Add 'secret' to report endpoints

Author: mikekucera

.env.defaults

@@ -10,3 +10,4 @@ FGSEA_PRERANKED_SERVICE_URL=https://fgseadev.baderlab.net/v1/preranked
 FGSEA_RNASEQ_SERVICE_URL=https://fgseadev.baderlab.net/v1/rnaseq
 EM_SERVICE_URL=https://emjavadev.baderlab.net/v1
 BRIDGEDB_URL=https://webservice.bridgedb.org
+REPORT_SECRET=baderlab

.env.local

@@ -10,3 +10,4 @@ FGSEA_PRERANKED_SERVICE_URL=http://localhost:8000/preranked
 FGSEA_RNASEQ_SERVICE_URL=http://localhost:8000/rnaseq
 EM_SERVICE_URL=http://localhost:8080/v1
 BRIDGEDB_URL=https://webservice.bridgedb.org
+REPORT_SECRET=baderlab

src/client/components/network-editor/export-controller.js

@@ -25,6 +25,7 @@ const Path = {
   DATA_ENRICH:   'data/enrichment_results.txt',
   DATA_RANKS:    'data/ranks.txt',
   DATA_GENESETS: 'data/gene_sets.gmt',
+  DATA_JSON:     'data/network.json',
   README:        'README.md'
 };
 
@@ -60,6 +61,7 @@ export class ExportController {
     const blob2 = await this._createNetworkImageBlob(ImageSize.LARGE);
     const blob3 = await this._createNetworkPDFBlob();
     const blob4 = await this._createSVGLegendBlob();
+    // const blob5 = await this._createNetworkJSONBlob();
     const files = await filesPromise;
     const readme = createREADME(this.controller);
 
@@ -69,6 +71,7 @@ export class ExportController {
     zip.file(Path.IMAGE_LARGE,   blob2);
     zip.file(Path.IMAGE_PDF,     blob3);
     zip.file(Path.IMAGE_LEGEND,  blob4);
+    // zip.file(Path.DATA_JSON,     blob5);
     zip.file(Path.DATA_ENRICH,   files[0]);
     zip.file(Path.DATA_RANKS,    files[1]);
     zip.file(Path.DATA_GENESETS, files[2]);
@@ -148,6 +151,16 @@ export class ExportController {
     return blob;
   }
 
+  async _createNetworkJSONBlob() {
+    const { cy } = this.controller;
+    const json = cy.json();
+    const blob = new Blob(
+      [ JSON.stringify(json, null, 2) ], {
+      type: 'text/plain'
+    });
+    return blob;
+  }
+
   async _createNetworkPDFBlob() {
     const { cy } = this.controller;
     const blob = await cy.pdf({

src/client/components/report/index.js

@@ -6,7 +6,7 @@ import { currentTheme } from '../../theme';
 import Report from './report';
 
 
-export function ReportHome() {
+export function ReportHome({ secret }) {
   const [ theme, setTheme ] = useState(currentTheme);
 
   useEffect(() => {
@@ -22,12 +22,13 @@ export function ReportHome() {
   return (
     <ThemeProvider theme={theme}>
       <CssBaseline />
-      <Report />
+      <Report secret={secret} />
     </ThemeProvider>
   );
 }
 
 ReportHome.propTypes = {
+  secret: PropTypes.string,
 };
 
 export default ReportHome;

src/client/components/report/report.js

@@ -1,4 +1,5 @@
 import React, { useState, useEffect } from 'react';
+import PropTypes from 'prop-types';
 import { getComparator } from '../network-editor/pathway-table';
 import { Select, MenuItem } from '@material-ui/core';
 import { Table, TableBody, TableCell, TableContainer, TableHead, TableRow, Paper } from '@material-ui/core';
@@ -17,34 +18,49 @@ const useStyles = makeStyles((theme) => ({
 }));
 
 
-export function Report() {
+async function fetchReport(secret) {
+  try {
+    const countRes = await fetch(`/api/report/count/${secret}`);
+    if(!countRes.ok) {
+      return 'error';
+    }
+    const networkRes = await fetch(`/api/report/networks/${secret}`);
+    if(!networkRes.ok) {
+      return 'error';
+    }
+
+    const counts = await countRes.json();
+    const networks = await networkRes.json();
+
+    return { counts, networks };
+  } catch(err) {
+    console.log(err);
+    return 'error';
+  }
+}
+
+
+export function Report({ secret }) {
   const classes = useStyles();
+
   const [ report, setReport ] = useState(null);
   const [ order, setOrder] = useState('desc');
   const [ orderBy, setOrderBy ] = useState('creationTime');
 
   useEffect(() => {
-    Promise.all([
-      fetch('/api/report/count').then(res => res.json()),
-      fetch('/api/report/networks').then(res => res.json())
-    ])
-    .then(([ counts, networks ]) => {
-      const report = { counts, networks };
-      console.log('report', report);
-      setReport(report);
-    })
-    .catch((error) => console.log(error));
+    fetchReport(secret).then(setReport);
   }, []);
 
-
   if(!report) {
     return <div> Loading... </div>;
+  } else if(report === 'error') {
+    return <div> Error fetching report. </div>;
   }
 
   const comparator = getComparator(order, orderBy);
   const sortedNetworks = report.networks.sort(comparator);
 
-  return <div>
+  return <div style={{padding: '10px'}}>
     <h1>EnrichmentMap:RNA-Seq - Usage Report</h1>
     <h3>Demo Networks: {report.counts.demo}</h3>
     <h3>User Created Networks ({report.counts.user}):</h3>
@@ -73,7 +89,7 @@ export function Report() {
             <TableCell align="right"><b>Type</b></TableCell>
             <TableCell align="right"><b>Creation Time</b></TableCell>
             <TableCell align="right"><b>Last Access Time</b></TableCell>
-            <TableCell align="right"><b>Open</b></TableCell>
+            <TableCell align="right"> </TableCell>
           </TableRow>
         </TableHead>
         <TableBody>
@@ -101,4 +117,8 @@ export function Report() {
   </div>;
 }
 
+Report.propTypes = {
+  secret: PropTypes.string,
+};
+
 export default Report;

src/client/router.js

@@ -40,10 +40,11 @@ export function Router() {
         )}
       />
       <Route
-        path='/report'
-        render={(props) => (
-          <ReportHome {...props} />
-        )}
+        path='/report/:secret'
+        render={(props) => {
+          const secret = _.get(props, ['match', 'params', 'secret'], _.get(props, 'secret'));
+          return <ReportHome secret={secret} />;
+        }}
       />
       <Route
         path='/document/:id/:secret'

src/server/env.js

@@ -14,6 +14,7 @@ export const LOG_LEVEL = process.env.LOG_LEVEL;
 export const BASE_URL = process.env.BASE_URL;
 export const UPLOAD_LIMIT = process.env.UPLOAD_LIMIT;
 export const TESTING = ('' + process.env.TESTING).toLowerCase() === 'true';
+export const REPORT_SECRET = process.env.REPORT_SECRET;
 
 // Service config
 export const FGSEA_PRERANKED_SERVICE_URL = process.env.FGSEA_PRERANKED_SERVICE_URL;

src/server/routes/api/report.js

@@ -1,12 +1,20 @@
 import Express from 'express';
 import Datastore from '../../datastore.js';
 import { writeCursorToResult } from './index.js';
+import { REPORT_SECRET } from '../../env.js';
 
 const http = Express.Router();
 
 // Return enrichment results in TSV format
-http.get('/count', async function(req, res, next) {
+http.get(`/count/:secret`, async function(req, res, next) {
+  
   try {
+    const { secret } = req.params;
+    if(secret !== REPORT_SECRET) {
+      res.sendStatus(404);
+      return;
+    }
+
     const counts = await Datastore.getNetworkCounts();
     res.send(JSON.stringify(counts));
 
@@ -16,8 +24,14 @@ http.get('/count', async function(req, res, next) {
 });
 
 // Return enrichment results in TSV format
-http.get('/networks', async function(req, res, next) {
+http.get(`/networks/:secret`, async function(req, res, next) {
   try {
+    const { secret } = req.params;
+    if(secret !== REPORT_SECRET) {
+      res.sendStatus(404);
+      return;
+    }
+
     const cursor = await Datastore.getNetworkStatsCursor();
     await writeCursorToResult(cursor, res);
     cursor.close();