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LoadPickListDefinition

Loads Pick List Definition content, provided in LexGrid canonical xml format.
Options:

  • -in,-input <uri> URI or path specifying location of the source file.
  • -v, -validate <int> Perform validation of the candidate resource without loading data.
    Supported levels of validation include:
    • 0 = Verify document is well-formed

    • 1 = Verify document is valid
      Example:

       

      LoadPickListDefinition -in "file:///path/to/file.xml"

LoadAllDefinitionsToResolvedValueSet

Loads All Value Set Definitions for a given uri as resolved coding scheme.
Options:

 

LoadAllDefinitionsToResolvedValueSet  -uri "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"
LoadValueSetDefinition.sh

Loads Value Set Definition content, provided in LexGrid canonical xml format.

Options:

  • -in, Input <uri> URI or path specifying location of the source file.
  • -v, Validate <int> Perform validation of the candidate

    resource without loading data.  Supported levels of validation include:

       0 = Verify document is well-formed

       1 = Verify document is valid


    Load Example:

     

    LoadValueSetDefinition -in "file:///path/to/file.xml"
SourceAssertedResolvedValueSetLoad

Loads all source asserted Value Sets from a given source.

Options:

   -cs, --codingScheme, usage="Name of Coding Scheme that asserts values sets"

   -v, --version, usage="Version of the coding scheme."

   -a, --association, usage="Relationship name asserted by the codingScheme")

   -t", --target", usage="Target to Source resolution.")

   -uri", --uri", usage="Base uri to build the conding scheme uri upon")

   -o", --owner", usage="Owener of the value set assertioin")

   -s", --sourceName", usage="Gives the name of the property to resolve the source value against")

 Load Example:

 

SourceAssertedResolvedValueSetLoad.sh -v "17.04d"
SourceAssertedValueSetDefinitionLoad

Loads all source asserted Value Sets from a given source.

Options:

   -cs, --codingScheme, usage="Name of Coding Scheme that asserts values sets"

   -v, --version, usage="Version of the coding scheme."

   -a, --association, usage="Relationship name asserted by the codingScheme"

   -t", --target", usage="Target to Source resolution."

   -uri", --uri", usage="Base uri to build the conding scheme uri upon"

   -o", --owner", usage="Owener of the value set assertioin"

   -s", --sourceName", usage="Gives the name of the property to resolve the source value against"

   -cd, --conceptDomainName" usage= "Gives the name of the property to resolve the concept domain value against"

Load Example:

 

SourceAssertedValueSetDefinitionLoad -v "17.04d"
SourceAssertedValueSetUpdate

Loads all source asserted Value Sets from a given source.
 
Options:
  -cs  -codingScheme - Name of Coding Scheme that asserts values sets
   default "NCI_Thesaurus"


  -pv --pversion - Previous version of the coding scheme.
   Optional default none


  -cv --cversion - Version of the coding scheme. User must input a current version.
   default none;


  -a --association - Relationship name asserted by the codingScheme.
   default association = "Concept_In_Subset";


  -t --target - Target to Source resolution.
   default target = "true";


  -uri --uri - Base uri to build the value set coding scheme uri upon.  
   defaul uri = "http://evs.nci.nih.gov/valueset/";


  -o --owner - Owner of the value set assertion.
   default owner="NCI";


  -s --sourceName - Gives the name of the property to resolve the source value against.
   default source = "Contributing_Source";


  -cd --conceptDomainName - Gives the name of the property to resolve the concept domain value against.
   defaultconceptDomainIndicator = "Semantic_Type";


  -sUri --schemeUri - Scheme Uri for the coding scheme containing the value set updates.
   defaultschemeUri = NCItSourceAssertedValueSetUpdateService.NCIT_URI;

Load Example:

 

SourceAssertedValueSetUpdate.sh -cv "17.04d"

Expert Admin Scripts (Focused on Mass Loads of Value Sets)

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Heap size:
Memory management for heap size is a particular issue when loading larger Terminologies such as SNOMED or the NCI Thesaurus. Users need to be prepared to increase heap size if loads crash with heap size errors.
Example:

 

-Xmx:4000m

 

Permanent Generation:
LexEVS now depends on some Permanent Generation memory management during runtime.

Typically set as follows:

 

-XX:MaxPermSize:256m

 

Installing Sample Vocabularies

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