meta-edc 1.0.6__py3-none-any.whl → 1.0.7__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- meta_analytics/dataframes/__init__.py +3 -0
- meta_analytics/dataframes/constants.py +1 -1
- meta_analytics/dataframes/enrolled/__init__.py +0 -1
- meta_analytics/dataframes/get_eos_df.py +15 -2
- meta_analytics/dataframes/get_glucose_df.py +149 -0
- meta_analytics/dataframes/get_glucose_fbg_df.py +27 -0
- meta_analytics/dataframes/get_glucose_fbg_ogtt_df.py +22 -0
- meta_analytics/dataframes/glucose_endpoints/endpoint_by_date.py +106 -120
- meta_analytics/dataframes/glucose_endpoints/glucose_endpoints_by_date.py +36 -227
- meta_analytics/dataframes/utils.py +18 -4
- meta_analytics/notebooks/hiv_regimens.ipynb +425 -0
- meta_analytics/notebooks/monitoring_report.ipynb +1561 -0
- meta_analytics/notebooks/pharmacy.ipynb +971 -0
- meta_analytics/utils.py +81 -0
- {meta_edc-1.0.6.dist-info → meta_edc-1.0.7.dist-info}/METADATA +4 -3
- {meta_edc-1.0.6.dist-info → meta_edc-1.0.7.dist-info}/RECORD +32 -18
- {meta_edc-1.0.6.dist-info → meta_edc-1.0.7.dist-info}/WHEEL +1 -1
- meta_edc-1.0.7.dist-info/licenses/AUTHORS.rst +8 -0
- meta_reports/migrations/0054_auto_20250422_2003.py +81 -0
- meta_reports/migrations/0055_alter_glucosesummary_table.py +17 -0
- meta_reports/migrations/0056_auto_20250422_2214.py +54 -0
- meta_reports/migrations/0057_auto_20250422_2224.py +54 -0
- meta_reports/migrations/0058_auto_20250422_2232.py +54 -0
- meta_reports/models/dbviews/glucose_summary/unmanaged_model.py +13 -1
- meta_reports/models/dbviews/glucose_summary/view_definition.py +8 -5
- meta_subject/form_validators/glucose_form_validator.py +16 -1
- meta_subject/forms/study_medication_form.py +5 -3
- meta_subject/migrations/0221_auto_20250402_1913.py +42 -0
- meta_subject/migrations/0222_alter_historicalstudymedication_stock_codes_and_more.py +46 -0
- meta_analytics/dataframes/enrolled/get_glucose_df.py +0 -122
- /meta_edc-1.0.6.dist-info/AUTHORS → /meta_analytics/dataframes/glucose_endpoints/utils.py +0 -0
- {meta_edc-1.0.6.dist-info → meta_edc-1.0.7.dist-info/licenses}/LICENSE +0 -0
- {meta_edc-1.0.6.dist-info → meta_edc-1.0.7.dist-info}/top_level.txt +0 -0
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"cell_type": "code",
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"id": "initial_id",
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"metadata": {
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"collapsed": true
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"source": [
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"%%capture\n",
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"import os\n",
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"from pathlib import Path\n",
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"import pandas as pd\n",
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"from dj_notebook import activate\n",
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"import numpy as np\n",
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"from django_pandas.io import read_frame\n",
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"\n",
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"env_file = os.environ[\"META_ENV\"]\n",
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"reports_folder = Path(os.environ[\"META_REPORTS_FOLDER\"])\n",
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"analysis_folder = Path(os.environ[\"META_ANALYSIS_FOLDER\"])\n",
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"pharmacy_folder = Path(os.environ[\"META_PHARMACY_FOLDER\"])\n",
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"plus = activate(dotenv_file=env_file)"
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],
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"outputs": [],
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"execution_count": null
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{
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"metadata": {},
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"cell_type": "code",
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"source": [
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"from edc_pharmacy.analytics.dataframes import no_stock_for_subjects_df\n",
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"from datetime import datetime\n",
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"from edc_registration.models import RegisteredSubject\n",
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"\n",
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"from edc_appointment.analytics import get_appointment_df\n",
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"from edc_appointment.constants import NEW_APPT\n",
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"from edc_pharmacy.models import StockRequest, Allocation, ReceiveItem, OrderItem, Lot\n",
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"\n",
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"from edc_pharmacy.analytics import get_next_scheduled_visit_for_subjects_df\n",
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"from meta_rando.models import RandomizationList\n",
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"from edc_pharmacy.models import Stock\n",
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"from edc_visit_schedule.models import SubjectScheduleHistory\n",
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"from django.apps import apps as django_apps\n",
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"from django.db.models import Count\n",
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"from django_pandas.io import read_frame\n",
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"from edc_visit_schedule.site_visit_schedules import site_visit_schedules\n",
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"from edc_pharmacy.models import Container\n",
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"from great_tables import GT, html, loc, style\n",
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"from PIL import Image\n"
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],
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"id": "a4c997d7adda770",
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"outputs": [],
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"execution_count": null
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"metadata": {},
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"cell_type": "code",
