(feat) O3-3316 Add support for encounter diagnosis #298

CynthiaKamau · 2024-05-28T11:48:58Z

Requirements

This PR has a title that briefly describes the work done including the ticket number. If there is a ticket, make sure your PR title includes a conventional commit label. See existing PR titles for inspiration.
My work conforms to the OpenMRS 3.0 Styleguide and design documentation.
My work includes tests or is validated by existing tests.

Summary

This feature attempts to introduce encounter diagnosis in RFE
Current RFE Schema :

{
      "label": "Reason for hospitalization:",
      "id": "hospReason",
      "questionOptions": {
	      "concept": "a8a07a48-1350-11df-a1f1-0026b9348838",
	      "rendering": "problem",
	      "rank": 1
      },
      "type": "diagnosis",
      "validators": []
 }

Proposed schema as in AFE :

{
    "label": "Test Diagnosis",
    "id": "DiagNosIS",
    "type": "diagnosis",
    "questionOptions": {
      "rendering": "repeating",
      "dataSource": "diagnoses",
      "diagnosis": {
        "isConfirmed": "true",
        "rank": 1
      }
    }
 }

Screenshots

Screen.Recording.2024-11-27.at.15.11.12.mov

Related Issue

Other

github-actions · 2024-05-28T11:52:02Z

Size Change: -263 kB (-17.32%) 👏

Total Size: 1.25 MB

Filename	Size	Change
`dist/539.js`	0 B	-263 kB (removed)	🏆

ℹ️ View Unchanged

Filename	Size	Change
`dist/151.js`	379 kB	0 B
`dist/225.js`	2.57 kB	0 B
`dist/254.js`	88.7 kB	0 B
`dist/277.js`	1.85 kB	0 B
`dist/300.js`	642 B	0 B
`dist/335.js`	968 B	0 B
`dist/353.js`	3.02 kB	0 B
`dist/41.js`	3.37 kB	0 B
`dist/540.js`	2.63 kB	0 B
`dist/55.js`	758 B	0 B
`dist/585.js`	112 kB	0 B
`dist/635.js`	14.4 kB	0 B
`dist/658.js`	263 kB	0 B
`dist/690.js`	11.5 kB	0 B
`dist/70.js`	483 B	0 B
`dist/979.js`	6.87 kB	0 B
`dist/99.js`	691 B	0 B
`dist/993.js`	3.09 kB	0 B
`dist/main.js`	355 kB	+63 B (+0.02%)
`dist/openmrs-esm-form-engine-lib.js`	3.8 kB	+1 B (+0.03%)

_{compressed-size-action}

samuelmale · 2024-05-29T09:13:41Z

src/components/encounter/encounter-form.component.tsx

+        const saveDiagnoses = await EncounterFormManager.saveDiagnosis(fields, savedEncounter);
+        if (saveDiagnoses) {
+          showSnackbar({
+            title: t('encounterDiagnosisSaved', 'Encounter diagnosis saved successfully'),
+            kind: 'success',
+            isLowContrast: true,
+          });
+        }


So the EncounterResource supports diagnoses as a create-able property shouldn't we be creating the diagnoses in a single transaction with the encounter?

Let me add it the same way we handle orders

brandones · 2024-06-19T15:05:18Z

@CynthiaKamau Ping, are you still working on this? Any blockers?

CynthiaKamau · 2024-06-19T15:43:23Z

@CynthiaKamau Ping, are you still working on this? Any blockers?

Yes, there some fixes that need to be done on the backend to complete the work

brandones · 2024-06-19T15:59:04Z

@CynthiaKamau Please provide links to the work or issues you're talking about. If there is no linkable issue/PR/talk/Slack, please tell us what work needs to be completed before this can move forward.

CynthiaKamau · 2024-06-19T16:31:01Z

@CynthiaKamau Please provide links to the work or issues you're talking about. If there is no linkable issue/PR/talk/Slack, please tell us what work needs to be completed before this can move forward.

This is the link to the backend pr

brandones · 2024-09-15T11:54:36Z

Ok @CynthiaKamau , looks like that backend PR is merged. Can we move forward with this?

CynthiaKamau · 2024-09-17T09:59:54Z

Ok @CynthiaKamau , looks like that backend PR is merged. Can we move forward with this?

Im working on it now

samuelmale

Nice work @CynthiaKamau! Are you planning on adding some test coverage?

samuelmale · 2024-09-25T12:06:08Z

src/processors/encounter/encounter-processor-helper.ts

@@ -300,6 +304,27 @@ export async function hydrateRepeatField(
        }),
    );
  }
+
+  //handle diagnoses
+  const unMappedDiagnosis = encounter.diagnoses.filter((diagnosis) => {


Suggested change

const unMappedDiagnosis = encounter.diagnoses.filter((diagnosis) => {

const unMappedDiagnoses = encounter.diagnoses.filter((diagnosis) => {

samuelmale · 2024-09-25T12:07:36Z

src/processors/encounter/encounter-processor-helper.ts

@@ -28,6 +29,7 @@ export function prepareEncounter(
  const obsForSubmission = [];
  prepareObs(obsForSubmission, formFields);
  const ordersForSubmission = prepareOrders(formFields);
+  const diagnosisForSubmission = prepareDiagnosis(formFields);


Suggested change

const diagnosisForSubmission = prepareDiagnosis(formFields);

const diagnosesForSubmission = prepareDiagnosis(formFields);

samuelmale · 2024-09-25T12:08:01Z

src/adapters/encounter-diagnosis-adapter.ts

+    context: FormProcessorContextProps,
+  ): Promise<any> {
+    const availableDiagnoses = sourceObject ?? (context.domainObjectValue as OpenmrsEncounter);
+    const matchedDiagnosis = availableDiagnoses.diagnoses?.find(


Suggested change

const matchedDiagnosis = availableDiagnoses.diagnoses?.find(

const matchedDiagnoses = availableDiagnoses.diagnoses?.find(

samuelmale · 2024-09-25T13:18:05Z

src/processors/encounter/encounter-form-processor.ts

@@ -166,6 +166,7 @@ export class EncounterFormProcessor extends FormProcessor {
    try {
      const { data: savedEncounter } = await saveEncounter(abortController, encounter, encounter.uuid);
      const saveOrders = savedEncounter.orders.map((order) => order.orderNumber);
+      const saveDiagnosis = savedEncounter.diagnoses.map((diagnosis) => diagnosis.display);


Suggested change

const saveDiagnosis = savedEncounter.diagnoses.map((diagnosis) => diagnosis.display);

const savedDiagnoses = savedEncounter.diagnoses.map((diagnosis) => diagnosis.display);

samuelmale · 2024-09-25T13:36:47Z

src/transformers/default-schema-transformer.ts

@@ -237,3 +240,19 @@ function handleQuestionsWithObsComments(sectionQuestions: Array<FormField>): Arr

  return augmentedQuestions;
 }
+
+function handleDiagnosesDataSource(question: FormField) {


I would simply name this: handleDiagnosis(...)

samuelmale · 2024-09-30T20:48:35Z

src/adapters/encounter-diagnoses-adapter.ts

+    sourceObject: OpenmrsResource,
+    context: FormProcessorContextProps,
+  ): Promise<any> {
+    const availableDiagnoses = sourceObject ?? (context.domainObjectValue as OpenmrsEncounter);


Suggested change

const availableDiagnoses = sourceObject ?? (context.domainObjectValue as OpenmrsEncounter);

const encounter = sourceObject ?? (context.domainObjectValue as OpenmrsEncounter);

samuelmale · 2024-09-30T20:55:11Z

src/adapters/encounter-diagnoses-adapter.ts

+    context: FormProcessorContextProps,
+  ): Promise<any> {
+    const availableDiagnoses = sourceObject ?? (context.domainObjectValue as OpenmrsEncounter);
+    const matchedDiagnoses = availableDiagnoses.diagnoses.find(


