diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 9942b856..92d40265 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -2,15 +2,17 @@ name: Build on: push: + paths-ignore: + - 'docs/**' branches: - main - - develop tags: - 'v*.*.*' pull_request: branches: - main - - develop + paths-ignore: + - 'docs/**' schedule: - cron: '0 1 * * *' merge_group: diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml new file mode 100644 index 00000000..e89538f2 --- /dev/null +++ b/.github/workflows/docs.yml @@ -0,0 +1,67 @@ +name: Docs + +on: + push: + paths: + - 'docs/**' + branches: + - main + tags: + - 'v*.*.*' + pull_request: + paths: + - 'docs/**' + branches: + - main + schedule: + - cron: '0 1 * * *' + merge_group: + +concurrency: + group: ${{ github.workflow }}-${{ github.event_name == 'pull_request' && github.ref || github.run_id }} + cancel-in-progress: true + +permissions: read-all + +jobs: + build-pages: + runs-on: ubuntu-24.04 + steps: + - name: Check out Git repository + uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + + - name: Setup Node + uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4 + with: + node-version-file: .nvmrc + cache: npm + cache-dependency-path: 'docs/package-lock.json' + + - name: Build + working-directory: docs + env: + DOCS_BASE: "/${{ github.event.repository.name }}/" + run: make build + + - name: Setup Pages + uses: actions/configure-pages@983d7736d9b0ae728b81ab479565c72886d7745b # v5 + + - name: Upload artifact + uses: actions/upload-pages-artifact@56afc609e74202658d3ffba0e8f6dda462b719fa # v3 + with: + path: docs/.vitepress/dist + + deploy-pages: + runs-on: ubuntu-24.04 + needs: [ build-pages ] + permissions: + pages: write + id-token: write + environment: + name: ${{ github.ref == 'refs/heads/main' && 'github-pages' || format('preview-{0}', github.ref_name) }} + url: ${{ steps.deployment.outputs.page_url }} + steps: + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@d6db90164ac5ed86f2b6aed7e0febac5b3c0c03e # v4 + diff --git a/.nvmrc b/.nvmrc new file mode 100644 index 00000000..fc6f56e1 --- /dev/null +++ b/.nvmrc @@ -0,0 +1 @@ +23.11.1 diff --git a/README.md b/README.md index c8b015e4..19503af1 100644 --- a/README.md +++ b/README.md @@ -22,306 +22,9 @@ This request is composed of two parts: The cohort definition (for who (which patients) should data be extracted) The data extraction (what data should be extracted) -## Prerequisites +## Documentation -TORCH interacts with the following components directly: - -- a CQL ready FHIR Server like [Blaze](https://github.com/samply/blaze) **OR - ** [FLARE](https://github.com/medizininformatik-initiative/flare) -- A FHIR Server / FHIR Search API -- Reverse Proxy (NGINX) - -The reverse proxy allows for integration into a site's multi-server infrastructure and provides a means of serving -the extracted data. - -## Verification - -For container images, we use cosign to sign images. This allows users to confirm the image was built by the expected CI -pipeline and has not been modified after publication. -``` -cosign verify "ghcr.io/medizininformatik-initiative/torch:v1.0.0" \ ---certificate-identity-regexp "https://github.com/medizininformatik-initiative/torch.*" \ ---certificate-oidc-issuer "https://token.actions.githubusercontent.com" \ ---certificate-github-workflow-ref="refs/tags/v1.0.0" \ --o text -``` -The expected output is: -``` -Verification for ghcr.io/medizininformatik-initiative/torch:v1.0.0 -- -The following checks were performed on each of these signatures: -- The cosign claims were validated -- Existence of the claims in the transparency log was verified offline -- The code-signing certificate was verified using trusted certificate authority certificates -``` -This output ensures that the image was build on the GitHub workflow on the repository -`medizininformatik-initiative/torch` and tag `v1.0.0`. - -### Cohort Selection - -TORCH supports CQL or FHIR Search for the cohort selection part. - -If your FHIR server does not support CQL itself then the FLARE component must be used to extract the -cohort based on the cohort definition of the **CRTDL**. - -The cohort evaluation strategy can be set using the TORCH_USE_CQL setting in -the [enviroment variables](#environment-variables) - -## Container version - -For simplicity torch is integrated in -the [feasibility-triangle](https://github.com/medizininformatik-initiative/feasibility-deploy/tree/main/feasibility-triangle) -of the feasibility-deploy repository, but can also be installed without it. - -For the latest build see: https://github.com/medizininformatik-initiative/torch/pkgs/container/torch - -## Environment Variables - -| Name | Default | Description | -|:----------------------------------------------------|:------------------------------------|:-----------------------------------------------------------------------------------------------------| -| SERVER_PORT | 8080 | The Port of the server to use | -| TORCH_PROFILE_DIR | structureDefinitions | The directory for profile definitions. | -| TORCH_MAPPING_CONSENT | mappings/consent-mappings_fhir.json | The file for consent mappings in FHIR format. | -| TORCH_MAPPING_TYPE_TO_CONSENT | mappings/type_to_consent.json | The file mapping Resource Types to time fields against which the consent is checked | -| TORCH_FHIR_USER | – | The FHIR server user. | -| TORCH_FHIR_PASSWORD | – | The FHIR server password. | -| TORCH_FHIR_OAUTH_ISSUER_URI | – | The URI for the OAuth issuer. | -| TORCH_FHIR_OAUTH_CLIENT_ID | – | The client ID for OAuth. | -| TORCH_FHIR_OAUTH_CLIENT_SECRET | – | The client secret for OAuth. | -| TORCH_FHIR_URL | – | The base URL of the FHIR server to use. | -| TORCH_FHIR_MAX_CONNECTIONS | 5 | The maximum number of concurrent connections to use - has to be (TORCH_MAXCONCURRENCY + 1) | -| TORCH_FHIR_PAGE_COUNT | 500 | The number of pages in a FHIR search response. | -| TORCH_FHIR_DISABLE_ASYNC | false | Set to `true` in order to disable use of [Asynchronous Interaction Request Pattern][5]. | -| TORCH_FLARE_URL | – | The base URL of the FLARE server to use. | -| TORCH_RESULTS_DIR | output/ | The directory for storing results. | -| TORCH_RESULTS_PERSISTENCE | PT2160H | Time Block for result persistence in ISO 8601
format in hours/minutes/seconds. Default 90 days | -| TORCH_BATCHSIZE | 500 | The batch size used for processing data. | -| TORCH_MAXCONCURRENCY | 4 | The maximum concurrency level for processing. | -| TORCH_MAPPINGS_FILE | ontology/mapping_cql.json | The file for ontology mappings using CQL. | -| TORCH_BUFFERSIZE | 100 | Size in MB of the webclientbuffer that interacts with the FHIR server | -| TORCH_CONCEPT_TREE_FILE | ontology/mapping_tree.json | The file for the concept tree mapping. | -| TORCH_DSE_MAPPING_TREE_FILE | ontology/dse_mapping_tree.json | The file for DSE concept tree mapping. | -| TORCH_USE_CQL | true | Flag indicating if CQL should be used. | -| TORCH_BASE_URL | – | The server name before the proxy from which torch is accessed | -| TORCH_OUTPUT_FILE_SERVER_URL | – | The URL to access Result location TORCH_RESULTS_DIR served by a proxy/fileserver | -| LOG_LEVEL
_DE_MEDIZININFORMATIKINITIATIVE_TORCH | info | Log level for torch core functionality. | -| LOG_LEVEL
_CA_UHN_FHIR | error | Log level for HAPI FHIR library. | -| SPRING_PROFILES_ACTIVE | active | The active Spring profile. | -| SPRING_CODEC_MAX_IN_MEMORY_SIZE | 100MB | The maximum in-memory size for Spring codecs. | - -## TORCH REST API (based on FHIR Bulk Data Request) - -Torch implements the FHIR [Asynchronous Bulk Data Request Pattern][2]. - -### $extract-data - -The $extract-data endpoint implements the kick-off request in the Async Bulk Pattern. It receives a FHIR parameters -resource with a **_crtdl_** parameter containing a -valueBase64Binary [CRTDL](https://github.com/medizininformatik-initiative/clinical-resource-transfer-definition-language). -All examples are with a torch configured with **http://localhost:8086**. - -```sh -scripts/create-parameters.sh src/test/resources/CRTDL/CRTDL_observation.json | curl -s 'http://localhost:8086/fhir/$extract-data' -H "Content-Type: application/fhir+json" -d @- -v -``` - -The Parameters resource created by `scripts/create-parameters.sh` look like this: - -``` -{ - "resourceType": "Parameters", - "parameter": [ - { - "name": "crtdl", - "valueBase64Binary": "" - } - ] -} -``` - -Optionally patient ids can be submitted for a known cohort, bypassing the cohort selection in the CRTDL: - -``` -{ - "resourceType": "Parameters", - "parameter": [ - { - "name": "crtdl", - "valueBase64Binary": "" - }, - { - "name": "patient", - "valueString": "" - }, - { - "name": "patient", - "valueString": "" - } - ] -} -``` - -#### Response - Error (e.g. unsupported search parameter) - -* HTTP Status Code of 4XX or 5XX - -#### Response - Success - -* HTTP Status Code of 202 Accepted -* Content-Location header with the absolute URL of an endpoint for subsequent status requests (polling location) - -That location header can be used in the following status query: -E.g. location:"/fhir/__status/1234" - -### Status Request - -Torch provides a Status Request Endpoint which can be called using the location from the extract Data Endpoint. - -```sh -curl -s http://localhost:8080/fhir/__status/{location} -``` - -#### Response - In-Progress - -* HTTP Status Code of 202 Accepted - -#### Response - Error - -* HTTP status code of 4XX or 5XX -* Content-Type header of application/fhir+json -* Operation Outcome with fatal issue - -#### Response - Complete - -* HTTP status of 200 OK -* Content-Type header of application/fhir+json -* A body containing a JSON file describing the file links to the batched transformation results - -```sh -curl -s 'http://localhost:8080/fhir/$extract-data' -H "Content-Type: application/fhir+json" -d '' -``` - -the result is a looks something like this: - -```json -{ - "requiresAccessToken": false, - "output": [ - { - "type": "Bundle", - "url": "http://localhost:8080/da4a1c56-f5d9-468c-b57a-b8186ea4fea8/6c88f0ff-0e9a-4cf7-b3c9-044c2e844cfc.ndjson" - }, - { - "type": "Bundle", - "url": "http://localhost:8080/da4a1c56-f5d9-468c-b57a-b8186ea4fea8/a4dd907c-4d98-4461-9d4c-02d62fc5a88a.ndjson" - }, - { - "type": "Bundle", - "url": "http://localhost:8080/da4a1c56-f5d9-468c-b57a-b8186ea4fea8/f33634bd-d51b-463c-a956-93409d96935f.ndjson" - } - ], - "request": "http://localhost:8080//fhir/$extract-data", - "deleted": [], - "transactionTime": "2024-09-05T12:30:32.711151718Z", - "error": [] -} - -``` - -## Output Files - -After [Response Complete](#response---complete) is returned the result files in ndjson format -are located in Output directory set in [enviroment variables](#environment-variables). -In the case of error an error.json can be found in the Output directory detailing the fatal error. - -Note that each patient batch is written to the output directory and the files are written before the process completes. -This can be used to track the progress of your data extraction. - -#### Download Data - -If a server is set up for the files e.g. NGINX, the files can be fetched by a Request on the URL set in -TORCH_OUTPUT_FILE_SERVER_URL in [enviroment variables](#environment-variables). - -```sh -curl -s "http://localhost:8080/da4a1c56-f5d9-468c-b57a-b8186ea4fea8/f33634bd-d51b-463c-a956-93409d96935f.ndjson" -``` - -### NDJSON: Result Bundles - -The ndjson will contain one **transaction bundle** per Patient. - -### Global Status Request - -Torch provides a Status Request Endpoint which provides a overview extract Data Endpoint. - -```sh -curl -s http://localhost:8080/fhir/__status/ -``` - -### Masked Fields - -Required fields that were not extracted and slices that are unknown in the Structure Definition are set to Data Absent -Reason "masked". - -For example a CRTDL only extracting Condition.onset will result in this: - -```json -{ - "resourceType": "Condition", - "id": "TestID", - "meta": { - "profile": [ - "https://www.medizininformatik-initiative.de/fhir/core/modul-diagnose/StructureDefinition/Diagnose" - ] - }, - "code": { - "extension": [ - { - "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", - "valueCode": "masked" - } - ] - }, - "subject": { - "extension": [ - { - "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", - "valueCode": "masked" - } - ] - }, - "onsetDateTime": "2024-10" -} -``` - -## Transfer Script - -TORCH provides a companion **transfer script** designed to automate the workflow of submitting a data extraction -request, polling the status, and transferring the resulting files to a target FHIR server. - -The transfer script will: - -1. Take the **CRTDL** and generate a FHIR parameters resource to send to TORCH. -2. Execute $extract-data operation on the TORCH server using parameters resource as input. -3. Poll the TORCH status endpoint until the export is complete. -4. Download the resulting patient-oriented FHIR bundles into a temp dir. -5. Upload these files to a configured target FHIR server using the `blazectl` tool. -6. Provide progress feedback and error handling at each step. - -### Usage Example - -```bash -./transfer-extraction-to-dup-fhir-server.sh -c src/test/resources/CRTDL/CRTDL_observation.json -t http://target-fhir-server:8080/fhir -``` - -### Environment Variables - -The transfer script respects several environment variables to configure server URLs, directories, retry counts, and -timing: - -| Variable | Default | Description | -|----------------|-----------------------|-----------------------------------------------------| -| TORCH_BASE_URL | http://localhost:8080 | Base URL of the TORCH server | -| MAX_RETRIES | 60 | Number of status polling attempts before timing out | -| SLEEP_SECONDS | 5 | Seconds to wait between polling attempts | +Documentation can be found [here](https://medizininformatik-initiative.github.io/torch/). ## Supported Features @@ -339,6 +42,7 @@ timing: - Auto Extracting modifiers - Black or Whitelisting of certain ElementIDs locally - Validating against Profiles +- Value Set based Slicing ## License diff --git a/docs/.gitignore b/docs/.gitignore new file mode 100644 index 00000000..9d329a87 --- /dev/null +++ b/docs/.gitignore @@ -0,0 +1,3 @@ +/node_modules/ +/.vitepress/cache +/.vitepress/dist diff --git a/docs/.vitepress/config.ts b/docs/.vitepress/config.ts new file mode 100644 index 00000000..95f30b52 --- /dev/null +++ b/docs/.vitepress/config.ts @@ -0,0 +1,85 @@ +import {withMermaid} from "vitepress-plugin-mermaid"; + +export default withMermaid({ + title: 'TORCH', + description: 'TORCH Documentation', + base: process.env.DOCS_BASE || '', + appearance: true, + lastUpdated: true, + themeConfig: { + siteTitle: false, + + editLink: { + pattern: 'https://github.com/medizininformatik-initiative/torch/edit/main/docs/:path', + text: 'Edit this page on GitHub' + }, + + socialLinks: [ + {icon: 'github', link: 'https://github.com/medizininformatik-initiative/torch'} + ], + + footer: { + message: 'Released under the Apache License 2.0', + }, + + search: { + provider: 'local' + }, + + outline: { + level: [2, 3] + }, + + nav: [ + {text: 'Home', link: '/'} + ], + + sidebar: [ + { + text: 'Home', + link: '/index.md', + activeMatch: '^/$' + }, + { + text: 'Overview', + link: '/overview.md', + activeMatch: '^/$' + }, + { + text: 'Getting Started', + link: '/getting-started', + activeMatch: '^/getting-started' + }, + { + text: 'Documentation', + link: '/documentation', + items: [ + {text: 'Configuration', link: '/configuration'}, + {text: 'API', link: '/api/api'}, + { + text: 'CRTDL', link: '/crtdl/crtdl', + items: [ + {text: 'Filter', link: '/crtdl/filter'}, + {text: 'Consent Key', link: '/crtdl/consent-key'} + ] + + }, + { + text: 'Implementation', + link: '/implementation/implementation-overview', + items: [ + {text: 'Consent', link: '/implementation/consent'}, + {text: 'Direct Loading', link: '/implementation/direct-load'}, + {text: 'Must Have Checking', link: '/implementation/must-have'}, + {text: 'Cascading Delete', link: '/implementation/cascading-delete'}, + {text: 'Reference Resolve', link: '/implementation/reference-resolve'}, + {text: 'Redaction', link: '/implementation/redaction'}, + {text: 'Data Extraction', link: '/implementation/data-extraction'} + ] + } + + ] + } + ] + } +}) diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 00000000..ddb9254f --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,7 @@ +install: + npm install + +build: install + npm run docs:build + +.PHONY: install build diff --git a/docs/api/api.md b/docs/api/api.md new file mode 100644 index 00000000..4b5bed57 --- /dev/null +++ b/docs/api/api.md @@ -0,0 +1,136 @@ +# API + +TORCH provides a FHIR REST API for extracting data based on the Clinical Resource Transfer Definition Language (CRTDL). +It implements the FHIR [Asynchronous Bulk Data Request Pattern](http://hl7.org/fhir/R5/async-bulk.html). + +### Key Features of the API + +- **Asynchronous Requests**: Supports long-running data extraction tasks. +- **FHIR Compliant**: Adheres to FHIR standards for resource representation. +- **CRTDL Integration**: Uses CRTDL definitions to specify data extraction rules. + +### API Endpoints + +- **`/$extract-data`**: Initiates a data extraction job based on a CRTDL definition. +- **`/__status`**: Checks the status of an ongoing data extraction job. +- **`/metadata`**: Provides metadata about the TORCH server and its capabilities. + +## TORCH REST API (based on FHIR Bulk Data Request) + +Torch implements the FHIR [Asynchronous Bulk Data Request Pattern][1]. + +### $extract-data + +The $extract-data endpoint implements the kick-off request in the Async Bulk Pattern. It receives a FHIR parameters +resource with a **_crtdl_** parameter containing a +valueBase64Binary [CRTDL](https://github.com/medizininformatik-initiative/clinical-resource-transfer-definition-language). +All examples are with a torch configured with **`http://localhost:8080`**. + +```sh +scripts/create-parameters.sh src/test/resources/CRTDL/CRTDL_observation.json | curl -s 'http://localhost:8080/fhir/$extract-data' -H "Content-Type: application/fhir+json" -d @- -v +``` + +The Parameters resource created by `scripts/create-parameters.sh` look like this: + +``` +{ + "resourceType": "Parameters", + "parameter": [ + { + "name": "crtdl", + "valueBase64Binary": "" + } + ] +} +``` + +Optionally patient ids can be submitted for a known cohort, bypassing the cohort selection in the CRTDL: + +``` +{ + "resourceType": "Parameters", + "parameter": [ + { + "name": "crtdl", + "valueBase64Binary": "" + }, + { + "name": "patient", + "valueString": "" + }, + { + "name": "patient", + "valueString": "" + } + ] +} +``` + +#### Response - Error (e.g. unsupported search parameter) + +* HTTP Status Code of 4XX or 5XX + +#### Response - Success + +* HTTP Status Code of 202 Accepted +* Content-Location header with the absolute URL of an endpoint for subsequent status requests (polling location) + +That location header can be used in the following status query: +E.g. location:"/fhir/__status/1234" + +### Status Request + +Torch provides a Status Request Endpoint which can be called using the location from the extract Data Endpoint. + +```sh +curl -s http://localhost:8080/fhir/__status/{location} +``` + +#### Response - In-Progress + +* HTTP Status Code of 202 Accepted + +#### Response - Error + +* HTTP status code of 4XX or 5XX +* Content-Type header of application/fhir+json +* Operation Outcome with fatal issue + +#### Response - Complete + +* HTTP status of 200 OK +* Content-Type header of application/fhir+json +* A body containing a JSON file describing the file links to the batched transformation results + +```sh +curl -s 'http://localhost:8080/fhir/$extract-data' -H "Content-Type: application/fhir+json" -d '' +``` + +the result is a looks something like this: + +```json +{ + "requiresAccessToken": false, + "output": [ + { + "type": "Bundle", + "url": "http://localhost:8080/da4a1c56-f5d9-468c-b57a-b8186ea4fea8/6c88f0ff-0e9a-4cf7-b3c9-044c2e844cfc.ndjson" + }, + { + "type": "Bundle", + "url": "http://localhost:8080/da4a1c56-f5d9-468c-b57a-b8186ea4fea8/a4dd907c-4d98-4461-9d4c-02d62fc5a88a.ndjson" + }, + { + "type": "Bundle", + "url": "http://localhost:8080/da4a1c56-f5d9-468c-b57a-b8186ea4fea8/f33634bd-d51b-463c-a956-93409d96935f.ndjson" + } + ], + "request": "http://localhost:8080//fhir/$extract-data", + "deleted": [], + "transactionTime": "2024-09-05T12:30:32.711151718Z", + "error": [] +} + +``` + +[1]: diff --git a/docs/configuration.md b/docs/configuration.md new file mode 100644 index 00000000..ed097a76 --- /dev/null +++ b/docs/configuration.md @@ -0,0 +1,250 @@ +# Configuration + +Torch is configured using environment variables that control its behavior and integration with a FHIR server. This allows +for flexible deployment and customization based on the specific requirements of your environment. + +## Configuration Overview + +This document provides an overview of the environment variables used to configure TORCH, including their default values +and descriptions. +These variables can be set in the application.yml file or as system environment variables when running the application. + +When running TORCH as a container, it is recommended to set these variables or pass them as environment variables during container startup. +## Backend + +### Environment Variables + +#### `SERVER_PORT` + +The port on which the server listens for incoming connections. +If running a container it is the port inside the container. + +**Default:** `8080` + +--- + +#### `TORCH_PROFILE_DIR` + +The directory path where profile definitions are stored. + +**Default:** `structureDefinitions` + +--- + +#### `TORCH_MAPPING_CONSENT` + +Path to the JSON file containing consent mappings formatted for FHIR. + +**Default:** `mappings/consent-mappings_fhir.json` + +--- + +#### `TORCH_MAPPING_TYPE_TO_CONSENT` + +File that maps FHIR Resource Types to their associated time fields used to check consent validity. + +**Default:** `mappings/type_to_consent.json` + +--- + +#### `TORCH_FHIR_USER` + +The username used for authentication with the FHIR server. + +**Default:** – (none) + +--- + +#### `TORCH_FHIR_PASSWORD` + +The password used for authentication with the FHIR server. + +**Default:** – (none) + +--- + +#### `TORCH_FHIR_OAUTH_ISSUER_URI` + +The URI of the OAuth issuer used for OAuth authentication. + +**Default:** – (none) + +--- + +#### `TORCH_FHIR_OAUTH_CLIENT_ID` + +Client ID used for OAuth authentication. + +**Default:** – (none) + +--- + +#### `TORCH_FHIR_OAUTH_CLIENT_SECRET` + +Client secret used for OAuth authentication. + +**Default:** – (none) + +--- + +#### `TORCH_FHIR_URL` + +Base URL of the FHIR server that TORCH connects to. + +**Default:** – (none) + +--- + +#### `TORCH_FHIR_MAX_CONNECTIONS` + +Maximum number of concurrent connections allowed to the FHIR server. Must be equal to `TORCH_MAXCONCURRENCY + 1`. + +**Default:** `5` + +--- + +#### `TORCH_FHIR_PAGE_COUNT` + +Number of entries per page in FHIR search responses. + +**Default:** `500` + +--- + +#### `TORCH_FHIR_DISABLE_ASYNC` + +Set to `true` to disable the use of the Asynchronous Interaction Request Pattern for FHIR operations. + +**Default:** `false` + +--- + +#### `TORCH_FLARE_URL` + +Base URL of the FLARE server used in the pipeline. + +**Default:** – (none) + +--- + +#### `TORCH_RESULTS_DIR` + +Directory path where results are stored. + +**Default:** `output/` + +--- + +#### `TORCH_RESULTS_PERSISTENCE` + +ISO 8601 duration indicating how long result files are persisted (e.g., `PT2160H` means 90 days). + +**Default:** `PT2160H` + +--- + +#### `TORCH_BATCHSIZE` + +Size of data batches processed at once. + +**Default:** `500` + +--- + +#### `TORCH_MAXCONCURRENCY` + +Maximum level of concurrency for data processing operations. + +**Default:** `4` + +--- + +#### `TORCH_MAPPINGS_FILE` + +Path to the file containing ontology mappings defined using Clinical Quality Language (CQL). + +**Default:** `ontology/mapping_cql.json` + +--- + +#### `TORCH_BUFFERSIZE` + +Size (in MB) of the buffer used by the web client interacting with the FHIR server. + +**Default:** `100` + +--- + +#### `TORCH_CONCEPT_TREE_FILE` + +File containing the concept tree mapping used for resource classification. + +**Default:** `ontology/mapping_tree.json` + +--- + +#### `TORCH_DSE_MAPPING_TREE_FILE` + +File containing the concept tree mapping specifically for DSE (Data Set Extensions). + +**Default:** `ontology/dse_mapping_tree.json` + +--- + +#### `TORCH_USE_CQL` + +Flag indicating whether to enable Clinical Quality Language (CQL) for processing. + +**Default:** `true` + +--- + +#### `TORCH_BASE_URL` + +Base server URL before any proxy, used for accessing TORCH directly. + +**Default:** – (none) + +--- + +#### `TORCH_OUTPUT_FILE_SERVER_URL` + +URL used to access the result files in `TORCH_RESULTS_DIR` via a proxy or file server. + +**Default:** – (none) + +--- + +#### `LOG_LEVEL_DE_MEDIZININFORMATIKINITIATIVE_TORCH` + +Logging level for core TORCH functionality. + +**Default:** `info` + +--- + +#### `LOG_LEVEL_CA_UHN_FHIR` + +Logging level for the HAPI FHIR library. + +**Default:** `error` + +--- + +#### `SPRING_PROFILES_ACTIVE` + +Active Spring profile used to configure the application context. + +**Default:** `active` + +--- + +#### `SPRING_CODEC_MAX_IN_MEMORY_SIZE` + +Maximum allowed in-memory size for Spring codecs when processing data. + +**Default:** `100MB` + +--- + +[5]: https://www.hl7.org/fhir/http.html#async "FHIR Asynchronous Interaction Request Pattern" diff --git a/docs/crtdl/consent-key.md b/docs/crtdl/consent-key.md new file mode 100644 index 00000000..d5c6aba0 --- /dev/null +++ b/docs/crtdl/consent-key.md @@ -0,0 +1,45 @@ +## Consent Key in CRTDL + +The consent key in the Cohort Selection of the CRTDL is used to specify the consent rules that apply +to the cohort definition and data extraction. It allows for per-patient, per-resource consent enforcement +during structured extraction. + +### Key Features + +- **Configurable** : Controlled via the `TORCH_MAPPING_CONSENT` environment variable. +- **Shipped with MII specific Consent Key Mapping**: The default consent key mapping is provided by the + MII [MII Consent Key Mapping](https://github.com/medizininformatik-initiative/torch/blob/main/mappings/consent-mappings_fhir.json). + +### Example CRTDL with Consent Key + +The following example shows how to use the consent key in a CRTDL definition. +The consent key is defined in the `inclusionCriteria` section, which specifies the conditions under which a patient is +included in the cohort. +Consent keys are indentified by the `context.code` field, which is set to **Einwilligung** (German for consent). +The key value is located as a termCode in this case with the code **yes-yes-no-yes**. + +```json +{ + "version": "http://to_be_decided.com/draft-1/schema#", + "display": "", + "inclusionCriteria": [ + [ + { + "context": { + "code": "Einwilligung", + "display": "Einwilligung", + "system": "fdpg.mii.cds", + "version": "1.0.0" + }, + "termCodes": [ + { + "code": "yes-yes-no-yes", + "display": "Verteilte, EU-DSGVO konforme Analyse, ohne Krankenassendaten, und mit Rekontaktierung", + "system": "fdpg.consent.combined" + } + ] + } + ] + ] +} + diff --git a/docs/crtdl/crtdl.md b/docs/crtdl/crtdl.md new file mode 100644 index 00000000..5cd8cb28 --- /dev/null +++ b/docs/crtdl/crtdl.md @@ -0,0 +1,195 @@ +## CRTDL + +The Clinical Resource Transfer Definition Language (CRTDL) is a JSON-based format used to define cohorts and data +extraction rules for TORCH. +It allows users to specify who to extract data for, what data