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CTS2 Authoring Development (see: org.lexevs.cts2.author.AuthoringOperation )

  • Association Authoring Operations (see: org.lexevs.cts2.author.AssociationAuthoringOperation )
    • Create association in an established coding scheme using the Revision model.
    • Create association in an established mapping dedicated coding scheme using the Revision model.
    • Create association mapping. Create mappings between coding schemes and persist as new coding scheme with default metadata settings. Persist using the Revision model.
    • Create association mapping. Create mappings between coding schemes and persist as a coding scheme with user defined metadata values. Persist using the Revision model.
    • Create association mapping: Create mappings between coding schemes with persisted concept values pulled from target schemes current in a LexEVS service instance. Persist using the Revision model.
    • Create association type. Create a new AssociationPredicate value and persist is using the Revision model.
  • ValueSet Authoring
    • (see: org.lexevs.cts2.author.ValueSetAuthoringOperation)

OWL/RDF Export

  • OWL/RDF Export functionality has been added, allowing the export of loaded LexEVS content into OWL format.
    • (see: org.LexGrid.LexBIG.Extensions.Export.OWL_Exporter)
  • Known issues/restrictions:
    • GForge #30058: AssociationData is not exported. Thus, the owl/rdf exporter cannot handle the owl:hasValue, owl:maxCardinality, owl:minCardinality, owl:cardinality constraints.

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  1. DB_PRIMARY_KEY_STRATEGY indicates which strategy will be used
  2. for the primary key of the database tables.
  3. WARNING - This cannot be change after the initial
  4. schema installation.
    #
  5. Allowable values include:
    #
    #"GUID"
    • Primary Keys are implemented as random GUIDs.
      #"SEQUENTIAL_INTEGER"
    • Primary Keys will be sequentially incremented
    • as Integer values.
      DB_PRIMARY_KEY_STRATEGY=GUID

 

Mapping Extension

(see: org.LexGrid.LexBIG.Extensions.Generic.MappingExtension) 

  • A general purpose Generic Extension for Mapping Coding Schemes has been introduced.

The main implemented features are:

  • Faster retrieval of Mapping ontology relationships as compared to standard CodedNodeGraph methods
  • Expanded Sorting capabilities to include:
    • Source Code
    • Target Code
    • Source Entity Description
    • Target Entity Description
    • Relationship Name
    • A Named Qualifier
  • Ability to count the number of codes that participate in a mapping ontology without having to traverse
  • Determine whether or not an Ontology can be considered a 'Mapping' Ontology.
    • A 'Mapping' Ontology is defined in this case as having at least ALL Relations containers marked as 'isMapping=true'

Supplement Extension

(see: org.LexGrid.LexBIG.Extensions.Generic.SupplementExtension)

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The main implemented features are:

    • Determine whether or not a giving Coding Scheme is acting as a Coding Scheme Supplement.
    • Resolve the Parent Coding Scheme of a given Coding Scheme Supplement.

Value Sets (gForge # 26650)

