Support for external terminology service #2832
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feordin
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This pull request introduces 5 alerts and fixes 1 when merging f431f72 into dd9129f - view on LGTM.com new alerts:
fixed alerts:
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| "ExternalTerminologyServer": "http://tx.fhir.org/r4", | ||
| "Validate": { | ||
| "CacheDurationInSeconds": 14400, | ||
| "ProfileValidationTerminologyServer": "http://hapi.fhir.org/baseR4" |
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One of the issues we had with this branch was the test severs not being reliable for running E2E tests. We wanted to replace them with our in house server, but that didn't get done in time.
We could skip all the E2E tests for terminology, but I don't feel great about including a feature that doesn't have tests run against it.
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This could be done with an in-memory terminology server making it less dependent on external systems.
* Support for external terminology server * Fixed Issue with $export * Bug #1459: FIxed issue with $export error code when request type is Batch or Transaction. * Resources can now be validated against US Core * Added tests for $validate using external terminology service TODO: Need to make tests better. * Updated US-Core profiles in normative from STU3 -> R4. Wrote Tests for $Validate on a patient resource against us-core. * Improved added tests Added GenderIdentity USCORE-profile to normative Set "Definitions.zip" as "content" and "Copy Always" so that its path can be found Modified some pre-existing tests so that they account for profile validation. * Fixed appsettings * Removed unrelated bug-fix code for ExportNotSupportedInBundle * Validate tests pass on STU3 and R4, most pass on R5. Fixed issue with ZipSource which prevented defintion file summaries from being loaded. Removed last bit of code irrelevant work. * Added ValueSet-BirthSex to R4 and R5 Validate Tests passing for all versions * Cleaned up csproj for Stu3, R4, and R5 .web * Updated TestConfiguration.json to use new external terminology service endpoint * Changed endpoint back to hapi Co-authored-by: Jared Erwin <[email protected]>
* Support for external terminology server * Fixed Issue with $export * Bug #1459: FIxed issue with $export error code when request type is Batch or Transaction. * Resources can now be validated against US Core * Added tests for $validate using external terminology service TODO: Need to make tests better. * Updated US-Core profiles in normative from STU3 -> R4. Wrote Tests for $Validate on a patient resource against us-core. * Improved added tests Added GenderIdentity USCORE-profile to normative Set "Definitions.zip" as "content" and "Copy Always" so that its path can be found Modified some pre-existing tests so that they account for profile validation. * Fixed appsettings * Removed unrelated bug-fix code for ExportNotSupportedInBundle * Validate tests pass on STU3 and R4, most pass on R5. Fixed issue with ZipSource which prevented defintion file summaries from being loaded. Removed last bit of code irrelevant work. * Added ValueSet-BirthSex to R4 and R5 Validate Tests passing for all versions * Cleaned up csproj for Stu3, R4, and R5 .web * Updated TestConfiguration.json to use new external terminology service endpoint * Changed endpoint back to hapi * Validate-Code operationHandler. OperationRequest, and OpeartionResponse. * ValueSet $Validate-Code is mostly working and testing is partially implemented using OntoServer as external TS * Added Testing for Get version of valueset $validate-code * Created Terminology Controller and profile validator now uses external terminology service by default * Implemented POST and GET $Validate-Code for both ValueSets and CodeSystems. Some E2E tests are implemented but more are to come. * Added more testing for $validate-code Implemented GET version of $lookup * $validate-code does not work for STU3 as the TS is on R4 Fixed error where some operations would return an error saying server could not read conformance statement. * Implemented $lookup and wrote E2E tests for said operation * Finished Implementing and testing $expand Cleaned up terminology related code. * Added logging when definitions folder is not found or external/fallback terminology service cannot be created Added ProfileValidationTerminologServer endpoint in the test configuration file * Fixed Test names in TerminologyOperationTests * Final code clean up before submitting PR Terminology related tests will be skipped if there is no external endpoint set. * Removed unused variable * Fixed bug where tests were failing because CreateAsync was using PUT request instead of POST * Added: Terminology Operation Filters for TerminologyControlle, Terminology Operations to Capability Statement Fixed: Batch tests failing because $lookup was assuming to not work, Tests failing due to InProcTestServer only available in local environment Improved code standard to fit with the rest of FHIR server codebase * Fixed Capability Statement * Added temporary operatioDefinition json files. * Added Operation definition for terminology operations. * Fixed problem with testConfiguration settings not being updated. Fixed small bug in TerminologyOperator * Removed code in CheckResults method from Terminology Operator that retried terminology operation if the error was related to conformance statement read issues. Fixed issue in bundle-batch that assumed $lookup was not implemented. * Added checks in terminology controller to make sure operation that is to be executed is enabled in appsettings. Added separate testconfiguration.json for each version of FHIR. Placed profiler resolver in a try catch if the profile validation terminology endpoint is empty * Removed old testconfiguration.json file that was causing tests to not be skipped when necessary. * Updated test configuration path in provision-deploy.yml Added terminology module logging messages to API.Resources.resx * Added break out of for each look once bool has been set to true in Lookup and Expand parameters filter. More code clean up * Fixed package.yml to account for separate, version specific, testconfiguration files. * Trying to fix build & deploy for test configuration * Corrected HAPI endpoint for STU3 in testconfiguration.json Corrected validate and terminology tests where they would break out of for each loop early. * Fixed tests that were not working correctly. * Fixed comment typo * Fixed Typos * Fixed test name typo. * $validate was already being added to the capability statement somewhere else within the FHIR service, so I removed it from where I was adding the terminology operations. Also fixed typo. * Added Terminology Operations Documentation. * Update TerminologyOperations.md * Update TerminologyOperations.md Co-authored-by: Jared Erwin <[email protected]>
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Description
Adds necessary support for configuring an external terminology service and creates endpoints to pass-thru terminology requests.
Related issues
Addresses [issue #].
Testing
Manual testing performed as well as automated tests added.
FHIR Team Checklist
Semver Change (docs)
Patch|Skip|Feature|Breaking (reason)
Semver=Feature