dkoslicki
commented
2 months ago @mohsenht Can you take a look at this?
Closed edeutsch closed 2 months ago
dkoslicki
commented
2 months ago @mohsenht Can you take a look at this?
mohsenht
commented
2 months ago @edeutsch Do you have failure logs for these tests?
edeutsch
commented
2 months ago I do, but they're pretty huge. Are you able to repro?
_______________________________________________________________________________________ test_glucose_diabetes _______________________________________________________________________________________
def test_glucose_diabetes():
query = {"operations": {"actions": [
"create_message",
"add_qnode(name=CHEBI:37626, key=n0)",
"add_qnode(name=MONDO:0005015, key=n1)",
"connect(action=connect_nodes, max_path_length=3)",
"filter_results(action=limit_number_of_results, max_results=30)",
"return(message=true, store=true)"
]}}
[response, message] = _do_arax_query(query)
assert response.status == 'OK'
> assert len(message.query_graph.edges) == 3
E AssertionError: assert 0 == 3
E + where 0 = len({})
E + where {} = {'edges': {},\n 'nodes': {'n0': {'categories': None,\n 'constraints': [],\n 'ids': ['CHEBI:37626'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'},\n 'n1': {'categories': None,\n 'constraints': [],\n 'ids': ['MONDO:0005015'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'}}}.edges
E + where {'edges': {},\n 'nodes': {'n0': {'categories': None,\n 'constraints': [],\n 'ids': ['CHEBI:37626'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'},\n 'n1': {'categories': None,\n 'constraints': [],\n 'ids': ['MONDO:0005015'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'}}} = {'auxiliary_graphs': None,\n 'knowledge_graph': {'edges': {}, 'nodes': {}},\n 'query_graph': {'edges': {},\n 'nodes': {'n0': {'categories': None,\n 'constraints': [],\n 'ids': ['CHEBI:37626'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'},\n 'n1': {'categories': None,\n 'constraints': [],\n 'ids': ['MONDO:0005015'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'}}},\n 'results': []}.query_graph
test_ARAX_connect.py:135: AssertionError
--------------------------------------------------------------------------------------- Captured stdout call ---------------------------------------------------------------------------------------No I can't reproduce it.
mohsenht
commented
2 months ago @edeutsch
Could you please confirm if you can see this error on the failure log?
"ERROR: Could not find main node id name to fill essence variable!"
edeutsch
commented
2 months ago Here's what I see:
======================================================================================== test session starts ========================================================================================
platform linux -- Python 3.9.18, pytest-7.2.2, pluggy-1.3.0 -- /usr/bin/python3.9
cachedir: .pytest_cache
rootdir: /mnt/data/orangeboard/test/RTX/code/ARAX/test
plugins: cov-4.1.0
collected 4 items
test_ARAX_connect.py::test_connect_ulcerative_colitis_to_adalimumab FAILED [ 25%]
test_ARAX_connect.py::test_connect_resveratrol_glyoxalase FAILED [ 50%]
test_ARAX_connect.py::test_connect_pde5i_alzheimer SKIPPED (need --runslow option to run) [ 75%]
test_ARAX_connect.py::test_glucose_diabetes FAILED [100%]
============================================================================================= FAILURES ==============================================================================================
___________________________________________________________________________ test_connect_ulcerative_colitis_to_adalimumab ___________________________________________________________________________
def test_connect_ulcerative_colitis_to_adalimumab():
query = {"operations": {"actions": [
"create_message",
"add_qnode(ids=MONDO:0005101, key=n00)",
"add_qnode(ids=UNII:FYS6T7F842, key=n01)",
"connect(action=connect_nodes, max_path_length=3)",
"return(message=true, store=false)"
]}}
[response, message] = _do_arax_query(query)
assert response.status == 'OK'
> assert len(message.query_graph.edges) == 3
E AssertionError: assert 0 == 3
E + where 0 = len({})
E + where {} = {'edges': {},\n 'nodes': {'n00': {'categories': None,\n 'constraints': [],\n 'ids': ['MONDO:0005101'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'},\n 'n01': {'categories': None,\n 'constraints': [],\n 'ids': ['UNII:FYS6T7F842'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'}}}.edges
E + where {'edges': {},\n 'nodes': {'n00': {'categories': None,\n 'constraints': [],\n 'ids': ['MONDO:0005101'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'},\n 'n01': {'categories': None,\n 'constraints': [],\n 'ids': ['UNII:FYS6T7F842'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'}}} = {'auxiliary_graphs': None,\n 'knowledge_graph': {'edges': {}, 'nodes': {}},\n 'query_graph': {'edges': {},\n 'nodes': {'n00': {'categories': None,\n 'constraints': [],\n 'ids': ['MONDO:0005101'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'},\n 'n01': {'categories': None,\n 'constraints': [],\n 'ids': ['UNII:FYS6T7F842'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'}}},\n 'results': []}.query_graph
test_ARAX_connect.py:93: AssertionError
--------------------------------------------------------------------------------------- Captured stderr call ----------------------------------------------------------------------------------------
2024-09-25T18:28:06.935869 INFO: (975536) [] ARAX Query launching on incoming Query
2024-09-25T18:28:06.935950 DEBUG: (975536) [] RTXConfiguration says maturity=development, current_branch=master, is_itrb_instance=False, arax_version=1.5.3, trapi_version=1.5.0
2024-09-25T18:28:06.935983 INFO: (975536) [] Creating an empty template TRAPI Response
2024-09-25T18:28:06.936134: DEBUG: In BiolinkHelper init
2024-09-25T18:28:06.938196: DEBUG: Loading BL lookup map...
2024-09-25T18:28:06.938245: DEBUG: Loading pickle file: /mnt/data/orangeboard/test/RTX/code/ARAX/BiolinkHelper/biolink_lookup_map_4.2.1_v4.pickle
2024-09-25T18:28:06.939959: DEBUG: Done loading BL lookup map
2024-09-25T18:28:06.943638 INFO: (975536) [] Examine input Query for needed information for dispatch
2024-09-25T18:28:06.943689 INFO: (975536) [] Found input processing plan. Sending to the ProcessingPlanExecutor
2024-09-25T18:28:06.943717 DEBUG: (975536) [] Entering execute_processing_plan
2024-09-25T18:28:06.943802 DEBUG: (975536) [] Connecting to ResponseCache
2024-09-25T18:28:06.998533 DEBUG: (975536) [] Creating ARAXMessenger instance
2024-09-25T18:28:06.998644 DEBUG: (975536) [] No starting messages were referenced. Will start with a blank template Message
2024-09-25T18:28:06.998686 INFO: (975536) [] Creating an empty template TRAPI Response
2024-09-25T18:28:06.998785: DEBUG: In BiolinkHelper init
2024-09-25T18:28:07.002907: DEBUG: Loading BL lookup map...
2024-09-25T18:28:07.003008: DEBUG: Loading pickle file: /mnt/data/orangeboard/test/RTX/code/ARAX/BiolinkHelper/biolink_lookup_map_4.2.1_v4.pickle
2024-09-25T18:28:07.006198: DEBUG: Done loading BL lookup map
2024-09-25T18:28:07.012391 DEBUG: (975536) [] Found actions
2024-09-25T18:28:07.012476 INFO: (975536) [] Parsing input actions list
2024-09-25T18:28:07.012519 DEBUG: (975536) [] Parsing action: create_message
2024-09-25T18:28:07.013060 DEBUG: (975536) [] Parsing action: add_qnode(ids=MONDO:0005101, key=n00)
2024-09-25T18:28:07.013698 DEBUG: (975536) [] Parsing action: add_qnode(ids=UNII:FYS6T7F842, key=n01)
2024-09-25T18:28:07.013777 DEBUG: (975536) [] Parsing action: connect(action=connect_nodes, max_path_length=3)
2024-09-25T18:28:07.013845 DEBUG: (975536) [] Parsing action: return(message=true, store=false)
2024-09-25T18:28:07.114415: DEBUG: In BiolinkHelper init
2024-09-25T18:28:07.116538: DEBUG: Loading BL lookup map...
2024-09-25T18:28:07.116588: DEBUG: Loading pickle file: /mnt/data/orangeboard/test/RTX/code/ARAX/BiolinkHelper/biolink_lookup_map_4.2.1_v4.pickle
2024-09-25T18:28:07.118273: DEBUG: Done loading BL lookup map
2024-09-25T18:28:07.118690 INFO: (975536) [] Processing action 'create_message' with parameters None
2024-09-25T18:28:07.118736 INFO: (975536) [] Creating an empty template TRAPI Response
2024-09-25T18:28:07.118798: DEBUG: In BiolinkHelper init
2024-09-25T18:28:07.120759: DEBUG: Loading BL lookup map...
2024-09-25T18:28:07.120806: DEBUG: Loading pickle file: /mnt/data/orangeboard/test/RTX/code/ARAX/BiolinkHelper/biolink_lookup_map_4.2.1_v4.pickle
2024-09-25T18:28:07.123323: DEBUG: Done loading BL lookup map
2024-09-25T18:28:07.125630 INFO: (975536) [] Processing action 'add_qnode' with parameters {'ids': 'MONDO:0005101', 'key': 'n00'}
2024-09-25T18:28:07.125689 INFO: (975536) [] Adding a QueryNode to Message with input parameters {'key': 'n00', 'ids': 'MONDO:0005101', 'name': None, 'categories': None, 'is_set': None, 'option_group_id': None}
2024-09-25T18:28:07.126047 DEBUG: (975536) [] Looking up ids ['MONDO:0005101'] in NodeSynonymizer
2024-09-25T18:28:07.126597 INFO: (975536) [] Processing action 'add_qnode' with parameters {'ids': 'UNII:FYS6T7F842', 'key': 'n01'}
2024-09-25T18:28:07.126648 INFO: (975536) [] Adding a QueryNode to Message with input parameters {'key': 'n01', 'ids': 'UNII:FYS6T7F842', 'name': None, 'categories': None, 'is_set': None, 'option_group_id': None}
2024-09-25T18:28:07.126867 DEBUG: (975536) [] Looking up ids ['UNII:FYS6T7F842'] in NodeSynonymizer
2024-09-25T18:28:07.127248 INFO: (975536) [] Processing action 'connect' with parameters {'action': 'connect_nodes', 'max_path_length': '3'}
2024-09-25T18:28:07.127916 INFO: (975536) [] Finding paths process has started
2024-09-25T18:28:07.411760 WARNING: (975536) [] Path UNII:FYS6T7F842_2 raised an exception: unable to open database file, db path: /mnt/data/orangeboard/test/RTX/code/ARAX/KnowledgeSources/NormalizedGoogleDistance/curie_ngd_v1.0_KG2.10.0.sqlite
2024-09-25T18:28:07.412336 WARNING: (975536) [] Path MONDO:0005101_1 raised an exception: unable to open database file, db path: /mnt/data/orangeboard/test/RTX/code/ARAX/KnowledgeSources/NormalizedGoogleDistance/curie_ngd_v1.0_KG2.10.0.sqlite
2024-09-25T18:28:07.452397 DEBUG: (975536) [] PathFinder found 0 paths
2024-09-25T18:28:07.452484 WARNING: (975536) [] Could not connect the nodes n01 and n00 with a max path length of 3.
2024-09-25T18:28:07.452964 DEBUG: (975536) [] Applying Connect to Message with parameters {'action': 'connect_nodes', 'max_path_length': 3, 'qnode_keys': ['n01', 'n00'], 'node_category_constraint': ''}
2024-09-25T18:28:07.453016 INFO: (975536) [] Processing action 'return' with parameters {'message': 'true', 'store': 'false'}
2024-09-25T18:28:07.453136 INFO: (975536) [] Processing is complete and resulted in 0 results.
________________________________________________________________________________ test_connect_resveratrol_glyoxalase ________________________________________________________________________________
def test_connect_resveratrol_glyoxalase():
query = {"operations": {"actions": [
"create_message",
"add_qnode(ids=PUBCHEM.COMPOUND:445154, key=n00)",
"add_qnode(ids=NCBIGene:2739, key=n01)",
"connect(action=connect_nodes, max_path_length=4)",
"return(message=true, store=false)"
]}}
[response, message] = _do_arax_query(query)
assert response.status == 'OK'
> assert len(message.query_graph.edges) == 3
E AssertionError: assert 0 == 3
E + where 0 = len({})
E + where {} = {'edges': {},\n 'nodes': {'n00': {'categories': None,\n 'constraints': [],\n 'ids': ['PUBCHEM.COMPOUND:445154'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'},\n 'n01': {'categories': None,\n 'constraints': [],\n 'ids': ['NCBIGene:2739'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'}}}.edges
E + where {'edges': {},\n 'nodes': {'n00': {'categories': None,\n 'constraints': [],\n 'ids': ['PUBCHEM.COMPOUND:445154'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'},\n 'n01': {'categories': None,\n 'constraints': [],\n 'ids': ['NCBIGene:2739'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'}}} = {'auxiliary_graphs': None,\n 'knowledge_graph': {'edges': {}, 'nodes': {}},\n 'query_graph': {'edges': {},\n 'nodes': {'n00': {'categories': None,\n 'constraints': [],\n 'ids': ['PUBCHEM.COMPOUND:445154'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'},\n 'n01': {'categories': None,\n 'constraints': [],\n 'ids': ['NCBIGene:2739'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'}}},\n 'results': []}.query_graph
test_ARAX_connect.py:106: AssertionError
--------------------------------------------------------------------------------------- Captured stderr call ----------------------------------------------------------------------------------------
2024-09-25T18:28:07.737691 INFO: (975536) [] ARAX Query launching on incoming Query
2024-09-25T18:28:07.737778 DEBUG: (975536) [] RTXConfiguration says maturity=development, current_branch=master, is_itrb_instance=False, arax_version=1.5.3, trapi_version=1.5.0
2024-09-25T18:28:07.737816 INFO: (975536) [] Creating an empty template TRAPI Response
2024-09-25T18:28:07.737884: DEBUG: In BiolinkHelper init
2024-09-25T18:28:07.739807: DEBUG: Loading BL lookup map...
