meta-edc 1.1.8__py3-none-any.whl → 1.1.12__py3-none-any.whl

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_ae/tests/holidays.csv

@@ -1,15 +0,0 @@
-2019-01-01,New Year's Day,tanzania
-2019-01-12,Zanzibar Revolution Day,tanzania
-2019-04-07,The Sheikh Abeid Amani Karume Day,tanzania
-2019-04-17,Easter Monday,tanzania
-2019-04-26,Union Day,tanzania
-2019-05-01,Labour Day,tanzania
-2019-06-26,Eid al-Fitr,tanzania
-2019-07-07,Saba Saba Day,tanzania
-2019-07-14,Good Friday,tanzania
-2019-08-08,Nane Nane Day,tanzania
-2019-10-14,Nyerere Day,tanzania
-2019-12-01,Mawlid Day,tanzania
-2019-12-09,Independence Day,tanzania
-2019-12-25,Christmas Day,tanzania
-2019-12-26,Boxing Day,tanzania

meta_ae/tests/tests/test_actions.py

@@ -1,126 +0,0 @@
-from django.core.exceptions import ObjectDoesNotExist
-from django.test import TestCase, override_settings
-from edc_action_item.models import ActionItem
-from edc_adverse_event.constants import (
-    AE_FOLLOWUP_ACTION,
-    AE_TMG_ACTION,
-    DEATH_REPORT_ACTION,
-    DEATH_REPORT_TMG_ACTION,
-)
-from edc_constants.constants import CLOSED, GRADE4, GRADE5, NEW
-from model_bakery import baker
-
-from meta_screening.tests.meta_test_case_mixin import MetaTestCaseMixin
-
-
-class TestActions(MetaTestCaseMixin, TestCase):
-    def test_ae_initial_creates_action(self):
-        subject_screening = self.get_subject_screening()
-        subject_consent = self.get_subject_consent(subject_screening)
-        ae_initial = baker.make_recipe(
-            "meta_ae.aeinitial", subject_identifier=subject_consent.subject_identifier
-        )
-
-        try:
-            action_item = ActionItem.objects.get(
-                action_identifier=ae_initial.action_identifier
-            )
-        except ObjectDoesNotExist:
-            self.fail("ObjectDoesNotExist unexpectedly raised.")
-        else:
-            self.assertEqual(action_item.status, CLOSED)
-            self.assertEqual(
-                action_item.subject_identifier, subject_consent.subject_identifier
-            )
-
-    def test_ae_initial_creates_ae_followup_action(self):
-        subject_screening = self.get_subject_screening()
-        subject_consent = self.get_subject_consent(subject_screening)
-        ae_initial = baker.make_recipe(
-            "meta_ae.aeinitial", subject_identifier=subject_consent.subject_identifier
-        )
-
-        action_item = ActionItem.objects.get(action_identifier=ae_initial.action_identifier)
-        try:
-            action_item = ActionItem.objects.get(
-                parent_action_item=action_item,
-                action_type__name=AE_FOLLOWUP_ACTION,
-                subject_identifier=subject_consent.subject_identifier,
-            )
-        except ObjectDoesNotExist:
-            self.fail("ObjectDoesNotExist unexpectedly raised.")
-        else:
-            self.assertEqual(action_item.status, NEW)
-
-    @override_settings(EDC_RANDOMIZATION_REGISTER_DEFAULT_RANDOMIZER=False)
-    def test_ae_initial_G4_creates_ae_tmg_action(self):
-        subject_screening = self.get_subject_screening()
-        subject_consent = self.get_subject_consent(subject_screening)
-        baker.make_recipe(
-            "meta_ae.aeinitial",
-            subject_identifier=subject_consent.subject_identifier,
-            ae_grade=GRADE4,
-        )
-
-        try:
-            ActionItem.objects.get(
-                action_type__name=AE_TMG_ACTION,
-                subject_identifier=subject_consent.subject_identifier,
-            )
-        except ObjectDoesNotExist:
-            self.fail("ObjectDoesNotExist unexpectedly raised.")
