Merge pull request #80 from EyeSeeTea/master

Release 3.7.0
3dbionotes-community · Apr 21, 2023 · acc12e0 · acc12e0
2 parents 421946d + fd9e99c
commit acc12e0
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diff --git a/app/assets/javascripts/3dbio_viewer/.nvmrc b/app/assets/javascripts/3dbio_viewer/.nvmrc
@@ -0,0 +1 @@
+v16.14.0
diff --git a/app/assets/javascripts/3dbio_viewer/package.json b/app/assets/javascripts/3dbio_viewer/package.json
@@ -19,7 +19,6 @@
         "react-dom": "^17.0.1",
         "react-draggable": "4.4.3",
         "react-dropzone": "^11.3.1",
-        "react-ga": "^3.3.0",
         "react-image-fallback": "^8.0.0",
         "react-markdown": "5.0.2",
         "react-router-dom": "^5.2.0",

diff --git a/app/assets/javascripts/3dbio_viewer/src/index.tsx b/app/assets/javascripts/3dbio_viewer/src/index.tsx
@@ -1,17 +1,9 @@
 import React from "react";
-import ReactGA from "react-ga";
 import ReactDOM from "react-dom";
 import "./index.css";
 import reportWebVitals from "./reportWebVitals";
 import App from "./webapp/pages/app/App";
 
-const gaAppId = "UA-93698320-1"; //UA-93698320-4 for development UA-93698320-1 for production
-ReactGA.initialize(gaAppId, {
-    debug: true,
-    titleCase: false,
-    useExistingGa: process.env.NODE_ENV !== "development",
-});
-
 ReactDOM.render(<App />, document.getElementById("root"));
 
 reportWebVitals();
diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/components/model-search/ModelSearch.tsx b/app/assets/javascripts/3dbio_viewer/src/webapp/components/model-search/ModelSearch.tsx
@@ -65,10 +65,7 @@ export const ModelSearch: React.FC<ModelSearchProps> = React.memo(props => {
 
     const openUploadWithAnalytics = React.useCallback(() => {
         openUpload();
-        sendAnalytics({
-            type: "event",
-            category: "dialog",
-            action: "open",
+        sendAnalytics("open_dialog", {
             label: "Upload Model",
         });
     }, [openUpload]);
@@ -152,11 +149,9 @@ function useDbModelSearch(modelType: ModelSearchType) {
     const search = React.useCallback(
         (query: string) => {
             setSearchState({ type: "searching" });
-            sendAnalytics({
-                type: "event",
-                category: "viewer_search_menu",
-                action: "search",
-                label: query,
+            sendAnalytics("search", {
+                on: "viewer",
+                query: query,
             });
 
             const searchType = modelType === "all" ? undefined : modelType;

diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/components/network/NetworkForm.tsx b/app/assets/javascripts/3dbio_viewer/src/webapp/components/network/NetworkForm.tsx
@@ -73,7 +73,7 @@ const NetworkForm: React.FC<NetworkFormProps> = React.memo(props => {
                     annotationsFile,
                 };
 
-                sendAnalytics({ type: "event", category: "viewer", action: "upload" });
+                sendAnalytics("upload", { type: "network", on: "viewer" });
 
                 return compositionRoot.buildNetwork
                     .execute({ network, onProgress })

diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/JumpToButton.tsx b/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/JumpToButton.tsx
@@ -21,10 +21,8 @@ export const JumpToButton: React.FC<JumpToButtonProps> = React.memo(props => {
 export function goToElement(DOMElementId: string) {
     // Use document.getElementById for simplicity. The orthodox approach would be to use refs,
     // but we'd need to pass them to all components that have an anchor.
-    sendAnalytics({
-        type: "event",
-        action: "jump_to",
-        category: "viewer",
+    sendAnalytics("jump_to", {
+        on: "viewer",
         label: DOMElementId,
     });
     const el = document.getElementById(DOMElementId);

diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/ProfilesButton.tsx b/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/ProfilesButton.tsx
@@ -21,10 +21,8 @@ export const ProfilesButton: React.FC<ProfilesButtonProps> = React.memo(props =>
 
     const setProfile = React.useCallback(
         (profileId: ProfileId) => {
-            sendAnalytics({
-                type: "event",
-                action: "set_profile",
-                category: "viewer",
+            sendAnalytics("set_profile", {
+                on: "viewer",
                 label: profileId,
             });
             onChange(profiles[profileId]);

diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/ToolsButton.tsx b/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/ToolsButton.tsx
@@ -30,10 +30,7 @@ export const ToolsButton: React.FC<ToolsButtonProps> = props => {
 
     const openNetworkWithAnalytics = React.useCallback(() => {
         openNetwork();
-        sendAnalytics({
-            type: "event",
-            category: "dialog",
-            action: "open",
+        sendAnalytics("open_dialog", {
             label: "Network",
         });
     }, [openNetwork]);

diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/components/viewer-selector/ViewerSelector.tsx b/app/assets/javascripts/3dbio_viewer/src/webapp/components/viewer-selector/ViewerSelector.tsx
@@ -47,7 +47,7 @@ export const ViewerSelector: React.FC<ViewerSelectorProps> = props => {
     const runModelSearchAction = React.useCallback<ModelSearchProps["onSelect"]>(
         (action, item) => {
             const newSelection = runAction(selection, action, item);
-            sendAnalytics({ type: "event", category: "viewer_search_menu", action: action });
+            sendAnalytics(action, { type: "viewer_search_menu", item: item.id });
             onSelectionChange(newSelection);
             closeSearch();
         },
@@ -56,10 +56,7 @@ export const ViewerSelector: React.FC<ViewerSelectorProps> = props => {
 
     const openSearchWithAnalytics = React.useCallback(() => {
         openSearch();
-        sendAnalytics({
-            type: "event",
-            category: "dialog",
-            action: "open",
+        sendAnalytics("open_dialog", {
             label: "Search",
         });
     }, [openSearch]);

diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/pages/app/App.tsx b/app/assets/javascripts/3dbio_viewer/src/webapp/pages/app/App.tsx
@@ -45,10 +45,6 @@ function App() {
 }
 
 const RouterTracking: React.FC = props => {
-    const location = useLocation();
-    React.useEffect(() => {
-        sendAnalytics({ type: "pageView", path: `/viewer${location.pathname}` });
-    }, [location.pathname]);
     return <>{props.children}</>;
 };
 

diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/utils/analytics.ts b/app/assets/javascripts/3dbio_viewer/src/webapp/utils/analytics.ts
@@ -1,44 +1,21 @@
-import ReactGA from "react-ga";
-import _ from "lodash";
-
-/* Non-redux GA analytics helpers. For Redux, check for example the <Citation> component. Steps:
-    - Import action.
-    - Create mapDispatchToProps.
-    - Add dispatch props to Props type.
-    - Use redux connect with mapDispatchToProps.
-    - Call dispatcher from props.
-*/
-
-type AnalyticsData = Event | PageView | OutboundLink;
-
-interface Event {
-    type: "event";
-    category: string;
-    action: string;
-    label?: string;
-}
-
-interface PageView {
-    type: "pageView";
-    path: string;
+declare global {
+    interface Window {
+        gtag?: (...args: []) => void;
+    }
 }
 
-interface OutboundLink {
-    type: "outboundLink";
-    label: string;
-}
+declare function gtag(type: "event", name: string, data?: object): void;
 
-export function sendAnalytics(data: AnalyticsData) {
-    switch (data.type) {
-        case "event":
-            ReactGA.event({ category: data.category, action: data.action, label: data.label });
-            break;
-        case "pageView":
-            ReactGA.set({ page: data.path });
-            ReactGA.pageview(data.path);
-            break;
-        case "outboundLink":
-            ReactGA.outboundLink({ label: data.label }, () => {});
-            break;
-    }
+export function sendAnalytics(name: string, data?: object) {
+    if (window.gtag !== undefined)
+        gtag(
+            "event",
+            name,
+            data && {
+                ...data,
+                location_hash: window.location.hash,
+                location_pathname: window.location.pathname,
+                location_href: window.location.href,
+            }
+        );
 }
diff --git a/app/assets/javascripts/3dbio_viewer/yarn.lock b/app/assets/javascripts/3dbio_viewer/yarn.lock
@@ -10585,11 +10585,6 @@ react-event-listener@^0.6.2:
     prop-types "^15.6.0"
     warning "^4.0.1"
 
-react-ga@^3.3.0:
-  version "3.3.0"
-  resolved "https://registry.yarnpkg.com/react-ga/-/react-ga-3.3.0.tgz#c91f407198adcb3b49e2bc5c12b3fe460039b3ca"
-  integrity sha512-o8RScHj6Lb8cwy3GMrVH6NJvL+y0zpJvKtc0+wmH7Bt23rszJmnqEQxRbyrqUzk9DTJIHoP42bfO5rswC9SWBQ==
-
 react-image-fallback@^8.0.0:
   version "8.0.0"
   resolved "https://registry.npmjs.org/react-image-fallback/-/react-image-fallback-8.0.0.tgz#18a88c3e011ee683f35fab1dd6e88eb5152b18ec"

diff --git a/app/assets/javascripts/covid19/.nvmrc b/app/assets/javascripts/covid19/.nvmrc
@@ -0,0 +1 @@
+v16.14.0
diff --git a/app/assets/javascripts/covid19/i18n/en.pot b/app/assets/javascripts/covid19/i18n/en.pot
@@ -5,8 +5,17 @@ msgstr ""
 "Content-Type: text/plain; charset=utf-8\n"
 "Content-Transfer-Encoding: 8bit\n"
 "Plural-Forms: nplurals=2; plural=(n != 1)\n"
-"POT-Creation-Date: 2022-11-23T13:00:39.368Z\n"
-"PO-Revision-Date: 2022-11-23T13:00:39.368Z\n"
+"POT-Creation-Date: 2023-04-03T01:34:38.763Z\n"
+"PO-Revision-Date: 2023-04-03T01:34:38.763Z\n"
+
+msgid "No ontologies found."
+msgstr ""
+
+msgid "No ontology terms found."
+msgstr ""
+
+msgid "No organisms found."
+msgstr ""
 
 msgid "Antibodies"
 msgstr ""
@@ -107,6 +116,18 @@ msgstr ""
 msgid "Compound"
 msgstr ""
 
+msgid "ID"
+msgstr ""
+
+msgid "Term"
+msgstr ""
+
+msgid "Description"
+msgstr ""
+
+msgid "Ontology"
+msgstr ""
+
 msgid "Search protein/organism/PDB ID/EMDB ID/UniProt ID"
 msgstr ""
 
@@ -216,9 +237,6 @@ msgstr ""
 msgid "Publication"
 msgstr ""
 
-msgid "ID"
-msgstr ""
-
 msgid "Authors"
 msgstr ""
 

diff --git a/app/assets/javascripts/covid19/package.json b/app/assets/javascripts/covid19/package.json
@@ -23,7 +23,6 @@
         "purify-ts": "^1.1.0",
         "react": "17.0.1",
         "react-dom": "17.0.1",
-        "react-ga": "^3.3.0",
         "react-router-dom": "^5.2.0",
         "react-scripts": "4.0.3",
         "styled-components": "^5.3.0",

diff --git a/app/assets/javascripts/covid19/src/compositionRoot.ts b/app/assets/javascripts/covid19/src/compositionRoot.ts
@@ -8,12 +8,16 @@ import { AddDynamicInfoToCovid19InfoUseCase } from "./domain/usecases/AddDynamic
 import { LocalStorageCacheRepository } from "./data/repositories/LocalStorageCacheRepository";
 import { LigandsApiRepository } from "./data/repositories/LigandsApiRepository";
 import { GetLigandImageDataResourcesUseCase } from "./domain/usecases/GetLigandImageDataResourcesUseCase";
+import { BionotesOntologyRepository } from "./data/repositories/BioOntologyRepository";
+import { BionotesOrganismRepository } from "./data/repositories/BionotesOrganismRepository";
 
 export function getCompositionRoot() {
     const covid19InfoRepository = new Covid19InfoFromJsonRepository();
     const dataGridRepository = new BrowserDataGridRepository();
     const cacheRepository = new LocalStorageCacheRepository();
     const ligandsRepository = new LigandsApiRepository();
+    const ontologyRepository = new BionotesOntologyRepository();
+    const organismRepository = new BionotesOrganismRepository();
 
     return {
         getCovid19Info: new GetCovid19InfoUseCase(covid19InfoRepository),
@@ -25,7 +29,11 @@ export function getCompositionRoot() {
             cacheRepository
         ),
         ligands: {
-            getIDR: new GetLigandImageDataResourcesUseCase(ligandsRepository),
+            getIDR: new GetLigandImageDataResourcesUseCase(
+                ligandsRepository,
+                ontologyRepository,
+                organismRepository
+            ),
         },
     };
 }