Allow non-auth mode.

Makefile

@@ -33,26 +33,39 @@ clean-studio:
 	@printf "Clean studio...\n"
 	@cd studio && rm -rf node_modules && rm -rf dist && yarn cache clean && cd ..
 
-build-studio:
+build-biomedgps-studio:
 	@printf "Building studio based on openapi...\n"
 	@mkdir -p assets
+	@cp studio/logo/biomedgps.png studio/public/assets/logo-white.png 
+	@cp studio/logo/biomedgps.png studio/src/assets/logo-white.png
+	@cp studio/logo/biomedgps.png studio/public/logo.png
 	# @cd studio && yarn && yarn openapi || true
 	@cd studio && yarn
-	@cd studio && yarn build:embed && cd ..
+	@cd studio && yarn build:biomedgps-embed && cd ..
+
+build-rapex-studio:
+	@printf "Building studio based on openapi...\n"
+	@mkdir -p assets
+	@cp studio/logo/rapex.png studio/public/assets/logo-white.png 
+	@cp studio/logo/rapex.png studio/src/assets/logo-white.png
+	@cp studio/logo/rapex.png studio/public/logo.png
+	# @cd studio && yarn && yarn openapi || true
+	@cd studio && yarn
+	@cd studio && yarn build:rapex-embed && cd ..
 
 build-biomedgps:
 	@cargo build --release
 
 build-biomedgps-linux:
 	@cargo build --release --target=x86_64-unknown-linux-musl
 
-build-mac: build-studio build-biomedgps
+build-mac: build-biomedgps-studio build-biomedgps
 	@printf "\nDone!\n"
 
-build-linux: build-studio build-biomedgps
+build-linux: build-biomedgps-studio build-biomedgps
 	@printf "\nDone!\n"
 
-build-linux-on-mac: build-studio build-biomedgps-linux
+build-linux-on-mac: build-biomedgps-studio build-biomedgps-linux
 	@printf "\nDone!\n"
 
 # You must run `make build-service` to build new api spec for studio when you change the api spec
@@ -66,8 +79,16 @@ changelog:
 	@python build/build_changelog.py --repo ../biominer-components --output-file ./studio/public/README/changelog.md --repo-name 'BioMedGPS UI'
 	@python build/build_changelog.py --repo . --output-file ./studio/public/README/changelog.md --repo-name BioMedGPS
 
-deploy: build-studio
+deploy: deploy-biomedgps
+
+deploy-biomedgps: build-biomedgps-studio
 	@docker run --rm -it -v "$(CURDIR)":/home/rust/src messense/rust-musl-cross:x86_64-musl cargo build --release
 	@rsync -avP target/x86_64-unknown-linux-musl/release/biomedgps target/x86_64-unknown-linux-musl/release/biomedgps-cli [email protected]:/data/biomedgps/bin
 	@rsync -avP --delete assets/index.html [email protected]:/var/www/html/biomedgps/index.html
-	@rsync -avP --delete assets [email protected]:/var/www/html/biomedgps/
+	@rsync -avP --delete assets [email protected]:/var/www/html/biomedgps/
+
+deploy-rapex: build-rapex-studio
+	@docker run --rm -it -v "$(CURDIR)":/home/rust/src messense/rust-musl-cross:x86_64-musl cargo build --release
+	@rsync -avP target/x86_64-unknown-linux-musl/release/biomedgps target/x86_64-unknown-linux-musl/release/biomedgps-cli [email protected]:/data/rapex/bin
+	@rsync -avP --delete assets/index.html [email protected]:/var/www/html/rapex/index.html
+	@rsync -avP --delete assets [email protected]:/var/www/html/rapex/

studio/config/routes.ts

@@ -1,4 +1,4 @@
-import { createElement } from "react";
+import { Children, createElement } from "react";
 import * as icons from "@ant-design/icons";
 import type { MenuDataItem } from '@ant-design/pro-components';
 
