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LexEVS Administration Links

Vocabulary Administration Overview

A set of administrative shell scripts are provided to manage the LexEVS Service. These scripts are provided for Windows (.bat) and Linux (.sh) operating systems and call wrapper classes for LexEVS administration API classes. These scripts are located in the {LEXBIG_DIRECTORY}/admin and {LEXBIG_DIRECTORY}/test directory. A full description of the options with an example is provided for each command line script.

Coding Scheme Metadata Access and Administration

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"
SupplementScheme

Utility to register, unregister, and list Coding Scheme Supplements.

Usage: SupplementScheme  [-r] [-u] [-l]

   [-parentUri parentUri]

   [-parentVersion parentVersion]

   [-supplementUri supplementUri]

   [-supplementVersion supplementVersion]

 

   -r  Register Coding Scheme as a Supplement

   -u Unregister Coding Scheme as a Supplement

   -l,--list List Supplements

   -parentUri <parentUri> Parent URI.

   -parentVersion <parentVersion> Parent Version.

   -supplementUri <supplementUri> Supplement URI.

   -supplementVersion <supplementVersion>Supplement Version.


Example:

  • SupplementScheme -u -parentUri "urn:oid:2.16.840.1.113883.3.26.1.1" -parentVersion "05.09e" -supplementUri "http://supplement.ontology.org" -supplementVersion "1.0.1"

Lucene Index Administration

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"

Misc Database Administration Scripts

ExportDDLScripts

Exports the database create/drop scripts.
Options:

  • -db, -databaseType, required=true, usage="Target database type.")
  • -p, -prefix Prefix to append to all tables
  • -o,-out Output directory, a required option

  • -f, -force Force output directory creation.

    Example:

     

    ExportDDLScripts -p lb -0 "file:///path/to/dir" -f

PasswordEncryptor

Encrypts the given password.
Argument:

  • -p,-password password for encryption.

Example:

 

PasswordEncryptor -p lexgrid
RebuildTransitivityTable

Rebuilds transitivity table associated with 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.

Example:

 

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

LexEVS Export Scripts

ExportLgXML

Exports content from the repository to a file in the LexGrid canonical XML format.
Usage:
ExportLgXML [-xc] [-an null] [-xall] -v null -u name -out uri [-xa] [-f]

  • -an,--associationsName Export associations with this name. Only valid with export type 'xa'

  • -f,-force If specified, allows the destination file to be overwritten if present.
  • -out,-output <uri> URI or path of the directory to contain the resulting XML file. The file name will be automatically derived from the coding scheme name.
  • -u,-urn <name> URN or local name of the coding scheme to export.
  • -v,-version The assigned tag/label or absolute version identifier of the coding scheme.
  • -xa,-exportAssociations Type of export: export only associations.
  • -xall,-exportAll Type of export: export all content. Default behavior.

  • -xc,-exportConcepts Type of export: export only concepts.

    Example:

     

    ExportLgXML -out "file:///path/to/dir" -u "NCI Thesaurus" -v "05.06e" -f

ExportOBO

Exports content from the repository to a file in the Open Biomedical Ontologies (OBO) format.
Options:

  • -out,-output <uri> URI or path of the directory to contain the resulting OBO file. The file name will be automatically derived from the coding scheme name.
  • -u,-urn <name> URN or local name of the coding scheme to export.
  • -v,-version <id> The assigned tag/label or absolute version identifier of the coding scheme.

  • -f,-force If specified, allows the destination file to be overwritten if present.

    Note

     

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

    Note:

     

    Available for Linux based OS only.



    Examples:

     

    ExportOBO -out "file:///path/to/dir" -f

     

     

    ExportOBO -out "file:///path/to/dir" -u "FBbt" -v "PRODUCTION" -f

ExportOwlRdf

Exports content from the repository to a file in OWL format.
Options:

  • -out,-output <uri> URI or path of the directory to contain the resulting OWL file. The file name will be automatically derived from the coding scheme name.
  • -u,-urn <name> URN or local name of the coding scheme to export.
  • -v,-version <id> The assigned tag/label or absolute version identifier of the coding scheme.

  • -f,-force If specified, allows the destination file to be overwritten if present.

    Note

     

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



    Examples:

     

    ExportOwlRdf -out "file:///path/to/dir" -f

     

     

    ExportOwlRdf -out "file:///path/to/dir" -u "sample" -v "1.0" -f

LexEVS Loader Scripts

Load

A generic loader script that allows for the selection of a Loader Extension.

Options:

   -in,--input <uri> URI or path specifying location of the source file

   -l, --loader <name> LexGrid Load Extension name

   -mf,--manifest <uri> URI or path specifying location of the manifest file

   -a, --activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated.

   -t, --tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.

 

Example:

 

LoadText -in "file:///path/to/file.txt" -a
  

LoadLgXML

Loads a vocabulary file, provided in LexGrid canonical xml format.
Options:

  • -in,-input <uri> URI specifying location of the source file.
  • -v, -validate <level> Perform validation of the candidate resource without loading data.  If specified, the '-a' and '-t' options are ignored.  Supported levels of validation include:
    • 0 = Verify document is well-formed
    • 1 = Verify document is valid
  • -a,-activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated.

  • -t, -tag <tagID> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.
    Load Example:

     

    LoadLgXML -in "file:///path/to/file.xml" -nf -a


    Validation Example:

     

    LoadLgXML -in "file:///path/to/file.xml" -v 0
LoadMedDRALoads a file specified in the Medical Dictionary for Regulatory Activities (MedDRA) format.

Options:
  •    -in,--input <uri> URI or path specifying location of the source file
  •    -mf,--manifest <uri> URI or path specifying location of the manifest file
  •    -v, --validate <int> Perform validation of the candidate  resource without loading data.  If specified, the '-a' and '-t' options are ignored.  Supported levels of validation include:0 = Verify document is valid
  •    -a, --activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated.
  •    -t, --tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.
  •    -cui  Uri to MRCONSO.RRF from the NCI Metathesaurus allows loading of CUI's  for a given term. (Slows load time considerably)


Load Example:

 

LoadMedDRA -in "file:///path/to/file.asc" -a

 

Validation Example:

 

LoadMedDRA -in "file:///path/to/file.asc" -v 0

 

Load CUI Example:

LoadMetaData

Loads optional XML-based metadata to be associated with an existing coding scheme.

  • -u,-urn <name> URN uniquely identifying the code system.
  • -v,-version <id> Version identifier.
  • -in,-input <uri> URI or path specifying location of the XML file.
  • -v,-validate <int> Perform validation of the input file without loading data.  If specified, the '-f', and '-o' options are ignored.  Supported levels of validation include:  0 = Verify document is valid
  • -o, -overwrite If specified, existing metadata for the code system will be erased. Otherwise, new metadata will be appended to existing metadata (if present).
  • -f,-force Force overwrite (no confirmation).

    Note

     

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


    Examples:

     

    LoadMetadata -in "file:///path/to/file.xml" -o

     

     

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

LoadMIFVocabulary

Loads from an the HL7 Vocabulary mif file.

 Options:
  •    -in,--input <uri> URI or path specifying location of the source file.
  •    -a, --activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated.
  •    -t, --tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.


Load Example:

 

LoadMIFVocabulary -in "file:///path/to/file.xml" -a
LoadMrMap

Loads mappings file(s), provided in UMLS RRF format. Specifically MRMAP.RRF and MRSAT.RRF.
Options:

LoadNCIHistory

Imports NCI History data to the LexEVS repository.
Options:

  • -in,-input <uri> URI specifying location of the history file
  • -vf,-versionFile <uri> URI specifying location of the file containing version identifiers for the history to be loaded.
  • -v, -validate <level>Perform validation of the candidate resource without loading data.  If specified, the '-r' option is ignored.  Supported levels of validation include:
    • 0 = Verify top 10 lines are correct format
    • 1 = Verify correct format for the entire file

  • -r, -replace If not specified, the provided history file will be added into the current history database; otherwise the current database will be replaced by the new content.
    Load Example:


    Validation Example:

     

    LoadNCIHistory -in "file:///path/to/history.file" -v 0

     

    Versions File Format Information:

     

    releaseDate | isLatest | releaseAgency | releaseId | releaseOrder | entityDescription

     

    Sample record:

     

    28-NOV-05 | false | [http://nci.nih.gov] | 05.10e | 26 | Editing of NCI Thesaurus 05.10e was completed on October 31, 2005.  Version 05.10e was October's fifth build in our development cycle.

