Merge from main repo: Release Version 2.1.2 (#2943)

.turbo/turbo-build.log

@@ -0,0 +1,4 @@
+
+> [email protected] build
+> tsc
+

README.md

@@ -1,29 +1,29 @@
 # Medplum Demo Bots
 
-This repo contains code for [Medplum Bots](https://docs.medplum.com/app/bots). Bots power many of the integrations you see in Medplum apps.  You can view your deployed bots online on the [Medplum App](https://app.medplum.com).
+This repo contains code for [Medplum Bots](https://docs.medplum.com/app/bots). Bots power many of the integrations you see in Medplum apps. You can view your deployed bots online on the [Medplum App](https://app.medplum.com).
 
 Bots make heavy use of the [Medplum JS Client Library](https://docs.medplum.com/typedoc/core/index.html).
 
 ## Setup
 
 To set up your bot deployment you will need to do the following:
 
-* [Create a Bot](https://app.medplum.com/admin/project) on Medplum and note its `id`. (All Bots in your account can be found [here](https://app.medplum.com/Bot))
-* Create a new typescript file (e.g. `my-bot.ts`) and copy the contents of `examples/hello-patient.ts` into your new file.
-* With the `id` of the Bot `id` in hand, add a section to `medplum.config.json` like so
+- [Create a Bot](https://app.medplum.com/admin/project) on Medplum and note its `id`. (All Bots in your account can be found [here](https://app.medplum.com/Bot))
+- Create a new typescript file (e.g. `my-bot.ts`) and copy the contents of `examples/hello-patient.ts` into your new file.
+- With the `id` of the Bot `id` in hand, add a section to `medplum.config.json` like so
 
 ```json
-    {
-      "name": "sample-account-setup",
-      "id": "aa3a0383-a97b-4172-b65d-430f6241646f",
-      "source": "src/examples/sample-account-setup.ts",
-      "dist": "dist/sample-account-setup.js"
-    }
+{
+  "name": "sample-account-setup",
+  "id": "aa3a0383-a97b-4172-b65d-430f6241646f",
+  "source": "src/examples/sample-account-setup.ts",
+  "dist": "dist/sample-account-setup.js"
+}
 ```
 
-* [Create an ClientApplication](https://app.medplum.com/ClientApplication/new) on Medplum. (All ClientApplications in your account can be found [here](https://app.medplum.com/ClientApplication))
-* Create a .env file locally by copying `.env.example` and put the `ClientId` and `ClientSecret` from the `ClientApplication` into the file.
-* (Optional) Create an [AccessPolicy]((https://app.medplum.com/AccessPolicy)) on Medplum that can only read/write Bots and add it to the Bot in the [admin panel](https://app.medplum.com/admin/project).
+- [Create an ClientApplication](https://app.medplum.com/ClientApplication/new) on Medplum. (All ClientApplications in your account can be found [here](https://app.medplum.com/ClientApplication))
+- Create a .env file locally by copying `.env.example` and put the `ClientId` and `ClientSecret` from the `ClientApplication` into the file.
+- (Optional) Create an [AccessPolicy](<(https://app.medplum.com/AccessPolicy)>) on Medplum that can only read/write Bots and add it to the Bot in the [admin panel](https://app.medplum.com/admin/project).
 
 ## Installation
 

medplum.config.json

@@ -47,6 +47,30 @@
       "id": "",
       "source": "src/stripe-bots/stripe-create-invoice.ts",
       "dist": "dist/stripe-bots/stripe-create-invoice.js"
+    },
+    {
+      "name": "merge-bot",
+      "id": "",
+      "source": "src/deduplication/merge-bot.ts",
+      "dist": "dist/deduplication/merge-bot.js"
+    },
+    {
+      "name": "patient-deduplication",
+      "id": "",
+      "source": "src/deduplication/patient-deduplication.ts",
+      "dist": "dist/deduplication/patient-deduplication.js"
+    },
+    {
+      "name": "find-matching-patients",
+      "id": "",
+      "source": "src/deduplication/find-matching-patients.ts",
+      "dist": "dist/deduplication/find-matching-patients.js"
+    },
+    {
+      "name": "merge-matching-patients",
+      "id": "",
+      "source": "src/deduplication/merge-matching-patients.ts",
+      "dist": "dist/deduplication/merge-matching-patients.js"
     }
   ]
 }

