Investigate Timeout Error about biothings_explorer HOT 4 CLOSED

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.

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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

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Implemented in: ea23686

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