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Section
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Panel
titleContents of this Page
Table of Contents
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Include Page
Menu LexEVS 6.0 Administration to Include
Menu LexEVS 6.0 Administration to Include

Vocabulary Administration Overview

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

If you are loading a large vocabulary such as SNOMED or the NCI Metathesaurus, then we recommend the use of these scripts over the GUI since adjusting system memory requirements can be accomplished by changing the load script with a text editor.

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
...
  • title
...
  • Note
...
  • 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
...
  • 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
...
  • 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
...
  • 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" 
...
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
...
  • 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
...
  • 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" 
...
LoadAllDefinitionsToResolvedValueSet
Loads Value Set Definition content, provided in LexGrid canonical xml format.
 Options:
  • -in,-input 
...
  •  <uri> 
...
  •  URI 
...
  •  or 
...
  •  path 
...
  •  specifying 
...
  •  location 
...
  •  of 
...
  •  the 
...
  •  source 
...
  •  file.
...
  • -v, 
...
  •  -validate 
...
  •  <int> 
...
  •  Perform 
...
  •  validation 
...
  •  of 
...
  •  the 
...
  •  candidate 
...
  •  resource 
...
  •  without 
...
  •  loading 
...
  •  data. 
...
  •  Supported 
...
  •  levels 
...
  •  of 
...
  •  validation 
...
  •  include:
...
    • 0 
...
    •  = 
...
    •  Verify 
...
    •  document 
...
    •  is 
...
    •  well-formed
...
    • 1 
...
    •  = 
...
    •  Verify 
...
    •  document 
...
    •  is 
...
    •  valid 
...

    •  Example:
...
    •  Code Block
...
    • LoadValueSetDefinition -in "file:///path/to/file.xml" 
Expert Admin Scripts (Focused on Mass Loads of Value Sets)
 
 Warning
These Scripts have a narrow focus on mass loads and removals of value sets. They can be very destructive.
   
Shell Script
Use and Function
LoadAllValueSetDefinitionsInDirectory
Loads All LexGrid XML formatted Value Set Definitions in a given directory. 
Highly recommended that the folder be cleaned of all non value set files and folders
Options:
    • -in, Path to directory

       Example:
       Code Block
      LoadAllValueSetDefinitionsInDirectory -in /path/to/directory
LoadAllDefinitionsToResolvedValueSet
Loads All Value Set Definitions for a given uri as resolved coding scheme. All compiled resolved value sets should be removed to insure resolution updates are correct with the current version of the source terminology.
Options:
RemoveAllValueSetDefinitions
WARNING: Removes all value set definitions without discrimination
Options:
None: Takes no input, removes all value set definitions in the system. Cannot be reversed.
Example:
 Code Block
 ./RemoveAllValueSetDefinitions.sh
 
 
RemoveAllResolvedValueSets
 WARNING:  REMOVES ALL RESOLVED VALUE SETS
Options: None, removes all resolved value sets from the system. Not reversible.
Example:
 Code Block
./RemoveAllResolvedValueSets.sh
LexEVS Validation Test Script
   
Shell Script
Use and Function
TestRunner
Located in {LEXBIG_DIRECTORY}/test. Runs the test suite by invoking the Ant launcher.
 Info
titleNote
The LexEVS runtime and database environments must still be configured prior to invoking the test suite. Running any option other than -v will cause a large set of junits to be run
Usage: TestRunner
  • -b, -brief Run the LexBIG test suite and produce a text report with overall statistics and details for failed tests only.
  • -f, -full Run the LexBIG test suite and produce an itemized list of all tests with indication of success/failure.
  • -x,-xml Run the LexBIG test suite and produce a report with extensive information for each test case in xml format.
  • -h,-html Run the LexBIG test suite and produce a report suitable for view in a standard web browser: this is the default
     if no other option is specified.
  • -v,-verify Basic verification that LexEVS is configured properly and basic systems are functioning. 
     Examples:
     Code Block
    TestRunner -v
    Run the full test suite of jUnits and save the report to an html file. (This can take quite some time.)
     Code Block
    TestRunner -f -h
    Run a verification of the LexEVS installation. A quick way to insure your system is up and running.
     Code Block
    TestRunner -v 
Command Line Scripts and Wrappers Overview
LexEVS provides a set of shell scripts and code wrappers that provide command line users standard options and automatic printouts of current coding schemes when performing administrative functions using the command line.
Displaying Current Coding Schemes
When you have coding Schemes Loaded to LexEVS many command line script calls will bring up a printout of a table of the loaded coding schemes to be used as a selective menu for other functions.
screenshot showing the printout of a table of the loaded coding schemesImage Added
Using Optional Parameters
A standard parameter interface allows users to customize command line calls to LexEVS. These options control things such as loader synchronicity, supplemental file locations, and fault conditions. Shell scripts contain comments on usage for each function wrappers options.
 Code Block
{code}|

h3. LexEVS Validation Test Script

|| Shell Script || Use and Function ||
| TestRunner | Located in \{LEXBIG_DIRECTORY\}/test. Runs the test suite by invoking the Ant launcher.
{info:title=Note}The LexEVS runtime and database environments must still be configured prior to invoking the test suite.  Running any option other than -v will cause a large set of junits to be run{info}
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}TestRunner -v{code}
Run the full test suite of jUnits and save the report to an html file. (This can take quite some time.)
{code}TestRunner -f -h{code}
Run a verification of the LexEVS installation.  A quick way to insure your system is up and running.
{code}TestRunner -v {code}|

h2. Command Line Scripts and Wrappers Overview

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

h3. Displaying Current Coding Schemes

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

!Command_Line_Scheme_List.JPG|alt="screenshot showing the printout of a table of the loaded coding schemes"!

h3. Using Optional Parameters

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

{code}
# 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 $@ 
{code}

h3. Setting Java Virtual Machine Options

Heap size:
Memory management for heap size is a particular issue when loading larger Terminologies such as SNOMED or the NCI Thesaurus.  Users need to be prepared to increase heap size if loads crash with heap
Setting Java Virtual Machine Options
Heap size:
 Memory management for heap size is a particular issue when loading larger Terminologies such as SNOMED or the NCI Thesaurus. Users need to be prepared to increase heap size if loads crash with heap size errors.
 Example:
 Code Block
-Xmx:4000m

Permanent Generation:
 LexEVS now depends on some Permanent Generation memory management during runtime.
Typically set as follows:
 Code Block
 size errors.
Example:
{code}
-Xmx:4000m
{code}

Permanent Generation:
LexEVS now depends on some Permanent Generation memory management during runtime. 

Typically set as follows:
{code}
-XX:MaxPermSize:256m
{code}

h2. Installing Sample Vocabularies

This LexEVS installation provides a sample vocabulary, 
Installing Sample Vocabularies
This LexEVS installation provides a sample vocabulary, Automobiles.xml, 
...
 that 
...
 can 
...
 be 
...
 loaded 
...
 into 
...
 the 
...
 database.
...
  1. In 
...
  1.  a 
...
  1. Command 
...
  1.  Prompt
...
  1.  window, 
...
  1.  enter 
...
  1.  the 
...
  1.  following 
...
  1.  to 
...
  1.  go 
...
  1.  to 
...
  1.  the 
...
  1.  example 
...
  1.  programs.
...
  1.  Code Block
...
  1. cd {LEXBIG_DIRECTORY}/examples
...
  2. To load an example vocabulary, run the LoadSampleData script, LoadSampleData.bat 
...
  1.  for 
...
  1.  Windows; 
...
  1.  LoadSampleData.sh 
...
  1.  for 
...
  1.  Linux.
...
  2. To 
...
  1.  load 
...
  1.  other 
...
  1.  example 
...
  1.  vocabularies, 
...
  1.  run 
...
  1.  the 
...
  1.  appropriate 
...
  1.  script 
...
  1.  for 
...
  1.  any 
...
  1.  sample 
...
  1.  vocabulary 
...
  1.  in 
...
  1.  {LEXBIG_DIRECTORY
...
  1. }/test/resources/testData.


{:=
 Info
title
Note
}
Vocabularies 
 
 cannot 
 
 be 
 
 loaded 
 
 until 
 
 configuration 
 
 of 
 
 the 
 
 LexEVS 
 
 runtime 
 
 and 
 
 database 
 
 server 
 
 are 
 complete. {info}

!Successful_Load_of_Sample_Vocabulary.jpg|alt="Displays the successful load of the sample vocabulary file."!

h3. Running the sample query programs

A set of sample programs are provided in the \
complete.
Displays the successful load of the sample vocabulary file.Image Added
Running the sample query programs
A set of sample programs are provided in the {LEXBIG_DIRECTORY
...
}/examples 
...
 directory. 
...
 To 
...
 run 
...
 the 
...
 sample 
...
 query 
...
 programs 
...
 successfully 
...
 a 
...
 vocabulary 
...
 must 
...
 be 
...
 loaded.
...
  1. Enter
     Code Block
    cd {LEXBIG_DIRECTORY}/
...
  1. examples
  2. Execute one of sample programs.
     .bat for windows or .sh for Linux. 
     FindPropsandAssocForCode.bat 
     FindRelatedCodes
Shows the output of example programs using sample vocabulary for finding properties and associations for a given codeImage Added
Installing NCI Vocabularies
NCI Thesaurus Vocabulary
This section describes the steps to download and install a full version of the NCI Thesaurus for the LexEVS Service.
  1. Using a web or ftp client go to URL: ftp://ftp1.nci.nih.gov/pub/cacore/EVS/
...

  1.  screenshot showing navigating to FTP directoryImage Added
  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"
 Info
titleNote
The NCI Thesaurus has grown large enough that it can no longer be loaded on many typical desktop machines. We recommend a 64-bit operating system running on a multiprocessor computer with a minimum of 4g of memory. Server class Linux machines are the typical target for these loads. The time to load NCI Thesaurus will vary depending on machine, memory, and disk speed. Expect a couple of hours for a higher end machine.
The following code sample shows the example output from load of NCI Thesaurus 05.12f
 Code Block
{code}

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

The following code sample shows the example 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

h4. Loading the Metathesaurus

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
Loading the Metathesaurus
This section describes the steps to download and install a full version of the NCI Metathesaurus for the LexEVS Service.
  1. Using a web or ftp client go to URL: ftp://ftp1.nci.nih.gov/pub/cacore/EVS/
...

  1.  screenshot showing navigating to ftp client in ExplorerImage Added
  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. 
...
  1.  RELEASE_INFO.RRF 
...
  1.  is 
...
  1.  required 
...
  1.  to 
...
  1.  be 
...
  1.  present 
...
  1.  for 
...
  1.  the 
...
  1.  load 
...
  1.  utility 
...
  1.  to 
...
  1.  work.
...
  2. Using 
...
  1.  the 
...
  1.  LexEVS 
...
  1.  utilities 
...
  1.  load 
...
  1.  the 
...
  1.  NCI 
...
  1.  Thesaurus
...
  1.  Code Block
...
  1. 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}/"
...
 Info
titleNote
NCI Metathesaurus contains many individual vocabularies some of which are large vocabularies in and of themselves. It requires many hours to load and index. It can require 36 hours on a multiprocessor machine with 6g plus memory. The total time to load NCI MetaThesaurus will vary depending on machine, memory, and disk speed. Because this loader uses a batch loading strategy it is less dependent on memory, but some users will see 3 or 4 day load times with average multiprocessor processing power.
Resuming Loads
Since this loader is resource hungry we provide the option to restart should you find your resource settings to be inadequate. Resuming loads which have crashed or been interrupted by server problems is possible using the ResumeBatchLoad script set.
  1. Using the LexEVS utilities load the NCI Thesaurus
     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"
...
NCI History
This section describes the steps to download and install a history file for NCI Thesaurus.
  1. Using a web or ftp client go to URL:
     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" 
 Info
titleNote
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.
  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"
...
  2. 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"
...
Tagging a Vocabulary
This section describes the steps to tag a coding scheme to be used via LexEVS API.
  1. Change directory to LexEVS administration directory. Enter:
     Code Block
    cd {LEXBIG_DIRECTORY}/admin
...
  2. Use the TagScheme to tag a coding system and version with a local tag name (e.g. 
...
  1.  PRODUCTION). 
...
  1.  This 
...
  1.  tag 
...
  1.  name 
...
  1.  can 
...
  1.  be 
...
  1.  used 
...
  1.  via 
...
  1.  LexEVS 
...
  1.  API 
...
  1.  for 
...
  1.  query 
...
  1.  restriction. 
...
  1.  Example:
...
  1.  Code Block
...
  1. TagScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "10.10d"  -t 
...
  1. "PRODUCTION"
...
IndexManagement
LexEVS indexes can be manually updated, removed and optimized by users. This is a useful function particularly when metadata, authoring and post processing may have taken place.
Remove Index
  1. Change directory to LexEVS administration directory. Enter:
     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 Added
     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 
...
  1.  RebuildIndex 
...
  1.  script 
...
  1.  to 
...
  1.  rebuild 
...
  1.  an 
...
  1.  index 
...
  1.  for 
...
  1.  a 
...
  1.  particular 
...
  1.  coding 
...
  1.  scheme.
...

  1.  Example:
...

  1.  Windows:
...

  1. RebuildIndex.bat
...

  1.  Linux:
...

  1. RebuildIndex.sh
...
  2. Interactive 
...
  1.  command: 
...
  1. Enter 
...
  1.  the 
...
  1.  number 
...
  1.  of 
...
  1.  the 
...
  1.  Coding 
...
  1.  Scheme 
...
  1.  to 
...
  1.  use, 
...
  1.  then 
...
  1.  <Enter>.
...
User 
...
 responds 
...
 with 
...
 column 
...
 number 
...
 for 
...
 appropriate 
...
 coding 
...
 scheme.
...
  1. Interactive 
...
  1.  command: 
...
  1. REBUILD 
...
  1.  INDEX 
...
  1.  FOR 
...
  1.  URI? 
...
  1.  <uri 
...
  1.  displayed 
...
  1.  here> 
...
  1.  ('Y' 
...
  1.  to 
...
  1.  confirm, 
...
  1.  any 
...
  1.  other 
...
  1.  key 
...
  1.  to 
...
  1.  cancel).
...
  1.  User 
...
  1.  responds 
...
  1.  with 
...
  1.  'Y
...
  1. '
  2. Command Line example:
     screenshot of command line interfaceImage Added
     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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