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0.6.0 - Improved FHIR Validation
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@hhund hhund released this 12 Jul 16:44
· 96 commits to main since this release
v0.6.0
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hhund Hauke Hund
GPG key ID: 15A40D58B4BF6C78
Learn about vigilant mode.
d1b1868
This commit was signed with the committer’s verified signature.
hhund Hauke Hund
GPG key ID: 15A40D58B4BF6C78
Learn about vigilant mode.

With the 0.6.0 release false-positive validation errors have been fixed and a new parameter to run the data-send process in a dry-run mode has been added. With the dry-run mode, the data-send process will abort before storing the encrypted GECCO transfer dataset in the local DSF FHIR server and starting the data-translate process at the GECCO Transfer Hub (GTH). In the dry-mode no actual data is being transferred to the GTH.

A new version of the stand-alone Validator has been released as well. In order to fix the false-positive validation errors with the stand-alone validator, delete the three files listed below from the cache folder at default location ${java.io.tmpdir}/codex_gecco_validation_cache/.

Additional information on the new process release and the stand-alone validator can be found in the process Wiki.

To upgrade the process plugin from 0.5.1 perform the following steps:

  1. Stop the DSF BPE

    docker-compose down

  2. Replace the 0.5.1 process plugin with the new codex-process-data-transfer-0.6.0.jar

    sudo rm /opt/bpe/process/codex-process-data-transfer-0.5.1.jar
sudo wget https://github.com/num-codex/codex-processes-ap1/releases/download/v0.6.0/codex-process-data-transfer-0.6.0.jar -P /opt/bpe/process
sudo chmod 440 /opt/bpe/process/codex-process-data-transfer-0.6.0.jar
sudo chown root:bpe /opt/bpe/process/codex-process-data-transfer-0.6.0.jar

  3. Delete a profile snapshot in /opt/bpe/cache/StructureDefinition and two expanded ValueSets in /opt/bpe/cache/ValueSet

    sudo rm /opt/bpe/cache/StructureDefinition/https_www.netzwerk-universitaetsmedizin.de_fhir_StructureDefinition_sars-cov-2-ab-pnl-ser-pl-ia_1.0.4.json.gz
sudo rm /opt/bpe/cache/ValueSet/https_www.netzwerk-universitaetsmedizin.de_fhir_ValueSet_rheumatological-immunological-diseases_1.0.5.json.gz
sudo rm /opt/bpe/cache/ValueSet/https_www.netzwerk-universitaetsmedizin.de_fhir_ValueSet_vaccines-snomed_1.0.5.json.gz

    The files will be recreated during the next startup of the BPE to fix false-positive validation errors.

  4. Modify the process exclude config in /opt/bpe/docker-compose.yml

    @@ -50,3 +50,3 @@
       ORG_HIGHMED_DSF_BPE_PROCESS_EXCLUDED: |
-        wwwnetzwerk-universitaetsmedizinde_dataTranslate/0.5.1
-        wwwnetzwerk-universitaetsmedizinde_dataReceive/0.5.1
+        wwwnetzwerk-universitaetsmedizinde_dataTranslate/0.6.0
+        wwwnetzwerk-universitaetsmedizinde_dataReceive/0.6.0

    Additional processes may be listed in your process exclude config.

  5. Start the DSF BPE

    docker-compose up -d && docker-compose logs -f

Caution: To start the data-send process in version 0.6.0, you will need to use appropriate Task resources. For 0.6.0 examples see the wiki.

Fixes include:

  • False-Positive validation errors generated for the SarsCoV2AbPnlSerPlIA, History of Vaccination and Rheumatological Immunological Diseases profiles have been fixed, requiring the deletion of three StructureDefinition/ValueSet cache enties.
  • Process outcomes of the data-translate and data-receive processes where not saved as ouput parameters in their respective start-process Task resources.
  • The test data generator used within the development test setup did not generate a UTF-8 encoded Bundle when executed on Windows machines.

Issues closed:

  • Add Missing BpmnErrors #86
  • Move Bundle Logging to Default off Logging Class #81
  • Fix Test Data BundleGenerator Encoding #80
  • Improve Status Output of Translate Process #79
  • add simulate flag to send process to "just" get validation output from send process #77
  • Validator Generates False-Positives #72
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