better method to wait for organism creation/deletion

test/__init__.py

@@ -1,3 +1,4 @@
+import time
 import unittest
 
 from arrow.apollo import get_apollo_instance
@@ -9,4 +10,23 @@ def setup_package():
 
 
 class ApolloTestCase(unittest.TestCase):
-    pass
+
+    def waitOrgDeleted(self, org_id):
+        """
+        Wait for an organism to be really deleted from Apollo
+        """
+
+        org_info = wa.organisms.show_organism(org_id)
+        if 'directory' in org_info:
+            time.sleep(1)
+            org_info = wa.organisms.show_organism(org_id)
+
+    def waitOrgCreated(self, org_id):
+        """
+        Wait for an organism to be really created from Apollo
+        """
+
+        org_info = wa.organisms.show_organism(org_id)
+        if 'directory' in org_info:
+            time.sleep(1)
+            org_info = wa.organisms.show_organism(org_id)

test/organism_test.py

@@ -94,13 +94,11 @@ def test_update_metadata(self):
 
     def test_delete_organism(self):
 
-        time.sleep(3)
-
         org_info = wa.organisms.show_organism('temp_org')
 
         wa.organisms.delete_organism(org_info['id'])
 
-        time.sleep(3)
+        self.waitOrgDeleted('temp_org')
 
         orgs = wa.organisms.get_organisms()
 
@@ -109,11 +107,9 @@ def test_delete_organism(self):
 
     def test_delete_organism_cn(self):
 
-        time.sleep(3)
-
         wa.organisms.delete_organism('temp_org')
 
-        time.sleep(3)
+        self.waitOrgDeleted('temp_org')
 
         orgs = wa.organisms.get_organisms()
 
@@ -122,8 +118,6 @@ def test_delete_organism_cn(self):
 
     def test_delete_features(self):
 
-        time.sleep(3)
-
         wa.annotations.load_gff3('temp_org', 'test-data/merlin.gff')
 
         org_info = wa.organisms.show_organism('temp_org')
@@ -142,8 +136,6 @@ def test_delete_features(self):
 
     def test_delete_features_cn(self):
 
-        time.sleep(3)
-
         wa.annotations.load_gff3('temp_org', 'test-data/merlin.gff')
 
         org_info = wa.organisms.show_organism('temp_org')
@@ -335,7 +327,7 @@ def test_add_organism(self):
         meta_back = json.loads(res['metadata'])
         assert 'bla' in meta_back and meta_back['bla'] == 'bli'
 
-        time.sleep(3)
+        self.waitOrgCreated('some_new_org')
 
         org_info = wa.organisms.show_organism('some_new_org')
 
@@ -349,6 +341,12 @@ def test_add_organism(self):
         assert 'bla' in meta_back and meta_back['bla'] == 'bli'
 
     def setUp(self):
+        # Make sure the organism is not already there
+        temp_org_info = wa.organisms.show_organism('temp_org')
+        if 'directory' in temp_org_info:
+            wa.organisms.delete_organism(temp_org_info['id'])
+            self.waitOrgDeleted('temp_org')
+
         org_info = wa.organisms.show_organism('alt_org')
         if 'directory' not in org_info:
             # Should not happen, but let's be tolerant...
@@ -357,14 +355,18 @@ def setUp(self):
             org_info = wa.organisms.show_organism('alt_org')
 
         wa.organisms.add_organism('temp_org', org_info['directory'])
+        self.waitOrgCreated('temp_org')
 
     def tearDown(self):
         org_info = wa.organisms.show_organism('temp_org')
 
         if org_info and 'id' in org_info:
             wa.organisms.delete_organism(org_info['id'])
 
+        self.waitOrgDeleted('temp_org')
+
         org_info = wa.organisms.show_organism('some_new_org')
 
         if org_info and 'id' in org_info:
             wa.organisms.delete_organism(org_info['id'])
+            self.waitOrgDeleted('some_new_org')

test/remote_test.py

@@ -11,13 +11,11 @@ class RemoteTest(ApolloTestCase):
 
     def test_delete_organism(self):
 
-        time.sleep(3)
-
         org_info = wa.organisms.show_organism('temp_org')
 
         wa.remote.delete_organism(org_info['id'])
 
-        time.sleep(3)
+        self.waitOrgDeleted('temp_org')
 
         orgs = wa.organisms.get_organisms()
 
