HowTo Build LexEVS Loaders

Table of Contents Font Color Key LexEVS Projects Involved lbAdmin lbImpl lbGUI lbInterfaces lbModel lgConverter lbTest

Font Color Key

• blue - indicates files to be created
• firebrick - indicates where MedDRA Loader code is called
• gray - indicates loader code provided (inherited) that you don't change
• red - indicates code you need to create or refactor appropriately

LexEVS Projects Involved

lbAdmin

• Package: org.LexGrid.LexBIG.admin
  • Class: ActiveScheme
  • Class: LoadMedDRA --PRIMARY ENTRY POINT---
    • org.LexGrid.LexBIG.Impl.loaders.MedDRALoaderImpl
      • validate()
      • BaseLoader.setCodingSchemeManifestURI()
      • load() ---START THE PROCESS---
      • If specified, sets associated tag on new schemes
        • BaseLoader.getCodingSchemeReferences()
      • if specified, activates new schemes
        • BaseLoader.getCodingSchemeReferences()
    • java.net.URI(used by MedDRA_Loader)
    • org.apache.commons.cli.Options (Used by URI)
• scripts:
  • LoadMedDRA.bat
  • LoadMedDRA.sh

lbImpl

• Package: org.LexGrid.LexBIG.Impl
  • Class: LexBIGServiceImpl
    • Method: registerExtensions()
      • Add line to register loader
      • new MedDRALoaderImpl().register();
  • Package:loaders
  • Class: MedDRALoaderImpl (extends BaseLoader implements MedDRA_Loader)
    • Code needs to be edited appropriately
    • Public method: finalize
    • Public method: getMedDRAVersion
    • Public method: getOntologyFormat
      • Requires OntologyFormat.MEDDRA to be defined in lbInterfaces
    • Public method: load
      • Calls BaseLoader.load
      • Nested within BaseLoader.load calls BaseLoader.baseLoad
        • Creates DoConversion
          • Calls run()
            • Calls doLoad!!!
            • register(loadedCodingSchemes)
            • doPostProcessing
            • doTransitiveAndIndex
            • doApplyManifest
            • register(loadedCodingSchemes)
            • Something with options
    • Public method: validate
    • Protected method: buildExtensionDescription
    • Protected method: declareAllowedOptions
    • Public method: doLoad
      • Called from BaseLoader.load
      • Creates instance of MedDRA2LGMain
        • Calls map() which returns a codingScheme object
        • Calls BaseLoader.persistCodingSchemeToDatabase()

lbGUI

• IGNORE

lbInterfaces

• Package: org.LexGrid.LexBIG.Extensions.Load
  • Interface: MedDRA_Loader(extends Loader)
  • Enum: OntologyFormat (Update with new loader name , i.e. MEDDRA)

lbModel

• Castor/src (files are created/deleted by Castor!!)
  • Package: org.LexGrid.LexBIG.Preferences.loader.MedDRALoadPreferences
    • Package: descriptors

lgConverter

• Package: edu.mayo.informatics.lexgrid.convert.directConversions
  • Package: medDRA
    • translation engine
    • Class: MedDRA2LGMain.java
    • Class: MedDRAFormatValidator
  • Package: TextCommon
    • Simple example to start learning how to build converter.
• Package: edu.mayo.informatics.lexgrid.convert.formats
  • Package: baseFormats
    • Class: CommonBase
    • Class: FileBase (useful for MedDRA??)
    • Class: URIBase (useful for MedDRA??)
  • Package: inputFormats
    • Class: MedDRA.java (need to define???)
• Package: edu.mayo.informatics.lexgrid.convert
  • Package: inserter
    • Class: CodingSchemeInserter (call??)
  • Package: options(??)
  • Package: utility
    • Package: loaderPreferences
      • Package: loaders
        • Class: MedDRAPreferenceLoader (not needed yet)

lbTest

• Package: edu.mayo.informatics.lexgrid.convert.directConversions.medDRA
• Package: org.LexGrid.LexBIG.Impl.testUtility
  • Class: LoadTestDataTest
    • public method: testLoadMedDRA