initial commit of pdbe engine

Adds support for queries to the Protein Data Bank Europe (PDBe).

1 files changed, 109 insertions, 0 deletions

diff --git a/tests/unit/engines/test_pdbe.py b/tests/unit/engines/test_pdbe.py
new file mode 100644
index 000000000..7aa8e2655
--- /dev/null
+++ b/tests/unit/engines/test_pdbe.py
@@ -0,0 +1,109 @@
+import mock
+from collections import defaultdict
+from searx.engines import pdbe
+from searx.testing import SearxTestCase
+
+
+class TestPdbeEngine(SearxTestCase):
+    def test_request(self):
+        query = 'test_query'
+        dicto = defaultdict(dict)
+        params = pdbe.request(query, dicto)
+        self.assertTrue('url' in params)
+        self.assertTrue('ebi.ac.uk' in params['url'])
+        self.assertTrue('data' in params)
+        self.assertTrue('q' in params['data'])
+        self.assertTrue(query in params['data']['q'])
+        self.assertTrue('wt' in params['data'])
+        self.assertTrue('json' in params['data']['wt'])
+        self.assertTrue('method' in params)
+        self.assertTrue(params['method'] == 'POST')
+
+    def test_response(self):
+        self.assertRaises(AttributeError, pdbe.response, None)
+        self.assertRaises(AttributeError, pdbe.response, [])
+        self.assertRaises(AttributeError, pdbe.response, '')
+        self.assertRaises(AttributeError, pdbe.response, '[]')
+
+        json = """
+{
+  "response": {
+    "docs": [
+      {
+        "citation_title": "X-ray crystal structure of ferric Aplysia limacina myoglobin in different liganded states.",
+        "citation_year": 1993,
+        "entry_author_list": [
+          "Conti E, Moser C, Rizzi M, Mattevi A, Lionetti C, Coda A, Ascenzi P, Brunori M, Bolognesi M"
+        ],
+        "journal": "J. Mol. Biol.",
+        "journal_page": "498-508",
+        "journal_volume": "233",
+        "pdb_id": "2fal",
+        "status": "REL",
+        "title": "X-RAY CRYSTAL STRUCTURE OF FERRIC APLYSIA LIMACINA MYOGLOBIN IN DIFFERENT LIGANDED STATES"
+      }
+    ],
+    "numFound": 1,
+    "start": 0
+  },
+  "responseHeader": {
+    "QTime": 0,
+    "params": {
+      "q": "2fal",
+      "wt": "json"
+    },
+    "status": 0
+  }
+}
+"""
+
+        response = mock.Mock(text=json)
+        results = pdbe.response(response)
+        self.assertEqual(type(results), list)
+        self.assertEqual(len(results), 1)
+        self.assertEqual(results[0]['title'],
+                         'X-RAY CRYSTAL STRUCTURE OF FERRIC APLYSIA LIMACINA MYOGLOBIN IN DIFFERENT LIGANDED STATES')
+        self.assertEqual(results[0]['url'], pdbe.pdbe_entry_url.format(pdb_id='2fal'))
+        self.assertEqual(results[0]['img_src'], pdbe.pdbe_preview_url.format(pdb_id='2fal'))
+        self.assertTrue('Conti E' in results[0]['content'])
+        self.assertTrue('X-ray crystal structure of ferric Aplysia limacina myoglobin in different liganded states.' in
+                        results[0]['content'])
+        self.assertTrue('1993' in results[0]['content'])
+
+        # Testing proper handling of PDB entries marked as obsolete
+        json = """
+{
+  "response": {
+    "docs": [
+      {
+        "citation_title": "Obsolete entry test",
+        "citation_year": 2016,
+        "entry_author_list": ["Doe J"],
+        "journal": "J. Obs.",
+        "journal_page": "1-2",
+        "journal_volume": "1",
+        "pdb_id": "xxxx",
+        "status": "OBS",
+        "title": "OBSOLETE ENTRY TEST",
+        "superseded_by": "yyyy"
+      }
+    ],
+    "numFound": 1,
+    "start": 0
+  },
+  "responseHeader": {
+    "QTime": 0,
+    "params": {
+      "q": "xxxx",
+      "wt": "json"
+    },
+    "status": 0
+  }
+}
+"""
+        response = mock.Mock(text=json)
+        results = pdbe.response(response)
+        self.assertEqual(type(results), list)
+        self.assertEqual(len(results), 1)
+        self.assertEqual(results[0]['title'], 'OBSOLETE ENTRY TEST (OBSOLETE)')
+        self.assertTrue(results[0]['content'].startswith('<em>This entry has been superseded by'))