https://github.com/samply/obds2fhir
https://github.com/samply/obds2fhir
adt fhir
Last synced: 3 months ago
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- Host: GitHub
- URL: https://github.com/samply/obds2fhir
- Owner: samply
- License: apache-2.0
- Created: 2020-11-23T11:35:47.000Z (over 4 years ago)
- Default Branch: develop
- Last Pushed: 2024-10-29T09:30:38.000Z (7 months ago)
- Last Synced: 2024-10-29T09:33:32.627Z (7 months ago)
- Topics: adt, fhir
- Language: XSLT
- Homepage:
- Size: 617 KB
- Stars: 2
- Watchers: 3
- Forks: 0
- Open Issues: 1
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# oBDS2FHIR / ADT2FHIR
oBDS2FHIR (also called ADT2FHIR) is a tool to transform files exported by German tumor documentation systems into FHIR bundles for use in the [Bridgehead](https://github.com/samply/bridgehead) (or other FHIR-based software).
Using the two XSLT files ([oBDS2MDS.xsl](https://github.com/samply/obds2fhir/blob/main/src/main/resources/oBDS2MDS_FHIR.xsl) and [MDS2FHIR.xsl](https://github.com/samply/obds2fhir/blob/main/src/main/resources/MDS2FHIR.xsl)), XML files conforming to [oBDS](https://basisdatensatz.de/xml/) or the legacy version [ADT/GEKID V2*](https://basisdatensatz.de/xml/) can be transformed into FHIR resources conforming to [de.dktk.oncology](https://simplifier.net/packages/de.dktk.oncology/).
This software was originally created for the [German Cancer Consortium's Clinical Communication Platform](https://dktk.dkfz.de/) and has since been made open source.
## Two names, one software
**ADT2FHIR** was originally developed in 2020 to integrate the ADT/GEKID dataset, which was hence renamed to Onkologischer Basisdatensatz (oBDS). Thus, ADT2FHIR is now also known as **oBDS2FHIR** (terms are used synonymously).
## Usage
The main method transforms oBDS compliant data into FHIR bundles.
Therefore, put your oBDS data in the input directory ```/clincial_data/Input_Patients```.
Optionally, you can (1) pseudonymize (e.g. see [Mainzelliste](https://bitbucket.org/medicalinformatics/mainzelliste)) and (2) import the data into a FHIR server (e.g. see [Blaze](https://github.com/samply/blaze)).
### Docker
oBDS2FHIR is designed for use with docker compose. To run, put the oBDS xml files in ```/clinical_data/Input_oBDS/``` and run:
```sh
docker-compose up
```
You need at least docker-compose version `1.29.2`.
The configuration is set in the ```docker-compose.yml``` file and is preconfigured as far as possible (you probably won't need to set **#commented** parameters):
###### Environment:
Set the environment variables either directly in Java oder via docker compose (start with the default values from the Dockerfile):
* ```FILE_PATH``` defines the directory of the clinical oBDS data in the docker container.
There souldn't be a reason to change this for docker.
* ```STORE_PATH``` defines the URL of the FHIR server API.
You can use the default value, when using the default BLAZE server (https://github.com/samply/blaze).
* ```STORE_AUTH``` sets the FHIR server authentication. *Leave it empty if there is no authentication.*
* ```IDENTIFIER_SYSTEM``` defines the system of the FHIR identifiers.
You can use the default value or set your own system URL.
* ```MAINZELLISTE_URL``` for pseudonymization in the transformation step; sets the URL of the pseudonymization service. *Leave it empty if there is no pseudonymization.*
* ```MAINZELLISTE_APIKEY``` sets the pseudonymization service authentication. *Leave it empty if there is no pseudonymization.*
* ```IDTYPE``` sets the pseudonym type. *Leave it empty if there is no pseudonymization.*
* ```SALT``` defines a random additional input for the hashing applied in generating the FHIR ids from oBDS. **Please do change this**
* ```SSL_CERTIFICATE_VALIDATION``` can be set to false **IF** your FHIR server is only accessible via https and you do **NOT** have a valid SSL certificate. Not recommended!
* ```ADD_DEPARTMENTS``` can be set to true if you want to add the departments that commited the patient report (=oBDS Melder). *Probably not necessary*.
###### Volumes:
* ```./clinical_data:/obds2fhir/clinical_data``` You can use the default value, which then mounts the host ```clinical_data``` directory to the docker container.
* ```/etc/bridgehead/traefik-tls:/.../:ro``` If you use https, please set the correct certificate path here (should work out of the box for use with Bridgeheads).
###### Network - extra_hosts:
* ``"host.docker.internal:host-gateway"`` If you run oBDS2FHIR in an additional docker-compose file on the same host and don't manage the docker network yourself, then use this configuration to enable access to other services (FHIR server; pseudonymization service).
## Notes
Assumes: Patient, Sample, Diagnose always have an Id, other Ids are optional.
-_Lokal_DKTK_ID_Pat_System_ needs to conform to https://www.hl7.org/fhir/datatypes.html#uri
You should modify the identifier system (replace http://dktk.dkfz.de/fhir/onco/core/CodeSystem/PseudonymArtCS with
a local URL). You can just make one up (or use the default), but note that this URL will be used as ```Identifier.system```
in the resulting FHIR Patient resources (```Identifer.value``` will either be (a) a hash based on patient master data or, if pseudonymization
is configured, (b) be replaced by a Mainzelliste-generated pseudonym).
Since ids are required in FHIR but optional in the oBDS XML schema, they are generated via content hashing
if not present. However, it is recommended to provide all optional ids in the imported oBDS XML files.
Additionally, ```Patient_ID```, ```Diagnosis_ID``` and ```Sample_ID``` are required.