meta-edc 1.0.7__py3-none-any.whl → 1.1.1__py3-none-any.whl

meta_analytics/notebooks/pharmacy.ipynb

@@ -2,10 +2,10 @@
  "cells": [
   {
    "cell_type": "code",
-   "id": "initial_id",
-   "metadata": {
-    "collapsed": true
-   },
+   "execution_count": null,
+   "id": "0",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "%%capture\n",
     "import os\n",
@@ -13,20 +13,20 @@
     "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)"
-   ],
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "1",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "from edc_pharmacy.analytics.dataframes import no_stock_for_subjects_df\n",
     "from datetime import datetime\n",
@@ -46,15 +46,85 @@
     "from edc_visit_schedule.site_visit_schedules import site_visit_schedules\n",
     "from edc_pharmacy.models import Container\n",
     "from great_tables import GT, html, loc, style\n",
-    "from PIL import Image\n"
-   ],
-   "id": "a4c997d7adda770",
+    "from PIL import Image\n",
+    "from edc_pdutils.dataframes.get_subject_visit import convert_visit_code_to_float\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2",
+   "metadata": {},
    "outputs": [],
-   "execution_count": null
+   "source": [
+    "from edc_model_to_dataframe import read_frame_edc\n",
+    "from meta_subject.models import FollowupExamination\n",
+    "\n",
+    "df = read_frame_edc(FollowupExamination.objects.all(), drop_sys_columns=True, drop_action_item_columns=True)\n",
+    "df = df.replace(\"none\", pd.NA)\n",
+    "df = df.replace(\"none\", pd.NA)\n",
+    "df = df.fillna(pd.NA)\n",
+    "convert_visit_code_to_float(df)"
+   ]
   },
   {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3",
    "metadata": {},
+   "outputs": [],
+   "source": [
+    "from edc_analytics.stata import get_stata_labels_from_model\n",
+    "\n",
+    "df = df[[\"subject_identifier\", \"subject_visit_id\", \"report_datetime\", \"visit_code\", \"site_id\", \"site_name\", \"visit_reason\", \"symptoms\",\"symptoms_detail\", \"symptoms_sought_care\", \"symptoms_g3\", \"symptoms_g4\", \"comment\"]].copy().reset_index(drop=True)\n",
+    "\n",
+    "df = df.astype(\n",
+    "    {col: \"Float64\" for col in df.select_dtypes(include=[\"float\", \"float64\"]).columns}\n",
+    ")\n",
+    "df_meds = df.astype(\n",
+    "    {col: \"Int64\" for col in df.select_dtypes(include=[\"int\", \"int64\"]).columns}\n",
+    ")\n",
+    "df = df.astype(\n",
+    "    {\n",
+    "        col: \"datetime64[ns]\"\n",
+    "        for col in df.select_dtypes(include=[\"datetime\", \"datetime64\"]).columns\n",
+    "    }\n",
+    ")\n",
+    "df = df.astype(\n",
+    "    {\n",
+    "        col: str\n",
+    "        for col in df.select_dtypes(include=[\"object\"]).columns\n",
+    "    }\n",
+    ")\n",
+    "df = df.fillna(pd.NA)\n",
+    "\n",
+    "variable_labels = {}\n",
+    "variable_labels.update(**get_stata_labels_from_model(df, model=\"meta_subject.followupexamination\", suffix=None))\n",
+    "\n",
+    "df.to_stata(\n",
+    "    path=analysis_folder / \"followupexamination.dta\",\n",
+    "    variable_labels=variable_labels,\n",
+    "    version=118,\n",
+    "    write_index=False,\n",
+    ")"
+   ]
+  },
+  {
    "cell_type": "code",
+   "execution_count": null,
+   "id": "4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "\n",
     "def get_great_table(df:pd.DataFrame, title:str, footnote:str|None=None):\n",
@@ -90,51 +160,61 @@
     "\n",
     "\n",
     "    )\n"
-   ],
-   "id": "6d4f230107499268",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6",
    "metadata": {},
+   "outputs": [],
+   "source": [
+    "start_from_appt_date = datetime(2025,5,15)"
+   ]
+  },
+  {
    "cell_type": "code",
+   "execution_count": null,
+   "id": "7",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# get rando\n",
     "df_rando = read_frame(RandomizationList.objects.values(\"subject_identifier\", \"assignment\").filter(subject_identifier__isnull=False))"
