Add 99717-49 Local Code to 76030-6 LOINC mapping

[jbiskie]

Adds 99717-49 Local Code to 76030-6 LOINC mapping

This PR:

• Adds a new local to LOINC mapping
• Refactors the hardcoded mapping in the transform class into a configurable arguments in transformation_definitions.json
• Adds additional unit tests to cover cases where the codingMap json argument is not structured as expected

Issue

#1452

This PR covers engineering tasks 1 and 2. Task 3 (Add RS E2E tests for the mapping transformation) will be addressed in another PR.

Checklist

• I have added tests to cover my changes
• I have added logging where useful (with appropriate log level)
• I have added JavaDocs where required
• I have updated the documentation accordingly

Note: You may remove items that are not applicable

[github-actions]

PR Reviewer Guide 🔍

Here are some key observations to aid the review process:

⏱️ Estimated effort to review: 2 🔵🔵⚪⚪⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ No major issues detected

[github-actions]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Score
Possible issue	Prevent potential overwriting of existing keys in the map Ensure that the key "99717-49" does not already exist in the codingMap to prevent overwriting an existing mapping. This can be done by checking if the key exists before putting a new value. etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/ruleengine/transformation/custom/MapLocalObservationCodes.java [155-160] -codingMap.put( - "99717-49", - new IdentifierCode( - "76030-6", - "IDS gene full mutation analysis in Blood or Tissue by Sequencing", - HapiHelper.LOINC_CODE)); +if (!codingMap.containsKey("99717-49")) { + codingMap.put( + "99717-49", + new IdentifierCode( + "76030-6", + "IDS gene full mutation analysis in Blood or Tissue by Sequencing", + HapiHelper.LOINC_CODE)); +} Suggestion importance[1-10]: 7 Why: The suggestion to check if a key already exists before adding it to the map is a good practice to avoid data integrity issues. This is particularly important in a map that might be accessed or modified in various parts of the application, ensuring that no existing data is unintentionally overwritten.	7

[jbiskie]

PR Code Suggestions ✨

Explore these optional code suggestions:
Category Suggestion Score
Possible issue
Prevent potential overwriting of existing keys in the map

7

Non-issue. IntelliJ flags duplicates.

[halprin]

We should also update our RS E2E tests to test this.

[jbiskie]

Manual RS end to end testing was successful. Used file 020 and added an extra OBX for 99717-49:

OBX|12|TX|^^^99717-49^New local code added^L|1|Negative|||N|||F|||20240711034913

transformed:

OBX|113|TX|76030-6^IDS gene full mutation analysis in Blood or Tissue by Sequencing^LN^99717-49^New local code added^L|1|Negative|||N|||F|||20240711034913

[basiliskus]

Seems like there are some extracted functions that have a single line of code and are used only once. Are they needed? There's a tradeoff when refactoring to extract code to functions and adding too many can create unnecessary overhead. If they are added to help understand what the code does, you could consider adding a comment instead

[basiliskus]

Looks like this is only used once, it has a single line and the content is pretty straightforward. Does it need to extracted into its own function?

[jorg3lopez]

Good suggestion. I'll inline the extracting method and keep the logging one as is to keep the logging logic in one area.

[basiliskus]

What I meant is that we probably don't need logUnmappedLocalCode as it's adding more abstraction without the benefits. You could directly call logger.logWarning without putting it into its own function

[sonarcloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
97.8% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud