Merge pull request #345 from mutalyzer/noninteractive-links

Links in standalone mode should retain this mode

mutalyzer/website/templates/name-checker.html

@@ -124,7 +124,7 @@
             <h4>Description relative to transcription start</h4>
             <p>(Not for use in LSDBs in case of protein-coding transcripts).</p>
           {% endif %}
-          <p><code><a href="{{ url_for('.name_checker', description=genomicDescription) }}">{{ genomicDescription }}</a></code></p>
+          <p><code><a href="{{ url_for('.name_checker', description=genomicDescription, standalone=standalone|int or None) }}">{{ genomicDescription }}</a></code></p>
         {% endif %}
 
         {% if chromDescription %}
@@ -138,7 +138,7 @@
             {% if i.endswith('?') %}
               <p><code>{{ i }}</code></p>
             {% else %}
-              <p><code><a href="{{ url_for('.name_checker', description=i) }}">{{ i }}</a></code></p>
+              <p><code><a href="{{ url_for('.name_checker', description=i, standalone=standalone|int or None) }}">{{ i }}</a></code></p>
             {% endif %}
           {% endfor %}
         {% endif %}

tests/test_website.py

@@ -9,6 +9,8 @@ import bz2
 from mock import patch
 import os
 from io import BytesIO
+import re
+import urlparse
 
 from Bio import Entrez
 import lxml.html
@@ -24,6 +26,19 @@ from fixtures import with_references
 # TODO: Tests for /upload.
 
 
+def get_links(data, path=None):
+    """
+    Extract all link targets, or only those targeting the specified path, from
+    the page and parse them.
+    """
+    def parse_link(link):
+        splitted = urlparse.urlsplit(link)
+        return splitted.path, urlparse.parse_qs(splitted.query)
+
+    links = [parse_link(link) for link in re.findall('href="([^"]+)"', data)]
+    return [(p, q) for p, q in links if path is None or p == path]
+
+
 @pytest.fixture
 def website():
     return create_app().test_client()
@@ -301,6 +316,22 @@ def test_check_noninteractive(website):
     assert 'Raw variant 1: deletion of 1' in r.data
 
 
+@with_references('NG_012772.1')
+def test_check_noninteractive_links(website):
+    """
+    Submitting non-interactively should have links to transcripts also
+    non-interactive.
+    """
+    r = website.get('/name-checker',
+                    query_string={'description': 'NG_012772.1:g.128del',
+                                  'standalone': '1'})
+    assert '0 Errors' in r.data
+
+    links = get_links(r.data, path='/name-checker')
+    assert len(links) >= 2
+    assert all(q['standalone'] == ['1'] for _, q in links)
+
+
 @with_references('NG_012772.1')
 def test_check_interactive_links(website):
     """
@@ -310,8 +341,10 @@ def test_check_interactive_links(website):
     r = website.get('/name-checker',
                     query_string={'description': 'NG_012772.1:g.128del'})
     assert '0 Errors' in r.data
-    assert 'href="/name-checker?description=NG_012772.1%3Ag.128del"' in r.data
-    assert 'href="/name-checker?description=NG_012772.1%28BRCA2_v001%29%3Ac.-5100del"' in r.data
+
+    links = get_links(r.data, path='/name-checker')
+    assert len(links) >= 2
+    assert all('standalone' not in q for _, q in links)
 
 
 def test_snp_converter_valid(website):