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Queue: PublicMetaMap
Subject: "Strings of death" bring down MetaMap server
Status: open
Created: Mon Jun 10 11:49:55 2013
Resolved: Not set
LastUpdated: Mon Jun 10 17:13:06 2013

Subject: 
Creator: 28
Created: 2013-06-10 15:49:55
Transaction: 1937
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: text/plain
ContentEncoding: none

Content: 
         >Category: mmtxT
         >Synopsis: "Strings of death" bring down MetaMap server
         >Confidential: no
         >Severity: critical
         >Priority: high
         >Class: sw-bug
         >Submitter-Id: mmtxWeb
         >Release: 
         >Environment:
         >Operating System - MetaMap: 
         >OS Version - 2.6.27.56-0.1-default x86_64 (Suse Linux Enterprise Server 11)
         >Java Version - Java 1.7
         >Description:
         Various strings found in clinical text (even simple ones) bring down the MetaMap server. They include simple strings such as the ones list in the reproduce section. I am using the version of MetaMap that Will Rogers sent me in March that fixes another bug related to clinical text.
         
         On the server side I get this output:
         /usr/local/share/public_mm/bin/SKRrun.12 /usr/local/share/public_mm/bin/mmserver12.BINARY.Linux -L 2012 -Z 12
         Server options: [port(8066),accepted_hosts(['127.0.0.1'])]
         Berkeley DB databases (USAbase 2012AA strict model) are open.
         Static variants will come from table varsan in /usr/local/share/public_mm/DB/DB.USAbase.2012AA.strict.
         Derivational Variants: Adj/noun ONLY.
         Accessing lexicon /usr/local/share/public_mm/lexicon/data/lexiconStatic2012.
         Variant generation mode: static.
         port:8066
         Established connection to Tagger Server on localhost.
         #### ERROR: process_text/4 failed for
         [[],"Allergies"]
         
         
         On the client side I get:
         
         
         AD\[email redacted]:~/bin/public_mm> bin/testapi.sh wi
         serverport: 8066
         options: []
         terms: wi
         input file: wi
         
         Error when querying Prolog Server: Not a fast prolog expression-1
         
         java.io.IOException: Not a fast prolog expression-1
                 at se.sics.prologbeans.FastParser.parseProlog(FastParser.java:104)
                 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(Met   aMapApiImpl.java:323)
                 at gov.nih.nlm.nls.metamap.MetaMapApiTest.process(MetaMapApiTest.java:62   )
                 at gov.nih.nlm.nls.metamap.MetaMapApiTest.main(MetaMapApiTest.java:304)
         Exception in thread "main" java.lang.RuntimeException: java.io.IOException: Not    a fast prolog expression-1
                 at gov.nih.nlm.nls.metamap.MetaMapApiImpl.processCitationsFromString(Met   aMapApiImpl.java:342)
                 at gov.nih.nlm.nls.metamap.MetaMapApiTest.process(MetaMapApiTest.java:62   )
                 at gov.nih.nlm.nls.metamap.MetaMapApiTest.main(MetaMapApiTest.java:304)
         Caused by: java.io.IOException: Not a fast prolog expression-1
                 at se.sics.prologbeans.FastParser.parseProlog(FastParser.java:104)
                 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(Met   aMapApiImpl.java:323)
                 ... 2 more
         AD\[email redacted]:~/bin/public_mm> cat wi
         
         Allergies
         
         AD\[email redacted]:~/bin/public_mm> echo $JAVA_HOME
         /opt/jdk
         AD\[email redacted]:~/bin/public_mm> ls -al /opt/jdk
         lrwxrwxrwx 1 root root 8 2013-01-17 11:26 /opt/jdk -> jdk1.7.0
         
         
         
         
         >How-To-Repeat:
         From the MetaMap directory
         ./test_api.sh wi
         
         Where wi is:"
         
         Allergies
         
         "
         
         or ./test_api.sh wo
         AD\[email redacted]:~/bin/public_mm> cat wo
         
         .
         Allergies
         .
         
         AD\[email redacted]:~/bin/public_mm>
         
         >Unformatted:




Subject: 
Creator: 28
Created: 2013-06-10 21:13:06
Transaction: 1943
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: text/html
ContentEncoding: none

Content: I'm not sure what is causing the issue you're having.  I haven't been able to re-produce it.   If you would like to try it,  I've built a new unstable distribution of the Java API server; this contains the latest updates to the MMServer.  It is available at:http://metamap.nlm.nih.gov/download/public_mm_linux_javaapi_2012_unstable.tar.bz2.

