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Create wiki/website for TORCH
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‎.github/workflows/build.yml‎

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push:
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branches:
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- main
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- develop
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tags:
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- 'v*.*.*'
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pull_request:
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branches:
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- main
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- develop
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paths-ignore:
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- 'docs/**'
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schedule:
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- cron: '0 1 * * *'
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merge_group:

‎.github/workflows/docs.yml‎

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name: Docs
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on:
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push:
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branches:
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- main
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tags:
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- 'v*.*.*'
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pull_request:
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branches:
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- main
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schedule:
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- cron: '0 1 * * *'
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merge_group:
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concurrency:
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group: ${{ github.workflow }}-${{ github.event_name == 'pull_request' && github.ref || github.run_id }}
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cancel-in-progress: true
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permissions: read-all
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jobs:
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build-pages:
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runs-on: ubuntu-24.04
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steps:
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- name: Check out Git repository
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uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
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- name: Setup Node
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uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4
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with:
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node-version-file: .nvmrc
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cache: npm
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cache-dependency-path: 'docs/package-lock.json'
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- name: Build
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working-directory: docs
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env:
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DOCS_BASE: "/${{ github.event.repository.name }}/"
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run: make build
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- name: Setup Pages
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uses: actions/configure-pages@983d7736d9b0ae728b81ab479565c72886d7745b # v5
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- name: Upload artifact
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uses: actions/upload-pages-artifact@56afc609e74202658d3ffba0e8f6dda462b719fa # v3
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with:
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path: docs/.vitepress/dist
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deploy-pages:
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if: github.ref == 'refs/heads/main'
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runs-on: ubuntu-24.04
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needs: [ build-pages ]
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permissions:
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pages: write
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id-token: write
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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steps:
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@d6db90164ac5ed86f2b6aed7e0febac5b3c0c03e # v4

‎.nvmrc‎

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23.11.1

‎docs/.gitignore‎

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/node_modules/
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/.vitepress/cache
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/.vitepress/dist

‎docs/.vitepress/config.ts‎

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import {withMermaid} from "vitepress-plugin-mermaid";
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export default withMermaid({
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title: 'TORCH',
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description: 'TORCH Documentation',
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base: process.env.DOCS_BASE || '',
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lastUpdated: true,
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themeConfig: {
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siteTitle: false,
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editLink: {
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pattern: 'https://github.com/medizininformatik-initiative/torch/edit/main/docs/:path',
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text: 'Edit this page on GitHub'
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},
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socialLinks: [
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{icon: 'github', link: 'https://github.com/medizininformatik-initiative/torch'}
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],
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footer: {
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message: 'Released under the <a href="https://www.apache.org/licenses/LICENSE-2.0">Apache License 2.0</a>',
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},
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search: {
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provider: 'local'
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},
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outline: {
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level: [2, 3]
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},
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nav: [
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{text: 'Home', link: '/'}
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],
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sidebar: [
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{
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text: 'Home',
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link: '/index.md',
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activeMatch: '^/$'
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},
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{
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text: 'Getting Started',
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link: '/getting-started',
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activeMatch: '^/getting-started'
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},
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{
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text: 'Documentation',
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link: '/documentation',
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items: [
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{text: 'Configuration', link: '/configuration'},
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{text: 'API', link: '/api/api'},
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{
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text: 'CRTDL', link: '/crtdl/crtdl',
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items: [
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{text: 'Filter', link: '/crtdl/filter'},
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{text: 'Consent Key', link: '/crtdl/consent_key'}
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]
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},
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{
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text: 'Implementation', items: [
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{text: 'Implementation Overview', link: '/implementation/implementation-overview'},
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{text: 'Consent', link: '/implementation/consent'},
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{text: 'Direct Loading', link: '/implementation/direct_load'},
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{text: 'Must Have Checking', link: '/implementation/must_have'},
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{text: 'Cascading Delete', link: '/implementation/cascading_delete'}
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]
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},
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{text: 'Architecture', link: '/architecture/architecture'},
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]
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}
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]
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}
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})

‎docs/Makefile‎

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install:
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npm install
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build: install
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npm run docs:build
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.PHONY: install build