@@ -26,11 +24,9 @@ def test_delete_organism(self):
 
     def test_delete_organism_cn(self):
 
-        time.sleep(3)
-
         wa.remote.delete_organism('temp_org')
 
-        time.sleep(3)
+        self.waitOrgDeleted('temp_org')
 
         orgs = wa.organisms.get_organisms()
 
@@ -39,9 +35,8 @@ def test_delete_organism_cn(self):
 
     def test_update_organism(self):
 
-        time.sleep(3)
-
         org_info = wa.organisms.show_organism('temp_org')
+        assert org_info['sequences'] == 1
 
         meta = {"bla": "bli"}
 
@@ -71,9 +66,8 @@ def test_update_organism(self):
 
     def test_update_organism_noreload(self):
 
-        time.sleep(3)
-
         org_info = wa.organisms.show_organism('temp_org')
+        assert org_info['sequences'] == 1
 
         meta = {"bla": "bli"}
 
@@ -103,9 +97,8 @@ def test_update_organism_noreload(self):
 
     def test_update_organism_newseq(self):
 
-        time.sleep(3)
-
         org_info = wa.organisms.show_organism('temp_org')
+        assert org_info['sequences'] == 1
 
         meta = {"bla": "bli"}
 
@@ -130,18 +123,17 @@ def test_update_organism_newseq(self):
         assert len(seqs) == 2
 
         seq = seqs[0]
-        assert seq['name'] == 'Merlin'
-        assert seq['length'] == 172788
-
-        seq = seqs[1]
         assert seq['name'] == 'Anotherseq'
         assert seq['length'] == 4730
 
-    def test_update_organism_changedseq(self):
+        seq = seqs[1]
+        assert seq['name'] == 'Merlin'
+        assert seq['length'] == 172788
 
-        time.sleep(3)
+    def test_update_organism_changedseq(self):
 
         org_info = wa.organisms.show_organism('temp_org')
+        assert org_info['sequences'] == 1
 
         meta = {"bla": "bli"}
 
@@ -166,18 +158,17 @@ def test_update_organism_changedseq(self):
         assert len(seqs) == 2
 
         seq = seqs[0]
-        assert seq['name'] == 'Merlin'
-        assert seq['length'] == 172188
-
-        seq = seqs[1]
         assert seq['name'] == 'Anotherseq'
         assert seq['length'] == 4730
 
-    def test_update_organism_newseq_noreload(self):
+        seq = seqs[1]
+        assert seq['name'] == 'Merlin'
+        assert seq['length'] == 172188
 
-        time.sleep(3)
+    def test_update_organism_newseq_noreload(self):
 
         org_info = wa.organisms.show_organism('temp_org')
+        assert org_info['sequences'] == 1
 
         meta = {"bla": "bli"}
 
@@ -207,9 +198,8 @@ def test_update_organism_newseq_noreload(self):
 
     def test_update_organism_changedseq_noreload(self):
 
-        time.sleep(3)
-
         org_info = wa.organisms.show_organism('temp_org')
+        assert org_info['sequences'] == 1
 
         meta = {"bla": "bli"}
 
@@ -254,14 +244,16 @@ def test_add_organism(self):
         meta_back = json.loads(res['metadata'])
         assert 'bla' in meta_back and meta_back['bla'] == 'bli'
 
-        time.sleep(3)
+        self.waitOrgCreated('some_new_org_remote')
 
         org_info = wa.organisms.show_organism('some_new_org_remote')
 
         wa.remote.delete_organism(org_info['id'])
+        self.waitOrgDeleted('some_new_org_remote')
 
         assert org_info['species'] == 'newspecies'
         assert org_info['genus'] == 'newgenus'
+        assert org_info['sequences'] == 1
         meta_back = json.loads(org_info['metadata'])
         assert 'bla' in meta_back and meta_back['bla'] == 'bli'
 
@@ -281,7 +273,10 @@ def tearDown(self):
         if org_info and 'id' in org_info:
             wa.organisms.delete_organism(org_info['id'])
 
+        self.waitOrgDeleted('temp_org')
+
         org_info = wa.organisms.show_organism('some_new_org_remote')
 
         if org_info and 'id' in org_info:
             wa.organisms.delete_organism(org_info['id'])
+            self.waitOrgDeleted('some_new_org_remote')