-   ],
-   "id": "1a5c145dc73ae1ca",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "8",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# get appointments\n",
     "df_appt = get_appointment_df()\n",
-    "print(f\"{len(df_appt[(df_appt.appt_status==NEW_APPT) & (df_appt.appt_datetime >= datetime(2025,4,4)) & (df_appt.appt_datetime < datetime(2026,3,1)) & (df_appt.visit_code!=1480.0)])} appointments after filtering\")"
-   ],
-   "id": "c0f532dc5f20aef6",
-   "outputs": [],
-   "execution_count": null
+    "print(f\"{len(df_appt[(df_appt.appt_status==NEW_APPT) & (df_appt.appt_datetime >= start_from_appt_date) & (df_appt.appt_datetime < datetime(2026,3,1)) & (df_appt.visit_code!=1480.0)])} appointments after filtering\")"
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "9",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# create a dataframe of subjects still on the 'schedule' schedule\n",
     "# use SubjectScheduleHistory where offschedule_datetime is null\n",
     "df_subject_schedule = read_frame(SubjectScheduleHistory.objects.values(\"subject_identifier\", \"visit_schedule_name\", \"schedule_name\", \"onschedule_datetime\", \"offschedule_datetime\").filter(offschedule_datetime__isnull=True, schedule_name=\"schedule\"))\n",
     "\n",
     "print(f\"{len(df_subject_schedule)} subjects currently onstudy\")"
-   ],
-   "id": "dd5fd238c0160518",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "10",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# for now merge with the unfiltered df_appt\n",
     "df_main = df_subject_schedule.merge(\n",
@@ -150,39 +230,41 @@
     "    (df_main.appt_status==NEW_APPT)\n",
     "].copy()\n",
     "print(f\"{len(df_main)} new appointments for subjects on study\")\n"
-   ],
-   "id": "13739396761c72c",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "11",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# number of appointments before extended all subjects out to 48m\n",
     "df_grouped = df_main[\n",
-    "    (df_main.appt_datetime >= datetime(2025,4,4)) &\n",
+    "    (df_main.appt_datetime >= start_from_appt_date) &\n",
     "    (df_main.appt_datetime < datetime(2026,3,1)) &\n",
     "    (df_main.visit_code!=1480.0)\n",
     "].visit_code.value_counts().reset_index(name=\"appointments\").sort_values(by=\"visit_code\", ascending=True).reset_index(drop=True)\n",
     "df_grouped[\"cumsum\"] = df_grouped.appointments.cumsum()\n",
     "df_grouped[\"cumsum\"].max()\n"
-   ],
-   "id": "fdf65539dce9fc30",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
-   "source": "df_main",
-   "id": "81d462e710e0ae61",
+   "execution_count": null,
+   "id": "12",
+   "metadata": {},
    "outputs": [],
-   "execution_count": null
+   "source": [
+    "df_main"
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "13",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# now extend everyone to 48 months.\n",
     "# Subjects are in the process of consenting for extended\n",
@@ -212,34 +294,36 @@
     "# merge df_main back in\n",
     "df_pivot = df_pivot.merge(df_main[[\"subject_identifier\", \"visit_code\", \"appt_datetime\", \"appt_status\"]], on=[\"subject_identifier\",\"visit_code\"], how=\"left\")\n",
     "df_pivot"
-   ],
-   "id": "9bd1bf18017c18f2",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
-   "source": "# len(df_pivot[(df_pivot.appt_datetime>=datetime(2025,1,1)) & (df_pivot.visit_code==MONTH48)])/3",
-   "id": "80ab2992c6ccb274",
+   "execution_count": null,
+   "id": "14",
+   "metadata": {},
    "outputs": [],
-   "execution_count": null
+   "source": [
+    "# len(df_pivot[(df_pivot.appt_datetime>=datetime(2025,1,1)) & (df_pivot.visit_code==MONTH48)])/3"
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "15",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# extend no one!\n",
     "# df_pivot = df_pivot[df_pivot.exists==1].copy()\n",
     "# df_pivot.reset_index(drop=True, inplace=True)\n"