      • Administrative functions :
        • Ability to load Value Set and Pick List Definitions in to LexGrid repository
        • Ability to remove Value Set and Pick List Definitions from LexGrid repository.
        • Ability to export Value Set and Pick List Definition in LexGrid XML format.
      • Query functions :
        • Ability to list all the Value Set and Pick List Definitions loaded in the system.
        • Ability to dynamically resolve Value Set and Pick List Definition with/without user supplied restrictions.
        • Ability to check if a concept code is part of given Value Set.
        • Ability to check if one Value Set is sub set of other Value Set.
        • Ability to apply restrictions like term, coding scheme version, etc and resolve Value Set and Pick List Definition.
        • Ability to list all the coding schemes referenced by a Value Set Definition.
        • Ability to list all Value Set Definition URIs that references a Coding Scheme. Etc.
      • Authoring functions :
        • Ability to load/update/remove Value Set Definition, DefinitionEntry and Properties using Versioning API.
      • Scripts :
        • LoadValueSetDefinition(.bat and .sh) –Loads Value Set Definition in LexGrid XML file into repository.
        • LoadPickListDefinition(.bat and .sh) – Loads Pick List Definition in LexGrid XML file into repository.
      • GUI :
        • New GUI (LB_VSD_GUI in gui folder of LexEVS API install directory) is developed to test all the functionalities that are available for Value Set Definitions. This tool should mainly be used for testing purpose and not in production. Here are few major functions available through this GUI tool:
          • Create new Value Set Definition
          • Update existing Value Set Definition
          • Remove existing Value Set Definition
          • Load Value Set and Pick List Definition from LexGrid XML file
          • List all Value Set and Pick List Definitions present in the system
          • Add/update/remove DefinitionEntries (rule sets)
          • Add/update/remove properties
          • Resolve Value Set and Pick List Definition using specific set of coding scheme and version that are loaded in the system
          • Ability to validate if the changes made returns desired result before saving changes to the database
          • Export Value Set and Pick List Definitions in LexGrid XML format
          • Following query functions are also available:
            • Filter by Coding Scheme Reference
            • Filter by Concept Domain
            • Check if concept code is valid entry in Value Set Resolution
            • Filter by a term
            • Check if one Value Set is subset of other
            • Filter by Value Set Definition Name
      • JUnit :
        • Junit to test all the Value Set functionalities are included in lbTest java package.
          • Org.LexGrid.valuedomain.test.VDAllTests.java – Loads test data, runs both Value Set and Pick list functionality tests, and removes loaded test data.

Note: Usage Context and Concept Domain is not included in this release, but will be in next release.

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Versioning is a new functionality that has been added to LexEVS API in this release. Versioning API is divided into two parts, loader and query API. For this release, loader API is included; query API will be included in next release.

      • Loader functions:
      • Loader enables the editing capability of a codingScheme, valueset and picklist.
        • Changes can be applied in XML format.
        • Changes can be applied in the form of LexGrid Java castor objects as well.
        • Loader maintains the history of changes applied to the versionable objects.
        • Types of changes that can be applied on a versionable object are

NEW – to create a new versionable element
MODIFY – to change the attributes of an existing versionable element
VERSIONABLE – to change (or schedule a change of) the status of a versionable element within the context of the containing service.
REMOVE – to remove a versionable element from the service. (Note that the versionable object will be removed completely from the system including the history. VERSIONABLE Retire should be used if the element and its history should remain)
DEPENDENT – no changes are to be made to the named element itself, but a versionable element whose identity is dependent upon this element is to undergo a change.

    • Loader validates each of the versionable object before loading it. Below are the criteria for a valid versionable object.
    • EntryState must be present.
    • If the change type is NEW
    • The object being loaded should not exist in lexEVS system. (Exception : The <Versionable Object> being added already exist.)
    • prevRevision of entryState should be null. (Exception : Changes of type NEW are not allowed to have previous revisions.)
    • If the change type is other than NEW
    • The object being revised should be present in the lexEVS system. (Exception : The codingScheme being revised doesn't exist.)
    • The object must have prevRevision, except when the versionable object is revised first time after the "initial load". (Initial load : CodingScheme/ValueSet/PickList loaded with out a user defined revision)
    • The prevRevision should match the newest revision id of the given versionable object that is already loaded in the lexEVS system. (Exception : Revision source is not in sync with the database revisions. Previous revision id does not match with the latest revision id of the <Versionable object>. Please update the authoring instance with all the revisions and regenerate the source. )
  • JUnit :
    • VersionableEventAuthoringTest in lbTest package.

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  • CodedNodeGraph results are retrieved on demand from the database. Depth and Breath of the graph are both expanded on demand, so graph traversal time should not be effected by ontology, number of AssociatedConcepts, resolve depth, etc.
  • AssociatedConcepts (and Resolved Entities, if needed) are retrieved in batches, instead of individually.
  • Limitations

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  • - Duplicate AssociatedConcepts may exist in the graph to prevent cycles. This is consistent with LexEVS 5.x.

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