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: "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: