meta-edc 0.3.7__py3-none-any.whl → 0.3.50__py3-none-any.whl

meta_reports/tasks.py

@@ -0,0 +1,12 @@
+from celery import shared_task
+
+
+@shared_task
+def update_endpoints_table(subject_identifiers: list[str] | None = None):
+    from meta_analytics.dataframes import GlucoseEndpointsByDate
+
+    if len(subject_identifiers) > 5:
+        subject_identifiers = []
+    cls = GlucoseEndpointsByDate(subject_identifiers=subject_identifiers)
+    cls.run()
+    return cls.to_model()

meta_reports/templates/meta_reports/columns/subject_identifier_column.html

@@ -0,0 +1 @@
+<a title="{{ title }}" href="{{ url }}?q={{ subject_identifier }}">{{ label|default:subject_identifier }}</a>

meta_reports/templates/meta_reports/endpoints_all_change_list_note.html

@@ -0,0 +1,12 @@
+Endpoints report shows subjects who have reached the protocol endpoint.
+<BR>
+<i>This report INCLUDES subjects who are no longer on-study. See also the <a href="{% url 'meta_reports_admin:meta_reports_endpoints_changelist' %}">Endpoints (DM)</a> report.</i>
+<BR>
+Pay attention to the "LAST_UPDATED" column. This tells you the last time the report was updated per subject.
+<BR>
+<BR>
+Unlike other reports, this report does not automatically update, but you can update it :
+<UL>
+    <LI>Place a check mark next to one or more subjects and select 'Regenerate selected report data' from the Action menu.</LI>
+    <li>If you select more than 5 subjects, records for ALL subjects will be refreshed.</li>
+</UL>

meta_reports/templates/meta_reports/endpoints_change_list_note.html

@@ -0,0 +1,12 @@
+Endpoints report shows subjects who have reached the protocol endpoint and should enroll to the DM Referral Schedule.
+<BR>
+<i>The report EXCLUDES subjects who are no longer on-study. See also the <a href="{% url 'meta_reports_admin:meta_reports_endpointsproxy_changelist' %}">Endpoints (DM): All</a> report.</i></i>
+<BR>
+Pay attention to the "LAST_UPDATED" column. This tells you the last time the report was updated per subject.
+<BR>
+<BR>
+Unlike other reports, this report does not automatically update, but you can update it :
+<UL>
+    <LI>Place a check mark next to one or more subjects and select 'Regenerate selected report data' from the Action menu.</LI>
+    <li>If you select more than 5 subjects, records for ALL subjects will be refreshed.</li>
+</UL>

meta_reports/tests/test_sql_gen.py

@@ -0,0 +1,5 @@
+from django.test import TestCase
+
+
+class TestSqlGen(TestCase):
+    pass

meta_reports/urls.py

@@ -0,0 +1,8 @@
+from django.urls.conf import path
+from django.views.generic import RedirectView
+
+app_name = "meta_reports"
+
+urlpatterns = [
+    path("", RedirectView.as_view(url=f"/{app_name}/admin/"), name="home_url"),
+]

meta_screening/admin/subject_screening_admin.py

@@ -79,6 +79,7 @@ class SubjectScreeningAdmin(ModelAdminSubjectDashboardMixin, SimpleHistoryAdmin)
         "hospital_identifier",
         "initials",
         "reasons_ineligible",
+        "id",
     )
 
     readonly_fields = (

meta_screening/form_validators/screening_part_two.py

@@ -80,7 +80,7 @@ class ScreeningPartTwoFormValidator(PrnFormValidatorMixin, FormValidator):
                 {
                     self.report_datetime_field_attr: (
                         "Cannot be before `Part One` report datetime. "
-                        f"Expected date after {dte}."
+                        f"Expected date after {dte}. Got {self.report_datetime}"
                     )
                 },
                 INVALID_ERROR,

meta_screening/migrations/0062_remove_icpreferral_site_and_more.py

@@ -0,0 +1,27 @@
+# Generated by Django 4.2.11 on 2024-03-27 19:41
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_screening", "0061_alter_historicalicpreferral_site_and_more"),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name="icpreferral",
+            name="site",
+        ),
+        migrations.RemoveField(
+            model_name="icpreferral",
+            name="subject_screening",
+        ),
+        migrations.DeleteModel(
+            name="HistoricalIcpReferral",
+        ),
+        migrations.DeleteModel(
+            name="IcpReferral",
+        ),
+    ]

meta_screening/migrations/0063_alter_historicalscreeningpartone_fasting_duration_str_and_more.py

