Investigate Timeout Error

[kevinxin90]

{
  "message": {
    "query_graph": {
      "nodes": {
        "n00": {
          "id": "name:Imatinib",
          "category": "biolink:ChemicalSubstance"
        },
        "n01": {
          "category": "biolink:Disease"
        },
        "n02": {
            "category": "biolink:Gene"
        }
      },
      "edges": {
        "e00": {
          "subject": "n00",
          "object": "n01",
          "predicate":"biolink:treats"
        },
        "e01": {
          "subject": "n01",
          "object": "n02",
          "predicate":"biolink:caused_by"
        }
      }
    }
  }
}

Above query results in a 504 timeout error in current BTE app. Need to investigate how that happens and how to set timeout on either express.js end or nginx end.

[kevinxin90]

The issue is caused by nginx settings on the server.

Based on this post.

We can update the nginx settings on the server located at /etc/nginx/nginx.conf

Add the following lines in the http section (note this set the timeout to be 5mins, can increase if needed.):

http {
fastcgi_read_timeout 300;
proxy_read_timeout 300;
}

Then reload nginx config

sudo service nginx reload

[kevinxin90]

Based on the log, it seems API query completes in a reasonable amount of time. However, it takes extremely long time to update node with the results (1 mins). Need to investigate why it takes such a long time.

[kevinxin90]

Previously, for each association, we update the knowledge graph (inputNode, outputNode, edge) using javascript spread operation. This is very inefficient. Now, it will first check if node/edge exists in knowledge graph, and then directly using dict assignment operation, which significantly reduce the time for this process.

Also, for nodeUpdate (which updates qNode with equivalent identifiers), we also apply the same logics and significantly cuts down the query time.

Now this query is able to completes within 20 seconds.

[kevinxin90]

Implemented in: ea23686