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Menu LexEVS 6.0 Administration to Include
Menu LexEVS 6.0 Administration to Include

...

Coding Scheme Metadata Access and Administration

Shell Script

Use and Function

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:

    Code Block
    ActivateScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e"

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:

    Code Block
    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:

    Code Block
     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

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:

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

Lucene Index Administration

Shell Script

Use and Function

CleanUpLuceneIndex

Clean up orphaned indexes.
Options:

  • -h, -help, Prints usage information

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

    Info
    titleNote

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



    Example:

    Code Block
    CleanUPLuceneIndex -r

OptimizeLuceneIndex

Optimizes the Common Lucene Index.
Options:

  • -h, -help, Prints usage information

RebuildIndex

Rebuilds indexes associated with the specified coding scheme.
Options:

  • -u,-urn <urn> URN uniquely identifying the code system.
  • -v, -version <versionId> Version identifier.
  • -i,-index <name> Name of the index extension to rebuild (if absent, rebuilds all built-in indices and named extensions).

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

    Example:

    Code Block
    RebuildIndex -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e" -i "myindex"

RemoveIndex

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

Info
titleNote

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.
  • -i,-index <name> Name of the index extension to clear.

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

    Example:

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

Misc Database Administration Scripts

Shell Script

Use and Function

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:

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

PasswordEncryptor

Encrypts the given password.
Argument:

  • -p,-password password for encryption.
    Example:

    Code Block
    PasswordEncryptor -p lexgrid

LexEVS Export Scripts

Shell Script

Use and Function

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]

  • -a,-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:

    Code Block
    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.
  • -nf,-noFail If specified, indicates that processing should not stop for recoverable errors

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

    Info
    titleNote

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

    Info
    titleNote

    Available for Linux based OS only.



    Examples:

    Code Block
    ExportOBO -out "file:///path/to/dir" -nf -f
    Code Block
    ExportOBO -out "file:///path/to/dir" -u "FBbt" -v "PRODUCTION" -nf -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.

    Info
    titleNote

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



    Examples:

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

LexEVS Loader Scripts

Shell Script

Use and Function

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 '-nf', -a' and '-t' options are ignored. Supported levels of validation include:
    • 0 = Verify document is well-formed
    • 1 = 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 <tagID> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.
    Load Example:

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


    Validation Example:

    Code Block
    LoadLgXML -in "file:///path/to/file.xml" -v 0

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 '-nf' and '-r' options are ignored. Supported levels of validation include:
    • 0 = Verify top 10 lines are correct format
    • 1 = Verify correct format for the entire file
  • -nf,-noFail If specified, indicates that processing should not stop for recoverable errors

  • -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:

    Code Block
    LoadNCIHistory -nf -in "file:///path/to/history.file" -vf "[file:///path/to/version.file]"


    Validation Example:

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

    Versions File Format Information:

    Code Block
    releaseDate | isLatest | releaseAgency | releaseId | releaseOrder | entityDescription

    Sample record:

    Code Block
    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:

    Code Block
    LoadOBO -in "file:///path/to/file.obo" -nf -a
    Code Block
    LoadOBO -in "file:///path/to/file.obo" -v 0

LoadOWL

Loads an OWL file.

Info
titleNote

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
  • -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 well-formed
    • 1 = 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.
    Example:

    Code Block
    LoadOWL -in "file:///path/to/somefile.owl" -nf -a
    Code Block
    LoadOWL -in "file:///path/to/somefile.owl" -v 0

LoadRadLexProtegeFrames

URI or path specifying location of the pprj file. Imports from a RadLex xml file to a LexBIG repository. Requires that the pprj file be configured with reference to a RadLex xml file as follows:

Code Block
([radlex_ProjectKB_Instance_66] of String (name "source_file_name") (string_value "radlex.xml"))" );

Example:

Code Block
java org.LexGrid.LexBIG.admin.LoadRadLexProtegeFrames
  • -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 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:

    Code Block
    java -Xmx800m -cp lgRuntime.jar -Djava.ext.dirs=../runtime/sqlDrivers org.LexGrid.LexBIG.admin.LoadRadLexProtegeFrames -in "file:///path/to/RadLex.pprj" -a -or- org.LexGrid.LexBIG.admin.LoadRadLexProtegeFrames -in "file:///path/to/RadLex.pprj" -v 0

LoadUMLSSemnet

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 '-nf', -a' and '-t' options are ignored. Supported levels of validation include:
    • 0 = Verify the existence of each required file
  • -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.

  • -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.
    Example:

    Code Block
    LoadUMLSSemnet -in "file:///path/to/directory/" -nf --a --il 1
    Code Block
    LoadUMLSSemnet -in "file:///path/to/directory/" -v 0

LoadFMA

Imports from an FMA database to a LexEVS repository. Requires that the pprj file be configured with a database URN, username, password for an FMA MySQL based database. The FMA.pprj file and MySQL dump file are available at http://sig.biostr.washington.edu/projects/fm/ upon registration.
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 well-formed
    • 1 = 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:

    Code Block
    LoadFMA -in "file:///path/to/FMA.pprj" -nf -a
    Code Block
    LoadFMA -in "file:///path/to/FMA.pprj" -v 0

LoadHL7RIM

Converts an HL7 RIM MS Access database to a LexGrid database

  • -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,-load preferences <uri> URI or path specifying location of the load preferences 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.
    Example:

    Code Block
    LoadHL7RIM -in "file:///path/to/file.mdb" -nf -a
    Code Block
    LoadHL7RIM -in "file:///path/to/file.mdb" -v 0

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 '-nf', '-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).

  • -nf,-noFail If specified, indicates that processing should not stop for recoverable errors

    Info
    titleNote

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


    Examples:

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

LoadMrMap

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

  • -inMap,-input <uri> URI or path specifying location of the MRMAP source file.

  • -inSat,-input <uri> URI or path specifying location of the MRSAT source file.
    Example:

    Code Block
    LoadMrMap -inMap "file:///path/to/MRMAP.RRF -inSat "file:///path/to/MRSAT.RRF"

Special Batch Loading Functions

Shell Script

Use and Function

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:

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

    Code Block
    LoadMetaBatch -in "file:///path/to/directory/"

LoadUMLBatch

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:

    Code Block
    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:

    Code Block
    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:

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

Scheme and Metadata Removal

Shell Script

Use and Function

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:

    Code Block
    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).

    Info
    titleNote

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


    Examples:

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

Pick List and Value Set Load Administration

Shell Script

Use and Function

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:

      Code Block
      LoadPickListDefinition -in "file:///path/to/file.xml"
LoadValueSetDefinition

LoadAllDefinitionsToResolvedValueSet

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
      Example:

      Code Block
      LoadValueSetDefinition -in "file:///path/to/file.xml"

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

 

Warning

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

Shell Script

Use and Function

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:

      Code Block
      LoadAllValueSetDefinitionsInDirectory -in /path/to/directory

LoadAllDefinitionsToResolvedValueSet

Loads All Value Set Definitions for a given uri as resolved coding scheme. All compiled resolved value sets should be removed to insure resolution updates are correct with the current version of the source terminology.

Options:

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:

Code Block
 ./RemoveAllValueSetDefinitions.sh

 

 
RemoveAllResolvedValueSets

 WARNING:  REMOVES ALL RESOLVED VALUE SETS

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

Example:

Code Block
./RemoveAllResolvedValueSets.sh

LexEVS Validation Test Script

Shell Script

Use and Function

TestRunner

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

Info
titleNote

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:

    Code Block
    TestRunner -v

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

    Code Block
    TestRunner -f -h

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

    Code Block
    TestRunner -v

Command Line Scripts and Wrappers Overview

...

Value Set and Pick List Scripts

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