Merge pull request qiita-spots#2002 from josenavas/fix-1998

Fixing 1998

Author: ElDeveloper

qiita_db/test/test_util.py

@@ -729,6 +729,7 @@ def test_supported_filepath_types(self):
         self.assertItemsEqual(obs, exp)
 
 
+@qiita_test_checker()
 class UtilTests(TestCase):
     """Tests for the util functions that do not need to access the DB"""
 
@@ -813,6 +814,8 @@ def test_generate_study_list(self):
         obs_info = qdb.util.generate_study_list([1, 2, 3, 4], False)
         self.assertEqual(obs_info, exp_info)
 
+        qdb.artifact.Artifact(4).visibility = 'public'
+        exp_info[0]['status'] = 'public'
         exp_info[0]['proc_data_info'] = [{
             'data_type': '18S',
             'algorithm': 'QIIME (Pick closed-reference OTUs)',
@@ -834,7 +837,13 @@ def test_generate_study_list(self):
                         '1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
                         '1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
                         '1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
-                        '1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']}, {
+                        '1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']}]
+        obs_info = qdb.util.generate_study_list([1, 2, 3, 4], True,
+                                                public_only=True)
+        self.assertEqual(obs_info, exp_info)
+
+        exp_info[0]['proc_data_info'].extend(
+           [{
             'data_type': '18S',
             'algorithm': 'QIIME (Pick closed-reference OTUs)',
             'pid': 5,
@@ -888,7 +897,7 @@ def test_generate_study_list(self):
                         '1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
                         '1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
                         '1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192'],
-            'data_type': '16S'}]
+            'data_type': '16S'}])
 
         obs_info = qdb.util.generate_study_list([1, 2, 3, 4], True)
         self.assertEqual(obs_info, exp_info)

qiita_db/util.py

@@ -1223,7 +1223,7 @@ def supported_filepath_types(artifact_type):
         return qdb.sql_connection.TRN.execute_fetchindex()
 
 
-def generate_study_list(study_ids, build_samples):
+def generate_study_list(study_ids, build_samples, public_only=False):
     """Get general study information
 
     Parameters
@@ -1233,6 +1233,8 @@ def generate_study_list(study_ids, build_samples):
     build_samples : bool
         If true the sample information for each process artifact within each
         study will be included
+    public_only : bool, optional
+        If true, return only public BIOM artifacts. Default: false.
 
     Returns
     -------
@@ -1289,6 +1291,14 @@ def generate_study_list(study_ids, build_samples):
                 LEFT JOIN qiita.artifact_type USING (artifact_type_id)
                 WHERE artifact_type='BIOM' AND
                     study_id = qiita.study.study_id) AS artifact_biom_ts,
+    - all the BIOM visibility sorted by artifact_id that belong to the study
+            (SELECT array_agg(visibility ORDER BY artifact_id)
+                FROM qiita.study_artifact
+                LEFT JOIN qiita.artifact USING (artifact_id)
+                LEFT JOIN qiita.artifact_type USING (artifact_type_id)
+                LEFT JOIN qiita.visibility USING (visibility_id)
+                WHERE artifact_type='BIOM' AND
+                    study_id = qiita.study.study_id) AS artifact_biom_vis,
     - all the visibilities of all artifacts that belong to the study
             (SELECT array_agg(DISTINCT visibility)
                 FROM qiita.study_artifact
@@ -1352,6 +1362,13 @@ def generate_study_list(study_ids, build_samples):
                     LEFT JOIN qiita.artifact_type USING (artifact_type_id)
                     WHERE artifact_type='BIOM' AND
                         study_id = qiita.study.study_id) AS artifact_biom_ts,
+                (SELECT array_agg(visibility ORDER BY artifact_id)
+                    FROM qiita.study_artifact
+                    LEFT JOIN qiita.artifact USING (artifact_id)
+                    LEFT JOIN qiita.artifact_type USING (artifact_type_id)
+                    LEFT JOIN qiita.visibility USING (visibility_id)
+                    WHERE artifact_type='BIOM' AND
+                        study_id = qiita.study.study_id) AS artifact_biom_vis,
                 (SELECT array_agg(DISTINCT visibility)
                     FROM qiita.study_artifact
                     LEFT JOIN qiita.artifact USING (artifact_id)
@@ -1414,8 +1431,10 @@ def generate_study_list(study_ids, build_samples):
                 to_loop = zip(
                     info['artifact_biom_ids'], info['artifact_biom_dts'],
                     info['artifact_biom_ts'], info['artifact_biom_params'],
-                    info['artifact_biom_cmd'])
-                for artifact_id, dt, ts, params, cmd in to_loop:
+                    info['artifact_biom_cmd'], info['artifact_biom_vis'])
+                for artifact_id, dt, ts, params, cmd, vis in to_loop:
+                    if public_only and vis != 'public':
+                        continue
                     proc_info = {'processed_date': str(ts)}
                     proc_info['pid'] = artifact_id
                     proc_info['data_type'] = dt
@@ -1476,6 +1495,7 @@ def generate_study_list(study_ids, build_samples):
             del info["artifact_biom_ts"]
             del info["artifact_biom_params"]
             del info['artifact_biom_cmd']
+            del info['artifact_biom_vis']
 
             infolist.append(info)
 

qiita_pet/handlers/study_handlers/listing_handlers.py

@@ -88,7 +88,8 @@ def _build_study_info(user, search_type, study_proc=None, proc_samples=None):
         # No studies left so no need to continue
         return []
 
-    return generate_study_list([s.id for s in study_set], build_samples)
+    return generate_study_list([s.id for s in study_set], build_samples,
+                               public_only=(search_type == 'public'))
 
 
 class ListStudiesHandler(BaseHandler):