meta-edc 1.0.6__py3-none-any.whl → 1.1.0__py3-none-any.whl

meta_analytics/notebooks/ven.ipynb

@@ -0,0 +1,191 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%%capture\n",
+    "import os\n",
+    "from pathlib import Path\n",
+    "import pandas as pd\n",
+    "from dj_notebook import activate\n",
+    "import numpy as np\n",
+    "from django_pandas.io import read_frame\n",
+    "\n",
+    "env_file = os.environ[\"META_ENV\"]\n",
+    "reports_folder = Path(os.environ[\"META_REPORTS_FOLDER\"])\n",
+    "analysis_folder = Path(os.environ[\"META_ANALYSIS_FOLDER\"])\n",
+    "pharmacy_folder = Path(os.environ[\"META_PHARMACY_FOLDER\"])\n",
+    "plus = activate(dotenv_file=env_file)\n",
+    "pd.set_option('future.no_silent_downcasting', True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from matplotlib import pyplot as plt\n",
+    "from matplotlib_venn import venn3, venn2\n",
+    "from meta_analytics.dataframes import get_screening_df\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_fbg_value(r):\n",
+    "    if not pd.isna(r[\"converted_fbg2_value\"]):\n",
+    "        return r[\"converted_fbg2_value\"]\n",
+    "    return r[\"converted_fbg_value\"]\n",
+    "\n",
+    "def get_ogtt_value(r):\n",
+    "    if not pd.isna(r[\"converted_ogtt2_value\"]):\n",
+    "        return r[\"converted_ogtt2_value\"]\n",
+    "    return r[\"converted_ogtt_value\"]\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from meta_analytics.dataframes import get_screening_df\n",
+    "\n",
+    "df_screening = get_screening_df()\n",
+    "df_screening[\"visit_code\"] = \"Enrol\"\n",
+    "df_screening[\"fbg_value\"] = df_screening.apply(get_fbg_value, axis=1)\n",
+    "df_screening[\"ogtt_value\"] = df_screening.apply(get_ogtt_value, axis=1)\n",
+    "df_screening[\"site_id\"] = df_screening.site.astype(int)\n",
+    "df_screening = df_screening.drop(columns=[\"site\"])\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df_screening.query(\"\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fbg = set(df_screening[df_screening.fbg_value>=7.0][[\"id\"]].id.to_list())\n",
+    "ogtt = set(df_screening[df_screening.ogtt_value>=11.1][[\"id\"]].id.to_list())\n",
+    "hba1c = set(df_screening[df_screening.hba1c_value>=6.5][[\"id\"]].id.to_list())\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "# plt.figure(figsize=(6, 6))\n",
+    "fig, ax = plt.subplots(figsize=(8, 8))\n",
+    "venn = venn3([fbg, ogtt, hba1c], set_labels=('FBG≥7.0 mmol/L', 'OGTT≥11.1 mmol/L', 'HBA1C≥6.5%'), ax=ax)\n",
+    "plt.title(\"Overlap in diabetes indicators for all screened patients (n=5552)\")\n",
+    "\n",
+    "region_ids = ['100', '010', '001']\n",
+    "for idx, region_id in enumerate(region_ids):\n",
+    "    patch = venn.get_patch_by_id(region_id)\n",
+    "    label = venn.set_labels[idx]\n",
+    "    if patch and label:\n",
+    "        label.set_color(patch.get_facecolor())\n",
+    "        label.set_fontweight('bold')\n",
+    "\n",
+    "# Show the plot\n",
+    "# plt.show()\n",
+    "plt.savefig(analysis_folder / \"meta3_venn.png\", bbox_inches='tight')\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "import matplotlib.pyplot as plt\n",
+    "from matplotlib_venn import venn2\n",
+    "from pathlib import Path\n",
+    "\n",
+    "# Define the output folder\n",
+    "analysis_folder = Path(\"analysis_output\")\n",
+    "analysis_folder.mkdir(parents=True, exist_ok=True)\n",
+    "\n",
+    "# Define the sets\n",
+    "set1 = set(['A', 'B', 'C', 'D'])\n",
+    "set2 = set(['C', 'D', 'E', 'F'])\n",
+    "\n",
+    "# Create the figure and axis\n",
+    "fig, ax = plt.subplots(figsize=(6, 6))\n",
+    "\n",
+    "# Draw the Venn diagram on the axis\n",
+    "venn2([set1, set2], set_labels=('Set 1', 'Set 2'), ax=ax)\n",
+    "\n",
+    "# Save the figure\n",
+    "fig.savefig(analysis_folder / \"meta3_venn.png\", bbox_inches='tight')\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9",
+   "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/vitals.ipynb