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"source": [
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"\n",
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"def get_great_table(df:pd.DataFrame, title:str, footnote:str|None=None):\n",
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" return (GT(df)\n",
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" .tab_header(title=html(title))\n",
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" .cols_align(align=\"left\", columns=[0])\n",
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" .cols_align(align=\"right\", columns=list(range(1, len(df.columns))))\n",
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" .opt_stylize(style=5)\n",
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" .opt_row_striping(row_striping=False)\n",
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" .opt_vertical_padding(scale=1.2)\n",
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" .opt_horizontal_padding(scale=1.0)\n",
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" .tab_options(\n",
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" stub_background_color=\"white\",\n",
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" row_group_border_bottom_style=\"hidden\",\n",
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" table_background_color=\"white\",\n",
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" table_font_size=12,\n",
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" )\n",
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" .tab_style(\n",
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" style=[style.fill(color=\"white\"), style.text(color=\"black\")],\n",
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" locations=loc.body(columns=list(range(len(df.columns))), rows=list(range(0, len(df)))),\n",
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" )\n",
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" .tab_style(\n",
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" style=[style.fill(color=\"lightgrey\"), style.text(color=\"black\")],\n",
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" locations=loc.body(columns=list(range(len(df.columns))), rows=[len(df)-1]),\n",
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" )\n",
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" .tab_source_note(source_note=html(footnote or \"\"))\n",
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" .tab_style(\n",
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" style=style.text(color=\"black\", size=\"small\"),\n",
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" locations=loc.footer(),\n",
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" )\n",
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"\n",
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"\n",
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" )\n"
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],
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"id": "6d4f230107499268",
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"cell_type": "code",
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"source": [
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"# get rando\n",
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"df_rando = read_frame(RandomizationList.objects.values(\"subject_identifier\", \"assignment\").filter(subject_identifier__isnull=False))"
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],
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"id": "1a5c145dc73ae1ca",
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"outputs": [],
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"execution_count": null
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{
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"metadata": {},
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"cell_type": "code",
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"source": [
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"# get appointments\n",
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"df_appt = get_appointment_df()\n",
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"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\")"
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],
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"id": "c0f532dc5f20aef6",
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"outputs": [],
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"execution_count": null
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"metadata": {},
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"cell_type": "code",
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"source": [
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"# create a dataframe of subjects still on the 'schedule' schedule\n",
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"# use SubjectScheduleHistory where offschedule_datetime is null\n",
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"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",
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"\n",
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"print(f\"{len(df_subject_schedule)} subjects currently onstudy\")"
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],
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"id": "dd5fd238c0160518",
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"outputs": [],
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"execution_count": null
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"metadata": {},
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"cell_type": "code",
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"source": [
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"# for now merge with the unfiltered df_appt\n",
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"df_main = df_subject_schedule.merge(\n",
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" df_appt[[\"appointment_id\", \"subject_identifier\", \"visit_code\", \"visit_code_str\", \"appt_datetime\", \"baseline_datetime\", \"endline_visit_code\", \"visit_code_sequence\", \"appt_status\"]],\n",
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" on=\"subject_identifier\",\n",
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" how=\"left\")\n",
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"# exclude unscheduled,\n",
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"df_main = df_main[\n",
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" (df_main.visit_code_sequence==0) &\n",
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" (df_main.visit_schedule_name==\"visit_schedule\") &\n",
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" (df_main.schedule_name==\"schedule\") &\n",
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" (df_main.visit_code<2000.0) &\n",
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" (df_main.appt_status==NEW_APPT)\n",
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"].copy()\n",
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"print(f\"{len(df_main)} new appointments for subjects on study\")\n"
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],
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"id": "13739396761c72c",
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"outputs": [],
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"execution_count": null
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"metadata": {},
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"cell_type": "code",
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"source": [
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"# number of appointments before extended all subjects out to 48m\n",
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"df_grouped = df_main[\n",
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" (df_main.appt_datetime >= datetime(2025,4,4)) &\n",
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" (df_main.appt_datetime < datetime(2026,3,1)) &\n",
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" (df_main.visit_code!=1480.0)\n",
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"].visit_code.value_counts().reset_index(name=\"appointments\").sort_values(by=\"visit_code\", ascending=True).reset_index(drop=True)\n",
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"df_grouped[\"cumsum\"] = df_grouped.appointments.cumsum()\n",
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"df_grouped[\"cumsum\"].max()\n"
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],
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"id": "fdf65539dce9fc30",
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"outputs": [],
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"execution_count": null
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"metadata": {},
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"cell_type": "code",
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"source": "df_main",
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"id": "81d462e710e0ae61",
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"metadata": {},
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"cell_type": "code",
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"source": [
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"# now extend everyone to 48 months.\n",
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"# Subjects are in the process of consenting for extended\n",
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"# followup. Assume ALL have done so by filling in all\n",
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"# subject schedules to 48m\n",
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"\n",
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"# pivot\n",
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"df_pivot = df_main[\n",
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" (df_main.visit_code_sequence==0) &\n",
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" (df_main.visit_code<2000.0)\n",
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"].pivot_table(index=\"subject_identifier\", columns='visit_code', values='appt_datetime', aggfunc='count')\n",
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"df_pivot.fillna(0, inplace=True)\n",
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"df_pivot.reset_index(inplace=True)\n",
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"df_pivot.rename_axis(\"\", axis=\"columns\", inplace=True)\n",
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"\n",
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"# melt\n",
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"df_pivot = df_pivot.melt(id_vars=\"subject_identifier\", var_name=\"visit_code\", value_name=\"exists\")\n",
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"df_pivot[\"visit_code\"] = df_pivot[\"visit_code\"].astype(float)\n",
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"df_pivot.sort_values([\"subject_identifier\", \"visit_code\"], ascending=True, inplace=True)\n",
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"df_pivot.reset_index(drop=True, inplace=True)\n",
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"\n",
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"# merge in baseline_datetime\n",
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"df_baseline = df_appt[df_appt.visit_code==1000.0][[\"subject_identifier\", \"baseline_datetime\"]]\n",
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"df_pivot = df_pivot.merge(df_baseline, on=[\"subject_identifier\"], how=\"left\")\n",
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"df_pivot.reset_index(drop=True, inplace=True)\n",
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"\n",
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"# merge df_main back in\n",
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"df_pivot = df_pivot.merge(df_main[[\"subject_identifier\", \"visit_code\", \"appt_datetime\", \"appt_status\"]], on=[\"subject_identifier\",\"visit_code\"], how=\"left\")\n",
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"id": "9bd1bf18017c18f2",
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"metadata": {},
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"cell_type": "code",
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"source": "# len(df_pivot[(df_pivot.appt_datetime>=datetime(2025,1,1)) & (df_pivot.visit_code==MONTH48)])/3",
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"id": "80ab2992c6ccb274",
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"cell_type": "code",
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"source": [
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"# extend no one!\n",
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"# df_pivot = df_pivot[df_pivot.exists==1].copy()\n",
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"# df_pivot.reset_index(drop=True, inplace=True)\n"
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],
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"id": "1e3098273f43e6b2",
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"metadata": {},
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"cell_type": "code",
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"source": [
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"# add appointments do not have an appt_datetime, so calculate\n",
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"# using the visit schedule relative to baseline_datetime\n",
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"visit_schedule = site_visit_schedules.get_visit_schedule(\"visit_schedule\")\n",
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"schedule = visit_schedule.schedules.get(\"schedule\")\n",
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"mapping = {k: visit.rbase for k,visit in schedule.visits.items()}\n",
|
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249
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+
"\n",
|
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250
|
+
"def estimate_appt_datetime(row):\n",
|
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251
|
+
" if pd.isna(row[\"appt_datetime\"]):\n",
|
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252
|
+
" row[\"appt_datetime\"] = row[\"baseline_datetime\"] + mapping.get(str(int(row[\"visit_code\"])))\n",
|
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253
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+
" return row\n",
|
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254
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+
"\n",
|
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255
|
+
"df_pivot = df_pivot.apply(estimate_appt_datetime, axis=1)\n",
|
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256
|
+
"df_pivot.sort_values(by=[\"subject_identifier\", \"visit_code\"], ascending=True, inplace=True)\n",
|
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257
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+
"df_pivot.reset_index(drop=True, inplace=True)\n",
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258
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+
"\n",
|
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259
|
+
"# merge in assignment\n",
|
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260
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+
"df_pivot = df_pivot.merge(df_rando, on=\"subject_identifier\", how=\"left\")\n",
|
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261
|
+
"df_pivot.reset_index(drop=True, inplace=True)\n",
|
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262
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+
"\n",
|
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263
|
+
"# flag added appointments as NEW\n",
|
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264
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+
"df_pivot.loc[df_pivot.exists==0.0, \"appt_status\"] = NEW_APPT\n",
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265
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+
"\n",
|
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266
|
+
"print(f\"{len(df_pivot)} appointments\")"
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267
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+
],
|
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268
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+
"id": "7483e4c8e47becc9",
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269
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+
"outputs": [],
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270
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+
"execution_count": null
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271
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+
},
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272
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+
{
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273
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+
"metadata": {},
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274
|
+
"cell_type": "code",
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275
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+
"source": [
|
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276
|
+
"# df_subject_appointments is a dataframe of appointments\n",
|
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277
|
+
"# - only include NEW appointments\n",
|
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278
|
+
"# - only include appts between today (2025,4,4) and before (2026,3,1).\n",
|
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279
|
+
"# - exclude the last visit (48m) since no meds are dispensed then.\n",
|
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280
|
+
"cutoff_date = datetime(2026,3,1)\n",
|
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281
|
+
"df_subject_appointments = df_pivot[\n",
|
|
282
|
+
" (df_pivot.appt_status==NEW_APPT) &\n",
|
|
283
|
+
" (df_pivot.appt_datetime >= datetime(2025,4,4)) &\n",
|
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284
|
+
" (df_pivot.appt_datetime < cutoff_date) &\n",
|
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285
|
+
" (df_pivot.visit_code!=1480.0)\n",
|
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286
|
+
"].copy()\n",
|
|
287
|
+
"print(f\"{len(df_subject_appointments)} appointments\")"
|
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288
|
+
],
|
|
289
|
+
"id": "12f04c24f098e88f",
|
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290
|
+
"outputs": [],
|
|
291
|
+
"execution_count": null
|
|
292
|
+
},
|
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293
|
+
{
|
|
294
|
+
"metadata": {},
|
|
295
|
+
"cell_type": "code",
|
|
296
|
+
"source": [
|
|
297
|
+
"n = df_subject_appointments.subject_identifier.nunique()\n",
|
|
298
|
+
"print(f\"{n} subjects\")\n"
|
|
299
|
+
],
|
|
300
|
+
"id": "c32531751a339390",
|
|
301
|
+
"outputs": [],
|
|
302
|
+
"execution_count": null
|
|
303
|
+
},
|
|
304
|
+
{
|
|
305
|
+
"metadata": {},
|
|
306
|
+
"cell_type": "code",
|
|
307
|
+
"source": "(len(df_subject_appointments[df_subject_appointments.appt_datetime>=datetime(2026,1,1)])/36)/5",
|
|
