Add search by name function.

Author: Jon Wedell

gateway.py

@@ -12,6 +12,7 @@
 import subprocess
 
 # Installed packages
+import requests
 import psycopg2
 from flask import Flask, request, jsonify, redirect, render_template, url_for
 from psycopg2.extras import DictCursor
@@ -142,6 +143,20 @@ def home_page():
     return render_template("search_by_structure.html")
 
 
+@application.route('/name')
+def name_search():
+    """ Render the name search."""
+
+    term = request.args.get('term', "")
+    if term:
+        results = requests.get('http://alatis.nmrfam.wisc.edu/search/inchi', params={'term': term}).json()
+    else:
+        results = []
+    var_dict = {'title': term, 'results': results}
+
+    return render_template("search_by_name.html", **var_dict)
+
+
 @application.route('/chemical_identifier_search')
 def identifier_search():
     """ Search for a compound by chemical identifier. """
@@ -156,81 +171,6 @@ def reroute():
     return redirect("query?term=%s" % term, code=302)
 
 
-@application.route('/search/results')
-def results():
-    """ Search results. """
-    var_dict = {'title': request.args.get('term', ""),
-                'results': search(local=True)}
-
-    return render_template("search.html", **var_dict)
-
-
-@application.route('/search/query')
-def search(local=False):
-    """ Search the DB. """
-
-    term = request.args.get('term', None)
-    if not term:
-        return "Specify term."
-
-    cur = get_postgres_connection(dictionary_cursor=True)[1]
-
-    limit = " LIMIT 75;"
-    if local:
-        limit = ";"
-
-    if request.args.get('debug', None):
-        return '''
-SELECT * FROM (
-SELECT id,db,term,termname,data_path,similarity(term, '%s') AS sml FROM search_terms
-  WHERE lower(term) LIKE lower('%s')
-UNION
-SELECT id,db,term,termname,data_path,similarity(term, '%s')  FROM search_terms
-  WHERE identical_term @@ plainto_tsquery('%s')
-UNION
-(SELECT cm.id::text, 'PubChem', coalesce(cn.name, 'Unknown Name'), 'Compound',
- 'pubchem/'||cm.id, 1 FROM compound_metadata AS cm
-  LEFT JOIN compound_name AS cn
-ON cn.id = cm.id WHERE cm.id=to_number('0'||'%s', '99999999999')::int ORDER BY cn.seq LIMIT 1)
-UNION
-(SELECT id::text, 'PubChem', name, 'Compound', 'pubchem/'||id, similarity(lower(name), lower(%s)) FROM compound_name
-  WHERE lower(name) LIKE lower('%s') LIMIT 50)) AS f
-ORDER by sml DESC, 2!='PubChem', id ASC LIMIT 75;''' % (term, term + "%", term, term, term, term, term + "%")
-
-    cur.execute('''
-SELECT * FROM (
-SELECT id,db as database,term,termname,data_path,similarity(term, %s) AS sml FROM search_terms
-  WHERE lower(term) LIKE lower(%s)
-UNION
-SELECT id,db,term,termname,data_path,similarity(term, %s)  FROM search_terms
-  WHERE identical_term @@ plainto_tsquery(%s)
-UNION
-(SELECT cm.id::text, 'PubChem', coalesce(cn.name, 'Unknown Name'), 'Compound',
- 'pubchem/'||cm.id, 1 FROM compound_metadata AS cm
-  LEFT JOIN compound_name AS cn
-  ON cn.id = cm.id WHERE cm.id=to_number('0'||%s, '99999999999')::int ORDER BY cn.seq LIMIT 1)
-UNION
-(SELECT id::text, 'PubChem', name, 'Compound', 'pubchem/'||id, similarity(lower(name), lower(%s)) FROM compound_name
-  WHERE lower(name) LIKE lower(%s) LIMIT 50)) AS f
-ORDER by sml DESC, database!='PubChem', id ASC''' + limit, [term, term + "%", term, term, term, term, term + "%"])
-
-    # First query
-    result = []
-    for item in cur.fetchall():
-        res = {"link": item['data_path'],
-               "db": item["database"],
-               "entry": item['id'],
-               "termname": item['termname'],
-               "term": unicode(item['term'], 'utf-8')}
-
-        result.append(res)
-
-    if not local:
-        return jsonify(result)
-
-    return result
-
-
 @application.route('/reload')
 def reload_db():
     """ Reload the DB."""

requirements.txt

@@ -1,2 +1,3 @@
 psycopg2-binary==2.7.6.1
 flask==1.0.2
+requests==2.19.1

static/search.css

@@ -10,7 +10,12 @@
 }
 
 ul.dropdown-content.select-dropdown li span {
-    color: #000; /* no need for !important :) */
+    color: #000;
+}
+
+.bold-blue {
+    font-weight: bold;
+    color: #000097;
 }
 
 .checkbox-indigo[type="checkbox"] + label:before{
@@ -35,4 +40,4 @@ ul.dropdown-content.select-dropdown li span {
     border-left: 2px solid transparent;
     border-right: 2px solid #fff;
     border-bottom: 2px solid #fff;
-}
+}

templates/base.html

@@ -37,19 +37,12 @@
             </nav>
 
             <div class="col s3">
-                <!-- Instant search bar
-                <div class="search">
-                    <form method="get" action="/search/results" target="_blank">
-                        <p><span style="font-weight: bold;">Search:</span>
-                            <input type="text" id="search" name="term" title="Search">
-                        </p>
-                   </form>
-                </div>-->
                 <div class="card blue lighten-2">
                     <div class="card-content">
                         <span class="card-title">News</span>
                         <ul>
                             <li><b>Aug 2018</b>: Initiation.</li>
+                            <li><b>March 2019</b>: Added <a href="{{url_for('name_search')}}" class="bold-blue">search by name</a> function.</li>
                         </ul>
                     </div>
                 </div>
@@ -86,13 +79,6 @@ <h5 class="black-text">Other Servers</h5>
     </footer>
 
 </div>
-<script type="text/javascript" src="/static/materialize.min.js"></script>
-<script>document.addEventListener('DOMContentLoaded', function() {
-var elems = document.querySelectorAll('select');
-var instances = M.FormSelect.init(elems, 'options');
-});
-
-</script>
 </body>
 </html>
 

templates/search_by_structure.html

@@ -71,7 +71,13 @@
     </fieldset>
 </form>
 
+<script type="text/javascript" src="/static/materialize.min.js"></script>
 <script>
+document.addEventListener('DOMContentLoaded', function() {
+var elems = document.querySelectorAll('select');
+var instances = M.FormSelect.init(elems, 'options');
+});
+
 document.getElementById('infile').onchange = function() {
     // document.getElementById('FORMAT').selectedIndex =
     $('#FORMAT').val(this.value.split('.').pop());