initial commit

LICENSE

+Copyright 2020 Benoit Favre
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+

README.md

+Demo site
+=========
+
+Simple website for searching a set of articles labelled with topics.
+
+Data
+----
+
+Data is assumed to be a liste of articles in json format with a field 'topic-pred' containing a list of topics.
+Example:
+
+```
+{
+  'title': 'Title of the article',
+  'abstract': 'Abstract of the article',
+  'authors': 'List of authors as a string',
+  'publication_date': '2020-05-28',
+  'url': 'https://url-to-full-text',
+  'topic-pred': [ 'topic1', 'topic2', ...]
+}
+```
+
+The included search engine is a very simple search engine implementing BM25 ranking after stopword removal.
+
+Running
+-------
+
+```
+npm install
+node create-db.js papers-with-topics.json
+npm start
+```

create-db.js

+const fs = require('fs');
+
+var load = function(filename) {
+  console.log('loading json...');
+  const articles = JSON.parse(fs.readFileSync(filename));
+  console.log(articles.length, 'articles');
+  console.log('saving in db...');
+  articles.sort((a, b) => -a.publication_date.localeCompare(b.publication_date));
+
+  const index = {};
+  var id = 0;
+  for(var article of articles) {
+    article._id = id;
+    for(var topic of article['topic-pred']) {
+      if(!(topic in index)) index[topic] = [];
+      index[topic].push(id);
+    }
+    id ++;
+  }
+
+  for(var topic in index) {
+    index[topic].sort((a, b) => -articles[a].publication_date.localeCompare(articles[b].publication_date));
+  }
+
+  var data = {
+    index: index,
+    articles: articles,
+  };
+
+  fs.writeFileSync('data.json', JSON.stringify(data));
+  console.log('indexing...');
+  const search_engine = require('./search');
+  search_engine.build_index(articles.map((doc) => doc.title + ' ' + doc.abstract));
+  search_engine.save_index('data.bm25');
+}
+
+if(process.argv.length < 3) {
+  console.log('usage: node create-db.js <json-data-path>');
+} else {
+  load(process.argv[2]);
+}
+

model.js

+"use strict"
+const fs = require('fs');
+
+const {index, articles} = JSON.parse(fs.readFileSync('data.json').toString());
+
+exports.read = (id, callback) => {
+  callback(null, articles[id]);
+};
+
+exports.for_topic = (topic, page, callback) => {
+  const num_per_page = 36;
+  topic = topic || 'All';
+  page = parseInt(page || 1);
+
+  var query = {'topic-pred': topic};
+  var results, num_found;
+  if(topic === 'All') {
+    results = articles.slice((page - 1) * num_per_page, page * num_per_page);
+    num_found = articles.length;
+  } else if(topic in index) {
+    results = index[topic].slice((page - 1) * num_per_page, page * num_per_page).map((id) => articles[id]);
+    num_found = index[topic].length;
+  } else {
+    results = [];
+    num_found = 0;
+  }
+  callback(null, {
+        results: results,
+        num_found: num_found, 
+        next_page: page + 1,
+        topic: topic,
+        page: page,
+        num_pages: parseInt(num_found / num_per_page) + 1,
+      });
+}
+
+const search_engine = require('./search');
+search_engine.load_index('data.bm25');
+
+exports.search = (query, page, callback) => {
+  const num_per_page = 32;
+  query = query || "";
+  page = parseInt(page || 1);
+
+  const found = search_engine.search(query);
+  const num_found = found.length;
+  const results = found.slice((page - 1) * num_per_page, page * num_per_page).map(result => articles[result[0]]);
+  callback(null, {
+      results: results,
+      num_found: num_found, 
+      query: query,
+      next_page: page + 1,
+      page: page,
+      num_pages: parseInt(num_found / num_per_page) + 1,
+    });
+};
+
+exports.topics = ['All', 'Prevention', 'Diagnosis', 'Treatment', 'Case Report', 'Mechanism', 'Transmission', 'Epidemic Forecasting', 'General Info'];
+
+exports.elidate = (articles) => {
+  articles = JSON.parse(JSON.stringify(articles)); // deep copy
+  for(var i = 0; i < articles.length; i++) {
+    var article = articles[i];
+    var authors = article.authors.split(';');
+    if(authors.length > 3) {
+      article['authors'] = authors.slice(0, 3).join(';') + ' et al.'; 
+    }
+    if(article.abstract.length > 200) article.abstract = article.abstract.substr(0, 200) + '...';
+  }
+  return articles;
+}

package-lock.json

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+        "unpipe": "1.0.0"
+      }
+    },
+    "safe-buffer": {
+      "version": "5.1.2",
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+        "debug": "2.6.9",
+        "depd": "~1.1.2",
+        "destroy": "~1.0.4",
+        "encodeurl": "~1.0.2",
+        "escape-html": "~1.0.3",
+        "etag": "~1.8.1",
+        "fresh": "0.5.2",
+        "http-errors": "~1.7.2",
+        "mime": "1.6.0",
+        "ms": "2.1.1",
+        "on-finished": "~2.3.0",
+        "range-parser": "~1.2.1",
+        "statuses": "~1.5.0"
+      },
+      "dependencies": {
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+      }
+    },
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+        "escape-html": "~1.0.3",
+        "parseurl": "~1.3.3",
+        "send": "0.17.1"
+      }
+    },
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+    },
+    "statuses": {
+      "version": "1.5.0",
+      "resolved": "https://registry.npmjs.org/statuses/-/statuses-1.5.0.tgz",
+      "integrity": "sha1-Fhx9rBd2Wf2YEfQ3cfqZOBR4Yow="
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+    },
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+      "resolved": "https://registry.npmjs.org/type-is/-/type-is-1.6.18.tgz",
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+      "requires": {
+        "media-typer": "0.3.0",
+        "mime-types": "~2.1.24"
+      }
+    },
+    "unpipe": {
+      "version": "1.0.0",
+      "resolved": "https://registry.npmjs.org/unpipe/-/unpipe-1.0.0.tgz",
+      "integrity": "sha1-sr9O6FFKrmFltIF4KdIbLvSZBOw="
+    },
+    "utils-merge": {
+      "version": "1.0.1",
+      "resolved": "https://registry.npmjs.org/utils-merge/-/utils-merge-1.0.1.tgz",
+      "integrity": "sha1-n5VxD1CiZ5R7LMwSR0HBAoQn5xM="
+    },
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+    }
+  }
+}

package.json

+{
+  "name": "paper-server",
+  "version": "1.0.0",
+  "description": "",
+  "main": "server.js",
+  "scripts": {
+    "test": "echo \"Error: no test specified\" && exit 1"
+  },
+  "author": "",
+  "license": "ISC",
+  "dependencies": {
+    "body-parser": "^1.19.0",
+    "express": "^4.17.1",
+    "mustache-express": "^1.3.0"
+  }
+}

search.js

+"use strict"
+var fs = require('fs');
+
+var stopwords = fs.readFileSync('stopwords.txt').toString().split('\n').reduce((set, line) => {set.add(line.trim()); return set}, new Set());
+
+var index = {
+  termFrequency: new Map(),
+  documentLength: [],
+  averageDocumentLength: 0,
+  k1: 1.2,
+  b: 0.75,
+}
+
+function tokenize(text) {
+  var tokens = [];
+  for(var word of text.trim().toLowerCase().replace(/[^a-z0-9-]/g, ' ').split(/\s+/)) {
+    if(!stopwords.has(word)) {
+      tokens.push(word);
+    }
+  }
+  return tokens;
+}
+
+function vectorize(text) {
+  var vector = new Map();
+  for(var word of tokenize(text)) {
+    if(!vector.has(word)) vector.set(word, 1);
+    else vector.set(word, 1 + vector.get(word));
+  }
+  return vector;
+}
+
+function add_to_index(text, id) {
+  const termFrequency = index.termFrequency;
+  var documentLength = 0;
+  vectorize(text).forEach((count, word) => {
+    if(!index.termFrequency.has(word)) termFrequency.set(word, []);
+    termFrequency.get(word).push(id, count);
+    documentLength += count;
+  });
+  return documentLength;
+}
+
+function build_index(entries) {
+  var i = 0;
+  for(var text of entries) {
+    const length = add_to_index(text, i);
+    index.documentLength.push(length);
+    index.averageDocumentLength += length;
+    i++;
+  }
+  index.averageDocumentLength /= index.documentLength.length;
+}
+
+function load_index(filename) {
+  index = JSON.parse(fs.readFileSync(filename).toString());
+  index.termFrequency = new Map(index.termFrequency);
+}
+
+function save_index(filename) {
+  const backup = index.termFrequency;
+  index.termFrequency = Array.from(backup.entries());
+  fs.writeFileSync(filename, JSON.stringify(index));
+  index.termFrequency = backup;
+}
+
+function inverseDocumentFrequency(word) {
+  if(index.termFrequency.has(word)) {
+    const documentFrequency = index.termFrequency.get(word).length / 2;
+    return Math.log( (index.documentLength.length - documentFrequency + 0.5) / (documentFrequency + 0.5) );
+  }
+  return 0;
+}
+
+function okapi_bm25(query) {
+  var found = new Map();
+  tokenize(query).forEach((word) => {
+    if(index.termFrequency.has(word)) {
+      const idf = inverseDocumentFrequency(word);
+      const entries = index.termFrequency.get(word);
+      for(var i = 0; i < entries.length; i += 2) {
+        const doc = entries[i], termFrequency = entries[i + 1];
+        const score = idf * (termFrequency * (index.k1 + 1)) / termFrequency + index.k1 * (1 - index.b + index.b * index.documentLength[doc] / index.averageDocumentLength);
+        if(!found.has(doc)) found.set(doc, score);
+        else found.set(doc, score + found.get(doc));
+      }
+    }
+  });
+  return found;
+}
+
+function search(query) {
+  query = query || "";
+
+  var found = okapi_bm25(query);
+  var results = Array.from(found.entries());
+  results.sort((a, b) => b[1] - a[1]);
+
+  return results;
+};
+
+//var docs = JSON.parse(fs.readFileSync(process.argv[2]).toString());
+//build_index(docs.map(doc => doc.title + ' ' + doc.abstract));
+//save_index('index.bm25');
+//load_index('index.bm25');
+//console.log(search('virus'));
+
+module.exports = {
+  build_index: build_index,
+  save_index: save_index,
+  load_index: load_index,
+  search: search,
+};
+

server.js

+"use strict"
+var express = require('express');
+var mustache = require('mustache-express');
+
+var model = require('./model');
+var app = express();
+
+app.engine('html', mustache());
+app.set('view engine', 'html');
+app.set('views', './views');
+
+app.use((req, res, next) => {
+  res.locals.topic_menu = model.topics.map((topic) => ({name: topic}));
+  return next();
+});
+
+app.get('/', (req, res) => {
+  res.redirect('/topic/All');
+});
+
+app.get('/article/:id', (req, res) => {
+  model.read(req.params.id, (err, doc) => {
+    if(err) {
+      res.status(500).send(err);
+    } else {
+      res.render('read', doc);
+    }
+  });
+});
+
+app.get('/topic/:topic', (req, res) => {
+  res.locals.topic_menu = model.topics.map((topic) => ({name: topic, active: topic === req.params.topic}));
+  model.for_topic(req.params.topic, req.query.page, (err, found) => {
+    found.results = model.elidate(found.results);
+    res.render('search', found);
+  });
+});
+
+app.get('/search', (req, res) => {
+  model.search(req.query.query, req.query.page, (err, found) => {
+    found.results = model.elidate(found.results);
+    res.render('search', found);
+  });
+});
+
+app.use(express.static('old/public'))
+
+app.listen(8892, () => console.log('listening on http://localhost:8892'));

stopwords.txt

+a
+about
+above
+across
+after
+afterwards
+again
+against
+al 
+all
+almost
+alone
+along
+already
+also
+although
+always
+am  
+among
+amongst
+an
+analyze
+and
+another
+any
+anyhow
+anyone
+anything
+anywhere
+applicable
+apply
+are
+around
+as
+assume
+at
+be
+became
+because
+become
+becomes
+becoming
+been
+before
+beforehand
+being
+below
+beside
+besides
+between
+beyond
+both
+but
+by
+came
+cannot
+cc  
+cm  
+come
+compare
+could
+de  
+dealing
+department
+depend
+did
+discover
+dl  
+do
+does
+during
+each
+ec
+ed
+effected
+eg
+either
+else
+elsewhere
+enough
+et  
+etc
+ever
+every
+everyone
+everything
+everywhere
+except
+find
+for
+found
+from
+further
+get
+give
+go
+gov
+had
+has
+have
+he
+hence
+her
+here
+hereafter
+hereby
+herein
+hereupon
+hers
+herself
+him
+himself
+his
+how
+however
+hr  
+ie
+if
+ii  
+iii  
+in
+inc
+incl
+indeed
+into
+investigate
+is
+it
+its
+itself
+j
+jour
+journal
+just
+kg  
+last
+latter
+latterly
+lb  
+ld 
+letter
+like
+ltd
+made
+make
+many
+may
+me
+meanwhile
+mg  
+might
+ml  
+mm  
+mo  
+more
+moreover
+most
+mostly
+mr
+much
+must
+my
+myself
+namely
+neither
+never
+nevertheless
+next
+no
+nobody
+noone
+nor
+not
+nothing
+now
+nowhere
+of
+off
+often
+on
+only
+onto
+or
+other
+others
+otherwise
+our
+ours
+ourselves
+out
+over
+own
+oz  
+per
+perhaps
+pm  
+precede
+presently
+previously
+pt  
+rather
+regarding
+relate
+said
+same
+seem
+seemed
+seeming
+seems
+seriously
+several
+she
+should
+show
+showed
+shown
+since
+so
+some
+somehow
+someone
+something
+sometime
+sometimes
+somewhere
+still
+studied
+sub 
+such
+take
+tell
+th  
+than
+that
+the
+their
+them
+themselves
+then
+thence
+there
+thereafter
+thereby
+therefore
+therein
+thereupon
+these
+they
+this
+thorough
+those
+though
+through
+throughout
+thru
+thus
+to
+together
+too
+toward
+towards
+try
+type
+ug  
+under
+unless
+until
+up
+upon
+us
+used
+using
+various
+very
+via
+was
+we
+were
+what
+whatever
+when
+whence
+whenever
+where
+whereafter
+whereas
+whereby
+wherein
+whereupon
+wherever
+whether
+which
+while
+whither
+who
+whoever
+whom
+whose
+why
+will
+with
+within
+without
+wk
+would
+wt
+yet
+you
+your
+yours
+yourself
+yourselves
+yr

views/footer.html

+
+</main>
+</html>
+

views/header.html

+<!doctype html>
+<html lang="en">
+  <head>
+    <meta charset="utf-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+    <title>CORD-19 topics</title>
+    <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.4.1/css/bootstrap.min.css" integrity="sha384-Vkoo8x4CGsO3+Hhxv8T/Q5PaXtkKtu6ug5TOeNV6gBiFeWPGFN9MuhOf23Q9Ifjh" crossorigin="anonymous">
+  </head>
+
+  <body>
+    <nav class="navbar navbar-expand-md navbar-dark bg-dark">
+      <div class="collapse navbar-collapse" id="navbarsExampleDefault">
+        <a class="navbar-brand" href="/">Topics:</a>
+        <div class="navbar-nav-scroll ">
+          <ul class="navbar-nav bd-navbar-nav flex-row">
+            {{#topic_menu}}
+            <li class="nav-item">
+              <a href="/topic/{{name}}" class="nav-link {{#active}}active{{/active}}">{{name}}</a>
+            </li>
+            {{/topic_menu}}
+          </ul>
+        </div>
+        <form class="form-inline my-2 my-lg-0 ml-auto" action="/search">
+          <input class="form-control mr-sm-2" type="text" placeholder="Requête" name="query" aria-label="Search" value="{{query}}">
+          <input class="btn btn-secondary my-2 my-sm-0" type="submit" value="Rechercher">
+        </form>
+      </div>
+    </nav>
+
+  <main role="main" class="container mt-3 mb-5">

views/read.html

+{{> header}}
+  <div class="row">
+    <div class="col">
+      <h1>{{title}}</h1>
+      <p class="text-muted">{{authors}}</p>
+      <p>{{publication_date}}</p>
+      <p>
+      {{#topic-pred}}
+      <span class="badge badge-secondary">{{.}}</span>
+      {{/topic-pred}}
+      </p>
+      <p><strong>Abstract :</strong> {{abstract}}</p>
+      <p>
+        <a class="btn btn-outline-primary" href="{{url}}" target="_blank">Read full-text</a>
+      </p>
+    </div>
+  </div>
+{{> footer}}

views/search.html

+{{> header}}
+
+
+  <div class="row row-cols-1 row-cols-md-2 row-cols-lg-3">
+      {{#results}}
+      <div class="col mb-3">
+          <div class="card mb-4 h-100">
+            <div class="card-body">
+              <h5 class="card-title"><a href="/article/{{_id}}">{{title}}</a></h5>
+              <h6 class="card-subtitle text-muted">{{authors}}</h6>
+              <p class="card-text">
+              {{#topic-pred}}
+              <span class="badge badge-secondary">{{.}}</span>
+              {{/topic-pred}}
+              </p>
+            </div>
+            <div class="card-footer">
+              <a class="btn btn-outline-primary" href="{{url}}">Full text</a>
+              <span class="card-text text-muted float-right">{{publication_date}}</span>
+            </div>
+          </div>
+      </div>
+      {{/results}}
+  </div>
+
+  {{#next_page}}
+  <div class="row">
+    <div class="col text-center">
+      {{num_found}} articles {{#page}} (page {{page}}/{{num_pages}}) {{/page}}
+      <a class="btn btn-primary ml-3" href="/topic/{{topic}}?page={{next_page}}">Next page</a>
+    </div>
+  </div>
+  {{/next_page}}
+
+{{> footer}}