-   ],
-   "id": "1e3098273f43e6b2",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "16",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# add appointments do not have an appt_datetime, so calculate\n",
     "# using the visit schedule relative to baseline_datetime\n",
@@ -264,14 +348,14 @@
     "df_pivot.loc[df_pivot.exists==0.0, \"appt_status\"] = NEW_APPT\n",
     "\n",
     "print(f\"{len(df_pivot)} appointments\")"
-   ],
-   "id": "7483e4c8e47becc9",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "17",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# df_subject_appointments is a dataframe of appointments\n",
     "# - only include NEW appointments\n",
@@ -280,51 +364,53 @@
     "cutoff_date = datetime(2026,3,1)\n",
     "df_subject_appointments = df_pivot[\n",
     "    (df_pivot.appt_status==NEW_APPT) &\n",
-    "    (df_pivot.appt_datetime >= datetime(2025,4,4)) &\n",
+    "    (df_pivot.appt_datetime >= start_from_appt_date) &\n",
     "    (df_pivot.appt_datetime < cutoff_date) &\n",
     "    (df_pivot.visit_code!=1480.0)\n",
     "].copy()\n",
     "print(f\"{len(df_subject_appointments)} appointments\")"
-   ],
-   "id": "12f04c24f098e88f",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "18",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "n = df_subject_appointments.subject_identifier.nunique()\n",
     "print(f\"{n} subjects\")\n"
-   ],
-   "id": "c32531751a339390",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
-   "source": "(len(df_subject_appointments[df_subject_appointments.appt_datetime>=datetime(2026,1,1)])/36)/5",
-   "id": "e7f520f32116ab1c",
+   "execution_count": null,
+   "id": "19",
+   "metadata": {},
    "outputs": [],
-   "execution_count": null
+   "source": [
+    "(len(df_subject_appointments[df_subject_appointments.appt_datetime>=datetime(2026,1,1)])/36)/5"
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "20",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# summarize the appointments\n",
     "df_summary = df_subject_appointments.visit_code.value_counts().reset_index(name=\"appointments\").sort_values(by=[\"visit_code\"], ascending=True)\n",
     "df_summary[\"cumsum\"] = df_summary.appointments.cumsum()\n",
     "df_summary"
-   ],
-   "id": "f38ead26da10a1ef",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "21",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "df = df_subject_appointments.assignment.value_counts(dropna=False).reset_index()\n",
     "df.rename(columns={\"count\":\"appointments\"}, inplace=True)\n",
@@ -335,18 +421,18 @@
     "# filter\n",
     "df.loc[len(df)] = {\"appointments\": df.appointments.sum(), \"bottles\": df.bottles.sum(), \"tablets\": df.tablets.sum()}\n",
     "df"
-   ],
-   "id": "b6a56657d02b04ac",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "22",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "gt = get_great_table(\n",
     "    df,\n",
-    "    \"Table 1: IMP Bottles of 128 needed<BR><small>as of 2025-04-04</small>\",\n",
+    "    \"Table 1: IMP Bottles of 128 needed<BR><small>as of 2025-05-15</small>\",\n",
     "    footnote=(\n",
     "        \"<ol>\"\n",
     "        \"<li>assume all participants consent for extended followup.\"\n",
@@ -356,14 +442,14 @@
     "        \"</ol>\"\n",
     "    ))\n",
     "gt.show()"
-   ],
-   "id": "f9bffc9c05c7fd41",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "23",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "\n",
     "# save as png\n",
@@ -372,14 +458,14 @@
     "image = Image.open(analysis_folder / \"pharmacy_tbl1.png\")\n",
     "image = image.resize((image.width * 6, image.height * 6), Image.LANCZOS)\n",
     "image.save(analysis_folder / \"pharmacy_tbl1.pdf\", \"PDF\", resolution=800, optimize=True, quality=95)"
-   ],
-   "id": "53247d65d251bebb",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "24",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# now lets look at the stock\n",