2024-09-25T18:28:07.739862: DEBUG: Loading pickle file: /mnt/data/orangeboard/test/RTX/code/ARAX/BiolinkHelper/biolink_lookup_map_4.2.1_v4.pickle
2024-09-25T18:28:07.741304: DEBUG: Done loading BL lookup map
2024-09-25T18:28:07.744183 INFO: (975536) [] Examine input Query for needed information for dispatch
2024-09-25T18:28:07.744226 INFO: (975536) [] Found input processing plan. Sending to the ProcessingPlanExecutor
2024-09-25T18:28:07.744253 DEBUG: (975536) [] Entering execute_processing_plan
2024-09-25T18:28:07.744322 DEBUG: (975536) [] Connecting to ResponseCache
2024-09-25T18:28:07.771656 DEBUG: (975536) [] Creating ARAXMessenger instance
2024-09-25T18:28:07.771736 DEBUG: (975536) [] No starting messages were referenced. Will start with a blank template Message
2024-09-25T18:28:07.771765 INFO: (975536) [] Creating an empty template TRAPI Response
2024-09-25T18:28:07.771823: DEBUG: In BiolinkHelper init
2024-09-25T18:28:07.858162: DEBUG: Loading BL lookup map...
2024-09-25T18:28:07.858260: DEBUG: Loading pickle file: /mnt/data/orangeboard/test/RTX/code/ARAX/BiolinkHelper/biolink_lookup_map_4.2.1_v4.pickle
2024-09-25T18:28:07.859761: DEBUG: Done loading BL lookup map
2024-09-25T18:28:07.861919 DEBUG: (975536) [] Found actions
2024-09-25T18:28:07.861972 INFO: (975536) [] Parsing input actions list
2024-09-25T18:28:07.862000 DEBUG: (975536) [] Parsing action: create_message
2024-09-25T18:28:07.862039 DEBUG: (975536) [] Parsing action: add_qnode(ids=PUBCHEM.COMPOUND:445154, key=n00)
2024-09-25T18:28:07.862094 DEBUG: (975536) [] Parsing action: add_qnode(ids=NCBIGene:2739, key=n01)
2024-09-25T18:28:07.862137 DEBUG: (975536) [] Parsing action: connect(action=connect_nodes, max_path_length=4)
2024-09-25T18:28:07.862178 DEBUG: (975536) [] Parsing action: return(message=true, store=false)
2024-09-25T18:28:07.862248: DEBUG: In BiolinkHelper init
2024-09-25T18:28:07.863893: DEBUG: Loading BL lookup map...
2024-09-25T18:28:07.863945: DEBUG: Loading pickle file: /mnt/data/orangeboard/test/RTX/code/ARAX/BiolinkHelper/biolink_lookup_map_4.2.1_v4.pickle
2024-09-25T18:28:07.865408: DEBUG: Done loading BL lookup map
2024-09-25T18:28:07.866128 INFO: (975536) [] Processing action 'create_message' with parameters None
2024-09-25T18:28:07.866170 INFO: (975536) [] Creating an empty template TRAPI Response
2024-09-25T18:28:07.866220: DEBUG: In BiolinkHelper init
2024-09-25T18:28:07.868066: DEBUG: Loading BL lookup map...
2024-09-25T18:28:07.868119: DEBUG: Loading pickle file: /mnt/data/orangeboard/test/RTX/code/ARAX/BiolinkHelper/biolink_lookup_map_4.2.1_v4.pickle
2024-09-25T18:28:07.869802: DEBUG: Done loading BL lookup map
2024-09-25T18:28:07.872296 INFO: (975536) [] Processing action 'add_qnode' with parameters {'ids': 'PUBCHEM.COMPOUND:445154', 'key': 'n00'}
2024-09-25T18:28:07.872380 INFO: (975536) [] Adding a QueryNode to Message with input parameters {'key': 'n00', 'ids': 'PUBCHEM.COMPOUND:445154', 'name': None, 'categories': None, 'is_set': None, 'option_group_id': None}
2024-09-25T18:28:07.872685 DEBUG: (975536) [] Looking up ids ['PUBCHEM.COMPOUND:445154'] in NodeSynonymizer
2024-09-25T18:28:07.873211 INFO: (975536) [] Processing action 'add_qnode' with parameters {'ids': 'NCBIGene:2739', 'key': 'n01'}
2024-09-25T18:28:07.873261 INFO: (975536) [] Adding a QueryNode to Message with input parameters {'key': 'n01', 'ids': 'NCBIGene:2739', 'name': None, 'categories': None, 'is_set': None, 'option_group_id': None}
2024-09-25T18:28:07.873466 DEBUG: (975536) [] Looking up ids ['NCBIGene:2739'] in NodeSynonymizer
2024-09-25T18:28:07.873847 INFO: (975536) [] Processing action 'connect' with parameters {'action': 'connect_nodes', 'max_path_length': '4'}
2024-09-25T18:28:07.874663 INFO: (975536) [] Finding paths process has started
2024-09-25T18:28:08.167920 WARNING: (975536) [] Path NCBIGene:2739_2 raised an exception: unable to open database file, db path: /mnt/data/orangeboard/test/RTX/code/ARAX/KnowledgeSources/NormalizedGoogleDistance/curie_ngd_v1.0_KG2.10.0.sqlite
2024-09-25T18:28:08.168687 WARNING: (975536) [] Path CHEBI:45713_2 raised an exception: unable to open database file, db path: /mnt/data/orangeboard/test/RTX/code/ARAX/KnowledgeSources/NormalizedGoogleDistance/curie_ngd_v1.0_KG2.10.0.sqlite
2024-09-25T18:28:08.205315 DEBUG: (975536) [] PathFinder found 0 paths
2024-09-25T18:28:08.205411 WARNING: (975536) [] Could not connect the nodes n01 and n00 with a max path length of 4.
