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Coding Scheme Metadata Access and Administration
Shell Script | Use and Function | ||
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ActivateScheme | Activates a coding scheme based on unique URN and version.
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DeactivateScheme | Deactivates a coding scheme based on unique URN and version.
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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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TagScheme | Associates a tag ID (e.g. 'PRODUCTION' or 'TEST') with a coding scheme URN and version.
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Lucene Index Administration
Shell Script | Use and Function | |||||||
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CleanUpLuceneIndex | Clean up orphaned indexes.
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OptimizeLuceneIndex | Optimizes the Common Lucene Index.
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RebuildIndex | Rebuilds indexes associated with the specified coding scheme.
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RemoveIndex | Clears an optional named index associated with the specified coding scheme.
Options:
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Misc Database Administration Scripts
Shell Script | Use and Function | ||
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ExportDDLScripts | Exports the database create/drop scripts.
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PasswordEncryptor | Encrypts the given password.
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LexEVS Export Scripts
Shell Script | Use and Function | ||||||||||||||
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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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ExportOwlRdf | Exports content from the repository to a file in OWL format.
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LexEVS Loader Scripts
Shell Script | Use and Function | |||||||||
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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.
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LoadOBO | Loads a file specified in the Open Biomedical Ontologies (OBO) format.
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LoadOWL | Loads an OWL file.
Options:
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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:
Example:
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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:
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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.
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LoadHL7RIM | Converts an HL7 RIM MS Access database to a LexGrid database
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LoadMetaData | Loads optional XML-based metadata to be associated with an existing coding scheme.
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LoadMrMap | Loads mappings file(s), provided in UMLS RRF format. Specifically MRMAP.RRF and MRSAT.RRF.
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Special Batch Loading Functions
Shell Script | Use and Function | ||
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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.
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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.
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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.
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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.
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Scheme and Metadata Removal
Shell Script | Use and Function | |||||||||
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RemoveScheme | Removes a coding scheme based on unique URN and version.
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RemoveMetadata | Clears optionally loaded metadata associated with the specified coding scheme.
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Pick List and Value Set Load Administration
Shell Script | Use and Function | ||
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LoadPickListDefinition | Loads Pick List Definition content, provided in LexGrid canonical xml format.
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LoadAllDefinitionsToResolvedValueSet | Loads Value Set Definition content, provided in LexGrid canonical xml format.
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Expert Admin Scripts (Focused on Mass Loads of Value Sets)
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These Scripts have a narrow focus on mass loads and removals of value sets. They can be very destructive. |
Shell Script | Use and Function | ||
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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:
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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:
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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:
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RemoveAllResolvedValueSets | WARNING: REMOVES ALL RESOLVED VALUE SETS Options: None, removes all resolved value sets from the system. Not reversible. Example:
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LexEVS Validation Test Script
TestRunner
Located in {LEXBIG_DIRECTORY}/test. Runs the test suite by invoking the Ant launcher.
Shell Script | Use and Function |
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TestRunner | Located in {LEXBIG_DIRECTORY}/test. Runs the test suite by invoking the Ant launcher. |
Usage: TestRunner
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Command Line Scripts and Wrappers Overview
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Value Set and Pick List Scripts
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