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There are three RF2 terminology loaders (Full, Snapshot, and Delta), a ClaML terminology loader, and a general terminology remover.

Loading RF2

The RF2 full loader will load a complete set of RF2 Full files (e.g. from a SNOMEDCT International release or an NRC release).  This is used to load an initial version of SNOMEDCT with history. This is implemented as a call to the snapshot loader (for the initial release) followed by a series of calls to the delta loader (for each incremental release. "Release info" objects are created for each contained release. 

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  • A profile indicating RF2-full must be specified
    • e.g. -PRF2-full
    • See profiles in the pom.xml
  • run.config.ts - the standard configuration file specified as a -D parameter
  • input.dir - the input directory for the RF2 data
  • terminology - the terminology value to use when loading
  • version - the (optional) terminology version, the value "latest" is used by default.
  • server - true/false indicating whether to run the mojo through the server 
  • loader.defaultPreferredNames.typeId - specified in the properties file specified by run.config.ts

    • This is the RF2 preferred description typeId to use for computing concept preferred names.

  • loader.defaultPreferredNames.refSetId - specified in the properties file specified by run.config.ts
    • This is the RF2 preferred description language refSetId to use for computing concept preferred names

  • loader.defaultPreferredNames.acceptabilityId - specified in the properties file specified by run.config.ts

    • This is the RF2 language refset acceptability typeId to use for computing concept preferred names

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  • A profile indicating RF2-snapshot must be specified
    • e.g. -PRF2-snapshot
    • See profiles in the pom.xml
  • run.config.ts - the standard configuration file specified as a -D parameter
  • input.dir - the input directory for the RF2 data
  • terminology - the terminology value to use when loading
  • version - the (optional) terminology version, the value "latest" is used by default.
  • server - true/false indicating whether to run the mojo through the server 
  • loader.defaultPreferredNames.typeId - specified in the properties file specified by run.config.ts

    • This is the RF2 preferred description typeId to use for computing concept preferred names.

  • loader.defaultPreferredNames.refSetId - specified in the properties file specified by run.config.ts
    • This is the RF2 preferred description language refSetId to use for computing concept preferred names

  • loader.defaultPreferredNames.acceptabilityId - specified in the properties file specified by run.config.ts

    • This is the RF2 language refset acceptability typeId to use for computing concept preferred names

 

The RF2 delta loader is used to process an incremental release delta of SNOMEDCT.  A "release info" object is created for the delta release.

Mojo: TerminologyRf2DeltaLoaderMojo.java (in admin/mojo/src/main/resources/java/org/ihtsdo/otf/ts/mojo)

Project: admin/loader

Configuration Parameters

  • A profile indicating RF2-delta must be specified
    • e.g. -PRF2-delta
    • See profiles in the pom.xml
  • run.config.ts - the standard configuration file specified as a -D parameter
  • input.dir - the input directory for the RF2 data
  • terminology - the terminology value to use when loading
  • server - true/false indicating whether to run the mojo through the server 
  • lastPublicationDate - the last published terminology version from which this delta is relative..
  • loader.defaultPreferredNames.typeId - specified in the properties file specified by run.config.ts

    • This is the RF2 preferred description typeId to use for computing concept preferred names.

  • loader.defaultPreferredNames.refSetId - specified in the properties file specified by run.config.ts
    • This is the RF2 preferred description language refSetId to use for computing concept preferred names

  • loader.defaultPreferredNames.acceptabilityId - specified in the properties file specified by run.config.ts

    • This is the RF2 language refset acceptability typeId to use for computing concept preferred names

 

Loading ClaML

The ClaML loader is used to load ClaML-based terminologies into the mapping tool.  This includes ICD10 which is natively in ClaML as well as other terminologies like ICD9CM and ICPC ICD9CM that have been converted to ClaML.

