'n_drugs' parameter appears to not function correctly when passing in an integer via a TRAPI Query

[DnlRKorn]

Hey all,

I'm playing around with toggling the number of results from a specific TRAPI query. When I run the following query

{ "message": {"query_graph": { "nodes": { "disease": { "ids": ["MONDO:0004975"] }, "chemical": { "categories": ["biolink:ChemicalEntity"] } }, "edges": { "t_edge": { "object": "disease", "subject": "chemical", "predicates": ["biolink:treats"], "knowledge_type": "inferred" } } } }, "operations": {"actions": [ "infer(action=drug_treatment_graph_expansion,node_curie=MONDO:0004975,qedge_id=t_edge,n_drugs=10)", "return(message=true, store=true)" ]} }

I get this response "description": "The n_drugs value must be a positive integer. The provided value was 10.

I'm pretty sure this is being caused by the following section of the code. https://github.com/RTXteam/RTX/blob/5945133b6358c73654102eb2892d47916d01747c/code/ARAX/ARAXQuery/ARAX_infer.py#L396-L405

When testing some of the other "operations":"actions" I was able to get them working. Looking at their parameter parsing I see it executes eval when the parameter passed in is a string, which causes the values to be properly read. https://github.com/RTXteam/RTX/blame/5945133b6358c73654102eb2892d47916d01747c/code/ARAX/ARAXQuery/ARAX_infer.py#L522

https://github.com/RTXteam/RTX/blob/5945133b6358c73654102eb2892d47916d01747c/code/ARAX/ARAXQuery/ARAX_infer.py#L544 https://github.com/RTXteam/RTX/blob/5945133b6358c73654102eb2892d47916d01747c/code/ARAX/ARAXQuery/ARAX_infer.py#L557 https://github.com/RTXteam/RTX/blob/5945133b6358c73654102eb2892d47916d01747c/code/ARAX/ARAXQuery/ARAX_infer.py#L570

Let me know if I can provide any more details for this!

[chunyuma]

Hi @DnlRKorn, thanks for reporting this error.

@edeutsch, I've fixed this error. Could you please help deploy the latest master code? Thanks!

[edeutsch]

sure, the latest master has been rolled out to the usual locations following the master branch.

 code/ARAX/ARAXQuery/ARAX_infer.py            |  61 +++++++++--------
 code/ARAX/Documentation/DSL_Documentation.md | 328 +++++++++++++++++++++++++++++++++++++++++++++---------------------------------------------
 code/ARAX/test/test_ARAX_infer.py            |  51 ++++++++++++--

[chunyuma]

Thanks @edeutsch! I'm wondering if it has been rolled out to the production server.

I just tested a query on arax.ncats.io:

{
        "message": {"query_graph": {
            "nodes": {
                "disease": {
                    "ids": ["MONDO:0004975"]
                },
                "chemical": {
                    "categories": ["biolink:ChemicalEntity"]
                }
            },
            "edges": {
                "t_edge": {
                    "object": "disease",
                    "subject": "chemical",
                    "predicates": ["biolink:treats"],
                    "knowledge_type": "inferred"
                }
            }
        }
        },
        "operations": {"actions": [
            "infer(action=drug_treatment_graph_expansion,node_curie=MONDO:0004975,qedge_id=t_edge,n_drugs=10,n_paths=10)",
            "return(message=true, store=true)"
        ]}
    }

It seems not to work. But when I tested it locally, it works for me (https://arax.ncats.io/?r=456).

[edeutsch]

@chunyuma will test on /beta to verify that works. Requests to roll out to production will be made this Friday.

[chunyuma]

Thanks @edeutsch.

Hi @DnlRKorn, we fixed this error on https://arax.ncats.io/beta. Please try it now. I tried it and it works.

[chunyuma]

Once it is rolled out to the production, we can close this issue.

[chunyuma]

close it as it has been resolved.