-
-    def test_ae_initial_G5_creates_death_report_action(self):
-        subject_screening = self.get_subject_screening()
-        subject_consent = self.get_subject_consent(subject_screening)
-        baker.make_recipe(
-            "meta_ae.aeinitial",
-            subject_identifier=subject_consent.subject_identifier,
-            ae_grade=GRADE5,
-        )
-        try:
-            ActionItem.objects.get(
-                action_type__name=DEATH_REPORT_ACTION,
-                subject_identifier=subject_consent.subject_identifier,
-            )
-        except ObjectDoesNotExist:
-            self.fail("ObjectDoesNotExist unexpectedly raised.")
-
-        self.assertRaises(
-            ObjectDoesNotExist,
-            ActionItem.objects.get,
-            action_type__name=DEATH_REPORT_TMG_ACTION,
-            subject_identifier=subject_consent.subject_identifier,
-        )
-
-    def test_death_report_create_death_report_tmg_action(self):
-        subject_screening = self.get_subject_screening()
-        subject_consent = self.get_subject_consent(subject_screening)
-        baker.make_recipe(
-            "meta_ae.aeinitial",
-            subject_identifier=subject_consent.subject_identifier,
-            ae_grade=GRADE5,
-        )
-        action_item = ActionItem.objects.get(
-            action_type__name=DEATH_REPORT_ACTION,
-            subject_identifier=subject_consent.subject_identifier,
-        )
-
-        baker.make_recipe(
-            "meta_ae.deathreport",
-            subject_identifier=subject_consent.subject_identifier,
-            action_identifier=action_item.action_identifier,
-        )
-
-        action_item.refresh_from_db()
-        self.assertEqual(action_item.status, CLOSED)
-
-        try:
-            action_item = ActionItem.objects.get(
-                action_type__name=DEATH_REPORT_TMG_ACTION,
-                subject_identifier=subject_consent.subject_identifier,
-            )
-        except ObjectDoesNotExist:
-            self.fail("ObjectDoesNotExist unexpectedly raised.")
-        else:
-            self.assertEqual(action_item.status, NEW)

meta_ae/tests/urls.py

@@ -1,10 +0,0 @@
-from django.contrib import admin
-from django.urls.conf import include, path
-
-from meta_ae.admin_site import meta_ae_admin
-
-urlpatterns = [
-    path("ae/", include("meta_ae.urls")),
-    path("admin/", meta_ae_admin.urls),
-    path("admin/", admin.site.urls),
-]

meta_analytics/notebooks/anu.ipynb

@@ -1,95 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "0",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "%%capture\n",
-    "import pandas as pd\n",
-    "from django_pandas.io import read_frame\n",
-    "from pathlib import Path\n",
-    "from dj_notebook import activate\n",
-    "\n",
-    "plus = activate(dotenv_file=\"/Users/erikvw/source/edc_source/meta-edc/.env\")\n",
-    "report_folder = Path(\"/Users/erikvw/Documents/ucl/protocols/meta3/reports/\")\n",
-    "# output is suppressed -- normally would spew out all the edc loading messages\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "1",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from edc_pdutils.dataframes import get_crf\n",
-    "\n",
-    "df_patient_history = get_crf(model=\"meta_subject.patienthistory\", subject_visit_model=\"meta_subject.subjectvisit\")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "2",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_blood_results_rft = get_crf(model=\"meta_subject.bloodresultsrft\", subject_visit_model=\"meta_subject.subjectvisit\")\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "3",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_patient_history.to_csv(Path(\"/Users/erikvw/Documents/ucl/protocols/meta3/analysis/\") / \"patient_history.csv\")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "4",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_blood_results_rft.to_csv(Path(\"/Users/erikvw/Documents/ucl/protocols/meta3/analysis/\") / \"bllod_results_rft.csv\")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "5",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_visit ="
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 2
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.6"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}

meta_analytics/notebooks/appointment_planning.ipynb

@@ -1,329 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "0",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "%%capture\n",
-    "import os\n",
-    "from pathlib import Path\n",
-    "import pandas as pd\n",
-    "from dj_notebook import activate\n",
-    "import numpy as np\n",
-    "from django_pandas.io import read_frame\n",
-    "\n",
-    "env_file = os.environ[\"META_ENV\"]\n",
-    "reports_folder = Path(os.environ[\"META_REPORTS_FOLDER\"])\n",
-    "analysis_folder = Path(os.environ[\"META_ANALYSIS_FOLDER\"])\n",
-    "pharmacy_folder = Path(os.environ[\"META_PHARMACY_FOLDER\"])\n",
-    "plus = activate(dotenv_file=env_file)\n",
-    "pd.set_option('future.no_silent_downcasting', True)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "1",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import pdfkit\n",
-    "from datetime import date\n",
-    "from edc_pdutils.dataframes import get_subject_visit\n",
-    "from meta_analytics.dataframes import get_glucose_fbg_ogtt_df, get_glucose_fbg_df\n",
-    "from meta_visit_schedule.constants import MONTH15, MONTH18, MONTH21, MONTH27, MONTH30, MONTH33, MONTH39\n",
-    "from meta_analytics.dataframes import GlucoseEndpointsByDate\n",
-    "from scipy.stats import chi2\n",
-    "from great_tables import loc, style, md\n",
-    "from meta_analytics.dataframes import get_eos_df\n",
-    "from meta_analytics.utils import df_as_great_table, df_as_great_table2\n",
-    "from meta_prn.models import LossToFollowup\n",
-    "from edc_visit_schedule.models import SubjectScheduleHistory\n",
-    "from edc_appointment.analytics import get_appointment_df\n",
-    "from edc_appointment.constants import NEW_APPT, CANCELLED_APPT, ONTIME_APPT, MISSED_APPT, SCHEDULED_APPT, COMPLETE_APPT, INCOMPLETE_APPT, IN_PROGRESS_APPT, UNSCHEDULED_APPT\n",
-    "from edc_constants.constants import YES\n",
-    "from meta_consent.models import SubjectConsentV1Ext"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "2",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "html_data = []\n",
-    "cutoff_date = date(2025,3, 31)\n",
-    "end_of_trial_date= date(2026,3, 1)\n",
-    "document_title = f\"<h2>Monitoring Report: {cutoff_date.strftime('%B %Y')}</h2><h5>Data Download: {cutoff_date.strftime('%d %B %Y')}</h5>\"\n",
-    "study_title = 'META3 - Metformin treatment for diabetes prevention in Africa'\n",
-    "pdf_filename = f\"monitoring_report_{cutoff_date.strftime('%Y%m%d')}.pdf\"\n",
-    "\n",