LoadOBO

Loads a file specified in the Open Biomedical Ontologies (OBO) 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. If specified, the '-nf', -a' and '-t' options are ignored. Supported levels of validation include:
    • 0 = Verify document is valid
  • -nf,-noFail If specified, indicates that processing should not stop for recoverable errors
  • -a, -activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated

  • -t, -tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.
    Examples:

     

    LoadOBO -in "file:///path/to/file.obo" -nf -a

     

     

    LoadOBO -in "file:///path/to/file.obo" -v 0

LoadOWL

Loads an OWL file.

Note

 

Load of the NCI Thesaurus should be performed via the LoadNCIThesOWL counterpart, since it will allow more precise handling of NCI semantics.

Options:

  • -in,-input <uri> URI or path specifying location of the source file
  • -mf,--manifest <uri> URI or path specifying location of the manifest file
  • -v, -validate <int> Perform validation of the candidate resource without loading data.  If specified, the '-a' and '-t' options are ignored.  Supported levels of validation include:
    • 0 = Verify document is well-formed
    • 1 = Verify document is valid
  • -a, -activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated

  • -t, -tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.
    Example:

     

    LoadOWL -in "file:///path/to/somefile.owl" -a

     

     

    LoadOWL -in "file:///path/to/somefile.owl" -v 0
LoadOWL2

 Loads an OWL file. You can provide a manifest file to configure coding scheme# meta data.

 Options:

  •    -in,--input <uri> URI or path specifying location of the source file
  •    -mf,--manifest <uri> URI or path specifying location of the manifest file
  •    -lp,--loaderPrefs<uri> URI or path specifying location of the loader preference file
  •    -v, --validate <int> Perform validation of the candidate resource without loading data.  If specified, the '-a' and '-t' options are ignored.  Supported levels of validation include:
  •          0 = Verify document is well-formed
  •          1 = Verify document is valid
  •    -a, --activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated.
  •    -t, --tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.


 Load Example:

 

LoadOWL2 -in "file:///path/to/somefile.owl" -a

 

 

LoadOWL2 -in "file:///path/to/somefile.owl" -v 0
LoadResolvedValueSetDefinition

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


 Options:
   -u, The valueset definition URI to use
   -l, The list of coding schemes to revolve against. The format is codingschemeName::version
   -csVersionTag, The tag to use for resolving coding scheme
       
Load Example:

 

LoadResolvedValueSetDefinition -u \"Automobiles:valuesetDefinitionURI\" -l \"Automobiles::version1, GM::version2\" -csVersionTag \"production\" ""

 


LoadText

Loads a file in LexGrid Text format.

Options:

   -in,--input <uri> URI or path specifying location of the source file

   -d, --delimiter <character> defaults to tab the character used to delimit pair or triple components and the nesting.

   -mf,--manifest <uri> URI or path specifying location of the manifest file.

   -v, --validate <int> Perform validation of the candidate resource without loading data.  If specified, the '-a' and '-t' options are ignored.  Supported levels of validation include:

      0 = Verify document is valid

   -a, --activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated.

   -t, --tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.

 

Load Example:

 

LoadText -in "file:///path/to/file.txt" -a
LoadText -in "file:///path/to/file.txt" -v 0
LoadUMLSHistory

Loads UMLS History


 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.  If specified, the '-a' and '-t' options are ignored.  Supported levels of validation include:

      0 = Verify document is valid

   -a, --activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated.

   -r, --replace Replace exisiting file.

   -t, --tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.


Load Example:

 

LoadUMLSHistory -in "file:///path/to/META.folder" -r
 LoadUMLSHistory -in "file:///path/to/META.folder" -v 0
LoadUMLSSemnet.sh

Loads the UMLS Semantic Network, provided as a collection of files in a single directory.  The following files are expected to be provided from the National Library of Medicine (NLM) distribution:
   - LICENSE.txt (text from distribution terms and conditions)
   - SRFIL.txt (File Description)
   - SRFIL.txt (Field Description)
   - SRDEF.txt (Basic information about the Semantic Types and Relations)
   - SRSTR.txt (Structure of the Network)
   - SRSTRE1.txt (Fully inherited set of Relations (UIs))
   - SRSTRE2.txt (Fully inherited set of Relations (Names))
   - SU.txt (Unit Record)
These files can be downloaded from the NLM web site at http://semanticnetwork.nlm.nih.gov/Download/index.html.

Options:

   -in,--input <uri> URI or path of the directory containing the NLM files

   -v, --validate <int> Perform validation of the candidate resource without loading data.  If specified, the '--a' and '-t' options are ignored.  Supported levels of validation include:

        0 = Verify the existence of each required file

   -a, --activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated.

