diff --git a/notebooks/radis_api.ipynb b/notebooks/radis_api.ipynb index 13f1315d..2c1b8402 100644 --- a/notebooks/radis_api.ipynb +++ b/notebooks/radis_api.ipynb @@ -2,62 +2,31 @@ "cells": [ { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ + "import os\n", "from datetime import date, datetime\n", "\n", "import requests\n", + "from dotenv import load_dotenv\n", "from IPython.display import display\n", "\n", + "load_dotenv(\"../.env.dev\")\n", + "\n", "base_url = \"http://localhost:8000/api/\"\n", "\n", - "document_id = \"gepacs_3dfidii5858-6633i4-ii398841\"\n", - "auth_token = \"f2e7412ca332a85e37f3fce88c6a1904fe35ad63\"" + "token = os.environ[\"ADMIN_AUTH_TOKEN\"]\n", + "\n", + "document_id = \"gepacs_3dfidii5858-6633i4-ii398841\"" ] }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Status Code: 201\n" - ] - }, - { - "data": { - "text/plain": [ - "{'id': 1003,\n", - " 'language': 'en',\n", - " 'metadata': {'study_instance_uid': '34343-34343-34343',\n", - " 'accession_number': '345348389',\n", - " 'series_instance_uid': '34343-676556-3343',\n", - " 'sop_instance_uid': '35858-384834-3843'},\n", - " 'modalities': ['CT', 'PET'],\n", - " 'document_id': 'gepacs_3dfidii5858-6633i4-ii398841',\n", - " 'pacs_aet': 'gepacs',\n", - " 'pacs_name': 'GE PACS',\n", - " 'pacs_link': 'http://gepacs.com/34343-34343-34343',\n", - " 'patient_id': '1234578',\n", - " 'patient_birth_date': '1976-05-23',\n", - " 'patient_sex': 'M',\n", - " 'study_description': 'CT of the Thorax',\n", - " 'study_datetime': '2000-08-10T00:00:00+00:53',\n", - " 'body': 'This is the report',\n", - " 'created_at': '2024-04-11T11:01:51.472801+02:00',\n", - " 'updated_at': '2024-04-11T11:01:51.472808+02:00',\n", - " 'groups': [2]}" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], + "outputs": [], "source": [ "# Create a new report\n", "\n", @@ -84,7 +53,7 @@ "}\n", "\n", "response = requests.post(\n", - " base_url + \"reports/\", json=data, headers={\"Authorization\": f\"Token {auth_token}\"}\n", + " base_url + \"reports/\", json=data, headers={\"Authorization\": f\"Token {token}\"}\n", ")\n", "\n", "print(f\"Status Code: {response.status_code}\")\n", @@ -93,39 +62,9 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "{'id': 1003,\n", - " 'language': 'en',\n", - " 'metadata': {'study_instance_uid': '34343-34343-34343',\n", - " 'accession_number': '345348389',\n", - " 'series_instance_uid': '34343-676556-3343',\n", - " 'sop_instance_uid': '35858-384834-3843'},\n", - " 'modalities': ['CT', 'PET'],\n", - " 'document_id': 'gepacs_3dfidii5858-6633i4-ii398841',\n", - " 'pacs_aet': 'gepacs',\n", - " 'pacs_name': 'GE PACS',\n", - " 'pacs_link': 'http://gepacs.com/34343-34343-34343',\n", - " 'patient_id': '1234578',\n", - " 'patient_birth_date': '1976-05-23',\n", - " 'patient_sex': 'M',\n", - " 'study_description': 'CT of the Thorax',\n", - " 'study_datetime': '2000-08-10T00:00:00+00:53',\n", - " 'body': 'This is the updated report',\n", - " 'created_at': '2024-04-11T11:01:51.472801+02:00',\n", - " 'updated_at': '2024-04-11T11:01:51.472808+02:00',\n", - " 'groups': [2]}" - ] - }, - "execution_count": 12, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "# Update an existing report\n", "\n", @@ -154,7 +93,7 @@ "response = requests.put(\n", " base_url + f\"reports/{document_id}/\",\n", " json=data,\n", - " headers={\"Authorization\": f\"Token {auth_token}\"},\n", + " headers={\"Authorization\": f\"Token {token}\"},\n", " params={\"upsert\": False},\n", ")\n", "\n", @@ -163,45 +102,15 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "{'id': 1003,\n", - " 'language': 'en',\n", - " 'metadata': {'study_instance_uid': '34343-34343-34343',\n", - " 'accession_number': '345348389',\n", - " 'series_instance_uid': '34343-676556-3343',\n", - " 'sop_instance_uid': '35858-384834-3843'},\n", - " 'modalities': ['CT', 'PET'],\n", - " 'document_id': 'gepacs_3dfidii5858-6633i4-ii398841',\n", - " 'pacs_aet': 'gepacs',\n", - " 'pacs_name': 'GE PACS',\n", - " 'pacs_link': 'http://gepacs.com/34343-34343-34343',\n", - " 'patient_id': '1234578',\n", - " 'patient_birth_date': '1976-05-23',\n", - " 'patient_sex': 'M',\n", - " 'study_description': 'CT of the Thorax',\n", - " 'study_datetime': '2000-08-10T01:07:00+02:00',\n", - " 'body': 'This is the report',\n", - " 'created_at': '2024-04-11T11:01:51.472801+02:00',\n", - " 'updated_at': '2024-04-11T11:01:51.472808+02:00',\n", - " 'groups': [2]}" - ] - }, - "execution_count": 13, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "# Fetch a report (without all document representations in full text search databases)\n", "\n", "response = requests.get(\n", " base_url + f\"reports/{document_id}\",\n", - " headers={\"Authorization\": f\"Token {auth_token}\"},\n", + " headers={\"Authorization\": f\"Token {token}\"},\n", ")\n", "\n", "response.json()" @@ -209,60 +118,15 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "{'id': 1003,\n", - " 'language': 'en',\n", - " 'metadata': {'study_instance_uid': '34343-34343-34343',\n", - " 'accession_number': '345348389',\n", - " 'series_instance_uid': '34343-676556-3343',\n", - " 'sop_instance_uid': '35858-384834-3843'},\n", - " 'modalities': ['CT', 'PET'],\n", - " 'document_id': 'gepacs_3dfidii5858-6633i4-ii398841',\n", - " 'pacs_aet': 'gepacs',\n", - " 'pacs_name': 'GE PACS',\n", - " 'pacs_link': 'http://gepacs.com/34343-34343-34343',\n", - " 'patient_id': '1234578',\n", - " 'patient_birth_date': '1976-05-23',\n", - " 'patient_sex': 'M',\n", - " 'study_description': 'CT of the Thorax',\n", - " 'study_datetime': '2000-08-10T01:07:00+02:00',\n", - " 'body': 'This is the report',\n", - " 'created_at': '2024-04-11T11:01:51.472801+02:00',\n", - " 'updated_at': '2024-04-11T11:01:51.472808+02:00',\n", - " 'groups': [2],\n", - " 'documents': {'vespa': {'pathId': '/document/v1/report/report/docid/gepacs_3dfidii5858-6633i4-ii398841',\n", - " 'id': 'id:report:report::gepacs_3dfidii5858-6633i4-ii398841',\n", - " 'fields': {'pacs_name': 'GE PACS',\n", - " 'modalities': ['CT', 'PET'],\n", - " 'document_id': 'gepacs_3dfidii5858-6633i4-ii398841',\n", - " 'language': 'en',\n", - " 'pacs_link': 'http://gepacs.com/34343-34343-34343',\n", - " 'patient_birth_date': 201657600,\n", - " 'body': 'This is the report',\n", - " 'patient_sex': 'M',\n", - " 'study_description': 'CT of the Thorax',\n", - " 'groups': [2],\n", - " 'patient_age': 24,\n", - " 'pacs_aet': 'gepacs',\n", - " 'study_datetime': 965862420}}}}" - ] - }, - "execution_count": 14, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "# Fetch a report with all document representations in full text search databases\n", "\n", "response = requests.get(\n", " base_url + f\"reports/{document_id}\",\n", - " headers={\"Authorization\": f\"Token {auth_token}\"},\n", + " headers={\"Authorization\": f\"Token {token}\"},\n", " params={\"full\": True},\n", ")\n", "\n", @@ -271,62 +135,24 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\n" - ] - } - ], + "outputs": [], "source": [ "# Delete a report\n", "\n", "response = requests.delete(\n", " base_url + f\"reports/{document_id}\",\n", - " headers={\"Authorization\": f\"Token {auth_token}\"},\n", + " headers={\"Authorization\": f\"Token {token}\"},\n", ")\n", "print(response)" ] }, { "cell_type": "code", - "execution_count": 16, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "{'id': 1004,\n", - " 'language': 'en',\n", - " 'metadata': {'study_instance_uid': '34343-34343-34343',\n", - " 'accession_number': '345348389',\n", - " 'series_instance_uid': '34343-676556-3343',\n", - " 'sop_instance_uid': '35858-384834-3843'},\n", - " 'modalities': ['CT', 'PET'],\n", - " 'document_id': 'gepacs_3dfidii5858-6633i4-ii398841',\n", - " 'pacs_aet': 'gepacs',\n", - " 'pacs_name': 'GE PACS',\n", - " 'pacs_link': 'http://gepacs.com/34343-34343-34343',\n", - " 'patient_id': '1234578',\n", - " 'patient_birth_date': '1976-05-23',\n", - " 'patient_sex': 'M',\n", - " 'study_description': 'CT of the Thorax',\n", - " 'study_datetime': '2000-08-10T00:00:00+00:53',\n", - " 'body': 'This is an upserted report',\n", - " 'created_at': '2024-04-11T11:01:54.724342+02:00',\n", - " 'updated_at': '2024-04-11T11:01:54.724355+02:00',\n", - " 'groups': [2]}" - ] - }, - "execution_count": 16, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "data = {\n", " \"document_id\": \"gepacs_3dfidii5858-6633i4-ii398841\",\n", @@ -353,7 +179,7 @@ "response = requests.put(\n", " base_url + f\"reports/{document_id}/\",\n", " json=data,\n", - " headers={\"Authorization\": f\"Token {auth_token}\"},\n", + " headers={\"Authorization\": f\"Token {token}\"},\n", " params={\"upsert\": True},\n", ")\n", "\n", @@ -362,21 +188,13 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\n" - ] - } - ], + "outputs": [], "source": [ "response = requests.delete(\n", " base_url + f\"reports/{document_id}\",\n", - " headers={\"Authorization\": f\"Token {auth_token}\"},\n", + " headers={\"Authorization\": f\"Token {token}\"},\n", ")\n", "print(response)" ] @@ -398,7 +216,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.2" + "version": "3.12.3" }, "orig_nbformat": 4 },