On Mon Jun 10 11:49:55 2013, wjrogers wrote:
>
> >Submitter: [email redacted]
> >Category: mmtxT
> >Synopsis: "Strings of death" bring down MetaMap server
> >Confidential: no
> >Severity: critical
> >Priority: high
> >Class: sw-bug
> >Submitter-Id: mmtxWeb
> >Originator: John Osborne ([email redacted])
> >Release:
> >Environment:
> >Operating System - MetaMap:
> >OS Version - 2.6.27.56-0.1-default x86_64 (Suse Linux Enterprise
> Server 11)
> >Java Version - Java 1.7
> >Description:
> Various strings found in clinical text (even simple ones) bring down
> the MetaMap server. They include simple strings such as the ones
> list in the reproduce section. I am using the version of MetaMap
> that Will Rogers sent me in March that fixes another bug related to
> clinical text.
>
> On the server side I get this output:
> /usr/local/share/public_mm/bin/SKRrun.12
> /usr/local/share/public_mm/bin/mmserver12.BINARY.Linux -L 2012 -Z
> 12
> Server options: [port(8066),accepted_hosts(['127.0.0.1'])]
> Berkeley DB databases (USAbase 2012AA strict model) are open.
> Static variants will come from table varsan in
> /usr/local/share/public_mm/DB/DB.USAbase.2012AA.strict.
> Derivational Variants: Adj/noun ONLY.
> Accessing lexicon
> /usr/local/share/public_mm/lexicon/data/lexiconStatic2012.
> Variant generation mode: static.
> port:8066
> Established connection to Tagger Server on localhost.
> #### ERROR: process_text/4 failed for
> [[],"Allergies"]
>
>
> On the client side I get:
>
>
> AD\[email redacted]:~/bin/public_mm> bin/testapi.sh wi
> serverport: 8066
> options: []
> terms: wi
> input file: wi
>
> Error when querying Prolog Server: Not a fast prolog expression-1
>
> java.io.IOException: Not a fast prolog expression-1
> at
> se.sics.prologbeans.FastParser.parseProlog(FastParser.java:104)
> 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(Met
> aMapApiImpl.java:323)
> at
> gov.nih.nlm.nls.metamap.MetaMapApiTest.process(MetaMapApiTest.java:62
> )
> at
> gov.nih.nlm.nls.metamap.MetaMapApiTest.main(MetaMapApiTest.java:304)
> Exception in thread "main" java.lang.RuntimeException:
> java.io.IOException: Not a fast prolog expression-1
> at
> gov.nih.nlm.nls.metamap.MetaMapApiImpl.processCitationsFromString(Met
> aMapApiImpl.java:342)
> at
> gov.nih.nlm.nls.metamap.MetaMapApiTest.process(MetaMapApiTest.java:62
> )
> at
> gov.nih.nlm.nls.metamap.MetaMapApiTest.main(MetaMapApiTest.java:304)
> Caused by: java.io.IOException: Not a fast prolog expression-1
> at
> se.sics.prologbeans.FastParser.parseProlog(FastParser.java:104)
> 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(Met
> aMapApiImpl.java:323)
> ... 2 more
> AD\[email redacted]:~/bin/public_mm> cat wi
>
> Allergies
>
> AD\[email redacted]:~/bin/public_mm> echo $JAVA_HOME
> /opt/jdk
> AD\[email redacted]:~/bin/public_mm> ls -al /opt/jdk
> lrwxrwxrwx 1 root root 8 2013-01-17 11:26 /opt/jdk -> jdk1.7.0
>
>
>
>
> >How-To-Repeat:
> From the MetaMap directory
> ./test_api.sh wi
>
> Where wi is:"
>
> Allergies
>
> "
>
> or ./test_api.sh wo
> AD\[email redacted]:~/bin/public_mm> cat wo
>
> .
> Allergies
> .
>
> AD\[email redacted]:~/bin/public_mm>
>
> >Unformatted:


Subject: [PublicMetamap #46] "Strings of death" bring down MetaMap server 
Creator: 1
Created: 2013-06-10 21:13:06
Transaction: 1944
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: text/plain
ContentEncoding: none

Content: I'm not sure what is causing the issue you're having. I haven't been able to
         re-produce it. If you would like to try it, I've built a new unstable
         distribution of the Java API server; this contains the latest updates to the
         MMServer. It is available
         at:http://metamap.nlm.nih.gov/download/public_mm_linux_javaapi_2012_unstable.tar.bz2.
         
         On Mon Jun 10 11:49:55 2013, wjrogers wrote:
         >
         > >Category: mmtxT
         > >Synopsis: "Strings of death" bring down MetaMap server
         > >Confidential: no
         > >Severity: critical
         > >Priority: high
         > >Class: sw-bug
         > >Submitter-Id: mmtxWeb
         > >Release:
         > >Environment:
         > >Operating System - MetaMap:
         > >OS Version - 2.6.27.56-0.1-default x86_64 (Suse Linux Enterprise
         > Server 11)
         > >Java Version - Java 1.7
         > >Description:
         > Various strings found in clinical text (even simple ones) bring down
         > the MetaMap server. They include simple strings such as the ones
         > list in the reproduce section. I am using the version of MetaMap
         > that Will Rogers sent me in March that fixes another bug related to
         > clinical text.
         >
         > On the server side I get this output:
         > /usr/local/share/public_mm/bin/SKRrun.12
         > /usr/local/share/public_mm/bin/mmserver12.BINARY.Linux -L 2012 -Z
         > 12
         > Server options: [port(8066),accepted_hosts(['127.0.0.1'])]
         > Berkeley DB databases (USAbase 2012AA strict model) are open.
         > Static variants will come from table varsan in
         > /usr/local/share/public_mm/DB/DB.USAbase.2012AA.strict.
         > Derivational Variants: Adj/noun ONLY.
         > Accessing lexicon
         > /usr/local/share/public_mm/lexicon/data/lexiconStatic2012.
         > Variant generation mode: static.
         > port:8066
         > Established connection to Tagger Server on localhost.
         > #### ERROR: process_text/4 failed for
         > [[],"Allergies"]
         >
         >
         > On the client side I get:
         >
         >
         > AD\[email redacted]:~/bin/public_mm> bin/testapi.sh wi
         > serverport: 8066
         > options: []
         > terms: wi
         > input file: wi
         >
         > Error when querying Prolog Server: Not a fast prolog expression-1
         >
         > java.io.IOException: Not a fast prolog expression-1
         > at
         > se.sics.prologbeans.FastParser.parseProlog(FastParser.java:104)
         > 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(Met
         > aMapApiImpl.java:323)
         > at
         > gov.nih.nlm.nls.metamap.MetaMapApiTest.process(MetaMapApiTest.java:62
         > )
         > at
         > gov.nih.nlm.nls.metamap.MetaMapApiTest.main(MetaMapApiTest.java:304)
         > Exception in thread "main" java.lang.RuntimeException:
         > java.io.IOException: Not a fast prolog expression-1
         > at
         > gov.nih.nlm.nls.metamap.MetaMapApiImpl.processCitationsFromString(Met
         > aMapApiImpl.java:342)
         > at
         > gov.nih.nlm.nls.metamap.MetaMapApiTest.process(MetaMapApiTest.java:62
         > )
         > at
         > gov.nih.nlm.nls.metamap.MetaMapApiTest.main(MetaMapApiTest.java:304)
         > Caused by: java.io.IOException: Not a fast prolog expression-1
         > at
         > se.sics.prologbeans.FastParser.parseProlog(FastParser.java:104)
         > 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(Met
         > aMapApiImpl.java:323)
         > ... 2 more
         > AD\[email redacted]:~/bin/public_mm> cat wi
         >
         > Allergies
         >
         > AD\[email redacted]:~/bin/public_mm> echo $JAVA_HOME
         > /opt/jdk
         > AD\[email redacted]:~/bin/public_mm> ls -al /opt/jdk
         > lrwxrwxrwx 1 root root 8 2013-01-17 11:26 /opt/jdk -> jdk1.7.0
         >
         >
         >
         >
         > >How-To-Repeat:
         > From the MetaMap directory
         > ./test_api.sh wi
         >
         > Where wi is:"
         >
         > Allergies
         >
         > "
         >
         > or ./test_api.sh wo
         > AD\[email redacted]:~/bin/public_mm> cat wo
         >
         > .
         > Allergies
         > .
         >
         > AD\[email redacted]:~/bin/public_mm>
         >
         > >Unformatted:
         



Subject: [PublicMetamap #46] "Strings of death" bring down MetaMap server 
Creator: 1
Created: 2013-06-10 21:13:06
Transaction: 1945
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: text/plain
ContentEncoding: none

Content: I'm not sure what is causing the issue you're having. I haven't been able to
         re-produce it. If you would like to try it, I've built a new unstable
         distribution of the Java API server; this contains the latest updates to the
         MMServer. It is available
         at:http://metamap.nlm.nih.gov/download/public_mm_linux_javaapi_2012_unstable.tar.bz2.
         
         On Mon Jun 10 11:49:55 2013, wjrogers wrote:
         >
         > >Category: mmtxT
         > >Synopsis: "Strings of death" bring down MetaMap server
         > >Confidential: no
         > >Severity: critical
         > >Priority: high
         > >Class: sw-bug
         > >Submitter-Id: mmtxWeb
         > >Release:
         > >Environment:
         > >Operating System - MetaMap:
         > >OS Version - 2.6.27.56-0.1-default x86_64 (Suse Linux Enterprise
         > Server 11)
         > >Java Version - Java 1.7
         > >Description:
         > Various strings found in clinical text (even simple ones) bring down
         > the MetaMap server. They include simple strings such as the ones
         > list in the reproduce section. I am using the version of MetaMap
         > that Will Rogers sent me in March that fixes another bug related to
         > clinical text.
         >
         > On the server side I get this output:
         > /usr/local/share/public_mm/bin/SKRrun.12
         > /usr/local/share/public_mm/bin/mmserver12.BINARY.Linux -L 2012 -Z
         > 12
         > Server options: [port(8066),accepted_hosts(['127.0.0.1'])]
         > Berkeley DB databases (USAbase 2012AA strict model) are open.
         > Static variants will come from table varsan in
         > /usr/local/share/public_mm/DB/DB.USAbase.2012AA.strict.
         > Derivational Variants: Adj/noun ONLY.
         > Accessing lexicon
         > /usr/local/share/public_mm/lexicon/data/lexiconStatic2012.
         > Variant generation mode: static.
         > port:8066
         > Established connection to Tagger Server on localhost.
         > #### ERROR: process_text/4 failed for
         > [[],"Allergies"]
         >
         >
         > On the client side I get:
         >
         >
         > AD\[email redacted]:~/bin/public_mm> bin/testapi.sh wi
         > serverport: 8066
         > options: []
         > terms: wi
         > input file: wi
         >
         > Error when querying Prolog Server: Not a fast prolog expression-1
         >
         > java.io.IOException: Not a fast prolog expression-1
         > at
         > se.sics.prologbeans.FastParser.parseProlog(FastParser.java:104)
         > 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(Met
         > aMapApiImpl.java:323)
         > at
         > gov.nih.nlm.nls.metamap.MetaMapApiTest.process(MetaMapApiTest.java:62
         > )
         > at
         > gov.nih.nlm.nls.metamap.MetaMapApiTest.main(MetaMapApiTest.java:304)
         > Exception in thread "main" java.lang.RuntimeException:
         > java.io.IOException: Not a fast prolog expression-1
         > at
         > gov.nih.nlm.nls.metamap.MetaMapApiImpl.processCitationsFromString(Met
         > aMapApiImpl.java:342)
         > at
         > gov.nih.nlm.nls.metamap.MetaMapApiTest.process(MetaMapApiTest.java:62
         > )
         > at
         > gov.nih.nlm.nls.metamap.MetaMapApiTest.main(MetaMapApiTest.java:304)
         > Caused by: java.io.IOException: Not a fast prolog expression-1
         > at
         > se.sics.prologbeans.FastParser.parseProlog(FastParser.java:104)
         > 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(Met
         > aMapApiImpl.java:323)
         > ... 2 more
         > AD\[email redacted]:~/bin/public_mm> cat wi
         >
         > Allergies
         >
         > AD\[email redacted]:~/bin/public_mm> echo $JAVA_HOME
         > /opt/jdk
         > AD\[email redacted]:~/bin/public_mm> ls -al /opt/jdk
         > lrwxrwxrwx 1 root root 8 2013-01-17 11:26 /opt/jdk -> jdk1.7.0
         >
         >
         >
         >
         > >How-To-Repeat:
         > From the MetaMap directory
         > ./test_api.sh wi
         >
         > Where wi is:"
         >
         > Allergies
         >
         > "
         >
         > or ./test_api.sh wo
         > AD\[email redacted]:~/bin/public_mm> cat wo
         >
         > .
         > Allergies
         > .
         >
         > AD\[email redacted]:~/bin/public_mm>
         >
         > >Unformatted:
         



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