fbg_datetime.date() - self.previous_fbg_datetime.date()).days > 6
         )
 
+    # def case_four(self) -> bool:
+    #     """FBG >= 20.0"""
+    #     return bool(
+    #         pd.notna(self.next_fbg_datetime)
+    #         and pd.notna(self.fbg_datetime)
+    #         and self.fbg_value >= self.fbg_threshold
+    #         and self.next_fbg_value >= self.fbg_threshold
+    #         and 0.0 < self.next_ogtt_value < self.ogtt_threshold
+    #         and self.fasted == YES
+    #         and self.next_fasted == YES
+    #         and (self.next_fbg_datetime.date() - self.fbg_datetime.date()).days > 6
+    #     )
+
 
 class EndpointByDate:
     """Given all timepoints for a subject, flag the first timepoint
@@ -113,6 +132,9 @@ class EndpointByDate:
       * case 2. FBG >= 7 x 2, first OGTT<11.1
       * case 3.  FBG >= 7 x 2, second OGTT<11.1
 
+    If the endpoint is reached by FBG+OGTT, the date of endpoint is
+    always the date of the second measurement.
+
     Additional criteria considered:
       1. any threshhold FBG must be taken while fasted (fasted=YES)
       2. threshhold FBG readings must be consecutive (no

meta_analytics/dataframes/glucose_endpoints/glucose_endpoints_by_date.py

@@ -6,9 +6,11 @@ from edc_constants.constants import NULL_STRING, YES
 
 from ..constants import (
     CASE_EOS,
+    CASE_FBG_ONLY,
     CASE_FBGS_WITH_FIRST_OGTT,
     CASE_FBGS_WITH_SECOND_OGTT,
     CASE_OGTT,
+    FBG_BEYOND_THRESHOLD,
     endpoint_cases,
     endpoint_columns,
 )
@@ -40,6 +42,7 @@ class GlucoseEndpointsByDate:
     """
 
     fbg_threshhold = 7.0
+    fbg_beyond_threshold = FBG_BEYOND_THRESHOLD
     ogtt_threshhold = 11.1
     endpoint_cls = EndpointByDate
     keep_cols = [  # noqa: RUF012
@@ -77,13 +80,15 @@ class GlucoseEndpointsByDate:
         ]
         self.endpoint_cases = {k: v for k, v in endpoint_cases.items() if k in self.case_list}
 
-        self.df = get_glucose_df().copy()
+        self.df = get_glucose_df(subject_identifiers=self.subject_identifiers).copy()
 
         # 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.sort_values(by=["subject_identifier", "fbg_datetime"]).reset_index(
-            drop=True
+        self.df = (
+            self.df.query("not (fbg_value.isna() and ogtt_value.isna())")
+            .sort_values(by=["subject_identifier", "fbg_datetime"])
+            .reset_index(drop=True)
         )
         self.working_df = self.df.copy()
         self.working_df["endpoint"] = 0
@@ -91,11 +96,11 @@ class GlucoseEndpointsByDate:
 
     def run(self):
         self.process_by_ogtt_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.get_subject_df(row["subject_identifier"])
             subject_df = self.endpoint_cls(
-                subject_df=subject_df,
+                subject_df=self.get_subject_df(row["subject_identifier"]),
                 fbg_threshhold=self.fbg_threshhold,
                 ogtt_threshhold=self.ogtt_threshhold,
             ).subject_df
@@ -105,6 +110,53 @@ class GlucoseEndpointsByDate:
         self.post_check_endpoint()
         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.
+        """
+        subject_endpoint_df = self.working_df.loc[
+            (self.working_df["fbg_value"] >= self.fbg_beyond_threshold)
+            # & (self.working_df["fasted"] == YES)
+        ].copy()
+
+        subject_endpoint_df = (
+            subject_endpoint_df.sort_values(by=["subject_identifier", "fbg_datetime"])
+            .reset_index(drop=True)
+            .drop_duplicates(subset=["subject_identifier"], keep="first")
+            .reset_index(drop=True)
+        )
+        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["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 process_by_ogtt_only(self):
         """Flag subjects that met endpoint by hitting the OGTT
         threshold.
@@ -126,7 +178,7 @@ class GlucoseEndpointsByDate:
         """
         subject_endpoint_df = self.working_df.loc[
             (self.working_df["ogtt_value"] >= self.ogtt_threshhold)
-            & (self.working_df["ogtt_value"] < 9999.99)
+            & (self.working_df["ogtt_value"] <= 9999.99)
             & (self.working_df["fasted"] == YES)
             & (self.working_df["fbg_value"].notna())
         ].copy()
@@ -292,8 +344,9 @@ class GlucoseEndpointsByDate:
                 how="left",
                 suffixes=("", "_y"),
             )
-        self.df = self.df.sort_values(by=["subject_identifier", "fbg_datetime"])
-        self.df = self.df.reset_index(drop=True)
+        self.df = self.df.sort_values(by=["subject_identifier", "fbg_datetime"]).reset_index(
+            drop=True
+        )
 
     def to_model(self):
         """Write endpoint_only_df to the Endpoints model"""

meta_analytics/dataframes/screening/get_screening_df.py

@@ -124,16 +124,12 @@ def get_screening_df(df: pd.DataFrame | None = None) -> pd.DataFrame:
     df_physical_exam = read_frame(qs_physical_exam)
     # merge w/ subject visit to get subject_identifier
     df_physical_exam = df_physical_exam.merge(
-        df_physical_exam,
         df_subject_visit[
             ["subject_visit", "subject_identifier", "visit_code", "visit_code_sequence"]
         ],
         on="subject_visit",
         how="left",
-    )
-    df_physical_exam = df_physical_exam[
-        ["subject_identifier", "visit_code", "visit_code_sequence", "waist_circumference"]
-    ]
+    )[["subject_identifier", "visit_code", "visit_code_sequence", "waist_circumference"]]
     df_physical_exam[["waist_circumference"]] = df_physical_exam[
         ["waist_circumference"]
     ].apply(pd.to_numeric)

meta_consent/migrations/0035_alter_historicalsubjectconsent_consent_definition_name_and_more.py

@@ -0,0 +1,43 @@
+# Generated by Django 5.2.7 on 2025-10-24 04:17
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_consent", "0034_remove_subjectconsentspfq_site_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="historicalsubjectconsent",
+            name="consent_definition_name",
+            field=models.CharField(
+                default="",
+                editable=False,
+                max_length=50,
+                verbose_name="Consent definition",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalsubjectconsentv1",
+            name="consent_definition_name",
+            field=models.CharField(
+                default="",
+                editable=False,
+                max_length=50,
+                verbose_name="Consent definition",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="subjectconsent",
+            name="consent_definition_name",
+            field=models.CharField(
+                default="",
+                editable=False,
+                max_length=50,
+                verbose_name="Consent definition",
+            ),
+        ),
+    ]

meta_dashboard/navbars.py

@@ -4,8 +4,6 @@ from edc_navbar import Navbar, NavbarItem, site_navbars
 from edc_pharmacy.navbars import pharmacy_navbar_item
 from edc_review_dashboard.navbars import navbar_item as review_navbar_item
 
-no_url_namespace = False  # True if settings.APP_NAME == "meta_dashboard" else False
-
 navbar = Navbar(name="meta_dashboard")
 
 
@@ -16,8 +14,7 @@ navbar.register(
         label="Screening",
         fa_icon="fa-user-plus",
         codename="edc_screening.view_screening_listboard",
-        url_name="screening_listboard_url",
-        no_url_namespace=no_url_namespace,
+        url_names_key="screening_listboard_url",
     )
 )
 
@@ -28,8 +25,7 @@ navbar.register(
         label="Subjects",
         fa_icon="fa-user-circle",
         codename="edc_subject_dashboard.view_subject_listboard",
-        url_name="subject_listboard_url",
-        no_url_namespace=no_url_namespace,
+        url_names_key="subject_listboard_url",
     )
 )
 

meta_dashboard/urls.py

@@ -13,28 +13,28 @@ app_name = "meta_dashboard"
 
 urlpatterns = SubjectListboardView.urls(
     namespace=app_name,
-    label="subject_listboard",
+    url_names_key="subject_listboard_url",
     identifier_pattern=ResearchProtocolConfig().subject_identifier_pattern,
 )
 urlpatterns += ScreeningListboardView.urls(
     namespace=app_name,
-    label="screening_listboard",
+    url_names_key="screening_listboard_url",
     identifier_label="screening_identifier",
     identifier_pattern=screening_identifier,
 )
 urlpatterns += SubjectDashboardView.urls(
     namespace=app_name,
-    label="subject_dashboard",
+    url_names_key="subject_dashboard_url",
     identifier_pattern=ResearchProtocolConfig().subject_identifier_pattern,
 )
 
 urlpatterns += AeListboardView.urls(
     namespace=app_name,
-    label="ae_listboard",
+    url_names_key="ae_listboard_url",
     identifier_pattern=ResearchProtocolConfig().subject_identifier_pattern,
 )
 urlpatterns += DeathReportListboardView.urls(
     namespace=app_name,
-    label="death_report_listboard",
+    url_names_key="death_report_listboard_url",
     identifier_pattern=ResearchProtocolConfig().subject_identifier_pattern,
 )

meta_dashboard/views/screening/listboard_view.py

@@ -11,7 +11,6 @@ class ListboardView(ScreeningListboardView):
         kwargs.update(meta_version=get_meta_version())
         return super().get_context_data(**kwargs)
 
-    def get_search_fields(self) -> list[str]:
+    def get_search_fields(self) -> tuple[str, ...]:
         fields = super().get_search_fields()
-        fields.append("hospital_identifier__exact")
-        return fields
+        return *fields, "hospital_identifier__exact"

meta_dashboard/views/subject/dashboard/dashboard_view.py

@@ -20,23 +20,22 @@ class DashboardView(SubjectDashboardView):
 
     def get_context_data(self, **kwargs) -> dict[str, Any]:
         """Add message if subject reaches DM Endpoint."""
-        context = super().get_context_data(**kwargs)
-        context.update(subject_consent_v1_ext=self.subject_consent_v1_ext)
+        kwargs.update(subject_consent_v1_ext=self.subject_consent_v1_ext)
         try:
             Endpoints.objects.get(subject_identifier=self.subject_identifier)
         except ObjectDoesNotExist:
             pass
         else:
             url = reverse("meta_reports_admin:meta_reports_glucosesummary_changelist")
-            url = f"{url}?q={self.subject_identifier}"
+            url = mark_safe(f"{url}?q={self.subject_identifier}")  # noqa: S308
             message = format_html(
                 '{text} <A href="{url}">{verbose_name}</A>',
                 text=_("Subject has reached the protocol endpoint. See "),
-                url=mark_safe(url),  # noqa: S308
+                url=url,
                 verbose_name=GlucoseSummary._meta.verbose_name,
             )
             self.message_user(message, level=messages.WARNING)
-        return context
+        return super().get_context_data(**kwargs)
 
     @property
     def subject_consent_v1_ext(self):

meta_dashboard/views/subject/listboard/listboard_view.py

@@ -11,7 +11,6 @@ class SubjectListboardView(BaseSubjectListboardView):
         kwargs.update(meta_version=get_meta_version())
         return super().get_context_data(**kwargs)
 
-    def get_search_fields(self) -> list[str]:
+    def get_search_fields(self) -> tuple[str, ...]:
         fields = super().get_search_fields()
-        fields.append("identity__exact")
-        return fields
+        return *fields, "identity__exact"

meta_edc/settings/debug.py

@@ -11,12 +11,12 @@ sys.stdout.write(f"Settings file {__file__}\n")
 # from django.core.cache import cache
 # cache.clear()
 # TZ Sites:
-SITE_ID = SiteID(default=20)  # Amana
+# SITE_ID = SiteID(default=20)  # Amana
 # SITE_ID = SiteID(default=10)  # Hindu Mandal
 # SITE_ID = SiteID(default=40)  # Mwananyamala
 # SITE_ID = SiteID(default=50)  # Mbagala
 # SITE_ID = SiteID(default=60)  # Mnazi-Moja
-# SITE_ID = SiteID(default=30)  # Temeke
+SITE_ID = SiteID(default=30)  # Temeke
 
 INDEX_PAGE = "http://localhost:8000"
 EDC_SITES_UAT_DOMAIN = False

{meta_edc-1.2.6.dist-info → meta_edc-1.2.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: meta-edc
-Version: 1.2.6
+Version: 1.2.8
 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
@@ -15,7 +15,7 @@ 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>=2.0.39
+Requires-Dist: clinicedc>=2.0.41
 Requires-Dist: edc-he>=1.2.0
 Requires-Dist: edc-microscopy>=1.2.0
 Requires-Dist: edc-mnsi>=1.2.0
@@ -89,8 +89,8 @@ Assuming you are logged into the account ``myaccount``:
     mkdir ~/edc && \
     cd ~/edc && \
     uv venv && \
-    uv pip install -U meta-edc==1.2.5 && \
-    wget https://raw.githubusercontent.com/meta-trial/meta-edc/1.2.5/manage.py && \
+    uv pip install -U meta-edc==1.2.7 && \
+    wget https://raw.githubusercontent.com/meta-trial/meta-edc/1.2.7/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==1.2.5 && \
+    uv pip install -U meta-edc==1.2.7 && \
     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