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

 

 

LexEVS 6.1 Loader Scripts

Shell Script

Use and Function

LoadMedDRA

 Loads 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.


Load Example:

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


Validation Example:

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

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:

Code Block
LoadMIFVocabulary -in "file:///path/to/file.xml" -a
Info
titleNote

This replaces the LoadHL7RIM script and function

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:

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

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

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

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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"

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RemoveMetadata

Clears optionally loaded metadata associated with the specified coding scheme.
Options

...

-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.

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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

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"

LexEVS Validation Test Script

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Shell Script

...

Use and Function

 ""

Special Batch Loading Functions

Scheme and Metadata Removal

Pick List and Value Set Load Administration

LexEVS Validation Test Script

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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

...

-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.

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Command Line Scripts and Wrappers Overview

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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 schemesImage Removed 

Using Optional Parameters

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  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

    Info
    titleNote

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

Value Set and Pick List Loading

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