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)