Merge pull request #155 from gyorilab/ner_download

Add NER download as CSV option in web UI

Author: bgyori

gilda/app/templates/ner_matches.html

@@ -7,7 +7,16 @@
 
     <div class="panel panel-default">
         <div class="panel-heading">
-            <h3 class="panel-title">Named Entity Recognition Results</h3>
+            <div class="row">
+                <div class="col-md-6">
+                    <h3 class="panel-title">Named Entity Recognition Results</h3>
+                </div>
+                <div class="col-md-6 text-right">
+                    <button onclick="download_csv()" class="btn btn-primary">
+                        <i class="fas fa-download"></i> Download CSV
+                    </button>
+                </div>
+            </div>
         </div>
         <div class="panel-body">
             <blockquote>
@@ -53,4 +62,19 @@ <h3 class="panel-title">Named Entity Recognition Results</h3>
             </tbody>
         </table>
     </div>
+
+    <script>
+    function download_csv() {
+        const csvData = `{{ csv_data | safe }}`;
+        const blob = new Blob([csvData], { type: 'text/csv' });
+        const url = window.URL.createObjectURL(blob);
+        const a = document.createElement('a');
+        a.setAttribute('hidden', '');
+        a.setAttribute('href', url);
+        a.setAttribute('download', 'ner_results.csv');
+        document.body.appendChild(a);
+        a.click();
+        document.body.removeChild(a);
+    }
+    </script>
 {% endblock %}

gilda/app/ui.py

@@ -1,4 +1,6 @@
 from textwrap import dedent
+import csv
+from io import StringIO
 
 from flask import Blueprint, render_template, request
 from flask_wtf import FlaskForm
@@ -110,11 +112,42 @@ def view_ner():
     form = NERForm()
     if form.validate_on_submit():
         annotations = form.get_annotations()
+
+        # Generate CSV data
+        si = StringIO()
+        writer = csv.writer(si)
+        writer.writerow([
+            "Start", "End", "Text", "Grounding", "Standard Name", "Score",
+            "Additional Groundings"
+        ])
+
+        # Write data
+        for annotation in annotations:
+            match = annotation.matches[0]
+            match_curie = match.term.get_curie()
+            additional_groundings = ", ".join(
+                curie for curie in match.get_grounding_dict().keys()
+                if curie != match_curie
+            )
+
+            writer.writerow([
+                f"{annotation.start}",
+                f"{annotation.end}",
+                annotation.text,
+                match_curie,
+                match.term.entry_name,
+                f"{match.score:.4f}",
+                additional_groundings
+            ])
+
+        csv_data = si.getvalue()
+
         return render_template(
             "ner_matches.html",
             annotations=annotations,
             version=version,
             text=form.text.data,
+            csv_data=csv_data,
             # Add a new form that doesn't auto-populate
             form=NERForm(formdata=None),
         )