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Add function to clean FHIR resource according to spec #71

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Merged
dmitryashutov merged 4 commits into from
May 21, 2025
Merged

Add function to clean FHIR resource according to spec #71

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ef71a58
Add function to clean FHIR resource according to spec
dmitryashutov May 21, 2025
f95ec98
1.11.2-0
dmitryashutov May 21, 2025
b3eab73
Remove commented code
dmitryashutov May 21, 2025
6d781e7
Rename dropNullsFromDicts to needToCleanResource
dmitryashutov May 21, 2025
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2 changes: 1 addition & 1 deletion package.json
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"name": "aidbox-react",
"version": "1.11.1",
"version": "1.11.2-0",
"scripts": {
"build": "tsc & rollup -c",
"prebuild": "rimraf lib/* & rimraf dist/*",
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44 changes: 20 additions & 24 deletions src/services/fhir.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ import { AxiosRequestConfig } from 'axios';
import { AidboxReference, AidboxResource, ValueSet, Bundle, BundleEntry, id } from 'shared/src/contrib/aidbox';

import { isFailure, RemoteDataResult, success, failure } from '../libs/remoteData';
import { cleanEmptyValues, removeNullsFromDicts } from '../utils/fhir';
import { cleanObject } from '../utils/fhir';
import { buildQueryParams } from './instance';
import { SearchParams } from './search';
import { service } from './service';
Expand Down Expand Up @@ -95,21 +95,20 @@ function getInactiveSearchParam(resourceType: string) {
export async function createFHIRResource<R extends AidboxResource>(
resource: R,
searchParams?: SearchParams,
dropNullsFromDicts = true
needToCleanResource = true
): Promise<RemoteDataResult<WithId<R>>> {
return service(create(resource, searchParams, dropNullsFromDicts));
return service(create(resource, searchParams, needToCleanResource));
}

export function create<R extends AidboxResource>(
resource: R,
searchParams?: SearchParams,
dropNullsFromDicts = true
needToCleanResource = true
): AxiosRequestConfig {
let cleanedResource = resource;
if (dropNullsFromDicts) {
cleanedResource = removeNullsFromDicts(cleanedResource);
if (needToCleanResource) {
cleanedResource = cleanObject(cleanedResource);
}
cleanedResource = cleanEmptyValues(cleanedResource);

return {
method: 'POST',
Expand All @@ -122,21 +121,20 @@ export function create<R extends AidboxResource>(
export async function updateFHIRResource<R extends AidboxResource>(
resource: R,
searchParams?: SearchParams,
dropNullsFromDicts = true
needToCleanResource = true
): Promise<RemoteDataResult<WithId<R>>> {
return service(update(resource, searchParams, dropNullsFromDicts));
return service(update(resource, searchParams, needToCleanResource));
}

export function update<R extends AidboxResource>(
resource: R,
searchParams?: SearchParams,
dropNullsFromDicts = true
needToCleanResource = true
): AxiosRequestConfig {
let cleanedResource = resource;
if (dropNullsFromDicts) {
cleanedResource = removeNullsFromDicts(cleanedResource);
if (needToCleanResource) {
cleanedResource = cleanObject(cleanedResource);
}
cleanedResource = cleanEmptyValues(cleanedResource);

if (searchParams) {
return {
Expand Down Expand Up @@ -261,18 +259,17 @@ export async function findFHIRResource<R extends AidboxResource>(

export async function saveFHIRResource<R extends AidboxResource>(
resource: R,
dropNullsFromDicts: boolean = true
needToCleanResource = true
): Promise<RemoteDataResult<WithId<R>>> {
return service(save(resource, dropNullsFromDicts));
return service(save(resource, needToCleanResource));
}

export function save<R extends AidboxResource>(resource: R, dropNullsFromDicts: boolean = true): AxiosRequestConfig {
const versionId = resource.meta && resource.meta.versionId;
export function save<R extends AidboxResource>(resource: R, needToCleanResource = true): AxiosRequestConfig {
let cleanedResource = resource;
if (dropNullsFromDicts) {
cleanedResource = removeNullsFromDicts(cleanedResource);
if (needToCleanResource) {
cleanedResource = cleanObject(cleanedResource);
}
cleanedResource = cleanEmptyValues(cleanedResource);
const versionId = cleanedResource.meta && cleanedResource.meta.versionId;

return {
method: resource.id ? 'PUT' : 'POST',
Expand All @@ -285,7 +282,7 @@ export function save<R extends AidboxResource>(resource: R, dropNullsFromDicts:
export async function saveFHIRResources<R extends AidboxResource>(
resources: R[],
bundleType: 'transaction' | 'batch',
dropNullsFromDicts: boolean = true
needToCleanResource = true
): Promise<RemoteDataResult<Bundle<WithId<R>>>> {
return service({
method: 'POST',
Expand All @@ -294,10 +291,9 @@ export async function saveFHIRResources<R extends AidboxResource>(
type: bundleType,
entry: resources.map((resource) => {
let cleanedResource = resource;
if (dropNullsFromDicts) {
cleanedResource = removeNullsFromDicts(cleanedResource);
if (needToCleanResource) {
cleanedResource = cleanObject(cleanedResource);
}
cleanedResource = cleanEmptyValues(cleanedResource);
const versionId = cleanedResource.meta && cleanedResource.meta.versionId;

return {
Expand Down
66 changes: 23 additions & 43 deletions src/utils/fhir.ts
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Original file line number Diff line number Diff line change
@@ -1,61 +1,41 @@
function isEmpty(data: any): boolean {
if (Array.isArray(data)) {
return data.length === 0;
}

if (typeof data === 'object' && data !== null) {
return Object.keys(data).length === 0;
}

return false;
function isEmptyObject(data: any) {
return typeof data === 'object' && !Array.isArray(data) && data !== null && Object.keys(data).length === 0;
}

export function cleanEmptyValues(data: any): any {
export function cleanObject(data: any, topLevel = true): any {
if (Array.isArray(data)) {
return data.map((item) => {
return isEmpty(item) ? null : cleanEmptyValues(item);
const cleanedArray = data.map((item) => {
const cleaned = cleanObject(item, false);
//NOTE: convert undefined → null
return cleaned === undefined ? null : cleaned;
});
}

if (typeof data === 'object' && data !== null) {
const cleaned: Record<string, any> = {};
for (const [key, value] of Object.entries(data)) {
const cleanedValue = cleanEmptyValues(value);
if (!isEmpty(cleanedValue)) {
cleaned[key] = cleanedValue;
}
//NOTE: Trim trailing nulls
while (cleanedArray.length > 0 && cleanedArray[cleanedArray.length - 1] === null) {
cleanedArray.pop();
}
return cleaned;
}

if (typeof data === 'undefined') {
return null;
}

return data;
}

function isNull(value: any): boolean {
return value === null || value === undefined;
}

export function removeNullsFromDicts(data: any): any {
if (Array.isArray(data)) {
return data.map(removeNullsFromDicts);
return cleanedArray.length > 0 ? cleanedArray : undefined;
}

if (typeof data === 'object' && data !== null) {
const result: Record<string, any> = {};

for (const [key, value] of Object.entries(data)) {
if (!isNull(value)) {
result[key] = removeNullsFromDicts(value);
const cleanedValue = cleanObject(value, false);

if (cleanedValue !== undefined && cleanedValue !== null && !isEmptyObject(cleanedValue)) {
result[key] = cleanedValue;
}
}
return result;
}

if (typeof data === 'undefined') {
return null;
const isEmptyResult = Object.keys(result).length === 0;

if (topLevel && isEmptyResult) {
return {};
}

return isEmptyResult ? undefined : result;
}

return data;
Expand Down
101 changes: 24 additions & 77 deletions tests/utils/fhir.spec.ts
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Original file line number Diff line number Diff line change
@@ -1,78 +1,25 @@
import { cleanEmptyValues, removeNullsFromDicts } from '../../src/utils/fhir';

describe('cleanEmptyValues', () => {
it('cleans null values from dictionaries and arrays recursively', () => {
expect(cleanEmptyValues({})).toEqual({});
expect(cleanEmptyValues({ str: '' })).toEqual({ str: '' });

expect(cleanEmptyValues({ nested: { nested2: [{}] } })).toEqual({
nested: { nested2: [null] },
});

expect(cleanEmptyValues({ nested: { nested2: {} } })).toEqual({});

expect(cleanEmptyValues({ item: [] })).toEqual({});
expect(cleanEmptyValues({ item: [null] })).toEqual({ item: [null] });

expect(cleanEmptyValues({ item: [null, { item: null }] })).toEqual({
item: [null, { item: null }],
});

expect(cleanEmptyValues({ item: [null, { item: null }, {}] })).toEqual({
item: [null, { item: null }, null],
});
});

it('cleans undefined values from dictionaries and arrays recursively', () => {
expect(cleanEmptyValues({})).toEqual({});
expect(cleanEmptyValues({ str: '' })).toEqual({ str: '' });

expect(cleanEmptyValues({ nested: { nested2: [{}] } })).toEqual({
nested: { nested2: [null] },
});

expect(cleanEmptyValues({ nested: { nested2: {} } })).toEqual({});

expect(cleanEmptyValues({ item: [] })).toEqual({});
expect(cleanEmptyValues({ item: [undefined] })).toEqual({ item: [null] });

expect(cleanEmptyValues({ item: [undefined, { item: undefined }] })).toEqual({
item: [null, { item: null }],
});

expect(cleanEmptyValues({ item: [undefined, { item: undefined }, {}] })).toEqual({
item: [null, { item: null }, null],
});
});
});

describe('removeNullsFromDicts', () => {
it('removes nulls from nested dictionaries but not from arrays', () => {
expect(removeNullsFromDicts({})).toEqual({});
expect(removeNullsFromDicts({ item: [] })).toEqual({ item: [] });
expect(removeNullsFromDicts({ item: [null] })).toEqual({ item: [null] });
expect(removeNullsFromDicts({ item: [null, { item: null }] })).toEqual({
item: [null, {}],
});
expect(removeNullsFromDicts({ item: [null, { item: null }, {}] })).toEqual({
item: [null, {}, {}],
});
});

it('removes undefined from nested dictionaries but not from arrays', () => {
expect(removeNullsFromDicts({})).toEqual({});
expect(removeNullsFromDicts({ item: [] })).toEqual({ item: [] });
expect(removeNullsFromDicts({ item: [undefined] })).toEqual({ item: [null] });
expect(removeNullsFromDicts({ item: [undefined, { item: undefined }] })).toEqual({
item: [null, {}],
});
expect(removeNullsFromDicts({ item: [null, { item: null }, {}] })).toEqual({
item: [null, {}, {}],
});
});
});

describe('combine two cleaning functions', () => {
const data = { item: [undefined, { item: undefined }, {}] };
expect(cleanEmptyValues(removeNullsFromDicts(data))).toEqual({ item: [null, null, null] });
import { cleanObject } from '../../src/utils/fhir';

test.each([
{ data: {}, expected: {} },
{ data: { str: '' }, expected: { str: '' } },
{ data: { item: null }, expected: {} },
{ data: { item: undefined }, expected: {} },
{ data: { nested: { nested2: [null, {}] } }, expected: {} },
{ data: { nested: { nested2: [undefined, {}] } }, expected: {} },
{ data: { item: [null, { item: null }, {}] }, expected: {} },
{ data: { item: [undefined, { item: undefined }, {}] }, expected: {} },
{ data: { item: [null, { item: null }] }, expected: {} },
{ data: { item: [undefined, { item: undefined }] }, expected: {} },
{ data: { item: [] }, expected: {} },
{
data: { nested: { nested2: [null, { nested3: 'some value' }, null] } },
expected: { nested: { nested2: [null, { nested3: 'some value' }] } },
},
{
data: { nested: { nested2: [undefined, { nested3: 'some value' }, undefined] } },
expected: { nested: { nested2: [null, { nested3: 'some value' }] } },
},
])('cleanObnject(). Test case: %o', ({ data, expected }) => {
expect(cleanObject(data)).toEqual(expected);
});