     "df_stock = read_frame(Stock.objects.values(\"code\", \"lot_id\", \"container__name\", \"confirmed\", \"allocated\", \"dispensed\", \"qty_in\", \"qty_out\", \"unit_qty_in\", \"unit_qty_out\").all(), verbose=False)\n",
@@ -390,14 +476,14 @@
     "df_stock = df_stock.merge(df_lot[[\"lot_id\", \"assignment\"]], on=\"lot_id\", how=\"left\")\n",
     "df_stock.rename(columns={\"container__name\":\"container\"}, inplace=True)\n",
     "df_stock.reset_index(drop=True, inplace=True)"
-   ],
-   "id": "6d280a4eeac931a0",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "25",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# merge in container columns\n",
     "df_container = read_frame(Container.objects.all())\n",
@@ -407,60 +493,64 @@
     "\n",
     "# calculate bal\n",
     "df_stock[\"bal\"] = df_stock[\"unit_qty_in\"] - df_stock[\"unit_qty_out\"]\n"
-   ],
-   "id": "a11c4b67752b965d",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "26",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# show the balance of tablets decanted to bottles by assignment (on the EDC)\n",
     "df2 = df_stock[df_stock.container_display_name==\"Bottle 128\"].groupby(by=[\"assignment\"]).bal.agg(\"sum\").reset_index()\n",
     "df2.loc[len(df2)] = {\"bal\": df2.bal.sum()}\n",
     "df2"
-   ],
-   "id": "7e275d7fb827535b",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "27",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# some bottles, as of today, have not been captured in the system\n",
     "# here is an estimate of what has been decanted into bottles but not labelled.\n",
     "# in the system, these tablets would appear on the EDC as still in buckets\n",
     "df3 = df2.copy()\n",
     "df3 = df3.drop(len(df3) - 1)\n",
-    "placebo_unlabelled = 21*128*128\n",
-    "active_unlabelled = 25*191*128\n",
+    "placebo_unlabelled = 0 # 21*128*128\n",
+    "active_unlabelled = 0 # 25*191*128\n",
     "\n",
     "# adding in the estimates, this is about what we have bottled\n",
     "df3.loc[df3.assignment==\"placebo\", \"bal\"] +=  placebo_unlabelled\n",
     "df3.loc[df3.assignment==\"active\", \"bal\"] +=  active_unlabelled\n",
     "df3.loc[len(df3)] = {\"bal\": df3.bal.sum()}\n",
     "df3"
-   ],
-   "id": "1d7134fe05417475",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "28",
+   "metadata": {},
+   "outputs": [],
    "source": [
-    "gt = get_great_table(df3, \"Table 2: IMP tablets in stock<BR><small>as of 2025-04-04</small>\", footnote=\"Includes recently decanted but unlabelled bottles\")\n",
+    "gt = get_great_table(\n",
+    "    df3,\n",
+    "    \"Table 2: IMP tablets in stock<BR><small>as of 2025-04-04</small>\",\n",
+    "    # footnote=\"Includes recently decanted but unlabelled bottles\"\n",
+    "    )\n",
     "gt.show()"
-   ],
-   "id": "7ab587c2d36d2e10",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "29",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# save as png\n",
     "gt.save(analysis_folder / \"pharmacy_tbl2.png\")\n",
@@ -468,71 +558,71 @@
     "image = Image.open(analysis_folder / \"pharmacy_tbl2.png\")\n",
     "image = image.resize((image.width * 6, image.height * 6), Image.LANCZOS)\n",
     "image.save(analysis_folder / \"pharmacy_tbl2.pdf\", \"PDF\", resolution=800, optimize=True, quality=95)"
-   ],
-   "id": "68374d9f02546d6f",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "30",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# tablets: ordered\n",
     "df_orderitems = read_frame(OrderItem.objects.all())\n",
     "df_orderitems.qty.sum()"
-   ],
-   "id": "9b67d6799735e116",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "31",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# tablets: received\n",
     "df_received_items = read_frame(ReceiveItem.objects.all())\n",
     "df_received_items.unit_qty.sum()"
-   ],
-   "id": "af0868a54913329",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "32",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# tablets: received into stock\n",