to extract, and how to handle consent and masking. + +### Key Features of CRTDL + +- **Cohort Definition**: Specify the population of interest using FHIR resources and criteria. +- **Data Extraction Rules**: Define which FHIR resources and fields to extract. +- **Consent Handling**: Integrate consent rules to ensure compliance with privacy regulations. + +--- +### CRTDL Structure + +A CRTDL definition is structured as a JSON object with the following key components: + +- **`inclusion criteria`**: Defines the population of interest. +- **`data extraction`**: Specifies the FHIR resources and fields to extract. + +--- +### Cohort Selection + +The cohort selection uses +the [CCDL](https://github.com/medizininformatik-initiative/clinical-cohort-definition-language/tree/main) (Clinical Cohort +Definition Definition Language) to define the population of interest. + +TORCH supports CQL or FHIR Search for the cohort selection execution. + +If your FHIR server does not support CQL, the FLARE component must be used to extract the cohort based on the cohort definition of the CRTDL. +Alternatively you can specify a list of patient IDs which TORCH will use to extract the data. + +The cohort evaluation strategy can be set using the TORCH_USE_CQL setting in +the [enviroment variables](./../configuration.md#environment-variables). + +Torch uses the [Consent Key](consent-key.md) to enforce consent rules during the cohort selection and data extraction +process. + +--- +### Data Extraction Selection + +The data extraction object contains an array defining **attributeGroups**, which bundle attributes together. + +Each group has an identifier for the group called **groupReference**, a list of attributes to be extracted +**attributes +** and a filter object containing exactly one time filter and many code filter. The code filter contains an array of codes to be filtered (see [filters](filter.md)). + +**Every data extraction must have exactly one attribute group that describes patient attributes**. + +An attribute to be extracted contains an attribute reference **attributeRef** and information if the attribute is +required **must-have** e.g. + +```json +{ + "attributeRef": "Medication.medicationCode", + "mustHave": true + + } +``` + + +If a **must have** condition is **violated**, it will result in a complete stop of the extraction for a **patient**. + +Filters definition have a list of **FHIR search parameter operations** containing the type supported, name and corresponding parameters. Currrently **token** and **date** are supported. + + + + + +```json +{ + "version": "http://json-schema.org/to-be-done/schema#", + "display": "", + "cohortDefinition": { + "version": "http://to_be_decided.com/draft-1/schema#", + "display": "", + "inclusionCriteria": [ + [ + { + "termCodes": [ + { + "code": "424144002", + "system": "http://snomed.info/sct", + "display": "Gegenwärtiges chronologisches Alter" + } + ], + "context": { + "code": "Patient", + "system": "fdpg.mii.cds", + "version": "1.0.0", + "display": "Patient" + }, + "valueFilter": { + "type": "quantity-comparator", + "unit": { + "code": "a", + "display": "a" + }, + "value": 18, + "comparator": "gt" + } + } + ], + [ + { + "termCodes": [ + { + "code": "263495000", + "system": "http://snomed.info/sct", + "display": "Geschlecht" + } + ], + "context": { + "code": "Patient", + "system": "fdpg.mii.cds", + "version": "1.0.0", + "display": "Patient" + }, + "valueFilter": { + "selectedConcepts": [ + { + "code": "female", + "display": "Female", + "system": "http://hl7.org/fhir/administrative-gender" + } + ], + "type": "concept" + } + } + ], + [ + { + "termCodes": [ + { + "code": "8-918", + "system": "http://fhir.de/CodeSystem/bfarm/ops", + "version": "2023", + "display": "Interdisziplinäre multimodale Schmerztherapie" + } + ], + "context": { + "code": "Procedure", + "system": "fdpg.mii.cds", + "version": "1.0.0", + "display": "Prozedur" + } + } + ] + + ], + "dataExtraction": { + "attributeGroups": [ + { + "groupReference": "https://www.medizininformatik-initiative.de/fhir/core/modul-labor/StructureDefinition/ObservationLab", + "attributes": [ + { + "attributeRef": "Observation.code", + "mustHave": false + }, + { + "attributeRef": "Observation.value", + "mustHave": true + } + ], + "filter": [ + { + "type": "token", + "name": "code", + "codes": [ + { + "code": "718-7", + "system": "http://loinc.org", + "display": "Hemoglobin [Mass/volume] in Blood" + }, + { + "code": "33509-1", + "system": "http://loinc.org", + "display": "Hemoglobin [Mass/volume] in Body fluid" + } + ] + }, + { + "type": "date", + "name": "date", + "start": "2021-09-09", + "end": "2021-10-09" + } + ] + } + ] + } + } +} + +``` diff --git a/docs/crtdl/filter.md b/docs/crtdl/filter.md new file mode 100644 index 00000000..615194b8 --- /dev/null +++ b/docs/crtdl/filter.md @@ -0,0 +1,42 @@ +## Filter + +In the crtdl date and token are supported as filter types. +For all filter types the `name` responds to a FHIR Search parameter which identfies how the filter should be applied. + +### Date Filter + +The date filter allows you to specify a date range for filtering resources. +It can be used to include or exclude resources based on their date attributes. + +```json +{ + "type": "date", + "name": "dateFilter", + "parameters": { + "start": "2023-01-01", + "end": "2023-12-31" + } +} +``` + +The `start` and `end` parameters define the range of dates to filter resources only **allow** a day wise granularity. + +### Token Filter + +Token filters allow you to filter resources based on specific codes or identifiers. +This is useful for filtering resources by specific concepts, such as LOINC codes or SNOMED codes. + +```json +{ + "type": "token", + "name": "codeFilter", + "parameters": { + "system": "http://loinc.org", + "code": "12345-6" + } +} + +``` + +The `system` parameter specifies the coding system (e.g., LOINC, SNOMED), and the `code` parameter specifies the +specific code to filter by. diff --git a/docs/documentation.md b/docs/documentation.md new file mode 100644 index 00000000..ef9395c2 --- /dev/null +++ b/docs/documentation.md @@ -0,0 +1,28 @@ +# Documentation Overview + +### Configuration + +TORCH is configured using environment variables that control its behavior and integration with FHIR servers. + +👉 Visit the [**Configuration**](./configuration.md) for a detailed list of environment variables and their descriptions. + +### API + +TORCH provides a FHIR REST API for extracting data based on the CRTDL. +It implements the FHIR [Asynchronous Bulk Data Request Pattern][1].. + +👉 Visit the [**API Documentation**](./api/api.md) for details on endpoints, request/response formats, and usage +examples. + +### CRTDL + +The Clinical Resource Transfer Definition Language (CRTDL) is a JSON format used to describe cohorts and data extraction +rules. + +👉 Visit the [**CRTDL Documentation**](./crtdl/crtdl.md) for a comprehensive guide on how to create and use CRTDL +definitions. + + +[1]: + + diff --git a/docs/drawio/ResourceLoader.drawio b/docs/drawio/ResourceLoader.drawio new file mode 100644 index 00000000..8ea0c7d5 --- /dev/null +++ b/docs/drawio/ResourceLoader.drawio @@ -0,0 +1,295 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + diff --git a/docs/drawio/redaction.drawio b/docs/drawio/redaction.drawio new file mode 100644 index 00000000..596f083d --- /dev/null +++ b/docs/drawio/redaction.drawio @@ -0,0 +1,338 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/drawio/reference_resolve.drawio b/docs/drawio/reference_resolve.drawio new file mode 100644 index 00000000..452495c7 --- /dev/null +++ b/docs/drawio/reference_resolve.drawio @@ -0,0 +1,135 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/getting-started.md b/docs/getting-started.md new file mode 100644 index 00000000..6f6bc57f --- /dev/null +++ b/docs/getting-started.md @@ -0,0 +1,68 @@ +## Getting Started + +### Quickstart + +Torch can be started with a single command using docker and by providing a configuration file e.g. .env. +See [Configuration](configuration.md) for details on the configuration options. +```sh +docker run -d --name torch -p 8080:8080 ghcr.io/medizininformatik-initiative/torch:1.0.0-alpha.7 --env-file [/path/to/.env] +``` + +### Install prerequisites + +TORCH interacts with the following components: + +- a CQL ready FHIR Server like [Blaze](https://github.com/samply/blaze) + or [FLARE](https://github.com/medizininformatik-initiative/flare) for Cohort +- A FHIR Server / FHIR Search API +- Reverse Proxy (NGINX) (set by configuration) + +The reverse proxy allows for integration into a site's multi-server infrastructure and provides a means of serving +the extracted data. In practice, it acts as a **sidecar container** for TORCH, handling the delivery of generated files. + +### Feasibility Deploy + +For simplicity torch is integrated in +the [feasibility-triangle](https://github.com/medizininformatik-initiative/feasibility-deploy/tree/main/feasibility-triangle) +of the feasibility-deploy repository, but can also be installed without it. + +## Transfer Script + +TORCH provides a companion **transfer script** designed to automate the workflow of submitting a data extraction +request, polling the status, and transferring the resulting files to a target FHIR server. + +The transfer script will: + +1. Take the **CRTDL** and generate a FHIR parameters resource to send to TORCH. +2. Execute $extract-data operation on the TORCH server using parameters resource as input. +3. Poll the TORCH status endpoint until the export is complete. +4. Download the resulting patient-oriented FHIR bundles into a temp dir. +5. Upload these files to a configured target FHIR server using the `blazectl` tool. +6. Provide progress feedback and error handling at each step. + +## Verification + +For container images, we use cosign to sign images. This allows users to confirm the image was built by the expected CI +pipeline and has not been modified after publication. + +``` +cosign verify "ghcr.io/medizininformatik-initiative/torch:v1.0.0" \ +--certificate-identity-regexp "https://github.com/medizininformatik-initiative/torch.*" \ +--certificate-oidc-issuer "https://token.actions.githubusercontent.com" \ +--certificate-github-workflow-ref="refs/tags/v1.0.0" \ +-o text +``` + +The expected output is: + +``` +Verification for ghcr.io/medizininformatik-initiative/torch:v1.0.0 -- +The following checks were performed on each of these signatures: +- The cosign claims were validated +- Existence of the claims in the transparency log was verified offline +- The code-signing certificate was verified using trusted certificate authority certificates +``` + +This output ensures that the image was build on the GitHub workflow on the repository +`medizininformatik-initiative/torch` and tag `v1.0.0`. + diff --git a/docs/implementation/cascading-delete.md b/docs/implementation/cascading-delete.md new file mode 100644 index 00000000..6634a5cf --- /dev/null +++ b/docs/implementation/cascading-delete.md @@ -0,0 +1,136 @@ +# Cascading Delete in Torch + +Cascading delete is a critical feature for the Torch FHIR data extraction system that ensures referential integrity +and proper cleanup when resources are removed during the extraction process. +It is done in a queue based bidirectional manner, in the directions (parent → child) and (child → parent). + +## Problem Context + +In FHIR systems, resources often reference each other through various relationship types: + +- **Patient → Observation, DiagnosticReport, Condition, etc.** +- **Encounter → Observation, Procedure, MedicationAdministration** +- **DiagnosticReport → Observation (results)** +- **Specimen → Observation (derived-from)** + +When resources fail validation checks (such as must-have conditions, consent requirements, or profile compliance), +they need to be removed from the extraction batch. +However, simply removing a resource can break referential integrity and leave "orphaned" resources that reference the +deleted resource. + +## Parent Child Relationships + +a parent-child relationship in Torch is defined by the extraction process. +A parent resource is one that is extracted first and may have child resources that depend on it (i.e. a referential +chain). + +- **Parent**: A resource that is referencing another reference. +- **Child + **: A resource that is referenced by a parent resource, such as a Patient or Encounter resource (child) being referenced by an Observation (parent). + +## Goal of Cascading Delete + +Remove all resources whose referential chains are broken due to the deletion of a resource. + +## Approach + +1. **Identify Parent-Child Relationships**: + During the reference resolve process, Torch identifies parent-child relationships based on the FHIR resource references in + the reference resolve. +2. **Mark Resources for Deletion**: + When a resource fails validation checks (consent,must-have), it is marked for deletion. +3. **Bi-directional Deletion** + - **Parent to Child**: + - If a parent resource is marked for deletion, all connections to its child resources are removed. + - If a child has no other parent, it is also marked for deletion. + - Directly loaded resources have a parent by default, so they are not deleted by this step. + - **Child to Parent**: + - If a child resource is marked for deletion, it removes its reference to the parent. + - If the parent has no other children: + - the reference has to be checked for must-have condition + - if the parent has no other children, and it was a must-have reference it is marked for deletion. +4. **Cleanup**: + - After all resources are processed, Torch performs a cleanup step to remove all resources marked for deletion. + - This ensures that no orphaned resources remain in the system. + +## Cascading Delete Referential Chain Examples + +✅ = kept +❌ = deleted +★ = must-have reference + +### Example 1: Child Deleted, Parent Kept + +``` +Patient/123 + └─ Encounter/abc + ├─ Observation/obs1 ❌ deleted + └─ Observation/obs2★ + ``` + +``` +Patient/123 ✅ kept + └─ Encounter/abc ✅ kept + ├─ Observation/obs1 ❌ deleted + └─ Observation/obs2★ ✅ kept + ``` + +### Example 2: Must Have Violation Results in Parent Deleted + +``` +Patient/456 + └─ Encounter/def + ├─ Observation/obs3 + └─ Observation/obs5★ ❌ deleted + ``` + +``` +Patient/456 ✅ kept + └─ Encounter/def ❌ deleted + ├─ Observation/obs3 ❌ deleted + └─ Observation/obs5★ ❌ deleted + ``` + +### Example 3: One Parent Deleted results in all children kept + +``` +Patient/456 +├─ Encounter/def ❌ deleted +│ ├─ Observation/obs3 +│ └─ Observation/obs5 +└─ Encounter/xyz + ├─ Observation/obs3 + └─ Observation/obs5 + ``` + +``` +Patient/456 ✅ kept +├─ Encounter/def ❌ deleted +│ ├─ Observation/obs3 ✅ kept +│ └─ Observation/obs5 ✅ kept +└─ Encounter/xyz ✅ kept + ├─ Observation/obs3 ✅ kept + └─ Observation/obs5 ✅ kept + ``` + +### Example 3: All Parents Deleted results in all children kept + +``` +Patient/456 ✅ kept +├─ Encounter/def ❌ deleted +│ ├─ Observation/obs3 +│ └─ Observation/obs5 +└─ Encounter/xyz ❌ deleted + ├─ Observation/obs3 + └─ Observation/obs5 + ``` + +``` +Patient/456 ✅ kept +├─ Encounter/def ❌ deleted +│ ├─ Observation/obs3 ❌ deleted +│ └─ Observation/obs5 ❌ deleted +└─ Encounter/xyz ❌ deleted + ├─ Observation/obs3 ❌ deleted + └─ Observation/obs5 ❌ deleted + ``` diff --git a/docs/implementation/cascading-delete.png b/docs/implementation/cascading-delete.png new file mode 100644 index 00000000..3aa7a898 Binary files /dev/null and b/docs/implementation/cascading-delete.png differ diff --git a/docs/implementation/consent.md b/docs/implementation/consent.md new file mode 100644 index 00000000..6ea7c08e --- /dev/null +++ b/docs/implementation/consent.md @@ -0,0 +1,73 @@ +# Consent Handling in TORCH + +TORCH implements **privacy-aware consent handling** to ensure that extracted data strictly complies with patient +permissions and applicable regulations. + +--- + +## 1. Consent Representation + +- TORCH supports the [FHIR Consent](https://www.hl7.org/fhir/consent.html) resource as the canonical way to represent + patient consent. +- Consent records define: + - **Who** has granted consent + - **What** data may be accessed + - **Purpose** and permitted actions + - **Conditions** or time limits + +--- + +## 2. Consent Evaluation + +Before any data extraction: + +1. TORCH retrieves a consent key from the CRTDL +2. For a batch all patient **Consent** resources are fetched from the FHIR server. +3. For the current extraction request the valid consent records are identified based on: + - Patient ID + - Status + - Provision codes + +4. Shift start of Consent by related Encounter if applicable: + - The assumption is that consents are valid from the start of the encounters that have the start of the consent + within + their encounter period. +5. Calculate the Consent Periods: + - order them oldest to newest (by Consent.dateTime) + - for each: + - add permits to the current consent period + - if denies are present subtract them from the current consent period +6. During extraction TORCH determines: + - Whether the requested resources lie within the consent period for patient as calculated based on the CRTDL. + - If any resources dates are outside the period, they are excluded from the result set. + +## 3. Enforcement in Data Processing + +- Data outside the specified consent period are excluded from the result set +- All enforcement happens **before** results are packaged into NDJSON bundles. + +--- + +## 4. Integration with CRTDL + +- CRTDL definitions can reference consent rules directly via the consent key in the cohort selection. +- This allows **per-patient, per-resource** consent enforcement during structured extraction. + +--- + +## 5. Limitations and Considerations + +- Consent records must be **up-to-date** and accurately reflect patient permissions. +- TORCH only supports the use of consent keys that are defined in the mapping configurations ( see [Configuration](../configuration.md)). +- The consent check is always defined for a specific field for each FHIR resource type. If no consent field is defined for a resource type, all resources of this type are considered as consented. + (see the specified + fields [type_to_consent.json](https://github.com/medizininformatik-initiative/torch/blob/main/mappings/type_to_consent.json)). + +--- +## Summary + +Consent handling in TORCH is: + +- **Standards-based** (FHIR