Compare revisions

Miłosz Grocholewski · Miłosz Grocholewski · Miłosz Grocholewski · Miłosz Grocholewski · Miłosz Grocholewski · Miłosz Grocholewski
--- a/package-lock.json
+++ b/package-lock.json
@@ -40,6 +40,7 @@
        "react-dropzone": "14.2.3",
        "react-redux": "8.1.3",
        "react-select": "5.9.0",
+        "react-use-websocket": "4.11.1",
        "sonner": "1.4.3",
        "tailwind-merge": "1.14.0",
        "tailwindcss": "3.4.13",
@@ -12275,6 +12276,11 @@
        "react-dom": ">=16.6.0"
      }
    },
+    "node_modules/react-use-websocket": {
+      "version": "4.11.1",
+      "resolved": "https://registry.npmjs.org/react-use-websocket/-/react-use-websocket-4.11.1.tgz",
+      "integrity": "sha512-39e8mK2a2A1h8uY3ePF45b2q0vwMOmaEy7J5qEhQg4n7vYa5oDLmqutG36kZQgAQ/3KCZS0brlGRbbZJ0+zfKQ=="
+    },
    "node_modules/read-cache": {
      "version": "1.0.0",
      "resolved": "https://registry.npmjs.org/read-cache/-/read-cache-1.0.0.tgz",
@@ -14457,9 +14463,9 @@
      "dev": true
    },
    "node_modules/ws": {
-      "version": "8.16.0",
+      "version": "8.17.1",
-      "resolved": "https://registry.npmjs.org/ws/-/ws-8.16.0.tgz",
+      "resolved": "https://registry.npmjs.org/ws/-/ws-8.17.1.tgz",
-      "integrity": "sha512-HS0c//TP7Ina87TfiPUz1rQzMhHrl/SG2guqRcTOIUYD2q8uhUdNHZYJUaQ8aTGPzCh+c6oawMKW35nFl1dxyQ==",
+      "integrity": "sha512-6XQFvXTkbfUOZOKKILFG1PDK2NDQs4azKQl26T0YS5CxqWLgXajbPZ+h4gZekJyRqFU8pvnbAbbs/3TgRPy+GQ==",
      "dev": true,
      "engines": {
        "node": ">=10.0.0"
@@ -23504,6 +23510,11 @@
        "prop-types": "^15.6.2"
      }
    },
+    "react-use-websocket": {
+      "version": "4.11.1",
+      "resolved": "https://registry.npmjs.org/react-use-websocket/-/react-use-websocket-4.11.1.tgz",
+      "integrity": "sha512-39e8mK2a2A1h8uY3ePF45b2q0vwMOmaEy7J5qEhQg4n7vYa5oDLmqutG36kZQgAQ/3KCZS0brlGRbbZJ0+zfKQ=="
+    },
    "read-cache": {
      "version": "1.0.0",
      "resolved": "https://registry.npmjs.org/read-cache/-/read-cache-1.0.0.tgz",
@@ -25133,9 +25144,9 @@
      }
    },
    "ws": {
-      "version": "8.16.0",
+      "version": "8.17.1",
-      "resolved": "https://registry.npmjs.org/ws/-/ws-8.16.0.tgz",
+      "resolved": "https://registry.npmjs.org/ws/-/ws-8.17.1.tgz",
-      "integrity": "sha512-HS0c//TP7Ina87TfiPUz1rQzMhHrl/SG2guqRcTOIUYD2q8uhUdNHZYJUaQ8aTGPzCh+c6oawMKW35nFl1dxyQ==",
+      "integrity": "sha512-6XQFvXTkbfUOZOKKILFG1PDK2NDQs4azKQl26T0YS5CxqWLgXajbPZ+h4gZekJyRqFU8pvnbAbbs/3TgRPy+GQ==",
      "dev": true,
      "requires": {}
    },

--- a/package.json
+++ b/package.json
@@ -54,6 +54,7 @@
    "react-dropzone": "14.2.3",
    "react-redux": "8.1.3",
    "react-select": "5.9.0",
+    "react-use-websocket": "4.11.1",
    "sonner": "1.4.3",
    "tailwind-merge": "1.14.0",
    "tailwindcss": "3.4.13",
@@ -64,7 +65,6 @@
    "zod-to-json-schema": "3.22.4"
  },
  "devDependencies": {
-    "@types/ol-ext": "npm:@siedlerchr/types-ol-ext@3.6.1",
    "@commitlint/cli": "17.8.1",
    "@commitlint/config-conventional": "17.8.1",
    "@testing-library/jest-dom": "6.1.6",

--- a/src/components/AppWrapper/AppWrapper.component.tsx
+++ b/src/components/AppWrapper/AppWrapper.component.tsx
@@ -4,6 +4,7 @@ import { ReactNode } from 'react';
 import { Provider } from 'react-redux';
 import { Toaster } from 'sonner';
 import { Modal } from '@/components/FunctionalArea/Modal';
+import { WebSocketEntityUpdatesProvider } from '@/utils/websocket-entity-updates/webSocketEntityUpdatesProvider';
 interface AppWrapperProps {
  children: ReactNode;
@@ -13,17 +14,19 @@ export const AppWrapper = ({ children }: AppWrapperProps): JSX.Element => {
  return (
    <MapInstanceProvider>
      <Provider store={store}>
-        <>
+        <WebSocketEntityUpdatesProvider>
-          <Modal />
+          <>
-          <Toaster
+            <Modal />
-            position="top-center"
+            <Toaster
-            visibleToasts={1}
+              position="top-center"
-            style={{
+              visibleToasts={1}
-              width: '700px',
+              style={{
-            }}
+                width: '700px',
-          />
+              }}
-          {children}
+            />
-        </>
+            {children}
+          </>
+        </WebSocketEntityUpdatesProvider>
      </Provider>
    </MapInstanceProvider>
  );

--- a/src/components/FunctionalArea/ContextMenu/ContextMenu.component.test.tsx
+++ b/src/components/FunctionalArea/ContextMenu/ContextMenu.component.test.tsx
@@ -8,6 +8,8 @@ import { act, render, screen } from '@testing-library/react';
 import { CONTEXT_MENU_INITIAL_STATE } from '@/redux/contextMenu/contextMenu.constants';
 import { bioEntityContentFixture } from '@/models/fixtures/bioEntityContentsFixture';
 import { PluginsContextMenu } from '@/services/pluginsManager/pluginContextMenu/pluginsContextMenu';
+import { modelElementFixture } from '@/models/fixtures/modelElementFixture';
+import { DEFAULT_ERROR } from '@/constants/errors';
 import { ContextMenu } from './ContextMenu.component';
 const renderComponent = (initialStore?: InitialStoreState): { store: StoreType } => {
@@ -97,31 +99,40 @@ describe('ContextMenu - Component', () => {
    it('should display uniprot id as option if it is provided', () => {
      renderComponent({
-        bioEntity: {
+        modelElements: {
-          data: [
+          data: {
-            {
+            0: {
-              searchQueryElement: bioEntityContentFixture.bioEntity.id.toString(),
+              data: [modelElementFixture],
              loading: 'succeeded',
-              error: { name: '', message: '' },
+              error: { message: '', name: '' },
-              data: [
-                {
-                  ...bioEntityContentFixture,
-                  bioEntity: {
-                    ...bioEntityContentFixture.bioEntity,
-                    fullName: 'BioEntity Full Name',
-                    references: [
-                      {
-                        ...bioEntityContentFixture.bioEntity.references[0],
-                        type: 'UNIPROT',
-                      },
-                    ],
-                  },
-                },
-              ],
            },
-          ],
+          },
-          loading: 'succeeded',
+          search: {
-          error: { message: '', name: '' },
+            data: [
+              {
+                searchQueryElement: modelElementFixture.id.toString(),
+                loading: 'succeeded',
+                error: DEFAULT_ERROR,
+                data: [
+                  {
+                    modelElement: {
+                      ...modelElementFixture,
+                      fullName: 'BioEntity Full Name',
+                      references: [
+                        {
+                          ...bioEntityContentFixture.bioEntity.references[0],
+                          type: 'UNIPROT',
+                        },
+                      ],
+                    },
+                    perfect: true,
+                  },
+                ],
+              },
+            ],
+            loading: 'pending',
+            error: DEFAULT_ERROR,
+          },
        },
        contextMenu: {
          ...CONTEXT_MENU_INITIAL_STATE,
@@ -144,31 +155,40 @@ describe('ContextMenu - Component', () => {
    it('should open molart modal when clicking on uniprot', async () => {
      const { store } = renderComponent({
-        bioEntity: {
+        modelElements: {
-          data: [
+          data: {
-            {
+            0: {
-              searchQueryElement: bioEntityContentFixture.bioEntity.id.toString(),
+              data: [modelElementFixture],
              loading: 'succeeded',
-              error: { name: '', message: '' },
+              error: { message: '', name: '' },
-              data: [
-                {
-                  ...bioEntityContentFixture,
-                  bioEntity: {
-                    ...bioEntityContentFixture.bioEntity,
-                    fullName: 'BioEntity Full Name',
-                    references: [
-                      {
-                        ...bioEntityContentFixture.bioEntity.references[0],
-                        type: 'UNIPROT',
-                      },
-                    ],
-                  },
-                },
-              ],
            },
-          ],
+          },
-          loading: 'succeeded',
+          search: {
-          error: { message: '', name: '' },
+            data: [
+              {
+                searchQueryElement: modelElementFixture.id.toString(),
+                loading: 'succeeded',
+                error: DEFAULT_ERROR,
+                data: [
+                  {
+                    modelElement: {
+                      ...modelElementFixture,
+                      fullName: 'BioEntity Full Name',
+                      references: [
+                        {
+                          ...bioEntityContentFixture.bioEntity.references[0],
+                          type: 'UNIPROT',
+                        },
+                      ],
+                    },
+                    perfect: true,
+                  },
+                ],
+              },
+            ],
+            loading: 'pending',
+            error: DEFAULT_ERROR,
+          },
        },
        contextMenu: {
          ...CONTEXT_MENU_INITIAL_STATE,

