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Queue: PublicMetaMap
Subject: Socket closes randomly if Metamap runs on a remote server
Status: open
Created: Mon Nov 19 08:53:28 2012
Resolved: Not set
LastUpdated: Mon Nov 19 08:56:47 2012

Subject: Socket closes randomly if Metamap runs on a remote server
Creator: 28
Created: 2012-11-19 13:53:28
Transaction: 1810
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: text/plain
ContentEncoding: none

Content: 
         >Category: mmtxT
         >Synopsis: Socket closes randomly if Metamap runs on a remote server
         >Confidential: no
         >Severity: serious
         >Priority: high
         >Class: sw-bug
         >Submitter-Id: mmtxWeb
         >Release:
         >Environment:
         >Operating System - MetaMap:
         >OS Version - Linux 3.2.24.1.amd64-smp Debian (Squeeze)
         >Java Version - Java 1.7
         >Description:
         Socket closes randomly if Metamap runs on a remote server.
         We are sending a request every 0.5 second. After a random number of 
         requests the following exception will be thrown:
         
         PBMonitor: need to interrupt read/write!
         Error when querying Prolog Server: Socket closed
         
         java.net.SocketException: Socket closed
         	at java.net.SocketInputStream.socketRead0(Native Method)
         	at java.net.SocketInputStream.read(SocketInputStream.java:129)
         	at java.io.BufferedInputStream.fill(BufferedInputStream.java:218)
         	at java.io.BufferedInputStream.read(BufferedInputStream.java:237)
         	at se.sics.prologbeans.FastParser.parseProlog(FastParser.java:96)
         	at se.sics.prologbeans.PrologSession.send(PrologSession.java:413)
         	at se.sics.prologbeans.PrologSession.executeQuery(PrologSession.java:350)
         	at 
         gov.nih.nlm.nls.metamap.MetaMapApiImpl.processCitationsFromString(MetaMapApiImpl.java:323)
         	at ...
         >How-To-Repeat:
         - Start Metamap on a Linux server
         - Send requests from a client
         - After a random number of requests an exception will be thrown
         
         >Unformatted:




Subject: 
Creator: 28
Created: 2012-11-19 13:56:46
Transaction: 1814
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: text/html
ContentEncoding: none

Content: 
         Sent message to requestor:
         
         Is it possible to combine requests by separating them with blank lines?
         
         Each MetaMap request can take a significant amount of time to complete. 
           The server may be running out resources before any pending requests 
         are completed.
         
         The MetaMap API's server is currently built on top of PrologBeans 
         written in SICS 
         (http://www.sics.se/sicstus/docs/latest4/html/sicstus.html/lib_002dprologbeans.html#lib_002dprologbeans) 
         and uses SICS's server implementation.
         
         
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