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LexEVS 6.0 functionality has been updated to provide many new features for terminology services. In the Tool Overview on the LexEVS 6.0 page, you can see an outline of this functionality. Changes were necessary to the existing LexEVS API and have been documented in the sections below. For help with the new APIs, see the LexEVS 6.0 Programmer's Guide. Before reading about each change, review the "What To Look For" section, which proposes a methodology that will help you find changes required in your code.
In the following sections you will find documentation on what may need to be changed in your code when moving from LexEVS 5 to LexEVS 6. Before you go to each section, you can search your code for these strings (without the surrounding quotes). If you get a hit or hits, then you will need to make some changes in that area of the code. Follow the link for the string that you got a hit on in order to determine what to do in each case. This list may not catch everything, but it is a great place to start.
For example Iterator<ResolvedConceptReference>
Iterator<ResolvedConceptReference> |
may need to be replaced by
Iterator<? extends ResolvedConceptReference> |
In 5.0 org.LexGrid.concepts.Concept and org.LexGrid.concepts.Instance were a subclass of org.LexGrid.concepts.Entity. These have been removed for 6.0. If you have used concept or instance in LexEVS 5.x ,then in 6.0 you will want to modify your code to use Entity instead.
In 5.0, for example, a concept can be defined as follows:
Concept concept = new Concept(); concept.setEntityCode("code"); concept.setEntityCodeNamespace("namespace"); concept.setIsDefined(true); concept.setIsAnonymous(false); concept.setIsActive(true); |
In 6.0, a concept entity is defined as follows:
Entity concept = new Entity(); concept.addEntityType(EntityTypes.CONCEPT.toString()); concept.setEntityCode("code"); concept.setEntityCodeNamespace("namespace"); concept.setIsDefined(true); concept.setIsAnonymous(false); concept.setIsActive(true); |
You may notice that we use the addEntityType method to specify the entity type of Concept. We use the same method for Instance. In 6.0 we define Instance as follows:
Entity instance = new Entity(); instance.addEntityType(EntityTypes.INSTANCE.toString()); instance.setEntityCode("code"); instance.setEntityCodeNamespace("namespace"); |
org.LexGrid.relations.Association is replaced by AssociationPredicate and AssociationEntity in 6.0. The AssociationPredicate class contains 'associationName' and 'sourceList' properties, and their get/set methods. AssociationEntity class contains the properties such as 'forwardName', 'isNavigable', 'isTransitive', 'reverseName' etc., plus their get/set methods. For example, in 5.0 an Association class can be created as follows:
Association association = new Association(); association.setAssociationName("name"); association.addSource(source); association.setForwardName("forwardName"); association.setIsNavigable(true); |
In 6.0 it is replaced by
AssociationPredicate associationPredicate = new AssociationPredicate(); associationPredicate.setAssociationName("name"); associationPredicate.addSource(source); AssociationEntity associationEntity = new AssociationEntity(); associationEntity.setEntityCode("name"); associationEntity.setForwardName("forwardName"); associationEntity.setIsNavigable(true); |
Resolve supplied ValueSetDefinition object: In 5.0, this method is defined under LexEVSValueDomainServices.
public ResolvedValueDomainDefinition resolveValueDomain(URI valueDomainURI, AbsoluteCodingSchemeVersionReferenceList csVersionList, String versionTag) throws LBException; |
In 6.0, the method is under LexEVSValueSetDefinitionServices. It is represented as follows:
public ResolvedValueSetDefinition resolveValueSetDefinition(URI valueSetDefinitionURI, String valueSetDefinitionRevisionId, AbsoluteCodingSchemeVersionReferenceList csVersionList, String versionTag, SortOptionList sortOptionList) throws LBException; |
Besides the return type change, two new input arguments have been added. valueSetDefinitionRevisionId which holds the information of the version of the value set definition and sortOptionList which represents the list of sort options to apply during resolution. If supplied, the sort algorithms will be applied in the order provided. Any algorithms not valid to be applied in context of node set iteration, as specified in the sort extension description, will result in an argument exception. Available algorithms can be retrieved through the LexBIGService getSortExtensions method after being defined to the LexBIGServiceManager extension registry. For example:
AbsoluteCodingSchemeVersionReferenceList acsvList = null; Util.displayMessage("Now select Code System to use to resolve Value Set Definition"); CodingSchemeSummary css = Util.promptForCodeSystem(); if (css != null) { acsvList = new AbsoluteCodingSchemeVersionReferenceList(); acsvList.addAbsoluteCodingSchemeVersionReference(Constructors.createAbsoluteCodingSchemeVersionReference(css.getCodingSchemeURI(), css.getRepresentsVersion())); } LexEVSValueSetDefinitionServices vsdServ = LexEVSValueSetDefinitionServicesImpl.defaultInstance(); ResolvedValueSetDefinition rVSD = null; try { rVSD = vsdServ.resolveValueSetDefinition(new URI("myUri"), null, acsvList, null, null); } catch (URISyntaxException e) { e.printStackTrace(); } |
A new resolve value set definition method is provided. It accepts a ValueSetDefinition object instead of a URI.