‎docs/api/api.md‎

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# API
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TORCH provides a FHIR REST API for extracting data based on the Clinical Resource Transfer Definition Language (CRTDL).
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It implements the FHIR [Asynchronous Bulk Data Request Pattern](http://hl7.org/fhir/R5/async-bulk.html).
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### Key Features of the API
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- **Asynchronous Requests**: Supports long-running data extraction tasks.
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- **FHIR Compliant**: Adheres to FHIR standards for resource representation.
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- **CRTDL Integration**: Uses CRTDL definitions to specify data extraction rules.
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### API Endpoints
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- **`/$extract-data`**: Initiates a data extraction job based on a CRTDL definition.
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- **`/status`**: Checks the status of an ongoing data extraction job.
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- **`/metadata`**: Provides metadata about the TORCH server and its capabilities.
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## TORCH REST API (based on FHIR Bulk Data Request)
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Torch implements the FHIR [Asynchronous Bulk Data Request Pattern][1].
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### $extract-data
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The $extract-data endpoint implements the kick-off request in the Async Bulk Pattern. It receives a FHIR parameters
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resource with a **_crtdl_** parameter containing a
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valueBase64Binary [CRTDL](https://github.com/medizininformatik-initiative/clinical-resource-transfer-definition-language).
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All examples are with a torch configured with **`http://localhost:8080`**.
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```sh
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scripts/create-parameters.sh src/test/resources/CRTDL/CRTDL_observation.json | curl -s 'http://localhost:8080/fhir/$extract-data' -H "Content-Type: application/fhir+json" -d @- -v
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```
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The Parameters resource created by `scripts/create-parameters.sh` look like this:
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```
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{
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"resourceType": "Parameters",
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"parameter": [
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{
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"name": "crtdl",
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"valueBase64Binary": "<Base64 encoded CRTDL>"
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}
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]
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}
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```
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Optionally patient ids can be submitted for a known cohort, bypassing the cohort selection in the CRTDL:
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```
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{
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"resourceType": "Parameters",
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"parameter": [
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{
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"name": "crtdl",
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"valueBase64Binary": "<Base64 encoded CRTDL>"
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},
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{
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"name": "patient",
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"valueString": "<Patient Id 1>"
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},
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{
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"name": "patient",
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"valueString": "<Patient Id 2>"
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}
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]
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}
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```
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#### Response - Error (e.g. unsupported search parameter)
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* HTTP Status Code of 4XX or 5XX
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#### Response - Success
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* HTTP Status Code of 202 Accepted
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* Content-Location header with the absolute URL of an endpoint for subsequent status requests (polling location)
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That location header can be used in the following status query:
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E.g. location:"/fhir/__status/1234"
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### Status Request
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Torch provides a Status Request Endpoint which can be called using the location from the extract Data Endpoint.
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```sh
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curl -s http://localhost:8080/fhir/__status/{location}
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```
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#### Response - In-Progress
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* HTTP Status Code of 202 Accepted
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#### Response - Error
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* HTTP status code of 4XX or 5XX
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* Content-Type header of application/fhir+json
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* Operation Outcome with fatal issue
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#### Response - Complete
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* HTTP status of 200 OK
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* Content-Type header of application/fhir+json
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* A body containing a JSON file describing the file links to the batched transformation results
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```sh
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curl -s 'http://localhost:8080/fhir/$extract-data' -H "Content-Type: application/fhir+json" -d '<query>'
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```
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the result is a looks something like this:
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```json
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{
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"requiresAccessToken": false,
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"output": [
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{
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"type": "Bundle",
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"url": "http://localhost:8080/da4a1c56-f5d9-468c-b57a-b8186ea4fea8/6c88f0ff-0e9a-4cf7-b3c9-044c2e844cfc.ndjson"
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},
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{
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"type": "Bundle",
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"url": "http://localhost:8080/da4a1c56-f5d9-468c-b57a-b8186ea4fea8/a4dd907c-4d98-4461-9d4c-02d62fc5a88a.ndjson"
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},
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{
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"type": "Bundle",
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"url": "http://localhost:8080/da4a1c56-f5d9-468c-b57a-b8186ea4fea8/f33634bd-d51b-463c-a956-93409d96935f.ndjson"
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}
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],
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"request": "http://localhost:8080//fhir/$extract-data",
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"deleted": [],
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"transactionTime": "2024-09-05T12:30:32.711151718Z",
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"error": []
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}
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```
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[1]: <http://hl7.org/fhir/R5/async-bulk.html>

‎docs/architecture/architecture.md‎

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# Architecture
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This project uses a Spring Boot backend and a TypeScript/JavaScript frontend. The backend exposes REST APIs and
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interacts with a FHIR server. The frontend communicates with the backend via HTTP.
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## Components
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- **Spring Boot Application**: Handles business logic and API endpoints.
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- **FHIR Server**: Stores and retrieves healthcare data.
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- **Reverse Proxy (NGINX)**: Routes requests and serves static content.
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- **Frontend (TypeScript/JavaScript)**: User interface for interacting with the system.
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## Data Flow
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[Consent](../implementation/consent.md).

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