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Queue: PublicMetaMap
Subject: Apparent single quote error
Status: resolved
Created: Thu Aug 29 15:49:18 2013
Resolved: Thu Nov 14 14:34:20 2013
LastUpdated: Thu Nov 14 14:34:20 2013

Subject: 
Creator: 28
Created: 2013-08-29 19:49:19
Transaction: 1966
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: text/plain
ContentEncoding: none

Content: 
         >Category: mmtxT
         >Synopsis: Apparent single quote error
         >Confidential: no
         >Severity: serious
         >Priority: medium
         >Class: sw-bug
         >Submitter-Id: mmtxWeb
         >Release: 
         >Environment:
         >Operating System - MetaMap: 
         >OS Version - Linux carasgaladon 3.10.7-1-ARCH #1 SMP PREEMPT Thu Aug 15 11:55:34 CEST 2013 x86_64 GNU/Linux
         >Java Version - Java 1.7
         >Description:
         Entering the following text causes Metamap to crash:
         
         non-contributory for premature CAD ; father had MI in his 70 's
         
         The Error is:
         
         #### ERROR: process_text/4 failed for
         ["non-contributory for premature CAD ; father had MI in his 70 's"]
         
         
         Removing the space between 70 and 's eliminates the problem and correct output is received. 
         >How-To-Repeat:
         Metamap run with the following information:
         
         /mnt/public_mm/bin/SKRrun.12 /mnt/public_mm/bin/metamap12.BINARY.Linux -L 2012 -Z 2012AA --XMLf --restrict_to_sts lbpr,lbtr,diap,patf,dsyn,mobd,comd,cgab,acab,inpo,anab,neop,virs,bact,sosy,topp,medd,strd,phsu,bodm,antb,clnd,drdd
                      Berkeley DB databases (USAbase 2012AA strict model) are open.
                      Static variants will come from table varsan in /mnt/public_mm/DB/DB.USAbase.2012AA.strict.
                      Derivational Variants: Adj/noun ONLY.
                      Accessing lexicon /mnt/public_mm/lexicon/data/lexiconStatic2012.
                      Variant generation mode: static.
                      
                      metamap12.BINARY.Linux (2012)
                      
                      Control options:
                      lexicon_year=2012
                      mm_data_year=2012AA
                      XMLf
                      restrict_to_sts=[lbpr,lbtr,diap,patf,dsyn,mobd,comd,cgab,acab,inpo,anab,neop,virs,bact,sosy,topp,medd,strd,phsu,bodm,antb,clnd,drdd]
         
         |: non-contributory for premature CAD ; father had MI in his 70 's
         |: 
         #### ERROR: process_text/4 failed for
         ["non-contributory for premature CAD ; father had MI in his 70 's"]
         
         
         >Unformatted:




Subject: [PublicMetamap #48] Apparent single quote error 
Creator: 1
Created: 2013-08-30 14:41:50
Transaction: 1977
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: text/plain
ContentEncoding: none

Content: 
         Fri Aug 30 10:41:50 2013: Request 48 was acted upon.
          Transaction: Given to flang by wjrogers
                Queue: PublicMetaMap
              Subject: Apparent single quote error
                Owner: flang
           Requestors: [email redacted]
               Status: new
          Ticket 
         
         
         This transaction appears to have no content



Subject: 
Creator: 28
Created: 2013-08-30 14:59:25
Transaction: 1980
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: text/html
ContentEncoding: none

Content: There is a fix that was planned for inclusion in 2013 version of MetaMap (to be released soon...).   The following is the unstable version which appears to not exhibit the problem:

http://metamap.nlm.nih.gov/download/public_mm_linux_binary_2012_unstable.tar.bz2

Extract the archive in the parent directory were you install the main distribution.  Then cd to the public_mm directory and re-run bin/install.sh.

You should be able to run the updated bin/metamap12 after running bin/install.sh.

Sincerely,
Willie Rogers
Subject: [PublicMetamap #48] Apparent single quote error 
Creator: 1
Created: 2013-08-30 14:59:25
Transaction: 1981
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: text/plain
ContentEncoding: none

Content: There is a fix that was planned for inclusion in 2013 version of MetaMap (to be
         released soon...). The following is the unstable version which appears to not
         exhibit the problem:
         
         http://metamap.nlm.nih.gov/download/public_mm_linux_binary_2012_unstable.tar.bz2
         
         Extract the archive in the parent directory were you install the main
         distribution. Then cd to the public_mm directory and re-run bin/install.sh.
         
         You should be able to run the updated bin/metamap12 after running
         bin/install.sh.
         
         Sincerely,
         Willie Rogers
         



Subject: [PublicMetamap #48] Apparent single quote error 
Creator: 1
Created: 2013-08-30 14:59:25
Transaction: 1982
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: text/plain
ContentEncoding: none

Content: There is a fix that was planned for inclusion in 2013 version of MetaMap (to be
         released soon...). The following is the unstable version which appears to not
         exhibit the problem:
         
         http://metamap.nlm.nih.gov/download/public_mm_linux_binary_2012_unstable.tar.bz2
         
         Extract the archive in the parent directory were you install the main
         distribution. Then cd to the public_mm directory and re-run bin/install.sh.
         
         You should be able to run the updated bin/metamap12 after running
         bin/install.sh.
         
         Sincerely,
         Willie Rogers
         



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