fix #2569

qiita_pet/handlers/qiita_redbiom.py

@@ -7,7 +7,6 @@
 # -----------------------------------------------------------------------------
 
 from requests import ConnectionError
-from future.utils import viewitems
 from collections import defaultdict
 import redbiom.summarize
 import redbiom.search
@@ -18,7 +17,6 @@
 
 from qiita_core.util import execute_as_transaction
 from qiita_db.util import generate_study_list_without_artifacts
-from qiita_db.study import Study
 
 from .base_handlers import BaseHandler
 
@@ -29,10 +27,10 @@ def get(self, search):
         self.render('redbiom.html')
 
     def _redbiom_metadata_search(self, query, contexts):
-        study_artifacts = defaultdict(list)
+        study_artifacts = defaultdict(lambda: defaultdict(list))
         message = ''
         try:
-            samples = redbiom.search.metadata_full(query, False)
+            redbiom_samples = redbiom.search.metadata_full(query, False)
         except ValueError:
             message = (
                 'Not a valid search: "%s", your query is too small '
@@ -43,13 +41,17 @@ def _redbiom_metadata_search(self, query, contexts):
                 'check the search help for more information on the queries.'
                 % query)
         if not message:
-            study_samples = defaultdict(list)
-            for s in samples:
-                study_samples[s.split('.', 1)[0]].append(s)
-            for sid, samps in viewitems(study_samples):
-                study_artifacts[sid] = {
-                    a.id: samps for a in Study(sid).artifacts(
-                        artifact_type='BIOM')}
+            study_artifacts = defaultdict(lambda: defaultdict(list))
+            for ctx in contexts:
+                # redbiom.fetch.data_from_samples returns a biom, which we
+                # will ignore, and a dict
+                _, data = redbiom.fetch.data_from_samples(ctx, redbiom_samples)
+                for vals in data.values():
+                    for idx in vals:
+                        print idx
+                        aid, sample_id = idx.split('_', 1)
+                        sid = sample_id.split('.', 1)[0]
+                        study_artifacts[sid][aid].append(sample_id)
 
         return message, study_artifacts
 
@@ -70,8 +72,7 @@ def _redbiom_taxon_search(self, query, contexts):
             # find the features with those taxonomies and then search
             # those features in the samples
             features = redbiom.fetch.taxon_descendents(ctx, query)
-            for idx in redbiom.util.ids_from(features, True, 'feature',
-                                             ctx):
+            for idx in redbiom.util.ids_from(features, True, 'feature', ctx):
                 aid, sample_id = idx.split('_', 1)
                 sid = sample_id.split('.', 1)[0]
                 study_artifacts[sid][aid].append(sample_id)

qiita_pet/test/test_qiita_redbiom.py

@@ -27,15 +27,13 @@ def test_post_metadata(self):
         response = self.post('/redbiom/', post_args)
         self.assertEqual(response.code, 200)
 
-        samples = ['1.SKD6.640190', '1.SKD9.640182', '1.SKD8.640184',
-                   '1.SKD5.640186', '1.SKD2.640178', '1.SKD4.640185',
-                   '1.SKD1.640179', '1.SKD3.640198', '1.SKD7.640191']
         exp_artifact_biom_ids = {
-            '5': samples, '4': samples, '7': samples, '6': samples}
+            '5': ['1.SKD2.640178'],
+            '4': ['1.SKD2.640178', '1.SKD8.640184']}
         response_body = loads(response.body)
         obs_artifact_biom_ids = response_body['data'][0].pop(
             'artifact_biom_ids')
-        self.assertItemsEqual(obs_artifact_biom_ids, exp_artifact_biom_ids)
+        self.assertDictEqual(obs_artifact_biom_ids, exp_artifact_biom_ids)
         exp = {'status': 'success', 'message': '', 'data': DATA}
         self.assertEqual(response_body, exp)