2024-09-25T18:28:08.205921 DEBUG: (975536) [] Applying Connect to Message with parameters {'action': 'connect_nodes', 'max_path_length': 4, 'qnode_keys': ['n01', 'n00'], 'node_category_constraint': ''}
2024-09-25T18:28:08.205973 INFO: (975536) [] Processing action 'return' with parameters {'message': 'true', 'store': 'false'}
2024-09-25T18:28:08.206091 INFO: (975536) [] Processing is complete and resulted in 0 results.
_______________________________________________________________________________________ test_glucose_diabetes _______________________________________________________________________________________
def test_glucose_diabetes():
query = {"operations": {"actions": [
"create_message",
"add_qnode(name=CHEBI:37626, key=n0)",
"add_qnode(name=MONDO:0005015, key=n1)",
"connect(action=connect_nodes, max_path_length=3)",
"filter_results(action=limit_number_of_results, max_results=30)",
"return(message=true, store=true)"
]}}
[response, message] = _do_arax_query(query)
assert response.status == 'OK'
> assert len(message.query_graph.edges) == 3
E AssertionError: assert 0 == 3
E + where 0 = len({})
E + where {} = {'edges': {},\n 'nodes': {'n0': {'categories': None,\n 'constraints': [],\n 'ids': ['CHEBI:37626'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'},\n 'n1': {'categories': None,\n 'constraints': [],\n 'ids': ['MONDO:0005015'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'}}}.edges
E + where {'edges': {},\n 'nodes': {'n0': {'categories': None,\n 'constraints': [],\n 'ids': ['CHEBI:37626'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'},\n 'n1': {'categories': None,\n 'constraints': [],\n 'ids': ['MONDO:0005015'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'}}} = {'auxiliary_graphs': None,\n 'knowledge_graph': {'edges': {}, 'nodes': {}},\n 'query_graph': {'edges': {},\n 'nodes': {'n0': {'categories': None,\n 'constraints': [],\n 'ids': ['CHEBI:37626'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'},\n 'n1': {'categories': None,\n 'constraints': [],\n 'ids': ['MONDO:0005015'],\n 'is_set': False,\n 'option_group_id': None,\n 'set_id': None,\n 'set_interpretation': 'BATCH'}}},\n 'results': []}.query_graph
test_ARAX_connect.py:135: AssertionError
--------------------------------------------------------------------------------------- Captured stdout call ----------------------------------------------------------------------------------------
DEBUG: Datetime now is: 2024-09-25 18:28:08.617898
DEBUG: Cutover date is: 2024-02-16 22:50:00
DEBUG: Since we're after the cutover date, use new us-east-1 S3 bucket arax-response-storage-2
--------------------------------------------------------------------------------------- Captured stderr call ----------------------------------------------------------------------------------------
2024-09-25T18:28:08.218238 INFO: (975536) [] ARAX Query launching on incoming Query
2024-09-25T18:28:08.218317 DEBUG: (975536) [] RTXConfiguration says maturity=development, current_branch=master, is_itrb_instance=False, arax_version=1.5.3, trapi_version=1.5.0
2024-09-25T18:28:08.218357 INFO: (975536) [] Creating an empty template TRAPI Response
2024-09-25T18:28:08.218436: DEBUG: In BiolinkHelper init
2024-09-25T18:28:08.220439: DEBUG: Loading BL lookup map...
