199/72 canvas/elation/athena contribution plumbing #3788

thomasyopes · 2025-05-05T17:36:48Z

Issues:

Dependencies

Downstream: 199/72 athena/elation client work for contribution #3799

Description

Migrates resource diff job to resource-type level computation instead of per individual resource
Moves the resource diff job start/get logic to a shared logic
Moves fetching of computed bundles pre-signed-urls (EHR and Resource Diff) to shared logic
Moves refreshing the EHR bundles to shared logic
Moves resource diff job routing to shared routes
Split shared file into domain specific elements + added utility files for bundles / jobs
Re-typed shared bundle code to use Medplum types, not custom types
Moves resource diff utility to fhir-deduplication folder and makes it non-ehr-specific

Testing

Local
- resource type workflow runs (including job updates)
- canvas level API interactions work on shared commands / jobs / routes (both internal and CX facing)
- diff utility produces the correct two output bundles.
Staging
- resource type workflow runs (including job updates)
- canvas level API interactions work on shared commands / jobs / routes (both internal and CX facing)
- diff utility produces the correct two output bundles.
Sandbox
- N/A
Production
- resource type workflow runs (including job updates)
- canvas level API interactions work on shared commands / jobs / routes (both internal and CX facing)
- diff utility produces the correct two output bundles.

Release Plan

Before shipping, throttle the start resource diff job lambda to
Merge this

Summary by CodeRabbit

New Features
- Added middleware to validate and process EHR source IDs in routes.
- Introduced new internal API endpoints for managing EHR patient resource diff jobs and bundles.
- Added utility modules for appointment date ranges, EHR client creation, JWT token handling, external ID parsing, and bundle operations.
- Introduced classes for cloud and local processing of resource diff bundle computations and EHR bundle refreshes.
- Added functions to compute resource differences and deduplicate FHIR resources with strict validation.
- Added new bundle types and resource type validations for improved EHR data handling.
- Added retry logic to API calls and SQS message sending for robustness.
Refactor
- Unified resource diff bundle creation and refresh logic, removing direction-based handling in favor of explicit bundle types and job IDs.
- Modularized shared utilities for JWT tokens, bundle operations, and mappings.
- Replaced direct bundle fetching with asynchronous job-based processing and parallel resource handling.
- Simplified EHR bundle refresh and resource diff start flows with improved job management and error handling.
- Updated resource type handling to use standardized supported resource types and schemas.
- Enhanced API request handling with centralized response validation and retry logic.
- Consolidated resource diff bundle computation methods into a single streamlined process.
- Updated import paths and code structure for better modularity and maintainability.
- Removed obsolete resource diff direction enums and related code.
Bug Fixes
- Improved validation for supported resource types and job status updates.
- Strengthened error handling and reporting in job processing and bundle operations.
- Fixed potential runtime errors by safely accessing resource properties and validating inputs.
Chores
- Removed obsolete endpoints, Lambda handlers, and infrastructure related to prior resource diff bundle initiation.
- Updated import paths and internal wiring to align with new utility modules and improved code structure.
- Cleaned up unused types, constants, and functions related to removed resource diff direction handling.
- Adjusted environment variables and permissions in infrastructure stacks to reflect removed components.
Documentation
- Enhanced API route parameter validation and documentation for better clarity and consistency.

Ref: ENG-82 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

coderabbitai · 2025-05-05T17:36:55Z

Walkthrough

This change set refactors and modularizes the EHR bundle/resource diff job infrastructure, removing legacy Canvas-specific resource diff logic and generalizing the workflow to support multiple EHRs. It introduces new utility modules for bundle and job management, updates API routes and handlers, and replaces direct Lambda invocations with SQS-driven job orchestration. Several files are deleted or replaced, type definitions are updated, and error handling and retry logic are improved throughout the codebase.

