Merge pull request #301 from cytoscape/feature/report

Feature/report
cytoscape · Jul 9, 2024 · 305fbe0 · 305fbe0
2 parents 1d9fd5c + 818e612
commit 305fbe0
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Showing 12 changed files with 287 additions and 7 deletions.
diff --git a/.env.defaults b/.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
diff --git a/.env.local b/.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
diff --git a/src/client/components/network-editor/export-controller.js b/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({

diff --git a/src/client/components/network-editor/pathway-table.js b/src/client/components/network-editor/pathway-table.js
@@ -244,24 +244,29 @@ const linkoutProps = { target: "_blank",  rel: "noreferrer", underline: "hover"
 const DEF_ORDER = 'desc';
 const DEF_ORDER_BY = 'nes';
 
-const descendingComparator = (a, b, orderBy) => {
+export const descendingComparator = (a, b, orderBy) => {
+  const aVal = a[orderBy], bVal = b[orderBy];
+
   // null values come last in ascending!
-  if (a[orderBy] == null) {
+  if (aVal == null) {
     return -1;
   }
-  if (b[orderBy] == null) {
+  if (bVal == null) {
     return 1;
   }
-  if (b[orderBy] < a[orderBy]) {
+  if(typeof aVal === 'string' && typeof bVal === 'string') {
+    return aVal.localeCompare(bVal, undefined, { sensitivity: 'accent' });
+  }
+  if (bVal < aVal) {
     return -1;
   }
-  if (b[orderBy] > a[orderBy]) {
+  if (bVal > aVal) {
     return 1;
   }
   return 0;
 };
 
-const getComparator = (order, orderBy) => {
+export const getComparator = (order, orderBy) => {
   return order === 'desc'
     ? (a, b) => descendingComparator(a, b, orderBy)
     : (a, b) => -descendingComparator(a, b, orderBy);

diff --git a/src/client/components/report/index.js b/src/client/components/report/index.js
@@ -0,0 +1,34 @@
+import React, { useEffect, useState } from 'react';
+import PropTypes from 'prop-types';
+import { ThemeProvider } from '@material-ui/core/styles';
+import CssBaseline from '@material-ui/core/CssBaseline';
+import { currentTheme } from '../../theme';
+import Report from './report';
+
+
+export function ReportHome({ secret }) {
+  const [ theme, setTheme ] = useState(currentTheme);
+
+  useEffect(() => {
+    // Listen for changes in the user's theme preference
+    const mediaQuery = window.matchMedia('(prefers-color-scheme: dark)');
+    const handleThemeChange = () => setTheme(currentTheme());
+    mediaQuery.addEventListener('change', handleThemeChange);
+    return () => {
+      mediaQuery.removeEventListener('change', handleThemeChange);
+    };
+  }, []);
+
+  return (
+    <ThemeProvider theme={theme}>
+      <CssBaseline />
+      <Report secret={secret} />
+    </ThemeProvider>
+  );
+}
+
+ReportHome.propTypes = {
+  secret: PropTypes.string,
+};
+
+export default ReportHome;
diff --git a/src/client/components/report/report.js b/src/client/components/report/report.js
@@ -0,0 +1,124 @@
+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';
+import { makeStyles } from '@material-ui/core/styles';
+
+
+const useStyles = makeStyles((theme) => ({
+  orderBy: {
+    margin: theme.spacing(1),
+    minWidth: 200,
+  },
+  order: {
+    margin: theme.spacing(1),
+    minWidth: 120,
+  },
+}));
+
+
+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(() => {
+    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 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>
+    <div style={{"float":"right"}} >
+      Sort:
+      &nbsp;&nbsp;
+      <Select value={orderBy} onChange={(event) => setOrderBy(event.target.value)} className={classes.orderBy}>
+        <MenuItem value="networkName">Name</MenuItem>
+        <MenuItem value="creationTime">Creation Time</MenuItem>
+        <MenuItem value="lastAccessTime">Last Accessed Time</MenuItem>
+      </Select>
+      &nbsp;
+      <Select value={order} onChange={(event) => setOrder(event.target.value)} className={classes.order}>
+        <MenuItem value="desc">Desc</MenuItem>
+        <MenuItem value="asc">Asc</MenuItem>
+      </Select>
+    </div>
+    <br></br>
+    <TableContainer component={Paper}>
+      <Table sx={{ minWidth: 650 }} aria-label="simple table">
+        <TableHead>
+          <TableRow>
+            <TableCell><b>Network Name</b></TableCell>
+            <TableCell align="right"><b>Nodes</b></TableCell>
+            <TableCell align="right"><b>Edges</b></TableCell>
+            <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"> </TableCell>
+          </TableRow>
+        </TableHead>
+        <TableBody>
+          {sortedNetworks.map(network => {
+            const createTime = new Date(network.creationTime).toLocaleString('en-CA');
+            const accessTime = new Date(network.lastAccessTime).toLocaleString('en-CA');
+            return (
+              <TableRow
+                key={network._id}
+                sx={{ '&:last-child td, &:last-child th': { border: 0 } }}
+              >
+                <TableCell component="th" scope="row">{network.networkName}</TableCell>
+                <TableCell align="right">{network.nodeCount}</TableCell>
+                <TableCell align="right">{network.edgeCount}</TableCell>
+                <TableCell align="right">{network.inputType}</TableCell>
+                <TableCell align="right">{createTime}</TableCell>
+                <TableCell align="right">{accessTime}</TableCell>
+                <TableCell align="right"><a href={`/document/${network._id}`} target="_blank" rel = "noopener noreferrer">open</a></TableCell>
+              </TableRow>
+            );
+          })}
+        </TableBody>
+      </Table>
+    </TableContainer>
+  </div>;
+}
+
+Report.propTypes = {
+  secret: PropTypes.string,
+};
+
+export default Report;
diff --git a/src/client/router.js b/src/client/router.js
@@ -5,6 +5,7 @@ import PageNotFound from './components/page-not-found';
 import { RecentNetworksController } from './components/recent-networks-controller';
 import { Home } from './components/home';
 import { NetworkEditor } from './components/network-editor';
+import { ReportHome } from './components/report';
 
 const recentNetworksController = new RecentNetworksController();
 
@@ -38,6 +39,13 @@ export function Router() {
           <Home {...props} recentNetworksController={recentNetworksController} />
         )}
       />
+      <Route
+        path='/report/:secret'
+        render={(props) => {
+          const secret = _.get(props, ['match', 'params', 'secret'], _.get(props, 'secret'));
+          return <ReportHome secret={secret} />;
+        }}
+      />
       <Route
         path='/document/:id/:secret'
         render={(props) => (

diff --git a/src/server/datastore.js b/src/server/datastore.js
@@ -752,6 +752,51 @@ class Datastore {
     return cursor;
   }
 
+
+  async getNetworkCounts() {
+    const result = await this.db
+      .collection(NETWORKS_COLLECTION)
+      .aggregate([
+        { $facet: {
+          'user': [
+            { $match: { demo: { $ne: true } }},
+            { $count: 'total' }
+          ],
+          'demo': [
+            { $match: { demo: true }},
+            { $count: 'total' }
+          ],
+        }},
+        { $project: {
+          "user": { $arrayElemAt: ["$user.total", 0] },
+          "demo": { $arrayElemAt: ["$demo.total", 0] },
+        }}
+      ]).toArray();
+
+    return result[0];
+  }
+
+
+  async getNetworkStatsCursor() {
+    const cursor = await this.db
+      .collection(NETWORKS_COLLECTION)
+      .aggregate([
+        { $match: { demo: { $ne: true } }},
+        { $project: { 
+          networkName: 1,
+          creationTime: 1,
+          lastAccessTime: 1,
+          geneSetCollection: 1,
+          inputType: 1,
+          nodeCount: { $size: '$network.elements.nodes' },
+          edgeCount: { $size: '$network.elements.edges' }
+        }}
+    ]);
+
+    return cursor;
+  }
+
+
 }
 
 const ds = new Datastore(); // singleton

diff --git a/src/server/env.js b/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;

diff --git a/src/server/index.js b/src/server/index.js
@@ -21,6 +21,7 @@ import indexRouter from './routes/index.js';
 import apiRouter from './routes/api/index.js';
 import createRouter, { createRouterErrorHandler } from './routes/api/create.js';
 import exportRouter from './routes/api/export.js';
+import reportRouter from './routes/api/report.js';
 
 import Datastore, { GMT_2 } from './datastore.js';
 
@@ -108,6 +109,7 @@ app.use('/', indexRouter);
 app.use('/api', apiRouter);
 app.use('/api/create', createRouter);
 app.use('/api/export', exportRouter);
+app.use('/api/report', reportRouter);
 
 // The error handler must be before any other error middleware and after all controllers
 if (SENTRY) {

diff --git a/src/server/routes/api/index.js b/src/server/routes/api/index.js
@@ -231,7 +231,7 @@ http.delete('/:netid/positions', async function(req, res, next) {
 });
 
 
-async function writeCursorToResult(cursor, res) {
+export async function writeCursorToResult(cursor, res) {
   res.write('[');
   if(await cursor.hasNext()) {
     const obj = await cursor.next();