Mojo: TerminologyClamlLoaderMojo.java (in admin/mojo/src/main/resources/java/org/ihtsdo/otf/mappingts/mojo)

Project: admin/loader

Configuration Parameters

  • A profile indicating ClaML must be specified
    • e.g. -PClaML
    • See profiles in the pom.xml
  • run.config.ts - the standard configuration file specified as a -D parameter
  • input.file - the input ClaML file
  • terminology - the ClaML-based terminology being loaded (e.g. ICD10)
  • version - the (optional) terminology version, the value "latest" is used by default
  • server - true/false indicating whether to run the mojo through the server 

 

Removing a Terminology

The terminology remover is used to remove any terminology (and version) from the database, regardless of what loader was used to load it.

Mojo: TerminologyRemoverMojo.java (in admin/mojo/src/main/resources/java/org/ihtsdo/otf/mappingts/mojo)

Project: admin/remover

Configuration Parameters

  • A profile of "Terminology" must be passed
  • run.config.ts - the standard configuration file specified as a -D parameter
  • terminology - the terminology to remove (e.g. ICPCICD9CM)
  • version - the terminology version to remove, the default is "latest"
  • server - true/false indicating whether to run the mojo through the server 

Sample

Sample command line call of the admin tool to load SNOMEDCT RF2 snapshot using the version "latest":

 

% cd ~/code/admin/loader
% mvn install -PRF2-snapshot -Drun.config.ts=/home/ec2-tomcat/config/config.properties -Dterminology=SNOMEDCT -Dinput.dir=/home/ec2-tomcat/data/snomedct-20140731-mini

 

Sample command line call of the admin tool to load SNOMEDCT RF2 full using the version "latest":

 

% cd ~/code/admin/loader
% mvn install -PRF2-full -Drun.config.ts=/home/
ihtsdo
ec2-tomcat/config/config.properties -Dterminology=SNOMEDCT -Dinput.dir=/home/
ihstdo
ec2-tomcat/data/snomedct-20140731
-snapshot
-minif

 

Sample command line call of the admin tool to load ICD9CM using the version "2013":

 

% cd ~/code/admin/loader
% mvn install -PClaML -Drun.config.ts=/home/ec2-tomcat/config/config.properties -Dterminology=ICD9CM -Dversion=2013 -Dinput.file=/home/ec2-tomcat/data/icd9cm-2013.xml

 

Sample command line call of the admin tool to remove ICPCID9CM:

 

% cd ~/code/admin/remover
% mvn install -PTerminology -Drun.config.ts=/home/ihtsdoec2-tomcat/config/config.properties -Dterminology=ICPC ICD9CM -Dversion=20102013

 

 

Sample Eclipse run configuration for loading SNOMEDCT RF2 snapshot:

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Sample Eclipse run configuration for loading SNOMED CT:Image Removed]SNOMEDCT RF2 full data set:

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Sample command line call of the admin tool to load ICD9CM using the version "2013"

Image Added

 

Sample Eclipse run configuration for removing ICPCICD9CM:

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Troubleshooting

Occasionally the load of a terminology will fail for one reason or another. If the process does not run to completion, it is a recommend practice to remove the terminology before attempting to import it again.

 

# stop the server
% service tomcat7 stop

 
# attempt to load ICPCICD9CM
% cd ~/code/admin/loader
% mvn install -PClaML -Drun.config.ts=/home/ihtsdoec2-tomcat/config/config.properties -Dterminology=ICPC ICD9CM -Dversion=20102013 -Dinput.file=/home/ihtsdoec2-tomcat/data/icpcicd9cm-22013.xml
 
... perhaps a failure occurs here during the process
 
# Run the remover
% cd ~/code/admin/remover
% mvn install -PTerminology -Drun.config.ts=/home/ec2-tomcat/ihtsdoconfigconfig/config.properties -Dterminology=ICPC ICD9CM -Dversion=20102013
 
# attempt to load ICPC ICD9CM again
% cd ~/code/admin/loader
% mvn install -PClaML -Drun.config.ts=/home/ihtsdoec2-tomcat/config/config.properties -Dterminology=ICPC ICD9CM -Dversion=20102013 -Dinput.file=/home/ihtsdoec2-tomcat/data/icpcicd9cm-22013.xml

 

 

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