Changes

File(s) / Path(s)	Change Summary
`packages/api/src/command/mapping/cx.ts`, `.../patient.ts`, `.../consolidated-recreate.ts`, `.../cx-mapping.ts`, `.../jwt-token.ts`, `.../athenahealth/command/process-patients-from-appointments.ts`, `.../athenahealth/command/sync-patient.ts`, `.../athenahealth/shared.ts`, `.../canvas/command/process-patients-from-appointments.ts`, `.../canvas/command/sync-patient.ts`, `.../canvas/shared.ts`, `.../elation/command/process-patients-from-appointments.ts`, `.../elation/command/sync-patient.ts`, `.../elation/shared.ts`, `.../healthie/command/process-patients-from-appointments.ts`, `.../healthie/command/sync-patient.ts`, `.../healthie/shared.ts`, `.../jwt-token.ts`, `.../shared.ts`, `.../routes/ehr/shared.ts`, `.../routes/internal/jwt-token/athenahealth.ts`, `.../canvas.ts`, `.../elation.ts`, `.../healthie.ts`	Updated import paths to new utility modules; no logic changes.
`packages/api/src/external/ehr/canvas/command/bundle/fetch-ehr-bundle.ts`, `.../fetch-resource-diff-bundle-pre-signed-urls.ts`, `.../job/create-resource-diff-bundles/get-job-payload.ts`, `.../job/create-resource-diff-bundles/start-job.ts`, `.../shared.ts`, `.../resource-diff.ts`, `.../jwt-token.ts`, `.../lambdas/src/ehr-start-resource-diff-bundles.ts`	Deleted legacy Canvas-specific and shared resource diff/bundle/job logic.
`packages/api/src/external/ehr/canvas/command/bundle/refresh-ehr-bundles.ts`	Replaced legacy refresh logic with a new function `refreshEhrBundles` supporting generalized parameters and single resource type refresh.
`packages/api/src/external/ehr/shared/utils/appointment.ts`, `.../client.ts`, `.../external-id.ts`, `.../fhir.ts`, `.../job.ts`, `.../jwt-token.ts`, `.../mappings.ts`, `.../patient.ts`, `.../bundle/functions.ts`, `.../bundle/types.ts`	Introduced new utility modules for appointment, client, external ID, FHIR, job, JWT token, mappings, patient, and bundle management.
`packages/api/src/external/ehr/shared/command/bundle/fetch-bundle-presignd-urls.ts`, `.../refresh-ehr-bundles.ts`	Added new generalized functions for fetching bundle pre-signed URLs and refreshing bundles across EHRs.
`packages/api/src/external/ehr/shared/job/bundle/create-resource-diff-bundles/get-job-payload.ts`, `.../start-job.ts`, `.../start-jobs-across-ehrs.ts`	Added new generalized job payload retrieval and job start logic for resource diff bundles.
`packages/api/src/routes/ehr/canvas/patient.ts`, `.../routes/internal/ehr/canvas/patient.ts`	Refactored/removed Canvas-specific resource diff endpoints and logic; migrated to shared, generic job/bundle handling.
`packages/api/src/routes/internal/ehr/index.ts`, `.../patient.ts`, `.../middleware.ts`	Added new internal EHR patient resource/job router and middleware for EHR ID validation.
`packages/api/src/routes/internal/medical/patient-job.ts`	Added route for completing patient jobs with no entries; minor doc updates.
`packages/core/src/external/ehr/api/api-shared.ts`	Added `validateAndLogResponse` utility for consistent API response validation/logging.
`packages/core/src/external/ehr/api/bundle/refresh-ehr-bundle.ts`, `.../job/complete-job.ts`, `.../job/create-resource-diff-bundles/set-entry-status.ts`, `.../job/set-entry-status.ts`	Added/updated functions for refreshing EHR bundles, completing jobs, and setting job entry status with improved error handling and retries.