Suggested change

const matchedDiagnoses = availableDiagnoses.diagnoses.find(

const matchedDiagnosis = availableDiagnoses.diagnoses.find(

samuelmale · 2024-09-30T21:08:59Z

src/adapters/encounter-diagnoses.test.ts

+  },
+];
+
+describe('EncounterDiagnosesAdapter', () => {


Can you add test case(s) around:

editing a value and the fact that the edited value gets voided

@CynthiaKamau I discovered a bug while testing the entire feature.
Issue: When you delete a diagnosis (using the form repeat controls) and launch the form again in edit mode, the deleted diagnosis still exists, meaning it was never voided. This is partly why I requested the tests.

try retesting now

samuelmale · 2024-09-30T21:10:29Z

src/processors/encounter/encounter-form-processor.ts

@@ -166,6 +166,7 @@ export class EncounterFormProcessor extends FormProcessor {
    try {
      const { data: savedEncounter } = await saveEncounter(abortController, encounter, encounter.uuid);
      const saveOrders = savedEncounter.orders.map((order) => order.orderNumber);
+      const saveDiagnoses = savedEncounter.diagnoses.map((diagnosis) => diagnosis.display);


Suggested change

const saveDiagnoses = savedEncounter.diagnoses.map((diagnosis) => diagnosis.display);

const savedDiagnoses = savedEncounter.diagnoses.map((diagnosis) => diagnosis.display);

(I would also rename saveOrders -> savedOrders)

samuelmale · 2024-09-30T21:17:50Z

src/processors/encounter/encounter-form-processor.ts

+      // handle diagnoses
+      if (saveDiagnoses.length) {
+        showSnackbar({
+          title: translateFn('diagnosisSaved', 'Diagnosis(s) saved successfully'),


Suggested change

title: translateFn('diagnosisSaved', 'Diagnosis(s) saved successfully'),

title: translateFn('diagnosisSaved', 'Diagnosis(es) saved successfully'),

samuelmale · 2024-09-30T21:24:14Z

src/processors/encounter/encounter-processor-helper.ts

@@ -300,6 +304,40 @@ export async function hydrateRepeatField(
        }),
    );
  }
+
+  const unMappedDiagnoses = encounter.diagnoses.filter((diagnosis) => {
+    return !assignedDiagnosesIds.includes(diagnosis?.diagnosis?.coded.uuid);


I think the Diagnosis should include the field's ID in it's formFieldPath otherwise we may end up including past diagnoses.

@CynthiaKamau did you see this?

yes, you can relook at the pr

samuelmale · 2024-09-30T21:28:43Z

src/processors/encounter/encounter-processor-helper.ts

+      sortedDiagnoses
+        .filter((diagnosis) => !diagnosis.voided)
+        .map(async (diagnosis) => {
+          const clone = cloneRepeatField(field, diagnosis, counter++);


Can you add a demo where we capture diagnoses with "repeat controls"?

brandones · 2024-10-10T16:37:59Z

Ping @samuelmale

samuelmale · 2024-10-14T12:20:13Z

@brandones I left a few more comments for @CynthiaKamau

samuelmale

Thanks for the great work @CynthiaKamau!

To make this more generic and practical, we need a way to extend the data source to load concepts from custom concept classes and, optionally, sets.

   questionOptions: {
      diagnosis: {
         rank?: number;
         isConfirmed?: boolean;
         conceptClasses?: Array<string>;
         conceptSet?: string;
      }
   }

cc: @ibacher

samuelmale · 2024-11-19T10:24:05Z

src/adapters/encounter-diagnoses-adapter.ts

+    diagnosis: {
+      coded: value,
+    },
+    certainty: 'CONFIRMED',


This should default to PROVISIONAL but can be override-able through question options; something like: isConfirmedDiagnosis

Initially we were to make the feature and schema similar to what is in AFE, has that changed ?

I'm not sure about AFE, but HFE and other standard forms in the RefApp, such as the visit note, all default to PROVISIONAL. With the increasing need to use the form engine to replace custom-developed forms, it's important to follow standard patterns.

How will confirmed diagnosis be handled ?

From the form-design perspective, the field maybe configured like:

"questionOptions": { "diagnosis": { "isConfirmed": true; } }

samuelmale · 2024-11-19T10:33:37Z

src/types/schema.ts

@@ -182,6 +182,7 @@ export interface FormQuestionOptions {
  comment?: string;
  orientation?: 'vertical' | 'horizontal';
  shownCommentOptions?: { validators?: Array<Record<string, any>>; hide?: { hideWhenExpression: string } };
+  rank?: number;


We should encapsulate all the supported options:

diagnosis: { rank?: number; isConfirmed?: boolean }

CynthiaKamau · 2024-11-20T08:15:51Z

Thanks for the great work @CynthiaKamau!

To make this more generic and practical, we need a way to extend the data source to load concepts from custom concept classes and, optionally, sets.
   questionOptions: {
      diagnosis: {
         rank?: number;
         isConfirmed?: boolean;
         conceptClasses?: Array<string>;
         conceptSet?: string;
      }
   }
cc: @ibacher

Is it supported by the backend ? I remember the question with the type problem had the same challenge

CynthiaKamau · 2024-11-20T08:16:52Z

Thanks for the great work @CynthiaKamau!
To make this more generic and practical, we need a way to extend the data source to load concepts from custom concept classes and, optionally, sets.
   questionOptions: {
      diagnosis: {
         rank?: number;
         isConfirmed?: boolean;
         conceptClasses?: Array<string>;
         conceptSet?: string;
      }
   }
cc: @ibacher
Are the concept classes and sets supported by the backend, or passing more than one concept ? I remember the question with the type problem had the same challenge

samuelmale · 2024-11-20T08:31:09Z

Is it supported by the backend ?

The short answer is yes! Through OpenMRS' REST API, it's possible to filter concepts by class (I believe this is what the underlying datasource is doing); Then for the set, you can fetch the provided concept and retrieve the set members.

I remember the question with the type problem had the same challenge

If I remember correctly, this was a pagination issue and the resolution was using a search-based mechanism as opposed to loading all concepts in a single request.

CynthiaKamau · 2024-11-20T08:44:25Z

Is it supported by the backend ?

The short answer is yes! Through OpenMRS' REST API, it's possible to filter concepts by class (I believe this is what the underlying datasource is doing); Then for the set, you can fetch the provided concept and retrieve the set members.

I remember the question with the type problem had the same challenge

If I remember correctly, this was a pagination issue and the resolution was using a search-based mechanism as opposed to loading all concepts in a single request.

I hope it will work for multiple concept classes

pirupius · 2024-11-21T11:23:39Z

src/adapters/encounter-diagnoses-adapter.ts

@@ -0,0 +1,80 @@
+import { type OpenmrsResource } from '@openmrs/esm-framework';


Rename the file name to singular encounter-diagnosis-adapter.ts

pirupius · 2024-11-21T11:38:44Z

src/adapters/encounter-diagnoses-adapter.ts

@@ -0,0 +1,80 @@
+import { type OpenmrsResource } from '@openmrs/esm-framework';
+import { type FormFieldValueAdapter, type FormProcessorContextProps } from '..';


These need to be combined with the ../types

pirupius · 2024-11-21T12:02:24Z

src/adapters/encounter-diagnoses.test.ts

@@ -0,0 +1,204 @@
+import { type FormContextProps } from '../provider/form-provider';


Rename this file to singular diagnosis as well

pirupius · 2024-11-21T12:02:45Z

src/adapters/encounter-diagnoses.test.ts

@@ -0,0 +1,204 @@
+import { type FormContextProps } from '../provider/form-provider';
+import { type FormField } from '../types';
+import { EncounterDiagnosesAdapter } from './encounter-diagnoses-adapter';


Trickle the changes to other files as well

pirupius · 2024-11-21T12:14:26Z

src/adapters/encounter-diagnoses-adapter.ts

+
+export let assignedDiagnosesIds: string[] = [];
+
+export const EncounterDiagnosesAdapter: FormFieldValueAdapter = {


Suggested change

export const EncounterDiagnosesAdapter: FormFieldValueAdapter = {

export const EncounterDiagnosisAdapter: FormFieldValueAdapter = {

We agreed to name it in plural since it can be more than one here

Plural makes sense for the variables because you are actually dealing with multiple but singular makes more sense for file names and for this case the function/class. Kinda the same way we have EncounterLocationAdapter and EncounterRoleAdapter

This is more similar to orders from what i understood, and its in plural, @samuelmale can also weigh in since it was part of his review

I think the singular version (EncounterDiagnosisAdapter) is better because it's more atomic and seems to follow the Single Responsibility Principle. For consistency, we should rename other adapters to align with this pattern.

pirupius · 2024-11-21T12:21:07Z

src/registry/inbuilt-components/inbuiltFieldValueAdapters.ts

@@ -61,4 +62,8 @@ export const inbuiltFieldValueAdapters: RegistryItem<FormFieldValueAdapter>[] =
    type: 'patientIdentifier',
    component: PatientIdentifierAdapter,
  },
+  {
+    type: 'diagnosis',
+    component: EncounterDiagnosesAdapter,


Suggested change

component: EncounterDiagnosesAdapter,

component: EncounterDiagnosisAdapter,

pirupius · 2024-11-21T12:24:54Z

src/processors/encounter/encounter-processor-helper.ts

+      return numberA - numberB; // Sort numerically based on formFieldPath
+    });
+
+  if (field.type === 'diagnosis') {


This might not specific to this PR but shouldn't we add an option to view the diagnosis in the Visit > encounters view.
How does the form look in read-only mode?

Let me do a screenshot

This might not specific to this PR but shouldn't we add an option to view the diagnosis in the Visit > encounters view. How does the form look in read-only mode?

They will be viewable there

They will be viewable there

The screen recording you shared doesn't show it. Maybe it's an old one

They will be viewable there

The screen recording you shared doesn't show it. Maybe it's an old one

Its on the video, if you check the diagnosis on the visits widget and compare it to the open form they are the same, minute 1:32

I think i should have been more clear, i meant the value for the diagnosis but i've also realized it's a similar behavior as the orders. There's a requirement to show the entered values (i.e Infection due to Entamoeba, Mucus in stool, etc) in the visits view but that's out of scope for this PR

Yea, but i have updated the video to show the diagnosis well, however, on the visits widget, voided diagnosis are also displayed

CynthiaKamau marked this pull request as draft May 28, 2024 11:49

CynthiaKamau force-pushed the O3-3316 branch from b959145 to 2d22e64 Compare May 28, 2024 11:51

samuelmale reviewed May 29, 2024

View reviewed changes

CynthiaKamau force-pushed the O3-3316 branch from c9635c2 to 7274df9 Compare June 4, 2024 10:28

CynthiaKamau force-pushed the O3-3316 branch 2 times, most recently from a40ba8d to 2415c6d Compare September 16, 2024 19:12

CynthiaKamau force-pushed the O3-3316 branch 2 times, most recently from e5de3c9 to 63ad98e Compare September 25, 2024 10:58

CynthiaKamau marked this pull request as ready for review September 25, 2024 10:58

samuelmale reviewed Sep 25, 2024

View reviewed changes

CynthiaKamau force-pushed the O3-3316 branch 2 times, most recently from bc33d5d to 089214e Compare September 30, 2024 10:54

CynthiaKamau requested a review from samuelmale September 30, 2024 10:55

samuelmale reviewed Sep 30, 2024

View reviewed changes

CynthiaKamau requested a review from samuelmale October 2, 2024 12:28

CynthiaKamau force-pushed the O3-3316 branch from d601ac0 to e77e0b3 Compare November 7, 2024 12:49

denniskigen requested review from denniskigen and pirupius November 7, 2024 13:18

samuelmale reviewed Nov 19, 2024

View reviewed changes

samuelmale requested a review from mogoodrich November 19, 2024 10:46

(test) O3-3925 Add test coverage for the ProgramStateAdapter

b9876d1

CynthiaKamau added 2 commits November 20, 2024 11:11

code review

619f2df

code review

1b338c3

CynthiaKamau force-pushed the O3-3316 branch 2 times, most recently from f726e01 to ca83cf3 Compare November 20, 2024 08:58

pirupius reviewed Nov 21, 2024

View reviewed changes

CynthiaKamau force-pushed the O3-3316 branch from ca83cf3 to e30f21c Compare November 21, 2024 12:49

code review

2acf728

CynthiaKamau force-pushed the O3-3316 branch from e30f21c to 2acf728 Compare November 27, 2024 12:13

CynthiaKamau requested review from samuelmale and pirupius November 27, 2024 12:23

samuelmale requested a review from ibacher November 27, 2024 22:59

	const unMappedDiagnosis = encounter.diagnoses.filter((diagnosis) => {
	const unMappedDiagnoses = encounter.diagnoses.filter((diagnosis) => {

	const diagnosisForSubmission = prepareDiagnosis(formFields);
	const diagnosesForSubmission = prepareDiagnosis(formFields);

	const matchedDiagnosis = availableDiagnoses.diagnoses?.find(
	const matchedDiagnoses = availableDiagnoses.diagnoses?.find(

	const saveDiagnosis = savedEncounter.diagnoses.map((diagnosis) => diagnosis.display);
	const savedDiagnoses = savedEncounter.diagnoses.map((diagnosis) => diagnosis.display);

	const availableDiagnoses = sourceObject ?? (context.domainObjectValue as OpenmrsEncounter);
	const encounter = sourceObject ?? (context.domainObjectValue as OpenmrsEncounter);

	const saveDiagnoses = savedEncounter.diagnoses.map((diagnosis) => diagnosis.display);
	const savedDiagnoses = savedEncounter.diagnoses.map((diagnosis) => diagnosis.display);

	title: translateFn('diagnosisSaved', 'Diagnosis(s) saved successfully'),
	title: translateFn('diagnosisSaved', 'Diagnosis(es) saved successfully'),

		@@ -0,0 +1,80 @@
		import { type OpenmrsResource } from '@openmrs/esm-framework';

		@@ -0,0 +1,80 @@
		import { type OpenmrsResource } from '@openmrs/esm-framework';
		import { type FormFieldValueAdapter, type FormProcessorContextProps } from '..';

		@@ -0,0 +1,204 @@
		import { type FormContextProps } from '../provider/form-provider';


		export let assignedDiagnosesIds: string[] = [];

		export const EncounterDiagnosesAdapter: FormFieldValueAdapter = {

	export const EncounterDiagnosesAdapter: FormFieldValueAdapter = {
	export const EncounterDiagnosisAdapter: FormFieldValueAdapter = {

	component: EncounterDiagnosesAdapter,
	component: EncounterDiagnosisAdapter,

(feat) O3-3316 Add support for encounter diagnosis #298

Are you sure you want to change the base?

(feat) O3-3316 Add support for encounter diagnosis #298

Conversation

CynthiaKamau commented May 28, 2024 • edited Loading

Requirements

Summary

Screenshots

Related Issue

Other

github-actions bot commented May 28, 2024 • edited Loading

Choose a reason for hiding this comment

Choose a reason for hiding this comment

brandones commented Jun 19, 2024

CynthiaKamau commented Jun 19, 2024

brandones commented Jun 19, 2024

CynthiaKamau commented Jun 19, 2024 • edited Loading

brandones commented Sep 15, 2024

CynthiaKamau commented Sep 17, 2024

samuelmale left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

brandones commented Oct 10, 2024

samuelmale commented Oct 14, 2024

samuelmale left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

CynthiaKamau commented Nov 20, 2024

CynthiaKamau commented Nov 20, 2024

samuelmale commented Nov 20, 2024

CynthiaKamau commented Nov 20, 2024

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

CynthiaKamau commented May 28, 2024 •

edited

Loading

github-actions bot commented May 28, 2024 •

edited

Loading

CynthiaKamau commented Jun 19, 2024 •

edited

Loading