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merged 1 commit into from
Jun 21, 2025
Merged

fix(core): Fix deduplication to properly handle references for MedicationDispense #4076

merged 1 commit into from
Jun 21, 2025

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@keshavsaharia keshavsaharia commented Jun 21, 2025 •
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metriport/metriport-internal#1040

Issues:

Dependencies

  • Upstream: None
  • Downstream: None

Description

I received a report that Surescripts conversion bundles had broken references for MedicationDispense, but I couldn't figure out anywhere that the logic would allow that to happen. I wrote an analysis script to test this, which showed that bundles with MedicationDispense were having their references broken by dangerouslyDeduplicateFhir. This is an issue that likely affects any FHIR bundle with MedicationDispense resources.

Screenshot 2025-06-20 at 7 41 19 PM

After implementing the fix, all patient bundles were deduplicating correctly with correct references.

Screenshot 2025-06-20 at 7 41 40 PM

Testing

Will test by deduplicating some large bundles.

  • Local
    • Use utils script to download large bundles and deduplicate
  • Staging
    • Run deduplication on staging bundles through Surescripts
  • Production
    • Run deduplication on production and monitor

Release Plan

  • Merge this

Summary by CodeRabbit

  • Bug Fixes
    • Ensured that MedicationDispense resources are correctly extracted and included alongside other medication-related data.
    • Extended deduplication and reference replacement processes to cover MedicationDispense resources.

@keshavsaharia
fix(core): fix to deduplication to avoid breaking references for Medi…
12eb5fe 
…cationDispense

metriport/metriport-internal#1040

Signed-off-by: Keshav Saharia <keshav@metriport.com>
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linear bot commented Jun 21, 2025

ENG-498 MedicationDispense bug in deduplicate

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coderabbitai bot commented Jun 21, 2025 •
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Walkthrough

The changes update the handling of the MedicationDispense FHIR resource type. Extraction logic now collects MedicationDispense resources from bundles, and deduplication logic includes MedicationDispense in medication-related resource processing, ensuring consistent treatment with other medication resource types.

Changes

File(s) Change Summary
packages/core/src/external/fhir/bundle/bundle.ts Updated extraction logic to collect and return MedicationDispense resources from FHIR bundles.
packages/core/src/fhir-deduplication/deduplicate-fhir.ts Included MedicationDispense in deduplication and medication reference replacement logic.

Sequence Diagram(s)

sequenceDiagram
    participant Client
    participant BundleExtractor
    participant Deduplicator

    Client->>BundleExtractor: extractFhirTypesFromBundle(bundle)
    BundleExtractor->>BundleExtractor: Collect MedicationDispense and other resources
    BundleExtractor-->>Client: ExtractedFhirTypes (includes medicationDispenses)

    Client->>Deduplicator: deduplicateFhir(ExtractedFhirTypes)
    Deduplicator->>Deduplicator: Deduplicate medications
    Deduplicator->>Deduplicator: Replace medication references in MedicationDispense and others
    Deduplicator-->>Client: Deduplicated FHIR resources
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📥 Commits

Reviewing files that changed from the base of the PR and between 5522a26 and 12eb5fe.

📒 Files selected for processing (2)
  • packages/core/src/external/fhir/bundle/bundle.ts (2 hunks)
  • packages/core/src/fhir-deduplication/deduplicate-fhir.ts (2 hunks)
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📓 Path-based instructions (1)
`**/*.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...

**/*.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 to build code that's idempotent whenever possible
  • Prefer functional programming style functions: small, deterministic, 1 input, 1 output
  • Minimize coupling / dependencies
  • Avoid modifying objects received as parameter
  • Only add comments to code to explain why something was done, not how it works
  • Naming
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    • constants, variables, functions: camelCase
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      the same type
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      like DB and HTTP; convert to undefined before sending inwards into the code
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    • Move literals to constants declared after imports when possible (avoid magic numbers)
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    and try to use out().log instead
  • Avoid multi-line logs
    • don't send objects as a second parameter to console.log() or out().log()
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  • scripts: top-level comments go after the import
  • packages/core/src/fhir-deduplication/deduplicate-fhir.ts
  • packages/core/src/external/fhir/bundle/bundle.ts
⏰ Context from checks skipped due to timeout of 90000ms (2)
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  • GitHub Check: Analyze (javascript)
🔇 Additional comments (6)
packages/core/src/fhir-deduplication/deduplicate-fhir.ts (3)

35-35: LGTM: MedicationDispense added to medication-related types.

This correctly includes MedicationDispense in the medication-related resource types, ensuring consistent handling with other medication resources.

64-64: LGTM: Medication references will be properly replaced.

Adding "medicationDispenses" to the reference replacement logic is correct, as the comment above explains that medication references must be replaced before deduplication.

68-75: ```shell
#!/bin/bash
set -e

1. List all deduplication functions in the fhir-deduplication directory

echo "=== Deduplication functions in fhir-deduplication ==="
rg -n "export function deduplicate" packages/core/src/fhir-deduplication/*.ts

2. Search for any 'Dispense' references in the same directory

echo "=== 'Dispense' references in fhir-deduplication ==="
rg -n "Dispense" packages/core/src/fhir-deduplication/*.ts

3. Show context around medicationDispenses usage in deduplicate-fhir.ts

echo "=== Context around medicationDispenses in deduplicate-fhir.ts ==="
rg -n "medicationDispens" packages/core/src/fhir-deduplication/deduplicate-fhir.ts -A3 -B3


</details>
<details>
<summary>packages/core/src/external/fhir/bundle/bundle.ts (3)</summary>

`384-384`: **Good organization: MedicationDispense array grouped with medication resources.**

Moving the `medicationDispenses` array declaration to be grouped with other medication-related arrays improves code organization and readability.

---

`420-421`: **LGTM: MedicationDispense extraction logic implemented correctly.**

The extraction logic for MedicationDispense resources follows the same pattern as other resource types and correctly adds them to the medicationDispenses array.

---

`502-502`: **LGTM: MedicationDispense included in extraction results.**

Correctly includes the medicationDispenses array in the returned ExtractedFhirTypes object, ensuring the extracted resources are available for downstream processing.

</details>

</blockquote></details>

</details>
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@keshavsaharia keshavsaharia marked this pull request as ready for review June 21, 2025 02:54
@keshavsaharia keshavsaharia added this pull request to the merge queue Jun 21, 2025
Merged via the queue into develop with commit 66cfe95 Jun 21, 2025
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@keshavsaharia keshavsaharia deleted the eng-498-medicationdispense-deduplication branch June 21, 2025 19:03
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@RamilGaripov RamilGaripov RamilGaripov approved these changes

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