Plugin-Visual-Seqviz/server.js at main · SynBioHub/Plugin-Visual-Seqviz · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
const express = require('express')

const path = require('path');
const request = require('request');
const serialize = require("serialize-javascript");

import filesToParts from "./io/filesToParts";

const app = express()
const port = 5000
const addr = "localhost"

app.use(express.json());
//app.use(express.static("public"));

app.get('/seqviz.js', function (req, res) {
  console.log('seqviz.js')
  res.sendFile(path.join(__dirname, 'public', 'seqviz.js'));
})

app.get('/Status', function (req, res) {
  console.log('Status')
  res.status(200).send('The plugin is up and running')
})

app.post('/Evaluate', function (req, res) {
  let type = req.body.type.toString();
  console.log('evaluate ' + type)
  if (type === 'Component' || type === 'ComponentDefinition') {
    res.status(200).send('The app can handle this input');
  } else {
    res.status(404).end();
  }
})

app.post('/Run', async (req, res) => {
  let url = req.body.complete_sbol.toString();
  let top_level = req.body.top_level.toString();
    let hostAddr = req.get('host');
    // Optional override via environment variable (use full host or include protocol)
    const overrideHost = process.env.SEQVIZ_HOST;
    const scriptUrl = overrideHost
      ? (overrideHost.match(/^https?:\/\//)
          ? overrideHost.replace(/\/$/, '') + '/seqviz.js'
          : 'http://' + overrideHost.replace(/\/$/, '') + '/seqviz.js')
      : `https://${hostAddr}/seqviz.js`;
  try {
    // Get SBOL file content string
    let csv;
    if(req.body.token) {
      csv = await getFileData(url, req.body.token);
    }
    else {
      csv = await getFileData(url);
    }
    // parse SBOL file to get data for sequence view rendering
    const {
      displayList,
      parts
    } = await filesToParts(csv, {
      topLevel: top_level
    });

    const propdata = {
      style: {
        height: 600,
        width: 1100
      },
      size: {
        width: 500,
        height: 600
      },
      displayList: displayList,
      parts: parts,
    }

    const theHtml = `<!doctype html>
                    <html>
                      <head><title>sequence view</title></head>
                      <body>
                        <div id="reactele"></div>
                        <script type="text/javascript">window.__INITIAL_DATA__ = ${serialize(propdata)}</script>
                          <script type="text/javascript" src="${scriptUrl}" charset="utf-8"></script>
                      </body>
                    </html>`;
    res.send(theHtml);
  } catch (err) {
    const theHtml = `<!doctype html>
                    <html>
                      <head><title>sequence view</title></head>
                      <body>
                        <div id="reactele">
                        Error when parsing this file to get sequence data!
                        ${err.toString()}
                        </div>
                      </body>
                    </html>`;
    res.send(theHtml);
  }
})

function getFileData(url, token=null) {
  return new Promise((resolve, reject) => {
    const options = {
      url: url,
      headers: {"Accept": "text/plain"}
    };
    if (token) {
      options.headers['X-authorization'] = token;
    }
    request.get(options, function (error, response, body) {
      if (!error && response.statusCode == 200) {
        return resolve(body);
      } else {
        console.log('error:', error);
        return reject(error);
      }
    });
  })
}

app.listen(port, () => console.log(`Example app listening at http://${addr}:${port}`))