Update OML mappings

[JFisk42]

This PR updates the OML mappings to use the new catchall mappings.

Test Steps:

1. OML Related tests should pass:
   1. ./gradlew :prime-router:testIntegration --tests "gov.cdc.prime.router.datatests.mappinginventory.omlo21.OMLO21Full" -Pforcetest
   2. ./gradlew :prime-router:testIntegration --tests "gov.cdc.prime.router.datatests.TranslationTests" -Pforcetest
2. All other tests should pass as well.

Changes

• OML FHIR -> HL7 mappings are no longer dependent upon deprecated mapping files (hl7_mapping/common; hl7_mapping/v251; etc.)
• Unused FHIR -> HL7 mappings have been removed
• Created end-to-end tests for OML HL7 -> FHIR -> HL7 mappings.
  • OML HL7 -> FHIR catchall mappings were updated to better support a maximally configured OML message.
    • ServiceRequest.specimen and ServiceRequest.supportingInfo were added to support this. Specimen.collection and Patient.relationship were updated as well.
      • The vast majority of test updates on this PR are related to these catchall updates.
    • OML support for the CE to CWE casting was added.
• Updated the OML data test files from translation-test-config.csv to reflect updates in the mappings
  • The .fhir file in the FHIR -> HL7 scenario will need to be verified and communicated with ETOR to ensure no breaking changes have been made. The significant differences here reflect the new and different fields being mapped in the OML HL7 -> FHIR conversion. #TODO

Checklist

Testing

• Tested locally?
• Ran ./prime test or ./gradlew testSmoke against local Docker ReportStream container?
• (For Changes to /frontend-react/...) Ran npm run lint:write?
• Added tests?

Process

• Are there licensing issues with any new dependencies introduced?
• Includes a summary of what a code reviewer should test/verify?
• Updated the release notes?
• Database changes are submitted as a separate PR?
• DevOps team has been notified if PR requires ops support?

To Be Done

Follow up issues still need to be logged:

• Ticket for Phase 2 of the OML mappings update. This will focus on adding any necessary new fields with a special focus on addressing fields that ETOR has documented as missing with the catchall uplift earlier this year.
• • Logged: https://app.zenhub.com/workspaces/platform-6182b02547c1130010f459db/issues/gh/cdcgov/prime-reportstream/16065
• A ticket to address a defect in the fhirdata cli tool which causes an exception when attempting to generate fhir data from a hl7 file. Unit tests should also be created for this command.
• • Logged: https://app.zenhub.com/workspaces/platform-6182b02547c1130010f459db/issues/gh/cdcgov/prime-reportstream/16066
• Possible ticket to add yml validation for conditional keywords. (ie NOT_NULL vs NOT NULL).
• • Logged: https://app.zenhub.com/workspaces/platform-6182b02547c1130010f459db/issues/gh/cdcgov/prime-reportstream/16081
• • I added a little bit of thoughts into the ticket. Because the oddity of this scenario, the juice may not be worth the squeeze to implement this.
• Ticket to remove any use of hl7v2Name (which used to be a valid extension url) from our code base.
• • Logged: https://app.zenhub.com/workspaces/platform-6182b02547c1130010f459db/issues/gh/cdcgov/prime-reportstream/16077

[github-actions]

Dependency Review

✅ No vulnerabilities or license issues or OpenSSF Scorecard issues found.

OpenSSF Scorecard

Package	Version	Score	Details

Scanned Manifest Files

[github-actions]

Test Results

1 232 tests  ±0   1 228 ✅ ±0   7m 34s ⏱️ -32s
  162 suites ±0       4 💤 ±0 
  162 files   ±0       0 ❌ ±0 

Results for commit fa0014e. ± Comparison against base commit 1bf38e8.

♻️ This comment has been updated with latest results.

[github-actions]

Integration Test Results

 54 files  +1   54 suites  +1   29m 33s ⏱️ + 1m 31s
413 tests +3  404 ✅ +3  9 💤 ±0  0 ❌ ±0 
416 runs  +3  407 ✅ +3  9 💤 ±0  0 ❌ ±0 

Results for commit fa0014e. ± Comparison against base commit 1bf38e8.

This pull request removes 1 and adds 4 tests. Note that renamed tests count towards both.

gov.cdc.prime.router.datatests.mappinginventory.orcobr.ORCOBRToServiceRequestDiagnosticReportTests ‑ test correctly handles the effective when OBR8 is not populated()

gov.cdc.prime.router.datatests.mappinginventory.omlo21.OMLO21Full ‑ test OML_O21 all segments()
gov.cdc.prime.router.datatests.mappinginventory.orcobr.ORCOBRToServiceRequestDiagnosticReportTests ‑ test correctly handles the effectiveDateTime when OBR8 is not populated()
gov.cdc.prime.router.datatests.mappinginventory.orcobr.ORCOBRToServiceRequestDiagnosticReportTests ‑ test correctly handles the effectivePeriod when OBR8 is populated()
gov.cdc.prime.router.datatests.mappinginventory.orcobr.ORCOBRToServiceRequestDiagnosticReportTests ‑ test populates OML specific fields for OML messages()

♻️ This comment has been updated with latest results.

[sonarcloud]

Quality Gate failed

Failed conditions
40.0% Coverage on New Code (required ≥ 80%)

See analysis details on SonarCloud

[JFisk42]

#TODO: I arrived at the contents of this file by using the fhirdata cli tool to generate the fhir from the expected hl7. I'm not sure how important some of these removed fields are to ETOR but I imagine they would be delighted if those one day showed up in the HL7 (and thus good to preserve in this file). When logging the ticket for the OML second pass I will also go through and see if any of these are low hanging fields to add that are mapped in the mapping inventory.

[JFisk42]

Couple points here: Logged a ticket for the follow up OML items. Posted in the ETOR channel to alert them to the changes coming down the pipe. Also remembered that a number of fields are enriched from ETOR-TI itself.

[JFisk42]

For some reason after pushing the last commit to fix the build, GitHub decided the backend didn't need to be built :/

[JFisk42]

Forgot to post these comments on Friday.

[mkalish]

Fantastic stuff! Only comment would be a few new test cases or test enhancements

[arnejduranovic]

Changes look good and new tickets appear ready for refinement, great work!