8000 ENG-392 Don't create consolidated on ingest by leite08 · Pull Request #3938 · metriport/metriport · GitHub
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ENG-392 Don't create consolidated on ingest #3938

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Merged
merged 4 commits into from
May 31, 2025
Merged

ENG-392 Don't create consolidated on ingest #3938

merged 4 commits into from
May 31, 2025

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leite08
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@leite08 leite08 commented May 31, 2025 •
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Dependencies

Description

Don't create consolidated on ingest.

Normalize consolidated loaded from S3 (b/c this is not done yet).

Throw error if consolidated is missing.

Also moves a function that was a left-over from the text only ingestion. Still useful on utils.

Testing

  • Local
    • ingestion works when consolidated found
    • ingestion fails when consolidated not found
    • consolidated gets normalized
  • Staging
    • pt created before 2025-06-01, not ingested yet, search works when consolidated found
    • pt created before 2025-06-01, not ingested yet, search fails when no consolidated
      • This is a situation that should never happen
    • pt already ingested, search works
    • ingestion through queue works when consolidated found
    • ingestion through queue fails when consolidated not found and msg goes to DLQ
    • consolidated gets normalized
  • Sandbox
    • none
  • Production
    • none

Release Plan

  • Merge this

Summary by CodeRabbit

  • Refactor

    • Simplified patient data processing by removing support for external API fetching and focusing on local file-based FHIR Bundle handling.
    • Streamlined bundle-to-text conversion by removing and consolidating related functions.
    • Improved data normalization by refining encounter filtering and preventing duplicate condition extensions.
    • Reduced infrastructure dependencies by eliminating environment variables and permissions related to FHIR bundle processing.

  • Chores

    • Cleaned up unused code, imports, and environment variables for improved maintainability.

@linear Linear
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linear bot commented May 31, 2025

ENG-392 [BE] Ingestion shouldn't create consolidated

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coderabbitai bot commented May 31, 2025 •
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Walkthrough

This change removes the ability to convert consolidated FHIR Bundles to text arrays via the getConsolidatedAsText function and the bundleToString utility. It updates ingestion logic to use a new getConsolidatedBundle helper, eliminates API-based resource fetching in a utility script, replaces encounter normalization with filtering, prevents duplicate chronicity extensions, and removes related Lambda dependencies in infrastructure code.

Changes

File(s) Change Summary
packages/core/src/command/consolidated/consolidated-get.ts Removed getConsolidatedAsText export and related imports.
packages/core/src/command/consolidated/search/fhir-resource/ingest-lexical.ts Updated ingestion to use new getConsolidatedBundle helper; refactored error handling and variable usage.
packages/core/src/external/fhir/export/string/bundle-to-string.ts Removed bundleToString export; updated documentation to focus on single-resource conversion; removed Bundle import.
packages/core/src/external/fhir/normalization/normalize-fhir.ts Replaced normalizeEncounters call with filterInvalidEncounters in normalization pipeline.
packages/core/src/external/fhir/normalization/resources/condition.ts Added check to avoid adding duplicate chronicity extensions to conditions.
packages/core/src/external/fhir/normalization/resources/encounter.ts Renamed normalizeEncounters function to filterInvalidEncounters without changing logic.
packages/infra/lib/lambdas-nested-stack.ts Removed all references, environment variables, and permissions related to fhirToBundleLambda.
packages/utils/src/open-search/semantic-text-from-consolidated.ts Removed API-based fetching; now only processes local bundle files; redefined local bundleToString function.

Sequence Diagram(s)

sequenceDiagram
    participant IngestionJob
    participant getConsolidatedBundle
    participant BundleNormalizer

    IngestionJob->>getConsolidatedBundle: Request consolidated bundle (cxId, patientId)
    getConsolidatedBundle->>BundleNormalizer: Normalize bundle
    BundleNormalizer-->>getConsolidatedBundle: Return normalized bundle
    getConsolidatedBundle-->>IngestionJob: Return bundle
    IngestionJob->>OpenSearch: Ingest bundle resources
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Reviewing files that changed from the base of the PR and between 41d1841 and d30cfc6.

