Implement a encoded search to json-ld wrapper.

[htsworkflow.git] / htsworkflow / submission / test / test_encoded.py

diff --git a/htsworkflow/submission/test/test_encoded.py b/htsworkflow/submission/test/test_encoded.py
index 21eed840e351a64fdbe47fcd6d48e192d07aafb3..675d944a4bc0bb33e1e1b78be7ba4608da64d511 100644 (file)
--- a/htsworkflow/submission/test/test_encoded.py
+++ b/htsworkflow/submission/test/test_encoded.py
@@ -66,6 +66,7 @@ class TestEncoded(TestCase):
         encode = ENCODED('test.encodedcc.org')
         url = encode.prepare_url(library['@id'])
         context = encode.create_jsonld_context(library, url)
+        self.assertEqual(context['@vocab'], 'http://test.encodedcc.org/profiles/library.json#')
         self.assertEqual(context['award'], linked_id )
         self._verify_context(context, 'library')
         # namespaces not added yet.
@@ -121,6 +122,51 @@ class TestEncoded(TestCase):
         self.assertEqual(obj['@context']['OBO'], 'http://purl.obolibrary.org/obo/')
 
 
+    def test_convert_search_to_jsonld(self):
+        example = {'count': {'biosamples': 2},
+                   'portal_title': 'ENCODE',
+                   'title': 'Search',
+                   'notification': 'Success',
+                   'filters': [],
+                   '@id': '/search/?searchTerm=wold',
+                   '@type': ['search'],
+                   'facets': [],
+                    '@graph': [{
+                    u'@id': u'/biosamples/ENCBS125ENC/',
+                    u'@type': [u'biosample', u'item'],
+                    u'accession': u'ENCBS125ENC',
+                    u'award.rfa': u'ENCODE2-Mouse',
+                    u'biosample_term_name': u'myocyte',
+                    u'biosample_type': u'in vitro differentiated cells',
+                    u'characterizations.length': [],
+                    u'constructs.length': [],
+                    u'lab.title': u'Barbara Wold, Caltech',
+                    u'life_stage': u'unknown',
+                    u'organism.name': u'mouse',
+                    u'source.title': u'Barbara Wold',
+                    u'status': u'CURRENT',
+                    u'treatments.length': []},
+                    {u'@id': u'/biosamples/ENCBS126ENC/',
+                    u'@type': [u'biosample', u'item'],
+                    u'accession': u'ENCBS126ENC',
+                    u'award.rfa': u'ENCODE2-Mouse',
+                    u'biosample_term_name': u'myocyte',
+                    u'biosample_type': u'in vitro differentiated cells',
+                    u'characterizations.length': [],
+                    u'constructs.length': [],
+                    u'lab.title': u'Barbara Wold, Caltech',
+                    u'life_stage': u'unknown',
+                    u'organism.name': u'mouse',
+                    u'source.title': u'Barbara Wold',
+                    u'status': u'CURRENT',
+                    u'treatments.length': []},
+                    ]}
+
+        encode = ENCODED('test.encodedcc.org')
+        result = encode.convert_search_to_jsonld(example)
+        for obj in result['@graph']:
+            self.assertNotIn('award.rfa', obj)
+
     def _verify_context(self, context, obj_type):
         for context_key in [None, obj_type]:
             for k in ENCODED_CONTEXT[context_key]: