Merge pull request #45 from MoffMade/4.2.9

4.2.9 bump, update_organism bugfix

README.rst

@@ -85,6 +85,8 @@ Or with the Arrow client:
 History
 -------
 
+- 4.2.9
+    - Bugfix to  update_organism when using suppress_output
 - 4.2.8
     - Added --suppress_output to update_organism
 - 4.2.7

apollo/organisms/__init__.py

@@ -125,11 +125,13 @@ def update_organism(self, organism_id, common_name, directory, blatdb=None, spec
         if suppress_output is not None and suppress_output is True:
             data['returnAllOrganisms'] = False
 
-        response = self.post('updateOrganismInfo', data)[0]
-
-        if len(response.keys()) == 0:
-            return self.show_organism(organism_id)
-        return response
+        response = self.post('updateOrganismInfo', data)
+        if type(response) is not list:
+            return response
+        if len(response) > 0:
+            return [x for x in response if x['commonName'] == common_name][0]
+        else:
+            return self.show_organism(common_name)
 
     def get_organisms(self, common_name=None):
         """

setup.py

@@ -16,7 +16,7 @@
 
 setup(
     name="apollo",
-    version='4.2.8',
+    version='4.2.9',
     description="Apollo API library",
     long_description=readme,
     author="Helena Rasche;Anthony Bretaudeau;Nathan Dunn",

test/organism_test.py

@@ -119,6 +119,19 @@ def test_delete_organism_cn(self):
         for org in orgs:
             assert org['commonName'] != 'temp_org'
 
+    def test_delete_organism_suppress(self):
+
+        org_info = self.waitOrgCreated('temp_org')
+
+        wa.organisms.delete_organism(org_info['id'], suppress_output=True)
+
+        self.waitOrgDeleted('temp_org')
+
+        orgs = wa.organisms.get_organisms()
+
+        for org in orgs:
+            assert org['commonName'] != 'temp_org'
+
     def test_delete_features(self):
 
         wa.annotations.load_gff3('temp_org', 'test-data/merlin.gff')
@@ -317,6 +330,31 @@ def test_update_organism_changedseq_noreload(self):
         assert seq['name'] == 'Merlin'
         assert seq['length'] == 172788
 
+    def test_update_organism_suppress(self):
+
+        other_org_info = wa.organisms.show_organism('test_organism')
+
+        org_info = wa.organisms.show_organism('temp_org')
+
+        wa.organisms.update_organism(org_info['id'], 'temp_org', other_org_info['directory'], species='updatedspecies', genus='updatedgenus', blatdb=other_org_info['directory'] + "/seq/genome.2bit", public=False, suppress_output=True)
+        # Returns useless stuff
+
+        time.sleep(3)
+        org_info = wa.organisms.show_organism('temp_org')
+
+        assert org_info['species'] == 'updatedspecies'
+        assert org_info['genus'] == 'updatedgenus'
+        assert org_info['blatdb'] == other_org_info['directory'] + "/seq/genome.2bit"
+        assert not org_info['publicMode']
+        assert org_info['sequences'] == 1
+
+        seqs = wa.organisms.get_sequences(org_info['id'])['sequences']
+        assert len(seqs) == 1
+
+        seq = seqs[0]
+        assert seq['name'] == 'Merlin'
+        assert seq['length'] == 172788
+
     def test_add_organism(self):
 
         org_info = wa.organisms.show_organism('test_organism')
@@ -341,6 +379,30 @@ def test_add_organism(self):
         meta_back = json.loads(org_info['metadata'])
         assert 'bla' in meta_back and meta_back['bla'] == 'bli'
 
+    def test_add_organism_suppress(self):
+
+        org_info = wa.organisms.show_organism('test_organism')
+
+        meta = {"bla": "bli"}
+        res = wa.organisms.add_organism('some_new_org', org_info['directory'], species='newspecies', genus='newgenus', blatdb=org_info['directory'] + "/seq/genome.2bit", metadata=meta, suppress_output=True)
+
+        assert res['species'] == 'newspecies'
+        assert res['genus'] == 'newgenus'
+        assert res['blatdb'] == org_info['directory'] + "/seq/genome.2bit"
+        meta_back = json.loads(res['metadata'])
+        assert 'bla' in meta_back and meta_back['bla'] == 'bli'
+
+        org_info = self.waitOrgCreated('some_new_org')
+
+        wa.organisms.delete_organism(org_info['id'])
+
+        assert org_info['species'] == 'newspecies'
+        assert org_info['genus'] == 'newgenus'
+        assert org_info['blatdb'] == org_info['directory'] + "/seq/genome.2bit"
+        assert not org_info['publicMode']
+        meta_back = json.loads(org_info['metadata'])
+        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')