Issues/39 internal bundle validation #68
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restart policy "no" makes it easier to debug issues related to crashing containers
This initial process validation task implementation requires 29 additional jars to be added to the BPE as regular (non-process) plugins. Alternatively we could release the process plugin as a tar.gz/zip or we might want to add the needed HAPI dependencies into the DSF BPE itself. This implementation contains some workarounds due to limitations of some classes in the dsf-fhir-validation module. The maven build produces a codex-process-data-transfer-0.5.0-SNAPSHOT.zip containing the codex-process-data-transfer-0.5.0-SNAPSHOT.jar and all dependency needed to start a stand-alone bundle/resource validator. Windows: java -cp codex-process-data-transfer-0.5.0-SNAPSHOT.jar;lib/* de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.ValidationMain some-bundle.json some-resource.xml Unix: java -cp codex-process-data-transfer-0.5.0-SNAPSHOT.jar:lib/* de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.ValidationMain some-bundle.json some-resource.xml The stand-alone validator outputs debug infos to System.err and the validation result to System.out. For a given single resource a OperationOutcome resource is produced and for a given Bundle, a bundle with added response.outcome per entry with be printed to System.out. The validator validates every json or xml file defined as command line argument. The validator can be configured using a application.properties file within the execution folder or via java system properties, meaning java command line parameters -Dfoo=bar. For configuration properties see classes de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.spring.config.ValidationConfig and de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.ValidationMain.TestConfig.
clients only initialize a trust store only ssl context, if key store and key store password are null.
Jersey based clients not use the ApacheConnectorProvider. Standard connector provider has no support for forwarding proxies. Added a ontology server connection test to the ValueSetExpansionClient and usage of to ValidatorMain.
The GECCO 1.0.5 radiology-procedures profile needs a min=0 config in the rule Procedure.code.coding:dicom in order for the HAPI Snapshot Generator to generate the correct StructureDefinition snapshot.
The contructor of ValidationPackageManagerImpl used in the ValidateDataLearningTest was missing the "dicom" fix, aka GeccoRadiologyProceduresCodingSliceMinFixer
issues/39_internal_bundle_validation
issues/39_internal_bundle_validation
Removed "-type" suffix from the error code CodeSystem/ValueSet. Removed not needed TODO comments. Changed log level from error to warning for first try ValueSet expansion errors (errors resulting in trying to expand via external terminology server next). Changed external terminology server for the test setup.
To start the dic-fhir service with a locally build DSF image use: docker-compose -f docker-compose.yml -f docker-compose.local-dsf-build.yml up dic-fhir
These changes depend on highmed/highmed-dsf#354 being merged.
Increased version numbers of log42-utils and crypto-utils dependencies to the latest versions.
Snapshots are only generate for StructureDefinitions from the root validation package and its dependencies. ValueSet are only expanded if they are part of binding rules from these StructureDefinitions. The binding strength can be configured.
change log level for errors during internal ValueSet expansion
Added getServerBase Method to GeccoClient interface and implementing classes. Removed geccoServerBase field from ReadData service, since it may not be configured (when testing without GECCO FHIR Server or at the GTH), resulting in a NullPointerException.
The file codex-processes-ap1-docker-test-setup/docker-compose.override.yml has been added to .gitignore and can now be used to defined local overrides. See https://docs.docker.com/compose/extends on how to use override files.
Added new environment variable to disable FHIR validation. Added new functionality to test if all resources are declaring at least on supported profile. A validation error is raised if no supported profile is defined. Profiles are supported if they are declared in the root validation package (currently de.gecco | 1.0.5) or are dependencies of the StructureDefinitions. Only profile with abstract = false and kind = resource are supported as claimed profiles by resources beeing validated.
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closes #39