-    "column_headers = {\"appt_datetime\": \"Appointment\", \"year\": \"Year\", \"month\": \"Month\", \"10\": \"Hindu Mandal\", \"20\": \"Amana\", \"30\": \"Temeke\", \"40\": \"Mwananyamala\", \"60\": \"Mnazi Moja\", \"total\": \"Total\"}\n",
-    "\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "3",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_visit = get_subject_visit(\"meta_subject.subjectvisit\")\n",
-    "df_visit = df_visit[df_visit.appt_datetime.dt.date<=cutoff_date]\n",
-    "df_appointments = get_appointment_df()\n",
-    "df_appointments[\"site_id\"] = df_appointments.site_id.astype(str)\n",
-    "cls = GlucoseEndpointsByDate()\n",
-    "cls.run()\n",
-    "df_endpoint = cls.endpoint_only_df.copy()\n",
-    "df_glucose = get_glucose_fbg_ogtt_df()\n",
-    "df_glucose_fbg = get_glucose_fbg_df()\n",
-    "df_glucose = pd.concat([df_glucose, df_glucose_fbg])\n",
-    "\n",
-    "enrolled = df_visit.copy()\n",
-    "enrolled[\"site_id\"] = enrolled[\"site_id\"].astype(str)\n",
-    "enrolled_pivot = (\n",
-    "    enrolled\n",
-    "    .query(\"visit_code==1000.0\").groupby([\"site_id\"])\n",
-    "    .size()\n",
-    "    .reset_index()\n",
-    "    .pivot_table(columns=\"site_id\", values=0, observed=True)\n",
-    ")\n",
-    "enrolled_pivot.columns.name=\"\"\n",
-    "enrolled_pivot[\"total\"] = enrolled_pivot[[\"10\", \"20\",\"30\",\"40\",\"60\"]].sum(axis=1)\n",
-    "\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "4",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Table 1f Future scheduled appointments per month\n",
-    "df_appt_pivot = (\n",
-    "    # df_appointments.query(\"appt_datetime<=@cutoff_date and appt_reason==@SCHEDULED_APPT and appt_timing==@ONTIME_APPT and ~appt_status.isin([@NEW_APPT])\")\n",
-    "    df_appointments.query(\"@cutoff_date<=appt_datetime<=@end_of_trial_date and appt_reason==@SCHEDULED_APPT and appt_timing==@ONTIME_APPT and appt_status.isin([@NEW_APPT])\")\n",
-    "    .set_index(\"appt_datetime\")\n",
-    "    .groupby(by=[\"site_id\", pd.Grouper(freq=\"ME\")])\n",
-    "    .size()\n",
-    "    .to_frame()\n",
-    "    .reset_index()\n",
-    "    .rename(columns={0:\"patients\"})\n",
-    "    .pivot(index=\"appt_datetime\", columns=\"site_id\", values=\"patients\")\n",
-    "    .reset_index()\n",
-    "    .fillna(0)\n",
-    ")\n",
-    "\n",
-    "df_appt_pivot.columns.name = None\n",
-    "df_appt_pivot[\"total\"] = df_appt_pivot.iloc[:,1:].sum(axis=1)\n",
-    "df_appt_pivot[\"appt_datetime\"] = df_appt_pivot.appt_datetime.dt.strftime(\"%Y-%m\")\n",
-    "sum_row = df_appt_pivot.select_dtypes(include='float64').sum()\n",
-    "sum_row['appt_datetime'] = 'Total-'\n",
-    "sum_row_df = pd.DataFrame(sum_row).T\n",
-    "df_appt_pivot = pd.concat([df_appt_pivot, sum_row_df], axis=0)\n",
-    "df_appt_pivot[[\"year\", \"month\"]] = df_appt_pivot[\"appt_datetime\"].str.split(\"-\", expand=True)\n",
-    "\n",
-    "df_appt_pivot2 = (\n",
-    "    # df_appointments.query(\"appt_datetime<=@cutoff_date and appt_reason==@SCHEDULED_APPT and appt_timing==@ONTIME_APPT and ~appt_status.isin([@NEW_APPT])\")\n",
-    "    df_appointments.query(\"@cutoff_date<=appt_datetime<=@end_of_trial_date and appt_reason==@SCHEDULED_APPT and appt_timing==@ONTIME_APPT and appt_status.isin([@NEW_APPT])\")\n",
-    "    .set_index(\"visit_code\")\n",
-    "    .groupby(by=[\"site_id\", \"visit_code\"])\n",
-    "    .agg([\"last\"])\n",
