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

meta_analytics/notebooks/pharmacy_stock_202410.ipynb

@@ -1,306 +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 meta_rando.models import RandomizationList\n",
-    "from meta_consent.models import SubjectConsent\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "2",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "cnt = 0\n",
-    "df_hm = pd.read_excel(\"/Users/erikvw/Documents/ucl/protocols/meta3/pharmacy/HINDU_MANDAL.xlsx\")\n",
-    "df_hm = df_hm.groupby(\"sid\").agg({\"qty\":\"sum\"})\n",
-    "cnt += len(df_hm)\n",
-    "print(\"df_hm\", len(df_hm), cnt)\n",
-    "\n",
-    "df_amana = pd.read_excel(\"/Users/erikvw/Documents/ucl/protocols/meta3/pharmacy/AMANA.xlsx\")\n",
-    "df_amana = df_amana.groupby(\"sid\").agg({\"qty\":\"sum\"})\n",
-    "cnt += len(df_amana)\n",
-    "print(\"df_amana\", len(df_amana), cnt)\n",
-    "\n",
-    "df_mnazi = pd.read_excel(\"/Users/erikvw/Documents/ucl/protocols/meta3/pharmacy/mnazi.xlsx\")\n",
-    "df_mnazi = df_mnazi.groupby(\"sid\").agg({\"qty\":\"sum\"})\n",
-    "cnt += len(df_mnazi)\n",
-    "print(\"df_mnazi\", len(df_mnazi), cnt)\n",
-    "\n",
-    "df_mwana = pd.read_excel(\"/Users/erikvw/Documents/ucl/protocols/meta3/pharmacy/MWANANYAMALA.xlsx\")\n",
-    "df_mwana = df_mwana.groupby(\"sid\").agg({\"qty\":\"sum\"})\n",
-    "cnt += len(df_mwana)\n",
-    "print(\"df_mwana\", len(df_mwana), cnt)\n",
-    "\n",
-    "df_temeke = pd.read_excel(\"/Users/erikvw/Documents/ucl/protocols/meta3/pharmacy/TEMEKE.xlsx\")\n",
-    "df_temeke = df_temeke.groupby(\"sid\").agg({\"qty\":\"sum\"})\n",
-    "cnt += len(df_temeke)\n",
-    "print(\"df_temeke\", len(df_temeke), cnt)\n",
-    "\n",
-    "df_sites = pd.concat([df_hm, df_amana, df_mnazi, df_mwana, df_temeke], axis=0)\n",
-    "df_sites"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "3",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# get rando, this is slow (col assignment is encrypted)\n",
-    "df_rando = read_frame(RandomizationList.objects.values(\"subject_identifier\", \"sid\", \"site_name\", \"assignment\", \"allocated_site\").all(), verbose=False)\n",
-    "df_rando = df_rando.rename(columns={\"allocated_site\": \"site_id\"})\n",
-    "df_rando = df_rando[[\"subject_identifier\", \"sid\", \"site_name\", \"assignment\", \"site_id\"]]\n",
-    "df_rando = df_rando.reset_index(drop=True)\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "4",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# merge rando w/ hindu_mandal\n",
-    "df_sites = df_sites.merge(df_rando, on='sid', how='left', suffixes=('', '_rando'))\n",
-    "df_sites = df_sites[[\"subject_identifier\", \"sid\", \"site_id\", \"qty\", \"site_name\", \"assignment\"]]\n",
-    "df_sites\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "5",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# merge hindu_mandal w/ consent to get \"consent_datetime\", \"gender\", \"dob\"\n",
-    "df_consent = read_frame(SubjectConsent.objects.values(\"subject_identifier\", \"consent_datetime\", \"gender\", \"dob\"), verbose=False)\n",
-    "df_consent[\"consent_datetime\"] = pd.to_datetime(df_consent[\"consent_datetime\"]).dt.tz_localize(None)\n",
-    "df_consent[\"consent_datetime\"] = df_consent[\"consent_datetime\"].dt.normalize()\n",
-    "df_sites = df_sites.merge(df_consent, on=\"subject_identifier\", how=\"left\")\n",
-    "df_sites"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "6",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_sites = df_sites.reset_index(drop=True)\n",
-    "df_sites\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "7",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_sites.site_name.value_counts()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "8",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_sites"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "9",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_sites[(df_sites.qty.notna())][\"site_name\"].value_counts()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "10",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_sites[(df_sites.subject_identifier.isna())][\"site_name\"].value_counts()\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "11",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# lists SIDs that do not match an allocated subject_identifier \n",
-    "export_errors_df = df_sites[(df_sites.subject_identifier.isna())][[\"subject_identifier\", \"sid\", \"site_id\", \"qty\", \"site_name\", \"consent_datetime\", \"gender\", \"dob\"]].copy()\n",
-    "export_errors_df = export_errors_df.reset_index(drop=True)\n",
-    "export_errors_df.to_csv(\"/Users/erikvw/Documents/ucl/protocols/meta3/pharmacy/imp_stock_20241016-errors.csv\")\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "12",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# safe file to show pharmacist and coordinators\n",
-    "export_wo_assignment_df = df_sites[(df_sites.subject_identifier.notna()) & (df_sites.qty.notna())][[\"subject_identifier\", \"sid\", \"site_id\", \"qty\", \"site_name\", \"consent_datetime\", \"gender\", \"dob\"]].copy()\n",
-    "export_wo_assignment_df = export_wo_assignment_df.reset_index(drop=True)\n",
-    "export_wo_assignment_df.to_csv(\"/Users/erikvw/Documents/ucl/protocols/meta3/pharmacy/imp_stock_20241016-calvin.csv\")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "13",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# this is a secure file, for Buma only!!\n",
-    "export_with_assignment_df = df_sites[(df_sites.subject_identifier.notna()) & (df_sites.qty.notna())][[\"subject_identifier\", \"sid\", \"site_id\", \"qty\", \"site_name\", \"consent_datetime\", \"gender\", \"dob\", \"assignment\"]].copy()\n",
-    "export_with_assignment_df = export_with_assignment_df.reset_index(drop=True)\n",
-    "export_with_assignment_df.to_csv(\"/Users/erikvw/Documents/ucl/protocols/meta3/pharmacy/imp_stock_20241016-buma.csv\")\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "14",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# summary of bottles\n",
-    "btl_df = export_wo_assignment_df.groupby(\"site_name\").agg({\"qty\":\"sum\"})\n",
-    "btl_df"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "15",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# summary of subjects\n",
-    "export_wo_assignment_df.site_name.value_counts()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "16",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# summary of tabs\n",
-    "btl_df * 128"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "17",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "(btl_df * 128).qty.sum()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "18",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_assign = export_with_assignment_df.groupby(\"assignment\").agg({\"qty\":\"sum\"})\n",
-    "df_assign"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "19",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_assign * 128"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "20",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "(df_assign * 128).qty.sum()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "21",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "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/qa.ipynb

@@ -1,273 +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",
-    "\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)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "1",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from edc_pharmacy.utils import get_stock_for_location_df\n",
-    "from edc_pharmacy.models import Location, Stock, Dispense, StockRequest\n",
-    "from django.db.models import Count\n",
-    "from edc_pharmacy.utils import get_instock_and_nostock_data\n",
-    "from edc_pharmacy.analytics import get_next_scheduled_visit_for_subjects_df\n",
-    "\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "2",
-   "metadata": {},
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "3",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "location = Location.objects.all()[2]\n",
-    "get_stock_for_location_df(location)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "4",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "\n",
-    "qs_stock = (\n",
-    "    Stock.objects.values(\n",
-    "        \"allocation__registered_subject__subject_identifier\",\n",
-    "        \"code\",\n",
-    "        \"dispense__dispense_identifier\",\n",
-    "        \"location__name\",\n",
-    "    )\n",
-    "    .filter(location=location, qty=1)\n",
-    "    .annotate(count=Count(\"allocation__registered_subject__subject_identifier\"))\n",
-    ")\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "5",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "qs_stock"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "6",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "Dispense.objects.all()[0].__dict__"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "7",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "Stock.objects.filter(dispense__isnull=False)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "8",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "stock_request = StockRequest.objects.get(request_identifier=\"000122\")\n",
-    "df_next_scheduled_visits = get_next_scheduled_visit_for_subjects_df(stock_request)\n",
-    "df_instock, df_nostock = get_instock_and_nostock_data(stock_request, df_next_scheduled_visits)\n",
-    "\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "9",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_instock"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "10",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_nostock"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "11",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "12",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "13",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "14",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "15",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "16",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "17",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from edc_pdutils.dataframes import get_appointments\n",
-    "\n",
-    "from edc_utils import get_utcnow\n",
-    "from edc_appointment.constants import NEW_APPT\n",
-    "from dateutil.relativedelta import relativedelta\n",
-    "from datetime import datetime\n",
-    "\n",
-    "df_appt = get_appointments()\n",
-    "\n",
-    "mask1 = (df_appt.visit_code.isin([1240.0, 1360.0, 1480.0]))\n",
-    "mask2 = (df_appt.appt_datetime > datetime(2026, 1, 1)) & (df_appt.appt_datetime < datetime(2026, 8, 1))\n",
-    "df = df_appt[(df_appt.appt_status==NEW_APPT) & mask1 & mask2]\n",
-    "df.subject_identifier.nunique()\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "18",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "\n",
-    "df = df_appt[(df_appt.appt_status!=NEW_APPT) & (df_appt.visit_code.isin([1240.0, 1360.0, 1480.0]))].visit_code.value_counts()\n",
-    "df.sum()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "19",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from tabulate import tabulate\n",
-    "print(tabulate(df.to_frame(), headers=\"keys\"))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "20",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "\n",
-    "df_appt.appt_datetime < datetime(2025, 12, 1)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "21",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "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/steering.ipynb

@@ -1,61 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "0",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "markdown",
-   "id": "1",
-   "metadata": {},
-   "source": [
-    "incidence of the endpoints (dm)\n",
-    "1st year (0-1)\n",
-    "2nd year (1-2)\n",
-    "\n",
-    "markers\n",
-    "- overall (met endpoint)\n",
-    "- hba1c (after baseline w/ hba1c >6.5)\n",
-    "- fbc\n",
-    "- ogtt\n",
-    "\n",
-    "other conditions\n",
-    "- numbers w/ SAE\n",
-    "- types of SAEs\n",
-    "- SAE's not reported at baseline\n",
-    "- "
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "2",
-   "metadata": {},
-   "source": []
-  }
- ],
- "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
-}