@@ -0,0 +1,184 @@
+# Generated by Django 5.0.4 on 2024-04-18 23:46
+
+import django.core.validators
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_screening", "0062_remove_icpreferral_site_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="historicalscreeningpartone",
+            name="fasting_duration_str",
+            field=models.CharField(
+                blank=True,
+                help_text="As reported by patient. Duration of fast. Format is `HHhMMm`. For example 1h23m, 12h7m, etc",
+                max_length=8,
+                null=True,
+                validators=[
+                    django.core.validators.RegexValidator(
+                        "^([0-9]{1,3}h([0-5]?[0-9]m)?)$",
+                        message="Invalid format. Expected something like 1h20m, 11h5m, etc. No spaces allowed.",
+                    )
+                ],
+                verbose_name="How long have they fasted in hours and/or minutes?",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalscreeningpartone",
+            name="repeat_fasting_duration_str",
+            field=models.CharField(
+                blank=True,
+                help_text="As reported by patient. Duration of fast. Format is `HHhMMm`. For example 1h23m, 12h7m, etc",
+                max_length=8,
+                null=True,
+                validators=[
+                    django.core.validators.RegexValidator(
+                        "^([0-9]{1,3}h([0-5]?[0-9]m)?)$",
+                        message="Invalid format. Expected something like 1h20m, 11h5m, etc. No spaces allowed.",
+                    )
+                ],
+                verbose_name="How long have they fasted in hours and/or minutes?",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalscreeningpartthree",
+            name="fasting_duration_str",
+            field=models.CharField(
+                blank=True,
+                help_text="As reported by patient. Duration of fast. Format is `HHhMMm`. For example 1h23m, 12h7m, etc",
+                max_length=8,
+                null=True,
+                validators=[
+                    django.core.validators.RegexValidator(
+                        "^([0-9]{1,3}h([0-5]?[0-9]m)?)$",
+                        message="Invalid format. Expected something like 1h20m, 11h5m, etc. No spaces allowed.",
+                    )
+                ],
+                verbose_name="How long have they fasted in hours and/or minutes?",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalscreeningpartthree",
+            name="repeat_fasting_duration_str",
+            field=models.CharField(
+                blank=True,
+                help_text="As reported by patient. Duration of fast. Format is `HHhMMm`. For example 1h23m, 12h7m, etc",
+                max_length=8,
+                null=True,
+                validators=[
+                    django.core.validators.RegexValidator(
+                        "^([0-9]{1,3}h([0-5]?[0-9]m)?)$",
+                        message="Invalid format. Expected something like 1h20m, 11h5m, etc. No spaces allowed.",
+                    )
+                ],
+                verbose_name="How long have they fasted in hours and/or minutes?",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalscreeningparttwo",
+            name="fasting_duration_str",
+            field=models.CharField(
+                blank=True,
+                help_text="As reported by patient. Duration of fast. Format is `HHhMMm`. For example 1h23m, 12h7m, etc",
+                max_length=8,
+                null=True,
+                validators=[
+                    django.core.validators.RegexValidator(
+                        "^([0-9]{1,3}h([0-5]?[0-9]m)?)$",
+                        message="Invalid format. Expected something like 1h20m, 11h5m, etc. No spaces allowed.",
+                    )
+                ],
+                verbose_name="How long have they fasted in hours and/or minutes?",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalscreeningparttwo",
+            name="repeat_fasting_duration_str",
+            field=models.CharField(
+                blank=True,
+                help_text="As reported by patient. Duration of fast. Format is `HHhMMm`. For example 1h23m, 12h7m, etc",
+                max_length=8,
+                null=True,
+                validators=[
+                    django.core.validators.RegexValidator(
+                        "^([0-9]{1,3}h([0-5]?[0-9]m)?)$",
+                        message="Invalid format. Expected something like 1h20m, 11h5m, etc. No spaces allowed.",
+                    )
+                ],
+                verbose_name="How long have they fasted in hours and/or minutes?",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalsubjectscreening",
+            name="fasting_duration_str",
+            field=models.CharField(
+                blank=True,
+                help_text="As reported by patient. Duration of fast. Format is `HHhMMm`. For example 1h23m, 12h7m, etc",
+                max_length=8,
+                null=True,
+                validators=[
+                    django.core.validators.RegexValidator(
+                        "^([0-9]{1,3}h([0-5]?[0-9]m)?)$",
+                        message="Invalid format. Expected something like 1h20m, 11h5m, etc. No spaces allowed.",
+                    )
+                ],
+                verbose_name="How long have they fasted in hours and/or minutes?",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalsubjectscreening",
+            name="repeat_fasting_duration_str",
+            field=models.CharField(
+                blank=True,
+                help_text="As reported by patient. Duration of fast. Format is `HHhMMm`. For example 1h23m, 12h7m, etc",
+                max_length=8,
+                null=True,
+                validators=[
+                    django.core.validators.RegexValidator(
+                        "^([0-9]{1,3}h([0-5]?[0-9]m)?)$",
+                        message="Invalid format. Expected something like 1h20m, 11h5m, etc. No spaces allowed.",
+                    )
+                ],
+                verbose_name="How long have they fasted in hours and/or minutes?",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="subjectscreening",
+            name="fasting_duration_str",
+            field=models.CharField(
+                blank=True,
+                help_text="As reported by patient. Duration of fast. Format is `HHhMMm`. For example 1h23m, 12h7m, etc",
+                max_length=8,
+                null=True,
+                validators=[
+                    django.core.validators.RegexValidator(
+                        "^([0-9]{1,3}h([0-5]?[0-9]m)?)$",
+                        message="Invalid format. Expected something like 1h20m, 11h5m, etc. No spaces allowed.",
+                    )
+                ],
+                verbose_name="How long have they fasted in hours and/or minutes?",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="subjectscreening",
+            name="repeat_fasting_duration_str",
+            field=models.CharField(
+                blank=True,
+                help_text="As reported by patient. Duration of fast. Format is `HHhMMm`. For example 1h23m, 12h7m, etc",
+                max_length=8,
+                null=True,
+                validators=[
+                    django.core.validators.RegexValidator(
+                        "^([0-9]{1,3}h([0-5]?[0-9]m)?)$",
+                        message="Invalid format. Expected something like 1h20m, 11h5m, etc. No spaces allowed.",
+                    )
+                ],
+                verbose_name="How long have they fasted in hours and/or minutes?",
+            ),
+        ),
+    ]

