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Issues/39 internal bundle validation #68
Commits on May 24, 2022
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changed restart policy to "no", DSF version to 0.6.0
restart policy "no" makes it easier to debug issues related to crashing containers
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initial validation impl., demo data now compliant with gecco 1.0.5 spec
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.
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Commits on May 25, 2022
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fixed client init code for trust store defined but no key store defined
clients only initialize a trust store only ssl context, if key store and key store password are null.
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fixed forward proxy support, added ontology server connection test
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.
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adds profile modifier to fix GECCO radiology-procedures missing min=0
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.
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Commits on May 27, 2022
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Added "dicom" fix to ValidationPackageManagerImpl constructor
The contructor of ValidationPackageManagerImpl used in the ValidateDataLearningTest was missing the "dicom" fix, aka GeccoRadiologyProceduresCodingSliceMinFixer
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Commits on Jun 6, 2022
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Commits on Jun 7, 2022
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Merge remote-tracking branch 'origin/develop' into
issues/39_internal_bundle_validation
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Merge remote-tracking branch 'origin/develop' into
issues/39_internal_bundle_validation
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Commits on Jun 11, 2022
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renamed error CodeSystem/ValueSet, removed comments, changed log level
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.
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Commits on Jun 12, 2022
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Commits on Jun 13, 2022
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added docker-compose file to override dsf images with local builds
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
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switched to DSF 0.7.0-SNAPSHOT, remove not needed code and dependencies
These changes depend on highmed/highmed-dsf#354 being merged.
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Commits on Jun 14, 2022
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removed not needed dependency management entries, some cleanup
Increased version numbers of log42-utils and crypto-utils dependencies to the latest versions.
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Commits on Jun 15, 2022
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Commits on Jun 16, 2022
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reworked StructureDefinition snapshot generation and ValueSet expansion
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.
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snapshots now added to validator if errors occurred during generation
change log level for errors during internal ValueSet expansion
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Commits on Jun 17, 2022
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Commits on Jun 18, 2022
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code cleanup/refactoring, NPE fix at ReadData when server not configured
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.
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fixed yml lint warnings, added docker-compose.override.yml to .gitignore
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.
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env variable to disable validation, error when profile not supported
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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