| container | mem | cpu |
|---|---|---|
| rtx_pr_2888 | 691MiB / 2GiB | 0.01% |
| check | result | detail |
|---|---|---|
| container rtx_pr_2888 running | ✓ pass | up |
| GET /api/arax/v1.4/status | ✓ pass | HTTP 200 |
| GET / serves the ARAX UI | ✓ pass | HTTP 200, body contains ARAX |
| GET /api/arax/v1.4/ui/ | ✓ pass | HTTP 200 |
| GET /api/arax/v1.4/meta_knowledge_graph | ✓ pass | HTTP 200 |
Skipping database check (pass --withdatabases to download/update databases) KP info cache is up to date. ============================= test session starts ============================== platform linux -- Python 3.12.3, pytest-8.1.1, pluggy-1.6.0 rootdir: /mnt/data/orangeboard/production/RTX configfile: pytest.ini plugins: anyio-4.15.1 collected 321 items test_ARAX_connect.py .s [ 0%] test_ARAX_expand.py ssss.s.ss.ssssssssssssss..s...s..sssss.......sssssss [ 16%] ......s.sss.....ss.. [ 23%] test_ARAX_filter_kg.py .s..sss.sss. [ 26%] test_ARAX_filter_results.py ...s.s..s [ 29%] test_ARAX_infer.py ........s.ssssssss [ 35%] test_ARAX_json_queries.py ..s.s [ 36%] test_ARAX_messenger.py .............. [ 41%] test_ARAX_overlay.py s...sssssssssssssssssssss [ 48%] test_ARAX_query.py . [ 49%] test_ARAX_ranker.py sssssssssssss [ 53%] test_ARAX_resultify.py .......s.s..s......s....ss...sssss...sss.ssssss [ 67%] test_ARAX_standup_queries.py ...ssss [ 70%] test_ARAX_synonymizer.py ......................... [ 77%] test_ARAX_translate.py ........ss. [ 81%] test_ARAX_workflows.py ..ssssss.sssssss.sssssss [ 88%] test_ARAX_xcrg_connect.py ......... [ 91%] test_compute_ngd.py ........................ [ 99%] test_result_transformer.py ... [100%] =========== 177 passed, 144 skipped, 1 warning in 158.23s (0:02:38) ============
| # | query | HTTP | s | results | KG nodes/edges | status |
|---|---|---|---|---|---|---|
| Example 1 | interacts_with (CHEBI:46195) | 200 | 1.89 | 58 | 59/132 | Success |
| Example 2 | treats inferred (MONDO:0015564) | 200 | 5.65 | 117 | 224/1536 | Success |
| Example 3 | affects qualified (NCBIGene:1576) | 200 | 3.55 | 500 | 506/1963 | Success |
| Pathfinder | pathfinder (MONDO:0005011 to MONDO:0005180) | 200 | 103.36 | 1 | 254/2401 | Success |
query Example 1
endpoint https://cicd.rtx.ai/2888/api/arax/v1.4/query
http 200
seconds 1.89
results 58
KG nodes 59
KG edges 132
status Success
error Normal completion
query_graph:
{
"edges": {
"e00": {
"object": "n01",
"predicates": [
"biolink:interacts_with"
],
"subject": "n00"
}
},
"nodes": {
"n00": {
"ids": [
"CHEBI:46195"
]
},
"n01": {
"categories": [
"biolink:Protein"
]
}
}
}
response body (first 4 KB, truncated):
{"biolink_version": "4.2.5", "context": "https://raw.githubusercontent.com/biolink/biolink-model/master/context.jsonld", "datetime": "2026-09-13 12:08:41", "description": "Normal completion", "http_status": 200, "id": "https://arax.ncats.io/api/arax/v1.4/response/545127", "info": null, "job_id": null, "logs": [{"code": "", "level": "DEBUG", "message": "in query_return_message", "timestamp": "2026-09-13T12:08:41.585882"}, {"code": "", "level": "INFO", "message": "ARAX Query launching on incoming Query", "timestamp": "2026-09-13T12:08:41.586056"}, {"code": "", "level": "DEBUG", "message": "RTXConfiguration says maturity=development, current_branch=test-xcrg-ranker, is_itrb_instance=False, arax_version=1.6.2, trapi_version=1.6.0", "timestamp": "2026-09-13T12:08:41.586130"}, {"code": "", "level": "DEBUG", "message": "NodeSynonymizer says NODE_NORMALIZER_URL=https://nodenorm-es.ci.transltr.io, NAME_RESOLVER_URL=https://name-resolution-sri.renci.org", "timestamp": "2026-09-13T12:08:41.586292"}, {"code": "", "level": "INFO", "message": "Creating an empty template TRAPI Response", "timestamp": "2026-09-13T12:08:41.586407"}, {"code": "", "level": "INFO", "message": "Examine input Query for needed information for dispatch", "timestamp": "2026-09-13T12:08:41.670448"}, {"code": "", "level": "INFO", "message": "Validating the input query graph", "timestamp": "2026-09-13T12:08:41.670533"}, {"code": "", "level": "DEBUG", "message": "Deserializing message", "timestamp": "2026-09-13T12:08:41.670590"}, {"code": "", "level": "INFO", "message": "Found input query_graph. Interpreting it and generating ARAXi processing plan to answer it", "timestamp": "2026-09-13T12:08:41.671166"}, {"code": "", "level": "DEBUG", "message": "Assessing the QueryGraph for basic information", "timestamp": "2026-09-13T12:08:41.716684"}, {"code": "", "level": "DEBUG", "message": "Found 2 nodes and 1 edges", "timestamp": "2026-09-13T12:08:41.716765"}, {"code": "", "level": "DEBUG", "message": "canonical_curies={'CHEBI:46195': {'preferred_curie': 'CHEBI:46195', 'preferred_name': 'Acetaminophen', 'preferred_category': 'biolink:SmallMolecule', 'all_categories': {'biolink:SmallMolecule': 17, 'biolink:MolecularEntity': 17, 'biolink:ChemicalEntity': 17, 'biolink:PhysicalEssence': 17, 'biolink:ChemicalOrDrugOrTreatment': 17, 'biolink:ChemicalEntityOrGeneOrGeneProduct': 17, 'biolink:ChemicalEntityOrProteinOrPolypeptide': 17, 'biolink:NamedThing': 17, 'biolink:PhysicalEssenceOrOccurrent': 17}}}, curie=CHEBI:46195", "timestamp": "2026-09-13T12:08:41.871451"}, {"code": "", "level": "DEBUG", "message": "The QueryGraph reference template is: n00(ids)-e00()-n01(categories=biolink:Protein)", "timestamp": "2026-09-13T12:08:41.871631"}, {"code": "", "level": "INFO", "message": "Found input processing plan. Sending to the ProcessingPlanExecutor", "timestamp": "2026-09-13T12:08:41.873065"}, {"code": "", "level": "DEBUG", "message": "Entering execute_processing_plan", "timestamp": "2026-09-13T12:08:41.873116"}, {"code": "", "level": "DEBUG", "message": "Connecting to ResponseCache", "timestamp": "2026-09-13T12:08:41.873313"}, {"code": "", "level": "DEBUG", "message": "Creating ARAXMessenger instance", "timestamp": "2026-09-13T12:08:41.899768"}, {"code": "", "level": "DEBUG", "message": "A single Message is ready and in hand", "timestamp": "2026-09-13T12:08:41.899843"}, {"code": "", "level": "DEBUG", "message": "Saving original query graph (has qnodes {'n00', 'n01'} and qedges {'e00': {'attribute_constraints': [],\n 'exclude': None,\n 'knowledge_type': None,\n 'object': 'n01',\n 'option_group_id': None,\n 'predicates': ['biolink:interacts_with'],\n 'qualifier_constraints': [],\n 'subject': 'n00'}})", "timestamp": "2026-09-13T12:08:41.900584"}, {"code": "", "level": "DEBUG", "message": "Found actions", "timestamp": "2026-09-13T12:08:41.900633"}, {"code": "", "level": "INFO", "message": "Parsing input actions list", "timestamp": "2026-09-13T12:08:41.900695"}, {"code": "", "level": "DEBUG", "message": "Parsing action: expand()", "timestamp": "2026-09-13T12:08:41.900720"}, {"code": "", "levquery Example 2
endpoint https://cicd.rtx.ai/2888/api/arax/v1.4/query
http 200
seconds 5.65
results 117
KG nodes 224
KG edges 1536
status Success
error Normal completion
query_graph:
{
"edges": {
"t_edge": {
"attribute_constraints": [],
"knowledge_type": "inferred",
"object": "on",
"predicates": [
"biolink:treats"
],
"qualifier_constraints": [],
"subject": "sn"
}
},
"nodes": {
"on": {
"categories": [
"biolink:Disease"
],
"constraints": [],
"ids": [
"MONDO:0015564"
],
"is_set": false
},
"sn": {
"categories": [
"biolink:ChemicalEntity"
],
"constraints": [],
"is_set": false
}
}
}
response body (first 4 KB, truncated):
{"biolink_version": "4.2.5", "context": "https://raw.githubusercontent.com/biolink/biolink-model/master/context.jsonld", "datetime": "2026-09-13 12:08:43", "description": "Normal completion", "http_status": 200, "id": "https://arax.ncats.io/api/arax/v1.4/response/545128", "info": null, "job_id": null, "logs": [{"code": "", "level": "DEBUG", "message": "in query_return_message", "timestamp": "2026-09-13T12:08:43.635225"}, {"code": "", "level": "INFO", "message": "ARAX Query launching on incoming Query", "timestamp": "2026-09-13T12:08:43.635378"}, {"code": "", "level": "DEBUG", "message": "RTXConfiguration says maturity=development, current_branch=test-xcrg-ranker, is_itrb_instance=False, arax_version=1.6.2, trapi_version=1.6.0", "timestamp": "2026-09-13T12:08:43.635446"}, {"code": "", "level": "DEBUG", "message": "NodeSynonymizer says NODE_NORMALIZER_URL=https://nodenorm-es.ci.transltr.io, NAME_RESOLVER_URL=https://name-resolution-sri.renci.org", "timestamp": "2026-09-13T12:08:43.635492"}, {"code": "", "level": "INFO", "message": "Creating an empty template TRAPI Response", "timestamp": "2026-09-13T12:08:43.635597"}, {"code": "", "level": "INFO", "message": "Examine input Query for needed information for dispatch", "timestamp": "2026-09-13T12:08:43.708561"}, {"code": "", "level": "INFO", "message": "Validating the input query graph", "timestamp": "2026-09-13T12:08:43.708635"}, {"code": "", "level": "DEBUG", "message": "Deserializing message", "timestamp": "2026-09-13T12:08:43.708685"}, {"code": "", "level": "INFO", "message": "Found input query_graph. Interpreting it and generating ARAXi processing plan to answer it", "timestamp": "2026-09-13T12:08:43.709195"}, {"code": "", "level": "DEBUG", "message": "Assessing the QueryGraph for basic information", "timestamp": "2026-09-13T12:08:43.742669"}, {"code": "", "level": "DEBUG", "message": "Found 2 nodes and 1 edges", "timestamp": "2026-09-13T12:08:43.742744"}, {"code": "", "level": "DEBUG", "message": "The QueryGraph reference template is: n00(ids)-e00()-n01(categories=biolink:ChemicalEntity)", "timestamp": "2026-09-13T12:08:43.742906"}, {"code": "", "level": "INFO", "message": "Found input processing plan. Sending to the ProcessingPlanExecutor", "timestamp": "2026-09-13T12:08:43.744255"}, {"code": "", "level": "DEBUG", "message": "Entering execute_processing_plan", "timestamp": "2026-09-13T12:08:43.744305"}, {"code": "", "level": "DEBUG", "message": "Connecting to ResponseCache", "timestamp": "2026-09-13T12:08:43.744501"}, {"code": "", "level": "DEBUG", "message": "Creating ARAXMessenger instance", "timestamp": "2026-09-13T12:08:43.766399"}, {"code": "", "level": "DEBUG", "message": "A single Message is ready and in hand", "timestamp": "2026-09-13T12:08:43.766470"}, {"code": "", "level": "DEBUG", "message": "Saving original query graph (has qnodes {'sn', 'on'} and qedges {'t_edge': {'attribute_constraints': [],\n 'exclude': None,\n 'knowledge_type': 'inferred',\n 'object': 'on',\n 'option_group_id': None,\n 'predicates': ['biolink:treats'],\n 'qualifier_constraints': [],\n 'subject': 'sn'}})", "timestamp": "2026-09-13T12:08:43.767265"}, {"code": "", "level": "DEBUG", "message": "Found actions", "timestamp": "2026-09-13T12:08:43.767301"}, {"code": "", "level": "INFO", "message": "Parsing input actions list", "timestamp": "2026-09-13T12:08:43.767360"}, {"code": "", "level": "DEBUG", "message": "Parsing action: expand()", "timestamp": "2026-09-13T12:08:43.767390"}, {"code": "", "level": "DEBUG", "message": "Parsing action: overlay(action=compute_ngd, virtual_relation_label=N1, subject_qnode_key=on, object_qnode_key=sn)", "timestamp": "2026-09-13T12:08:43.768123"}, {"code": "", "level": "DEBUG", "message": "Parsing action: filter_kg(action=remove_general_concept_nodes,perform_action=True)", "timestamp": "2026-09-13T12:08:43.768189"}, {"code": "", "level": "DEBUG", "message": "Parsing action: resultify()", "timestamp": "2026-09-13T12:08:43.768229"}, {"code": "", "level": "DEBUG", "message": "Parsing action: filter_results(action=limit_number_of_results, max_results=500)", "timesquery Example 3
endpoint https://cicd.rtx.ai/2888/api/arax/v1.4/query
http 200
seconds 3.55
results 500
KG nodes 506
KG edges 1963
status Success
error Normal completion
query_graph:
{
"edges": {
"t_edge": {
"knowledge_type": "inferred",
"object": "on",
"predicates": [
"biolink:affects"
],
"qualifier_constraints": [
{
"qualifier_set": [
{
"qualifier_type_id": "biolink:object_aspect_qualifier",
"qualifier_value": "activity_or_abundance"
},
{
"qualifier_type_id": "biolink:object_direction_qualifier",
"qualifier_value": "increased"
}
]
}
],
"subject": "sn"
}
},
"nodes": {
"on": {
"categories": [
"biolink:Gene"
],
"ids": [
"NCBIGene:1576"
]
},
"sn": {
"categories": [
"biolink:ChemicalEntity"
]
}
}
}
response body (first 4 KB, truncated):
{"biolink_version": "4.3.2", "context": "https://raw.githubusercontent.com/biolink/biolink-model/master/context.jsonld", "datetime": "2026-09-13 12:08:49", "description": "Normal completion", "http_status": 200, "id": "https://arax.ncats.io/api/arax/v1.4/response/545129", "info": null, "job_id": null, "logs": [{"code": "", "level": "DEBUG", "message": "in query_return_message", "timestamp": "2026-09-13T12:08:49.678491"}, {"code": "", "level": "INFO", "message": "ARAX Query launching on incoming Query", "timestamp": "2026-09-13T12:08:49.678628"}, {"code": "", "level": "DEBUG", "message": "RTXConfiguration says maturity=development, current_branch=test-xcrg-ranker, is_itrb_instance=False, arax_version=1.6.2, trapi_version=1.6.0", "timestamp": "2026-09-13T12:08:49.678688"}, {"code": "", "level": "DEBUG", "message": "NodeSynonymizer says NODE_NORMALIZER_URL=https://nodenorm-es.ci.transltr.io, NAME_RESOLVER_URL=https://name-resolution-sri.renci.org", "timestamp": "2026-09-13T12:08:49.678755"}, {"code": "", "level": "INFO", "message": "Creating an empty template TRAPI Response", "timestamp": "2026-09-13T12:08:49.678848"}, {"code": "", "level": "INFO", "message": "Examine input Query for needed information for dispatch", "timestamp": "2026-09-13T12:08:49.758666"}, {"code": "", "level": "INFO", "message": "Validating the input query graph", "timestamp": "2026-09-13T12:08:49.758742"}, {"code": "", "level": "DEBUG", "message": "Deserializing message", "timestamp": "2026-09-13T12:08:49.758786"}, {"code": "", "level": "INFO", "message": "Found input query_graph. Interpreting it and generating ARAXi processing plan to answer it", "timestamp": "2026-09-13T12:08:49.759364"}, {"code": "", "level": "DEBUG", "message": "Assessing the QueryGraph for basic information", "timestamp": "2026-09-13T12:08:49.792609"}, {"code": "", "level": "DEBUG", "message": "Found 2 nodes and 1 edges", "timestamp": "2026-09-13T12:08:49.792701"}, {"code": "", "level": "DEBUG", "message": "The QueryGraph reference template is: n00(ids)-e00()-n01(categories=biolink:ChemicalEntity)", "timestamp": "2026-09-13T12:08:49.792869"}, {"code": "", "level": "INFO", "message": "QueryGraphInterpreter recognized query_graph as an xCRG MVP2 query: triggering xCRG subsystem.", "timestamp": "2026-09-13T12:08:50.713368"}, {"code": "", "level": "INFO", "message": "Found input processing plan. Sending to the ProcessingPlanExecutor", "timestamp": "2026-09-13T12:08:50.713442"}, {"code": "", "level": "DEBUG", "message": "Entering execute_processing_plan", "timestamp": "2026-09-13T12:08:50.713476"}, {"code": "", "level": "DEBUG", "message": "Connecting to ResponseCache", "timestamp": "2026-09-13T12:08:50.713645"}, {"code": "", "level": "DEBUG", "message": "Creating ARAXMessenger instance", "timestamp": "2026-09-13T12:08:50.737321"}, {"code": "", "level": "DEBUG", "message": "A single Message is ready and in hand", "timestamp": "2026-09-13T12:08:50.737407"}, {"code": "", "level": "DEBUG", "message": "Saving original query graph (has qnodes {'sn', 'on'} and qedges {'t_edge': {'attribute_constraints': [],\n 'exclude': None,\n 'knowledge_type': 'inferred',\n 'object': 'on',\n 'option_group_id': None,\n 'predicates': ['biolink:affects'],\n 'qualifier_constraints': [{'qualifier_set': [{'qualifier_type_id': 'biolink:object_aspect_qualifier',\n 'qualifier_value': 'activity_or_abundance'},\n {'qualifier_type_id': 'biolink:object_direction_qualifier',\n 'qualifier_value': 'increased'}]}],\n 'subject': 'sn'}})", "timestamp": "2026-09-13T12:08:50.738989"}, {"code": "", "level": "DEBUG", "message": "Found actions", "timestamp": "2026-09-13T12:08:50.739041"}, {"code": "", "level": "INFO", "message": "Parsing input actions list", "timestamp": "2026-09-13T12:08:50.739102"}, {"code": "", "level": "DEBUG", "message": "Parsing action: connect(action=xcrg)", "timestamp": "2026-09-13T12:08:50.739137"}, {"code": "", "level": "INFO", "message": "Processing action 'connect'query Pathfinder
endpoint https://cicd.rtx.ai/2888/api/arax/v1.4/query
http 200
seconds 103.36
results 1
KG nodes 254
KG edges 2401
status Success
error Normal completion
query_graph:
{
"nodes": {
"n0": {
"ids": [
"MONDO:0005011"
]
},
"n1": {
"ids": [
"MONDO:0005180"
]
}
},
"paths": {
"p0": {
"object": "n1",
"predicates": [
"biolink:related_to"
],
"subject": "n0"
}
}
}
response body (first 4 KB, truncated):
{"biolink_version": "4.2.5", "context": "https://raw.githubusercontent.com/biolink/biolink-model/master/context.jsonld", "datetime": "2026-09-13 12:08:53", "description": "Normal completion", "http_status": 200, "id": "https://arax.ncats.io/api/arax/v1.4/response/545130", "info": null, "job_id": null, "logs": [{"code": "", "level": "DEBUG", "message": "in query_return_message", "timestamp": "2026-09-13T12:08:53.653937"}, {"code": "", "level": "INFO", "message": "ARAX Query launching on incoming Query", "timestamp": "2026-09-13T12:08:53.654076"}, {"code": "", "level": "DEBUG", "message": "RTXConfiguration says maturity=development, current_branch=test-xcrg-ranker, is_itrb_instance=False, arax_version=1.6.2, trapi_version=1.6.0", "timestamp": "2026-09-13T12:08:53.654166"}, {"code": "", "level": "DEBUG", "message": "NodeSynonymizer says NODE_NORMALIZER_URL=https://nodenorm-es.ci.transltr.io, NAME_RESOLVER_URL=https://name-resolution-sri.renci.org", "timestamp": "2026-09-13T12:08:53.654231"}, {"code": "", "level": "INFO", "message": "Creating an empty template TRAPI Response", "timestamp": "2026-09-13T12:08:53.654334"}, {"code": "", "level": "INFO", "message": "Examine input Query for needed information for dispatch", "timestamp": "2026-09-13T12:08:53.738341"}, {"code": "", "level": "INFO", "message": "Validating the input query graph", "timestamp": "2026-09-13T12:08:53.738411"}, {"code": "", "level": "DEBUG", "message": "Deserializing message", "timestamp": "2026-09-13T12:08:53.738453"}, {"code": "", "level": "INFO", "message": "Found input query_graph. Interpreting it and generating ARAXi processing plan to answer it", "timestamp": "2026-09-13T12:08:53.738988"}, {"code": "", "level": "DEBUG", "message": "Assessing the QueryGraph for basic information", "timestamp": "2026-09-13T12:08:53.772289"}, {"code": "", "level": "DEBUG", "message": "Found 2 nodes and 0 edges", "timestamp": "2026-09-13T12:08:53.772368"}, {"code": "", "level": "DEBUG", "message": "canonical_curies={'MONDO:0005011': {'preferred_curie': 'MONDO:0005011', 'preferred_name': 'Crohn disease', 'preferred_category': 'biolink:Disease', 'all_categories': {'biolink:Disease': 15, 'biolink:DiseaseOrPhenotypicFeature': 15, 'biolink:BiologicalEntity': 15, 'biolink:ThingWithTaxon': 15, 'biolink:NamedThing': 15}}}, curie=MONDO:0005011", "timestamp": "2026-09-13T12:08:53.919124"}, {"code": "", "level": "DEBUG", "message": "canonical_curies={'MONDO:0005180': {'preferred_curie': 'MONDO:0005180', 'preferred_name': 'Parkinson disease', 'preferred_category': 'biolink:Disease', 'all_categories': {'biolink:Disease': 16, 'biolink:DiseaseOrPhenotypicFeature': 16, 'biolink:BiologicalEntity': 16, 'biolink:ThingWithTaxon': 16, 'biolink:NamedThing': 16}}}, curie=MONDO:0005180", "timestamp": "2026-09-13T12:08:53.935855"}, {"code": "", "level": "DEBUG", "message": "The QueryGraph reference template is: n00(ids)-e00()-", "timestamp": "2026-09-13T12:08:53.936003"}, {"code": "", "level": "INFO", "message": "QueryGraphInterpreter recognized query_graph as a 'pathfinder' query: triggering pathfinder subsystem.", "timestamp": "2026-09-13T12:08:53.936251"}, {"code": "", "level": "INFO", "message": "Found input processing plan. Sending to the ProcessingPlanExecutor", "timestamp": "2026-09-13T12:08:53.936306"}, {"code": "", "level": "DEBUG", "message": "Entering execute_processing_plan", "timestamp": "2026-09-13T12:08:53.936337"}, {"code": "", "level": "DEBUG", "message": "Connecting to ResponseCache", "timestamp": "2026-09-13T12:08:53.936553"}, {"code": "", "level": "DEBUG", "message": "Creating ARAXMessenger instance", "timestamp": "2026-09-13T12:08:53.957812"}, {"code": "", "level": "DEBUG", "message": "A single Message is ready and in hand", "timestamp": "2026-09-13T12:08:53.957889"}, {"code": "", "level": "DEBUG", "message": "Saving original query graph (has qnodes {'n1', 'n0'} and paths {'p0': {'constraints': None,\n 'object': 'n1',\n 'predicates': ['biolink:related_to'],\n 'subject': 'n0'}})", "timestamp": "2026-09-13T12:08:53.958620"}, {"code": "", "level": "DEBUG", "message": "Found act[2026-09-13T11:58:55Z] wrote the status page /var/www/arax-preview/index.html [2026-09-13T11:58:55Z] step 1/10 validating host setup [2026-09-13T11:58:55Z] PR 2888, branch test-xcrg-ranker, sha ab228be695bc63d40b144fdf8f691e2862a01c1d, force yes, fast-only no [2026-09-13T11:58:55Z] container rtx_pr_2888, image rtx:pr-2888, port 127.0.0.1:12888 [2026-09-13T11:58:55Z] public url https://cicd.rtx.ai/2888/ [2026-09-13T11:58:55Z] step 2/10 deciding how to deploy [2026-09-13T11:58:55Z] mode: full rebuild (--force was given) [2026-09-13T11:58:55Z] step 3/10 clearing the previous deploy of PR 2888 and checking the host [2026-09-13T11:59:03Z] preflight: 1 other preview(s) on the host, limit 3 [2026-09-13T11:59:03Z] preflight: 160 GB free of 485 GB on the docker root, floor 48 GB [2026-09-13T11:59:03Z] preflight: 6302 MB memory available, minimum 2048 MB [2026-09-13T11:59:03Z] preflight: 127.0.0.1:12888 is free [2026-09-13T12:05:02Z] step 5/10 starting rtx_pr_2888 on 127.0.0.1:12888, capped at 2g memory and 1.5 cpus 310e6996a0afd3cf99792055648a606aa0fe96cb2ef0c0e5b7b0231c131e8c61 [2026-09-13T12:05:03Z] verified rtx_pr_2888 is on the PR head ab228be695bc63d40b144fdf8f691e2862a01c1d [2026-09-13T12:05:03Z] step 6/10 setting up databases and starting the services [2026-09-13T12:05:03Z] creating database symlinks Downloading any missing databases from arax-databases.rtx.ai to /mnt/data/orangeboard/databases cohd_database (/mnt/data/orangeboard/production/RTX/code/ARAX/KnowledgeSources/COHD_local/data/COHDdatabase_v1.0_KG2.8.0.db) not present locally, downloading or symlinking now...... curie_to_pmids (/mnt/data/orangeboard/production/RTX/code/ARAX/KnowledgeSources/NormalizedGoogleDistance/curie_to_pmids_v1.0_tier0-20260621.sqlite) not present locally, downloading or symlinking now...... curie_ngd (/mnt/data/orangeboard/production/RTX/code/ARAX/KnowledgeSources/NormalizedGoogleDistance/curie_ngd_v1.0_tier0-20260621.sqlite) not present locally, downloading or symlinking now...... kg2c_sqlite (/mnt/data/orangeboard/production/RTX/code/ARAX/KnowledgeSources/KG2c/tier0-info-for-overlay_v1.0_tier0-20260621.sqlite) not present locally, downloading or symlinking now...... fda_approved_drugs (/mnt/data/orangeboard/production/RTX/code/ARAX/KnowledgeSources/fda_approved_drugs_v1.0.pickle) not present locally, downloading or symlinking now...... autocomplete (/mnt/data/orangeboard/production/RTX/code/autocomplete/autocomplete_v1.0_tier0-20260621.sqlite) not present locally, downloading or symlinking now...... explainable_dtd_db (/mnt/data/orangeboard/production/RTX/code/ARAX/KnowledgeSources/Prediction/ExplainableDTD_v1.0_tier0-20260621-all_with_paths.db) not present locally, downloading or symlinking now...... Local paths: cohd_database: /mnt/data/orangeboard/production/RTX/code/ARAX/KnowledgeSources/COHD_local/data/COHDdatabase_v1.0_KG2.8.0.db curie_to_pmids: /mnt/data/orangeboard/production/RTX/code/ARAX/KnowledgeSources/NormalizedGoogleDistance/curie_to_pmids_v1.0_tier0-20260621.sqlite curie_ngd: /mnt/data/orangeboard/production/RTX/code/ARAX/KnowledgeSources/NormalizedGoogleDistance/curie_ngd_v1.0_tier0-20260621.sqlite kg2c_sqlite: /mnt/data/orangeboard/production/RTX/code/ARAX/KnowledgeSources/KG2c/tier0-info-for-overlay_v1.0_tier0-20260621.sqlite fda_approved_drugs: /mnt/data/orangeboard/production/RTX/code/ARAX/KnowledgeSources/fda_approved_drugs_v1.0.pickle autocomplete: /mnt/data/orangeboard/production/RTX/code/autocomplete/autocomplete_v1.0_tier0-20260621.sqlite explainable_dtd_db: /mnt/data/orangeboard/production/RTX/code/ARAX/KnowledgeSources/Prediction/ExplainableDTD_v1.0_tier0-20260621-all_with_paths.db Remote locations: cohd_database: rtxconfig@arax-databases.rtx.ai:/home/rtxconfig/KG2.8.0/COHDdatabase_v1.0_KG2.8.0.db curie_to_pmids: rtxconfig@arax-databases.rtx.ai:/home/rtxconfig/tier0-20260621/curie_to_pmids_v1.0_tier0-20260621.sqlite curie_ngd: rtxconfig@arax-databases.rtx.ai:/home/rtxconfig/tier0-20260621/curie_ngd_v1.0_tier0-20260621.sqlite kg2c_sqlite: rtxconfig@arax-databases.rtx.ai:/home/rtxconfig/tier0-20260621/tier0-info-for-overlay_v1.0_tier0-20260621.sqlite fda_approved_drugs: rtxconfig@arax-databases.rtx.ai:/home/rtxconfig/tier0-20260408/fda_approved_drugs_v1.0.pickle autocomplete: rtxconfig@arax-databases.rtx.ai:/home/rtxconfig/tier0-20260621/autocomplete_v1.0_tier0-20260621.sqlite explainable_dtd_db: rtxconfig@arax-databases.rtx.ai:/home/rtxconfig/tier0-20260621/ExplainableDTD_v1.0_tier0-20260621-all_with_paths.db Docker paths: cohd_database: /mnt/data/orangeboard/databases/KG2.8.0/COHDdatabase_v1.0_KG2.8.0.db curie_to_pmids: /mnt/data/orangeboard/databases/tier0-20260621/curie_to_pmids_v1.0_tier0-20260621.sqlite curie_ngd: /mnt/data/orangeboard/databases/tier0-20260621/curie_ngd_v1.0_tier0-20260621.sqlite kg2c_sqlite: /mnt/data/orangeboard/databases/tier0-20260621/tier0-info-for-overlay_v1.0_tier0-20260621.sqlite fda_approved_drugs: /mnt/data/orangeboard/databases/tier0-20260408/fda_approved_drugs_v1.0.pickle autocomplete: /mnt/data/orangeboard/databases/tier0-20260621/autocomplete_v1.0_tier0-20260621.sqlite explainable_dtd_db: /mnt/data/orangeboard/databases/tier0-20260621/ExplainableDTD_v1.0_tier0-20260621-all_with_paths.db saving new version file to /mnt/data/orangeboard/production/RTX/code/ARAX/KnowledgeSources/db_versions.json On database cohd_database in _download_to_mnt() Database already exists, no need to download On database curie_to_pmids in _download_to_mnt() Database already exists, no need to download On database curie_ngd in _download_to_mnt() Database already exists, no need to download On database kg2c_sqlite in _download_to_mnt() Database already exists, no need to download On database fda_approved_drugs in _download_to_mnt() Database already exists, no need to download On database autocomplete in _download_to_mnt() Database already exists, no need to download On database explainable_dtd_db in _download_to_mnt() Database already exists, no need to download [2026-09-13T12:05:04Z] building the KP info cache The process with process ID 47 has STARTED refreshing the KP info caches - Getting meta info from infores:retriever The process with process ID 47 has FINISHED refreshing the KP info caches [2026-09-13T12:05:07Z] starting apache2, RTX_OpenAPI_production and RTX_Complete * Starting Apache httpd web server apache2 AH00558: apache2: Could not reliably determine the server's fully qualified domain name, using 172.17.0.3. Set the 'ServerName' directive globally to suppress this message * * Starting system RTX_OpenAPI_production daemon ...done. * Starting system RTX_Complete daemon ...done. [2026-09-13T12:05:08Z] step 7/10 writing /etc/nginx/arax-preview.d/2888.conf [2026-09-13T12:05:08Z] wrote shared /etc/nginx/arax-preview.d/_rtxcomplete.conf pointing at port 12888 nginx: the configuration file /etc/nginx/nginx.conf syntax is ok nginx: configuration file /etc/nginx/nginx.conf test is successful [2026-09-13T12:05:09Z] nginx reloaded [2026-09-13T12:05:09Z] step 8/10 polling http://127.0.0.1:12888/api/arax/v1.4/status for up to 900s curl: (22) The requested URL returned error: 503 Service Unavailable curl: (22) The requested URL returned error: 503 Service Unavailable [2026-09-13T12:05:29Z] health check passed [2026-09-13T12:05:29Z] step 9/10 checking the public URL [2026-09-13T12:05:29Z] public url ok: https://cicd.rtx.ai/2888/ [2026-09-13T12:05:29Z] step 10/10 done ===================================================== ARAX preview deployed pr 2888 branch test-xcrg-ranker sha ab228be695bc63d40b144fdf8f691e2862a01c1d mode full reason --force was given url https://cicd.rtx.ai/2888/ port 127.0.0.1:12888 container rtx_pr_2888 image rtx:pr-2888 nginx /etc/nginx/arax-preview.d/2888.conf =====================================================
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Building wheels for collected packages: ipython-cypher, SQLAlchemy, pickledb, ujson, MarkupSafe, neo4j-driver, catrax-xcrg, neo4jrestclient, neobolt, neotime, stringcase, atomicwrites, pytest-logging
Building wheel for ipython-cypher (setup.py): started
Building wheel for ipython-cypher (setup.py): finished with status 'done'
Created wheel for ipython-cypher: filename=ipython_cypher-0.2.6-py3-none-any.whl size=13255 sha256=19169166db6e8227cf2debfdc7c181eacf286fab17071e2668a909c6e4461cf2
Stored in directory: /root/.cache/pip/wheels/a2/9a/6a/cbfdb7a2dcdead1c98798e360577e7f7e1378a568489d94640
Building wheel for SQLAlchemy (setup.py): started
Building wheel for SQLAlchemy (setup.py): finished with status 'done'
Created wheel for SQLAlchemy: filename=SQLAlchemy-1.4.47-cp312-cp312-linux_x86_64.whl size=1611568 sha256=0c3ad340235f6da1067275953d48d005d6576b5c3a1d27cb3c6e996a1c7307c1
Stored in directory: /root/.cache/pip/wheels/03/c7/09/4e868814a13d1e9a6fca219ba3b9bf30b0c064e5c7841497b2
Building wheel for pickledb (setup.py): started
Building wheel for pickledb (setup.py): finished with status 'done'
Created wheel for pickledb: filename=pickleDB-0.9.2-py3-none-any.whl size=4254 sha256=266007bc4c9d7d0de059d6e47052904d8e68977c2dda5d6f8c57379b36885dfd
Stored in directory: /root/.cache/pip/wheels/db/04/8d/3ee89a9642b0cf26e5b5660209326052b3e7ba6b5ce805f605
Building wheel for ujson (pyproject.toml): started
Building wheel for ujson (pyproject.toml): finished with status 'done'
Created wheel for ujson: filename=ujson-5.4.0-cp312-cp312-linux_x86_64.whl size=43015 sha256=9d8e73a17128905110d79c9774535a14b661fd88e5021db11b36ef20b39b921f
Stored in directory: /root/.cache/pip/wheels/d8/4d/fc/4737a6e4b748ee5f033a790b57d318c9c8e32d4300b977879b
Building wheel for MarkupSafe (setup.py): started
Building wheel for MarkupSafe (setup.py): finished with status 'done'
Created wheel for MarkupSafe: filename=MarkupSafe-2.1.2-cp312-cp312-linux_x86_64.whl size=27932 sha256=c8075ca82591e8c231345a442cf7080ddfc46b6fa7c24b3c2baedb7c9fe14467
Stored in directory: /root/.cache/pip/wheels/2c/40/ee/f5dc47077cc22aa7698564d653641f839cbe388a9be7a8a8e7
Building wheel for neo4j-driver (setup.py): started
Building wheel for neo4j-driver (setup.py): finished with status 'done'
Created wheel for neo4j-driver: filename=neo4j_driver-1.7.6-py3-none-any.whl size=32622 sha256=dcb7a10aeef2ca3d04b09c28e83f772710a27f2530609f078242364c8a810f8b
Stored in directory: /root/.cache/pip/wheels/09/68/2b/fdc98933c64886e37def8ede490fd48a190b50340948769ba8
Building wheel for catrax-xcrg (pyproject.toml): started
Building wheel for catrax-xcrg (pyproject.toml): finished with status 'done'
Created wheel for catrax-xcrg: filename=catrax_xcrg-0.1.0-py3-none-any.whl size=39060 sha256=533035d7856d539790bffa81b7017ad37ec087fac0db67428241a8de23f7bb7e
Stored in directory: /root/.cache/pip/wheels/66/f2/de/823a9b1919b0011d0316d50d053dd9274f693289af6e3fc49a
Building wheel for neo4jrestclient (setup.py): started
Building wheel for neo4jrestclient (setup.py): finished with status 'done'
Created wheel for neo4jrestclient: filename=neo4jrestclient-2.1.1-py2.py3-none-any.whl size=78547 sha256=1f1fdaec286ed63ed3ad21acfbdb12d4b0484e609b27c065705b0c79ab6ad25b
Stored in directory: /root/.cache/pip/wheels/67/eb/e9/f6d0a8066269bd38c0ed27df7c7b1b3efcaa728b7e97f3d641
Building wheel for neobolt (setup.py): started
Building wheel for neobolt (setup.py): finished with status 'done'
Created wheel for neobolt: filename=neobolt-1.7.17-py3-none-any.whl size=37161 sha256=4686cd84833e493d9c6a0faffdbfccb4e7f349a63c0f4115862c510182acfddf
Stored in directory: /root/.cache/pip/wheels/f3/86/66/faab2d0d10bb77d82ebd6810dae20fd0866f84d99a6ae86019
Building wheel for neotime (setup.py): started
Building wheel for neotime (setup.py): finished with status 'done'
Created wheel for neotime: filename=neotime-1.7.4-py3-none-any.whl size=20546 sha256=be0204942028b96b1dafd4c6db41e2eadc05aab5003e5ec65d2be22633a041a0
Stored in directory: /root/.cache/pip/wheels/31/cf/5a/d8e1e0c7910917c9f592a7e16782a40ae6130d7e4d55352f4c
Building wheel for stringcase (setup.py): started
Building wheel for stringcase (setup.py): finished with status 'done'
Created wheel for stringcase: filename=stringcase-1.2.0-py3-none-any.whl size=3569 sha256=99e755f603db85b37d110afa82618cf0c0748bccffdf4938414d473d1b99209e
Stored in directory: /root/.cache/pip/wheels/37/76/84/09143757ac9846675769f3649fc2aa936ec40255783a23ba52
Building wheel for atomicwrites (setup.py): started
Building wheel for atomicwrites (setup.py): finished with status 'done'
Created wheel for atomicwrites: filename=atomicwrites-1.4.1-py2.py3-none-any.whl size=6942 sha256=60dd205497a1afbd02d27b1499ea689921a2f2802820af95e8d6d8f6c2fa3d5c
Stored in directory: /root/.cache/pip/wheels/6b/37/a4/ae30755673c2d1e07228f13b4491fcaef62438f771d5012d07
Building wheel for pytest-logging (setup.py): started
Building wheel for pytest-logging (setup.py): finished with status 'done'
Created wheel for pytest-logging: filename=pytest_logging-2015.11.4-py3-none-any.whl size=4335 sha256=bfb37e06f8e44328a68dbce757372485735ac87e9ec3ca5f5e530a8604017abe
Stored in directory: /root/.cache/pip/wheels/53/cc/87/84a1b820986ced026baa0b549b27a0a0daf8a12fcd506bf3b5
Successfully built ipython-cypher SQLAlchemy pickledb ujson MarkupSafe neo4j-driver catrax-xcrg neo4jrestclient neobolt neotime stringcase atomicwrites pytest-logging
Attempting uninstall: click
Found existing installation: click 8.1.3
Uninstalling click-8.1.3:
Successfully uninstalled click-8.1.3
[91mWARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
[0mRemoving intermediate container df98108660f9
---> 4c8a76e4392c
Step 38/51 : RUN cd /mnt/data/orangeboard/production/RTX && python3 -m pip install 'connexion[swagger-ui]' --break-system-packages
---> Running in f5d1845276f5
Requirement already satisfied: connexion[swagger-ui] in /usr/local/lib/python3.12/dist-packages (2.14.2)
Requirement already satisfied: clickclick<21,>=1.2 in /usr/local/lib/python3.12/dist-packages (from connexion[swagger-ui]) (20.10.2)
Requirement already satisfied: jsonschema<5,>=2.5.1 in /usr/local/lib/python3.12/dist-packages (from connexion[swagger-ui]) (4.26.0)
Requirement already satisfied: PyYAML<7,>=5.1 in /usr/local/lib/python3.12/dist-packages (from connexion[swagger-ui]) (6.0.2)
Requirement already satisfied: requests<3,>=2.9.1 in /usr/local/lib/python3.12/dist-packages (from connexion[swagger-ui]) (2.32.3)
Requirement already satisfied: inflection<0.6,>=0.3.1 in /usr/local/lib/python3.12/dist-packages (from connexion[swagger-ui]) (0.5.1)
Requirement already satisfied: werkzeug<2.3,>=1.0 in /usr/local/lib/python3.12/dist-packages (from connexion[swagger-ui]) (2.2.3)
Requirement already satisfied: packaging>=20 in /usr/local/lib/python3.12/dist-packages (from connexion[swagger-ui]) (26.3)
Requirement already satisfied: flask<2.3,>=1.0.4 in /usr/local/lib/python3.12/dist-packages (from connexion[swagger-ui]) (2.2.5)
Requirement already satisfied: itsdangerous>=0.24 in /usr/local/lib/python3.12/dist-packages (from connexion[swagger-ui]) (2.2.0)
Requirement already satisfied: swagger-ui-bundle<0.1,>=0.0.2 in /usr/local/lib/python3.12/dist-packages (from connexion[swagger-ui]) (0.0.9)
Requirement already satisfied: click>=4.0 in /usr/local/lib/python3.12/dist-packages (from clickclick<21,>=1.2->connexion[swagger-ui]) (8.5.0)
Requirement already satisfied: Jinja2>=3.0 in /usr/local/lib/python3.12/dist-packages (from flask<2.3,>=1.0.4->connexion[swagger-ui]) (3.1.6)
Requirement already satisfied: attrs>=22.2.0 in /usr/local/lib/python3.12/dist-packages (from jsonschema<5,>=2.5.1->connexion[swagger-ui]) (26.1.0)
Requirement already satisfied: jsonschema-specifications>=2023.03.6 in /usr/local/lib/python3.12/dist-packages (from jsonschema<5,>=2.5.1->connexion[swagger-ui]) (2025.9.1)
Requirement already satisfied: referencing>=0.28.4 in /usr/local/lib/python3.12/dist-packages (from jsonschema<5,>=2.5.1->connexion[swagger-ui]) (0.37.0)
Requirement already satisfied: rpds-py>=0.25.0 in /usr/local/lib/python3.12/dist-packages (from jsonschema<5,>=2.5.1->connexion[swagger-ui]) (2026.6.3)
Requirement already satisfied: charset-normalizer<4,>=2 in /usr/local/lib/python3.12/dist-packages (from requests<3,>=2.9.1->connexion[swagger-ui]) (3.5.1)
Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.12/dist-packages (from requests<3,>=2.9.1->connexion[swagger-ui]) (3.19)
Requirement already satisfied: urllib3<3,>=1.21.1 in /usr/local/lib/python3.12/dist-packages (from requests<3,>=2.9.1->connexion[swagger-ui]) (2.5.0)
Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.12/dist-packages (from requests<3,>=2.9.1->connexion[swagger-ui]) (2026.7.22)
Requirement already satisfied: MarkupSafe>=2.1.1 in /usr/local/lib/python3.12/dist-packages (from werkzeug<2.3,>=1.0->connexion[swagger-ui]) (2.1.2)
Requirement already satisfied: typing-extensions>=4.4.0 in /usr/local/lib/python3.12/dist-packages (from referencing>=0.28.4->jsonschema<5,>=2.5.1->connexion[swagger-ui]) (4.16.0)
[91mWARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
[0mRemoving intermediate container f5d1845276f5
---> ddb568d5540c
Step 39/51 : RUN python3 -c "import requests; import click; import connexion; print('All packages imported successfully')" || (echo "ERROR: Packages not found" && exit 1)
---> Running in e7e295833cb8
All packages imported successfully
Removing intermediate container e7e295833cb8
---> b1d60d48c19e
Step 40/51 : RUN chown -R rt:rt /mnt/data/orangeboard/production/RTX
---> Running in 19ae83581b63
Removing intermediate container 19ae83581b63
---> 9b0cb43579ed
Step 41/51 : RUN export DEVAREA=production
---> Running in 6ca8a5f4994a
Removing intermediate container 6ca8a5f4994a
---> 1cb8069c8715
Step 42/51 : RUN cat /mnt/data/orangeboard/production/RTX/code/UI/OpenAPI/python-flask-server/RTX_OpenAPI | sed 's/template/production/g' > /etc/init.d/RTX_OpenAPI_production
---> Running in 6c0e3b47e041
Removing intermediate container 6c0e3b47e041
---> 50c4472b32a3
Step 43/51 : RUN chmod 700 /etc/init.d/RTX_OpenAPI_production
---> Running in 77725c040f99
Removing intermediate container 77725c040f99
---> 286ba10e0a60
Step 44/51 : RUN su - rt -c "cd /mnt/data/orangeboard/production/RTX/code/UI/OpenAPI/python-flask-server && cp -p RTX_OpenAPI RTX_OpenAPI_production && sed -i 's/template/production/g' RTX_OpenAPI_production"
---> Running in c9e30b7326a9
Removing intermediate container c9e30b7326a9
---> 1cfea079c845
Step 45/51 : RUN su - rt -c "cd /mnt/data/orangeboard/production/RTX/code/UI/OpenAPI/python-flask-server && cp -p RTX_OpenAPI.start RTX_OpenAPI_production.start && sed -i 's/template/production/g' RTX_OpenAPI_production.start"
---> Running in f675bf780df4
Removing intermediate container f675bf780df4
---> 7282a4c15315
Step 46/51 : RUN update-rc.d RTX_OpenAPI_production defaults
---> Running in bdfec148bb4e
Removing intermediate container bdfec148bb4e
---> fd9811050af1
Step 47/51 : RUN cat /mnt/data/orangeboard/production/RTX/code/autocomplete/RTX_Complete | sed 's/devED/production/g' > /etc/init.d/RTX_Complete
---> Running in d546b17bd7b0
Removing intermediate container d546b17bd7b0
---> dbdd58970049
Step 48/51 : RUN chmod 700 /etc/init.d/RTX_Complete
---> Running in 0c4e6c8251c1
Removing intermediate container 0c4e6c8251c1
---> 29ff408dd5d6
Step 49/51 : RUN cd /mnt/data/orangeboard/production/RTX/code/autocomplete && sed -i 's/devED/production/g' RTX_Complete.start
---> Running in 569e280964c6
Removing intermediate container 569e280964c6
---> 471e7c67cf43
Step 50/51 : RUN update-rc.d RTX_Complete defaults
---> Running in ed77d9ef9239
Removing intermediate container ed77d9ef9239
---> cacf8380fbc1
Step 51/51 : RUN su - rt -c "cd /mnt/data/orangeboard/production/RTX/code/ && echo 'Github actions ARAX test suite' > config.domain"
---> Running in 2fd004cbd90a
Removing intermediate container 2fd004cbd90a
---> 19bf8a2ef162
Successfully built 19bf8a2ef162
Successfully tagged rtx:pr-2888