`packages/core/src/external/ehr/api/job/initialize-job.ts`, `.../update-job-total.ts`, `.../sync-patient.ts`, `.../link-patient.ts`	Updated to use retry logic and centralized response validation.
`packages/core/src/external/ehr/bundle/bundle-shared.ts`	Added/updated type guards and resource type validation for bundle operations.
`packages/core/src/external/ehr/bundle/command/create-or-replace-bundle.ts`, `.../fetch-bundle.ts`	Improved error handling, resource type validation, and retry logic for S3 operations.
`packages/core/src/external/ehr/bundle/create-resource-diff-bundles/steps/compute/ehr-compute-resource-diff-bundles-local.ts`, `.../ehr-compute-resource-diff-bundles.ts`, `.../utils.ts`	Refactored diff computation logic to batch processing, stricter validation, and improved deduplication.
`packages/core/src/external/ehr/bundle/create-resource-diff-bundles/steps/compute/ehr-compute-resource-diff-bundles-cloud.ts`, `.../factory.ts`, `.../ehr-compute-resource-diff-bundles.ts`	Added SQS-based cloud handler and updated interfaces for diff bundle computation.
`packages/core/src/external/ehr/bundle/create-resource-diff-bundles/steps/start/ehr-start-resource-diff-bundles-local.ts`	Refactored to remove legacy resource validation, streamline resource type iteration, and manage job totals/completion.
`packages/core/src/external/ehr/bundle/job/create-resource-diff-bundles/create-resource-diff-bundle-shared.ts`	Added shared types/utilities for diff bundle job requests and SQS group IDs.
`packages/core/src/external/ehr/bundle/job/create-resource-diff-bundles/steps/refresh/ehr-refresh-ehr-bundles-cloud.ts`, `.../ehr-refresh-ehr-bundles-factory.ts`, `.../ehr-refresh-ehr-bundles-local.ts`, `.../ehr-refresh-ehr-bundles.ts`	Added/updated cloud/local handlers and interfaces for refreshing EHR bundles.
`packages/core/src/external/ehr/bundle/refresh-ehr-bundles/ehr-refresh-ehr-bundles-local.ts`	Enhanced job lifecycle/error handling and resource type iteration for EHR bundle refresh.
`packages/core/src/external/ehr/canvas/index.ts`	Refactored to generalize resource type/bundle handling, update method signatures, and remove direction-based logic.
`packages/core/src/external/ehr/elation/link-patient/elation-link-patient-cloud.ts`, `.../healthie/link-patient/healthie-link-patient-cloud.ts`, `.../sync-patient/ehr-sync-patient-cloud.ts`	Wrapped SQS message sending in retry logic.
`packages/core/src/fhir-deduplication/compute-resources-xor.ts`	Added function for computing XOR of FHIR resource sets with validation and deduplication.
`packages/shared/src/interface/external/ehr/fhir-resource.ts`	Unified resource types with external FHIR types, exported supported resource types, and updated bundle creation signatures.
`packages/infra/lib/ehr-nested-stack.ts`, `.../api-stack.ts`, `.../api-stack/api-service.ts`	Removed all references to legacy start resource diff bundles queue/lambda, updated permissions, and environment variables.
`packages/lambdas/src/ehr-compute-resource-diff-bundles.ts`, `.../ehr-refresh-ehr-bundles.ts`	Updated Lambda handlers to new message formats, resource type handling, and error reporting.

Sequence Diagram(s)

Generalized Resource Diff Bundle Job Flow

sequenceDiagram
    participant API as API Route
    participant JobStarter as startCreateResourceDiffBundlesJob
    participant JobDB as PatientJob Store
    participant BundleRefresher as refreshEhrBundles
    participant SQS as SQS Queue
    participant Lambda as Lambda Worker
    participant S3 as S3 Storage

    API->>JobStarter: POST /internal/ehr/:ehrId/patient/:id/resource/diff (start job)
    JobStarter->>JobDB: Create patient job (type: resource-diff)
    JobStarter->>BundleRefresher: For each supported resource type, refreshEhrBundles(...)
    BundleRefresher->>SQS: Send refresh job message
    SQS->>Lambda: Trigger Lambda for refresh
    Lambda->>S3: Create/replace empty diff bundles (Metriport-only, EHR-only)
    Lambda->>SQS: Send compute diff job message
    SQS->>Lambda: Trigger Lambda for compute
    Lambda->>S3: Fetch resources, compute diff, update bundles
    Lambda->>JobDB: Update job entry status (successful/failed)

Fetching Resource Diff Job Payload

sequenceDiagram
    participant API as API Route
    participant JobDB as PatientJob Store
    participant BundleFetcher as fetchBundlePreSignedUrls

    API->>JobDB: Fetch patient job by jobId
    alt job.status == "completed"
        API->>BundleFetcher: fetchBundlePreSignedUrls(...)
        BundleFetcher->>API: Return pre-signed URLs
        API->>API: Compose and return job payload with URLs
    else
        API->>API: Return job payload (no URLs)
    end

Refreshing EHR Bundles

sequenceDiagram
    participant API as API Route
    participant BundleRefresher as refreshEhrBundles
    participant SQS as SQS Queue
    participant Lambda as Lambda Worker
    participant S3 as S3 Storage

    API->>BundleRefresher: POST /internal/ehr/:ehrId/patient/:id/resource/refresh
    BundleRefresher->>SQS: Send refresh job message
    SQS->>Lambda: Trigger Lambda for refresh
    Lambda->>S3: Refresh EHR bundle for resource type
    Lambda->>JobDB: Update job entry status

JWT Token Management (Generalized)

sequenceDiagram
    participant API as API Route
    participant JWTUtils as checkJwtToken/saveJwtToken
    participant TokenStore as JWT Token Store

    API->>JWTUtils: checkJwtToken({token, source})
    JWTUtils->>TokenStore: getJwtToken({token, source})
    TokenStore-->>JWTUtils: Token info
    JWTUtils-->>API: {active, expired?}

    API->>JWTUtils: saveJwtToken({token, source, exp, data})
    JWTUtils->>TokenStore: findOrCreateJwtToken(...)
    TokenStore-->>JWTUtils: (persisted)
    JWTUtils-->>API: (done)

SQS-Based Resource Diff Computation

sequenceDiagram
    participant JobStarter as startCreateResourceDiffBundlesJob
    participant SQS as SQS Queue
    participant Lambda as Lambda Worker
    participant S3 as S3 Storage

    JobStarter->>SQS: Send compute diff job message (per resource type)
    SQS->>Lambda: Trigger Lambda for compute
    Lambda->>S3: Fetch resources, compute diff, update bundles
    Lambda->>JobDB: Update job entry status

These diagrams represent the new modular, EHR-agnostic resource diff and bundle management workflows, reflecting the new control flow and infrastructure introduced by this change set.

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Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

thomasyopes · 2025-05-05T20:02:59Z

packages/api/src/external/ehr/jwt-token.ts

moved into /shared/utils/jwt-token.ts

thomasyopes · 2025-05-05T20:04:04Z

packages/api/src/external/ehr/shared.ts

JWT stuff moved into /shared/utils/jwt-token.ts
Appointments stuff moved into /shared/utils/appointment.ts
External ID stuff moved into /shared/utils/external-id.ts
Client stuff moved into /shared/utils/client.ts

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

… 199-elation-contribution Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

thomasyopes · 2025-05-06T18:55:38Z

packages/api/src/command/medical/patient/consolidated-recreate.ts

@@ -56,7 +55,6 @@ export async function recreateConsolidated({
      createResourceDiffBundles({
        cxId: patient.cxId,
        patientId: patient.id,
-        direction: ResourceDiffDirection.METRIPORT_ONLY,


The resource diff job now computes both directions at once.

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

thomasyopes · 2025-05-06T19:49:08Z

packages/api/src/external/ehr/canvas/shared.ts

@@ -45,7 +48,3 @@ export async function createCanvasClient(
    getClient: CanvasApi.create,
  });
 }
-
-export function getCreateCanvasResourceDiffBundlesJobType(direction: ResourceDiffDirection) {


Moved to jobs utils file

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

thomasyopes · 2025-05-06T20:40:30Z

packages/api/src/external/ehr/shared/utils/appointment.ts

Taken from old shared file.

Thomas Yopes added 2 commits May 1, 2025 11:13

feat(healthie): small fix

341f568

Ref: ENG-82 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

feat(ehr): contribution

bf0ca87

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

Thomas Yopes added 11 commits May 5, 2025 10:40

feat(ehr): add general complete endpoint

e6a7f14

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

feat(ehr): adding contribution

696db7e

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

feat(ehr): more updates

b413d48

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

feat(ehr): fixing imports

b1235c0

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

feat(ehr): refresh in both directions

3c87872

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

feat(ehr): combining the diffs

78bf417

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

feat(ehr): fixing reffresh

df26b3c

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

feat(ehr): core fix

0a9880e

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

feat(ehr): removing direction

76f5dc6

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

feat(ehr): fixing imports

2d4f9fd

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

feat(ehr): dedicated file

a652eac

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

thomasyopes commented May 5, 2025

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packages/api/src/external/ehr/jwt-token.ts Outdated

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moved into /shared/utils/jwt-token.ts

thomasyopes commented May 5, 2025

View reviewed changes

Thomas Yopes added 5 commits May 5, 2025 13:24

feat(ehr): more fixes

731f456

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

feat(ehr): fixing retries

1444010

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

feat(ehr): fixing retry stuff

9ffd9b6

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

Merge branch 'develop' of https://github.com/metriport/metriport into…

0e7c80c

… 199-elation-contribution Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

feat(ehr): fixing contribution

cf461b8

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

thomasyopes commented May 6, 2025

View reviewed changes

Thomas Yopes added 2 commits May 6, 2025 11:57

feat(ehr): mappings fix

85539d7

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

feat(ehr): small edits

1c24c4d

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

thomasyopes commented May 6, 2025

View reviewed changes

Thomas Yopes added 4 commits May 6, 2025 12:52

feat(ehr): promise all for fetching bundles

f6276c7

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

feat(ehr): small edits

621b0e5

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

feat(ehr): more tsdoc work

1666caa

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

feat(ehr): tsdoc

bbbae86

Ref: ENG-199 Ref: #1040 Signed-off-by: Thomas Yopes <thomasyopes@Thomass-MBP.attlocal.net>

thomasyopes commented May 6, 2025

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packages/api/src/external/ehr/shared/utils/appointment.ts Outdated

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Taken from old shared file.

This was referenced Jun 6, 2025

feat(healthie): supporting group sessions #3773

Merged

Eng 281 canvas writeback #3981

Merged

This was referenced Jun 17, 2025

Eng 433 scheduler for patient job #3997

Merged

feat(ehr): elation contribution #4082

Merged

This was referenced Jul 3, 2025

feat(ehr): re-running dq on appointment fetching past cooldown #4147

Merged

Eng 412 healthie contribution #4143

Merged

RELEASE elation contribution w/ monitoring #4164

Merged

coderabbitai bot mentioned this pull request Jul 10, 2025

feat: associate patient to multiple facilities #4173

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11 tasks

coderabbitai bot mentioned this pull request Aug 5, 2025

feat(ehr): response fixes #4303

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5 tasks

coderabbitai bot mentioned this pull request Aug 14, 2025

feat(ehr): sollis contribute ehr summaries + remove bad encounters #4346

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coderabbitai bot mentioned this pull request Aug 28, 2025

feat(ehr): extra athenahealth validation on department id #4483

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Testing

Release Plan

Summary by CodeRabbit

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Walkthrough

Changes

Sequence Diagram(s)

Generalized Resource Diff Bundle Job Flow

Fetching Resource Diff Job Payload

Refreshing EHR Bundles

JWT Token Management (Generalized)

SQS-Based Resource Diff Computation

Chat

Support

CodeRabbit Commands (Invoked using PR comments)

Other keywords and placeholders

CodeRabbit Configuration File (.coderabbit.yaml)

Documentation and Community

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thomasyopes May 5, 2025

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thomasyopes May 5, 2025

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thomasyopes May 6, 2025

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thomasyopes May 6, 2025

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thomasyopes commented May 5, 2025 •

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