📒 Files selected for processing (3)
  • packages/core/src/external/fhir/normalization/normalize-fhir.ts (2 hunks)
  • packages/core/src/external/fhir/normalization/resources/condition.ts (2 hunks)
  • packages/core/src/external/fhir/normalization/resources/encounter.ts (1 hunks)
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`**/*.ts`: - Use the Onion Pattern to organize a package's code in layers - Try to use immutable code and avoid sharing state across different functions, objects, and systems - Try...

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  • max column length is 100 chars
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  • packages/core/src/external/fhir/normalization/normalize-fhir.ts
  • packages/core/src/external/fhir/normalization/resources/encounter.ts
  • packages/core/src/external/fhir/normalization/resources/condition.ts
🧬 Code Graph Analysis (1)
packages/core/src/external/fhir/normalization/normalize-fhir.ts (1)
packages/core/src/external/fhir/normalization/resources/encounter.ts (1)
  • filterInvalidEncounters (6-18)
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🔇 Additional comments (5)
packages/core/src/external/fhir/normalization/resources/condition.ts (2)

22-25: LGTM! Proper duplicate chronicity extension prevention.

The log 8000 ic correctly prevents duplicate chronicity extensions by checking for existing ones before creating new ones. The early return from the forEach iteration is the appropriate behavior here.

7-8: Import addition looks good.

The new import for findChronicityExtension is properly added and used consistently with the existing import pattern.

packages/core/src/external/fhir/normalization/normalize-fhir.ts (2)

7-7: Good import update for clarity.

The import change from normalizeEncounters to filterInvalidEncounters better reflects the function's actual behavior of filtering out invalid encounters rather than normalizing them.

36-40: Improved variable naming and function call.

The updated function call and variable naming (validEncounters instead of normalizedEncounters) more accurately represents what the function does - filtering invalid encounters rather than normalizing them.

packages/core/src/external/fhir/normalization/resources/encounter.ts (1)

6-9: Excellent function rename for clarity.

The rename from normalizeEncounters to filterInvalidEncounters much better describes what this function actually does - it filters out encounters that don't have a reason, location, or type, rather than normalizing encounter data. This improves code readability and maintainability.

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leite08 added 3 commits May 31, 2025 18:31
@leite08
refactor: ingestion lambda don't recreate consolidated
c7653b2 
Ref eng-392

Signed-off-by: Rafael Leite <2132564+leite08@users.noreply.github.com>
@leite08
refactor: move unused ingestion code to utils
a81c18b 
Ref eng-392

Signed-off-by: Rafael Leite <2132564+leite08@users.noreply.github.com>
@leite08
refactor(core): normalize consolidated bundle +
41d1841 
- normalize consolidated bundle
- throw on missing consolidated bundle

Ref eng-392

Signed-off-by: Rafael Leite <2132564+leite08@users.noreply.github.com>
@leite08 leite08 force-pushed the eng-392-dont-create-consolidated-on-ingest branch from 35d1a7e to 41d1841 Compare May 31, 2025 21:52
@leite08 leite08 changed the base branch from develop to eng371-fix-hydration May 31, 2025 21:52
@leite08 leite08 marked this pull request as ready for review May 31, 2025 21:56
@leite08 leite08 mentioned this pull request May 31, 2025
Merged
4 tasks
Base automatically changed from eng371-fix-hydration to develop May 31, 2025 22:00
@leite08
fix(core): single chronic extension in normalization
d30cfc6 
Ref eng-392

Signed-off-by: Rafael Leite <2132564+leite08@users.noreply.github.com>
@leite08 leite08 mentioned this pull request May 31, 2025
Merged
1 task
@leite08 leite08 added this pull request to the merge queue May 31, 2025
Merged via the queue into develop with commit afe037a May 31, 2025
18 checks passed
@leite08 leite08 deleted the eng-392-dont-create-consolidated-on-ingest branch May 31, 2025 22:50
@leite08 leite08 mentioned this pull request May 31, 2025
Merged
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This was referenced Jun 1, 2025
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