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ActivateScheme

Activates a coding scheme based on unique URN and version.
Options:

  • -u,-urn <urn> URN uniquely identifying the code system.
  • -v,-version <versionId> Version identifier.

  • -f,-force Force activation (no confirmation).

    Example:

     

    ActivateScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e"
CleanUpMetadata

Clean up metadata entries that are orphaned.

Options:

   -h, --help, Prints usage information

   -f,--force, Force removal without prompting of metadata that doesn't have a corresponding coding scheme entry(orphaned).

Example:

 

CleanUpMetadata -f

DeactivateScheme

Deactivates a coding scheme based on unique URN and version.
Options:

  • -u,-urn <urn> URN uniquely identifying the code system.
  • -v,-version <versionId> Version identifier.
  • -d,-date <yyyy-MM-dd,HH:mm:ss> Date and time for deactivation to take effect; immediate if not specified.

  • -f,-force Force deactivation (no confirmation).

    Example:

     

    DeactivateScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e" -d "01/31/2099,12:00:00

ListExtensions

List registered extensions to the LexEVS runtime environment.
Options:

  • -a,-all List all extensions (default, override by specifying other options).
  • -i,-index List index extensions.
  • -m,-match List match algorithm extensions.
  • -s,-sort List sort algorithm extensions.

  • -g,-generic List generic extensions.

    Example:

     

    ListExtensions -a

ListSchemes

List all currently registered vocabularies.
Options:

  • -b,-brief List only coding scheme name, version, urn, and tags (default).
  • -f,-full List full detail for each scheme.

    Example: ListSchemes
LoadManifest

Load manifest data onto the codingscheme based on unique URN and version.

Options:

   -u,--urn "urn"; URN uniquely identifying the code system.

   -v,--version "versionId"; Version identifier.

   -mf,--manifest "manifest"; location of manifest xml file.

 

Note: If either the URN or the version values are unspecified, a list of available coding schemes will be presented for user selection.

Example:

 

LoadManifest -u \"urn:oid:2.16.840.1.113883.3.26.1.1\" -v \"05.09e\" -mf \"file://path//to//manifest.xml\""
LoadManifest -mf \"file://path//to//manifest.xml\"
RemoveTagScheme

Removes a tag ID (e.g. 'PRODUCTION' or 'TEST') from a coding scheme URN and version.

Options:

   -u,--urn <urn> URN uniquely identifying the code system.

   -v,--version <id> Version identifier.

 

Note: If the URN and version values are unspecified, a list of available coding schemes will be presented for user selection.

Example:

 

RemoveTagScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e"
RemoveVSResolvedFromCodingScheme

Removes a resolved ValueSet based on coding scheme and version that was used for its resolution.

 

Options:

   -l, List of coding scheme versions to match when removing the ResolvedValueSet.

   -f,--force Force de-activation and removal without confirmation.

Example:

 

RemoveVSResolvedFromCodingSchemes  -l -l \"source.coding.scheme.uri::version1, second.source.uri::version2\" -f
RemoveResolvedValueSet

Removes a resolved ValueSet

Options:

   -l, The list of resolved value sets to remove, separated by comma. format "resolvedValueSetUri1::version1, resolvedValueSetUri2::version2,...".

   -f,--force Force de-activation and removal without confirmation.

 

Load Example:

 

RemoveResolvedValueSet  -l \"resolvedValueSetUri1::version1, resolvedValueSetUri2::version2\" -f
RemoveValueSetDefinition

Removes a coding scheme based on unique URN and version.

Options:

   -u,--urn <urn> URN uniquely identifying the code system.

 

Note: If the URN and version values are unspecified, a list of available coding schemes will be presented for user selection.

Example:

 

RemoveValueSetDefinition

 

RemoveValueSetDefinition -u http://evs.nci.nih.gov/Valueset/C100110

TagScheme

Associates a tag ID (e.g. 'PRODUCTION' or 'TEST') with a coding scheme URN and version.
Options:

  • -u,-urn <urn> URN uniquely identifying the code system.
  • -v,-version <versionId> Version identifier.

  • -t,-tag The tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.

    Example:

     

    TagScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v 05.09e" -t "TEST"

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BuildAssertedValueSetIndex

Builds indexes associated with the source asserted value sets of the specified coding scheme.

Options:

   -u,--urn <urn> URN uniquely identifying the code system.

   -v,--version <id> Version identifier.

   -f,--force Force clear (no confirmation).

 

Note: If the URN and version values are unspecified, a list of available coding schemes will be presented for user selection.

Load Example:

 

BuildAssertedValueSetIndex -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e"
BuildResolvedAndAssertedValueSetIndexes

Builds indexes associated with the source asserted value sets of the specified coding scheme. Adds the value set entities of any resolved value sets external to the asserted source

Options:

   -u,--urn <urn> URN uniquely identifying the code system.

   -v,--version <id> Version identifier.

   -f,--force Force clear (no confirmation).

 

Note: If the URN and version values are unspecified, a list of available coding schemes will be presented for user selection.

 Example:

 

BuildResolvedAndAssertedValueSetIndex -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e"

CleanUpLuceneIndex

Clean up orphaned indexes.
Options:

  • -h, -help, Prints usage information

  • -r, -reindex, Reindex any missing indices.

    Note

     

    Lucene Clean Up can only be executed in the default Single Index Mode.



    Example:

     

    CleanUPLuceneIndex -r

RebuildIndex

Rebuilds indexes associated with the specified coding scheme.
Options:

  • -u,-urn <urn> URN uniquely identifying the code system.
  • -v, -version <versionId> Version identifier.

  • -f,-force Force clear (no confirmation).

    Example:

     

    RebuildIndex -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e"

RemoveIndex

Clears an optional named index associated with the specified coding scheme.

Note

 

Built-in indices required by the LexEVS runtime cannot be removed.

Options:

  • -u,-urn <urn> URN uniquely identifying the code system.
  • -v,-version <versionId> Version identifier.

  • -f,-force Force clear (no confirmation).

    Example:

     

    RemoveIndex -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e"

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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"

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

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