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Introduction
This document is a section of the Administration Guide.
Vocabulary Administration Overview
A set of administrative utilities are provided to manage the LexEVS Service. These utilities are provided for Windows (.bat) and Linux (.sh) operating systems. Each of the commands is located in the {LEXBIG_DIRECTORY}/admin and {LEXBIG_DIRECTORY}/test directory. A full description of the options with example is provided for each of the administration utilities.
Administrative Program | Description | ||
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ActivateScheme | Activates a coding scheme based on unique URN and version.
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ClearOrphanedResources | Clean up orphaned resources - databases and indexes.
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DeactivateScheme | Deactivates a coding scheme based on unique URN and version.
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ExportLgXML | Exports content from the repository to a file in the LexGrid canonical XML format.
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ExportOBO | Exports content from the repository to a file in the Open Biomedical Ontologies (OBO) format.
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ExportOWL | Exports content from the repository to a file in OWL format.
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ListExtensions | List registered extensions to the LexEVS runtime environment.
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ListSchemes | List all currently registered vocabularies.
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LoadLgXML | Loads a vocabulary file, provided in LexGrid canonical xml format.
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LoadNCIHistory | Imports NCI History data to the LexEVS repository. |
Options:
- -in,-input
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- <uri>
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- URI
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- specifying
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- location
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- of
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- the
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- history
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- file
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- -vf,-versionFile
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- <uri>
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- URI
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- specifying
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- location
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- of
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- the
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- file
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- containing
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- version
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- identifiers
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- for
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- the
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- history
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- to
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- be
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- loaded.
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- -v,
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- -validate
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- <level>
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- Perform
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- validation
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- of
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- the
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- candidate
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- resource
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- without
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- loading
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- data.
...
- If
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- specified,
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- the
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- '-nf'
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- and
...
- '-r'
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- options
...
- are
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- ignored.
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- Supported
...
- levels
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- of
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- validation
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- include:
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- 0
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- =
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- Verify
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- top
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- 10
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- lines
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- are
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- correct
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- format
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- 1
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- =
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- Verify
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- correct
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- format
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- for
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- the
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- entire
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- file
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- -nf,-noFail
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- If
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- specified,
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- indicates
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- that
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- processing
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- should
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- not
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- stop
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- for
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- recoverable
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- errors
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- -r,
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- -replace
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- If
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- not
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- specified,
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- the
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- provided
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- history
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- file
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- will
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- be
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- added
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- into
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- the
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- current
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- history
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- database;
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- otherwise
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- the
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- current
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- database
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- will
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- be
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- replaced
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- by
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- the
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- new
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- content.
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Load Example:
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Code Block
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LoadNCIHistory -nf -in "file:///path/to/history.file" -vf "file:///path/to/version.file"
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Validation Example:
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Code Block
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LoadNCIHistory -in "file:///path/to/history.file" -v 0
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Versions File Format Information:Code Block releaseDate | isLatest | releaseAgency | releaseId | releaseOrder | entityDescription
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Sample record:
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Code Block
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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.
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|LoadNCIMeta
Loads the NCI MetaThesaurus, provided as a collection of RRF files.
Options:- -in,-input
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- <uri>
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- The
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- directory
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- containing
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- the
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- RRF
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- files;
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- in
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- URI
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- format.
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- -v,
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- -validate
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- <level>
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- Perform
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- validation
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- of
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- the
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- candidate
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- resource
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- without
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- loading
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- data.
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- If
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- specified,
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- the
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- '-nf',
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- -a'
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- and
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- '-t'
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- options
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- are
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- ignored.
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- Supported
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- levels
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- of
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- validation
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- include:
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- 0
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- =
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- Verify
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- first
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- 1000
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- lines
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- per
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- required
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- file
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- -nf,-noFail
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- If
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- specified,
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- indicates
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- that
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- processing
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- should
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- not
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- stop
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- for
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- recoverable
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- errors
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- -a,
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- -activate
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- ActivateScheme
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- on
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- successful
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- load;
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- if
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- unspecified
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- the
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- vocabulary
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- is
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- loaded
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- but
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- not
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- activated
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- -t,
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- -tag
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- <tagID>
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- An
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- optional
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- tag
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- ID
...
- (e.g.
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- 'PRODUCTION'
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- or
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- 'TEST')
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- to
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- assign.
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Load Example:
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Code Block
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LoadNCIMeta -in "file:///path/to/directory" -nf -a
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Validation Example:
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Code Block
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LoadNCIMeta -in "file:///path/to/directory" -v 0
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|LoadNCIThesOWL
Loads an OWL file containing a version of the NCI Thesaurus ...
Options:- -in,-input
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- <uri>
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- URI
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- specifying
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- location
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- of
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- the
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- source
...
- file
...
- -v,
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- -validate
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- <level>
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- Perform
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- validation
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- of
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- the
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- candidate
...
- resource
...
- without
...
- loading
...
- data.
...
- If
...
- specified,
...
- the
...
- '-nf',
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- -a'
...
- and
...
- '-t'
...
- options
...
- are
...
- ignored.
...
- Supported
...
- levels
...
- of
...
- validation
...
- include:
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- 0
...
- =
...
- Verify
...
- document
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- is
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- well-formed
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- 1
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- =
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- Verify
...
- document
...
- is
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- valid
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- -nf,
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- -noFail
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- If
...
- specified,
...
- indicates
...
- that
...
- processing
...
- should
...
- not
...
- stop
...
- for
...
- recoverable
...
- errors.
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- -a,
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- -activate
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- ActivateScheme
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- on
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- successful
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- load;
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- if
...
- unspecified
...
- the
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- vocabulary
...
- is
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- loaded
...
- but
...
- not
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- activated.
...
- -t,
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- -tag
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- <tagID>
...
- An
...
- optional
...
- tag
...
- ID
...
- (e.g.
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- 'PRODUCTION'
...
- or
...
- 'TEST')
...
- to
...
- assign.
...
Load Example:
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Code Block
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LoadNCIThesOWL -in "file:///path/to/thesaurus.owl" -nf -a
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Validation Example:
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Code Block
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LoadNCIThesOWL -in "file:///path/to/thesaurus.owl" -v 0
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|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',
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- -a'
...
- and
...
- '-t'
...
- options
...
- are
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- 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,
...
- -
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- activate
...
- ActivateScheme
...
- on
...
- successful
...
- load;
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- if
...
- unspecified
...
- the
...
- vocabulary
...
- is
...
- loaded
...
- but
...
- not
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- activated
...
- -t,
...
- -tag
...
- <id>
...
- An
...
- optional
...
- tag
...
- ID
...
- (e.g.
...
- 'PRODUCTION'
...
- or
...
- 'TEST')
...
- to
...
- assign.
...
Example:
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Code Block LoadOBO -in "file:///path/to/file.obo" -nf -a
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|Code Block LoadOBO -in "file:///path/to/file.obo" -v 0
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LoadOWL
Loads an OWL file.
Info title 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
- -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 LoadOWL -in "file:///path/to/somefile.owl" -nf -a
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|Code Block LoadOWL -in "file:///path/to/somefile.owl" -v 0
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LoadUMLSDatabase
Loads UMLS content,
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provided
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as
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a
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collection
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of
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RRF
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files
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in
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a
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single
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directory.
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Files
...
may
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comprise
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the
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entire
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UMLS
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distribution
...
or
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pruned
...
via
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the
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MetamorphoSys
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tool.
...
A
...
complete
...
list
...
of
...
source
...
vocabularies
...
is
...
available
...
online
...
at
...
...
Options:
...
- -in,
...
- -input
...
- <uri>
...
- Location
...
- of
...
- the
...
- source
...
- database.
...
- Typically
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- this
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- is
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- specified
...
- in
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- the
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- form
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- of
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- a
...
- URL
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- that
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- indicates
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- the
...
- database
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- server,
...
- port,
...
- name,
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- and
...
- optional
...
- properties.
...
- -u,
...
- -uid
...
- User
...
- ID
...
- for
...
- authenticated
...
- access,
...
- if
...
- required
...
- and
...
- not
...
- specified
...
- as
...
- part
...
- of
...
- the
...
- input
...
- URL.
...
- -p,-
...
- pwd
...
- Password
...
- for
...
- authenticated
...
- access,
...
- if
...
- required
...
- and
...
- not
...
- specified
...
- as
...
- part
...
- of
...
- the
...
- input
...
- URL.
...
- -d,-
...
- driver
...
- Name
...
- of
...
- the
...
- JDBC
...
- driver
...
- to
...
- use
...
- when
...
- accessing
...
- the
...
- database.
...
- -s,
...
- -sources
...
- Comma-delimited
...
- list
...
- of
...
- source
...
- vocabularies
...
- to
...
- load.
...
- If
...
- absent,
...
- all
...
- available
...
- vocabularies
...
- are
...
- loaded.
...
- -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.
...
Examples:Code Block LoadUMLSDatabase -in "jdbc:postgresql://localhost:5432/lexgrid" -d "org.postgresql.Driver" -u "myDatabaseUser" -p "myPassword" -s "ICD9CM_2005,ICD9CM_2006" -nf -a
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|Code Block LoadUMLSDatabase -in "jdbc:postgresql://localhost:5432/lexgrid" -d "org.postgresql.Driver" -u "myDatabaseUser" -p "myPassword" -v 0
...
LoadUMLSFiles
Loads UMLS content,
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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
...
...
Options:
...
- -in,
...
- -input
...
- <uri>
...
- URI
...
- or
...
- path
...
- of
...
- the
...
- directory
...
- containing
...
- the
...
- NLM
...
- files
...
- -s,-
...
- sources
...
- Comma-delimited
...
- list
...
- of
...
- source
...
- vocabularies
...
- to
...
- load.
...
- If
...
- absent,
...
- all
...
- available
...
- vocabularies
...
- are
...
- loaded.
...
- -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.
...
Examples:Code Block LoadUMLSFiles -in "file:///path/to/directory/" -s "ICD9CM_2005,ICD9CM_2006" -nf -a
...
Code Block LoadUMLSFiles -in "file:///path/to/directory/" -v 0
...
|Info title Note UMLS Metathesaurus RRF files are a very large fileset. Many users prefer to subset these files using the Metamorphosys tool included with the UMLS Metathesaurus in order to move a single terminology from a central location of these files. When generating source RRF files from the Metathesaurus, the Metamorphosys tool should be set to output versionless source abbreviations rather than versioned source abbreviations. Failing to do so before loading RRF files to LexEVS will cause an incomplete database to be created leaving the association and concept tables empty
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.
...
Examples: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/
...
...
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.
...
Example: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.
...
Examples:
...
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.
...
Options:
...
- -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
...
title
...
Note
...
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"
...
|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 title 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.
...
- -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" -i "myindex"
...
|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"
...
|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"
...
|TestRunner
Located in {LEXBIG_DIRECTORY}/test.
...
Executes
...
a
...
suite
...
of
...
tests
...
for
...
the
...
LexEVS
...
installation.
...
Info
...
title
...
Note
...
The
...
LexEVS
...
runtime
...
and
...
database
...
environments
...
must
...
still
...
be
...
configured
...
prior
...
to
...
invoking
...
the
...
test
...
suite.
...
Options:
...
- -b,-brief
...
- Runs
...
- the
...
- LexEVS
...
- test
...
- suite
...
- and
...
- produce
...
- a
...
- text
...
- report
...
- with
...
- overall
...
- statistics
...
- and
...
- details
...
- for
...
- failed
...
- tests
...
- only.
...
- -f,-full
...
- Runs
...
- the
...
- LexEVS
...
- test
...
- suite
...
- and
...
- produce
...
- an
...
- itemized
...
- list
...
- of
...
- all
...
- tests
...
- with
...
- indication
...
- of
...
- success/failure.
...
- -h,-html
...
- Runs
...
- the
...
- LexEVS
...
- test
...
- suite
...
- and
...
- produce
...
- a
...
- report
...
- suitable
...
- for
...
- view
...
- in
...
- a
...
- standard
...
- web
...
- browser.
...
- -x,-xml
...
- Runs
...
- the
...
- LexEVS
...
- test
...
- suite
...
- and
...
- produce
...
- a
...
- report
...
- with
...
- extensive
...
- information
...
- for
...
- each
...
- test
...
- case
...
- in
...
- xml
...
- format.
...
Example:
...
Code Block
...
TestRunner -f -h
...
|TransferScheme
Tool to help gather information necessary to transfer data from one SQL server to another.
Options:- -u,-urn
...
- The
...
- Coding
...
- Scheme
...
- URN
...
- or
...
- local
...
- name
...
- to
...
- transfer.
...
- -v,-version
...
- The
...
- version
...
- of
...
- the
...
- coding
...
- scheme
...
- to
...
- transfer.
...
Example:
...
Code Block
...
TransferScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v 05.09e"
...
Installing Sample Vocabularies
This LexEVS installation provides the UMLS Semantic Net and a sampling of the NCI Thesaurus content (sample.owl)
...
that
...
can
...
be
...
loaded
...
into
...
the
...
database.
...
- In
...
- a
...
- Command
...
- Prompt
...
- window,
...
- enter
...
- the
...
- following
...
- to
...
- go
...
- to
...
- the
...
- example
...
- programs:
...
Code Block
...
cd {LEXBIG_DIRECTORY
...
}/examples
- To load the example vocabularies, run the appropriate LoadSampleData script (<tt>LoadSampleData.bat</tt>
...
- for
...
- Windows;
...
- <tt>LoadSampleData.sh</tt>
...
- for
...
- Linux).
...
Info title Note Vocabularies should not be loaded until configuration of the LexEVS runtime and database server are complete.
The following figure 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 have been loaded.
- Enter:
Code Block cd {LEXBIG_DIRECTORY}/examples
...
- Execute one of sample programs. .bat for windows or .sh for Linux.
- FindConceptNameForCode.bat
- FindPropsandAssocForCode.bat
- FindRelatedCodes
- FindTreeforCodeAndAssoc
The following figure shows sample program output 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.
- Using a web or ftp client go to URL: ftp://ftp1.nci.nih.gov/pub/cacore/EVS/
...
- Select the version of NCI Thesaurus OWL you wish to download. Save the file to a directory on your machine.
- 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
- Using the LexEVS utilities load the NCI Thesaurus
Code Block cd {LexBIG_DIRECTORY}/admin
...
For
...
- Windows
...
- installation
...
- use
...
- the
...
- following
...
- command:
...
Code Block
...
LoadNCIThesOWL.bat -nf -in "file:///{NCI_THESAURUS_DIRECTORY}/Thesaurus_05.12f.owl"
...
For
...
- Linux
...
- installation
...
- use
...
- the
...
- following
...
- command:
...
Code Block
...
LoadNCIThesOWL.sh -nf -in "file:///{NCI_THESAURUS_DIRECTORY}/Thesaurus_05.12f.owl"
Info title Note This step will require about three hours on a Pentium 3.0 Ghz machine. The total time to load NCI Thesaurus will vary depending on machine, memory, and disk speed.
The following example shows output from load of NCI Thesaurus 05.12f:
Code Block |
---|
{code} {info:title=Note}This step will require about three hours on a Pentium 3.0 Ghz machine. The total time to load NCI Thesaurus will vary depending on machine, memory, and disk speed.{info} The following example shows output from load of NCI Thesaurus 05.12f: {code} ... [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 {code} h3. NCI Metathesaurus vocabulary This section describes the steps to download and install a full version of the NCI Metathesaurus for the LexEVS Service. # Using a web or ftp client go to URL: |
NCI Metathesaurus vocabulary
This section describes the steps to download and install a full version of the NCI Metathesaurus for the LexEVS Service.
- Using a web or ftp client go to URL: ftp://ftp1.nci.nih.gov/pub/cacore/EVS/
...
- Select the version of NCI Metathesaurus RRF you wish to download. Save the file to a directory on your machine.
- 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.
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Info
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title
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Note
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RELEASE_INFO.RRF
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is
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required
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to
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be
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present
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for
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the
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load
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utility
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to
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work.
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- Using the LexEVS utilities load the NCI Thesaurus
Code Block cd {LexBIG_DIRECTORY}/admin
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For
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- Windows
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- installation
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- use
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- the
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- following
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- command:
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Code Block
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LoadNCIMeta.bat -nf -in "file:///{NCI_METATHESAURUS_DIRECTORY}/"
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For
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- Linux
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- installation
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- use
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- the
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- following
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- command:
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Code Block
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LoadNCIMeta.sh -nf -in "file:///{NCI_THESAURUS_DIRECTORY}/"
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Info | ||
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NCI Metathesaurus contains many individual vocabularies and requires several hours to load and index. This step requires about 15 hours on a Pentium 3.0 Ghz machine with 7200rpm disk. The total time to load NCI MetaThesaurus will vary depending on machine, memory, and disk speed. |
NCI History
This section describes the steps to download and install a history file for NCI Thesaurus.
- Using a web or ftp client go to URL: ftp://ftp1.nci.nih.gov/pub/cacore/EVS/
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- 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.
- 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
- Using the LexEVS utilities load the NCI Thesaurus:
Code Block cd {LexBIG_DIRECTORY}/admin_*</tt>
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For
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- Windows
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- installation
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- use
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- the
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- following
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- command:
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Code Block
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LoadNCIHistory.bat -nf -in "file:///{NCI_HISTORY_DIRECTORY}" -vf "file:///NCI_HISTORY_DIRECTORY}/VersionFile"
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For
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- Linux
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- installation
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- use
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- the
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- following
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- command:
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Code Block
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LoadNCIHistory.sh -nf -in "file:///{NCI_HISTORY_DIRECTORY}" -vf "file:///NCI_HISTORY_DIRECTORY}/VersionFile"
Info | ||
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If a {code} {info:title=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. {info} h2. Deactivating and Removing a Vocabulary This section describes the steps to deactivate a coding scheme and remove coding scheme from LexEVS Service. # Change directory to LexEVS administration directory. Enter: {code} |
Deactivating and Removing a Vocabulary
This section describes the steps to deactivate a coding scheme and remove coding scheme from LexEVS Service.
- Change directory to LexEVS administration directory. Enter:
Code Block cd {LEXBIG_DIRECTORY}/admin_*
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- 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 "05.12f"
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- 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 "05.12f"
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Tagging a Vocabulary
This section describes the steps to tag a coding scheme to be used via LexEVS API.
- Change directory to LexEVS administration directory and enter:
Code Block cd {LEXBIG_DIRECTORY}/admin_*
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- Use the TagScheme to tag a coding system and version with a local tag name (e.g.
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- PRODUCTION).
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- This
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- tag
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- name
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- can
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- be
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- used
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- via
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- LexEVS
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- API
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- for
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- query
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- restriction.
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- Example:
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Code Block
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TagScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.12f" -t "PRODUCTION"
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