From a9bc74d071aa7e6f72151bdbf5a08aecc103fa77 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <p.gawron@atcomp.pl>
Date: Tue, 31 Dec 2024 14:32:47 +0100
Subject: [PATCH] use new publication endpoint
---
.../PublicationsModal/PublicationsModal.tsx | 12 +-
...PublicationsModalLayout.component.test.tsx | 20 +-
.../utils/getBasePublications.test.ts | 16 +-
.../utils/getBasePublications.ts | 16 +-
.../utils/getStandarizedPublications.ts | 8 +-
.../mapBasePublicationToStandarized.test.ts | 14 +-
.../utils/mapBasePublicationToStandarized.ts | 7 +-
.../utils/useDownloadPublicationsAsCSVFile.ts | 4 +-
.../FilterBySubmapHeader.test.tsx | 4 +-
src/models/mocks/publicationsResponseMock.ts | 351 +++++++++---------
src/models/pageableSchema.ts | 2 +-
src/models/publicationsResponseSchema.ts | 10 -
src/models/publicationsSchema.ts | 8 +-
.../publications/publications.selectors.ts | 11 +-
src/redux/publications/publications.thunks.ts | 18 +-
src/redux/publications/publications.types.ts | 4 +-
src/types/models.ts | 6 +-
17 files changed, 248 insertions(+), 263 deletions(-)
delete mode 100644 src/models/publicationsResponseSchema.ts
diff --git a/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModal.tsx b/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModal.tsx
index 69cbc09b..e37d378e 100644
--- a/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModal.tsx
+++ b/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModal.tsx
@@ -19,13 +19,13 @@ export const PublicationsModal = (): JSX.Element => {
const parsedData: PublicationsTableData[] | undefined = useMemo(() => {
const dd = data?.map(item => ({
- pubmedId: item.publication.article.pubmedId,
- title: item.publication.article.title,
- authors: item.publication.article.authors,
- journal: item.publication.article.journal,
- year: item.publication.article.year,
+ pubmedId: item.article.pubmedId,
+ title: item.article.title,
+ authors: item.article.authors,
+ journal: item.article.journal,
+ year: item.article.year,
elementsOnMap: JSON.stringify(item.elements) || EMPTY_ARRAY_STRING, // table data accepts only string | string[]
- submaps: mapsNames[item.elements[FIRST_ARRAY_ELEMENT].modelId],
+ submaps: mapsNames[item.elements[FIRST_ARRAY_ELEMENT].model],
}));
return dd || [];
}, [data, mapsNames]);
diff --git a/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/PublicationsModalLayout.component.test.tsx b/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/PublicationsModalLayout.component.test.tsx
index aa7755b5..95bf0cd7 100644
--- a/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/PublicationsModalLayout.component.test.tsx
+++ b/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/PublicationsModalLayout.component.test.tsx
@@ -8,7 +8,7 @@ import { apiPath } from '@/redux/apiPath';
import { downloadFileFromBlob } from '@/redux/export/export.utils';
import { StoreType } from '@/redux/store';
import { BioEntityContent, Publication } from '@/types/models';
-import { mockNetworkResponse } from '@/utils/mockNetworkResponse';
+import { mockNetworkNewAPIResponse } from '@/utils/mockNetworkResponse';
import {
InitialStoreState,
getReduxWrapperWithStore,
@@ -28,7 +28,7 @@ const THIRD_ELEMENT_ID = 300;
const FOURTH_ELEMENT_ID = 400;
const BASE_PUBLICATION: Publication =
- PUBLICATIONS_DEFAULT_SEARCH_FIRST_10_MOCK.data[FIRST_ARRAY_ELEMENT];
+ PUBLICATIONS_DEFAULT_SEARCH_FIRST_10_MOCK.content[FIRST_ARRAY_ELEMENT];
const BASE_ELEMENT = BASE_PUBLICATION.elements[FIRST_ARRAY_ELEMENT];
const PUBLICATION: Publication = {
...BASE_PUBLICATION,
@@ -36,22 +36,22 @@ const PUBLICATION: Publication = {
{
...BASE_ELEMENT,
id: FIRST_ELEMENT_ID,
- modelId: FIRST_MODEL_ID,
+ model: FIRST_MODEL_ID,
},
{
...BASE_ELEMENT,
id: SECOND_ELEMENT_ID,
- modelId: SECOND_MODEL_ID,
+ model: SECOND_MODEL_ID,
},
{
...BASE_ELEMENT,
id: THIRD_ELEMENT_ID,
- modelId: THIRD_MODEL_ID, // model id duplicate
+ model: THIRD_MODEL_ID, // model id duplicate
},
{
...BASE_ELEMENT,
id: FOURTH_ELEMENT_ID,
- modelId: THIRD_MODEL_ID, // model id duplicate