Consent) +- Per Patient and per Resource +- Only checks specific fields of the patient compartment resource diff --git a/docs/implementation/consent.png b/docs/implementation/consent.png new file mode 100644 index 00000000..dc39a64e Binary files /dev/null and b/docs/implementation/consent.png differ diff --git a/docs/implementation/data-extraction.md b/docs/implementation/data-extraction.md new file mode 100644 index 00000000..476d1c30 --- /dev/null +++ b/docs/implementation/data-extraction.md @@ -0,0 +1,29 @@ +# Data Extraction + +By directly loading and reference resolving resources are assigned to all attribute groups by which they should be +extracted. + +The extraction process consists of the following 2 steps: +1. **Attribute Extraction**: Extract only the attributes specified in the profiles. +2. **Redaction**: Remove any unnecessary data from the resources according to predefined rules and fixes resources to + ensure compliance with the profiles. + see [Redaction](redaction.md) for details. + +## Attribute Extraction + +Attribute extraction is based on the attribute groups defined in the CRTDL and the profiles referenced there. +It is based on fhir path expressions that are evaluated against the resources. +The extraction process is as follows: +1. Merge extraction behaviour e.g. if multiple attribute groups extract the same attribute, the union of all extraction + rules is applied. + Also hierarchical extraction is supported e.g. if a parent element is extracted the children elements don't need to + be extracted explicitly. +2. Evaluate FHIR Path expressions against the resources to extract the specified attributes. +3. Write the extracted attributes to the output resources using HAPI Terser. + +### Limitations and Considerations +- **Nested List Handling**: Fhir path is evaluated at the element level, so if elements are within nested lists, the + extraction may not behave as expected, since the nested list structure is not considered during evaluation and + therefore not preserved. + * For this reason only extracting elements until the first list level is supported, e.g. `Patient.name` is supported + but `Patient.name.given` is not. diff --git a/docs/implementation/direct-load.md b/docs/implementation/direct-load.md new file mode 100644 index 00000000..1081bbb5 --- /dev/null +++ b/docs/implementation/direct-load.md @@ -0,0 +1,86 @@ +# Handling Attribute Groups Directly + +TORCH distinguishes between directly loaded and refrenced attributeGroups, where referenced attributeGroups are identified by the flag +`IncludeReferenceOnly`. +Directly loaded attributeGroups can be loaded directly as their inclusion in the extraction does not depend on any referencing. + +TORCH loads all resources of the directly loaded attributeGroups based on the Fhir Profile specified in the attribute group and the filters applied to the attribute group. +I.e. resources are loaded based on the Fhir Profile specified in the attribute group and +the [filters](../crtdl/filter.md) applied to +the attribute group. + +The processing has two separate workflows due to the different nature of the resources: + +1. **Core Resources + **: These are resources that are outside the patient compartment (no direct link to Patient - e.g. Medication). +2. **Patient Resources**: These are resources that are directly loaded and processed for each patient. + +## 1. Directly Loaded Core Attribute Groups + +Core attributes are simply loaded and processed in a single step. + +This means that all resources that are part of the core attribute group are loaded and processed in a single fhir search +request. + +- After that a profile and must-have check is done on the resources. + - Must-have conditions are violated if **not a single** resource passes this check. +- If any **must-have** condition is violated, the extraction is fully stopped for the job. +- At the same time it is sufficient if the must-have conditions are fulfilled for a single "global" resource. + +```mermaid +flowchart TD + Start[Start Core Attribute Processing] --> Load[Load all core resources in single FHIR search request] + Load --> Profile[Profile check on resources] + Profile --> MustHave[Must-have check on resources] + MustHave --> Check{Any must-have condition violated?} + Check -->|yes| Stop[Stop extraction for job] + Check -->|no| Global[At least one resource fulfills must-have condition] + Global --> Complete[Core processing complete] + style Stop fill: #ffcccc + style Complete fill: #ccffcc + style CoreWorkflow fill: #e1f5fe +``` + +## 2. Directly Loaded Patient Attribute Groups + +Patient attribute groups are loaded and processed for each patient. + +All resources from a patient attribute group are loaded and processed in a single fhir search request +and then assigned to their patient. + +- First the consent is checked for each of the loaded resources and only resources that pass the consent check are processed further. + - When **no consent** key is defined, all resources are considered to be consenting by + default. +- A profile and must-have check is done on every resource. + +- If after the group processing a must-have condition is violated, the respective patient is marked for deletion. Once all patients are processed, + all resources (including the patient resource itself) for a patient marked for deletion are deleted. If no resources are left the whole batch is deleted. + +```mermaid +flowchart TD + Start[Start Patient Attribute Processing] --> ForEach[For each patient] + ForEach --> Load[Load patient resources in single FHIR search request] + Load --> Assign[Assign resources to patient] + Assign --> Consent[Consent check on patient resources] + Consent --> ConsentKey{Consent key defined?} + ConsentKey -->|no| AllConsent[All resources considered consenting by default] + ConsentKey -->|yes| OnlyConsent[Process only consenting resources] + AllConsent --> ProfileCheck[Profile and must-have check on every resource] + OnlyConsent --> ProfileCheck + ProfileCheck --> MustHaveViolated{Group processing violated must-have condition?} + MustHaveViolated -->|yes| MarkDelete[Mark patient for deletion] + MustHaveViolated -->|no| PatientComplete[Patient processing complete] + MarkDelete --> MorePatients{More patients to process?} + PatientComplete --> MorePatients + MorePatients -->|yes| ForEach + MorePatients -->|no| DeleteMarked[Delete marked patient resources from batch] + DeleteMarked --> AnyLeft{Any patients left in batch?} + AnyLeft -->|no| DeleteBatch[Delete entire batch] + AnyLeft -->|yes| BatchComplete[Batch processing complete] + style MarkDelete fill: #ffeeaa + style DeleteBatch fill: #ffcccc + style BatchComplete fill: #ccffcc + style PatientWorkflow fill: #f3e5f5 +``` + + diff --git a/docs/implementation/implementation-overview.md b/docs/implementation/implementation-overview.md new file mode 100644 index 00000000..ce4ebc42 --- /dev/null +++ b/docs/implementation/implementation-overview.md @@ -0,0 +1,57 @@ +## Implementation Overview + +#### Pipeline Overview + +The TORCH pipeline consists of several key components that work together to extract and process data from FHIR servers +based on the Clinical Resource Transfer Definition Language (CRTDL). The main components of the pipeline are: + +- **CRTDL Definition**: A JSON-based definition that specifies the cohort and data extraction rules. +- **Cohort Selection**: Uses FHIR Search or CQL to identify the population +- **Data Extraction**: Extracts FHIR resources based on the CRTDL definition. +- **Consent Handling**: Applies consent rules to ensure compliance with privacy regulations. +- **Output Generation**: Produces FHIR-compliant resources in NDJSON format. + +#### Pipeline Steps + +1. **Validate CRTDL Definition**: Ensure the CRTDL definition is correctly formatted and contains valid criteria. +2. **Cohort Evaluation**: Evaluate the cohort via FHIR Search or CQL, unless patient IDs passed directly as parameter. +3. **Preprocessing of directly loaded core Resources + **: Directly loaded core resources are processed first, as to ensure the results can be shared over all patients. +4. **Handling Patient Resources + **: For each patient, the pipeline processes the resources according to the CRTDL definition. +5. **Handling Core Resources**: Patients can load new core resources, which are then postprocessed. +6. **Writing Output**: The final output is written in NDJSON format, with each patient’s data in a separate bundle. + +```mermaid +flowchart TD + A[CRTDL] --> B{valid CRTDL?} + B -->|no| C[Error] + B -->|yes| D{cohort given as parameter?} + D -->|no| E[Execute Cohort Selection CCDL] + D -->|yes| F[Handle directly loaded Core Attribute Groups] + E --> G{Which method?} + G --> H[CQL] + G --> I[Flare] + H --> J[Fetch Patients] + I --> J + J --> F + F --> K[Resolve References] + K --> L[Cascading Delete] + L --> M[Initialize patient batch with preprocessed core data] + M --> N[Fetch and build batch consent] + N --> O[Handle directly loaded Patient Attribute Groups] + O --> P[Resolve References] + P --> Q[Cascading Delete] + Q --> R[Extraction] + R --> S[Update Core Data] + S --> T[Write out Results] + T --> U[NdJson] + S --> V{All Patient Batches handled?} + V -->|yes| W[Resolve References] + V -->|no| T + W --> X[Cascading Delete] + X --> Y[Extraction] + Y --> T + style C fill: #ffcccc + style U fill: #ccffcc +``` diff --git a/docs/implementation/must-have.md b/docs/implementation/must-have.md new file mode 100644 index 00000000..3ebadffb --- /dev/null +++ b/docs/implementation/must-have.md @@ -0,0 +1,36 @@ +## Must Have Checking in TORCH Pipeline + +The must have checking i.e. ensuring required elements are present is a crucial step to ensure +that the extracted data meets the criteria defined in the Clinical Resource Transfer Definition Language (CRTDL). +Required elements are defined in the CRTDL using a must have flag. + +Must Have checking is performed after resources are loaded from the FHIR server and during the reference resolve step. + +Must have conditions can be violated in two ways: +1. A resource is missing a required attribute as defined in the CRTDL. +2. A resource is missing a required reference to another resource as defined in the CRTDL. + +So the must-have checking is done in two steps: + +## 1. **Field Must Have Check** + +Based on fhir path expressions, the must have check verifies that all required attributes specified in the CRTDL are +filled in a resource. +If any required attribute is missing, the extraction for that resource is stopped, and an error is logged. + +## 2. **Reference Resolve** + +The first Must Have Check is done on the resources that are loaded directly from the FHIR server. +References are only checked for existence, not for correctness. + +A reference attribute in the CRTDL can be marked as must have and has a link to other attribute groups, +that define the requirements for the referenced resource. + +During **Reference Resolve**, TORCH will does the basic must have check on the resolved reference with the linked +attribute +groups. +So not only does the reference need to be resolved, but the referenced resource also needs to pass the must have check +for the linked attribute groups. +If any must have condition is violated, the referencing resource is marked for deletion and then cleaned up during +the [cascading delete](cascading-delete.md) step. + diff --git a/docs/implementation/redaction.md b/docs/implementation/redaction.md new file mode 100644 index 00000000..e268464a --- /dev/null +++ b/docs/implementation/redaction.md @@ -0,0 +1,121 @@ +# Redaction + +Torch redacts resources after extracting the specified attributes and resolving references before packaging them into +NDJSON bundles. + +The redaction ensures that not only the requested information is included in the output, but also that any +unnecessary data is removed according to predefined rules. + +During the reference resolve and loading of resources a resource is associated with all profiles that were used to +extract it. + +## 1. Redaction Rules + +- **Strict Structure Definition Adherence**: Resources are redacted to strictly adhere to the structure defined in the + requested profiles. + That means for example if a profile only allows a subset of address fields, all other fields are removed from the + output. +- **Strict Extension Handling**: Only extensions explicitly allowed in the profile are retained. All other extensions + except for Data Absent Reason are removed. + +- **Reference Handling**: References to other resources are preserved if they were part of the reference resolve + process. + References to resources not included in the extraction are removed to prevent dangling references. + +- **Empty Element Removal**: Elements that become empty after redaction are removed from the resource to maintain a + clean structure. + +- **"Half-Open" Slicing**: With the strict structure definition adherence, Torch implements a "half-open" slicing + approach. + This means that if slicing is open in the profile, additional slices not defined in the profile are removed. + Exception is with multiple profiles per resource, where the first known profile is selected greedily. + + +- **Data Absent Reason Setting**: If an element is removed due to redaction or extraction but is required by the + profile, + it is replaced with a Data Absent Reason extension to indicate that the data was intentionally omitted. + +## 2. Redaction Process + +Recursive Walk through Resource: + +1. **Profile Identification**: Determine the profile(s) associated with the resource to understand the structure and + allowed elements. + Associate the resource with the all profiles associated with it during the extraction process. + **multiple profiles per resource are supported** the context for the profiles (i.e. the element id in the structure + definition) is tracked in parallel for all profiles. + +2. **Element Evaluation**: For each element in the resource, evaluate whether it is allowed by the profile. + 1. Handle Slicing + 2. Handle Extensions + 3. (if not primitive) Handle Children + +3. Handling Children + 1. descend into children (update context for profiles) + 2. resolve references (remove references to resources not identified during reference resolve) + 3. if empty set Data Absent Reason if required by any profile + +## 3. Limitations and Considerations + +- **Profile Accuracy**: The effectiveness of redaction relies heavily on the accuracy and completeness of the profiles + used. + Incomplete profiles may lead to unintended data retention or removal. + +- **Value Sets Binding Slices**: Since TORCH does not have its own terminology service, value sets binding slices are + not fully supported. + This means that if a slice is defined based on a value set, TORCH cannot enforce the inclusion or exclusion of + elements based on that value set and + only support the structural definition of the slice with the code system. + +- **No slicing Rules**: Torch does not support slicing rules like "open" or "closed" in the profiles. + It implements a "half-open" approach where additional slices not defined in the profile are removed, except when + multiple profiles per resource are used. + +- **No Slicing Ordering**: Torch does not enforce any specific ordering of slices or elements within the resource. + That means that it does not check if the order of elements in the resource matches the order defined in the profile. + +## 4. Summary + +Torch's redaction process is designed to ensure that extracted resources strictly adhere to the defined profiles, +removing any unnecessary or disallowed data while preserving essential references and structure. + +```mermaid +flowchart TD + A[FHIR Resource + Profiles] --> B[Profile Association] + B --> C[Multiple Profiles per Resource Supported] + C --> D[Recursive Element Walk] + D --> E[Element Evaluation] + E --> F[Handle Slicing] + F --> G["Half-Open Slicing:
Remove undefined slices"] + G --> H[Handle Extensions] + H --> I["Strict Extension Filtering:
Keep only allowed + Data Absent Reason"] + I --> J{Primitive Element?} + J -->|Yes| K[Element Complete] + J -->|No| L[Handle Children] + L --> M[Descend into Children] + M --> N[Update Profile Context] + N --> O[Resolve References] + O --> P{Reference in Extraction?} + P -->|No| Q[Remove Dangling Reference] + P -->|Yes| R[Preserve Reference] + Q --> S{Element Empty?} + R --> S + S -->|Yes & Required| T[Set Data Absent Reason] + S -->|Yes & Optional| U[Remove Empty Element] + S -->|No| V[Keep Element] + K --> W{More Elements?} + T --> W + U --> W + V --> W + W -->|Yes| D + W -->|No| X[Redacted Resource] + X --> Y[Strict Profile Adherence Achieved] + style A fill: #e1f5fe + style B fill: #f3e5f5 + style G fill: #fff3e0 + style I fill: #fff3e0 + style Q fill: #ffcdd2 + style T fill: #fff3e0 + style U fill: #ffcdd2 + style Y fill: #c8e6c9 +``` diff --git a/docs/implementation/reference-resolve.md b/docs/implementation/reference-resolve.md new file mode 100644 index 00000000..3f0f3b1a --- /dev/null +++ b/docs/implementation/reference-resolve.md @@ -0,0 +1,23 @@ +## Reference Resolve + +Torch needs to resolve references in the extracted data to ensure that all resources are correctly extracted and linked. +This is done in the **Reference Resolve** step of the Torch pipeline. + +### Resolving References + +Torch manages for each Attribute Group the Resources that have been assigned to it. +This assignment is called a ResourceGroup (e.g. AttributeGroup_Observation,Observation1). + +To resolve references, Torch uses the following steps for each Patient or the Core Resources: + +1. **Get all valid ResourceGroups**: Torch retrieves all ResourceGroups that are valid for the current extraction. +2. **Extract References**: For each ResourceGroup, Torch extracts the references from the resources. +3. **Load References**: Torch checks if it already loaded the referenced resources in its cache. + - If the resource is not loaded, Torch bundles all references and loads them in a single FHIR search request. +4. **Assign References**: Torch assigns the loaded resources to the ResourceGroup. + - Performs a [must-have check](must-have.md) on the loaded resources. + - For Patient resources, it also checks if the resources are allowed by the patient's [consent](consent.md). + - If any must-have condition is violated, the referencing resource group is