Arax pathfinder

[mohsenht]

Hi @maximusunc,

Please review this pull request.

[codecov]

Codecov Report

❌ Patch coverage is 2.82486% with 172 lines in your changes missing coverage. Please review.
✅ Project coverage is 34.48%. Comparing base (928e4d8) to head (ce1a5e6).
⚠️ Report is 5 commits behind head on main.

Files with missing lines	Patch %	Lines
workers/arax_pathfinder/worker.py	0.00%	111 Missing ⚠️
workers/arax/worker.py	0.00%	35 Missing ⚠️
shepherd_utils/inject_shepherd_arax_provenance.py	0.00%	26 Missing ⚠️

Files with missing lines	Coverage Δ
shepherd_server/main.py	0.00% <ø> (ø)
shepherd_utils/config.py	100.00% <100.00%> (ø)
shepherd_utils/inject_shepherd_arax_provenance.py	0.00% <0.00%> (ø)
workers/arax/worker.py	0.00% <0.00%> (ø)
workers/arax_pathfinder/worker.py	0.00% <0.00%> (ø)

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[maximusunc]

I tried running a query through the ARAX pathfinder and it's unclear what happened. I got these logs:

arax_pathfinder  | 2026-02-04T16:02:05.361576: DEBUG: lookup map not here! /tmp/biolink/biolink_lookup_map_4.2.5_v5.pickle
arax_pathfinder  | 2026-02-04T16:02:07.267560: INFO: Building local Biolink 4.2.5 ancestor/descendant lookup map because one doesn't yet exist
arax_pathfinder  | [2026-02-04 16:02:07,299: INFO/shepherd.arax.pathfinder.e3355332.00527f4e]: Model release date: 12/01/2025
arax_pathfinder  | [2026-02-04 16:02:07,299: INFO/shepherd.arax.pathfinder.e3355332.00527f4e]: Finding paths process has started
arax_pathfinder  | [2026-02-04 16:02:07,300: INFO/shepherd.arax.pathfinder.e3355332.00527f4e]: Expanding CHEBI:45783
arax_pathfinder  | [2026-02-04 16:02:07,301: INFO/shepherd.arax.pathfinder.e3355332.00527f4e]: Expanding MONDO:0004979

but nothing else before it was timed out after 5 minutes. I sent it Imatinib->Asthma.

[mohsenht]

Hi @maximusunc,

I changed the parameters to make it faster for now. I will get back to Shepherd-pathfinder and check it probably next week to figure out what the problem is.

[maximusunc]

When testing with Imatinib->Asthma, your Pathfinder is returning 0 paths. Is this intended?

[maximusunc]

I'm not sure if your pathfinder code is asynchronous or not, but this call is blocking and so your pathfinder implementation can only handle one query at a time. Is this intended?

[mohsenht]

Hi @maximusunc

Could you please provide me your json query that you sent and got 0 paths?

[mohsenht]

Here is my query and I got result for this one.

{
    "message": {
        "query_graph": {
            "nodes": {
                "n0": {
                    "ids": [
                        "CHEBI:31690"
                    ]
                },
                "n1": {
                    "ids": [
                        "MONDO:0004979"
                    ]
                }
            },
            "paths": {
                "p0": {
                    "subject": "n0",
                    "object": "n1",
                    "predicates": [
                        "biolink:related_to"
                    ],
                    "constraints": []
                }
            }
        }
    }
}

[mohsenht]

It is now can handle multiple queries.