@@ -0,0 +1,263 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%%capture\n",
+    "import os\n",
+    "import pandas as pd\n",
+    "from dj_notebook import activate\n",
+    "from pathlib import Path\n",
+    "env_file = os.environ[\"META_ENV\"]\n",
+    "analysis_folder = Path(os.environ[\"META_ANALYSIS_FOLDER\"])\n",
+    "reports_folder = Path(os.environ[\"META_ANALYSIS_FOLDER\"])\n",
+    "plus = activate(dotenv_file=env_file)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from edc_pdutils.dataframes import get_crf\n",
+    "from edc_appointment.analytics import get_appointment_df\n",
+    "from edc_appointment.constants import MISSED_APPT\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df_visit = get_crf(\"meta_subject.glucosefbg\", subject_visit_model=\"meta_subject.subjectvisit\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df_missedvisit = get_crf(\"meta_subject.subjectvisitmissed\", subject_visit_model=\"meta_subject.subjectvisit\")\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df_missedvisit[df_missedvisit.appt_timing!=MISSED_APPT]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "dffbg = get_crf(\"meta_subject.glucosefbg\", subject_visit_model=\"meta_subject.subjectvisit\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "dffbg[dffbg.fbg_value<=3.0][[\"subject_identifier\", \"visit_code\", \"fbg_value\"]]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "dfglu = get_crf(\"meta_subject.glucose\", subject_visit_model=\"meta_subject.subjectvisit\")\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "dfglu.fbg_value.describe()\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "10",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df_appt = get_appointment_df()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "11",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df_appt"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "12",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "dffbg.visit_code.value_counts()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "13",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "dfglu.visit_code.value_counts()\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "14",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df = df_appt.merge(dffbg[[\"subject_identifier\", \"visit_code\", \"fbg_value\"]], on=[\"subject_identifier\", \"visit_code\"], how=\"left\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "15",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df[df.visit_code==1005.0].appt_status.value_counts()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "16",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df[(df.visit_code==1005.0) & (df.fbg_value.isna())].appt_status.value_counts()\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "17",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from datetime import datetime\n",
+    "\n",
+    "df[(df.visit_code==1005.0) & (df.fbg_value.isna()) & (df.appt_datetime<=pd.to_datetime(datetime(2024,3,4)))].appt_status.value_counts()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "18",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "missed_subjects = [\n",
+    "    \"105-60-0164-5\",\n",
+    "    \"105-20-0384-3\",\n",
+    "    \"105-60-0196-7\",\n",
+    "    \"105-60-0157-9\",\n",
+    "    \"105-40-0324-7\",\n",
+    "    \"105-30-0118-4\",\n",
+    "]\n",
+    "\n",
+    "df[(df.visit_code==1005.0) & (df.fbg_value.isna()) & (df.appt_datetime<=pd.to_datetime(datetime(2024,3,4)))].subject_identifier"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "19",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df[(df.visit_code==1005.0) & (df.fbg_value.isna()) & (df.appt_datetime<=pd.to_datetime(datetime(2024,3,4))) & (df.appt_timing) ][[\"subject_identifier\", \"appt_timing\", \"appt_status\", \"visit_code\"]]\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "20",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df_appt[df_appt.subject_identifier==\"105-60-0157-9\"]"
+   ]
+  },
+  {
+   "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/utils.py