package.json

@@ -1,7 +1,6 @@
 {
-  "type": "module",
   "name": "medplum-demo-bots",
-  "version": "2.0.29",
+  "version": "2.1.2",
   "description": "Medplum Demo Bots",
   "scripts": {
     "build": "tsc",
@@ -14,23 +13,23 @@
   "author": "Medplum <[email protected]>",
   "license": "Apache-2.0",
   "devDependencies": {
-    "@medplum/cli": "2.0.29",
-    "@medplum/core": "2.0.29",
-    "@medplum/eslint-config": "2.0.29",
-    "@medplum/fhirtypes": "2.0.29",
-    "@medplum/mock": "2.0.29",
-    "@types/node": "20.4.5",
-    "@types/node-fetch": "2.6.4",
+    "@medplum/cli": "2.1.2",
+    "@medplum/core": "2.1.2",
+    "@medplum/eslint-config": "2.1.2",
+    "@medplum/fhirtypes": "2.1.2",
+    "@medplum/mock": "2.1.2",
+    "@types/node": "20.6.2",
+    "@types/node-fetch": "2.6.5",
     "@types/ssh2-sftp-client": "9.0.0",
-    "@vitest/coverage-v8": "0.33.0",
-    "@vitest/ui": "0.33.0",
+    "@vitest/coverage-v8": "0.34.4",
+    "@vitest/ui": "0.34.4",
     "form-data": "4.0.0",
-    "node-fetch": "2.6.12",
+    "node-fetch": "2.7.0",
     "pdfmake": "0.2.7",
     "ssh2-sftp-client": "9.1.0",
-    "stripe": "12.14.0",
-    "typescript": "5.1.6",
-    "vitest": "0.33.0"
+    "stripe": "13.6.0",
+    "typescript": "5.2.2",
+    "vitest": "0.34.4"
   },
   "eslintConfig": {
     "extends": [
@@ -39,9 +38,10 @@
   },
   "prettier": {
     "printWidth": 120,
-    "singleQuote": true
+    "singleQuote": true,
+    "trailingComma": "es5"
   },
   "dependencies": {
-    "esbuild": "0.18.17"
+    "esbuild": "0.19.3"
   }
 }

src/deduplication/README.md

@@ -0,0 +1,95 @@
+# Patient Deduplication Demo
+
+This folder contains a reference implementation for a simple, human-in-the-loop patient deduplication pipeline, based on the guidance in [Patient Deduplication Architectures](https://www.medplum.com/docs/fhir-datastore/patient-deduplication#architecture-overview).
+
+The implementation consists of two bots:
+
+- [`find-matching-patients`](./find-matching-patients.ts) - Identifies duplicated Patients and performs a series of steps:
+  - Check for the first name, last name, birth date, and zip code.
+  - If it's a match, it will check a list to see if it's not on the doNotMatch list
+  - Creates a `RiskAssessment`, with a numeric score, representing the candidate match.
+  - Creates a `Task` for a human to review the match
+- [`merge-matching-patients`](./merge-matching-patients.ts) -The other that merges the two Patients into one
+  - [Link the Patient records](https://www.medplum.com/docs/fhir-datastore/patient-deduplication#linking-patient-records-in-fhir)
+  - [Merge the Contact info](https://www.medplum.com/docs/fhir-datastore/patient-deduplication#merge-rules)
+  - [Rewrite Clinical Resource](https://www.medplum.com/docs/fhir-datastore/patient-deduplication#rewriting-references-from-clinical-data)
+  - Delete the source record, if the user has requested it
+
+This implementation also consists of FHIR bundles with sample data, which can be uploaded using the [batch upload tool](https://www.medplum.com/docs/tutorials/importing-sample-data):
+
+- [patient-data.json](./patient-data.json) - Three sample `Patient` resources, two of whom are known duplicates, and one of which is a false positive
+- [merge-questionnaire.json](./merge-questionnaire.json) - An example `Questionnaire` resource that describes a form that a reviewer might use to evaluate a candidate match.
+
+## Setup
+
+To run and deploy your Bot do the following steps:
+
+Install:
+
+```bash
+npm i
+```
+
+Build:
+
+```bash
+npm run build
+```
+
+Test:
+
+```bash
+npm t
+```
+
+[Create first Bot](https://www.medplum.com/docs/cli#bots) :
+
+```bash
+npx medplum bot create find-matching-patients <project id> "src/deduplication/find-matching-patients.ts" "dist/deduplication/find-matching-patients.js"
+```
+
+[Deploy first Bot](https://www.medplum.com/docs/cli#bots) :
+
+```bash
+npx medplum bot deploy find-matching-patients
+```
+
+```bash
+Update bot code.....
+Success! New bot version: <botID>
+Deploying bot...
+Deploy result: All OK
+```
+
+Set up a `Subscription` following the instructions [here](https://www.medplum.com/docs/bots/bot-basics#executing-automatically-using-a-subscription) to trigger the Bot when a `Patient` record is updated.
+
+- Critera: `Patient?active=true`
+- Endpoint: `Bot/:find-matching-patients-bot-id`
+
+[Create second Bot](https://www.medplum.com/docs/cli#bots) :
+
+```bash
+npx medplum bot create merge-matching-patients <project id> "src/deduplication/merge-matching-patients.ts" "dist/deduplication/merge-matching-patients.js"
+```
+
+[Deploy second Bot](https://www.medplum.com/docs/cli#bots) :
+
+```bash
+npx medplum bot deploy merge-matching-patients
+```
+
+You will see the following in your command prompt if all goes well:
+
+```bash
+Update bot code.....
+Success! New bot version: <botID>
+Deploying bot...
+Deploy result: All OK
+```
+
+Use the [batch upload tool](https://www.medplum.com/docs/tutorials/importing-sample-data) to import the [merge questionnaire](./merge-questionnaire.json)
+
+Set up a `Subscription` following the instructions [here](https://www.medplum.com/docs/bots/bot-basics#executing-automatically-using-a-subscription) to trigger the bot when the questionnaire is submitted.
+
+- Critera: `QuestionnaireResponse?questionnaire=Questionnaire/:merge-questionnaire-id`
+- Endpoint: `Bot/:merge-matching-patients-bot-id`

src/deduplication/find-matching-patients.test.ts

@@ -0,0 +1,72 @@
+import {
+  ContentType,
+  MedplumClient,
+  createReference,
+  getReferenceString,
+  indexSearchParameterBundle,
+  indexStructureDefinitionBundle,
+  resolveId,
+} from '@medplum/core';
+import { readJson } from '@medplum/definitions';
+import { Bundle, List, Patient, SearchParameter } from '@medplum/fhirtypes';
+import { MockClient } from '@medplum/mock';
+import { handler } from './find-matching-patients';
+import patientData from './patient-data.json';
+
+interface TestContext {
+  medplum: MedplumClient;
+}
+
+// npm t src/examples/patient-deduplication.test.ts
+// This test demostrates a automatically linking patients with three matching identifiers
+describe('Link Patient', async () => {
+  // Load the FHIR definitions to enable search parameter indexing
+  beforeAll(() => {
+    indexStructureDefinitionBundle(readJson('fhir/r4/profiles-types.json') as Bundle);
+    indexStructureDefinitionBundle(readJson('fhir/r4/profiles-resources.json') as Bundle);
+    indexSearchParameterBundle(readJson('fhir/r4/search-parameters.json') as Bundle<SearchParameter>);
+  });
+
+  // Load the sample data from patient-data.json
+  beforeEach<TestContext>(async (context) => {
+    context.medplum = new MockClient();
+    await context.medplum.executeBatch(patientData as Bundle);
+  });
+
+  test<TestContext>('Created RiskAssessment', async ({ medplum }) => {
+    // Read the patient
+    const patients = await medplum.searchResources('Patient', { given: 'Alex' });
+
+    await handler(medplum, { input: patients?.[0] as Patient, contentType: ContentType.FHIR_JSON, secrets: {} });
+
+    // We expect two risk assessments to be created for the two candidate matches
+    const riskAssessments = await medplum.searchResources('RiskAssessment');
+    expect(riskAssessments.length).toBe(2);
+    expect(riskAssessments.every((assessment) => resolveId(assessment.subject) === patients[0].id));
+  });
+
+  test<TestContext>('Does not create RiskAssessment due to doNotMatch List', async ({ medplum }) => {
+    // Read two patients that should not be matched
+    const alexSmith = await medplum.searchOne('Patient', { given: 'Alex', gender: 'male' });
+    const alexisSmith = await medplum.searchOne('Patient', { given: 'Alex', gender: 'female' });
+
+    if (!alexSmith || !alexisSmith) {
+      throw new Error('Missing Input Patient');
+    }
+
+    // Add each patient to the other's
+    const doNotMatchAlex = (await medplum.searchOne('List', { subject: getReferenceString(alexSmith) })) as List;
+    const doNotMatchAlexis = (await medplum.searchOne('List', { subject: getReferenceString(alexisSmith) })) as List;
+    doNotMatchAlex.entry = [{ item: createReference(alexisSmith) }];
+    doNotMatchAlexis.entry = [{ item: createReference(alexSmith) }];
+    await medplum.updateResource(doNotMatchAlex);
+    await medplum.updateResource(doNotMatchAlexis);
+
+    await handler(medplum, { input: alexSmith, contentType: ContentType.FHIR_JSON, secrets: {} });
+
+    const riskAssessment = await medplum.searchResources('RiskAssessment');
+    expect(riskAssessment.length).toBe(1);
+    expect(riskAssessment?.[0]?.subject?.reference).toBe(getReferenceString(alexSmith));
+    expect(riskAssessment?.[0]?.basis?.[0]).not.toBe(getReferenceString(alexisSmith));
+  });
+});