308
|
+
"id": "e7f520f32116ab1c",
|
|
309
|
+
"outputs": [],
|
|
310
|
+
"execution_count": null
|
|
311
|
+
},
|
|
312
|
+
{
|
|
313
|
+
"metadata": {},
|
|
314
|
+
"cell_type": "code",
|
|
315
|
+
"source": [
|
|
316
|
+
"# summarize the appointments\n",
|
|
317
|
+
"df_summary = df_subject_appointments.visit_code.value_counts().reset_index(name=\"appointments\").sort_values(by=[\"visit_code\"], ascending=True)\n",
|
|
318
|
+
"df_summary[\"cumsum\"] = df_summary.appointments.cumsum()\n",
|
|
319
|
+
"df_summary"
|
|
320
|
+
],
|
|
321
|
+
"id": "f38ead26da10a1ef",
|
|
322
|
+
"outputs": [],
|
|
323
|
+
"execution_count": null
|
|
324
|
+
},
|
|
325
|
+
{
|
|
326
|
+
"metadata": {},
|
|
327
|
+
"cell_type": "code",
|
|
328
|
+
"source": [
|
|
329
|
+
"df = df_subject_appointments.assignment.value_counts(dropna=False).reset_index()\n",
|
|
330
|
+
"df.rename(columns={\"count\":\"appointments\"}, inplace=True)\n",
|
|
331
|
+
"df[\"bottles\"] = df.appointments * 3\n",
|
|
332
|
+
"df[\"tablets\"] = df.bottles * 128\n",
|
|
333
|
+
"\n",
|
|
334
|
+
"# we need this many bottles / tablets by assignment\n",
|
|
335
|
+
"# filter\n",
|
|
336
|
+
"df.loc[len(df)] = {\"appointments\": df.appointments.sum(), \"bottles\": df.bottles.sum(), \"tablets\": df.tablets.sum()}\n",
|
|
337
|
+
"df"
|
|
338
|
+
],
|
|
339
|
+
"id": "b6a56657d02b04ac",
|
|
340
|
+
"outputs": [],
|
|
341
|
+
"execution_count": null
|
|
342
|
+
},
|
|
343
|
+
{
|
|
344
|
+
"metadata": {},
|
|
345
|
+
"cell_type": "code",
|
|
346
|
+
"source": [
|
|
347
|
+
"gt = get_great_table(\n",
|
|
348
|
+
" df,\n",
|
|
349
|
+
" \"Table 1: IMP Bottles of 128 needed<BR><small>as of 2025-04-04</small>\",\n",
|
|
350
|
+
" footnote=(\n",
|
|
351
|
+
" \"<ol>\"\n",
|
|
352
|
+
" \"<li>assume all participants consent for extended followup.\"\n",
|
|
353
|
+
" \"<li>Need 3 bottles every three months\"\n",
|
|
354
|
+
" \"<li>48m appointment is excluded\"\n",
|
|
355
|
+
" \"<li>Only prepare for appointments scheduled before 2026-03-01.\"\n",
|
|
356
|
+
" \"</ol>\"\n",
|
|
357
|
+
" ))\n",
|
|
358
|
+
"gt.show()"
|
|
359
|
+
],
|
|
360
|
+
"id": "f9bffc9c05c7fd41",
|
|
361
|
+
"outputs": [],
|
|
362
|
+
"execution_count": null
|
|
363
|
+
},
|
|
364
|
+
{
|
|
365
|
+
"metadata": {},
|
|
366
|
+
"cell_type": "code",
|
|
367
|
+
"source": [
|
|
368
|
+
"\n",
|
|
369
|
+
"# save as png\n",
|
|
370
|
+
"gt.save(analysis_folder / \"pharmacy_tbl1.png\")\n",
|
|
371
|
+
"# export to PDF\n",
|
|
372
|
+
"image = Image.open(analysis_folder / \"pharmacy_tbl1.png\")\n",
|
|
373
|
+
"image = image.resize((image.width * 6, image.height * 6), Image.LANCZOS)\n",
|
|
374
|
+
"image.save(analysis_folder / \"pharmacy_tbl1.pdf\", \"PDF\", resolution=800, optimize=True, quality=95)"
|
|
375
|
+
],
|
|
376
|
+
"id": "53247d65d251bebb",
|
|
377
|
+
"outputs": [],
|
|
378
|
+
"execution_count": null
|
|
379
|
+
},
|
|
380
|
+
{
|
|
381
|
+
"metadata": {},
|
|
382
|
+
"cell_type": "code",
|
|
383
|
+
"source": [
|
|
384
|
+
"# now lets look at the stock\n",
|
|
385
|
+
"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",
|
|
386
|
+
"\n",
|
|
387
|
+
"# merge in assignment\n",
|
|
388
|
+
"df_lot = read_frame(Lot.objects.values(\"id\", \"assignment__name\").all(), verbose=False)\n",
|
|
389
|
+
"df_lot.rename(columns={\"id\":\"lot_id\", \"assignment__name\": \"assignment\"}, inplace=True)\n",
|
|
390
|
+
"df_stock = df_stock.merge(df_lot[[\"lot_id\", \"assignment\"]], on=\"lot_id\", how=\"left\")\n",
|
|
391
|
+
"df_stock.rename(columns={\"container__name\":\"container\"}, inplace=True)\n",
|
|
392
|
+
"df_stock.reset_index(drop=True, inplace=True)"
|
|
393
|
+
],
|
|
394
|
+
"id": "6d280a4eeac931a0",
|
|
395
|
+
"outputs": [],
|
|
396
|
+
"execution_count": null
|
|
397
|
+
},
|
|
398
|
+
{
|
|
399
|
+
"metadata": {},
|
|
400
|
+
"cell_type": "code",
|
|
401
|
+
"source": [
|
|
402
|
+
"# merge in container columns\n",
|
|
403
|
+
"df_container = read_frame(Container.objects.all())\n",
|
|
404
|
+
"df_container.rename(columns={\"name\": \"container\", \"display_name\": \"container_display_name\", \"units\": \"container_units\", \"qty\": \"container_qty\"}, inplace=True)\n",
|
|
405
|
+
"df_stock = df_stock.merge(df_container[[\"container\", \"container_display_name\", \"container_type\", \"container_units\", \"container_qty\"]], on=\"container\", how=\"left\")\n",
|
|
406
|
+
"df_stock.reset_index(drop=True, inplace=True)\n",
|
|
407
|
+
"\n",
|
|
408
|
+
"# calculate bal\n",
|
|
409
|
+
"df_stock[\"bal\"] = df_stock[\"unit_qty_in\"] - df_stock[\"unit_qty_out\"]\n"
|
|
410
|
+
],
|
|
411
|
+
"id": "a11c4b67752b965d",
|
|
412
|
+
"outputs": [],
|
|
413
|
+
"execution_count": null
|
|
414
|
+
},
|
|
415
|
+
{
|
|
416
|
+
"metadata": {},
|
|
417
|
+
"cell_type": "code",
|
|
418
|
+
"source": [
|
|
419
|
+
"# show the balance of tablets decanted to bottles by assignment (on the EDC)\n",
|
|
420
|
+
"df2 = df_stock[df_stock.container_display_name==\"Bottle 128\"].groupby(by=[\"assignment\"]).bal.agg(\"sum\").reset_index()\n",
|
|
421
|
+
"df2.loc[len(df2)] = {\"bal\": df2.bal.sum()}\n",
|
|
422
|
+
"df2"
|
|
423
|
+
],
|
|
424
|
+
"id": "7e275d7fb827535b",
|
|
425
|
+
"outputs": [],
|
|
426
|
+
"execution_count": null
|
|
427
|
+
},
|
|
428
|
+
{
|
|
429
|
+
"metadata": {},
|
|
430
|
+
"cell_type": "code",
|
|
431
|
+
"source": [
|
|
432
|
+
"# some bottles, as of today, have not been captured in the system\n",
|
|
433
|
+
"# here is an estimate of what has been decanted into bottles but not labelled.\n",
|
|
434
|
+
"# in the system, these tablets would appear on the EDC as still in buckets\n",
|
|
435
|
+
"df3 = df2.copy()\n",
|
|
436
|
+
"df3 = df3.drop(len(df3) - 1)\n",
|
|
437
|
+
"placebo_unlabelled = 21*128*128\n",
|
|
438
|
+
"active_unlabelled = 25*191*128\n",
|
|
439
|
+
"\n",
|
|
440
|
+
"# adding in the estimates, this is about what we have bottled\n",
|
|
441
|
+
"df3.loc[df3.assignment==\"placebo\", \"bal\"] += placebo_unlabelled\n",
|
|
442
|
+
"df3.loc[df3.assignment==\"active\", \"bal\"] += active_unlabelled\n",
|
|
443
|
+
"df3.loc[len(df3)] = {\"bal\": df3.bal.sum()}\n",
|
|
444
|
+
"df3"
|
|
445
|
+
],
|
|
446
|
+
"id": "1d7134fe05417475",
|
|
447
|
+
"outputs": [],
|
|
448
|
+
"execution_count": null
|
|
449
|
+
},
|
|
450
|
+
{
|
|
451
|
+
"metadata": {},
|
|
452
|
+
"cell_type": "code",
|
|
453
|
+
"source": [
|
|
454
|
+
"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",
|
|
455
|
+
"gt.show()"
|
|
456
|
+
],
|
|
457
|
+
"id": "7ab587c2d36d2e10",
|
|
458
|
+
"outputs": [],
|
|
459
|
+
"execution_count": null
|
|
460
|
+
},
|
|
461
|
+
{
|
|
462
|
+
"metadata": {},
|
|
463
|
+
"cell_type": "code",
|
|
464
|
+
"source": [
|
|
465
|
+
"# save as png\n",
|
|
466
|
+
"gt.save(analysis_folder / \"pharmacy_tbl2.png\")\n",
|
|
467
|
+
"# export to PDF\n",
|
|
468
|
+
"image = Image.open(analysis_folder / \"pharmacy_tbl2.png\")\n",
|
|
469
|
+
"image = image.resize((image.width * 6, image.height * 6), Image.LANCZOS)\n",
|
|
470
|
+
"image.save(analysis_folder / \"pharmacy_tbl2.pdf\", \"PDF\", resolution=800, optimize=True, quality=95)"
|
|
471
|
+
],
|
|
472
|
+
"id": "68374d9f02546d6f",
|
|
473
|
+
"outputs": [],
|
|
474
|
+
"execution_count": null
|
|
475
|
+
},
|
|
476
|
+
{
|
|
477
|
+
"metadata": {},
|
|
478
|
+
"cell_type": "code",
|
|
479
|
+
"source": [
|
|
480
|
+
"# tablets: ordered\n",
|
|
481
|
+
"df_orderitems = read_frame(OrderItem.objects.all())\n",
|
|
482
|
+
"df_orderitems.qty.sum()"
|
|
483
|
+
],
|
|
484
|
+
"id": "9b67d6799735e116",
|
|
485
|
+
"outputs": [],
|
|
486
|
+
"execution_count": null
|
|
487
|
+
},
|
|
488
|
+
{
|
|
489
|
+
"metadata": {},
|
|
490
|
+
"cell_type": "code",
|
|
491
|
+
"source": [
|
|
492
|
+
"# tablets: received\n",
|
|
493
|
+
"df_received_items = read_frame(ReceiveItem.objects.all())\n",
|
|
494
|
+
"df_received_items.unit_qty.sum()"
|
|
495
|
+
],
|
|
496
|
+
"id": "af0868a54913329",
|
|
497
|
+
"outputs": [],
|
|
498
|
+
"execution_count": null
|
|
499
|
+
},
|
|
500
|
+
{
|
|
501
|
+
"metadata": {},
|
|
502
|
+
"cell_type": "code",
|
|
503
|
+
"source": [
|
|
504
|
+
"# tablets: received into stock\n",
|
|
505
|
+
"df_stock[df_stock.container_type==\"bucket\"].unit_qty_in.sum()"
|
|
506
|
+
],
|
|
507
|
+
"id": "82b0df34b49377f0",
|
|
508
|
+
"outputs": [],
|
|
509
|
+
"execution_count": null
|
|
510
|
+
},
|
|
511
|
+
{
|
|
512
|
+
"metadata": {},
|
|
513
|
+
"cell_type": "code",
|
|
514
|
+
"source": [
|
|
515
|
+
"# tablets: decanted from buckets into bottles\n",
|
|
516
|
+
"df_stock[df_stock.container_type==\"bucket\"].unit_qty_out.sum()"
|
|
517
|
+
],
|
|
518
|
+
"id": "1d1383219f8fd0a4",
|
|
519
|
+
"outputs": [],
|
|
520
|
+
"execution_count": null
|
|
521
|
+
},
|
|
522
|
+
{
|
|
523
|
+
"metadata": {},
|
|
524
|
+
"cell_type": "code",
|
|
525
|
+
"source": [
|
|
526
|
+
"# tablets: total in bottles\n",
|
|
527
|
+
"df_stock[df_stock.container_type==\"Bottle\"].unit_qty_in.sum()"
|
|
528
|
+
],
|
|
529
|
+
"id": "d928f610d5427f39",
|
|
530
|
+
"outputs": [],
|
|
531
|
+
"execution_count": null
|
|
532
|
+
},
|
|
533
|
+
{
|
|
534
|
+
"metadata": {},
|
|
535
|
+
"cell_type": "code",
|
|
536
|
+
"source": [
|
|
537
|
+
"# tablets: total bottles available / not yet dispensed BY ASSIGNMENT\n",
|
|
538
|
+
"# the total matches the total above for column \"bal\"\n",
|
|
539
|
+
"df4 = df_stock[(df_stock.container_type==\"Bottle\") & (df_stock.confirmed==True) & (df_stock.dispensed==True)].groupby(by=[\"assignment\"]).unit_qty_in.sum().reset_index()\n",
|
|
540
|
+
"df4[\"subtotal\"] = np.nan\n",
|
|
541
|
+
"df4.loc[len(df4)] = {\"subtotal\": df4.unit_qty_in.sum()}\n",
|
|
542
|
+
"df4[\"dispensed\"] = True\n",
|
|
543
|
+
"\n",
|
|
544
|
+
"df5 = df_stock[(df_stock.container_type==\"Bottle\") & (df_stock.confirmed==True) & (df_stock.dispensed==False)].groupby(by=[\"assignment\"]).unit_qty_in.sum().reset_index()\n",
|
|
545
|
+
"df5.loc[df5.assignment==\"placebo\", \"unit_qty_in\"] += placebo_unlabelled\n",
|
|
546
|
+
"df5.loc[df5.assignment==\"active\", \"unit_qty_in\"] += active_unlabelled\n",
|
|
547
|
+
"df5[\"subtotal\"] = np.nan\n",
|
|
548
|
+
"df5.loc[len(df5)] = {\"subtotal\" : df5.unit_qty_in.sum()}\n",
|
|
549
|
+
"df5[\"dispensed\"] = False\n",
|
|
550
|
+
"\n",
|
|
551
|
+
"df6 = pd.concat([df4, df5])\n",
|
|
552
|
+
"df6[\"total\"] = np.nan\n",
|
|
553
|
+
"df6.reset_index(drop=True, inplace=True)\n",
|
|
554
|
+
"df6.loc[len(df6)] = {\"total\": df6.subtotal.sum()}\n",
|
|
555
|
+
"df6 = df6[[\"dispensed\", \"assignment\", \"unit_qty_in\", \"subtotal\", \"total\"]]\n",
|
|
556
|
+
"df6"
|
|
557
|
+
],
|
|
558
|
+
"id": "6600690d6e88a1b2",
|
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559
|
+
"outputs": [],
|
|
560
|
+
"execution_count": null
|
|
561
|
+
},
|
|
562
|
+
{
|
|
563
|
+
"metadata": {},
|
|
564
|
+
"cell_type": "code",
|
|
565
|
+
"source": "",
|
|
566
|
+
"id": "3ad00099e744f41b",
|
|
567
|
+
"outputs": [],
|
|
568
|
+
"execution_count": null
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|
569
|
+
},
|
|
570
|
+
{
|
|
571
|
+
"metadata": {},
|
|
572
|
+
"cell_type": "code",
|
|
573
|
+
"source": "",
|
|
574
|
+
"id": "c460fa84e9fc004e",
|
|
575
|
+
"outputs": [],
|
|
576
|
+
"execution_count": null
|
|
577
|
+
},
|
|
578
|
+
{
|
|
579
|
+
"metadata": {},
|
|
580
|
+
"cell_type": "code",
|
|
581
|
+
"source": "",
|
|
582
|
+
"id": "428d31f52ed17823",
|
|
583
|
+
"outputs": [],
|
|
584
|
+
"execution_count": null
|
|
585
|
+
},
|
|
586
|
+
{
|
|
587
|
+
"metadata": {},
|
|
588
|
+
"cell_type": "code",
|
|
589
|
+
"source": [
|
|
590
|
+
"from meta_visit_schedule.constants import MONTH36\n",
|
|
591
|
+
"\n",
|
|
592
|
+
"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))]"
|
|
593
|
+
],
|
|
594
|
+
"id": "49a7b405b7973ae3",
|
|
595
|
+
"outputs": [],
|
|
596
|
+
"execution_count": null
|
|
597
|
+
},
|
|
598
|
+
{
|
|
599
|
+
"metadata": {},
|
|
600
|
+
"cell_type": "code",
|
|
601
|
+
"source": [
|
|
602
|
+
"def remove_subjects_where_stock_on_site(stock_request: StockRequest, df: pd.DataFrame):\n",
|
|
603
|
+
" stock_model_cls = django_apps.get_model(\"edc_pharmacy.Stock\")\n",
|
|
604
|
+
" qs_stock = (\n",
|
|
605
|
+
" stock_model_cls.objects.values(\n",
|
|
606
|
+
" \"allocation__registered_subject__subject_identifier\", \"code\"\n",
|
|
607
|
+
" )\n",
|
|
608
|
+
" .filter(location=stock_request.location, qty=1)\n",
|
|
609
|
+
" .annotate(count=Count(\"allocation__registered_subject__subject_identifier\"))\n",
|
|
610
|
+
" )\n",
|
|
611
|
+
" df_stock = read_frame(qs_stock)\n",
|
|
612
|
+
" df_stock = df_stock.rename(\n",
|
|
613
|
+
" columns={\n",
|
|
614
|
+
" \"allocation__registered_subject__subject_identifier\": \"subject_identifier\",\n",
|
|
615
|
+
" \"count\": \"stock_qty\",\n",
|
|
616
|
+
" }\n",
|
|
617
|
+
" )\n",
|
|
618
|
+
" if not df.empty and not df_stock.empty:\n",
|
|
619
|
+
" df_subject = df.copy()\n",
|
|
620
|
+
" df_subject[\"code\"] = None\n",
|
|
621
|
+
" df = df.merge(df_stock, on=\"subject_identifier\", how=\"left\")\n",
|
|
622
|
+
" for index, row in df.iterrows():\n",
|
|
623
|
+
" qty_needed = stock_request.containers_per_subject - len(df[df.subject_identifier == row.subject_identifier])\n",
|
|
624
|
+
" if qty_needed > 0:\n",
|
|
625
|
+
" for _ in range(0, qty_needed):\n",
|
|
626
|
+
" df = pd.concat([df, df_subject])\n",
|
|
627
|
+
" else:\n",
|
|
628
|
+
" df[\"code\"] = None\n",
|
|
629
|
+
" df[\"stock_qty\"] = 0.0\n",
|
|
630
|
+
" df = df.reset_index(drop=True)\n",
|
|
631
|
+
" return df\n"
|
|
632
|
+
],
|
|
633
|
+
"id": "491b43957fe1c756",
|
|
634
|
+
"outputs": [],
|
|
635
|
+
"execution_count": null
|
|
636
|
+
},
|
|
637
|
+
{
|
|
638
|
+
"metadata": {},
|
|
639
|
+
"cell_type": "code",
|
|
640
|
+
"source": [
|
|
641
|
+
"def pad_with_null_rows(df, qty_needed):\n",
|
|
642
|
+
" padded_data = []\n",
|
|
643
|
+
" for index, row in df.iterrows():\n",
|
|
644
|
+
" customer = row['subject']\n",
|
|
645
|
+
" products = row['product_code']\n",
|
|
646
|
+
" # Pad the products list with None to make its length x\n",
|
|
647
|
+
" products += [None] * (qty_needed - len(products))\n",
|
|
648
|
+
" # Create x rows for each customer\n",
|
|
649
|
+
" for product in products:\n",
|
|
650
|
+
" padded_data.append({'customer': customer, 'product_code': product})\n",
|
|
651
|
+
" return pd.DataFrame(padded_data)"
|
|
652
|
+
],
|
|
653
|
+
"id": "14fd36a1e0e158b9",
|
|
654
|
+
"outputs": [],
|
|
655
|
+
"execution_count": null
|
|
656
|
+
},
|
|
657
|
+
{
|
|
658
|
+
"metadata": {},
|
|
659
|
+
"cell_type": "code",
|
|
660
|
+
"source": [
|
|
661
|
+
"pk = \"5455cf66-b8e5-449c-a1e8-24d3325026d7\"\n",
|
|
662
|
+
"stock_request = StockRequest.objects.get(pk=pk)\n"
|
|
663
|
+
],
|
|
664
|
+
"id": "ee9423599bad2c6f",
|
|
665
|
+
"outputs": [],
|
|
666
|
+
"execution_count": null
|
|
667
|
+
},
|
|
668
|
+
{
|
|
669
|
+
"metadata": {},
|
|
670
|
+
"cell_type": "code",
|
|
671
|
+
"source": [
|
|
672
|
+
"df_subjects = get_next_scheduled_visit_for_subjects_df(stock_request)\n",
|
|
673
|
+
"df_subjects"
|
|
674
|
+
],
|
|
675
|
+
"id": "f5b22e507f36170d",
|
|
676
|
+
"outputs": [],
|
|
677
|
+
"execution_count": null
|
|
678
|
+
},
|
|
679
|
+
{
|
|
680
|
+
"metadata": {},
|
|
681
|
+
"cell_type": "code",
|
|
682
|
+
"source": "",
|
|
683
|
+
"id": "8918d8cd6b2ae777",
|
|
684
|
+
"outputs": [],
|
|
685
|
+
"execution_count": null
|
|
686
|
+
},
|
|
687
|
+
{
|
|
688
|
+
"metadata": {},
|
|
689
|
+
"cell_type": "code",
|
|
690
|
+
"source": [
|
|
691
|
+
"df = df_subjects.copy()\n",
|
|
692
|
+
"stock_model_cls = django_apps.get_model(\"edc_pharmacy.Stock\")\n",
|
|
693
|
+
"qs_stock = (\n",
|
|
694
|
+
" stock_model_cls.objects.values(\n",
|
|
695
|
+
" \"allocation__registered_subject__subject_identifier\", \"code\"\n",
|
|
696
|
+
" )\n",
|
|
697
|
+
" .filter(location=stock_request.location, qty=1)\n",
|
|
698
|
+
" .annotate(count=Count(\"allocation__registered_subject__subject_identifier\"))\n",
|
|
699
|
+
")\n",
|
|
700
|
+
"df_stock = read_frame(qs_stock)\n",
|
|
701
|
+
"df_stock = df_stock.rename(\n",
|
|
702
|
+
" columns={\n",
|
|
703
|
+
" \"allocation__registered_subject__subject_identifier\": \"subject_identifier\",\n",
|
|
704
|
+
" \"count\": \"stock_qty\",\n",
|
|
705
|
+
" }\n",
|
|
706
|
+
")\n",
|
|
707
|
+
"df_stock"
|
|
708
|
+
],
|
|
709
|
+
"id": "164302f67cec31be",
|
|
710
|
+
"outputs": [],
|
|
711
|
+
"execution_count": null
|
|
712
|
+
},
|
|
713
|
+
{
|
|
714
|
+
"metadata": {},
|
|
715
|
+
"cell_type": "code",
|
|
716
|
+
"source": "df.merge(df_stock, on=\"subject_identifier\", how=\"left\")",
|
|
717
|
+
"id": "8c1c3f0b594bdf3",
|
|
718
|
+
"outputs": [],
|
|
719
|
+
"execution_count": null
|
|
720
|
+
},
|
|
721
|
+
{
|
|
722
|
+
"metadata": {},
|
|
723
|
+
"cell_type": "code",
|
|
724
|
+
"source": [
|
|
725
|
+
"if not df.empty and not df_stock.empty:\n",
|
|
726
|
+
" df_subject = df.copy()\n",
|
|
727
|
+
" df_subject[\"code\"] = None\n",
|
|
728
|
+
" df = df.merge(df_stock, on=\"subject_identifier\", how=\"left\")\n",
|
|
729
|
+
" for index, row in df.iterrows():\n",
|
|
730
|
+
" qty_needed = stock_request.containers_per_subject - len(df[df.subject_identifier == row.subject_identifier])\n",
|
|
731
|
+
" if qty_needed > 0:\n",
|
|
732
|
+
" for _ in range(0, qty_needed):\n",
|
|
733
|
+
" df = pd.concat([df, df_subject])\n",
|
|
734
|
+
"else:\n",
|
|
735
|
+
" df[\"code\"] = None\n",
|
|
736
|
+
"df[\"stock_qty\"] = 0.0\n",
|
|
737
|
+
"df = df.reset_index(drop=True)\n",
|
|
738
|
+
"df"
|
|
739
|
+
],
|
|
740
|
+
"id": "ba3541a4e2cdfde6",
|
|
741
|
+
"outputs": [],
|
|
742
|
+
"execution_count": null
|
|
743
|
+
},
|
|
744
|
+
{
|
|
745
|
+
"metadata": {},
|
|
746
|
+
"cell_type": "code",
|
|
747
|
+
"source": "df.loc[df.index.repeat(3)]",
|
|
748
|
+
"id": "5ba4eff2efc5f3eb",
|
|
749
|
+
"outputs": [],
|
|
750
|
+
"execution_count": null
|
|
751
|
+
},
|
|
752
|
+
{
|
|
753
|
+
"metadata": {},
|
|
754
|
+
"cell_type": "code",
|
|
755
|
+
"source": [
|
|
756
|
+
"if not df.empty and not df_stock.empty:\n",
|
|
757
|
+
" df = df.merge(df_stock, on=\"subject_identifier\", how=\"left\")\n",
|
|
758
|
+
"else:\n",
|
|
759
|
+
" df[\"code\"] = None\n",
|
|
760
|
+
"df[\"stock_qty\"] = 0.0\n",
|
|
761
|
+
"df = df.reset_index(drop=True)\n",
|
|
762
|
+
"df"
|
|
763
|
+
],
|
|
764
|
+
"id": "79507f3726dd23ac",
|
|
765
|
+
"outputs": [],
|
|
766
|
+
"execution_count": null
|
|
767
|
+
},
|
|
768
|
+
{
|
|
769
|
+
"metadata": {},
|
|
770
|
+
"cell_type": "code",
|
|
771
|
+
"source": [
|
|
772
|
+
"df = remove_subjects_where_stock_on_site(stock_request, df_subjects)\n",
|
|
773
|
+
"df"
|
|
774
|
+
],
|
|
775
|
+
"id": "a23aafeb660d5a9c",
|
|
776
|
+
"outputs": [],
|
|
777
|
+
"execution_count": null
|
|
778
|
+
},
|
|
779
|
+
{
|
|
780
|
+
"metadata": {},
|
|
781
|
+
"cell_type": "code",
|
|
782
|
+
"source": [
|
|
783
|
+
"df_instock = df[~df.code.isna()]\n",
|
|
784
|
+
"df_instock = df_instock.reset_index(drop=True)\n",
|
|
785
|
+
"df_instock = df_instock.sort_values(by=[\"subject_identifier\"])\n",
|
|
786
|
+
"\n",
|
|
787
|
+
"df_nostock = df[df.code.isna()]\n",
|
|
788
|
+
"df_nostock = df_nostock.reset_index(drop=True)\n",
|
|
789
|
+
"df_nostock = df_nostock.loc[\n",
|
|
790
|
+
" df_nostock.index.repeat(stock_request.containers_per_subject)\n",
|
|
791
|
+
"].reset_index(drop=True)\n",
|
|
792
|
+
"df_nostock = df_nostock.sort_values(by=[\"subject_identifier\"])\n",
|
|
793
|
+
"df_nostock[\"code\"] = df_nostock[\"code\"].fillna(\"---\")\n"
|
|
794
|
+
],
|
|
795
|
+
"id": "f8e386caf276b53e",
|
|
796
|
+
"outputs": [],
|
|
797
|
+
"execution_count": null
|
|
798
|
+
},
|
|
799
|
+
{
|
|
800
|
+
"metadata": {},
|
|
801
|
+
"cell_type": "code",
|
|
802
|
+
"source": "",
|
|
803
|
+
"id": "85715500af7721de",
|
|
804
|
+
"outputs": [],
|
|
805
|
+
"execution_count": null
|
|
806
|
+
},
|
|
807
|
+
{
|
|
808
|
+
"metadata": {},
|
|
809
|
+
"cell_type": "code",
|
|
810
|
+
"source": "",
|
|
811
|
+
"id": "acf8453d693c288e",
|
|
812
|
+
"outputs": [],
|
|
813
|
+
"execution_count": null
|
|
814
|
+
},
|
|
815
|
+
{
|
|
816
|
+
"metadata": {},
|
|
817
|
+
"cell_type": "code",
|
|
818
|
+
"source": "no_stock_for_subjects_df()",
|
|
819
|
+
"id": "73171a433d5b5882",
|
|
820
|
+
"outputs": [],
|
|
821
|
+
"execution_count": null
|
|
822
|
+
},
|
|
823
|
+
{
|
|
824
|
+
"metadata": {},
|
|
825
|
+
"cell_type": "code",
|
|
826
|
+
"source": "df_schedule = read_frame(SubjectScheduleHistory.objects.values(\"subject_identifier\", \"visit_schedule_name\",\"schedule_name\", \"offschedule_datetime\").all())\n",
|
|
827
|
+
"id": "5721c4cf5f08d681",
|
|
828
|
+
"outputs": [],
|
|
829
|
+
"execution_count": null
|
|
830
|
+
},
|
|
831
|
+
{
|
|
832
|
+
"metadata": {},
|
|
833
|
+
"cell_type": "code",
|
|
834
|
+
"source": [
|
|
835
|
+
"df_schedule = df_schedule[(df_schedule.visit_schedule_name==\"visit_schedule\") & (df_schedule.schedule_name==\"schedule\") & df_schedule.offschedule_datetime.isna()]\n",
|
|
836
|
+
"df_schedule.reset_index(drop=True, inplace=True)"
|
|
837
|
+
],
|
|
838
|
+
"id": "621196fa35e00e9c",
|
|
839
|
+
"outputs": [],
|
|
840
|
+
"execution_count": null
|
|
841
|
+
},
|
|
842
|
+
{
|
|
843
|
+
"metadata": {},
|
|
844
|
+
"cell_type": "code",
|
|
845
|
+
"source": [
|
|
846
|
+
"df_stock = read_frame(Stock.objects.all(), verbose=False)\n",
|
|
847
|
+
"df_stock_on_site = df_stock[(df_stock.confirmed_at_site==True) & (df_stock.dispensed==False)].copy()\n",
|
|
848
|
+
"df_stock_on_site.reset_index(drop=True, inplace=True)\n",
|
|
849
|
+
"df_stock_on_site = df_stock_on_site.drop(columns=[\"subject_identifier\"])\n"
|
|
850
|
+
],
|
|
851
|
+
"id": "8abada4ffb0db4f0",
|
|
852
|
+
"outputs": [],
|
|
853
|
+
"execution_count": null
|
|
854
|
+
},
|
|
855
|
+
{
|
|
856
|
+
"metadata": {},
|
|
857
|
+
"cell_type": "code",
|
|
858
|
+
"source": [
|
|
859
|
+
"df_allocation = read_frame(Allocation.objects.values(\"id\", \"registered_subject\").all(), verbose=False)\n",
|
|
860
|
+
"df_rs = read_frame(RegisteredSubject.objects.values(\"id\", \"subject_identifier\").all(), verbose=False)\n",
|
|
861
|
+
"df_allocation = df_allocation.merge(df_rs[[\"id\", \"subject_identifier\"]], how=\"left\", left_on=\"registered_subject\", right_on=\"id\", suffixes=[\"_allocation\", \"_rs\"])"
|
|
862
|
+
],
|
|
863
|
+
"id": "624ebc7e51e679bd",
|
|
864
|
+
"outputs": [],
|
|
865
|
+
"execution_count": null
|
|
866
|
+
},
|
|
867
|
+
{
|
|
868
|
+
"metadata": {},
|
|
869
|
+
"cell_type": "code",
|
|
870
|
+
"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\")",
|
|
871
|
+
"id": "394e569ac1649719",
|
|
872
|
+
"outputs": [],
|
|
873
|
+
"execution_count": null
|
|
874
|
+
},
|
|
875
|
+
{
|
|
876
|
+
"metadata": {},
|
|
877
|
+
"cell_type": "code",
|
|
878
|
+
"source": [
|
|
879
|
+
"df = pd.merge(df_schedule[[\"subject_identifier\", 'offschedule_datetime']], df_stock_on_site, on=\"subject_identifier\", how=\"left\")\n",
|
|
880
|
+
"df= df[df.code.isna()][[\"subject_identifier\", ]].sort_values(by=[\"subject_identifier\"]).reset_index(drop=True)"
|
|
881
|
+
],
|
|
882
|
+
"id": "1ab7350cfb29eab4",
|
|
883
|
+
"outputs": [],
|
|
884
|
+
"execution_count": null
|
|
885
|
+
},
|
|
886
|
+
{
|
|
887
|
+
"metadata": {},
|
|
888
|
+
"cell_type": "code",
|
|
889
|
+
"source": [
|
|
890
|
+
"df_appt = get_next_scheduled_visit_for_subjects_df()\n",
|
|
891
|
+
"df_appt = df_appt[[\"subject_identifier\", \"site_id\", \"visit_code\", \"appt_datetime\", \"baseline_datetime\"]].copy()\n",
|
|
892
|
+
"df_appt.reset_index(drop=True, inplace=True)"
|
|
893
|
+
],
|
|
894
|
+
"id": "f29cc9c6c1234c34",
|
|
895
|
+
"outputs": [],
|
|
896
|
+
"execution_count": null
|
|
897
|
+
},
|
|
898
|
+
{
|
|
899
|
+
"metadata": {},
|
|
900
|
+
"cell_type": "code",
|
|
901
|
+
"source": [
|
|
902
|
+
"\n",
|
|
903
|
+
"df = df.merge(df_appt, how=\"left\", on=\"subject_identifier\")\n",
|
|
904
|
+
"df = df[(df.appt_datetime.notna())]\n",
|
|
905
|
+
"df.reset_index(drop=True, inplace=True)"
|
|
906
|
+
],
|
|
907
|
+
"id": "9e3e3f429a1995ec",
|
|
908
|
+
"outputs": [],
|
|
909
|
+
"execution_count": null
|
|
910
|
+
},
|
|
911
|
+
{
|
|
912
|
+
"metadata": {},
|
|
913
|
+
"cell_type": "code",
|
|
914
|
+
"source": [
|
|
915
|
+
"utc_now = pd.Timestamp.utcnow().tz_localize(None)\n",
|
|
916
|
+
"df[\"relative_days\"] = (df.appt_datetime - utc_now).dt.days\n",
|
|
917
|
+
"df_final = df[(df.relative_days >= -105)].copy()\n",
|
|
918
|
+
"df_final.reset_index(drop=True, inplace=True)\n",
|
|
919
|
+
"df_final"
|
|
920
|
+
],
|
|
921
|
+
"id": "d6570f1e94ac23bb",
|
|
922
|
+
"outputs": [],
|
|
923
|
+
"execution_count": null
|
|
924
|
+
},
|
|
925
|
+
{
|
|
926
|
+
"metadata": {},
|
|
927
|
+
"cell_type": "code",
|
|
928
|
+
"source": "RegisteredSubject.objects.filter(site_id=10)",
|
|
929
|
+
"id": "6aef5bb0e7caf4e8",
|
|
930
|
+
"outputs": [],
|
|
931
|
+
"execution_count": null
|
|
932
|
+
},
|
|
933
|
+
{
|
|
934
|
+
"metadata": {},
|
|
935
|
+
"cell_type": "code",
|
|
936
|
+
"source": "",
|
|
937
|
+
"id": "1e6126bbe8d04c70",
|
|
938
|
+
"outputs": [],
|
|
939
|
+
"execution_count": null
|
|
940
|
+
},
|
|
941
|
+
{
|
|
942
|
+
"metadata": {},
|
|
943
|
+
"cell_type": "code",
|
|
944
|
+
"source": "",
|
|
945
|
+
"id": "1ee6ef823e6a543d",
|
|
946
|
+
"outputs": [],
|
|
947
|
+
"execution_count": null
|
|
948
|
+
}
|
|
949
|
+
],
|
|
950
|
+
"metadata": {
|
|
951
|
+
"kernelspec": {
|
|
952
|
+
"display_name": "Python 3",
|
|
953
|
+
"language": "python",
|
|
954
|
+
"name": "python3"
|
|
955
|
+
},
|
|
956
|
+
"language_info": {
|
|
957
|
+
"codemirror_mode": {
|
|
958
|
+
"name": "ipython",
|
|
959
|
+
"version": 2
|
|
960
|
+
},
|
|
961
|
+
"file_extension": ".py",
|
|
962
|
+
"mimetype": "text/x-python",
|
|
963
|
+
"name": "python",
|
|
964
|
+
"nbconvert_exporter": "python",
|
|
965
|
+
"pygments_lexer": "ipython2",
|
|
966
|
+
"version": "2.7.6"
|
|
967
|
+
}
|
|
968
|
+
},
|
|
969
|
+
"nbformat": 4,
|
|
970
|
+
"nbformat_minor": 5
|
|
971
|
+
}
|