MySQL error?

[dkoslicki]

I'm seeing an error I haven't run into before; on https://arax.test.transltr.io/ the DSL

add_qnode(ids=NCBIGene:4233, key=n0)
add_qnode(ids=MONDO:0021117, key=n1)
connect(action=connect_nodes,max_path_length=3,shortest_path= false)
# connect(action=connect_nodes,max_path_length=3)
resultify()
filter_results(action=limit_number_of_results, max_results=100)

Gives a log message of:

2024-02-01T03:19:38.626488 DEBUG: Number of edges in KG with attributes is 733
2024-02-01T03:19:38.627183 DEBUG: Number of edges in KG by attribute Counter({None: 1745, 'biolink:knowledge_level': 59, 'biolink:agent_type': 50, 'max phase for indication': 32, 'agent_type': 9, 'pValue': 2, 'score': 2})
2024-02-01T03:19:38.627212 INFO: Transforming results to TRAPI 1.4 format (moving 'virtual' nodes/edges to support graphs)
2024-02-01T03:19:38.627234 DEBUG: Original input QG contained qnodes {'arax_connect_node_1', 'n1', 'n0'} and qedges {'connected_edge_2', 'connected_edge_1', 'connected_edge_3', 'subclass:n1--n1'}
2024-02-01T03:19:38.627245 DEBUG: Non-orphan qnodes in original QG are: {'arax_connect_node_1', 'n1', 'n0'}
2024-02-01T03:19:38.629921 DEBUG: Replacing ARAX's internal edited QG with the original input QG..
2024-02-01T03:19:38.629955 DEBUG: Virtual qedge keys moved to support_graphs were: set()
2024-02-01T03:19:38.629966 DEBUG: There are a total of 0 AuxiliaryGraphs.
2024-02-01T03:19:38.629975 INFO: Done transforming results to TRAPI 1.4 format (i.e., using support_graphs)
2024-02-01T03:19:38.630009 DEBUG: Storing resulting Message
2024-02-01T03:19:38.630027 DEBUG: Writing response record to MySQL
2024-02-01T03:19:38.633112 ERROR: Unable to store response record in MySQL   # <-----------
2024-02-01T03:22:39.151312 DEBUG: Query is still progressing...

Is there something up with our response cache/DB?

Tagging @edeutsch though let me know if someone else might know more

[dkoslicki]

Related to this, trying it out on CI instead of TEST, a different error gets thrown, but a full TRAPI message is returned, but just not rendered: and it seems to have a full response graph that is being rendered. Is this perhaps a UI issue @isbluis

[edeutsch]

hmm, I do not see anything obviously amiss. I can log in to the MySQL and execute commands manually. The recent activity views seems to show reasonable activity near your query time:

The errors appear to be processes rather than talking to the MySQL server.

So I'm guessing a transient error, unless you can repro it?

[edeutsch]

looks like the error is a KeyError in Resultify?

[isbluis]

Hi @dkoslicki . The returned TRAPI does not contain any results, so none are rendered:

However, you can still view and explore the Knowledge Graph:

It appears (to me) that the UI is displaying as much of the returned data as it is able to, but please feel free to re-tag me if this is not the case. Thanks!

[dkoslicki]

Thanks both; I'll keep working on it

[saramsey]

Any updates on this one? I guess it's not occurring too frequently in the wild?

[dkoslicki]

Yeah, I haven't been able to reproduce this error, so it's probably safe to close and I'll just keep an eye out for it