meta-edc 1.1.0__py3-none-any.whl → 1.1.2__py3-none-any.whl

meta_analytics/README.rst

@@ -1,5 +1,4 @@
-
-
+pip install -U pdfkit great_tables scipy django_pandas dj_notebook
 
 import pandas as pd
 import numpy as np

meta_analytics/dataframes/glucose_endpoints/glucose_endpoints_by_date.py

@@ -304,6 +304,14 @@ class GlucoseEndpointsByDate:
         model_cls = django_apps.get_model(model)
         if self.subject_identifiers:
             model_cls.objects.filter(subject_identifier__in=self.subject_identifiers).delete()
+            df = (
+                self.endpoint_only_df[
+                    self.endpoint_only_df["subject_identifier"].isin(self.subject_identifiers)
+                ]
+                .copy()
+                .sort_values(by=["subject_identifier"])
+                .reset_index(drop=True)
+            )
         else:
             model_cls.objects.all().delete()
         created = 0

meta_analytics/notebooks/endpoints/meta_endpoints_by_date.ipynb

@@ -10,8 +10,10 @@
     "%%capture\n",
     "import os\n",
     "from pathlib import Path\n",
+    "\n",
     "import pandas as pd\n",
     "from dj_notebook import activate\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",
@@ -29,13 +31,13 @@
    "source": [
     "import numpy as np\n",
     "import io\n",
-    "import msoffcrypto\n",
+    "# import msoffcrypto\n",
     "import mempass\n",
     "\n",
     "from datetime import datetime\n",
     "from edc_appointment.constants import ONTIME_APPT, NEW_APPT, CANCELLED_APPT, MISSED_APPT\n",
     "from edc_pdutils.dataframes import get_crf, get_subject_visit\n",
-    "from tabulate import tabulate\n",
+    "# from tabulate import tabulate\n",
     "from meta_analytics.dataframes import get_glucose_fbg_ogtt_df, get_glucose_fbg_df\n",
     "from meta_analytics.dataframes import GlucoseEndpointsByDate\n",
     "from meta_analytics.dataframes import get_glucose_df\n",
@@ -78,16 +80,6 @@
    "id": "5",
    "metadata": {},
    "outputs": [],
-   "source": [
-    "cls.endpoint_only_df"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "6",
-   "metadata": {},
-   "outputs": [],
    "source": [
     "df_glu = get_glucose_df()\n",
     "df_glu.query(\"subject_identifier=='105-40-0379-1'\")\n",
@@ -100,7 +92,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -110,7 +102,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -120,7 +112,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -130,7 +122,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -140,7 +132,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -151,7 +143,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "11",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -161,7 +153,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "13",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -180,7 +172,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "13",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -218,7 +210,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -229,7 +221,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -289,7 +281,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -333,7 +325,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "18",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -345,7 +337,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "19",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -357,7 +349,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "20",
+   "id": "19",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -369,7 +361,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "21",
+   "id": "20",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -381,7 +373,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "22",
+   "id": "21",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -392,7 +384,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "23",
+   "id": "22",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -405,7 +397,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "24",
+   "id": "23",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -429,7 +421,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "25",
+   "id": "24",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -470,7 +462,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "26",
+   "id": "25",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -483,7 +475,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "27",
+   "id": "26",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -497,13 +489,13 @@
     "df['Total'] = df[['10', '20', '30', '40', '60']].sum(axis=1)\n",
     "df.fillna(0, inplace=True)\n",
     "df\n",
-    "print(tabulate(df[['label', '10', '20', '30', '40', '60', 'Total']], showindex=False, headers=\"keys\", tablefmt=\"simple_grid\"))\n"
+    "# print(tabulate(df[['label', '10', '20', '30', '40', '60', 'Total']], showindex=False, headers=\"keys\", tablefmt=\"simple_grid\"))\n"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "28",
+   "id": "27",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -513,7 +505,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "29",
+   "id": "28",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -523,7 +515,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "30",
+   "id": "29",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -533,7 +525,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "31",
+   "id": "30",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -543,7 +535,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "32",
+   "id": "31",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -553,7 +545,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "33",
+   "id": "32",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -563,7 +555,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "34",
+   "id": "33",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -573,7 +565,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "35",
+   "id": "34",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -586,7 +578,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "36",
+   "id": "35",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -598,7 +590,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "37",
+   "id": "36",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -609,7 +601,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "38",
+   "id": "37",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -621,7 +613,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "39",
+   "id": "38",
    "metadata": {},
    "outputs": [],
    "source": [