--- a/src/components/FunctionalArea/ContextMenu/ContextMenu.component.tsx
+++ b/src/components/FunctionalArea/ContextMenu/ContextMenu.component.tsx
-import { searchedBioEntityElementUniProtIdSelector } from '@/redux/bioEntity/bioEntity.selectors';
 import { contextMenuSelector } from '@/redux/contextMenu/contextMenu.selector';
 import { closeContextMenu } from '@/redux/contextMenu/contextMenu.slice';
 import { useAppDispatch } from '@/redux/hooks/useAppDispatch';
@@ -9,12 +8,13 @@ import { twMerge } from 'tailwind-merge';
 import { FIRST_ARRAY_ELEMENT, SECOND_ARRAY_ELEMENT, ZERO } from '@/constants/common';
 import { PluginsContextMenu } from '@/services/pluginsManager/pluginContextMenu/pluginsContextMenu';
-import { BioEntity, NewReaction } from '@/types/models';
+import { ModelElement, NewReaction } from '@/types/models';
 import { ClickCoordinates } from '@/services/pluginsManager/pluginContextMenu/pluginsContextMenu.types';
 import { currentModelSelector } from '@/redux/models/models.selectors';
 import { mapDataLastPositionSelector } from '@/redux/map/map.selectors';
 import { DEFAULT_ZOOM } from '@/constants/map';
 import { OutsideClickWrapper } from '@/shared/OutsideClickWrapper';
+import { searchedModelElementUniProtIdSelector } from '@/redux/modelElements/modelElements.selector';
 export const ContextMenu = (): React.ReactNode => {
  const pluginContextMenu = PluginsContextMenu.menuItems;
@@ -22,7 +22,7 @@ export const ContextMenu = (): React.ReactNode => {
  const lastPosition = useAppSelector(mapDataLastPositionSelector);
  const dispatch = useAppDispatch();
  const { isOpen, coordinates } = useAppSelector(contextMenuSelector);
-  const unitProtId = useAppSelector(searchedBioEntityElementUniProtIdSelector);
+  const unitProtId = useAppSelector(searchedModelElementUniProtIdSelector);
  const isUnitProtIdAvailable = (): boolean => unitProtId !== undefined;
@@ -49,7 +49,10 @@ export const ContextMenu = (): React.ReactNode => {
  const modelId = model ? model.id : ZERO;
  const handleCallback = (
-    callback: (coordinates: ClickCoordinates, element: BioEntity | NewReaction | undefined) => void,
+    callback: (
+      coordinates: ClickCoordinates,
+      element: ModelElement | NewReaction | undefined,
+    ) => void,
  ) => {
    return () => {
      closeContextMenuFunction();

--- a/src/components/FunctionalArea/Modal/EditOverlayModal/EditOverlayModal.component.test.tsx
+++ b/src/components/FunctionalArea/Modal/EditOverlayModal/EditOverlayModal.component.test.tsx
@@ -94,6 +94,7 @@ describe('EditOverlayModal - component', () => {
        login: 'test',
        role: 'user',
        userData: null,
+        token: null,
      },
      modal: {
        isOpen: true,
@@ -132,6 +133,7 @@ describe('EditOverlayModal - component', () => {
        login: 'test',
        role: 'user',
        userData: null,
+        token: null,
      },
      modal: {
        isOpen: true,
@@ -171,6 +173,7 @@ describe('EditOverlayModal - component', () => {
        login: 'test',
        role: 'user',
        userData: null,
+        token: null,
      },
      modal: {
        isOpen: true,
@@ -218,6 +221,7 @@ describe('EditOverlayModal - component', () => {
        login: 'test',
        role: 'user',
        userData: null,
+        token: null,
      },
      modal: {
        isOpen: true,

--- a/src/components/FunctionalArea/Modal/EditOverlayModal/hooks/useEditOverlay.test.ts
+++ b/src/components/FunctionalArea/Modal/EditOverlayModal/hooks/useEditOverlay.test.ts
@@ -15,6 +15,7 @@ describe('useEditOverlay', () => {
        login: 'test',
        role: 'user',
        userData: null,
+        token: null,
      },
      modal: {
        isOpen: true,
@@ -54,6 +55,7 @@ describe('useEditOverlay', () => {
        login: 'test',
        role: 'user',
        userData: null,
+        token: null,
      },
      modal: {
        isOpen: true,
@@ -96,6 +98,7 @@ describe('useEditOverlay', () => {
        login: null,
        role: 'user',
        userData: null,
+        token: null,
      },
      modal: {
        isOpen: true,
@@ -134,6 +137,7 @@ describe('useEditOverlay', () => {
        login: 'test',
        role: 'user',
        userData: null,
+        token: null,
      },
      modal: {
        isOpen: true,
@@ -173,6 +177,7 @@ describe('useEditOverlay', () => {
        login: null,
        role: 'user',
        userData: null,
+        token: null,
      },
      modal: {
        isOpen: true,

--- a/src/components/FunctionalArea/Modal/OverviewImagesModal/OverviewImagesModal.component.test.tsx
+++ b/src/components/FunctionalArea/Modal/OverviewImagesModal/OverviewImagesModal.component.test.tsx
@@ -18,6 +18,8 @@ jest.mock('./utils/useOverviewImageSize', () => ({
  })),
 }));
+const PROJECT_DIRECTORY = 'directory';
 const renderComponent = (initialStoreState: InitialStoreState = {}): { store: StoreType } => {
  const { Wrapper, store } = getReduxWrapperWithStore(initialStoreState);
@@ -42,6 +44,7 @@ describe('OverviewImagesModal - component', () => {
            ...projectFixture,
            overviewImageViews: [],
            topOverviewImage: PROJECT_OVERVIEW_IMAGE_MOCK,
+            directory: PROJECT_DIRECTORY,
          },
          loading: 'succeeded',
          error: { message: '', name: '' },
@@ -70,6 +73,7 @@ describe('OverviewImagesModal - component', () => {
            ...projectFixture,
            overviewImageViews: [PROJECT_OVERVIEW_IMAGE_MOCK],
            topOverviewImage: PROJECT_OVERVIEW_IMAGE_MOCK,
+            directory: PROJECT_DIRECTORY,
          },
          loading: 'succeeded',
          error: { message: '', name: '' },
@@ -91,7 +95,7 @@ describe('OverviewImagesModal - component', () => {
    it('should render image with valid src', () => {
      const imageElement = screen.getByAltText('overview');
-      const result = `${BASE_MAP_IMAGES_URL}/map_images/${PROJECT_OVERVIEW_IMAGE_MOCK.filename}`;
+      const result = `${BASE_MAP_IMAGES_URL}/map_images/${PROJECT_DIRECTORY}/${PROJECT_OVERVIEW_IMAGE_MOCK.filename}`;
      expect(imageElement.getAttribute('src')).toBe(result);
    });

--- a/src/components/FunctionalArea/Modal/OverviewImagesModal/utils/useOverviewImage.test.ts
+++ b/src/components/FunctionalArea/Modal/OverviewImagesModal/utils/useOverviewImage.test.ts
@@ -7,6 +7,8 @@ import { getReduxWrapperWithStore } from '@/utils/testing/getReduxWrapperWithSto
 import { renderHook } from '@testing-library/react';
 import { useOverviewImage } from './useOverviewImage';
+const PROJECT_DIRECTORY = 'directory';
 describe('useOverviewImage - hook', () => {
  describe('when image data is invalid', () => {
    const { Wrapper } = getReduxWrapperWithStore({
@@ -15,6 +17,7 @@ describe('useOverviewImage - hook', () => {
          ...projectFixture,
          overviewImageViews: [],
          topOverviewImage: PROJECT_OVERVIEW_IMAGE_MOCK,
+          directory: PROJECT_DIRECTORY,
        },
        loading: 'succeeded',
        error: { message: '', name: '' },
@@ -48,6 +51,7 @@ describe('useOverviewImage - hook', () => {
          ...projectFixture,
          overviewImageViews: [PROJECT_OVERVIEW_IMAGE_MOCK],
          topOverviewImage: PROJECT_OVERVIEW_IMAGE_MOCK,
+          directory: PROJECT_DIRECTORY,
        },
        loading: 'succeeded',
        error: { message: '', name: '' },
@@ -66,7 +70,7 @@ describe('useOverviewImage - hook', () => {
    });
    it('should return default size of image and valid imageUrl', () => {
-      const imageUrl = `${BASE_MAP_IMAGES_URL}/map_images/${PROJECT_OVERVIEW_IMAGE_MOCK.filename}`;
+      const imageUrl = `${BASE_MAP_IMAGES_URL}/map_images/${PROJECT_DIRECTORY}/${PROJECT_OVERVIEW_IMAGE_MOCK.filename}`;
      expect(result.current).toMatchObject({
        imageUrl,
@@ -88,6 +92,7 @@ describe('useOverviewImage - hook', () => {
            },
          ],
          topOverviewImage: PROJECT_OVERVIEW_IMAGE_MOCK,
+          directory: PROJECT_DIRECTORY,
        },
        loading: 'succeeded',
        error: { message: '', name: '' },
@@ -109,7 +114,7 @@ describe('useOverviewImage - hook', () => {
    );
    it('should return size of image and valid imageUrl', () => {
-      const imageUrl = `${BASE_MAP_IMAGES_URL}/map_images/${PROJECT_OVERVIEW_IMAGE_MOCK.filename}`;
+      const imageUrl = `${BASE_MAP_IMAGES_URL}/map_images/${PROJECT_DIRECTORY}/${PROJECT_OVERVIEW_IMAGE_MOCK.filename}`;
      expect(result.current).toMatchObject({
        imageUrl,

--- a/src/components/FunctionalArea/Modal/OverviewImagesModal/utils/useOverviewImageUrl.test.ts
+++ b/src/components/FunctionalArea/Modal/OverviewImagesModal/utils/useOverviewImageUrl.test.ts
@@ -6,6 +6,8 @@ import { getReduxWrapperWithStore } from '@/utils/testing/getReduxWrapperWithSto
 import { renderHook } from '@testing-library/react';
 import { useOverviewImageUrl } from './useOverviewImageUrl';
+const PROJECT_DIRECTORY = 'directory';
 describe('useOverviewImageUrl - hook', () => {
  describe('when currentImage data is valid', () => {
    const { Wrapper } = getReduxWrapperWithStore({
@@ -14,6 +16,7 @@ describe('useOverviewImageUrl - hook', () => {
          ...projectFixture,
          overviewImageViews: [],
          topOverviewImage: PROJECT_OVERVIEW_IMAGE_MOCK,
+          directory: PROJECT_DIRECTORY,
        },
        loading: 'succeeded',
        error: { message: '', name: '' },
@@ -41,6 +44,7 @@ describe('useOverviewImageUrl - hook', () => {
          ...projectFixture,
          overviewImageViews: [PROJECT_OVERVIEW_IMAGE_MOCK],
          topOverviewImage: PROJECT_OVERVIEW_IMAGE_MOCK,
+          directory: PROJECT_DIRECTORY,
        },
        loading: 'succeeded',
        error: { message: '', name: '' },
@@ -58,7 +62,7 @@ describe('useOverviewImageUrl - hook', () => {
      const { result } = renderHook(() => useOverviewImageUrl(), { wrapper: Wrapper });
      expect(result.current).toBe(
-        `${BASE_MAP_IMAGES_URL}/map_images/${PROJECT_OVERVIEW_IMAGE_MOCK.filename}`,
+        `${BASE_MAP_IMAGES_URL}/map_images/${PROJECT_DIRECTORY}/${PROJECT_OVERVIEW_IMAGE_MOCK.filename}`,
      );
    });
  });

--- a/src/components/FunctionalArea/Modal/OverviewImagesModal/utils/useOverviewImageUrl.ts
+++ b/src/components/FunctionalArea/Modal/OverviewImagesModal/utils/useOverviewImageUrl.ts
 import { BASE_MAP_IMAGES_URL } from '@/constants';
-import { currentOverviewImageSelector } from '@/redux/project/project.selectors';
+import {
+  currentOverviewImageSelector,
+  projectDirectorySelector,
+} from '@/redux/project/project.selectors';
 import { useSelector } from 'react-redux';
 export const useOverviewImageUrl = (): string => {
  const currentImage = useSelector(currentOverviewImageSelector);
+  const directory = useSelector(projectDirectorySelector);
-  if (!currentImage) {
+  if (!currentImage || !directory) {
    return '';
  }
-  return `${BASE_MAP_IMAGES_URL}/map_images/${currentImage.filename}`;
+  return `${BASE_MAP_IMAGES_URL}/map_images/${directory}/${currentImage.filename}`;
 };
--- a/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsTable/ElementsOnMapCell/ElementLink/ElementLink.component.test.tsx
+++ b/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsTable/ElementsOnMapCell/ElementLink/ElementLink.component.test.tsx
@@ -5,7 +5,7 @@ import { apiPath } from '@/redux/apiPath';
 import { DEFAULT_POSITION } from '@/redux/map/map.constants';
 import { INITIAL_STORE_STATE_MOCK } from '@/redux/root/root.fixtures';
 import { AppDispatch, RootState } from '@/redux/store';
-import { BioEntity, MapModel } from '@/types/models';
+import { MapModel, PublicationElement } from '@/types/models';
 import { mockNetworkNewAPIResponse } from '@/utils/mockNetworkResponse';
 import {
  InitialStoreState,
@@ -14,12 +14,12 @@ import {
 import { render, screen, waitFor } from '@testing-library/react';
 import { HttpStatusCode } from 'axios';
 import { MockStoreEnhanced } from 'redux-mock-store';
-import { isReactionBioEntity } from '@/redux/reactions/isReactionBioentity';
+import { isReactionElement } from '@/redux/reactions/isReactionElement';
 import { ElementLink } from './ElementLink.component';
 const mockedAxiosNewClient = mockNetworkNewAPIResponse();
-const TARGET_ELEMENT: BioEntity = {
+const TARGET_ELEMENT: PublicationElement = {
  ...bioEntityResponseFixture.content[FIRST_ARRAY_ELEMENT].bioEntity,
  id: 123,
  model: 52,
@@ -36,20 +36,20 @@ const OTHER_MODEL: MapModel = {
 };
 interface Props {
-  target: BioEntity;
+  target: PublicationElement;
 }
-const getElementText = (bioEntity: BioEntity): string => {
+const getElementText = (element: PublicationElement): string => {
-  const isReaction = isReactionBioEntity(bioEntity);
+  const isReaction = isReactionElement(element);
  const prefix = isReaction ? 'Reaction: ' : 'Element: ';
-  return prefix + bioEntity.elementId;
+  return prefix + element.elementId;
 };
-const getSearchQuery = (bioEntity: BioEntity): string => {
+const getSearchQuery = (element: PublicationElement): string => {
-  const isReaction = isReactionBioEntity(bioEntity);
+  const isReaction = isReactionElement(element);
-  return (isReaction ? 'reaction:' : 'element:') + bioEntity.id;
+  return (isReaction ? 'reaction:' : 'element:') + element.id;
 };
 const renderComponent = (
@@ -86,10 +86,10 @@ describe('ElementLink - component', () => {
    });
    it('should should show element id', async () => {
-      const bioEntity = TARGET_ELEMENT;
+      const element = TARGET_ELEMENT;
      await waitFor(() => {
-        expect(screen.getByText(getElementText(bioEntity))).toBeInTheDocument();
+        expect(screen.getByText(getElementText(element))).toBeInTheDocument();
      });
    });
  });
@@ -116,10 +116,10 @@ describe('ElementLink - component', () => {
        },
      );
-      const bioEntity = TARGET_ELEMENT;
+      const element = TARGET_ELEMENT;
      await waitFor(() => {
-        const link = screen.getByText(getElementText(bioEntity));
+        const link = screen.getByText(getElementText(element));
        link.click();
        const actions = store.getActions();
@@ -148,7 +148,7 @@ describe('ElementLink - component', () => {
        expect(actions).toEqual(
          expect.arrayContaining([
            expect.objectContaining({
-              payload: getSearchQuery(bioEntity),
+              payload: getSearchQuery(element),
              type: 'drawer/openSearchDrawerWithSelectedTab',
            }),
          ]),
@@ -206,10 +206,10 @@ describe('ElementLink - component', () => {
        },
      );
-      const bioEntity = TARGET_ELEMENT;
+      const element = TARGET_ELEMENT;
      await waitFor(() => {
-        const link = screen.getByText(getElementText(bioEntity));
+        const link = screen.getByText(getElementText(element));
        link.click();
        const actions = store.getActions();
@@ -238,7 +238,7 @@ describe('ElementLink - component', () => {
        expect(actions).toEqual(
          expect.arrayContaining([
            expect.objectContaining({
-              payload: getSearchQuery(bioEntity),
+              payload: getSearchQuery(element),
              type: 'drawer/openSearchDrawerWithSelectedTab',
            }),
          ]),

--- a/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsTable/ElementsOnMapCell/ElementLink/ElementLink.component.tsx
+++ b/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsTable/ElementsOnMapCell/ElementLink/ElementLink.component.tsx
@@ -13,11 +13,11 @@ import { closeModal } from '@/redux/modal/modal.slice';
 import { modelsNameMapSelector } from '@/redux/models/models.selectors';
 import { getSearchData } from '@/redux/search/search.thunks';
 import { PluginsEventBus } from '@/services/pluginsManager/pluginsEventBus';
-import { BioEntity } from '@/types/models';
+import { PublicationElement } from '@/types/models';
-import { isReactionBioEntity } from '@/redux/reactions/isReactionBioentity';
+import { isReactionElement } from '@/redux/reactions/isReactionElement';
 interface Props {
-  target: BioEntity;
+  target: PublicationElement;
 }
 export const ElementLink = ({ target }: Props): JSX.Element => {
@@ -26,7 +26,7 @@ export const ElementLink = ({ target }: Props): JSX.Element => {
  const currentModelId = useAppSelector(mapModelIdSelector);
  const mapsNames = useAppSelector(modelsNameMapSelector);
-  const isReaction = isReactionBioEntity(target);
+  const isReaction = isReactionElement(target);
  const isMapAlreadyOpened = (modelId: number): boolean =>
    openedMaps.some(map => map.modelId === modelId);

--- a/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsTable/ElementsOnMapCell/ElementsOnMapCell.component.test.tsx
+++ b/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsTable/ElementsOnMapCell/ElementsOnMapCell.component.test.tsx
 import { INITIAL_STORE_STATE_MOCK } from '@/redux/root/root.fixtures';
 import { AppDispatch, RootState } from '@/redux/store';
-import { BioEntity } from '@/types/models';
+import { PublicationElement } from '@/types/models';
 import {
  InitialStoreState,
  getReduxStoreWithActionsListener,
 } from '@/utils/testing/getReduxStoreActionsListener';
 import { render, screen, waitFor } from '@testing-library/react';
 import { MockStoreEnhanced } from 'redux-mock-store';
-import { bioEntityFixture } from '@/models/fixtures/bioEntityFixture';
+import { isReactionElement } from '@/redux/reactions/isReactionElement';
-import { isReactionBioEntity } from '@/redux/reactions/isReactionBioentity';
+import { publicationElementFixture } from '@/models/fixtures/publicationElementFixture';
 import { ElementsOnMapCell } from './ElementsOnMapCell.component';
 interface Props {
-  targets: BioEntity[];
+  targets: PublicationElement[];
 }
 const renderComponent = (
@@ -33,8 +33,8 @@ const renderComponent = (
  );
 };
-const elementFixture = { ...bioEntityFixture, idReaction: undefined };
+const elementFixture = { ...publicationElementFixture, idReaction: undefined };
-const reactionFixture = { ...bioEntityFixture, idReaction: '123' };
+const reactionFixture = { ...publicationElementFixture, idReaction: '123' };
 const mockTargets = [{ ...elementFixture }, { ...reactionFixture }];
@@ -49,7 +49,7 @@ describe('ElementsOnMapCell - component', () => {
    await waitFor(() => {
      // type as elementId
-      const isReaction = isReactionBioEntity(bioEntity);
+      const isReaction = isReactionElement(bioEntity);
      const prefix = isReaction ? 'Reaction: ' : 'Element: ';
      expect(screen.getByText(prefix + bioEntity.elementId)).toBeInTheDocument();
    });

--- a/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsTable/ElementsOnMapCell/ElementsOnMapCell.component.tsx
+++ b/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsTable/ElementsOnMapCell/ElementsOnMapCell.component.tsx
 import { ONE } from '@/constants/common';
-import { BioEntity } from '@/types/models';
+import { PublicationElement } from '@/types/models';
 import { ElementLink } from './ElementLink';
 interface Props {
-  targets: BioEntity[];
+  targets: PublicationElement[];
 }
 export const ElementsOnMapCell = ({ targets }: Props): JSX.Element => {

--- a/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsTable/PublicationsTable.component.tsx
+++ b/src/components/FunctionalArea/Modal/PublicationsModal/PublicationsTable/PublicationsTable.component.tsx
@@ -23,7 +23,7 @@ import {
 } from '@tanstack/react-table';
 import { useRef, useState } from 'react';
 import { z } from 'zod';
-import { bioEntitySchema } from '@/models/bioEntitySchema';
+import { publicationElementSchema } from '@/models/publicationElementSchema';
 import { ElementsOnMapCell } from './ElementsOnMapCell';
 import { FilterBySubmapHeader } from './FilterBySubmapHeader/FilterBySubmapHeader.component';
 import { DEFAULT_PAGE_SIZE } from './PublicationsTable.constants';
@@ -74,9 +74,7 @@ const columns = [
    cell: ({ getValue }): JSX.Element => {
      try {
        const valueObject: unknown = JSON.parse(getValue());
-        // eslint-disable-next-line no-console
+        const targets = z.array(publicationElementSchema).parse(valueObject);
-        console.log(valueObject);
-        const targets = z.array(bioEntitySchema).parse(valueObject);
        return <ElementsOnMapCell targets={targets} />;
      } catch (error) {

--- a/src/components/FunctionalArea/TopBar/ClearAnchorsButton/ClearAnchorsButton.component.test.tsx
+++ b/src/components/FunctionalArea/TopBar/ClearAnchorsButton/ClearAnchorsButton.component.test.tsx
@@ -49,7 +49,7 @@ describe('ClearAnchorsButton - component', () => {
      { payload: undefined, type: 'contextMenu/closeContextMenu' },
      { payload: undefined, type: 'reactions/resetReactionsData' },
      { payload: undefined, type: 'search/clearSearchData' },
-      { payload: undefined, type: 'bioEntityContents/clearBioEntities' },
+      { payload: undefined, type: 'modelElements/clearSearchModelElements' },
      { payload: undefined, type: 'drugs/clearDrugsData' },
      { payload: undefined, type: 'chemicals/clearChemicalsData' },
    ]);
@@ -75,7 +75,7 @@ describe('ClearAnchorsButton - component', () => {
      { payload: undefined, type: 'contextMenu/closeContextMenu' },
      { payload: undefined, type: 'reactions/resetReactionsData' },
      { payload: undefined, type: 'search/clearSearchData' },
-      { payload: undefined, type: 'bioEntityContents/clearBioEntities' },
+      { payload: undefined, type: 'modelElements/clearSearchModelElements' },
      { payload: undefined, type: 'drugs/clearDrugsData' },
      { payload: undefined, type: 'chemicals/clearChemicalsData' },
    ]);

--- a/src/components/FunctionalArea/TopBar/ClearAnchorsButton/ClearAnchorsButton.component.tsx
+++ b/src/components/FunctionalArea/TopBar/ClearAnchorsButton/ClearAnchorsButton.component.tsx
-import { clearBioEntities } from '@/redux/bioEntity/bioEntity.slice';
 import { clearChemicalsData } from '@/redux/chemicals/chemicals.slice';
 import { closeContextMenu } from '@/redux/contextMenu/contextMenu.slice';
 import { resultDrawerOpen } from '@/redux/drawer/drawer.selectors';
@@ -11,6 +10,7 @@ import { Button } from '@/shared/Button';
 import { Icon } from '@/shared/Icon';
 import React from 'react';
 import { useSelector } from 'react-redux';
+import { clearSearchModelElements } from '@/redux/modelElements/modelElements.slice';
 export const ClearAnchorsButton = (): React.ReactNode => {
  const dispatch = useAppDispatch();
@@ -31,7 +31,7 @@ export const ClearAnchorsButton = (): React.ReactNode => {
    dispatch(clearSearchData());
    // Reset old pins data
-    dispatch(clearBioEntities());
+    dispatch(clearSearchModelElements());
    dispatch(clearDrugsData());
    dispatch(clearChemicalsData());
  };

--- a/src/components/FunctionalArea/TopBar/User/User.component.test.tsx
+++ b/src/components/FunctionalArea/TopBar/User/User.component.test.tsx
@@ -126,6 +126,7 @@ describe('AuthenticatedUser component', () => {
      login: null,
      role: null,
      userData: null,
+      token: null,
    });
  });

--- a/src/components/Map/Drawer/BioEntityDrawer/AssociatedSubmap/AssociatedSubmap.component.test.tsx
+++ b/src/components/Map/Drawer/BioEntityDrawer/AssociatedSubmap/AssociatedSubmap.component.test.tsx
 import { SIZE_OF_ARRAY_WITH_ONE_ELEMENT, ZERO } from '@/constants/common';
-import { bioEntityContentFixture } from '@/models/fixtures/bioEntityContentsFixture';
 import { MODELS_MOCK_SHORT } from '@/models/mocks/modelsMock';
-import {
+import { BIOENTITY_INITIAL_STATE_MOCK } from '@/redux/bioEntity/bioEntity.mock';
-  BIOENTITY_INITIAL_STATE_MOCK,
-  BIO_ENTITY_LINKING_TO_SUBMAP_DATA_MOCK,
-  BIO_ENTITY_LINKING_TO_SUBMAP,
-} from '@/redux/bioEntity/bioEntity.mock';
 import { DRAWER_INITIAL_STATE } from '@/redux/drawer/drawer.constants';
 import {
  initialMapDataFixture,
@@ -21,6 +16,12 @@ import {
 import { act, render, screen } from '@testing-library/react';
 import { HISTAMINE_MAP_ID, MAIN_MAP_ID } from '@/constants/mocks';
 import { ModelElementsState } from '@/redux/modelElements/modelElements.types';
+import {
+  MODEL_ELEMENT_LINKING_TO_SUBMAP,
+  MODEL_ELEMENTS_SEARCH_LINKING_TO_SUBMAP_DATA_MOCK,
+} from '@/redux/modelElements/modelElements.mock';
+import { DEFAULT_ERROR } from '@/constants/errors';
+import { modelElementFixture } from '@/models/fixtures/modelElementFixture';
 import { AssociatedSubmap } from './AssociatedSubmap.component';
 const renderComponent = (initialStoreState: InitialStoreState = {}): { store: StoreType } => {
@@ -43,21 +44,27 @@ describe('AssociatedSubmap - component', () => {
    renderComponent({
      bioEntity: {
        ...BIOENTITY_INITIAL_STATE_MOCK,
-        data: BIO_ENTITY_LINKING_TO_SUBMAP_DATA_MOCK,
      },
      drawer: {
        ...DRAWER_INITIAL_STATE,
        bioEntityDrawerState: {
-          bioentityId: bioEntityContentFixture.bioEntity.id,
+          bioentityId: modelElementFixture.id,
          drugs: {},
          chemicals: {},
        },
      },
      modelElements: {
-        [MAIN_MAP_ID]: {
+        data: {
-          data: [BIO_ENTITY_LINKING_TO_SUBMAP],
+          [MAIN_MAP_ID]: {
-          loading: 'succeeded',
+            data: [MODEL_ELEMENT_LINKING_TO_SUBMAP],
-          error: { message: '', name: '' },
+            loading: 'succeeded',
+            error: { message: '', name: '' },
+          },
+        },
+        search: {
+          data: MODEL_ELEMENTS_SEARCH_LINKING_TO_SUBMAP_DATA_MOCK,
+          loading: 'idle',
+          error: DEFAULT_ERROR,
        },
      } as ModelElementsState,
      models: {
@@ -81,21 +88,27 @@ describe('AssociatedSubmap - component', () => {
      },
      bioEntity: {
        ...BIOENTITY_INITIAL_STATE_MOCK,
-        data: BIO_ENTITY_LINKING_TO_SUBMAP_DATA_MOCK,
      },
      drawer: {
        ...DRAWER_INITIAL_STATE,
        bioEntityDrawerState: {
-          bioentityId: bioEntityContentFixture.bioEntity.id,
+          bioentityId: modelElementFixture.id,
          drugs: {},
          chemicals: {},
        },
      },
      modelElements: {
-        [MAIN_MAP_ID]: {
+        data: {
-          data: [BIO_ENTITY_LINKING_TO_SUBMAP],
+          [MAIN_MAP_ID]: {
-          loading: 'succeeded',
+            data: [MODEL_ELEMENT_LINKING_TO_SUBMAP],
-          error: { message: '', name: '' },
+            loading: 'succeeded',
+            error: { message: '', name: '' },
+          },
+        },
+        search: {
+          data: MODEL_ELEMENTS_SEARCH_LINKING_TO_SUBMAP_DATA_MOCK,
+          loading: 'idle',
+          error: DEFAULT_ERROR,
        },
      } as ModelElementsState,
      models: {
@@ -118,19 +131,25 @@ describe('AssociatedSubmap - component', () => {
        },
        bioEntity: {
          ...BIOENTITY_INITIAL_STATE_MOCK,
-          data: BIO_ENTITY_LINKING_TO_SUBMAP_DATA_MOCK,
        },
        modelElements: {
-          0: {
+          data: {
-            data: [BIO_ENTITY_LINKING_TO_SUBMAP],
+            0: {
-            loading: 'succeeded',
+              data: [MODEL_ELEMENT_LINKING_TO_SUBMAP],
-            error: { message: '', name: '' },
+              loading: 'succeeded',
+              error: { message: '', name: '' },
+            },
+          },
+          search: {
+            data: MODEL_ELEMENTS_SEARCH_LINKING_TO_SUBMAP_DATA_MOCK,
+            loading: 'idle',
+            error: DEFAULT_ERROR,
          },
        } as ModelElementsState,
        drawer: {
          ...DRAWER_INITIAL_STATE,
          bioEntityDrawerState: {
-            bioentityId: bioEntityContentFixture.bioEntity.id,
+            bioentityId: modelElementFixture.id,
            drugs: {},
            chemicals: {},
          },
@@ -151,7 +170,6 @@ describe('AssociatedSubmap - component', () => {
        modelName: 'Histamine signaling',
        lastPosition: { x: 0, y: 0, z: 0 },
      });
      const openSubmapButton = screen.getByRole('button', { name: 'Open submap' });
      await act(() => {
        openSubmapButton.click();
@@ -184,19 +202,25 @@ describe('AssociatedSubmap - component', () => {
        },
        bioEntity: {
          ...BIOENTITY_INITIAL_STATE_MOCK,
-          data: BIO_ENTITY_LINKING_TO_SUBMAP_DATA_MOCK,
        },
        modelElements: {
-          [MAIN_MAP_ID]: {
+          data: {
-            data: [BIO_ENTITY_LINKING_TO_SUBMAP],
+            [MAIN_MAP_ID]: {
-            loading: 'succeeded',
+              data: [MODEL_ELEMENT_LINKING_TO_SUBMAP],
-            error: { message: '', name: '' },
+              loading: 'succeeded',
+              error: { message: '', name: '' },
+            },
+          },
+          search: {
+            data: MODEL_ELEMENTS_SEARCH_LINKING_TO_SUBMAP_DATA_MOCK,
+            loading: 'idle',
+            error: DEFAULT_ERROR,
          },
        } as ModelElementsState,
        drawer: {
          ...DRAWER_INITIAL_STATE,
          bioEntityDrawerState: {
-            bioentityId: bioEntityContentFixture.bioEntity.id,
+            bioentityId: modelElementFixture.id,
            drugs: {},
            chemicals: {},
          },
No results found