chore: resolve merge conflicts

CHANGELOG

 minerva-front (19.0.0~alpha.0) stable; urgency=medium
   * Feature: support for matomo (#289)
+  * Feature: allow plugin to not have a panel (#306)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 18 Oct 2024 13:00:00 +0200
 
+minerva-front (18.0.2) stable; urgency=medium
+  * Bug fix: Terms of Service modal is not hidden by Select project modal when
+    login via ORCID (#305)
+  * Bug fix: when downloading map there was missing spinner indicating the
+    download is in progress (#297)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 30 Oct 2024 13:00:00 +0200
+
 minerva-front (18.0.1) stable; urgency=medium
   * Bug fix: show cookie baner only when cookie baner link is provided (#304)
+  * Bug fix: when link to submap is provided add submap name (#303)
+  * Bug fix: some old maps could not be opened (#311)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 24 Oct 2024 13:00:00 +0200
 

docs/plugins/plugins.md

@@ -11,6 +11,7 @@ Your plugin should utilize the `window.minerva.plugins.registerPlugin` method fo
   pluginName: string;
   pluginVersion: string;
   pluginUrl: string;
+  withoutPanel: boolean | undefined;
 }
 ```
 
@@ -21,6 +22,7 @@ window.minerva.plugins.registerPlugin({
   pluginName: 'Your Plugin Name',
   pluginVersion: '1.8.3',
   pluginUrl: 'https://example.com/plugins/plugin.js',
+  withoutPanel: false,
 });
 ```
 
@@ -28,17 +30,17 @@ window.minerva.plugins.registerPlugin({
 
 The `window.minerva.plugins.registerPlugin` method returns object with `element` property which is a DOM element, allowing your plugin to append its HTML content to the DOM. Use this element to create and modify the HTML structure of your plugin.
 
-```
+```javascript
 // Plugin registration
 const { element } = window.minerva.plugins.registerPlugin({
-  pluginName: "Your Plugin Name",
-  pluginVersion: "1.0.0",
-  pluginUrl: "your-plugin-url",
+  pluginName: 'Your Plugin Name',
+  pluginVersion: '1.0.0',
+  pluginUrl: 'your-plugin-url',
 });
 