@@ -10,26 +10,40 @@ export const routes = [
     component: './Home',
   },
   {
-    path: '/knowledge-table',
-    name: 'Knowledge Table',
-    icon: 'table',
-    hideInMenu: true,
-    component: './KnowledgeTable',
-    category: 'knowledge-graph'
-  },
-  {
-    path: '/predict-model',
-    name: 'Predict Drugs/Targets',
-    icon: 'history',
-    component: './ModelConfig',
-    category: 'predict-model'
+    path: '/analyze-omics-data',
+    name: 'Analyze Omics Data',
+    icon: 'LineChartOutlined',
+    disabled: true,
+    component: './Home',
   },
   {
-    path: '/knowledge-graph',
-    name: 'Explain Your Results',
-    icon: 'comment',
-    component: './KnowledgeGraph',
-    category: 'knowledge-graph'
+    path: '/predict-explain',
+    name: 'Predict & Explain',
+    icon: 'link',
+    routes: [
+      {
+        path: '/predict-explain/knowledge-table',
+        name: 'Knowledge Table',
+        icon: 'table',
+        hideInMenu: true,
+        component: './KnowledgeTable',
+        category: 'knowledge-graph'
+      },
+      {
+        path: '/predict-explain/predict-model',
+        name: 'Predict Drugs/Targets',
+        icon: 'history',
+        component: './ModelConfig',
+        category: 'predict-model'
+      },
+      {
+        path: '/predict-explain/knowledge-graph',
+        name: 'Explain Your Results',
+        icon: 'comment',
+        component: './KnowledgeGraph',
+        category: 'knowledge-graph'
+      },
+    ]
   },
   {
     path: '/mecfs-longcovid',

studio/package.json

@@ -7,14 +7,16 @@
   "scripts": {
     "dev": "max dev",
     "build": "max build",
-    "build:embed": "cross-env UMI_APP_IS_STATIC=true UMI_ENV=embed UMI_APP_AUTH0_CLIENT_ID=Y08FauV1dAEiocNIZt5LiOifzNgXr6Uo UMI_APP_AUTH0_DOMAIN=biomedgps.jp.auth0.com max build",
+    "build:biomedgps-embed": "cross-env UMI_APP_IS_STATIC=true UMI_ENV=embed UMI_APP_AUTH0_CLIENT_ID=Y08FauV1dAEiocNIZt5LiOifzNgXr6Uo UMI_APP_AUTH0_DOMAIN=biomedgps.jp.auth0.com max build",
+    "build:rapex-embed": "cross-env UMI_APP_IS_STATIC=true UMI_ENV=embed max build",
     "build:analyze": "cross-env ANALYZE=true max build",
     "format": "prettier --cache --write .",
     "postinstall": "max setup",
     "setup": "max setup",
     "start": "npm run dev",
     "start:local-dev": "cross-env UMI_APP_API_PREFIX=http://localhost:3000 max dev",
-    "start:remote-dev": "cross-env UMI_APP_API_PREFIX=https://drugs.3steps.cn UMI_APP_AUTH0_CLIENT_ID=Y08FauV1dAEiocNIZt5LiOifzNgXr6Uo UMI_APP_AUTH0_DOMAIN=biomedgps.jp.auth0.com max dev",
+    "start:biomedgps-remote-dev": "cross-env UMI_APP_API_PREFIX=https://drugs.3steps.cn UMI_APP_AUTH0_CLIENT_ID=Y08FauV1dAEiocNIZt5LiOifzNgXr6Uo UMI_APP_AUTH0_DOMAIN=biomedgps.jp.auth0.com max dev",
+    "start:rapex-remote-dev": "cross-env UMI_APP_API_PREFIX=https://rapex.prophetdb.org max dev",
     "openapi": "max openapi"
   },
   "dependencies": {

studio/public/README/about.md

@@ -16,7 +16,7 @@ Construct and integrate <b>knowledge graph</b>, <b>multi-omics data</b> and <b>d
 
 ## Features
 
-### <a href="https://drugs.3steps.cn/#/predict-model">Predict Drug/Target</a> Module
+### <a href="https://drugs.3steps.cn/#/predict-explain/predict-model">Predict Drug/Target</a> Module
 
 - [x] Predict known drugs for your queried disease (Drug Repurposing).
 - [x] Predict new indications for your queried drug.
@@ -26,7 +26,7 @@ Construct and integrate <b>knowledge graph</b>, <b>multi-omics data</b> and <b>d
 
 <p></p>
 
-### <a href="https://drugs.3steps.cn/#/knowledge-graph">Explain Your Results</a> Module
+### <a href="https://drugs.3steps.cn/#/predict-explain/knowledge-graph">Explain Your Results</a> Module
 
 - [x] Knowledge graph studio for graph query, visualization and analysis.
 - [x] Graph neural network for drug discovery, disease mechanism, biomarker screening and discovering response to toxicant exposure.

studio/src/app.tsx

@@ -4,7 +4,7 @@ import { RequestConfig, history, RuntimeConfig, request as UmiRequest } from 'um
 import { PageLoading, SettingDrawer } from '@ant-design/pro-components';
 import { Auth0Provider } from '@auth0/auth0-react';
 import { CustomSettings, AppVersion } from '../config/defaultSettings';
-import { getJwtAccessToken, logout, logoutWithRedirect, getUsername } from '@/components/util';
+import { getJwtAccessToken, logout, logoutWithRedirect, getUsername, isAuthEnabled } from '@/components/util';
 
 // import * as Sentry from "@sentry/react";
 
@@ -141,6 +141,10 @@ export async function getInitialState(): Promise<{
 }
 
 export function rootContainer(container: React.ReactNode): React.ReactNode {
+  if (!isAuthEnabled()) {
+    return container;
+  }
+
   return (
     <Auth0Provider
       domain={AUTH0_DOMAIN}
@@ -177,7 +181,9 @@ export const layout: RuntimeConfig = (initialState: any) => {
 
       // You can modify the css style of the menu item at the global.less file.
       var spans = document.querySelectorAll('span.ant-pro-base-menu-horizontal-item-text');
+      console.log("Add new-tag to ME/CFS: ", spans);
       spans.forEach(function (span) {
+        console.log("span.innerHTML: ", span.innerHTML);
         if (span.innerHTML.startsWith("ME/CFS")) {
           span.classList.add('new-tag');
         }

studio/src/components/Header/index.tsx

@@ -1,7 +1,7 @@
 import { QuestionCircleOutlined, InfoCircleOutlined, UserOutlined, FieldTimeOutlined, LogoutOutlined } from '@ant-design/icons';
 import { Space, Menu, Button, message, Dropdown } from 'antd';
 import React, { useEffect, useState } from 'react';
-import { getJwtAccessToken, logoutWithRedirect } from '@/components/util';
+import { getJwtAccessToken, logoutWithRedirect, isAuthEnabled } from '@/components/util';
 import { useAuth0 } from "@auth0/auth0-react";
 import type { MenuProps } from 'antd';
 import { history } from 'umi';
@@ -160,14 +160,17 @@ const GlobalHeaderRight: React.FC<GlobalHeaderRightProps> = (props) => {
         <Button type="text" icon={<InfoCircleOutlined />} style={{ height: '40px' }}>About</Button>
       </Dropdown>
       {
-        !isAuthenticated ? (
+        isAuthEnabled() &&
+          !isAuthenticated ? (
           <Button type={isAuthenticated ? 'default' : 'primary'} onClick={() => loginWithRedirect()}>
             Sign In / Sign Up
           </Button>
         ) : (
-          <Dropdown menu={{ items: userItems, onClick: onClick }} placement="bottomLeft">
+          isAuthEnabled() ?
+            <Dropdown menu={{ items: userItems, onClick: onClick }} placement="bottomLeft">
               <Button type="primary" icon={<UserOutlined />}>{username}</Button>
-          </Dropdown>
+            </Dropdown>
+            : <Button type="primary" icon={<UserOutlined />}>{username}</Button>
         )
       }
     </Space>

studio/src/components/util.ts

@@ -89,7 +89,28 @@ export const logout = () => {
     localStorage.removeItem('redirectUrl');
 }
 
+export const isAuthEnabled = () => {
+    console.log("isAuthEnabled: ", process.env.UMI_APP_AUTH0_CLIENT_ID);
+    return process.env.UMI_APP_AUTH0_CLIENT_ID ? true : false
+}
+
+export const isAuthenticated = () => {
+    if (getUsername()) {
+        return true
+    }
+
+    if (!isAuthEnabled()) {
+        return true
+    }
+
+    return false
+}
+
 export const logoutWithRedirect = () => {
+    if (!isAuthEnabled()) {
+        return
+    }
+
     logout();
     // Save the current hash as the redirect url
     let currentUrl = window.location.hash.split("#").pop();

studio/src/components/webllm.ts

@@ -1,27 +1,6 @@
 import { ChatModule, InitProgressReport } from "@mlc-ai/web-llm";
 import { message } from "antd";
 
-export const getJwtAccessToken = (): string | null => {
-    let jwtToken = null;
-    // Check if the cookie exists
-    if (document.cookie && document.cookie.includes("jwt_access_token=")) {
-        // Retrieve the cookie value
-        // @ts-ignore
-        jwtToken = document.cookie
-            .split("; ")
-            .find((row) => row.startsWith("jwt_access_token="))
-            .split("=")[1];
-    }
-
-    if (jwtToken) {
-        console.log("JWT access token found in the cookie.");
-        return jwtToken;
-    } else {
-        console.log("JWT access token not found in the cookie.");
-        return null;
-    }
-}
-
 export const initChat = async () => {
     // const chat = new webllm.ChatWorkerClient(new Worker(
     //   new URL('./assets/web-llm.worker.js', import.meta.url),

studio/src/global.less

@@ -38,6 +38,16 @@ body,
   .ant-pro-top-nav-header-logo img {
     height: 45px;
   }
+
+  // For mix layout
+  .ant-pro-global-header {
+    height: 100%;
+  }
+
+  .ant-pro-global-header-logo a>svg,
+  .ant-pro-global-header-logo a>img {
+    height: 45px;
+  }
 }
 