-    "    .size()\n",
-    "    .to_frame()\n",
-    "    .reset_index()\n",
-    "    .rename(columns={0:\"patients\"})\n",
-    "    .pivot(index=\"visit_code\", columns=\"site_id\", values=\"patients\")\n",
-    "    .reset_index()\n",
-    "    .fillna(0)\n",
-    ")\n",
-    "\n",
-    "df_appt_pivot2.columns.name = None\n",
-    "df_appt_pivot2[\"total\"] = df_appt_pivot2.iloc[:,1:].sum(axis=1)\n",
-    "df_appt_pivot2[\"visit_code\"] = df_appt_pivot2.visit_code.astype(str)\n",
-    "sum_row = df_appt_pivot2.select_dtypes(include='float64').sum()\n",
-    "sum_row['visit_code'] = 'Total-'\n",
-    "sum_row_df = pd.DataFrame(sum_row).T\n",
-    "df_appt_pivot2 = pd.concat([df_appt_pivot2, sum_row_df], axis=0)\n",
-    "\n",
-    "# df_appt_pivot2[[\"year\", \"month\"]] = df_appt_pivot2[\"appt_datetime\"].str.split(\"-\", expand=True)\n",
-    "\n",
-    "\n",
-    "df_appt_pivot2"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "5",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "def get_df_appt(criteria:str):\n",
-    "    df_appt = (\n",
-    "        df_appointments.query(\"@cutoff_date<=appt_datetime<=@end_of_trial_date and appt_reason==@SCHEDULED_APPT and appt_timing==@ONTIME_APPT and appt_status.isin([@NEW_APPT]) and visit_code<2000.0\")\n",
-    "        .groupby([\"site_id\",  \"appt_datetime\"])\n",
-    "        .agg(\"last\")\n",
-    "        .reset_index()\n",
-    "        .query(criteria)\n",
-    "        .set_index(\"appt_datetime\")\n",
-    "        .groupby(by=[\"site_id\", pd.Grouper(freq=\"ME\")])\n",
-    "        .size()\n",
-    "        .to_frame()\n",
-    "        .reset_index()\n",
-    "        .rename(columns={0:\"patients\"})\n",
-    "        .pivot(index=\"appt_datetime\", columns=\"site_id\", values=\"patients\")\n",
-    "        .reset_index()\n",
-    "        .fillna(0)\n",
-    "    )\n",
-    "    df_appt.columns.name = None\n",
-    "    df_appt[\"total\"] = df_appt.iloc[:,1:].sum(axis=1)\n",
-    "    sum_row = df_appt.select_dtypes(include='float64').sum()\n",
-    "    sum_row_df = pd.DataFrame(sum_row).T\n",
-    "    df_appt = pd.concat([df_appt, sum_row_df], axis=0)\n",
-    "    df_appt[\"appt_datetime\"] = df_appt.appt_datetime.dt.strftime(\"%Y-%m\")\n",
-    "    df_appt[[\"year\", \"month\"]] = df_appt[\"appt_datetime\"].str.split(\"-\", expand=True)\n",
-    "    df_appt[\"year\"] = df_appt[\"year\"].fillna(\"Total\")\n",
-    "    return df_appt\n",
-    "\n",
-    "\n",
-    "gt = df_as_great_table2(\n",
-    "    get_df_appt(criteria=\"visit_code.isin([1360.0, 1480.0])\"),\n",
-    "    title=\"Table 1f: Participants who will complete followup on 1360 or 1480 before 2026-03-01\",\n",
-    "    # subtitle=\"Visit codes 1360 or 1480 only\",\n",
-    "    rowname_col=\"month\",\n",
-    "    groupname_col=\"year\",\n",
-    ")\n",
-    "gt = (\n",
-    "    gt\n",
-    "    .cols_label({k:v for k, v in column_headers.items() if k!=\"label\"})\n",
-    "    .cols_align(align=\"center\", columns=[\"appt_datetime\", \"10\", \"20\", \"30\", \"40\", \"60\", \"total\"])\n",
-    "    .cols_align(align=\"left\", columns=[\"month\", \"year\"])\n",
-    "    .fmt_number(columns=[\"10\", \"20\", \"30\", \"40\", \"60\", \"total\"], decimals=0)\n",
-    "    .tab_source_note(source_note=f\"Scheduled appointment date is on or after {cutoff_date.strftime('%d %B %Y')} and before {end_of_trial_date.strftime('%d %B %Y')}.\")\n",
