Fix 2689

qiita_db/meta_util.py

@@ -301,41 +301,36 @@ def sizeof_fmt(value, position):
 
 
 def get_lat_longs():
-    """Retrieve the latitude and longitude of all the samples in the DB
+    """Retrieve the latitude and longitude of all the public samples in the DB
 
     Returns
     -------
     list of [float, float]
         The latitude and longitude for each sample in the database
     """
-    portal_table_ids = [
-        s.id for s in qdb.portal.Portal(qiita_config.portal).get_studies()]
-
     with qdb.sql_connection.TRN:
-        # getting all tables in the portal
-        sql = """SELECT DISTINCT table_name
-                 FROM information_schema.columns
-                 WHERE table_name SIMILAR TO 'sample_[0-9]+'
-                    AND SPLIT_PART(table_name, '_', 2)::int IN %s
-                    AND table_schema = 'qiita'"""
-        qdb.sql_connection.TRN.add(sql, [tuple(portal_table_ids)])
-
-        # we are going to create multiple union selects to retrieve the
-        # latigute and longitude of all available studies. Note that UNION in
-        # PostgreSQL automatically removes duplicates
-        sql_query = """
-            SELECT CAST(sample_values->>'latitude' AS FLOAT),
-                   CAST(sample_values->>'longitude' AS FLOAT)
-            FROM qiita.%s
-            WHERE isnumeric(sample_values->>'latitude') AND
-                  isnumeric(sample_values->>'longitude')"""
-        sql = [sql_query % s
-               for s in qdb.sql_connection.TRN.execute_fetchflatten()]
-        sql = ' UNION '.join(sql)
-        qdb.sql_connection.TRN.add(sql)
-
-        # note that we are returning set to remove duplicates
-        return qdb.sql_connection.TRN.execute_fetchindex()
+        # getting all the public studies
+        studies = qdb.study.Study.get_by_status('public')
+
+        results = []
+        if studies:
+            # we are going to create multiple union selects to retrieve the
+            # latigute and longitude of all available studies. Note that
+            # UNION in PostgreSQL automatically removes duplicates
+            sql_query = """
+                SELECT CAST(sample_values->>'latitude' AS FLOAT),
+                       CAST(sample_values->>'longitude' AS FLOAT)
+                FROM qiita.sample_%d
+                WHERE isnumeric(sample_values->>'latitude') AND
+                      isnumeric(sample_values->>'longitude')"""
+            sql = [sql_query % s.id for s in studies]
+            sql = ' UNION '.join(sql)
+            qdb.sql_connection.TRN.add(sql)
+
+            # note that we are returning set to remove duplicates
+            results = qdb.sql_connection.TRN.execute_fetchindex()
+
+        return results
 
 
 def generate_biom_and_metadata_release(study_status='public'):

qiita_db/test/test_meta_util.py

@@ -137,6 +137,14 @@ def test_validate_filepath_access_by_user(self):
         qdb.study.Study.delete(study.id)
 
     def test_get_lat_longs(self):
+        # no public studies should return an empty array
+        obs = qdb.meta_util.get_lat_longs()
+        self.assertItemsEqual(obs, [])
+
+        old_visibility = {}
+        for pt in qdb.study.Study(1).prep_templates():
+            old_visibility[pt] = pt.artifact.visibility
+            pt.artifact.visibility = 'public'
         exp = [
             [74.0894932572, 65.3283470202],
             [57.571893782, 32.5563076447],
@@ -163,10 +171,12 @@ def test_get_lat_longs(self):
             [95.2060749748, 27.3592668624],
             [78.3634273709, 74.423907894],
             [38.2627021402, 3.48274264219]]
-
         obs = qdb.meta_util.get_lat_longs()
         self.assertItemsEqual(obs, exp)
 
+        for k, v in old_visibility.iteritems():
+            k.artifact.visibility = v
+
     def test_get_lat_longs_EMP_portal(self):
         info = {
             'timeseries_type_id': 1,
@@ -206,7 +216,7 @@ def test_get_lat_longs_EMP_portal(self):
         qiita_config.portal = 'EMP'
 
         obs = qdb.meta_util.get_lat_longs()
-        exp = [[42.42, 41.41]]
+        exp = []
 
         self.assertItemsEqual(obs, exp)
         qdb.metadata_template.sample_template.SampleTemplate.delete(st.id)
@@ -222,7 +232,7 @@ def test_update_redis_stats(self):
             ('number_of_samples', {'sandbox': '0', 'public': '0',
                                    'private': '27'}, r_client.hgetall),
             ('num_users', '4', r_client.get),
-            ('lat_longs', EXP_LAT_LONG, r_client.get),
+            ('lat_longs', '[]', r_client.get),
             ('num_studies_ebi', '1', r_client.get),
             ('num_samples_ebi', '27', r_client.get),
             ('number_samples_ebi_prep', '54', r_client.get),
@@ -394,21 +404,5 @@ def test_generate_biom_and_metadata_release(self):
                     bdr = qdb.sql_connection.TRN.execute()
 
 
-EXP_LAT_LONG = (
-    '[[60.1102854322, 74.7123248382], [23.1218032799, 42.838497795],'
-    ' [3.21190859967, 26.8138925876], [74.0894932572, 65.3283470202],'
-    ' [53.5050692395, 31.6056761814], [12.6245524972, 96.0693176066],'
-    ' [43.9614715197, 82.8516734159], [10.6655599093, 70.784770579],'
-    ' [78.3634273709, 74.423907894], [82.8302905615, 86.3615778099],'
-    ' [44.9725384282, 66.1920014699], [4.59216095574, 63.5115213108],'
-    ' [57.571893782, 32.5563076447], [40.8623799474, 6.66444220187],'
-    ' [95.2060749748, 27.3592668624], [38.2627021402, 3.48274264219],'
-    ' [13.089194595, 92.5274472082], [84.0030227585, 66.8954849864],'
-    ' [68.51099627, 2.35063674718], [29.1499460692, 82.1270418227],'
-    ' [35.2374368957, 68.5041623253], [12.7065957714, 84.9722975792],'
-    ' [0.291867635913, 68.5945325743], [85.4121476399, 15.6526750776],'
-    ' [68.0991287718, 34.8360987059]]')
-
-
 if __name__ == '__main__':
     main()