 // Modify plugin's HTML structure
 const yourContent = document.createElement('div');
-yourContent.textContent = "Your Plugin Content";
+yourContent.textContent = 'Your Plugin Content';
 element.appendChild(yourContent);
 ```
 

index.d.ts

@@ -3,15 +3,12 @@ import { fitBounds } from '@/services/pluginsManager/map/fitBounds';
 import { getOpenMapId } from '@/services/pluginsManager/map/getOpenMapId';
 import { triggerSearch } from '@/services/pluginsManager/map/triggerSearch';
 import { MinervaConfiguration } from '@/services/pluginsManager/pluginsManager';
-import { MapInstance } from '@/types/map';
 import { getModels } from '@/services/pluginsManager/map/models/getModels';
 import { openMap } from '@/services/pluginsManager/map/openMap';
 import { getCenter } from '@/services/pluginsManager/map/position/getCenter';
 import { setCenter } from '@/services/pluginsManager/map/position/setCenter';
-import { triggerSearch } from '@/services/pluginsManager/map/triggerSearch';
 import { getZoom } from '@/services/pluginsManager/map/zoom/getZoom';
 import { setZoom } from '@/services/pluginsManager/map/zoom/setZoom';
-import { MinervaConfiguration } from '@/services/pluginsManager/pluginsManager';
 import { getDisease } from '@/services/pluginsManager/project/data/getDisease';
 import { getName } from '@/services/pluginsManager/project/data/getName';
 import { getOrganism } from '@/services/pluginsManager/project/data/getOrganism';
@@ -29,6 +26,7 @@ type Plugin = {
   pluginName: string;
   pluginVersion: string;
   pluginUrl: string;
+  withoutPanel: boolean | undefined;
 };
 
 type RegisterPlugin = ({ pluginName, pluginVersion, pluginUrl }: Plugin) => {

src/components/FunctionalArea/MapNavigation/MapNavigation.component.test.tsx

@@ -9,11 +9,9 @@ import {
   getReduxWrapperWithStore,
 } from '@/utils/testing/getReduxWrapperWithStore';
 import { act, render, screen, within } from '@testing-library/react';
+import { HISTAMINE_MAP_ID, MAIN_MAP_ID } from '@/constants/mocks';
 import { MapNavigation } from './MapNavigation.component';
 
-const MAIN_MAP_ID = 5053;
-const HISTAMINE_MAP_ID = 5052;
-
 const renderComponent = (initialStoreState: InitialStoreState = {}): { store: StoreType } => {
   const { Wrapper, store } = getReduxWrapperWithStore(initialStoreState);
 

src/components/FunctionalArea/Modal/ToSModal/ToSModal.component.tsx

@@ -3,7 +3,7 @@ import { useAppDispatch } from '@/redux/hooks/useAppDispatch';
 import { Button } from '@/shared/Button';
 
 import { getSessionValid, logout, updateUser } from '@/redux/user/user.thunks';
-import { closeModal } from '@/redux/modal/modal.slice';
+import { closeModal, openSelectProjectModal } from '@/redux/modal/modal.slice';
 import { userSelector } from '@/redux/user/user.selectors';
 import { useAppSelector } from '@/redux/hooks/useAppSelector';
 import { termsOfServiceValSelector } from '@/redux/configuration/configuration.selectors';
@@ -15,13 +15,14 @@ export const ToSModal: React.FC = () => {
   const termsOfService = useAppSelector(termsOfServiceValSelector);
 
   const updateUserTosHandler = async (): Promise<void> => {
-    // eslint-disable-next-line no-console
-    console.log('update');
     if (userData) {
       const user = { ...userData, termsOfUseConsent: true };
       await dispatch(updateUser(user));
       await dispatch(getSessionValid());
       dispatch(closeModal());
+      if (userData.orcidId && userData.orcidId !== '') {
+        dispatch(openSelectProjectModal());
+      }
     }
   };
 

src/components/Map/Drawer/AvailablePluginsDrawer/LoadPlugin/LoadPlugin.component.tsx

@@ -16,7 +16,9 @@ export const LoadPlugin = ({ plugin }: Props): JSX.Element => {
     hash: plugin.hash,
     pluginUrl: plugin.urls[0],
     onPluginLoaded: () => {
-      dispatch(setCurrentDrawerPluginHash(plugin.hash));
+      if (!plugin.withoutPanel) {
+        dispatch(setCurrentDrawerPluginHash(plugin.hash));
+      }
     },
   });
 

src/components/Map/Drawer/AvailablePluginsDrawer/LoadPlugin/hooks/useLoadPlugin.ts

@@ -3,7 +3,7 @@ import { useAppSelector } from '@/redux/hooks/useAppSelector';
 import { isActiveLegendSelector } from '@/redux/legend/legend.selectors';
 import { removePluginLegend, setDefaultLegendId } from '@/redux/legend/legend.slice';
 import {
-  allActivePluginsSelector,
+  allActivePluginsWithPanelSelector,
   isPluginActiveSelector,
   isPluginLoadingSelector,
   isPluginSelectedSelector,
@@ -42,12 +42,12 @@ export const useLoadPlugin = ({
   const isPluginLoading = useAppSelector(state => isPluginLoadingSelector(state, hash));
   const isPluginSelected = useAppSelector(state => isPluginSelectedSelector(state, hash));
   const isActivePluginLegend = useAppSelector(state => isActiveLegendSelector(state, hash));
-  const allActivePlugins = useAppSelector(allActivePluginsSelector);
+  const allActivePluginsWithPanel = useAppSelector(allActivePluginsWithPanelSelector);
 
   const dispatch = useAppDispatch();
 
   const setLastPluginAsCurrentActivePlugin = (): void => {
-    const newAllActivePlugins = allActivePlugins.filter(p => p.hash !== hash);
+    const newAllActivePlugins = allActivePluginsWithPanel.filter(p => p.hash !== hash);
     const lastActivePlugin = newAllActivePlugins.pop();
     if (lastActivePlugin) {
       dispatch(setCurrentDrawerPluginHash(lastActivePlugin.hash));

src/components/Map/Drawer/BioEntityDrawer/AssociatedSubmap/AssociatedSubmap.component.tsx

@@ -19,7 +19,7 @@ export const AssociatedSubmap = (): React.ReactNode => {
       data-testid="associated-submap"
       className="flex flex-row flex-nowrap items-center justify-between"
     >
-      <p>Associated Submap: </p>
+      <p>Associated Submap: {relatedSubmap.name}</p>
       <Button className="max-h-8" variantStyles="ghost" onClick={openSubmap}>
         Open submap
       </Button>

src/components/Map/Drawer/SearchDrawerWrapper/GroupedSearchResults/BioEntitiesAccordion/BioEntitiesAccordion.component.test.tsx

@@ -11,6 +11,7 @@ import {
 } from '@/utils/testing/getReduxWrapperWithStore';
 import { render, screen } from '@testing-library/react';
 import { MockStoreEnhanced } from 'redux-mock-store';
+import { HISTAMINE_MAP_ID, MAIN_MAP_ID, PRKN_SUBSTRATES_MAP_ID } from '@/constants/mocks';
 import { BioEntitiesAccordion } from './BioEntitiesAccordion.component';
 
 const renderComponent = (initialStoreState: InitialStoreState = {}): { store: StoreType } => {
@@ -95,10 +96,22 @@ describe('BioEntitiesAccordion - component', () => {
       },
     });
 
-    expect(screen.getByText('Content (10)')).toBeInTheDocument();
-    expect(screen.getByText('Core PD map (2)')).toBeInTheDocument();
-    expect(screen.getByText('Histamine signaling (5)')).toBeInTheDocument();
-    expect(screen.getByText('PRKN substrates (3)')).toBeInTheDocument();
+    const countHistamine = bioEntitiesContentFixture.filter(
+      content => content.bioEntity.model === HISTAMINE_MAP_ID,
+    ).length;
+    const countCore = bioEntitiesContentFixture.filter(
+      content => content.bioEntity.model === MAIN_MAP_ID,
+    ).length;
+    const countPrkn = bioEntitiesContentFixture.filter(
+      content => content.bioEntity.model === PRKN_SUBSTRATES_MAP_ID,
+    ).length;
+
+    const countAll = bioEntitiesContentFixture.length;
+
+    expect(screen.getByText(`Content (${countAll})`)).toBeInTheDocument();
+    expect(screen.getByText(`Core PD map (${countCore})`)).toBeInTheDocument();
+    expect(screen.getByText(`Histamine signaling (${countHistamine})`)).toBeInTheDocument();
+    expect(screen.getByText(`PRKN substrates (${countPrkn})`)).toBeInTheDocument();
   });
 
   it('should fire toggleIsContentTabOpened on accordion item button click', () => {

src/components/Map/Drawer/SearchDrawerWrapper/ResultsList/PinsList/PinsListItem/PinsListItem.component.test.tsx

@@ -62,6 +62,11 @@ const renderComponent = (
 };
 
 describe('PinsListItem - component ', () => {
+  drugsFixture[0].targets[0].targetParticipants[0].link = 'https://example.com/plugin.js';
+  drugsFixture[0].targets[0].targetParticipants[1].link = 'https://example.com/plugin.js';
+  chemicalsFixture[0].targets[0].targetParticipants[0].link = 'https://example.com/plugin.js';
+  chemicalsFixture[0].targets[0].targetParticipants[1].link = 'https://example.com/plugin.js';
+
   it('should display full name of pin', () => {
     renderComponent(DRUGS_PIN.name, DRUGS_PIN.pin, 'drugs', BIO_ENTITY, INITIAL_STORE_STATE);
 

src/components/Map/Drawer/SubmapsDrawer/SubmapItem/DownloadSubmap/DownloadSubmap.component.tsx

@@ -2,18 +2,34 @@ import { formatsHandlersSelector } from '@/redux/configuration/configuration.sel
 import { Button } from '@/shared/Button';
 import { useSelect } from 'downshift';
 import { useSelector } from 'react-redux';
+import Image from 'next/image';
+import spinnerIcon from '@/assets/vectors/icons/spinner.svg';
+import { useState } from 'react';
+import { downloadFileFromUrl } from '@/redux/export/export.utils';
 import { SUBMAP_DOWNLOAD_HANDLERS_NAMES } from './DownloadSubmap.constants';
 import { useGetSubmapDownloadUrl } from './utils/useGetSubmapDownloadUrl';
 
-export const DownloadSubmap = (): JSX.Element => {
+export const DownloadSubmap = (): React.ReactNode => {
   const formatsHandlers = useSelector(formatsHandlersSelector);
   const formatsHandlersItems = Object.entries(formatsHandlers);
   const getSubmapDownloadUrl = useGetSubmapDownloadUrl();
 
-  const { isOpen, getToggleButtonProps, getMenuProps } = useSelect({
+  const [isDownloading, setIsDownloading] = useState<boolean>(false);
+
+  const { isOpen, getToggleButtonProps, getMenuProps, closeMenu } = useSelect({
     items: formatsHandlersItems,
   });
 
+  const downloadSubmap = (handler: string) => {
+    return function () {
+      closeMenu();
+      setIsDownloading(true);
+      downloadFileFromUrl(getSubmapDownloadUrl({ handler })).finally(function () {
+        setIsDownloading(false);
+      });
+    };
+  };
+
   return (
     <div className="relative">
       <Button
@@ -22,6 +38,15 @@ export const DownloadSubmap = (): JSX.Element => {
         className="mr-4"
         {...getToggleButtonProps()}
       >
+        {isDownloading && (
+          <Image
+            src={spinnerIcon}
+            alt="spinner icon"
+            height={12}
+            width={12}
+            className="mr-5 animate-spin"
+          />
+        )}
         Download
       </Button>
       <ul
@@ -34,14 +59,13 @@ export const DownloadSubmap = (): JSX.Element => {
         {isOpen &&
           formatsHandlersItems.map(([formatId, handler]) => (
             <li key={formatId}>
-              <a
-                className="flex flex-col border-t px-4 py-2 shadow-sm"
-                href={getSubmapDownloadUrl({ handler })}
-                target="_blank"
-                download
+              <Button
+                variantStyles="ghost"
+                className="flex w-full flex-col border-t px-4 py-2 shadow-sm"
+                onClick={downloadSubmap(handler)}
               >
-                <span>{SUBMAP_DOWNLOAD_HANDLERS_NAMES[formatId]}</span>
-              </a>
+                {SUBMAP_DOWNLOAD_HANDLERS_NAMES[formatId]}
+              </Button>
             </li>
           ))}
       </ul>

src/components/Map/MapViewer/MapViewerVector/utils/shapes/coords/getCenter.ts

@@ -8,10 +8,18 @@ export default function getCenter(coords: Array<Coordinate>): Coordinate {
   let maxY = -Infinity;
 
   coords.forEach(([x, y]) => {
-    if (x < minX) minX = x;
-    if (x > maxX) maxX = x;
-    if (y < minY) minY = y;
-    if (y > maxY) maxY = y;
+    if (x < minX) {
+      minX = x;
+    }
+    if (x > maxX) {
+      maxX = x;
+    }
+    if (y < minY) {
+      minY = y;
+    }
+    if (y > maxY) {
+      maxY = y;
+    }
   });
 
   const centerX = (minX + maxX) / 2;

src/components/Map/MapViewer/utils/listeners/mapSingleClick/handleAliasResults.test.ts

@@ -209,8 +209,6 @@ describe('handleAliasResults - util', () => {
           'entityNumber/addNumbersToEntityNumberData',
           'project/getBioEntityById/fulfilled',
           'entityNumber/addNumbersToEntityNumberData',
-          'reactions/getByIds/pending',
-          'reactions/getByIds/fulfilled',
           'project/getMultiBioEntity/fulfilled',
           'drawer/selectTab',
           'drawer/openBioEntityDrawerById',

src/components/Map/PluginsDrawer/PluginsHeader/PluginHeaderInfo/PluginHeaderInfo.component.tsx

@@ -17,7 +17,9 @@ export const PluginHeaderInfo = ({ plugin }: Props): JSX.Element => {
     hash: plugin.hash,
     pluginUrl: plugin.urls[FIRST_ARRAY_ELEMENT],
     onPluginLoaded: () => {
-      dispatch(setCurrentDrawerPluginHash(plugin.hash));
+      if (!plugin.withoutPanel) {
+        dispatch(setCurrentDrawerPluginHash(plugin.hash));
+      }
     },
   });
 

src/components/Map/PluginsDrawer/PluginsHeader/PluginOpenButton/LoadPluginElement/LoadPluginElement.component.tsx

@@ -19,7 +19,9 @@ export const LoadPluginElement = ({ plugin }: LoadPluginButtonProps): JSX.Elemen
     hash,
     pluginUrl: urls[FIRST_ARRAY_ELEMENT],
     onPluginLoaded: () => {
-      dispatch(setCurrentDrawerPluginHash(hash));
+      if (!plugin.withoutPanel) {
+        dispatch(setCurrentDrawerPluginHash(hash));
+      }
     },
   });
 

src/components/Map/PluginsDrawer/PluginsTabs/PluginSingleTab/PluginSingleTab.component.tsx

@@ -21,7 +21,9 @@ export const PluginSingleTab = ({ plugin }: Props): JSX.Element => {
   });
 
   const onPluginTabClick = (): void => {
-    dispatch(setCurrentDrawerPluginHash(plugin.hash));
+    if (!plugin.withoutPanel) {
+      dispatch(setCurrentDrawerPluginHash(plugin.hash));
+    }
   };
 
   const onPluginUnload = (event: React.MouseEvent<HTMLDivElement>): void => {

src/components/Map/PluginsDrawer/PluginsTabs/PluginsTabs.component.tsx

 /* eslint-disable jsx-a11y/click-events-have-key-events */
 import { ZERO } from '@/constants/common';
 import { useAppSelector } from '@/redux/hooks/useAppSelector';
-import { allActivePluginsSelector } from '@/redux/plugins/plugins.selectors';
+import { allActivePluginsWithPanelSelector } from '@/redux/plugins/plugins.selectors';
 import { useMemo } from 'react';
 import { PluginSingleTab } from './PluginSingleTab';
 
 export const PluginsTabs = (): JSX.Element => {
-  const allActivePlugins = useAppSelector(allActivePluginsSelector);
+  const allActivePlugins = useAppSelector(allActivePluginsWithPanelSelector);
   const isPluginsEmpty = allActivePlugins.length === ZERO;
 
   const pluginsTabs = allActivePlugins.map(plugin => (

src/constants/mocks.ts

-// eslint-disable-next-line no-magic-numbers
-export const MODEL_IDS_MOCK = [5052, 5053, 5054];
+export const MAIN_MAP_ID = 5053;
+export const HISTAMINE_MAP_ID = 5052;
+export const PRKN_SUBSTRATES_MAP_ID = 5054;
+export const MODEL_IDS_MOCK = [HISTAMINE_MAP_ID, MAIN_MAP_ID, PRKN_SUBSTRATES_MAP_ID];

src/models/bioEntitySchema.ts

@@ -34,7 +34,7 @@ export const bioEntitySchema = z.object({
     .number()
     .optional()
     .transform(height => height ?? ZERO),
-  visibilityLevel: z.string(),
+  visibilityLevel: z.string().nullable(),
   transparencyLevel: z.string().nullable().optional(),
   synonyms: z.array(z.string()),
   formerSymbols: z.array(z.string()).nullable().optional(),
@@ -46,13 +46,13 @@ export const bioEntitySchema = z.object({
   activity: z.boolean().optional(),
   structuralState: z.optional(structuralStateSchema.nullable()),
   hypothetical: z.boolean().nullable().optional(),
-  boundaryCondition: z.boolean().optional(),
-  constant: z.boolean().optional(),
+  boundaryCondition: z.boolean().optional().nullable(),
+  constant: z.boolean().optional().nullable(),
   initialAmount: z.number().nullable().optional(),
   initialConcentration: z.number().nullable().optional(),
   charge: z.number().nullable().optional(),
   substanceUnits: z.string().nullable().optional(),
-  onlySubstanceUnits: z.boolean().optional(),
+  onlySubstanceUnits: z.boolean().optional().nullable(),
   modificationResidues: z.optional(z.array(modificationResiduesSchema)),
   complex: z.number().nullable().optional(),
   compartment: z.number().nullable().optional(),

src/models/compartmentPathwaySchema.ts

@@ -32,7 +32,7 @@ export const compartmentPathwayDetailsSchema = z.object({
   formula: z.null(),
   fullName: z.string().nullable(),
   glyph: z.any(),
-  hierarchyVisibilityLevel: z.string(),
+  hierarchyVisibilityLevel: z.string().nullable(),
   homomultimer: z.null(),
   hypothetical: z.null(),
   id: z.number().gt(-1),