meta_screening/migrations/0064_remove_historicalscreeningpartone_fasting_duration_minutes_and_more.py

@@ -0,0 +1,126 @@
+# Generated by Django 4.2.11 on 2024-05-16 00:51
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        (
+            "meta_screening",
+            "0063_alter_historicalscreeningpartone_fasting_duration_str_and_more",
+        ),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name="historicalscreeningpartone",
+            name="fasting_duration_minutes",
+        ),
+        migrations.RemoveField(
+            model_name="historicalscreeningpartone",
+            name="repeat_fasting_duration_minutes",
+        ),
+        migrations.RemoveField(
+            model_name="historicalscreeningpartthree",
+            name="fasting_duration_minutes",
+        ),
+        migrations.RemoveField(
+            model_name="historicalscreeningpartthree",
+            name="repeat_fasting_duration_minutes",
+        ),
+        migrations.RemoveField(
+            model_name="historicalscreeningparttwo",
+            name="fasting_duration_minutes",
+        ),
+        migrations.RemoveField(
+            model_name="historicalscreeningparttwo",
+            name="repeat_fasting_duration_minutes",
+        ),
+        migrations.RemoveField(
+            model_name="historicalsubjectscreening",
+            name="fasting_duration_minutes",
+        ),
+        migrations.RemoveField(
+            model_name="historicalsubjectscreening",
+            name="repeat_fasting_duration_minutes",
+        ),
+        migrations.RemoveField(
+            model_name="subjectscreening",
+            name="fasting_duration_minutes",
+        ),
+        migrations.RemoveField(
+            model_name="subjectscreening",
+            name="repeat_fasting_duration_minutes",
+        ),
+        migrations.AddField(
+            model_name="historicalscreeningpartone",
+            name="fasting_duration_delta",
+            field=models.DurationField(
+                blank=True, help_text="system calculated value", null=True
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicalscreeningpartone",
+            name="repeat_fasting_duration_delta",
+            field=models.DurationField(
+                blank=True, help_text="system calculated value", null=True
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicalscreeningpartthree",
+            name="fasting_duration_delta",
+            field=models.DurationField(
+                blank=True, help_text="system calculated value", null=True
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicalscreeningpartthree",
+            name="repeat_fasting_duration_delta",
+            field=models.DurationField(
+                blank=True, help_text="system calculated value", null=True
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicalscreeningparttwo",
+            name="fasting_duration_delta",
+            field=models.DurationField(
+                blank=True, help_text="system calculated value", null=True
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicalscreeningparttwo",
+            name="repeat_fasting_duration_delta",
+            field=models.DurationField(
+                blank=True, help_text="system calculated value", null=True
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicalsubjectscreening",
+            name="fasting_duration_delta",
+            field=models.DurationField(
+                blank=True, help_text="system calculated value", null=True
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicalsubjectscreening",
+            name="repeat_fasting_duration_delta",
+            field=models.DurationField(
+                blank=True, help_text="system calculated value", null=True
+            ),
+        ),
+        migrations.AddField(
+            model_name="subjectscreening",
+            name="fasting_duration_delta",
+            field=models.DurationField(
+                blank=True, help_text="system calculated value", null=True
+            ),
+        ),
+        migrations.AddField(
+            model_name="subjectscreening",
+            name="repeat_fasting_duration_delta",
+            field=models.DurationField(
+                blank=True, help_text="system calculated value", null=True
+            ),
+        ),
+    ]

meta_screening/migrations/0065_auto_20240516_0352.py

@@ -0,0 +1,31 @@
+# Generated by Django 4.2.11 on 2024-05-16 00:52
+from django.db import migrations
+from edc_model.utils import duration_hm_to_timedelta
+from tqdm import tqdm
+
+
+def update_duration(apps, schema_editor):
+    model_cls = apps.get_model("meta_screening.subjectscreening")
+    qs = model_cls.objects.all()
+    total = qs.count()
+    for obj in tqdm(qs, total=total):
+        if obj.fasting_duration_str:
+            tdelta = duration_hm_to_timedelta(obj.fasting_duration_str)
+            obj.fasting_duration_delta = tdelta
+            obj.save_base(update_fields=["fasting_duration_delta"])
+        if obj.repeat_fasting_duration_str:
+            tdelta = duration_hm_to_timedelta(obj.repeat_fasting_duration_str)
+            obj.repeat_fasting_duration_delta = tdelta
+            obj.save_base(update_fields=["repeat_fasting_duration_delta"])
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        (
+            "meta_screening",
+            "0064_remove_historicalscreeningpartone_fasting_duration_minutes_and_more",
+        ),
+    ]
+
+    operations = [migrations.RunPython(update_duration)]

meta_screening/migrations/0066_alter_historicalscreeningpartone_fasting_duration_delta_and_more.py

@@ -0,0 +1,103 @@
+# Generated by Django 4.2.11 on 2024-05-16 01:21
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_screening", "0065_auto_20240516_0352"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="historicalscreeningpartone",
+            name="fasting_duration_delta",
+            field=models.DurationField(
+                blank=True,
+                help_text="system calculated to microseconds. (hours=microseconds/3.6e+9)",
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalscreeningpartone",
+            name="repeat_fasting_duration_delta",
+            field=models.DurationField(
+                blank=True,
+                help_text="system calculated to microseconds. (hours=microseconds/3.6e+9)",
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalscreeningpartthree",
+            name="fasting_duration_delta",
+            field=models.DurationField(
+                blank=True,
+                help_text="system calculated to microseconds. (hours=microseconds/3.6e+9)",
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalscreeningpartthree",
+            name="repeat_fasting_duration_delta",
+            field=models.DurationField(
+                blank=True,
+                help_text="system calculated to microseconds. (hours=microseconds/3.6e+9)",
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalscreeningparttwo",
+            name="fasting_duration_delta",
+            field=models.DurationField(
+                blank=True,
+                help_text="system calculated to microseconds. (hours=microseconds/3.6e+9)",
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalscreeningparttwo",
+            name="repeat_fasting_duration_delta",
+            field=models.DurationField(
+                blank=True,
+                help_text="system calculated to microseconds. (hours=microseconds/3.6e+9)",
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalsubjectscreening",
+            name="fasting_duration_delta",
+            field=models.DurationField(
+                blank=True,
+                help_text="system calculated to microseconds. (hours=microseconds/3.6e+9)",
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalsubjectscreening",
+            name="repeat_fasting_duration_delta",
+            field=models.DurationField(
+                blank=True,
+                help_text="system calculated to microseconds. (hours=microseconds/3.6e+9)",
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="subjectscreening",
+            name="fasting_duration_delta",
+            field=models.DurationField(
+                blank=True,
+                help_text="system calculated to microseconds. (hours=microseconds/3.6e+9)",
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="subjectscreening",
+            name="repeat_fasting_duration_delta",
+            field=models.DurationField(
+                blank=True,
+                help_text="system calculated to microseconds. (hours=microseconds/3.6e+9)",
+                null=True,
+            ),
+        ),
+    ]

meta_screening/migrations/0067_alter_historicalscreeningpartone_report_datetime_and_more.py

@@ -0,0 +1,84 @@
+# Generated by Django 4.2.11 on 2024-06-03 16:46
+
+from django.db import migrations, models
+import edc_model.validators.date
+import edc_protocol.validators
+import edc_utils.date
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        (
+            "meta_screening",
+            "0066_alter_historicalscreeningpartone_fasting_duration_delta_and_more",
+        ),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="historicalscreeningpartone",
+            name="report_datetime",
+            field=models.DateTimeField(
+                default=edc_utils.date.get_utcnow,
+                help_text="Date and time of report.",
+                validators=[
+                    edc_protocol.validators.datetime_not_before_study_start,
+                    edc_model.validators.date.datetime_not_future,
+                ],
+                verbose_name="Report Date and Time",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalscreeningpartthree",
+            name="report_datetime",
+            field=models.DateTimeField(
+                default=edc_utils.date.get_utcnow,
+                help_text="Date and time of report.",
+                validators=[
+                    edc_protocol.validators.datetime_not_before_study_start,
+                    edc_model.validators.date.datetime_not_future,
+                ],
+                verbose_name="Report Date and Time",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalscreeningparttwo",
+            name="report_datetime",
+            field=models.DateTimeField(
+                default=edc_utils.date.get_utcnow,
+                help_text="Date and time of report.",
+                validators=[
+                    edc_protocol.validators.datetime_not_before_study_start,
+                    edc_model.validators.date.datetime_not_future,
+                ],
+                verbose_name="Report Date and Time",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalsubjectscreening",
+            name="report_datetime",
+            field=models.DateTimeField(
+                default=edc_utils.date.get_utcnow,
+                help_text="Date and time of report.",
+                validators=[
+                    edc_protocol.validators.datetime_not_before_study_start,
+                    edc_model.validators.date.datetime_not_future,
+                ],
+                verbose_name="Report Date and Time",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="subjectscreening",
+            name="report_datetime",
+            field=models.DateTimeField(
+                default=edc_utils.date.get_utcnow,
+                help_text="Date and time of report.",
+                validators=[
+                    edc_protocol.validators.datetime_not_before_study_start,
+                    edc_model.validators.date.datetime_not_future,
+                ],
+                verbose_name="Report Date and Time",
+            ),
+        ),
+    ]

meta_screening/models/__init__.py

@@ -1,4 +1,4 @@
-from .icp_referral import IcpReferral
+# from .icp_referral import IcpReferral
 from .proxy_models import ScreeningPartOne, ScreeningPartThree, ScreeningPartTwo
 from .signals import update_p3_ltfu_on_post_save
 from .subject_refusal import SubjectRefusal

meta_screening/tests/holidays.csv

@@ -12,4 +12,4 @@
 2019-12-01,Mawlid Day,tanzania
 2019-12-09,Independence Day,tanzania
 2019-12-25,Christmas Day,tanzania
-2019-12-26,Boxing Day,tanzania
+2019-12-26,Boxing Day,tanzania