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

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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 
 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
...
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.
 Code Block

# 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 $@ 

...
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:
 Code Block

-Xmx:4000m

Permanent Generation:
 LexEVS now depends on some Permanent Generation memory management during runtime.
Typically set as follows:
 Code Block

-XX:MaxPermSize:256m

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.
     Code Block
    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.
...
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
     Code Block
    cd {LEXBIG_DIRECTORY}/examples
  2. Execute one of sample programs.
     .bat for windows or .sh for Linux. 
     FindPropsandAssocForCode.bat 
     FindRelatedCodes
...
  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
     Code Block
    cd {LexBIG_DIRECTORY}/admin
  • For Windows installation use the following command
     Code Block
    LoadOWL.bat -in "file:///{NCI_THESAURUS_DIRECTORY}/Thesaurus_10.10d.owl"
  • For Linux installation use the following command
     Code Block
    LoadOWL.sh -in "file:///{NCI_THESAURUS_DIRECTORY}/Thesaurus_10.10d.owl"
...
The following code sample shows the example output from load of NCI Thesaurus 05.12f
 Code Block

[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

...
  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
     Code Block
    cd {LexBIG_DIRECTORY}/admin
  • For Windows installation use the following command
     Code Block
    LoadMetaBatch.bat -in "file:///{NCI_METATHESAURUS_DIRECTORY}/"
    For Linux installation use the following command
     Code Block
    LoadMetaBatch.sh -in "file:///{NCI_THESAURUS_DIRECTORY}/"
...
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
     Code Block
    cd {LexBIG_DIRECTORY}/admin
  • For Windows installation use the following command
     Code Block
    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
     Code Block
    ResumeMetaBatch.sh -in "file:///{NCI_THESAURUS_DIRECTORY}/" -s "NCI Metathesaurus" -uri "urn:oid:2.16.840.1.113883.3.26.1.2" -version "200601"
...
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:
     No Format
    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
     Code Block
    cd {LexBIG_DIRECTORY}/admin
  • For Windows installation use the following command:
     Code Block
    LoadNCIHistory.bat -nf -in "file:///{NCI_HISTORY_DIRECTORY}" -vf "[file:///NCI_HISTORY_DIRECTORY]}/VersionFile"
  • For Linux installation use the following command:
     Code Block
    LoadNCIHistory.sh -nf -in "file:///{NCI_HISTORY_DIRECTORY}" -vf "[file:///{NCI_HISTORY_DIRECTORY]}/VersionFile" 
...
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:
     Code Block
    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:
     Code Block
    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:
     Code Block
    RemoveScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "10.10d"
...
This section describes the steps to tag a coding scheme to be used via LexEVS API.
  1. Change directory to LexEVS administration directory. Enter:
     Code Block
    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:
     Code Block
    TagScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "10.10d"  -t "PRODUCTION"
...
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:
     Code Block
    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 interfaceImage Modified
     Info
    titleNote
    Concepts cannot be resolved without an index. Rebuilding the index is required.
Rebuild Index
  1. Change directory to LexEVS administration directory. Enter
     Code Block
    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>.
...
  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 interfaceImage Modified
     Info
    titleNote
    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
...
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