marked for deletion. +5. **Update ResourceGroup**: The ResourceGroup is updated with the loaded resources and their references. +6. **Repeat for all ResourceGroups**: Torch repeats the process for all newly added ResourceGroups until all references + are resolved. diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 00000000..c173abff --- /dev/null +++ b/docs/index.md @@ -0,0 +1,38 @@ +--- +layout: home +title: TORCH +hero: + name: TORCH + text: Transfer Of Resources in Clinical Healthcare + tagline: Structure-guided extraction of clinical data from FHIR servers + actions: + - theme: brand + text: Overview + link: /overview + - theme: brand + text: Get Started + link: /getting-started + - theme: alt + text: API + link: /api/api + - theme: alt + text: Configuration + link: configuration + - theme: alt + text: Documentation + link: documentation + - theme: alt + text: View on GitHub + link: https://github.com/medizininformatik-initiative/torch + +features: + - title: Fast & Privacy-Aware + icon: 🔍 + details: Extract structured data using CRTDL with consent enforcement. + - title: Output Ready + icon: 📦 + details: Generates FHIR-compliant NDJSON bundles per patient ready to upload into a data use specific FHIR server. + - title: License + icon: 📝 + details: Apache 2.0 — see LICENSE for details. +--- diff --git a/docs/overview.md b/docs/overview.md new file mode 100644 index 00000000..5ab7f81d --- /dev/null +++ b/docs/overview.md @@ -0,0 +1,83 @@ +# TORCH - Transfer Of Resources in Clinical Healthcare + +## Goal + +**T**ransfer **O**f **R**esources in **C**linical **H**ealthcare or **Torch** is a project that aims to provide +a service that allows the local execution of structured data extraction queries on a FHIR-server. + +The main goal of TORCH is to automate the extraction of structured clinical data from FHIR servers as defined by +a well defined query language the so called [Clinical Resource Transfer Definition Language (CRTDL)](crtdl/crtdl.md) . + +This is vital inside clinical research networks, where data from multiple institutions needs to be aggregated for centralized and decentralized analysis. + +Manual extraction and transformation of data is time-consuming and error-prone, especially in a decentralized scenario. + +TORCH aims to solve this problem by providing a tool that can extract data based on a well-defined +**human-readable** structure and apply consent rules to ensure consent compliance. +This structure can then be used to extract data from multiple institutions in a consistent manner. + +A exemplary use case based on the [German Medical Informatics Initiative (MII)](https://www.medizininformatik-initiative.de/en/), where TORCH is used to extract data from hospital FHIR servers for a centralized analysis based on the +[Clinical Resource Transfer Definition Language (CRTDL)](crtdl/crtdl.md) is shown below: + +```mermaid +flowchart TD + R["Researcher"] + FP["Feasibility Portal"] + AP["Approval Authority"] + DIC["Data Integration Center"] + DMS["Data Management Institution"] + RP[Research Proposal Review] + T["⚙ TORCH"] + PP["⚙ Post-Processing System"] + R -->|Research Idea| FP + FP -->|Research Proposal with CRTDL| RP + RP --> AP + AP -->|Approved| DIC + T --> PP + DIC -->|Execute Data Extraction| T + PP -->|Extracted Data| DIC + DIC -->|Transfer Data| DMS + DMS -->|Centrally Postprocessed Data| R +``` + +## Features + +TORCH provides a range of features to support standardized and consent-aware data extraction: + +- **Required Fields Validation**: + Ensures that mandatory fields defined in the CRTDL are present in the extracted resources. +- **Consent Handling**: Applies consent rules as defined in the CRTDL to guarantee compliance during data extraction. +- **Reference Resolution**: + Resolves references between resources while maintaining referential integrity. +- **Slicing and Extensions**: Supports slicing and FHIR extensions to handle institution-specific resource structures. +- **Profile Adherence**: + Only keeps elements from extracted resources as specified by specific FHIR profiles (see [Redaction](implementation/redaction)). +- **FHIR Bulk Data Access**: + Implements the [FHIR Bulk Data Access](api/api.md) specification for efficient large-scale data extraction. +- **FHIR-to-FHIR Transfer**: + Creates extracted data in a FHIR-compliant format ready for import into another FHIR server or further FHIR based processing - ensuring maximum interoperability. + +## Limitations + +- **Value Sets Binding Slices**: + Since TORCH does not have its own terminology service, it does not support slicing by value set bindings. +- **FHIR Version Support**: TORCH currently supports only + **FHIR R4**. Other versions (e.g., DSTU2, R5) are not supported. +- **On the fly profile support**: TORCH only supports a + **set FHIR of profiles + ** given at program startup via config by mounting all valid Structure Definitions (see [Configuration](configuration.md)). +- **Nested Resources**: TORCH does not handle + **deeply nested resources**; they are currently treated as a single field rather than fully resolved structures. +- **Performance Constraints**: Large-scale extraction is bound by the + **FHIR Bulk Data Access specification** and server capabilities; + performance may vary depending on server implementation. +- **Consent Complexity**: Consent handling is limited to + **rule-based approaches defined in the CRTDL**. Complex or non-standard consent models may require customization. +- **Interoperability**: TORCH ensures FHIR compliance but does not guarantee interoperability with + **all vendor-specific FHIR implementations**. + +## License + +TORCH is licensed under the Apache License, Version 2.0. See the [LICENSE](https://github.com/medizininformatik-initiative/torch/tree/main/LICENSE) file for details. + + diff --git a/docs/package-lock.json b/docs/package-lock.json new file mode 100644 index 00000000..f4e5eea2 --- /dev/null +++ b/docs/package-lock.json @@ -0,0 +1,3689 @@ +{ + "name": "docs", + "version": "1.0.0", + "lockfileVersion": 3, + "requires": true, + "packages": { + "": { + "devDependencies": { + "mermaid": "^11.10.0", + "vitepress": "^1.2.3", + "vitepress-plugin-mermaid": "^2.0.17" + } + }, + "node_modules/@algolia/abtesting": { + "version": "1.1.0", + "resolved": "https://registry.npmjs.org/@algolia/abtesting/-/abtesting-1.1.0.tgz", + "integrity": "sha512-sEyWjw28a/9iluA37KLGu8vjxEIlb60uxznfTUmXImy7H5NvbpSO6yYgmgH5KiD7j+zTUUihiST0jEP12IoXow==", + "dev": true, + "dependencies": { + "@algolia/client-common": "5.35.0", + "@algolia/requester-browser-xhr": "5.35.0", + "@algolia/requester-fetch": "5.35.0", + "@algolia/requester-node-http": "5.35.0" + }, + "engines": { + 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"docs:preview": "vitepress preview " + } +} diff --git a/src/main/java/de/medizininformatikinitiative/torch/consent/ConsentFetcher.java b/src/main/java/de/medizininformatikinitiative/torch/consent/ConsentFetcher.java index ae58f72d..75fa8f0c 100644 --- a/src/main/java/de/medizininformatikinitiative/torch/consent/ConsentFetcher.java +++ b/src/main/java/de/medizininformatikinitiative/torch/consent/ConsentFetcher.java @@ -42,7 +42,7 @@ public class ConsentFetcher { private final ProvisionExtractor provisionExtractor; /** - * Constructs a new {@code ConsentHandler} with the specified dependencies. + * Constructs a new {@code ConsentFetcher} with the specified dependencies. * * @param dataStore The {@link DataStore} service for Server Calls. * @param mapper The {@link ConsentCodeMapper} for mapping consent codes. @@ -55,7 +55,7 @@ public ConsentFetcher(DataStore dataStore, ConsentCodeMapper mapper, ProvisionEx } private static Query getConsentQuery(PatientBatch batch) { - return Query.of("Consent", batch.compartmentSearchParam("Consent").appendParam("_profile:below", stringValue(CDS_CONSENT_PROFILE_URL))); + return Query.of("Consent", (batch.compartmentSearchParam("Consent").appendParam("status", stringValue("active"))).appendParam("_profile:below", stringValue(CDS_CONSENT_PROFILE_URL))); } /** diff --git a/src/main/java/de/medizininformatikinitiative/torch/service/DirectResourceLoader.java b/src/main/java/de/medizininformatikinitiative/torch/service/DirectResourceLoader.java index aeb2cc9b..cfe8c325 100644 --- a/src/main/java/de/medizininformatikinitiative/torch/service/DirectResourceLoader.java +++ b/src/main/java/de/medizininformatikinitiative/torch/service/DirectResourceLoader.java @@ -52,7 +52,6 @@ public DirectResourceLoader(DataStore dataStore, DseMappingTreeBase dseMappingTr this.dseMappingTreeBase = dseMappingTreeBase; this.structureDefinitionsHandler = structureDefinitionHandler; this.profileMustHaveChecker = profileMustHaveChecker; - } /** @@ -179,9 +178,7 @@ private Mono processPatientSingleAttributeGroup(Annotat .doOnNext(tuple -> { PatientResourceBundle bundle = mutableBundles.get(tuple.patientId); if (profileMustHaveChecker.fulfilled(tuple.resource, group)) { - safeGroup.add(tuple.patientId); - System.out.println("Ref" + group.groupReference() + "Type" + group.resourceType() + " ID " + group.id()); bundle.put(tuple.resource, group.id(), true); } else { bundle.put(tuple.resource, group.id(), false);