def testCreateNewKEGGVersion(self): """ Test adding one gene to an existing KEGG set """ selected_kegg_term = self.kegg_sets[1] geneset_response = loader.load_to_tribe(self.main_config_file, selected_kegg_term, prefer_update=True) self.assertEqual( geneset_response['title'], 'KEGG-Pathway-hsa00020: Citrate cycle ' '(TCA cycle) - H**o sapiens (human)') self.assertEqual(geneset_response['tip_item_count'], 10) # Adding random gene 5432 selected_kegg_term['annotations'] = { 1431: [], 1737: [], 1738: [], 1743: [], 2271: [], 3417: [], 3418: [], 3419: [], 3420: [], 3421: [], 5432: [] } version_response = loader.load_to_tribe(self.main_config_file, selected_kegg_term, prefer_update=True) self.assertEqual(len(version_response['annotations']), 11)
def testLoadGOToTribe(self): geneset_response = loader.load_to_tribe(self.main_config_file, self.go_terms[0]) self.assertEqual(geneset_response['title'], 'GO-BP-0000006:la liga') self.assertEqual(geneset_response['tip_item_count'], 3)
def testLoadKEGGToTribe(self): geneset_response = loader.load_to_tribe(self.main_config_file, self.kegg_sets[0]) self.assertEqual( geneset_response['title'], 'KEGG-Pathway-hsa00010: Glycolysis / ' 'Gluconeogenesis - H**o sapiens (human)') self.assertEqual(geneset_response['tip_item_count'], 10)
def testCreateNewDOVersion(self): """ Test adding one term and removing one term from an existing DO term """ selected_do_term = self.do_terms[1] geneset_response = loader.load_to_tribe( self.main_config_file, selected_do_term, prefer_update=True) self.assertEqual(geneset_response['title'], 'DO-0014667:disease of metabolism') self.assertEqual(geneset_response['tip_item_count'], 6) # Remove gene 5468, add random gene 4321 selected_do_term['annotations'] = { 4160: [], 8431: [], 51738: [], 5443: [], 6492: [], 4321: []} version_response = loader.load_to_tribe( self.main_config_file, selected_do_term, prefer_update=True) self.assertEqual(len(version_response['annotations']), 6)
def testCreateNewGOVersion(self): """ Test removing one gene from an existing GO term """ selected_go_term = self.go_terms[1] geneset_response = loader.load_to_tribe( self.main_config_file, selected_go_term, prefer_update=True) self.assertEqual(geneset_response['title'], 'GO-BP-0000007:european team') self.assertEqual(geneset_response['tip_item_count'], 4) # Remove gene 'A0A024R1V6' selected_go_term['annotations'] = { 'A0A024R214': [], 'A0A024QZP7': [], 'A0A024R216': []} version_response = loader.load_to_tribe( self.main_config_file, selected_go_term, prefer_update=True) self.assertEqual(len(version_response['annotations']), 3)
def testCreatingAlreadyExistingGeneset(self): """ Testing that if we try to create an already created geneset and annotations have not changed, fail gracefully. """ selected_go_term = self.go_terms[2] geneset_response = loader.load_to_tribe( self.main_config_file, selected_go_term, prefer_update=True) self.assertEqual(geneset_response['title'], 'GO-BP-0000005:premier league') self.assertEqual(geneset_response['tip_item_count'], 1) # Do not change the annotations, just try to save to Tribe again response = loader.load_to_tribe( self.main_config_file, selected_go_term, prefer_update=True) self.assertEqual(response['status_code'], 409) self.assertEqual( response['content'], 'There is already a geneset with the slug ' '"go0000005-h**o-sapiens" and annotations {\'A0A024R214\': []} ' 'saved in Tribe. A new geneset has not been saved.')
def testLoadDOToTribe(self): geneset_response = loader.load_to_tribe(self.main_config_file, self.do_terms[0]) self.assertEqual(geneset_response['title'], 'DO-374:nutrition disease') self.assertEqual(geneset_response['tip_item_count'], 6)