     "df_stock[df_stock.container_type==\"bucket\"].unit_qty_in.sum()"
-   ],
-   "id": "82b0df34b49377f0",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "33",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# tablets: decanted from buckets into bottles\n",
     "df_stock[df_stock.container_type==\"bucket\"].unit_qty_out.sum()"
-   ],
-   "id": "1d1383219f8fd0a4",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "34",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# tablets: total in bottles\n",
     "df_stock[df_stock.container_type==\"Bottle\"].unit_qty_in.sum()"
-   ],
-   "id": "d928f610d5427f39",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "35",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# tablets: total bottles available / not yet dispensed BY ASSIGNMENT\n",
     "# the total matches the total above for column \"bal\"\n",
@@ -554,50 +644,50 @@
     "df6.loc[len(df6)] = {\"total\": df6.subtotal.sum()}\n",
     "df6 = df6[[\"dispensed\", \"assignment\", \"unit_qty_in\", \"subtotal\", \"total\"]]\n",
     "df6"
-   ],
-   "id": "6600690d6e88a1b2",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
-   "source": "",
-   "id": "3ad00099e744f41b",
+   "execution_count": null,
+   "id": "36",
+   "metadata": {},
    "outputs": [],
-   "execution_count": null
+   "source": []
   },
   {
-   "metadata": {},
    "cell_type": "code",
-   "source": "",
-   "id": "c460fa84e9fc004e",
+   "execution_count": null,
+   "id": "37",
+   "metadata": {},
    "outputs": [],
-   "execution_count": null
+   "source": []
   },
   {
-   "metadata": {},
    "cell_type": "code",
-   "source": "",
-   "id": "428d31f52ed17823",
+   "execution_count": null,
+   "id": "38",
+   "metadata": {},
    "outputs": [],
-   "execution_count": null
+   "source": []
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "39",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "from meta_visit_schedule.constants import MONTH36\n",
     "\n",
     "df_appt[(df_appt.visit_code_str==MONTH36) & (df_appt.appt_datetime >= datetime(2024,12,15)) & (df_appt.appt_status==NEW_APPT) & (df_appt.appt_datetime <= datetime(2026,2,28))]"
-   ],
-   "id": "49a7b405b7973ae3",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "40",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "def remove_subjects_where_stock_on_site(stock_request: StockRequest, df: pd.DataFrame):\n",
     "    stock_model_cls = django_apps.get_model(\"edc_pharmacy.Stock\")\n",
@@ -629,14 +719,14 @@
     "    df[\"stock_qty\"] = 0.0\n",
     "    df = df.reset_index(drop=True)\n",
     "    return df\n"
-   ],
-   "id": "491b43957fe1c756",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "41",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "def pad_with_null_rows(df, qty_needed):\n",
     "    padded_data = []\n",
@@ -649,44 +739,44 @@
     "        for product in products:\n",
     "            padded_data.append({'customer': customer, 'product_code': product})\n",
     "    return pd.DataFrame(padded_data)"
-   ],
-   "id": "14fd36a1e0e158b9",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "42",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "pk = \"5455cf66-b8e5-449c-a1e8-24d3325026d7\"\n",
     "stock_request = StockRequest.objects.get(pk=pk)\n"
-   ],
-   "id": "ee9423599bad2c6f",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "43",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "df_subjects = get_next_scheduled_visit_for_subjects_df(stock_request)\n",
     "df_subjects"
-   ],
-   "id": "f5b22e507f36170d",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
-   "source": "",
-   "id": "8918d8cd6b2ae777",
+   "execution_count": null,
+   "id": "44",
+   "metadata": {},
    "outputs": [],
-   "execution_count": null
+   "source": []
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "45",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "df = df_subjects.copy()\n",
     "stock_model_cls = django_apps.get_model(\"edc_pharmacy.Stock\")\n",
@@ -705,22 +795,24 @@
     "    }\n",
     ")\n",
     "df_stock"
-   ],
-   "id": "164302f67cec31be",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
-   "source": "df.merge(df_stock, on=\"subject_identifier\", how=\"left\")",
-   "id": "8c1c3f0b594bdf3",
+   "execution_count": null,
+   "id": "46",
+   "metadata": {},
    "outputs": [],
-   "execution_count": null
+   "source": [
+    "df.merge(df_stock, on=\"subject_identifier\", how=\"left\")"
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "47",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "if not df.empty and not df_stock.empty:\n",
     "    df_subject = df.copy()\n",
@@ -736,22 +828,24 @@
     "df[\"stock_qty\"] = 0.0\n",
     "df = df.reset_index(drop=True)\n",
     "df"
-   ],
-   "id": "ba3541a4e2cdfde6",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
-   "source": "df.loc[df.index.repeat(3)]",
-   "id": "5ba4eff2efc5f3eb",
+   "execution_count": null,
+   "id": "48",
+   "metadata": {},
    "outputs": [],
-   "execution_count": null
+   "source": [
+    "df.loc[df.index.repeat(3)]"
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "49",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "if not df.empty and not df_stock.empty:\n",
     "    df = df.merge(df_stock, on=\"subject_identifier\", how=\"left\")\n",
@@ -760,25 +854,25 @@
     "df[\"stock_qty\"] = 0.0\n",
     "df = df.reset_index(drop=True)\n",
     "df"
-   ],
-   "id": "79507f3726dd23ac",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "50",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "df = remove_subjects_where_stock_on_site(stock_request, df_subjects)\n",
     "df"
-   ],
-   "id": "a23aafeb660d5a9c",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "51",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "df_instock = df[~df.code.isna()]\n",
     "df_instock = df_instock.reset_index(drop=True)\n",
@@ -791,160 +885,165 @@
     "].reset_index(drop=True)\n",
     "df_nostock = df_nostock.sort_values(by=[\"subject_identifier\"])\n",
     "df_nostock[\"code\"] = df_nostock[\"code\"].fillna(\"---\")\n"
-   ],
-   "id": "f8e386caf276b53e",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
-   "source": "",
-   "id": "85715500af7721de",
+   "execution_count": null,
+   "id": "52",
+   "metadata": {},
    "outputs": [],
-   "execution_count": null
+   "source": []
   },
   {
-   "metadata": {},
    "cell_type": "code",
-   "source": "",
-   "id": "acf8453d693c288e",
+   "execution_count": null,
+   "id": "53",
+   "metadata": {},
    "outputs": [],
-   "execution_count": null
+   "source": []
   },
   {
-   "metadata": {},
    "cell_type": "code",
-   "source": "no_stock_for_subjects_df()",
-   "id": "73171a433d5b5882",
+   "execution_count": null,
+   "id": "54",
+   "metadata": {},
    "outputs": [],
-   "execution_count": null
+   "source": [
+    "no_stock_for_subjects_df()"
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
-   "source": "df_schedule = read_frame(SubjectScheduleHistory.objects.values(\"subject_identifier\", \"visit_schedule_name\",\"schedule_name\", \"offschedule_datetime\").all())\n",
-   "id": "5721c4cf5f08d681",
+   "execution_count": null,
+   "id": "55",
+   "metadata": {},
    "outputs": [],
-   "execution_count": null
+   "source": [
+    "df_schedule = read_frame(SubjectScheduleHistory.objects.values(\"subject_identifier\", \"visit_schedule_name\",\"schedule_name\", \"offschedule_datetime\").all())\n"
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "56",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "df_schedule = df_schedule[(df_schedule.visit_schedule_name==\"visit_schedule\") & (df_schedule.schedule_name==\"schedule\")  & df_schedule.offschedule_datetime.isna()]\n",
     "df_schedule.reset_index(drop=True, inplace=True)"
-   ],
-   "id": "621196fa35e00e9c",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "57",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "df_stock = read_frame(Stock.objects.all(), verbose=False)\n",
     "df_stock_on_site = df_stock[(df_stock.confirmed_at_site==True) & (df_stock.dispensed==False)].copy()\n",
     "df_stock_on_site.reset_index(drop=True, inplace=True)\n",
     "df_stock_on_site = df_stock_on_site.drop(columns=[\"subject_identifier\"])\n"
-   ],
-   "id": "8abada4ffb0db4f0",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "58",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "df_allocation =  read_frame(Allocation.objects.values(\"id\", \"registered_subject\").all(), verbose=False)\n",
     "df_rs = read_frame(RegisteredSubject.objects.values(\"id\", \"subject_identifier\").all(), verbose=False)\n",
     "df_allocation = df_allocation.merge(df_rs[[\"id\", \"subject_identifier\"]], how=\"left\", left_on=\"registered_subject\", right_on=\"id\", suffixes=[\"_allocation\", \"_rs\"])"
-   ],
-   "id": "624ebc7e51e679bd",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
-   "source": "df_stock_on_site = df_stock_on_site.merge(df_allocation[[\"id_allocation\", \"subject_identifier\"]], how=\"left\", left_on=\"allocation\", right_on=\"id_allocation\")",
-   "id": "394e569ac1649719",
+   "execution_count": null,
+   "id": "59",
+   "metadata": {},
    "outputs": [],
-   "execution_count": null
+   "source": [
+    "df_stock_on_site = df_stock_on_site.merge(df_allocation[[\"id_allocation\", \"subject_identifier\"]], how=\"left\", left_on=\"allocation\", right_on=\"id_allocation\")"
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "60",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "df = pd.merge(df_schedule[[\"subject_identifier\", 'offschedule_datetime']], df_stock_on_site, on=\"subject_identifier\", how=\"left\")\n",
     "df= df[df.code.isna()][[\"subject_identifier\", ]].sort_values(by=[\"subject_identifier\"]).reset_index(drop=True)"
-   ],
-   "id": "1ab7350cfb29eab4",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "61",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "df_appt = get_next_scheduled_visit_for_subjects_df()\n",
     "df_appt = df_appt[[\"subject_identifier\", \"site_id\", \"visit_code\", \"appt_datetime\", \"baseline_datetime\"]].copy()\n",
     "df_appt.reset_index(drop=True, inplace=True)"
-   ],
-   "id": "f29cc9c6c1234c34",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "62",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "\n",
     "df = df.merge(df_appt, how=\"left\", on=\"subject_identifier\")\n",
     "df = df[(df.appt_datetime.notna())]\n",
     "df.reset_index(drop=True, inplace=True)"
-   ],
-   "id": "9e3e3f429a1995ec",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
+   "execution_count": null,
+   "id": "63",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "utc_now = pd.Timestamp.utcnow().tz_localize(None)\n",
     "df[\"relative_days\"] = (df.appt_datetime - utc_now).dt.days\n",
     "df_final = df[(df.relative_days >= -105)].copy()\n",
     "df_final.reset_index(drop=True, inplace=True)\n",
     "df_final"
-   ],
-   "id": "d6570f1e94ac23bb",
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
-   "source": "RegisteredSubject.objects.filter(site_id=10)",
-   "id": "6aef5bb0e7caf4e8",
+   "execution_count": null,
+   "id": "64",
+   "metadata": {},
    "outputs": [],
-   "execution_count": null
+   "source": [
+    "RegisteredSubject.objects.filter(site_id=10)"
+   ]
   },
   {
-   "metadata": {},
    "cell_type": "code",
-   "source": "",
-   "id": "1e6126bbe8d04c70",
+   "execution_count": null,
+   "id": "65",
+   "metadata": {},
    "outputs": [],
-   "execution_count": null
+   "source": []
   },
   {
-   "metadata": {},
    "cell_type": "code",
-   "source": "",
-   "id": "1ee6ef823e6a543d",
+   "execution_count": null,
+   "id": "66",
+   "metadata": {},
    "outputs": [],
-   "execution_count": null
+   "source": []
   }
  ],
  "metadata": {