@@ -0,0 +1,81 @@
+import pandas as pd
+from great_tables import GT, html, loc, style
+
+
+def df_as_great_table(
+    df_table: pd.DataFrame,
+    title=None,
+    subtitle=None,
+):
+    """Used by monitoring report"""
+    return (
+        GT(df_table)
+        .tab_header(title=html(f'<div class="table-header">{title}</div>'), subtitle=subtitle)
+        .cols_align(align="left", columns=[0, 1])
+        .cols_align(align="right", columns=list(range(2, len(df_table.columns))))
+        .opt_stylize(style=3)
+        .opt_row_striping(row_striping=True)
+        .opt_vertical_padding(scale=1.2)
+        .opt_horizontal_padding(scale=1.0)
+        .tab_options(
+            table_width="100%",
+            stub_background_color="snow",
+            row_group_border_bottom_style="hidden",
+            row_group_padding=0.5,
+            row_group_background_color="snow",
+            table_background_color="snow",
+            table_font_size=10,
+        )
+        .tab_style(
+            style=[style.fill(color="snow"), style.text(color="black")],
+            locations=loc.body(
+                columns=list(range(0, len(df_table.columns))),
+                rows=list(range(0, len(df_table))),
+            ),
+        )
+        .tab_style(
+            style=[style.fill(color="lightgray"), style.text(color="black")],
+            locations=loc.body(
+                columns=[0],
+                rows=list(range(0, len(df_table))),
+            ),
+        )
+    )
+
+
+def df_as_great_table2(
+    df_table: pd.DataFrame,
+    title=None,
+    subtitle=None,
+    rowname_col: str | None = None,
+    groupname_col: str | None = None,
+):
+    """Used by monitoring report"""
+    rowname_col = rowname_col or "label"
+    groupname_col = groupname_col or "visit_code"
+    return (
+        GT(df_table, rowname_col=rowname_col, groupname_col=groupname_col)
+        .tab_header(title=html(f'<div class="table-header">{title}</div>'), subtitle=subtitle)
+        .cols_align(align="left", columns=[0, 1])
+        .cols_align(align="right", columns=list(range(2, len(df_table.columns))))
+        .opt_stylize(style=3)
+        .opt_row_striping(row_striping=True)
+        .opt_vertical_padding(scale=1.2)
+        .opt_horizontal_padding(scale=1.0)
+        .tab_options(
+            table_width="100%",
+            stub_background_color="snow",
+            row_group_border_bottom_style="hidden",
+            row_group_padding=0.5,
+            row_group_background_color="snow",
+            table_background_color="snow",
+            table_font_size=10,
+        )
+        .tab_style(
+            style=[style.fill(color="snow"), style.text(color="black")],
+            locations=loc.body(
+                columns=list(range(0, len(df_table.columns))),
+                rows=list(range(0, len(df_table))),
+            ),
+        )
+    )

meta_edc/settings/debug.py

@@ -11,8 +11,9 @@ print(f"Settings file {__file__}")
 # SITE_ID = SiteID(default=10)  # Hindu Mandal
 # SITE_ID = SiteID(default=40)  # Mwananyamala
 # SITE_ID = SiteID(default=50)  # Mbagala
-SITE_ID = SiteID(default=60)  # Mnazi-Moja
-# SITE_ID = SiteID(default=30)  # Temeke
+# SITE_ID = SiteID(default=60)  # Mnazi-Moja
+SITE_ID = SiteID(default=30)  # Temeke
+
 INDEX_PAGE = "http://localhost:8000"
 EDC_SITES_UAT_DOMAIN = False
 DEBUG = True

meta_edc/urls.py

@@ -51,6 +51,7 @@ urlpatterns = [
     *paths_for_urlpatterns("edc_protocol_incident"),
     *paths_for_urlpatterns("edc_qol"),
     *paths_for_urlpatterns("edc_randomization"),
+    *paths_for_urlpatterns("edc_reportable"),
     *paths_for_urlpatterns("edc_refusal"),
     *paths_for_urlpatterns("edc_registration"),
     *paths_for_urlpatterns("edc_review_dashboard"),

{meta_edc-1.0.6.dist-info → meta_edc-1.1.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: meta-edc
-Version: 1.0.6
+Version: 1.1.0
 Summary: META Trial EDC (http://www.isrctn.com/ISRCTN76157257)
 Home-page: https://github.com/meta-trial/meta-edc
 Author: Erik van Widenfelt
@@ -683,7 +683,7 @@ License:                     GNU GENERAL PUBLIC LICENSE
 Keywords: django,clinicedc,META EDC,EDC,clinical trials
 Classifier: Environment :: Web Environment
 Classifier: Framework :: Django
-Classifier: Framework :: Django :: 5.1
+Classifier: Framework :: Django :: 5.2
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
@@ -692,12 +692,13 @@ Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Requires-Python: >=3.12
 Description-Content-Type: text/x-rst
 License-File: LICENSE
-License-File: AUTHORS
-Requires-Dist: edc==1.0.9
+License-File: AUTHORS.rst
+Requires-Dist: edc==1.1.0
 Requires-Dist: edc-microscopy
 Requires-Dist: beautifulsoup4
 Requires-Dist: celery[redis]
 Requires-Dist: django-pylabels
+Dynamic: license-file
 
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