2024-09-25T18:28:08.220494: DEBUG: Loading pickle file: /mnt/data/orangeboard/test/RTX/code/ARAX/BiolinkHelper/biolink_lookup_map_4.2.1_v4.pickle
2024-09-25T18:28:08.222158: DEBUG: Done loading BL lookup map
2024-09-25T18:28:08.224271 INFO: (975536) [] Examine input Query for needed information for dispatch
2024-09-25T18:28:08.224317 INFO: (975536) [] Found input processing plan. Sending to the ProcessingPlanExecutor
2024-09-25T18:28:08.224344 DEBUG: (975536) [] Entering execute_processing_plan
2024-09-25T18:28:08.224430 DEBUG: (975536) [] Connecting to ResponseCache
2024-09-25T18:28:08.250543 DEBUG: (975536) [] Creating ARAXMessenger instance
2024-09-25T18:28:08.250614 DEBUG: (975536) [] No starting messages were referenced. Will start with a blank template Message
2024-09-25T18:28:08.250641 INFO: (975536) [] Creating an empty template TRAPI Response
2024-09-25T18:28:08.250694: DEBUG: In BiolinkHelper init
2024-09-25T18:28:08.252459: DEBUG: Loading BL lookup map...
2024-09-25T18:28:08.252509: DEBUG: Loading pickle file: /mnt/data/orangeboard/test/RTX/code/ARAX/BiolinkHelper/biolink_lookup_map_4.2.1_v4.pickle
2024-09-25T18:28:08.253915: DEBUG: Done loading BL lookup map
2024-09-25T18:28:08.255879 DEBUG: (975536) [] Found actions
2024-09-25T18:28:08.255931 INFO: (975536) [] Parsing input actions list
2024-09-25T18:28:08.255958 DEBUG: (975536) [] Parsing action: create_message
2024-09-25T18:28:08.255998 DEBUG: (975536) [] Parsing action: add_qnode(name=CHEBI:37626, key=n0)
2024-09-25T18:28:08.256053 DEBUG: (975536) [] Parsing action: add_qnode(name=MONDO:0005015, key=n1)
2024-09-25T18:28:08.256097 DEBUG: (975536) [] Parsing action: connect(action=connect_nodes, max_path_length=3)
2024-09-25T18:28:08.256138 DEBUG: (975536) [] Parsing action: filter_results(action=limit_number_of_results, max_results=30)
2024-09-25T18:28:08.256179 DEBUG: (975536) [] Parsing action: return(message=true, store=true)
2024-09-25T18:28:08.256257: DEBUG: In BiolinkHelper init
2024-09-25T18:28:08.257867: DEBUG: Loading BL lookup map...
2024-09-25T18:28:08.257914: DEBUG: Loading pickle file: /mnt/data/orangeboard/test/RTX/code/ARAX/BiolinkHelper/biolink_lookup_map_4.2.1_v4.pickle
2024-09-25T18:28:08.259307: DEBUG: Done loading BL lookup map
2024-09-25T18:28:08.259683 INFO: (975536) [] Processing action 'create_message' with parameters None
2024-09-25T18:28:08.259719 INFO: (975536) [] Creating an empty template TRAPI Response
2024-09-25T18:28:08.259763: DEBUG: In BiolinkHelper init
2024-09-25T18:28:08.261337: DEBUG: Loading BL lookup map...
2024-09-25T18:28:08.261384: DEBUG: Loading pickle file: /mnt/data/orangeboard/test/RTX/code/ARAX/BiolinkHelper/biolink_lookup_map_4.2.1_v4.pickle
2024-09-25T18:28:08.262918: DEBUG: Done loading BL lookup map
2024-09-25T18:28:08.266148 INFO: (975536) [] Processing action 'add_qnode' with parameters {'name': 'CHEBI:37626', 'key': 'n0'}
2024-09-25T18:28:08.266219 INFO: (975536) [] Adding a QueryNode to Message with input parameters {'key': 'n0', 'ids': None, 'name': 'CHEBI:37626', 'categories': None, 'is_set': None, 'option_group_id': None}
2024-09-25T18:28:08.266556 DEBUG: (975536) [] Looking up id for name 'CHEBI:37626' in NodeSynonymizer
2024-09-25T18:28:08.267199 INFO: (975536) [] Creating QueryNode with ids '['CHEBI:37626']' for name 'CHEBI:37626'
2024-09-25T18:28:08.267306 INFO: (975536) [] Processing action 'add_qnode' with parameters {'name': 'MONDO:0005015', 'key': 'n1'}
2024-09-25T18:28:08.267348 INFO: (975536) [] Adding a QueryNode to Message with input parameters {'key': 'n1', 'ids': None, 'name': 'MONDO:0005015', 'categories': None, 'is_set': None, 'option_group_id': None}
2024-09-25T18:28:08.267572 DEBUG: (975536) [] Looking up id for name 'MONDO:0005015' in NodeSynonymizer
2024-09-25T18:28:08.268029 INFO: (975536) [] Creating QueryNode with ids '['MONDO:0005015']' for name 'MONDO:0005015'
2024-09-25T18:28:08.268127 INFO: (975536) [] Processing action 'connect' with parameters {'action': 'connect_nodes', 'max_path_length': '3'}
2024-09-25T18:28:08.268794 INFO: (975536) [] Finding paths process has started
2024-09-25T18:28:08.552881 WARNING: (975536) [] Path MONDO:0005015_2 raised an exception: unable to open database file, db path: /mnt/data/orangeboard/test/RTX/code/ARAX/KnowledgeSources/NormalizedGoogleDistance/curie_ngd_v1.0_KG2.10.0.sqlite
2024-09-25T18:28:08.570173 WARNING: (975536) [] Path CHEBI:37626_1 raised an exception: unable to open database file, db path: /mnt/data/orangeboard/test/RTX/code/ARAX/KnowledgeSources/NormalizedGoogleDistance/curie_ngd_v1.0_KG2.10.0.sqlite
2024-09-25T18:28:08.593826 DEBUG: (975536) [] PathFinder found 0 paths
2024-09-25T18:28:08.593918 WARNING: (975536) [] Could not connect the nodes n1 and n0 with a max path length of 3.