public ResolvedValueSetDefinition resolveValueSetDefinition(ValueSetDefinition vsDef, AbsoluteCodingSchemeVersionReferenceList csVersionList, String versionTag, SortOptionList sortOptionList) throws LBException; |
Resolve supplied PickListDefinition object. In 5.0, LexEVSPickListServices provides this function. Two methods are defined as follows:
public ResolvedPickListEntryList resolvePickList(String pickListId, Integer sortType) throws LBException; |
public ResolvedPickListEntryList resolvePickList(String pickListId, boolean sortByText) throws LBException; |
In 6.0, these methods are defined in LexEVSPickListDefinitionServices.java.
public ResolvedPickListEntryList resolvePickList(String pickListId, Integer sortType, AbsoluteCodingSchemeVersionReferenceList csVersionList, String versionTag) throws LBException; |
public ResolvedPickListEntryList resolvePickList(String pickListId, boolean sortByText, AbsoluteCodingSchemeVersionReferenceList csVersionList, String versionTag) throws LBException; |
Argument 'csVersionList' and 'versionTag' are added. 'csVersionList' represents a list of coding scheme URI's and versions to be used. These will be used only if they are present in the service. If absent, the most recent version will be used instead. 'versionTag' is the tag (e.g "devel", "production", ...) to be used to reconcile coding schemes when more than one is present. Note that non-tagged versions will be used if the tagged version is missing. An example using integer to indicate the sort type is shown as follows:
AbsoluteCodingSchemeVersionReferenceList incsvrl = new AbsoluteCodingSchemeVersionReferenceList(); incsvrl.addAbsoluteCodingSchemeVersionReference(Constructors.createAbsoluteCodingSchemeVersionReference("urn:oid:11.11.0.1", "1.1")); ResolvedPickListEntryList pls = _pickListService.resolvePickList("SRITEST:FA:MicrobialStructureOntologyMinusMCell", 1, incsvrl, "production"); |
The new resolvePickList method can be passed in a PickListDefinition object instead of pickListId.
public ResolvedPickListEntryList resolvePickList(PickListDefinition pickList, boolean sortByText, AbsoluteCodingSchemeVersionReferenceList csVersionList, String versionTag) throws LBException; |
public ResolvedPickListEntryList resolvePickListForTerm(String pickListId, String term, String matchAlgorithm, String language, String[] context, boolean sortByText,A bsoluteCodingSchemeVersionReferenceList csVersionList, String versionTag) throws LBException; |
More restriction arguments have been added to the new resolvePickListForTerm method, such as: 'term', 'matchAlgorithm', 'languange', and 'context'. The argument 'term' is required. An example is shown below:
ResolvedPickListEntryList pickLists = getPickListService().resolvePickListForTerm("SRITEST:AUTO:AllDomesticButGM", "Jaguar", MatchAlgorithms.exactMatch.name(), "english", null, false, null, null); |
In 6.0 you also can resolve a pick list by revision. The code below is the new method:
public PickListDefinition resolvePickListByRevision(String pickListId, String revisionId, Integer sortOrder) throws LBRevisionException; |
Note: the return type of this method is PickListDefinition instead of ResolvedPickListEntryList.
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