-    "    .tab_style(\n",
-    "        style=[\n",
-    "            style.text(color=\"black\", weight=\"bold\"),\n",
-    "            style.fill(color=\"lightgray\")\n",
-    "        ],\n",
-    "        locations=loc.row_groups()\n",
-    "    )\n",
-    ")\n",
-    "html_data.append(gt.as_raw_html())\n",
-    "gt.show()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "6",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "\n",
-    "gt = df_as_great_table2(\n",
-    "    get_df_appt(criteria=\"~visit_code.isin([1360.0, 1480.0])\"),\n",
-    "    title=\"Table 1f: Participants who will NOT complete followup on 1360 or 1480 before 2026-03-01\",\n",
-    "    rowname_col=\"month\",\n",
-    "    groupname_col=\"year\",\n",
-    ")\n",
-    "gt = (\n",
-    "    gt\n",
-    "    .cols_label({k:v for k, v in column_headers.items() if k!=\"label\"})\n",
-    "    .cols_align(align=\"center\", columns=[\"appt_datetime\", \"10\", \"20\", \"30\", \"40\", \"60\", \"total\"])\n",
-    "    .cols_align(align=\"left\", columns=[\"month\", \"year\"])\n",
-    "    .fmt_number(columns=[\"10\", \"20\", \"30\", \"40\", \"60\", \"total\"], decimals=0)\n",
-    "    .tab_source_note(source_note=f\"Scheduled appointment date is on or after {cutoff_date.strftime('%d %B %Y')} and before {end_of_trial_date.strftime('%d %B %Y')}.\")\n",
-    "    .tab_style(\n",
-    "        style=[\n",
-    "            style.text(color=\"black\", weight=\"bold\"),\n",
-    "            style.fill(color=\"lightgray\")\n",
-    "        ],\n",
-    "        locations=loc.row_groups()\n",
-    "    )\n",
-    ")\n",
-    "html_data.append(gt.as_raw_html())\n",
-    "gt.show()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "7",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# gather raw html\n",
-    "raw_html = [f'<div class=\"page-break\">{s}</div>' for s in html_data]\n",
-    "style_css = \"\"\"\n",
-    "<style>\n",
-    "  .page-break {\n",
-    "    page-break-inside: avoid; /* Always add page break before this element */\n",
-    "  }\n",
-    "  .table-header {\n",
-    "    font-weight: bold;\n",
-    "    font-size: 18px;\n",
-    "    text-align: center;\n",
-    "    border-bottom: None;\n",
-    "  }\n",
-    "</style>\n",
-    "\"\"\"\n",
-    "raw_html = ''.join(raw_html)\n",
-    "raw_html = f'<!DOCTYPE html>\\n<html lang=\"en\">\\n{style_css}\\n<head>\\n<meta charset=\"utf-8\"/>\\n</head>\\n<body>\\n' + document_title + raw_html + '\\n</body>\\n</html>\\n'"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "8",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "pdfkit.from_string(raw_html, str(analysis_folder / pdf_filename),\n",
-    "options={\n",
-    "    'footer-center': 'Page [page] of [topage]',\n",
-    "    'footer-font-size': '8',\n",
-    "    'footer-spacing': '5',\n",
-    "    'encoding': \"UTF-8\",\n",
-    "    'margin-top':'10mm',\n",
-    "    'margin-right':'15mm',\n",
-    "    'margin-bottom':'15mm',\n",
-    "    'margin-left':'15mm',\n",
-    "    'header-center': study_title,\n",
-    "    'header-font-size': '6',\n",
-    "    'header-spacing': '0',\n",
-    "    'disable-javascript': None,\n",
-    "    'no-outline': None,\n",
-    "},\n",
-    "verbose=True)"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 2
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.6"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}