   -t, --tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.

   -il,--InheritanceLevel <int> If specified, indicates the extent of inherited relationships to import.  

        0 = none; 1 = all; 2 = all except is_a (default).

        All direct relationships are imported, regardless of option.

Load Example:

 

LoadUMLSSemnet -in "file:///path/to/directory/" -a
LoadUMLSSemnet -in "file:///path/to/directory/" -v 0

Special Batch Loading Functions

LoadMetaBatch

Loads the NCI MetaThesaurus, provided as a collection of RRF files, using a batch loading strategy allowing a faster, more memory efficient load to occur.
Options:

LoadUmlsBatch

Loads UMLS content, provided as a collection of RRF files in a single directory. Files may comprise the entire UMLS distribution or pruned via the MetamorphoSys tool. A complete list of source vocabularies is available online at http://www.nlm.nih.gov/research/umls/metaa1.html.
Options:

  • -in,-input <uri> URI or path of the directory containing the NLM files

  • -s,-source vocabularies to load.
    Example:

     

    LoadUMLSBatch -in "file:///path/to/directory/" -s "PSY"

ResumeMetaBatch

Resume a UMLS load. Loads will usually be restartable if they fail due to an error. The loader will keep all loaded content and restart at the point of failure.
Options:

  • -in,-input <uri> URI or path of the directory containing the NLM files
  • -s,-source vocabulary to resume.
  • -uri,-uri of vocabulary to resume.

  • -version,-version of vocabulary to resume.
    Example:

     

    ResumeMetaBatch -in "file:///path/to/directory/" -s "PSY" -uri "urn:123.4" -version "2.0"

ResumeUmlsBatch

Resume a UMLS load. Loads will usually be restartable if they fail due to an error. The loader will keep all loaded content and restart at the point of failure.
Options:

  • -in,-input <uri> URI or path of the directory containing the NLM files
  • -s,-source vocabulary to resume.
  • -uri,-uri of vocabulary to resume.

  • -version,-version of vocabulary to resume.
    Example:

     

    ResumeUmlsBatch.sh -in "file:///path/to/directory/" -s "PSY" -uri "urn:123.4" -version "2.0"

Scheme and Metadata Removal

RemoveScheme

Removes 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 deactivation and removal without confirmation.
    Example:

     

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

RemoveMetadata

Clears optionally loaded metadata associated with 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.


    Examples:

     

    RemoveMetadata

     

     

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

Pick List and Value Set Load Administration

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"
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)

 

 

These Scripts have a narrow focus on mass loads and removals of value sets. They can be very destructive.

LoadAllValueSetDefinitionsInDirectory

Loads All LexGrid XML formatted Value Set Definitions in a given directory. 

Highly recommended that the folder be cleaned of all non value set files and folders

Options:

    • -in, Path to directory


      Example:

       

      LoadAllValueSetDefinitionsInDirectory -in /path/to/directory

RemoveAllValueSetDefinitions

WARNING: Removes all value set definitions without discrimination

Options:

None: Takes no input, removes all value set definitions in the system. Cannot be reversed.

Example:

 

./RemoveAllValueSetDefinitions.sh

 

 
RemoveAllResolvedValueSets

WARNING:  REMOVES ALL RESOLVED VALUE SETS

Options: None, removes all resolved value sets from the system. Not reversible.

Example:

 

./RemoveAllResolvedValueSets.sh

LexEVS Validation Test Script

TestRunner

Located in {LEXBIG_DIRECTORY}/test. Runs the test suite by invoking the Ant launcher.

Note

 

The LexEVS runtime and database environments must still be configured prior to invoking the test suite. Running any option other than -v will cause a large set of junits to be run

Usage: TestRunner

  • -b, -brief Run the LexBIG test suite and produce a text report with overall statistics and details for failed tests only.
  • -f, -full Run the LexBIG test suite and produce an itemized list of all tests with indication of success/failure.
  • -x,-xml Run the LexBIG test suite and produce a report with extensive information for each test case in xml format.
  • -h,-html Run the LexBIG test suite and produce a report suitable for view in a standard web browser: this is the default
    if no other option is specified.

  • -v,-verify Basic verification that LexEVS is configured properly and basic systems are functioning.
    Examples:

     

    TestRunner -v

     

    Run the full test suite of jUnits and save the report to an html file. (This can take quite some time.)

     

    TestRunner -f -h

     

    Run a verification of the LexEVS installation. A quick way to insure your system is up and running.

     

    TestRunner -v

Command Line Scripts and Wrappers Overview

LexEVS provides a set of shell scripts and code wrappers that provide command line users standard options and automatic printouts of current coding schemes when performing administrative functions using the command line.

Displaying Current Coding Schemes

When you have coding Schemes Loaded to LexEVS many command line script calls will bring up a printout of a table of the loaded coding schemes to be used as a selective menu for other functions.

screenshot showing the printout of a table of the loaded coding schemes

Using Optional Parameters

A standard parameter interface allows users to customize command line calls to LexEVS. These options control things such as loader synchronicity, supplemental file locations, and fault conditions. Shell scripts contain comments on usage for each function wrappers options.

 

# Loads an OWL file. You can provide a manifest file to configure coding scheme
# meta data.
#
# Options:
# -in,--input <uri> URI or path specifying location of the source file
# -mf,--manifest <uri> URI or path specifying location of the manifest file
# -lp,--loaderPrefs<uri> URI or path specifying location of the loader preference file
# -a, --activate ActivateScheme on successful load; if unspecified the
# vocabulary is loaded but not activated.
# -t, --tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.
#
# Example: LoadOWL -in "file:///path/to/somefile.owl" -a
#
java -Xmx3000m -XX:MaxPermSize=256M -cp "../runtime/lbPatch.jar:../runtime/lbRuntime.jar"
 
org.LexGrid.LexBIG.admin.LoadOWL $@

 

Setting Java Virtual Machine Options

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

 

Installing Sample Vocabularies

This LexEVS installation provides a sample vocabulary, Automobiles.xml, that can be loaded into the database.

  1. In a Command Prompt window, enter the following to go to the example programs.

     

    cd {LEXBIG_DIRECTORY}/examples
  2. To load an example vocabulary, run the LoadSampleData script, LoadSampleData.bat for Windows; LoadSampleData.sh for Linux.
  3. To load other example vocabularies, run the appropriate script for any sample vocabulary in {LEXBIG_DIRECTORY}/test/resources/testData.

Note

 

Vocabularies cannot be loaded until configuration of the LexEVS runtime and database server are complete.

Displays the successful load of the sample vocabulary file.

Running the sample query programs

A set of sample programs are provided in the {LEXBIG_DIRECTORY}/examples directory. To run the sample query programs successfully a vocabulary must be loaded.

  1. Enter

     

    cd {LEXBIG_DIRECTORY}/examples
  2. Execute one of sample programs.
    .bat for windows or .sh for Linux.
    FindPropsandAssocForCode.bat
    FindRelatedCodes

Shows the output of example programs using sample vocabulary for finding properties and associations for a given code

Installing NCI Vocabularies

NCI Thesaurus Vocabulary

This section describes the steps to download and install a full version of the NCI Thesaurus for the LexEVS Service.

  1. Using a web or ftp client go to URL: ftp://ftp1.nci.nih.gov/pub/cacore/EVS/
    screenshot showing navigating to FTP directory
  2. Select the version of NCI Thesaurus OWL you wish to download. Save the file to a directory on your machine.
  3. Extract the OWL file from the zip download and save in a directory on your machine. This directory will be referred to as NCI_THESAURUS_DIRECTORY

  4. Using the LexEVS utilities load the NCI Thesaurus

     

    cd {LexBIG_DIRECTORY}/admin

  • For Windows installation use the following command

     

    LoadOWL.bat -in "file:///{NCI_THESAURUS_DIRECTORY}/Thesaurus_10.10d.owl"

  • For Linux installation use the following command

     

    LoadOWL.sh -in "file:///{NCI_THESAURUS_DIRECTORY}/Thesaurus_10.10d.owl"

Note

 

The NCI Thesaurus has grown large enough that it can no longer be loaded on many typical desktop machines. We recommend a 64-bit operating system running on a multiprocessor computer with a minimum of 4g of memory. Server class Linux machines are the typical target for these loads. The time to load NCI Thesaurus will vary depending on machine, memory, and disk speed. Expect a couple of hours for a higher end machine.

The following code sample shows the example output from load of NCI Thesaurus 05.12f

 

[LexBIG] Processing TOP Node... Retired_Kind
[LexBIG] Clearing target of NCI_Thesaurus...
[LexBIG] Writing NCI_Thesaurus to target...
[LexBIG] Finished loading DB - loading transitive expansion table
[LexBIG] ComputeTransitive - Processing Anatomic_Structure_Has_Location
[LexBIG] ComputeTransitive - Processing Anatomic_Structure_is_Physical_Part_of
[LexBIG] ComputeTransitive - Processing Biological_Process_Has_Initiator_Process
[LexBIG] ComputeTransitive - Processing Biological_Process_Has_Result_Biological_Process
[LexBIG] ComputeTransitive - Processing Biological_Process_Is_Part_of_Process
[LexBIG] ComputeTransitive - Processing Conceptual_Part_Of
[LexBIG] ComputeTransitive - Processing Disease_Excludes_Finding
[LexBIG] ComputeTransitive - Processing Disease_Has_Associated_Disease
[LexBIG] ComputeTransitive - Processing Disease_Has_Finding
[LexBIG] ComputeTransitive - Processing Disease_May_Have_Associated_Disease
[LexBIG] ComputeTransitive - Processing Disease_May_Have_Finding
[LexBIG] ComputeTransitive - Processing Gene_Product_Has_Biochemical_Function
[LexBIG] ComputeTransitive - Processing Gene_Product_Has_Chemical_Classification
[LexBIG] ComputeTransitive - Processing Gene_Product_is_Physical_Part_of
[LexBIG] ComputeTransitive - Processing hasSubtype
[LexBIG] Finished building transitive expansion - building index
[LexBIG] Getting a results from sql (a page if using mysql)
[LexBIG] Indexed 0 concepts.
[LexBIG] Indexed 5000 concepts.
[LexBIG] Indexed 10000 concepts.
[LexBIG] Indexed 15000 concepts.
[LexBIG] Indexed 20000 concepts.
[LexBIG] Indexed 25000 concepts.
[LexBIG] Indexed 30000 concepts.
[LexBIG] Indexed 35000 concepts.
[LexBIG] Indexed 40000 concepts.
[LexBIG] Indexed 45000 concepts.
[LexBIG] Indexed 46000 concepts.
[LexBIG] Getting a results from sql (a page if using mysql)
[LexBIG] Closing Indexes Mon, 27 Feb 2006 01:44:22
[LexBIG] Finished indexing

 

NCI Metathesaurus Vocabulary

Loading the Metathesaurus

This section describes the steps to download and install a full version of the NCI Metathesaurus for the LexEVS Service.

  1. Using a web or ftp client go to URL: ftp://ftp1.nci.nih.gov/pub/cacore/EVS/
    screenshot showing navigating to ftp client in Explorer
  2. Select the version of NCI Metathesaurus RRF you wish to download. Save the file to a directory on your machine.
  3. Extract the RRF files from the zip download and save in a directory on your machine. This directory will be referred to as NCI_METATHESAURUS_DIRECTORY. RELEASE_INFO.RRF is required to be present for the load utility to work.

  4. Using the LexEVS utilities load the NCI Thesaurus

     

    cd {LexBIG_DIRECTORY}/admin

  • For Windows installation use the following command

     

    LoadMetaBatch.bat -in "file:///{NCI_METATHESAURUS_DIRECTORY}/"

     

    For Linux installation use the following command

     

    LoadMetaBatch.sh -in "file:///{NCI_THESAURUS_DIRECTORY}/"

Note

 

NCI Metathesaurus contains many individual vocabularies some of which are large vocabularies in and of themselves. It requires many hours to load and index. It can require 36 hours on a multiprocessor machine with 6g plus memory. The total time to load NCI MetaThesaurus will vary depending on machine, memory, and disk speed. Because this loader uses a batch loading strategy it is less dependent on memory, but some users will see 3 or 4 day load times with average multiprocessor processing power.

Resuming Loads

Since this loader is resource hungry we provide the option to restart should you find your resource settings to be inadequate. Resuming loads which have crashed or been interrupted by server problems is possible using the ResumeBatchLoad script set.

  1. Using the LexEVS utilities load the NCI Thesaurus

     

    cd {LexBIG_DIRECTORY}/admin

  • For Windows installation use the following command

     

    ResumeMetaBatch.bat -in "file:///{NCI_METATHESAURUS_DIRECTORY}/" -s "NCI Metathesaurus" -uri "urn:oid:2.16.840.1.113883.3.26.1.2" -version "200601"

  • For Linux installation use the following command

     

    ResumeMetaBatch.sh -in "file:///{NCI_THESAURUS_DIRECTORY}/" -s "NCI Metathesaurus" -uri "urn:oid:2.16.840.1.113883.3.26.1.2" -version "200601"

NCI History

This section describes the steps to download and install a history file for NCI Thesaurus.

  1. Using a web or ftp client go to URL:

    ftp://ftp1.nci.nih.gov/pub/cacore/EVS/
  2. Select the version of NCI History you wish to download. Save the file to a directory on your machine. Select the VersionFile download to the same directory as the history file.
  3. Extract the History files from the zip download and save in a directory on your machine. This directory will be referred to as NCI_HISTORY_DIRECTORY

  4. Using the LexEVS utilities load the NCI Thesaurus

     

    cd {LexBIG_DIRECTORY}/admin

  • For Windows installation use the following command:

     

    LoadNCIHistory.bat -nf -in "file:///{NCI_HISTORY_DIRECTORY}" -vf "[file:///NCI_HISTORY_DIRECTORY]}/VersionFile"

  • For Linux installation use the following command:

     

    LoadNCIHistory.sh -nf -in "file:///{NCI_HISTORY_DIRECTORY}" -vf "[file:///{NCI_HISTORY_DIRECTORY]}/VersionFile"

Note

 

If a 'releaseId' occurs twice in the file, the last occurrence will be stored. If LexEVS already knows about a releaseId (from a previous history load), the information is updated to match what is provided in the file. This file has to be provided to the load API on every load because you will need to maintain it in the future as each new release is made. We have created this file that should be valid as of today from the information that we found in the archive folder on your ftp server. You can find this file in the 'resources' directory of the LexEVS install.

Deactivating and Removing a Vocabulary

This section describes the steps to deactivate a coding scheme and remove coding scheme from LexEVS Service.

  1. Change directory to LexEVS administration directory. Enter:

     

    cd {LEXBIG_DIRECTORY}/admin

  2. Use the DeactiveScheme utility to prevent access to coding scheme. Once a coding scheme is deactivated, client programs will not be able to access the content for the specific coding scheme and version. Example:

     

    DeactivateScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "10.10d"

  3. Use RemoveScheme utility to remove coding scheme from LexEVS service and database.
    Example:

     

    RemoveScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "10.10d"

Tagging a Vocabulary

This section describes the steps to tag a coding scheme to be used via LexEVS API.

  1. Change directory to LexEVS administration directory. Enter:

     

    cd {LEXBIG_DIRECTORY}/admin

  2. Use the TagScheme to tag a coding system and version with a local tag name (e.g. PRODUCTION). This tag name can be used via LexEVS API for query restriction. Example:

     

    TagScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "10.10d"  -t "PRODUCTION"

IndexManagement

LexEVS indexes can be manually updated, removed and optimized by users. This is a useful function particularly when metadata, authoring and post processing may have taken place.

Remove Index

  1. Change directory to LexEVS administration directory. Enter:

     

    cd {LEXBIG_DIRECTORY}/admin
  2. Use RemoveIndex script to remove an index for a particular coding scheme.
    Example:
    Windows:
    RemoveIndex.bat
    Linux:
    RemoveIndex.sh
  3. Interactive commmand: Enter the number of the Coding Scheme to use, then <Enter>. User responds with column number for appropriate coding scheme.
  4. Interactive command: CLEAR? ('Y' to confirm, any other key to cancel). User responds with 'Y'

  5. Command Line example:
    screenshot of the command line interface

    Note

     

    Concepts cannot be resolved without an index. Rebuilding the index is required.

Rebuild Index

  1. Change directory to LexEVS administration directory. Enter

     

    cd {LEXBIG_DIRECTORY}/admin
  2. Use RebuildIndex script to rebuild an index for a particular coding scheme.
    Example:
    Windows:
    RebuildIndex.bat
    Linux:
    RebuildIndex.sh
  3. Interactive command: Enter the number of the Coding Scheme to use, then <Enter>.

User responds with column number for appropriate coding scheme.

  1. Interactive command: REBUILD INDEX FOR URI? <uri displayed here> ('Y' to confirm, any other key to cancel). User responds with 'Y'

  2. Command Line example:
    screenshot of command line interface

    Note

     

    It may be useful and performance enhancing to run OptimizeLuceneIndex script after removing and rebuilding.

Value Set and Pick List Loading

Value Set and Pick List Scripts

: