fix #1987

Author: antgonza

qiita_db/artifact.py

@@ -334,6 +334,15 @@ def create(cls, filepaths, artifact_type, name=None, prep_template=None,
                 qdb.sql_connection.TRN.add(sql, sql_args, many=True)
 
                 instance = cls(a_id)
+                # inheriting visibility
+                visibilities = {a.visibility for a in instance.parents}
+                # set based on the "lowest" visibility
+                if 'sandbox' in visibilities:
+                    instance.visibility = 'sandbox'
+                elif 'private' in visibilities:
+                    instance.visibility = 'private'
+                else:
+                    instance.visibility = 'public'
             else:
                 dtype_id = qdb.util.convert_to_id(prep_template.data_type(),
                                                   "data_type")

qiita_db/support_files/patches/47.sql

@@ -0,0 +1,5 @@
+-- Jan 15, 2017
+-- Inherit the status of the study to all it's artifacts.
+-- This code is much easier using python so check that patch
+
+SELECT 1;

qiita_db/support_files/patches/python_patches/47.py

@@ -0,0 +1,30 @@
+from qiita_db.study import Study
+
+
+class ForRecursion(object):
+    """for some strange reason, my guess is how we are executing the patches
+    recursion doesn't work directly so decided to use a class to make it
+    work"""
+
+    @classmethod
+    def change_status(cls, artifact, status):
+        for a in artifact.children:
+            try:
+                a.visibility = status
+            except:
+                # print so we know which changes failed and we can deal by hand
+                print "failed aid: %d, status %s" % (artifact.id, status)
+                return
+            cls.change_status(a, status)
+
+
+studies = Study.get_by_status('private').union(
+    Study.get_by_status('public')).union(Study.get_by_status('sandbox'))
+# just getting the base artifacts, no parents
+artifacts = {a for s in studies for a in s.artifacts() if not a.parents}
+
+# inheriting status
+fr = ForRecursion
+for a in artifacts:
+    status = a.visibility
+    fr.change_status(a, status)

qiita_db/test/test_artifact.py

@@ -668,7 +668,7 @@ def test_create_processed(self):
         self.assertEqual(obs.name, 'noname')
         self.assertTrue(before < obs.timestamp < datetime.now())
         self.assertEqual(obs.processing_parameters, exp_params)
-        self.assertEqual(obs.visibility, 'sandbox')
+        self.assertEqual(obs.visibility, 'private')
         self.assertEqual(obs.artifact_type, "Demultiplexed")
         self.assertEqual(obs.data_type, qdb.artifact.Artifact(1).data_type)
         self.assertTrue(obs.can_be_submitted_to_ebi)
@@ -700,7 +700,7 @@ def test_create_copy_files(self):
         self.assertEqual(obs.name, 'noname')
         self.assertTrue(before < obs.timestamp < datetime.now())
         self.assertEqual(obs.processing_parameters, exp_params)
-        self.assertEqual(obs.visibility, 'sandbox')
+        self.assertEqual(obs.visibility, 'private')
         self.assertEqual(obs.artifact_type, "Demultiplexed")
         self.assertEqual(obs.data_type, qdb.artifact.Artifact(1).data_type)
         self.assertTrue(obs.can_be_submitted_to_ebi)
@@ -732,7 +732,7 @@ def test_create_biom(self):
         self.assertEqual(obs.name, 'noname')
         self.assertTrue(before < obs.timestamp < datetime.now())
         self.assertEqual(obs.processing_parameters, exp_params)
-        self.assertEqual(obs.visibility, 'sandbox')
+        self.assertEqual(obs.visibility, 'private')
         self.assertEqual(obs.artifact_type, 'BIOM')
         self.assertEqual(obs.data_type, qdb.artifact.Artifact(2).data_type)
         self.assertFalse(obs.can_be_submitted_to_ebi)

qiita_db/test/test_util.py

@@ -98,8 +98,8 @@ def test_convert_to_id_bad_value(self):
 
     def test_get_artifact_types(self):
         obs = qdb.util.get_artifact_types()
-        exp = {'SFF': 1, 'FASTA_Sanger': 2, 'FASTQ': 3, 'FASTA': 4,
-               'per_sample_FASTQ': 5, 'Demultiplexed': 6, 'BIOM': 7}
+        exp = {'Demultiplexed': 6, 'FASTA_Sanger': 2, 'FASTQ': 3, 'BIOM': 7,
+               'per_sample_FASTQ': 5, 'SFF': 1, 'FASTA': 4}
         self.assertEqual(obs, exp)
 
         obs = qdb.util.get_artifact_types(key_by_id=True)