Unwanted conditions to notes schema #15764

lucero-v · 2024-09-03T16:35:50Z

This PR adds a schema for converting unwanted conditions to notes to be used with MARS OTC data

Test Steps:

Add the following rules to a receiver transform

  - name: observation-result-with-aoe
    resource:
      - "%resource.result.resolve().where(code.coding.extension('https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code').value.where(code in ('840539006))) | %resource.basedOn.resolve().supportingInfo.resolve()"

  - name: order-note
    resource: "%resource.basedOn.resolve().note | %resource.result.resolve().where(code.coding.extension('https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code').value.where(code in ('840539006')).exists().not())"
    schema: classpath:/metadata/hl7_mapping/receivers/Common/observation-to-nte/unwanted-conditions-to-notes.yml

Here we are indicating that all results that do not have a code of '840539006' (COVID) should go through the new unwanted-conditions-to-notes schema

Run a multiplex test and verify that all other conditions except for COVID are shown as NTE segments on the resulting message.

Changes

added unwanted-conditions-to-notes schema
added integration test

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?

Linked Issues

Fixes #issue

To Be Done

Create GitHub issues to track the work remaining, if any

#issue

…cording to MARS

github-actions · 2024-09-03T16:36:05Z

Dependency Review

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

OpenSSF Scorecard

Package	Version	Score	Details

Scanned Manifest Files

github-actions · 2024-09-03T16:48:58Z

Test Results

1 229 tests ±0 1 225 ✅ ±0 7m 8s ⏱️ +7s
161 suites ±0 4 💤 ±0
161 files ±0 0 ❌ ±0

Results for commit 73a56f0. ± Comparison against base commit 6f4c038.

♻️ This comment has been updated with latest results.

github-actions · 2024-09-03T17:10:21Z

Integration Test Results

53 files ±0 53 suites ±0 27m 59s ⏱️ -7s
410 tests +1 401 ✅ +1 9 💤 ±0 0 ❌ ±0
413 runs +1 404 ✅ +1 9 💤 ±0 0 ❌ ±0

Results for commit 73a56f0. ± Comparison against base commit 6f4c038.

♻️ This comment has been updated with latest results.

…onreportable-to-notes

GilmoreA6 · 2024-09-05T15:39:48Z

...ter/src/testIntegration/resources/datatests/FHIR_to_HL7/mars_unwanted_condition_to_notes.hl7

+ORC|RE|bfe0d734-06a8-472e-bf6a-cad808150c4e^Testing Lab^12D4567890^CLIA|bfe0d734-06a8-472e-bf6a-cad808150c4e^Testing Lab^12D4567890^CLIA|||||||||1245319599^McTester^Phil^^^^^^NPI&2.16.840.1.113883.4.6&ISO^L^^^NPI||(530) 867 5309^WPN^PH^^1^530^8675309^^^^^(530) 867 5309|20240828174209+0000||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA|(530) 867 5309^WPN^PH^^1^530^8675309^^^^^(530) 867 5309|321 Ocean Drive^^Denver^CO^80210^USA
+OBR|1|bfe0d734-06a8-472e-bf6a-cad808150c4e^Testing Lab^12D4567890^CLIA|bfe0d734-06a8-472e-bf6a-cad808150c4e^Testing Lab^12D4567890^CLIA|96123-5^SARS-CoV-2 (COVID-19) RdRp gene [Presence] in Upper respiratory specimen by NAA with probe detection^LN|||20240828172709+0000|||||||||1245319599^McTester^Phil^^^^^^NPI&2.16.840.1.113883.4.6&ISO^L^^^NPI|(530) 867 5309^WPN^PH^^1^530^8675309^^^^^(530) 867 5309|||||20240828174209+0000|||F
+NTE|1||This is a note
+NTE|2|0|OBX filtered for identifier = 96123-5 - COVID-19; value = 260373001 - Detected. OBX was removed due to your jurisdictional reporting rules indicating this result is not reportable.


This value in NTE-2 should not be numeric, This should be one of the values in table HL70105 "O", "L" or "P"

Can we also add a test where multiple observations are converted to notes?

Ah, nice catch, thanks. Also added test with Flu A, Flu B, and COVID.

…reportable-to-notes

GilmoreA6

Good Job!

sonarcloud · 2024-09-10T21:57:35Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

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Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump @playwright/test in /frontend-react in the playwright group (#15807) Bumps the playwright group in /frontend-react with 1 update: [@playwright/test](https://github.com/microsoft/playwright). Updates `@playwright/test` from 1.46.1 to 1.47.0 - [Release notes](https://github.com/microsoft/playwright/releases) - [Commits](microsoft/playwright@v1.46.1...v1.47.0) --- updated-dependencies: - dependency-name: "@playwright/test" dependency-type: direct:development update-type: version-update:semver-minor dependency-group: playwright ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * disable smoke tests for receiver status temporarily (#15836) * Engagement/jessica/15541 cli add code to condition (#15803) * Added code to condition to the fhirdata cli tool * added schema that handles converting unwanted conditions to notes acccording to MARS (#15764) * Bump the react-query group across 1 directory with 2 updates (#15838) Bumps the react-query group with 2 updates in the /frontend-react directory: [@tanstack/react-query](https://github.com/TanStack/query/tree/HEAD/packages/react-query) and [@tanstack/react-query-devtools](https://github.com/TanStack/query/tree/HEAD/packages/react-query-devtools). Updates `@tanstack/react-query` from 5.51.23 to 5.55.4 - [Release notes](https://github.com/TanStack/query/releases) - [Commits](https://github.com/TanStack/query/commits/v5.55.4/packages/react-query) Updates `@tanstack/react-query-devtools` from 5.51.23 to 5.55.4 - [Release notes](https://github.com/TanStack/query/releases) - [Commits](https://github.com/TanStack/query/commits/v5.55.4/packages/react-query-devtools) --- updated-dependencies: - dependency-name: "@tanstack/react-query" dependency-type: direct:production update-type: version-update:semver-minor dependency-group: react-query - dependency-name: "@tanstack/react-query-devtools" dependency-type: direct:production update-type: version-update:semver-minor dependency-group: react-query ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Joseph Andersen <[email protected]> * Bump express from 4.19.2 to 4.20.0 in /frontend-react (#15837) Bumps [express](https://github.com/expressjs/express) from 4.19.2 to 4.20.0. - [Release notes](https://github.com/expressjs/express/releases) - [Changelog](https://github.com/expressjs/express/blob/master/History.md) - [Commits](expressjs/express@4.19.2...4.20.0) --- updated-dependencies: - dependency-name: express dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump @okta/okta-signin-widget in /frontend-react in the okta group (#15809) Bumps the okta group in /frontend-react with 1 update: [@okta/okta-signin-widget](https://github.com/okta/okta-signin-widget). Updates `@okta/okta-signin-widget` from 7.21.2 to 7.23.0 - [Release notes](https://github.com/okta/okta-signin-widget/releases) - [Changelog](https://github.com/okta/okta-signin-widget/blob/master/webpack.release.config.js) - [Commits](okta/okta-signin-widget@okta-signin-widget-7.21.2...okta-signin-widget-7.23.0) --- updated-dependencies: - dependency-name: "@okta/okta-signin-widget" dependency-type: direct:production update-type: version-update:semver-minor dependency-group: okta ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump the vitest group in /frontend-react with 3 updates (#15457) Bumps the vitest group in /frontend-react with 3 updates: [@vitest/coverage-istanbul](https://github.com/vitest-dev/vitest/tree/HEAD/packages/coverage-istanbul), [@vitest/ui](https://github.com/vitest-dev/vitest/tree/HEAD/packages/ui) and [vitest](https://github.com/vitest-dev/vitest/tree/HEAD/packages/vitest). Updates `@vitest/coverage-istanbul` from 2.0.4 to 2.0.5 - [Release notes](https://github.com/vitest-dev/vitest/releases) - [Commits](https://github.com/vitest-dev/vitest/commits/v2.0.5/packages/coverage-istanbul) Updates `@vitest/ui` from 2.0.4 to 2.0.5 - [Release notes](https://github.com/vitest-dev/vitest/releases) - [Commits](https://github.com/vitest-dev/vitest/commits/v2.0.5/packages/ui) Updates `vitest` from 2.0.4 to 2.0.5 - [Release notes](https://github.com/vitest-dev/vitest/releases) - [Commits](https://github.com/vitest-dev/vitest/commits/v2.0.5/packages/vitest) --- updated-dependencies: - dependency-name: "@vitest/coverage-istanbul" dependency-type: direct:development update-type: version-update:semver-patch dependency-group: vitest - dependency-name: "@vitest/ui" dependency-type: direct:development update-type: version-update:semver-patch dependency-group: vitest - dependency-name: vitest dependency-type: direct:development update-type: version-update:semver-patch dependency-group: vitest ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Joseph Andersen <[email protected]> * Bump bridgecrewio/checkov-action from 12.2867.0 to 12.2869.0 (#15845) Bumps [bridgecrewio/checkov-action](https://github.com/bridgecrewio/checkov-action) from 12.2867.0 to 12.2869.0. - [Release notes](https://github.com/bridgecrewio/checkov-action/releases) - [Commits](bridgecrewio/checkov-action@6429623...08a0f07) --- updated-dependencies: - dependency-name: bridgecrewio/checkov-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Engagement/jessica/15405 cleanup deidentification enrichment (#15821) * Changed where the files used and produced by the remove pii test live as well as delete the output file after the test runs * Engagement/jessica/15540 fhirdata specify receiver (#15800) * Added the ability to specify the receiver settings for the fhirdata command * Made the receiver schema optional if the receiver is specified. * Checking the receiver for their format and using it. if applicable. Applying enrichment schemas across the board if a receiver is specified and has them * Engagement/jessica/15406 download report cleanup (#15847) * Capturing the report not existing error so that we can return a pretty one. Fixing a condition in the pii removal yml. Returning a prettier body for a report * Bump chromaui/action from 11.7.1 to 11.8.0 (#15848) Bumps [chromaui/action](https://github.com/chromaui/action) from 11.7.1 to 11.8.0. - [Release notes](https://github.com/chromaui/action/releases) - [Commits](chromaui/action@b984808...95f238d) --- updated-dependencies: - dependency-name: chromaui/action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * #15217 - Implement smoke test user flow for Last Mile Failures (#15843) * #15217 - Implement smoke test user flow for Last Mile Failures * Fixed linting issues * Fixed linting issues --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: etanb <[email protected]> Co-authored-by: Jack Wang <[email protected]> Co-authored-by: Angela DeGolier <[email protected]> Co-authored-by: chris-kuryak <[email protected]> Co-authored-by: OTT SATHNGAM <[email protected]> Co-authored-by: JessicaWNava <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: etanb <[email protected]> Co-authored-by: Penelope Lischer <[email protected]> Co-authored-by: Brick Green <[email protected]> Co-authored-by: victor-chaparro <[email protected]> Co-authored-by: James Gilmore <[email protected]> Co-authored-by: Joseph Andersen <[email protected]> Co-authored-by: lucero-v <[email protected]>

added schema that handles converting unwanted conditions to notes acc…

535b783

…cording to MARS

lucero-v requested a review from a team as a code owner September 3, 2024 16:35

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lucero-v self-assigned this Sep 3, 2024

lucero-v requested review from oslynn, GilmoreA6, victor-chaparro and JessicaWNava September 3, 2024 18:52

lucero-v linked an issue Sep 3, 2024 that may be closed by this pull request

Convert unwanted conditions to notes in a FHIR to HL7 transform for MARS OTC data #15584

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fix resource on test-transform

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JessicaWNava mentioned this pull request Sep 4, 2024

Test functionality of RADX MARS OTC Condition to Note Conversion feature #14693

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Merge remote-tracking branch 'origin/master' into engagement/lucero/n…

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…onreportable-to-notes

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lucero-v added the onboarding-ops Work related to onboarding with a partner. Addressed by the Onboarding & Operations team in RS. label Sep 5, 2024

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lucero-v temporarily deployed to staging September 9, 2024 23:18 — with GitHub Actions Inactive

fixed typo, added better test for unwanted condition to notes

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Merge branch 'master' into engagement/lucero/nonreportable-to-notes

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Merge branch 'master' into engagement/lucero/nonreportable-to-notes

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Merge branch 'master' into engagement/lucero/nonreportable-to-notes

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Merge branch 'master' into engagement/lucero/nonreportable-to-notes

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lucero-v merged commit bf44b02 into master Sep 10, 2024
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Unwanted conditions to notes schema #15764

Unwanted conditions to notes schema #15764

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Unwanted conditions to notes schema #15764

Unwanted conditions to notes schema #15764

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