A query returns error "500"

PathwayCommons / cpath2

Biological pathway data integration and access platform (Pathway Commons)

http://www.pathwaycommons.org/pc2/

MIT License

6 stars 5 forks source link

A query returns error "500" #257

Closed IgorRodchenkov closed 7 years ago

IgorRodchenkov commented 7 years ago

Fails:

http://www.pathwaycommons.org/pc2/graph?kind=neighborhood&format=binary_sif&source=PDGFRA&source=FGF9&source=LIF&source=CNTF&source=PTN&source=EDNRB&source=OLIG2&source=S100B&source=OLIG1&source=GFAP

or (its short version)

http://www.pathwaycommons.org/pc2/graph?kind=neighborhood&format=binary_sif&source=PDGFRA,FGF9,LIF,CNTF,PTN,EDNRB,OLIG2,S100B,OLIG1,GFAP

Most of other queries/genes - ok; also, it quickly gets BioPAX data if you remove '&format=binary_sif', which makes me think it might be the converter, i.e. Paxtools pattern module, performance/bug as well.

IgorRodchenkov commented 7 years ago

It's in fact error "504" ("Gateway Timeout") on the (proxy) server side, according to the log.

IgorRodchenkov commented 7 years ago

From the nginx/error.log:

2016/10/04 07:50:53 [error] 23958#0: *4315974 upstream timed out (110: Connection timed out) while reading response header from upstream, client: 192.168.188.82, server: , request: "GET /pc2/graph?kind=neighborhood&format=binary_sif&source=PDGFRA&source=FGF9&source=LIF&source=CNTF&source=PTN&source=EDNRB&source=OLIG2&source=S100B&source=OLIG1&source=GFAP HTTP/1.1", upstream: "http://127.0.0.1:8280/pc2/graph?kind=neighborhood&format=binary_sif&source=PDGFRA&source=FGF9&source=LIF&source=CNTF&source=PTN&source=EDNRB&source=OLIG2&source=S100B&source=OLIG1&source=GFAP", host: "192.168.81.153:48080"

IgorRodchenkov commented 7 years ago

FYI: despite this issue, PCViz got and displayed the network because it sits on the same server with PC2 service, and PCViz converts to SIF using own java code/service and using only three interaction types (BioPAX patterns) unlike the PC2 service that uses all the types (but neighbor_of), which takes too long to generate from large sub-networks...

IgorRodchenkov commented 7 years ago

Well, after I've increased timeouts on the PC proxy, new error is now returned by our lab's main Apache:

Proxy Error
The proxy server received an invalid response from an upstream server.
The proxy server could not handle the request GET /pc2/graph.
Reason: Error reading from remote server
Apache/2.2.22 (Debian) Server at www.pathwaycommons.org Port 80

IgorRodchenkov commented 7 years ago

Also, such graph queries as in the example, can quickly result in hundreds of Megabytes of biopax data to be downloaded by a client, which sometimes takes twenty or more minutes to get; and these look keep the server busy!..

IgorRodchenkov commented 7 years ago

Fixed in Paxtools, which, once the PC server is rebuilt and restarted, fixes this issue as well (the example query takes about two minutes to return the result).