 .ant-pro-sider.ant-layout-sider.ant-pro-sider-fixed {
@@ -71,6 +81,7 @@ ol {
 
     &-thead>tr,
     &-tbody>tr {
+
       >th,
       >td {
         white-space: pre;
@@ -85,7 +96,7 @@ ol {
 
 // Compatible with IE11
 @media screen and(-ms-high-contrast: active),
-  (-ms-high-contrast: none) {
+(-ms-high-contrast: none) {
   body .ant-design-pro>.ant-layout {
     min-height: 100vh;
   }
@@ -146,7 +157,8 @@ ol {
 // For Markdown Table
 .markdown-viewer {
   tr:nth-child(odd) {
-    background-color: #f2f2f2; /* 灰色 */
+    background-color: #f2f2f2;
+    /* 灰色 */
   }
 
   tr:nth-child(even) {
@@ -171,4 +183,4 @@ ol {
   border-radius: 2px;
   vertical-align: super;
   line-height: 1;
-}
+}

studio/src/pages/Home/index.tsx

@@ -184,16 +184,16 @@ const HomePage: React.FC = () => {
         console.log('Search:', value);
 
         if (value && name) {
-            history.push(`/knowledge-table?nodeId=${value}&nodeName=${name}`);
+            history.push(`/predict-explain/knowledge-table?nodeId=${value}&nodeName=${name}`);
             return;
         }
 
         const filtered = filter(nodeOptions, (item) => item.value === value);
         if (filtered.length === 0 || !filtered[0]?.metadata) {
-            history.push(`/knowledge-table?nodeId=${value}`);
+            history.push(`/predict-explain/knowledge-table?nodeId=${value}`);
         } else {
             const metadata = filtered[0].metadata;
-            history.push(`/knowledge-table?nodeId=${value}&nodeName=${metadata.name}`);
+            history.push(`/predict-explain/knowledge-table?nodeId=${value}&nodeName=${metadata.name}`);
         }
     };
 
@@ -236,7 +236,7 @@ const HomePage: React.FC = () => {
                     <h4 style={{ textAlign: 'center', fontSize: '16px', lineHeight: '24px' }}>
                         Enter a gene/protein, disease, drug or symptom name to find and explain related known knowledges in our platform.
                         <br />
-                        If you want to predict new knowledges, please go to the <a onClick={() => { history.push('/predict-model'); }}>Predict Drug/Target</a> page.
+                        If you want to predict new knowledges, please go to the <a onClick={() => { history.push('/predict-explain/predict-model'); }}>Predict Drug/Target</a> page.
                         <br />
                         Please click the following examples to see the results.
                     </h4>

studio/src/pages/KnowledgeGraph/index.tsx

@@ -1,4 +1,4 @@
-import { getUsername, logoutWithRedirect } from '@/components/util';
+import { isAuthenticated, logoutWithRedirect } from '@/components/util';
 import { Row, Col, Button, message as AntMessage, Empty } from 'antd';
 import { KnowledgeGraph } from 'biominer-components';
 import React, { useEffect, useState, memo, Suspense } from 'react';
@@ -22,13 +22,10 @@ const KnowledgeGraphWithChatBot: React.FC = () => {
   const [chatBoxVisible, setChatBoxVisible] = useState<boolean>(false)
   const [span, setSpan] = useState<number>(kgFullSpan)
   const ChatBox = React.lazy(() => import('@/components/ChatBox'));
-  const [username, setUsername] = useState<string | undefined>(undefined);
 
   useEffect(() => {
-    const username = getUsername();
-    setUsername(username);
-
-    if (!username) {
+    console.log("isAuthenticated in KnowledgeGraph: ", isAuthenticated());
+    if (!isAuthenticated()) {
       logoutWithRedirect();
     }
   }, [])
@@ -41,7 +38,7 @@ const KnowledgeGraphWithChatBot: React.FC = () => {
     }
   }, [chatBoxVisible])
 
-  return username && <Row gutter={8} className="chat-ai-container">
+  return isAuthenticated() && <Row gutter={8} className="chat-ai-container">
     {
       chatBoxVisible ? (
         <Col xxl={24 - span} xl={24 - span} lg={24 - span} md={24} sm={24} xs={24}>