remove . at beginning of token file

FHIR-2450
ncbi · Aug 7, 2024 · f3e0f81 · f3e0f81
1 parent 7bf89e9
commit f3e0f81
Showing 1 changed file with 41 additions and 22 deletions.
diff --git a/jupyter/pilot/Notebook01_phs002921_URECA_subject_phenotype.ipynb b/jupyter/pilot/Notebook01_phs002921_URECA_subject_phenotype.ipynb
@@ -2,32 +2,21 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 7,
    "id": "d4b50729-08c1-43d2-91aa-edc93194f03a",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "====== start time: 2024-08-02 17:36:44\n",
-      "https://dbgap-api.ncbi.nlm.nih.gov/fhir-jpa-pilot1/x1/ResearchSubject?study=phs002921\n",
-      "Total patients fetched: 1035\n",
-      "Accumulative patients with observations: 1\n",
-      "Accumulative patients with observations: 2\n",
-      "Data written to patient_observations.csv\n",
-      "====== end time: 2024-08-02 17:37:18\n",
-      "===========Elapsed time: 0 minutes and 34 seconds.\n"
-     ]
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-08-07T19:32:03.428830Z",
+     "start_time": "2024-08-07T19:31:34.565851Z"
     }
-   ],
+   },
    "source": [
     "import os\n",
     "import requests\n",
     "import csv\n",
     "from datetime import datetime\n",
     "from time import sleep\n",
-    "from fhir_fetcher import fetch_all_data  # Ensure this module is available and handles paging through all records\n",
+    "from fhir_fetcher import fetch_all_data  # Ensure this module is available \n",
+    "# and handles paging through all records\n",
     "\n",
     "def fetch_patient_observations(session, fhir_base_url, patient_id):\n",
     "    qstr = f'Observation?subject=Patient/{patient_id}'\n",
@@ -64,7 +53,7 @@
     "    ###############################################################################################\n",
     "    # get the token from https://www.ncbi.nlm.nih.gov/gap/power-user-portal/.  \n",
     "    #  Scroll down and click on the \"Task Specific Token\" button to get the light-weight version of the dbGaP RAS Passport.\n",
-    "    #  Save the file into a text. In my example, it is saved to .task-specific-token_all.txt. \n",
+    "    #  Save the file into a text. In my example, it is saved to task-specific-token_all.txt. \n",
     "    ###############################################################################################\n",
     "    TST_PATH = '~/dev/fhir/task-specific-token-all.txt'  \n",
     "    fhir_base_url = \"https://dbgap-api.ncbi.nlm.nih.gov/fhir-jpa-pilot1/x1\"\n",
@@ -129,15 +118,45 @@
     "\n",
     "if __name__ == \"__main__\":\n",
     "    main()\n"
-   ]
+   ],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "====== start time: 2024-08-07 15:31:34\n",
+      "https://dbgap-api.ncbi.nlm.nih.gov/fhir-jpa-pilot1/x1/ResearchSubject?study=phs002921\n",
+      "Total patients fetched: 1035\n",
+      "Accumulative patients with observations: 1\n",
+      "Accumulative patients with observations: 2\n",
+      "Data written to patient_observations.csv\n",
+      "====== end time: 2024-08-07 15:32:03\n",
+      "===========Elapsed time: 0 minutes and 28 seconds.\n"
+     ]
+    }
+   ],
+   "execution_count": 3
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "id": "73d4fd89-d458-4f4d-8e0a-e8bb23027492",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-08-07T19:31:25.033138Z",
+     "start_time": "2024-08-07T19:31:25.029617Z"
+    }
+   },
+   "source": [],
+   "outputs": [],
+   "execution_count": 2
+  },
+  {
    "metadata": {},
+   "cell_type": "code",
    "outputs": [],
-   "source": []
+   "execution_count": null,
+   "source": "",
+   "id": "e688d9da99c28d00"
   }
  ],
  "metadata": {