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Queue: PublicMetaMap
Subject: Instability when metamap server options and API metamap options both set
Status: stalled
Created: Wed Feb 27 17:49:36 2013
Resolved: Not set
LastUpdated: Tue Jun 11 10:28:17 2013

Subject: 
Creator: 28
Created: 2013-02-27 22:49:36
Transaction: 1838
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: text/plain
ContentEncoding: none

Content: 
         >Category: mmtxT
         >Synopsis: Instability when metamap server options and API metamap options both set
         >Confidential: no
         >Severity: serious
         >Priority: medium
         >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 1.6
         >Description:
         When running with options (I used combinations of word sense disambiguation and source vocabulary selection) in the MetaMap API in conjunction with source settings and word sense disambiguation settings in the metamap server instability results. By unstable I mean that source vocabulary restriction no longer works and a variable number of mapping candidates are generated - different on each run.
         
         I eventually realized I had been running the mmserver with options that I was trying to set in the API - then it went away. It caused a lot of grief though. :)
         >How-To-Repeat:
         Run the metamap server with source configuration options set, for example)
         
         bin/mmserver12 -y -R SNOMEDCT
         
         
         Now in the MetaMap API:
         		MetaMapApi api = new MetaMapApiImpl();
         	    List theOptions = new ArrayList();
         	    theOptions.add("-y");
                     theOptions.add("-R SNOMEDCT"); 
         if (theOptions.size() > 0) {
         	      api.setOptions(theOptions);
         	    }
         	    List resultList = api.processCitationsFromString("Hypertension");
         
         >Unformatted:




Subject: Instability when metamap server options and API metamap
Creator: 28
Created: 2013-03-05 14:08:18
Transaction: 1847
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: text/html
ContentEncoding: none

Content: Unfortunately, there is currently no easy way to fix this problem without requiring a significant rewrite to portions of MetaMap which we currently don't have resources to do.  Some options currently only work during the invocation of the MetaMap server.

Sincerely,
Willie Rogers


On Wed Feb 27 17:49:36 2013, wjrogers wrote:
>
> >Submitter: [email redacted]
> >Category: mmtxT
> >Synopsis: Instability when metamap server options and API metamap
> options both set
> >Confidential: no
> >Severity: serious
> >Priority: medium
> >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 1.6
> >Description:
> When running with options (I used combinations of word sense
> disambiguation and source vocabulary selection) in the MetaMap API
> in conjunction with source settings and word sense disambiguation
> settings in the metamap server instability results. By unstable I
> mean that source vocabulary restriction no longer works and a
> variable number of mapping candidates are generated - different on
> each run.
>
> I eventually realized I had been running the mmserver with options
> that I was trying to set in the API - then it went away. It caused
> a lot of grief though. :)
> >How-To-Repeat:
> Run the metamap server with source configuration options set, for
> example)
>
> bin/mmserver12 -y -R SNOMEDCT
>
>
> Now in the MetaMap API:
> MetaMapApi api = new MetaMapApiImpl();
> List<String> theOptions = new ArrayList<String>();
> theOptions.add("-y");
> theOptions.add("-R SNOMEDCT");
> if (theOptions.size() > 0) {
> api.setOptions(theOptions);
> }
> List<Result> resultList =
> api.processCitationsFromString("Hypertension");
>
> >Unformatted:


Subject: [PublicMetamap #38] Instability when metamap server options and API metamap 
Creator: 1
Created: 2013-03-05 14:08:19
Transaction: 1848
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: text/plain
ContentEncoding: none

Content: Unfortunately, there is currently no easy way to fix this problem without
         requiring a significant rewrite to portions of MetaMap which we currently don't
         have resources to do. Some options currently only work during the invocation of
         the MetaMap server.
         
         Sincerely,
         Willie Rogers
         
         
         On Wed Feb 27 17:49:36 2013, wjrogers wrote:
         >
         > >Category: mmtxT
         > >Synopsis: Instability when metamap server options and API metamap
         > options both set
         > >Confidential: no
         > >Severity: serious
         > >Priority: medium
         > >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 1.6
         > >Description:
         > When running with options (I used combinations of word sense
         > disambiguation and source vocabulary selection) in the MetaMap API
         > in conjunction with source settings and word sense disambiguation
         > settings in the metamap server instability results. By unstable I
         > mean that source vocabulary restriction no longer works and a
         > variable number of mapping candidates are generated - different on
         > each run.
         >
         > I eventually realized I had been running the mmserver with options
         > that I was trying to set in the API - then it went away. It caused
         > a lot of grief though. :)
         > >How-To-Repeat:
         > Run the metamap server with source configuration options set, for
         > example)
         >
         > bin/mmserver12 -y -R SNOMEDCT
         >
         >
         > Now in the MetaMap API:
         > MetaMapApi api = new MetaMapApiImpl();
         > List theOptions = new ArrayList();
         > theOptions.add("-y");
         > theOptions.add("-R SNOMEDCT");
         > if (theOptions.size() > 0) {
         > api.setOptions(theOptions);
         > }
         > List resultList =
         > api.processCitationsFromString("Hypertension");
         >
         > >Unformatted:
         



Subject: [PublicMetamap #38] Instability when metamap server options and API metamap 
Creator: 1
Created: 2013-03-05 14:08:19
Transaction: 1849
Parent: 0
MessageId: [email redacted]
Filename: 
ContentType: text/plain
ContentEncoding: none

Content: Unfortunately, there is currently no easy way to fix this problem without
         requiring a significant rewrite to portions of MetaMap which we currently don't
         have resources to do. Some options currently only work during the invocation of
         the MetaMap server.
         
         Sincerely,
         Willie Rogers
         
         
         On Wed Feb 27 17:49:36 2013, wjrogers wrote:
         >
         > >Category: mmtxT
         > >Synopsis: Instability when metamap server options and API metamap
         > options both set
         > >Confidential: no
         > >Severity: serious
         > >Priority: medium
         > >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 1.6
         > >Description:
         > When running with options (I used combinations of word sense
         > disambiguation and source vocabulary selection) in the MetaMap API
         > in conjunction with source settings and word sense disambiguation
         > settings in the metamap server instability results. By unstable I
         > mean that source vocabulary restriction no longer works and a
         > variable number of mapping candidates are generated - different on
         > each run.
         >
         > I eventually realized I had been running the mmserver with options
         > that I was trying to set in the API - then it went away. It caused
         > a lot of grief though. :)
         > >How-To-Repeat:
         > Run the metamap server with source configuration options set, for
         > example)
         >
         > bin/mmserver12 -y -R SNOMEDCT
         >
         >
         > Now in the MetaMap API:
         > MetaMapApi api = new MetaMapApiImpl();
         > List theOptions = new ArrayList();
         > theOptions.add("-y");
         > theOptions.add("-R SNOMEDCT");
         > if (theOptions.size() > 0) {
         > api.setOptions(theOptions);
         > }
         > List resultList =
         > api.processCitationsFromString("Hypertension");
         >
         > >Unformatted:
         



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