2024-09-25T18:28:08.594397 DEBUG: (975536) [] Applying Connect to Message with parameters {'action': 'connect_nodes', 'max_path_length': 3, 'qnode_keys': ['n1', 'n0'], 'node_category_constraint': ''}
2024-09-25T18:28:08.594448 INFO: (975536) [] Processing action 'filter_results' with parameters {'action': 'limit_number_of_results', 'max_results': '30'}
2024-09-25T18:28:08.594546 DEBUG: (975536) [] Before filtering, there are 0 results
2024-09-25T18:28:08.594629 WARNING: (975536) [] filter_results called with no results.
2024-09-25T18:28:08.594662 DEBUG: (975536) [] Applying Overlay to Message with parameters {'action': 'limit_number_of_results', 'max_results': '30'}
2024-09-25T18:28:08.595233 DEBUG: (975536) [] Query graph is {'edges': {},
'nodes': {'n0': {'categories': None,
'constraints': [],
'ids': ['CHEBI:37626'],
'is_set': False,
'option_group_id': None,
'set_id': None,
'set_interpretation': 'BATCH'},
'n1': {'categories': None,
'constraints': [],
'ids': ['MONDO:0005015'],
'is_set': False,
'option_group_id': None,
'set_id': None,
'set_interpretation': 'BATCH'}}}
2024-09-25T18:28:08.595287 INFO: (975536) [] Processing action 'return' with parameters {'message': 'true', 'store': 'true'}
2024-09-25T18:28:08.595373 DEBUG: (975536) [] Storing resulting Message
2024-09-25T18:28:08.595416 DEBUG: (975536) [] Writing response record to MySQL
INFO: Attempting to write to S3 bucket us-east-1:arax-response-storage-2:/responses/302578.json
2024-09-25T18:28:08.827611 INFO: (975536) [] INFO: Successfully wrote /responses/302578.json to us-east-1 S3 bucket arax-response-storage-2 in 0.2086940947920084 seconds
2024-09-25T18:28:08.828964 INFO: (975536) [] Result was stored with id 302578. It can be viewed at https://arax.ncats.io/?r=302578
2024-09-25T18:28:08.829009 INFO: (975536) [] Processing is complete and resulted in 0 results.
2024-09-25T18:28:08.829036 INFO: (975536) [] Resulting Message id is 302578 and is available to fetch via /response endpoint.
========================================================================================= warnings summary ==========================================================================================
../../../../../../../../usr/local/lib/python3.9/dist-packages/connexion/decorators/validation.py:16
../../../../../../../../usr/local/lib/python3.9/dist-packages/connexion/decorators/validation.py:16
/usr/local/lib/python3.9/dist-packages/connexion/decorators/validation.py:16: DeprecationWarning: Accessing jsonschema.draft4_format_checker is deprecated and will be removed in a future release. Instead, use the FORMAT_CHECKER attribute on the corresponding Validator.
from jsonschema import Draft4Validator, ValidationError, draft4_format_checker
../../../../../../../../usr/local/lib/python3.9/dist-packages/connexion/json_schema.py:16
../../../../../../../../usr/local/lib/python3.9/dist-packages/connexion/json_schema.py:16
/usr/local/lib/python3.9/dist-packages/connexion/json_schema.py:16: DeprecationWarning: jsonschema.RefResolver is deprecated as of v4.18.0, in favor of the https://github.com/python-jsonschema/referencing library, which provides more compliant referencing behavior as well as more flexible APIs for customization. A future release will remove RefResolver. Please file a feature request (on referencing) if you are missing an API for the kind of customization you need.
from jsonschema import Draft4Validator, RefResolver
../../../../../../../../usr/local/lib/python3.9/dist-packages/connexion/json_schema.py:17
/usr/local/lib/python3.9/dist-packages/connexion/json_schema.py:17: DeprecationWarning: jsonschema.exceptions.RefResolutionError is deprecated as of version 4.18.0. If you wish to catch potential reference resolution errors, directly catch referencing.exceptions.Unresolvable.
from jsonschema.exceptions import RefResolutionError, ValidationError # noqa
../ARAXQuery/ARAX_query_tracker.py:29
/mnt/data/orangeboard/test/RTX/code/ARAX/ARAXQuery/ARAX_query_tracker.py:29: MovedIn20Warning: Deprecated API features detected! These feature(s) are not compatible with SQLAlchemy 2.0. To prevent incompatible upgrades prior to updating applications, ensure requirements files are pinned to "sqlalchemy<2.0". Set environment variable SQLALCHEMY_WARN_20=1 to show all deprecation warnings. Set environment variable SQLALCHEMY_SILENCE_UBER_WARNING=1 to silence this message. (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
Base = declarative_base()
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
====================================================================================== short test summary info ======================================================================================
FAILED test_ARAX_connect.py::test_connect_ulcerative_colitis_to_adalimumab - AssertionError: assert 0 == 3
FAILED test_ARAX_connect.py::test_connect_resveratrol_glyoxalase - AssertionError: assert 0 == 3
FAILED test_ARAX_connect.py::test_glucose_diabetes - AssertionError: assert 0 == 3
============================================================================= 3 failed, 1 skipped, 6 warnings in 3.66s ==============================================================================unable to open database file, db path: /mnt/data/orangeboard/test/RTX/code/ARAX/KnowledgeSources/NormalizedGoogleDistance/curie_ngd_v1.0_KG2.10.0.sqlite
How could we upload the database into https://arax.ncats.io/ ?
@sundareswarpullela @edeutsch
edeutsch
commented
2 months ago aha, good eye!
-rw-r--r-- 1 rt rt 45538795520 Aug 26 23:08 ExplainableDTD_v1.0_KG2.10.0.db
-rw-r----- 1 rt rt 38928822272 Aug 11 05:32 ExplainableDTD_v1.0_KG2.8.4_refreshedTo_KG2.10.0.db
-rw-r----- 1 rt rt 1135886336 Aug 11 05:33 autocomplete_v1.0_KG2.10.0.sqlite
-rw-r--r-- 1 rt rt 1173290500 Aug 26 23:09 chemical_gene_embeddings_v1.0.KG2.10.0.npz
-rw-r----- 1 10006 users 1351049216 Aug 30 20:43 curie_ngd_v1.0_KG2.10.0.sqlite
-rw-r----- 1 rt rt 1630752768 Aug 11 05:37 curie_to_pmids_v1.0_KG2.10.0.sqlite
-rw-r----- 1 rt rt 70465 Aug 11 05:37 fda_approved_drugs_v1.0_KG2.10.0c.pickle
-rw-r----- 1 rt rt 5 Aug 11 05:37 fda_approved_drugs_v1.0_KG2.10.0c.pickle_TEST
-rw-r----- 1 rt rt 41387450368 Aug 11 06:01 kg2c_v1.0_KG2.10.0.sqlite
-rw-r----- 1 rt rt 602877952 Aug 11 06:01 kg2c_v1.0_KG2.10.0.sqlite_TEST
drwxrwxrwx 2 root root 4096 Aug 30 21:01 md5_sums/
-rw-r----- 1 rt rt 9706194 Aug 11 06:01 meta_kg_v1.0_KG2.10.0c.json
-rw-r----- 1 rt rt 107369 Aug 11 06:01 meta_kg_v1.0_KG2.10.0c.json_TEST
-rw-r----- 1 rt rt 17360637952 Aug 11 06:13 node_synonymizer_v1.0_KG2.10.0.sqlite
-rw-r--r-- 1 rt rt 2146578816 Aug 26 23:13 xcrg_decrease_model_v1.0.KG2.10.0.pt
-rw-r--r-- 1 rt rt 1336957664 Aug 26 23:11 xcrg_increase_model_v1.0.KG2.10.0.ptI will fix file ownership. Maybe that's it!
edeutsch
commented
2 months ago that fixed it!
============================================================================= 3 passed, 1 skipped, 4 warnings in 33.80s =============================================================================thanks so much!
On arax.ncats.io the following tests are failing consistently: