meta-edc 1.1.10__py3-none-any.whl → 1.1.13__py3-none-any.whl

meta_subject/models/signals.py

@@ -1,3 +1,5 @@
+import contextlib
+
 from django.apps import apps as django_apps
 from django.core.exceptions import ObjectDoesNotExist
 from django.db.models.signals import post_save, pre_save
@@ -23,7 +25,7 @@ from .subject_visit import SubjectVisit
     sender=StudyMedication,
     dispatch_uid="study_medication_on_pre_save",
 )
-def study_medication_on_pre_save(sender, instance, raw, **kwargs):
+def study_medication_on_pre_save(sender, instance, raw, **kwargs):  # noqa: ARG001
     """Create a prescription if one does not exist
 
     All refills are created against the prescription
@@ -35,7 +37,7 @@ def study_medication_on_pre_save(sender, instance, raw, **kwargs):
         subject_consent = get_consent_model_cls().objects.get(
             subject_identifier=instance.subject_visit.subject_identifier,
         )
-        try:
+        with contextlib.suppress(PrescriptionAlreadyExists):
             create_prescription(
                 subject_identifier=subject_consent.subject_identifier,
                 report_datetime=subject_consent.consent_datetime,
@@ -43,8 +45,6 @@ def study_medication_on_pre_save(sender, instance, raw, **kwargs):
                 medication_names=[METFORMIN],
                 site=subject_consent.site,
             )
-        except PrescriptionAlreadyExists:
-            pass
 
 
 @receiver(
@@ -53,7 +53,7 @@ def study_medication_on_pre_save(sender, instance, raw, **kwargs):
     sender=Delivery,
     dispatch_uid="update_pregnancy_notification_on_delivery_post_save",
 )
-def update_pregnancy_notification_on_delivery_post_save(sender, instance, raw, **kwargs):
+def update_pregnancy_notification_on_delivery_post_save(sender, instance, raw, **kwargs):  # noqa: ARG001
     """Updates PregnancyNotification model instance when the delivery form is submitted.
 
     Sets delivered=True and delivery_datetime
@@ -73,7 +73,7 @@ def update_pregnancy_notification_on_delivery_post_save(sender, instance, raw, *
     sender=Delivery,
     dispatch_uid="update_schedule_on_delivery_post_save",
 )
-def update_schedule_on_delivery_post_save(sender, instance, raw, **kwargs):
+def update_schedule_on_delivery_post_save(sender, instance, raw, **kwargs):  # noqa: ARG001
     """Takes a participant off the SCHEDULE_PREGNANCY schedule when
     delivery model is submitted.
 
@@ -97,10 +97,8 @@ def update_schedule_on_delivery_post_save(sender, instance, raw, **kwargs):
             delivery = Delivery.objects.get(
                 subject_visit__subject_identifier=instance.subject_identifier,
             )
-            offschedule_datetime = (
-                delivery.delivery_datetime
-                if delivery.delivery_datetime > last_subject_visit.report_datetime
-                else last_subject_visit.report_datetime
+            offschedule_datetime = max(
+                last_subject_visit.report_datetime, delivery.delivery_datetime
             )
             offschedule_model_cls.objects.create(
                 subject_identifier=instance.subject_identifier,
@@ -114,10 +112,14 @@ def update_schedule_on_delivery_post_save(sender, instance, raw, **kwargs):
     dispatch_uid="update_glucose_endpoints_for_subject_on_post_save",
 )
 def update_glucose_endpoints_for_subject_on_post_save(
-    sender, instance, raw, update_fields, **kwargs
+    sender,
+    instance,
+    raw,
+    update_fields,
+    **kwargs,  # noqa: ARG001
 ):
     if not raw and not update_fields and sender in [Glucose, GlucoseFbg]:
-        from meta_analytics.dataframes import GlucoseEndpointsByDate
+        from meta_analytics.dataframes import GlucoseEndpointsByDate  # noqa: PLC0415
 
         cls = GlucoseEndpointsByDate(
             subject_identifiers=[instance.subject_visit.subject_identifier]

meta_subject/models/subject_visit.py

@@ -48,7 +48,7 @@ class SubjectVisit(
 
     unschedule_detail = models.TextField(
         verbose_name="If 'unschedule', please provide further details, if any",
-        null=True,
+        default="",
         blank=True,
     )
 

meta_subject/models/urine_dipstick_test.py

@@ -14,7 +14,7 @@ class UrineDipstickTest(CrfModelMixin, edc_models.BaseUuidModel):
     )
 
     not_performed_reason = models.CharField(
-        verbose_name="If NO, provide reason", max_length=150, null=True, blank=True
+        verbose_name="If NO, provide reason", max_length=150, default="", blank=True
     )
 
     ketones = models.CharField(

meta_subject/models/urine_pregnancy.py

@@ -17,7 +17,7 @@ class UrinePregnancy(CrfWithActionModelMixin, edc_models.BaseUuidModel):
     )
 
     not_performed_reason = models.CharField(
-        verbose_name="If NO, provide reason", max_length=150, null=True, blank=True
+        verbose_name="If NO, provide reason", max_length=150, default="", blank=True
     )
 
     assay_date = models.DateField(verbose_name="Urine βhCG date", blank=True, null=True)

meta_visit_schedule/visit_schedules/__init__.py

@@ -9,3 +9,5 @@ style = color_style()
 
 sys.stdout.write(style.SUCCESS("Notice: loading visit schedule for phase 3 **** \n"))
 site_visit_schedules.register(visit_schedule)
+
+__all__ = ["schedule", "visit_schedule"]

meta_visit_schedule/visit_schedules/phase_three/__init__.py

@@ -1,2 +1,4 @@
 from .schedule import schedule
 from .visit_schedule import visit_schedule
+
+__all__ = ["schedule", "visit_schedule"]

meta_visit_schedule/visit_schedules/phase_three/schedule.py

@@ -47,10 +47,10 @@ from .crfs import (
     crfs_48m,
     crfs_d1,
     crfs_missed,
+    crfs_w2,
 )
 from .crfs import crfs_prn as default_crfs_prn
 from .crfs import crfs_unscheduled as default_crfs_unscheduled
-from .crfs import crfs_w2
 from .requisitions import (
     requisitions_1m,
     requisitions_3m,
@@ -70,10 +70,10 @@ from .requisitions import (
     requisitions_45m,
     requisitions_48m,
     requisitions_d1,
+    requisitions_w2,
 )
 from .requisitions import requisitions_prn as default_requisitions_prn
 from .requisitions import requisitions_unscheduled as default_requisitions_unscheduled
-from .requisitions import requisitions_w2
 
 
 class Visit(BaseVisit):

meta_visit_schedule/visit_schedules/phase_three/schedule_dm_referral.py

@@ -6,8 +6,7 @@ from edc_visit_schedule.visit import Crf, CrfCollection, Visit
 from meta_consent.consents import consent_v1
 
 from ...constants import DM_BASELINE, DM_FOLLOWUP, SCHEDULE_DM_REFERRAL
-from .crfs import crfs_missed
-from .crfs import crfs_prn
+from .crfs import crfs_missed, crfs_prn
 from .crfs import crfs_prn as default_crfs_prn
 
 crfs_baseline = CrfCollection(

meta_visit_schedule/visit_schedules/phase_three/schedule_pregnancy.py

@@ -6,8 +6,7 @@ from edc_visit_schedule.visit import Visit
 from meta_consent.consents import consent_v1
 
 from ...constants import DELIVERY, SCHEDULE_PREGNANCY
-from .crfs import crfs_missed
-from .crfs import crfs_prn
+from .crfs import crfs_missed, crfs_prn
 from .crfs import crfs_prn as default_crfs_prn
 from .crfs_pregnancy import crfs_pregnancy
 

meta_analytics/.ipynb_checkpoints/get_tables-checkpoint.py

@@ -1,105 +0,0 @@
-from datetime import datetime
-from pathlib import Path
-
-import pandas as pd
-from edc_analytics.custom_tables import (
-    AgeTable,
-    ArtTable,
-    BmiTable,
-    BpTable,
-    FastingTable,
-    FbgOgttTable,
-    FbgTable,
-    GenderTable,
-    HbA1cTable,
-    OgttTable,
-    WaistCircumferenceTable,
-)
-
-from meta_analytics.dataframes import get_glucose_tested_only_df, get_screening_df
-from meta_analytics.tables import EligibleP12Table, HasDmTable
-
-
-class Data:
-    def __init__(self, label: str, table_df: pd.DataFrame, data_df: pd.DataFrame):
-        self.label = label
-        self.table_df = table_df
-        self.data_df = data_df
-
-    def __repr__(self):
-        return f"{self.label} obs={len(self.data_df)}"
-
-    def to_csv(
-        self, folder: str | None = None, filename: str | None = None, cols: int | None = None
-    ):
-        folder = folder or "/Users/erikvw/Documents/ucl/protocols/meta3/reports/"
-        cols = cols or 5
-        datestamp = datetime.now().strftime("%Y%m%d%H%M")
-        filename = filename or f"meta3_table_{self.label}_{datestamp}.csv"
-        path = Path(folder) / filename
-        self.table_df.iloc[:, :cols].to_csv(
-            path_or_buf=path, encoding="utf-8", index=0, sep="|"
-        )
-
-
-def get_tables() -> dict[str, Data]:
-    """
-    results = get_table()
-    results.get("fbg").to_csv(folder="/Users/erikvw/Documents/")
-    """
-    df_screening = get_screening_df()
-    df_has_dm = df_screening[(df_screening["has_dm"] == "Yes")]
-    df_no_dm = df_screening[(df_screening["has_dm"] == "No")]
-    df_fbg = get_glucose_tested_only_df(df_screening)
-
-    df_not_tested = df_no_dm.copy()
-    df_not_eligible_p1p2 = df_not_tested[
-        ~(
-            (df_not_tested["eligible_part_one"] == "Yes")
-            & (df_not_tested["eligible_part_two"] == "Yes")
-        )
-    ]
-    df_not_tested.drop(df_not_eligible_p1p2.index, inplace=True)
-    df_not_tested.drop(df_fbg.index, inplace=True)
-
-    df_stats = pd.DataFrame(
-        {
-            "df": ["df_screening", "df_has_dm", "df_no_dm", "df_not_tested", "df_fbg"],
-            "count": [
-                len(df_screening),
-                len(df_has_dm),
-                len(df_no_dm),
-                len(df_not_tested),
-                len(df_fbg),
-            ],
-        }
-    )
-
-    results = {"stats": df_stats}
-    for key, df in {
-        "screening": df_screening,
-        "has_dm": df_has_dm,
-        "no_dm": df_no_dm,
-        "not_tested": df_not_tested,
-        "fbg": df_fbg,
-    }.items():
-        dfs = []
-        for tbl_cls in [
-            GenderTable,
-            AgeTable,
-            WaistCircumferenceTable,
-            BmiTable,
-            BpTable,
-            ArtTable,
-            FastingTable,
-            FbgTable,
-            OgttTable,
-            FbgOgttTable,
-            HbA1cTable,
-            EligibleP12Table,
-            HasDmTable,
-        ]:
-            tbl = tbl_cls(main_df=df)
-            dfs.append(tbl.table_df)
-        results.update({key: Data(key, pd.concat(list(dfs)), df)})
-    return results

meta_edc-1.1.10.dist-info/METADATA

@@ -1,89 +0,0 @@
-Metadata-Version: 2.4
-Name: meta-edc
-Version: 1.1.10
-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
-Author-email: Erik van Widenfelt <ew2789@gmail.com>, Jonathan Willitts <j.willitts@ucl.ac.uk>
-License-Expression: GPL-3.0-or-later
-License-File: LICENSE
-Classifier: Environment :: Web Environment
-Classifier: Framework :: Django
-Classifier: Framework :: Django :: 5.2
-Classifier: Intended Audience :: Developers
-Classifier: Intended Audience :: Science/Research
-Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-Requires-Dist: beautifulsoup4>=4.13.4
-Requires-Dist: celery[redis]>=5.5.3
-Requires-Dist: django-pylabels>=1.0.1
-Requires-Dist: edc>=1.2.0
-Requires-Python: >=3.12
-Description-Content-Type: text/x-rst
-
-|pypi| |actions| |codecov| |downloads|
-
-
-META Edc
---------
-
-Metformin treatment in Africa- META
-
-* https://www.ucl.ac.uk/global-health/research/z-research/respond-africa/metformin-treatment-africa-meta
-* https://www.inteafrica.org/related-projects/meta-trial/
-* https://www.lstmed.ac.uk/research/departments/international-public-health/respond-africa/meta
-* http://www.isrctn.com/ISRCTN76157257
-
-py 3.12 / DJ 5.1.5 / edc 1.0.3 (META3)
-
-This codebase is used for two randomized clinical trials:
-
-____
-
-META PHASE II:
-
-(final version `0.1.77 <https://github.com/meta-trial/meta-edc/tree/0.1.77>`_)
-
-Metformin Treatment for Diabetes Prevention in Africa: META Trial
-TASO, MRC/UVRI/LSHTM, NIMR – TZ and Liverpool School of Tropical Medicine (ISRCTN76157257)
-http://www.isrctn.com/ISRCTN76157257
-
-____
-
-META PHASE III:
-
-A randomised placebo-controlled double-blind phase III trial to determine the effects of metformin versus placebo on the incidence of diabetes in HIV-infected persons with pre-diabetes in Tanzania.
-
-Liverpool School of Tropical Medicine
-
-EDCTP grant number: RIA2018CO-2513
-
-Trial registration: ISCRTN 77382043
-
-https://ico.org.uk/ESDWebPages/Entry/Z4763134
-
-____
-
-See also https://github.com/clinicedc/edc
-
-|django|
-
-To setup a demo system, see https://github.com/meta-trial/meta3-sample
-
-
-.. |pypi| image:: https://img.shields.io/pypi/v/meta-edc.svg
-    :target: https://pypi.python.org/pypi/meta-edc
-
-.. |actions| image:: https://github.com/meta-trial/meta-edc/actions/workflows/build.yml/badge.svg
-  :target: https://github.com/meta-trial/meta-edc/actions/workflows/build.yml
-
-.. |codecov| image:: https://codecov.io/gh/meta-trial/meta-edc/branch/develop/graph/badge.svg
-  :target: https://codecov.io/gh/meta-trial/meta-edc
-
-.. |downloads| image:: https://pepy.tech/badge/meta-edc
-   :target: https://pepy.tech/project/meta-edc
-
-.. |django| image:: https://www.djangoproject.com/m/img/badges/djangomade124x25.gif
-   :target: http://www.djangoproject.com/
-   :alt: Made with Django