+ model: THIRD_MODEL_ID, // model id duplicate
},
],
};
@@ -77,7 +77,7 @@ jest.mock('../utils/fetchElementData');
})[id] as BioEntityContent,
);
-const mockedAxiosClient = mockNetworkResponse();
+const mockedAxiosNewClient = mockNetworkNewAPIResponse();
const renderComponent = (initialStore?: InitialStoreState): { store: StoreType } => {
const { Wrapper, store } = getReduxWrapperWithStore(initialStore);
@@ -96,11 +96,11 @@ const renderComponent = (initialStore?: InitialStoreState): { store: StoreType }
describe('PublicationsModalLayout - component', () => {
const length = 1;
- mockedAxiosClient
+ mockedAxiosNewClient
.onGet(apiPath.getPublications({ params: { length } }))
.reply(HttpStatusCode.Ok, {
...PUBLICATIONS_DEFAULT_SEARCH_FIRST_10_MOCK,
- data: [PUBLICATION],
+ content: [PUBLICATION],
});
it('should render download csv button', () => {
@@ -114,7 +114,7 @@ describe('PublicationsModalLayout - component', () => {
publications: {
data: {
...PUBLICATIONS_DEFAULT_SEARCH_FIRST_10_MOCK,
- data: [PUBLICATION],
+ content: [PUBLICATION],
filteredSize: length,
},
loading: 'succeeded',
diff --git a/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/getBasePublications.test.ts b/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/getBasePublications.test.ts
index ffa8191a..ca246ead 100644
--- a/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/getBasePublications.test.ts
+++ b/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/getBasePublications.test.ts
@@ -1,11 +1,11 @@
import { apiPath } from '@/redux/apiPath';
-import { mockNetworkResponse } from '@/utils/mockNetworkResponse';
+import { mockNetworkNewAPIResponse } from '@/utils/mockNetworkResponse';
import { HttpStatusCode } from 'axios';
import { showToast } from '@/utils/showToast';
import { PUBLICATIONS_DEFAULT_SEARCH_FIRST_10_MOCK } from '../../../../../../models/mocks/publicationsResponseMock';
import { getBasePublications } from './getBasePublications';
-const mockedAxiosClient = mockNetworkResponse();
+const mockedAxiosNewClient = mockNetworkNewAPIResponse();
jest.mock('./../../../../../../utils/showToast');
@@ -13,17 +13,19 @@ describe('getBasePublications - util', () => {
const length = 10;
it('should return valid data if provided', async () => {
- mockedAxiosClient
+ mockedAxiosNewClient
.onGet(apiPath.getPublications({ params: { length } }))
- .reply(HttpStatusCode.Ok, PUBLICATIONS_DEFAULT_SEARCH_FIRST_10_MOCK);
+ .reply(HttpStatusCode.Ok, JSON.stringify(PUBLICATIONS_DEFAULT_SEARCH_FIRST_10_MOCK));
const result = await getBasePublications({ length });
- expect(result).toStrictEqual(PUBLICATIONS_DEFAULT_SEARCH_FIRST_10_MOCK.data);
+ expect(result).toStrictEqual(
+ JSON.parse(JSON.stringify(PUBLICATIONS_DEFAULT_SEARCH_FIRST_10_MOCK.content)),
+ );
});
it('should return empty array if data structure is invalid', async () => {
- mockedAxiosClient
+ mockedAxiosNewClient
.onGet(apiPath.getPublications({ params: { length } }))
.reply(HttpStatusCode.Ok, { randomObject: true });
@@ -33,7 +35,7 @@ describe('getBasePublications - util', () => {
});
it('should return empty array and show toast error if http error', async () => {
- mockedAxiosClient
+ mockedAxiosNewClient
.onGet(apiPath.getPublications({ params: { length } }))
.reply(HttpStatusCode.BadRequest);
diff --git a/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/getBasePublications.ts b/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/getBasePublications.ts
index d149d031..e58c2f9f 100644
--- a/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/getBasePublications.ts
+++ b/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/getBasePublications.ts
@@ -1,11 +1,12 @@
-import { publicationsResponseSchema } from '@/models/publicationsResponseSchema';
import { apiPath } from '@/redux/apiPath';
import { PUBLICATIONS_FETCHING_ERROR_PREFIX } from '@/redux/publications/publications.constatns';
-import { axiosInstance } from '@/services/api/utils/axiosInstance';
-import { Publication, PublicationsResponse } from '@/types/models';
+import { axiosInstanceNewAPI } from '@/services/api/utils/axiosInstance';
+import { FilteredPageOf, Publication } from '@/types/models';
import { validateDataUsingZodSchema } from '@/utils/validateDataUsingZodSchema';
import { getErrorMessage } from '@/utils/getErrorMessage';
import { showToast } from '@/utils/showToast';
+import { pageableSchema } from '@/models/pageableSchema';
+import { publicationSchema } from '@/models/publicationsSchema';
interface Args {
length: number;
@@ -13,13 +14,16 @@ interface Args {
export const getBasePublications = async ({ length }: Args): Promise<Publication[]> => {
try {
- const response = await axiosInstance.get<PublicationsResponse>(
+ const response = await axiosInstanceNewAPI.get<FilteredPageOf<Publication>>(
apiPath.getPublications({ params: { length } }),
);
- const isDataValid = validateDataUsingZodSchema(response.data, publicationsResponseSchema);
+ const isDataValid = validateDataUsingZodSchema(
+ response.data,
+ pageableSchema(publicationSchema),
+ );
- return isDataValid ? response.data.data : [];
+ return isDataValid ? response.data.content : [];
} catch (error) {
const errorMessage = getErrorMessage({ error, prefix: PUBLICATIONS_FETCHING_ERROR_PREFIX });
showToast({
diff --git a/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/getStandarizedPublications.ts b/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/getStandarizedPublications.ts
index c59d2e00..894f194b 100644
--- a/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/getStandarizedPublications.ts
+++ b/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/getStandarizedPublications.ts
@@ -14,17 +14,17 @@ export const getStandarizedPublications = async ({
publications,
modelNameIdMap,
}: Args): Promise<StandarizedPublication[]> => {
- const getStandarizedPublicationsFuncs = publications.map(
+ const getStandardizedPublicationsFuncs = publications.map(
publication => () =>
mapBasePublicationToStandarized(publication, {
modelNameIdMap,
}),
);
- const standarizedPublications = await runInSequence<StandarizedPublication>(
- getStandarizedPublicationsFuncs,
+ const standardizedPublications = await runInSequence<StandarizedPublication>(
+ getStandardizedPublicationsFuncs,
SEQUENCE_CHUNK_SIZE,
);
- return standarizedPublications;
+ return standardizedPublications;
};
diff --git a/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/mapBasePublicationToStandarized.test.ts b/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/mapBasePublicationToStandarized.test.ts
index 3a556eff..05cbe84f 100644
--- a/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/mapBasePublicationToStandarized.test.ts
+++ b/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/mapBasePublicationToStandarized.test.ts
@@ -23,7 +23,7 @@ const MODEL_NAME_ID_MAP: Record<number, string> = {
};
const BASE_PUBLICATION: Publication =
- PUBLICATIONS_DEFAULT_SEARCH_FIRST_10_MOCK.data[FIRST_ARRAY_ELEMENT];
+ PUBLICATIONS_DEFAULT_SEARCH_FIRST_10_MOCK.content[FIRST_ARRAY_ELEMENT];
const BASE_ELEMENT = BASE_PUBLICATION.elements[FIRST_ARRAY_ELEMENT];
const PUBLICATION: Publication = {
...BASE_PUBLICATION,
@@ -31,22 +31,22 @@ const PUBLICATION: Publication = {
{
...BASE_ELEMENT,
id: FIRST_ELEMENT_ID,
- modelId: FIRST_MODEL_ID,
+ model: FIRST_MODEL_ID,
},
{
...BASE_ELEMENT,
id: SECOND_ELEMENT_ID,
- modelId: SECOND_MODEL_ID,
+ model: SECOND_MODEL_ID,
},
{
...BASE_ELEMENT,
id: THIRD_ELEMENT_ID,
- modelId: THIRD_MODEL_ID, // model id duplicate
+ model: THIRD_MODEL_ID, // model id duplicate
},
{
...BASE_ELEMENT,
id: FOURTH_ELEMENT_ID,
- modelId: THIRD_MODEL_ID, // model id duplicate
+ model: THIRD_MODEL_ID, // model id duplicate
},
],
};
@@ -80,7 +80,7 @@ const getFuncResult = async (
describe('mapBasePublicationToStandarized - util', () => {
it('should return valid pubmedId, journal, year and title', async () => {
const results = await getFuncResult(PUBLICATION);
- const { pubmedId, journal, year, title } = PUBLICATION.publication.article;
+ const { pubmedId, journal, year, title } = PUBLICATION.article;
expect(results.pubmedId).toBe(pubmedId);
expect(results.journal).toBe(journal);
@@ -90,7 +90,7 @@ describe('mapBasePublicationToStandarized - util', () => {
it('should return joined authors', async () => {
const results = await getFuncResult(PUBLICATION);
- const { authors } = PUBLICATION.publication.article;
+ const { authors } = PUBLICATION.article;
expect(results.authors).toBe(authors.join(','));
});
diff --git a/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/mapBasePublicationToStandarized.ts b/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/mapBasePublicationToStandarized.ts
index 84b7d269..dea109c1 100644
--- a/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/mapBasePublicationToStandarized.ts
+++ b/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/mapBasePublicationToStandarized.ts
@@ -13,13 +13,10 @@ export const mapBasePublicationToStandarized = async (
publication: Publication,
options: Options,
): Promise<StandarizedPublication> => {
- const {
- publication: { article },
- elements,
- } = publication;
+ const { article, elements } = publication;
const { modelNameIdMap } = options;
const { title, authors, journal, year, pubmedId } = article;
- const modelNames = elements.map(({ modelId }) => modelNameIdMap[modelId]);
+ const modelNames = elements.map(({ model }) => modelNameIdMap[model]);
const elementsData = await Promise.all(elements.map(async ({ id }) => fetchElementData(`${id}`)));
const elementsIds = elementsData
.filter((element): element is BioEntityContent => element !== undefined)
diff --git a/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/useDownloadPublicationsAsCSVFile.ts b/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/useDownloadPublicationsAsCSVFile.ts
index 531faf9c..cdd58d24 100644
--- a/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/useDownloadPublicationsAsCSVFile.ts
+++ b/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsModalLayout/utils/useDownloadPublicationsAsCSVFile.ts
@@ -41,12 +41,12 @@ export const useDownloadPublicationsAsCSVFile = (): UseDownloadPublicationsAsCSV
? searchedPublicationsList
: await getAllBasePublications();
- const standarizedPublications = await getStandarizedPublications({
+ const standardizedPublications = await getStandarizedPublications({
publications,
modelNameIdMap,
});
- return standarizedPublications;
+ return standardizedPublications;
};
const downloadPublicationsAsCSVFile = async (): Promise<void> => {
diff --git a/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsTable/FilterBySubmapHeader/FilterBySubmapHeader.test.tsx b/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsTable/FilterBySubmapHeader/FilterBySubmapHeader.test.tsx
index f238cef3..237c4c98 100644
--- a/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsTable/FilterBySubmapHeader/FilterBySubmapHeader.test.tsx
+++ b/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsTable/FilterBySubmapHeader/FilterBySubmapHeader.test.tsx
@@ -3,7 +3,7 @@ import { Provider } from 'react-redux';
import configureMockStore from 'redux-mock-store';
import thunk from 'redux-thunk';
import { act } from 'react-dom/test-utils';
-import { mockNetworkResponse } from '@/utils/mockNetworkResponse';
+import { mockNetworkNewAPIResponse } from '@/utils/mockNetworkResponse';
import {
InitialStoreState,
getReduxWrapperWithStore,
@@ -16,7 +16,7 @@ import { MODELS_MOCK } from '@/models/mocks/modelsMock';
import { FIRST_ARRAY_ELEMENT, ZERO } from '@/constants/common';
import { FilterBySubmapHeader } from './FilterBySubmapHeader.component';
-mockNetworkResponse();
+mockNetworkNewAPIResponse();
const renderComponent = (initialStoreState: InitialStoreState = {}): { store: StoreType } => {
const { Wrapper, store } = getReduxWrapperWithStore(initialStoreState);
diff --git a/src/models/mocks/publicationsResponseMock.ts b/src/models/mocks/publicationsResponseMock.ts
index c165eb98..01240a65 100644
--- a/src/models/mocks/publicationsResponseMock.ts
+++ b/src/models/mocks/publicationsResponseMock.ts
@@ -1,283 +1,266 @@
-import { PublicationsResponse } from '@/types/models';
+import { FilteredPageOf, Publication } from '@/types/models';
+import { bioEntityFixture } from '@/models/fixtures/bioEntityFixture';
-export const PUBLICATIONS_DEFAULT_SEARCH_FIRST_10_MOCK: PublicationsResponse = {
- data: [
+export const PUBLICATIONS_DEFAULT_SEARCH_FIRST_10_MOCK: FilteredPageOf<Publication> = {
+ content: [
{
elements: [
{
+ ...bioEntityFixture,
id: 19519,
- modelId: 52,
- type: 'REACTION',
+ model: 52,
},
],
- publication: {
- article: {
- title: 'The glutamate receptor ion channels.',
- authors: ['Dingledine R', ' Borges K', ' Bowie D', ' Traynelis SF.'],
- journal: 'Pharmacological reviews',
- year: 1999,
- link: 'https://www.ncbi.nlm.nih.gov/pubmed/10049997',
- pubmedId: '10049997',
- citationCount: 2458,
- },
+ article: {
+ title: 'The glutamate receptor ion channels.',
+ authors: ['Dingledine R', ' Borges K', ' Bowie D', ' Traynelis SF.'],
+ journal: 'Pharmacological reviews',
+ year: 1999,
+ link: 'https://www.ncbi.nlm.nih.gov/pubmed/10049997',
+ pubmedId: '10049997',
+ citationCount: 2458,
},
},
{
elements: [
{
+ ...bioEntityFixture,
id: 16167,
- modelId: 61,
- type: 'REACTION',
+ model: 61,
},
],
- publication: {
- article: {
- title: 'Regulation of JNK signaling by GSTp.',
- authors: [
- 'Adler V',
- ' Yin Z',
- ' Fuchs SY',
- ' Benezra M',
- ' Rosario L',
- ' Tew KD',
- ' Pincus MR',
- ' Sardana M',
- ' Henderson CJ',
- ' Wolf CR',
- ' Davis RJ',
- ' Ronai Z.',
- ],
- journal: 'The EMBO journal',
- year: 1999,
- link: 'https://www.ncbi.nlm.nih.gov/pubmed/10064598',
- pubmedId: '10064598',
- citationCount: 656,
- },
+ article: {
+ title: 'Regulation of JNK signaling by GSTp.',
+ authors: [
+ 'Adler V',
+ ' Yin Z',
+ ' Fuchs SY',
+ ' Benezra M',
+ ' Rosario L',
+ ' Tew KD',
+ ' Pincus MR',
+ ' Sardana M',
+ ' Henderson CJ',
+ ' Wolf CR',
+ ' Davis RJ',
+ ' Ronai Z.',
+ ],
+ journal: 'The EMBO journal',
+ year: 1999,
+ link: 'https://www.ncbi.nlm.nih.gov/pubmed/10064598',
+ pubmedId: '10064598',
+ citationCount: 656,
},
},
{
elements: [
{
+ ...bioEntityFixture,
id: 17823,
- modelId: 52,
- type: 'REACTION',
+ model: 52,
},
{
+ ...bioEntityFixture,
id: 19461,
- modelId: 52,
- type: 'REACTION',
+ model: 52,
},
],
- publication: {
- article: {
- title:
- 'Generic signals and specific outcomes: signaling through Ca2+, calcineurin, and NF-AT.',
- authors: ['Crabtree GR.'],
- journal: 'Cell',
- year: 1999,
- link: 'https://www.ncbi.nlm.nih.gov/pubmed/10089876',
- pubmedId: '10089876',
- citationCount: 454,
- },
+ article: {
+ title:
+ 'Generic signals and specific outcomes: signaling through Ca2+, calcineurin, and NF-AT.',
+ authors: ['Crabtree GR.'],
+ journal: 'Cell',
+ year: 1999,
+ link: 'https://www.ncbi.nlm.nih.gov/pubmed/10089876',
+ pubmedId: '10089876',
+ citationCount: 454,
},
},
{
elements: [
{
+ ...bioEntityFixture,
id: 18189,
- modelId: 52,
- type: 'REACTION',
+ model: 52,
},
{
+ ...bioEntityFixture,
id: 18729,
- modelId: 52,
- type: 'REACTION',
+ model: 52,
},
],
- publication: {
- article: {
- title: 'G protein regulation of adenylate cyclase.',
- authors: ['Simonds WF.'],
- journal: 'Trends in pharmacological sciences',
- year: 1999,
- link: 'https://www.ncbi.nlm.nih.gov/pubmed/10101967',
- pubmedId: '10101967',
- citationCount: 139,
- },
+ article: {
+ title: 'G protein regulation of adenylate cyclase.',
+ authors: ['Simonds WF.'],
+ journal: 'Trends in pharmacological sciences',
+ year: 1999,
+ link: 'https://www.ncbi.nlm.nih.gov/pubmed/10101967',
+ pubmedId: '10101967',
+ citationCount: 139,
},
},
{
elements: [
{
+ ...bioEntityFixture,
id: 16077,
- modelId: 58,
- type: 'REACTION',
+ model: 58,
},
{
+ ...bioEntityFixture,
id: 16135,
- modelId: 58,
- type: 'REACTION',
+ model: 58,
},
],
- publication: {
- article: {
- title:
- 'Akt promotes cell survival by phosphorylating and inhibiting a Forkhead transcription factor.',
- authors: [
- 'Brunet A',
- ' Bonni A',
- ' Zigmond MJ',
- ' Lin MZ',
- ' Juo P',
- ' Hu LS',
- ' Anderson MJ',
- ' Arden KC',
- ' Blenis J',
- ' Greenberg ME.',
- ],
- journal: 'Cell',
- year: 1999,
- link: 'https://www.ncbi.nlm.nih.gov/pubmed/10102273',
- pubmedId: '10102273',
- citationCount: 4019,
- },
+ article: {
+ title:
+ 'Akt promotes cell survival by phosphorylating and inhibiting a Forkhead transcription factor.',
+ authors: [
+ 'Brunet A',
+ ' Bonni A',
+ ' Zigmond MJ',
+ ' Lin MZ',
+ ' Juo P',
+ ' Hu LS',
+ ' Anderson MJ',
+ ' Arden KC',
+ ' Blenis J',
+ ' Greenberg ME.',
+ ],
+ journal: 'Cell',
+ year: 1999,
+ link: 'https://www.ncbi.nlm.nih.gov/pubmed/10102273',
+ pubmedId: '10102273',
+ citationCount: 4019,
},
},
{
elements: [
{
+ ...bioEntityFixture,
id: 15955,
- modelId: 55,
- type: 'REACTION',
+ model: 55,
},
],
- publication: {
- article: {
- title: 'Ca2+-induced apoptosis through calcineurin dephosphorylation of BAD.',
- authors: [
- 'Wang HG',
- ' Pathan N',
- ' Ethell IM',
- ' Krajewski S',
- ' Yamaguchi Y',
- ' Shibasaki F',
- ' McKeon F',
- ' Bobo T',
- ' Franke TF',
- ' Reed JC.',
- ],
- journal: 'Science (New York, N.Y.)',
- year: 1999,
- link: 'https://www.ncbi.nlm.nih.gov/pubmed/10195903',
- pubmedId: '10195903',
- citationCount: 708,
- },
+ article: {
+ title: 'Ca2+-induced apoptosis through calcineurin dephosphorylation of BAD.',
+ authors: [
+ 'Wang HG',
+ ' Pathan N',
+ ' Ethell IM',
+ ' Krajewski S',
+ ' Yamaguchi Y',
+ ' Shibasaki F',
+ ' McKeon F',
+ ' Bobo T',
+ ' Franke TF',
+ ' Reed JC.',
+ ],
+ journal: 'Science (New York, N.Y.)',
+ year: 1999,
+ link: 'https://www.ncbi.nlm.nih.gov/pubmed/10195903',
+ pubmedId: '10195903',
+ citationCount: 708,
},
},
{
elements: [
{
+ ...bioEntityFixture,
id: 15937,
- modelId: 55,
- type: 'REACTION',
+ model: 55,
},
{
+ ...bioEntityFixture,
id: 15955,
- modelId: 55,
- type: 'REACTION',
+ model: 55,
},
],
- publication: {
- article: {
- title:
- 'The proapoptotic activity of the Bcl-2 family member Bim is regulated by interaction with the dynein motor complex.',
- authors: ['Puthalakath H', ' Huang DC', " O'Reilly LA", ' King SM', ' Strasser A.'],
- journal: 'Molecular cell',
- year: 1999,
- link: 'https://www.ncbi.nlm.nih.gov/pubmed/10198631',
- pubmedId: '10198631',
- citationCount: 662,
- },
+ article: {
+ title:
+ 'The proapoptotic activity of the Bcl-2 family member Bim is regulated by interaction with the dynein motor complex.',
+ authors: ['Puthalakath H', ' Huang DC', " O'Reilly LA", ' King SM', ' Strasser A.'],
+ journal: 'Molecular cell',
+ year: 1999,
+ link: 'https://www.ncbi.nlm.nih.gov/pubmed/10198631',
+ pubmedId: '10198631',
+ citationCount: 662,
},
},
{
elements: [
{
+ ...bioEntityFixture,
id: 15948,
- modelId: 55,
- type: 'REACTION',
+ model: 55,
},
],
- publication: {
- article: {
- title:
- 'An APAF-1.cytochrome c multimeric complex is a functional apoptosome that activates procaspase-9.',
- authors: ['Zou H', ' Li Y', ' Liu X', ' Wang X.'],
- journal: 'The Journal of biological chemistry',
- year: 1999,
- link: 'https://www.ncbi.nlm.nih.gov/pubmed/10206961',
- pubmedId: '10206961',
- citationCount: 1162,
- },
+ article: {
+ title:
+ 'An APAF-1.cytochrome c multimeric complex is a functional apoptosome that activates procaspase-9.',
+ authors: ['Zou H', ' Li Y', ' Liu X', ' Wang X.'],
+ journal: 'The Journal of biological chemistry',
+ year: 1999,
+ link: 'https://www.ncbi.nlm.nih.gov/pubmed/10206961',
+ pubmedId: '10206961',
+ citationCount: 1162,
},
},
{
elements: [
{
+ ...bioEntityFixture,
id: 16286,
- modelId: 62,
- type: 'REACTION',
+ model: 62,
},
],
- publication: {
- article: {
- title:
- 'Biochemical characterization and crystal structure determination of human heart short chain L-3-hydroxyacyl-CoA dehydrogenase provide insights into catalytic mechanism.',
- authors: [
- 'Barycki JJ',
- " O'Brien LK",
- ' Bratt JM',
- ' Zhang R',
- ' Sanishvili R',
- ' Strauss AW',
- ' Banaszak LJ.',
- ],
- journal: 'Biochemistry',
- year: 1999,
- link: 'https://www.ncbi.nlm.nih.gov/pubmed/10231530',
- pubmedId: '10231530',
- citationCount: 56,
- },
+ article: {
+ title:
+ 'Biochemical characterization and crystal structure determination of human heart short chain L-3-hydroxyacyl-CoA dehydrogenase provide insights into catalytic mechanism.',
+ authors: [
+ 'Barycki JJ',
+ " O'Brien LK",
+ ' Bratt JM',
+ ' Zhang R',
+ ' Sanishvili R',
+ ' Strauss AW',
+ ' Banaszak LJ.',
+ ],
+ journal: 'Biochemistry',
+ year: 1999,
+ link: 'https://www.ncbi.nlm.nih.gov/pubmed/10231530',
+ pubmedId: '10231530',
+ citationCount: 56,
},
},
{
elements: [
{
+ ...bioEntityFixture,
id: 17780,
- modelId: 52,
- type: 'REACTION',
+ model: 52,
},
{
+ ...bioEntityFixture,
id: 17937,
- modelId: 52,
- type: 'REACTION',
+ model: 52,
},
],
- publication: {
- article: {
- title: 'The Ca-calmodulin-dependent protein kinase cascade.',
- authors: ['Soderling TR.'],
- journal: 'Trends in biochemical sciences',
- year: 1999,
- link: 'https://www.ncbi.nlm.nih.gov/pubmed/10366852',
- pubmedId: '10366852',
- citationCount: 322,
- },
+ article: {
+ title: 'The Ca-calmodulin-dependent protein kinase cascade.',
+ authors: ['Soderling TR.'],
+ journal: 'Trends in biochemical sciences',
+ year: 1999,
+ link: 'https://www.ncbi.nlm.nih.gov/pubmed/10366852',
+ pubmedId: '10366852',
+ citationCount: 322,
},
},
],
- totalSize: 159,
+ totalElements: 159,
filteredSize: 1586,
- length: 10,
- page: 0,
+ size: 10,
+ number: 0,
+ numberOfElements: 10,
+ totalPages: 16,
};
diff --git a/src/models/pageableSchema.ts b/src/models/pageableSchema.ts
index 9ec3a540..4e772ffc 100644
--- a/src/models/pageableSchema.ts
+++ b/src/models/pageableSchema.ts
@@ -7,7 +7,7 @@ export const pageableSchema = <T extends ZodTypeAny>(type: T) =>
totalPages: z.number().nonnegative(),
totalElements: z.number().nonnegative(),
numberOfElements: z.number().nonnegative(),
- size: z.number().positive(),
+ size: z.number().nonnegative(),
number: z.number().nonnegative(),
content: z.array(type),
});
diff --git a/src/models/publicationsResponseSchema.ts b/src/models/publicationsResponseSchema.ts
deleted file mode 100644
index 5bdcca5b..00000000
--- a/src/models/publicationsResponseSchema.ts
+++ /dev/null
@@ -1,10 +0,0 @@
-import { z } from 'zod';
-import { publicationSchema } from './publicationsSchema';
-
-export const publicationsResponseSchema = z.object({
- data: z.array(publicationSchema),
- totalSize: z.number(),
- filteredSize: z.number(),
- length: z.number(),
- page: z.number(),
-});
diff --git a/src/models/publicationsSchema.ts b/src/models/publicationsSchema.ts
index b1574088..14ac77ff 100644
--- a/src/models/publicationsSchema.ts
+++ b/src/models/publicationsSchema.ts
@@ -1,10 +1,8 @@
import { z } from 'zod';
-import { targetElementSchema } from './targetElementSchema';
+import { bioEntitySchema } from '@/models/bioEntitySchema';
import { articleSchema } from './articleSchema';
export const publicationSchema = z.object({
- elements: z.array(targetElementSchema),
- publication: z.object({
- article: articleSchema,
- }),
+ elements: z.array(bioEntitySchema),
+ article: articleSchema,
});
diff --git a/src/redux/publications/publications.selectors.ts b/src/redux/publications/publications.selectors.ts
index 8ed16fac..202156a9 100644
--- a/src/redux/publications/publications.selectors.ts
+++ b/src/redux/publications/publications.selectors.ts
@@ -11,20 +11,23 @@ export const publicationsDataSelector = createSelector(
export const publicationsListDataSelector = createSelector(
publicationsDataSelector,
- data => data?.data,
+ data => data?.content,
);
/** totalSize is number of pages */
-export const totalSizeSelector = createSelector(publicationsDataSelector, data => data?.totalSize);
+export const totalSizeSelector = createSelector(
+ publicationsDataSelector,
+ data => data?.totalElements,
+);
export const filteredSizeSelector = createSelector(
publicationsDataSelector,
data => data?.filteredSize,
);
-export const currentPageSelector = createSelector(publicationsDataSelector, data => data?.page);
+export const currentPageSelector = createSelector(publicationsDataSelector, data => data?.number);
export const paginationSelector = createSelector(publicationsDataSelector, data => ({
- pageIndex: data?.page || ZERO,
+ pageIndex: data?.number || ZERO,
pageSize: 10,
}));
diff --git a/src/redux/publications/publications.thunks.ts b/src/redux/publications/publications.thunks.ts
index 4c03def9..c173c620 100644
--- a/src/redux/publications/publications.thunks.ts
+++ b/src/redux/publications/publications.thunks.ts
@@ -1,23 +1,29 @@
import { createAsyncThunk } from '@reduxjs/toolkit';
import { validateDataUsingZodSchema } from '@/utils/validateDataUsingZodSchema';
-import { axiosInstance } from '@/services/api/utils/axiosInstance';
-import { PublicationsResponse } from '@/types/models';
-import { publicationsResponseSchema } from '@/models/publicationsResponseSchema';
+import { axiosInstanceNewAPI } from '@/services/api/utils/axiosInstance';
import { ThunkConfig } from '@/types/store';
import { getError } from '@/utils/error-report/getError';
+import { FilteredPageOf, Publication } from '@/types/models';
+import { pageableSchema } from '@/models/pageableSchema';
+import { publicationSchema } from '@/models/publicationsSchema';
import { GetPublicationsParams } from './publications.types';
import { apiPath } from '../apiPath';
import { PUBLICATIONS_FETCHING_ERROR_PREFIX } from './publications.constatns';
export const getPublications = createAsyncThunk<
- PublicationsResponse | undefined,
+ FilteredPageOf<Publication> | undefined,
GetPublicationsParams,
ThunkConfig
>('publications/getPublications', async params => {
try {
- const response = await axiosInstance.get<PublicationsResponse>(apiPath.getPublications(params));
+ const response = await axiosInstanceNewAPI.get<FilteredPageOf<Publication>>(
+ apiPath.getPublications(params),
+ );
- const isDataValid = validateDataUsingZodSchema(response.data, publicationsResponseSchema);
+ const isDataValid = validateDataUsingZodSchema(
+ response.data,
+ pageableSchema(publicationSchema),
+ );
return isDataValid ? response.data : undefined;
} catch (error) {
diff --git a/src/redux/publications/publications.types.ts b/src/redux/publications/publications.types.ts
index 2654b800..792e7544 100644
--- a/src/redux/publications/publications.types.ts
+++ b/src/redux/publications/publications.types.ts
@@ -1,10 +1,10 @@
import { FetchDataState } from '@/types/fetchDataState';
-import { PublicationsResponse } from '@/types/models';
+import { FilteredPageOf, Publication } from '@/types/models';
export type SortColumn = '' | 'pubmedId' | 'title' | 'authors' | 'journal' | 'year' | 'level';
export type SortOrder = 'asc' | 'desc';
-export type PublicationsState = FetchDataState<PublicationsResponse> & {
+export type PublicationsState = FetchDataState<FilteredPageOf<Publication>> & {
sortColumn: SortColumn;
sortOrder: SortOrder;
selectedModelId?: string;
diff --git a/src/types/models.ts b/src/types/models.ts
index af20167b..b01270f9 100644
--- a/src/types/models.ts
+++ b/src/types/models.ts
@@ -49,7 +49,6 @@ import {
import { overviewImageView } from '@/models/overviewImageView';
import { pluginSchema } from '@/models/pluginSchema';
import { projectSchema } from '@/models/projectSchema';
-import { publicationsResponseSchema } from '@/models/publicationsResponseSchema';
import { publicationSchema } from '@/models/publicationsSchema';
import { referenceSchema } from '@/models/referenceSchema';
import { sessionSchemaValid } from '@/models/sessionValidSchema';
@@ -150,7 +149,6 @@ export type Color = z.infer<typeof colorSchema>;
export type Statistics = z.infer<typeof statisticsSchema>;
export type CompartmentPathway = z.infer<typeof compartmentPathwaySchema>;
export type CompartmentPathwayDetails = z.infer<typeof compartmentPathwayDetailsSchema>;
-export type PublicationsResponse = z.infer<typeof publicationsResponseSchema>;
export type Publication = z.infer<typeof publicationSchema>;
export type ExportNetwork = z.infer<typeof exportNetworkchema>;
export type ExportElements = z.infer<typeof exportElementsSchema>;
@@ -180,4 +178,8 @@ export type PageOf<T> = {
content: T[];
};
+export type FilteredPageOf<T> = PageOf<T> & {
+ filteredSize: number;
+};
+
export type OAuth = z.infer<typeof oauthSchema>;
--
GitLab