LexEVS 6.0 CTS2 Association Authoring Operation API

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Introduction

LexEVS CTS2 Code System Authoring API provides capability to author Code System and its contents.

Here are the authoring functions that can be performed on Associations in a Code System:

Create

This function provides capability to create:

New Association
Add Qualifiers to the Association
Determine Source and Target Code Systems for the Association
New Coding Scheme consisting of mappings of one system's concepts to another.
New Mapping for an existing mapping scheme
New Association for an existing coding scheme.

Status Change

This function provides capability to update Status attributes:

Association Status

Interface

org.lexevs.cts2.LexEvsCTS2 cts2 = org.lexevs.cts2.LexEvsCTS2Impl.defaultInstance();
org.lexevs.cts2.author.AssociationAuthoringOperation associationAuthoring = 
cts2.getAuthoringOperation().getAssociationAuthoringOperation();

Revision Information

Authoring requires information helping to determine whether the edited coding scheme element is new or revises an existing association. This requires not only a containing revision, but also a entry state object for each versionable element of the Association being created. A single object of each is passed into the association creating method providing mandatory information about this revision which in most use cases here is a new association.

org.LexGrid.versions.Revision

Revision object has following attributes:

java.lang.String changeAgent - (Optional) The source that participated in this particular change.
java.lang.String changeInstruction - (Optional) A human or machine readable set of instructions on how to apply this change.
java.lang.String revisionId - (Mandatory) The unique identifier of this revision.
java.lang.Long editOrder - (Optional) The relative order that this revision is to be applied if in a systemRelease.
java.util.Date revisionDate - (Optional) The end date for which this version is operative (considered commited).
java.lang.String description - (Optional) The description of the resource/change.
java.lang.String systemReleaseURI - (Optional) The official URI of this release

org.LexGrid.versions.EntryState

java.lang.String containingRevision - (Mandatory)The revision that contains this particular entry state change
private java.lang.Long relativeOrder - (Optional)The relative order that this state change should be applied within the context of the containing revision
private org.LexGrid.versions.types.ChangeType changeType - (Context determined. NEW for new association)The type of change that occurred between this state and the previous.
private java.lang.String prevRevision - (Optional)The unique identifier of the state of this entry was at prior to this change.

Association Authoring Functions

Create Association Operations

createAssociation(boolean createMappingScheme, Revision revision, EntryState entryState, AbsoluteCodingSchemeVersionReference mappingScheme, AbsoluteCodingSchemeVersionReference sourceCodeSystemIdentifier, AbsoluteCodingSchemeVersionReference targetCodeSystemIdentifier, String sourceConceptCodeIdentifier, String targetConceptCodeIdentifier, String relationsContainerName, String associationType, AssociationQualification[] associationQualifiers)

Description:	Creates new Association
Input:	boolean createMappingScheme - create a mapping coding scheme if one does not exist org.LexGrid.versions.Revision revision - create a mapping coding scheme if one does not exist org.LexGrid.versions.EntryState entryState - revision data container granular to the versionable class. Aorg.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference mappingScheme - existing mapping scheme, required if adding mapped association org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference sourceCodeSystemIdentifier - minimum code system identification org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference targetCodeSystemIdentifier - minimum code system identification java.lang.String sourceConceptCodeIdentifier - source concept code java.lang.String targetConceptCodeIdentifier - target concept code java.lang.String relationsContainerName - relations container identifier java.lang.String associationType - association type identifier org.LexGrid.relations.AssociationQualification[] associationQualifiers - qualifications to add to this association
Output:	*org.LexGrid.relations.AssociationSource* - Created Association Structure
Exception:	*org.LexGrid.LexBIG.Exceptions.LBException*
Sample Call:	Step 1: Create Revision Elements: Revision revision = new Revision(); - initalize Revision object revision.setChangeAgent("Mayo Foundation"); - Set the change agent if desired Text changeInstructions = new Text(); - initialize Text Object changeInstructions.setContent("To be applied at next source release"); - Define change instructions if desired. revision.setChangeInstructions(changeInstructions); - Set change instructions revision.setEditOrder(new Long(1)); - Set edit order EntityDescription entityDescription = new EntityDescription(); - Initialize EntityDescription Object entityDescription.setContent("TestCTS2AssociationRevision"); - Set content for this object revision.setEntityDescription(entityDescription); - Set revision entityDescription EntryState entryState = new EntryState(); - Initialize EntryStateObject entryState.setChangeType(ChangeType.NEW); - This is a new association -- set ChangeType to "NEW" entryState.setContainingRevision("FirstRevision_12_09_2010"); - Define the revision identifier entryState.setRelativeOrder(new Long(1)); - Set relative order Step 2: Define a source scheme: AbsoluteCodingSchemeVersionReference sourceCodeSystemIdentifier = new AbsoluteCodingSchemeVersionReference(); sourceCodeSystemIdentifier.setCodingSchemeURN("http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"); sourceCodeSystemIdentifier.setCodingSchemeVersion(10.10a); Step 3: Define a target scheme: AbsoluteCodingSchemeVersionReference targetCodeSystemIdentifier = new AbsoluteCodingSchemeVersionReference(); targetCodeSystemIdentifier.setCodingSchemeURN("urn:oid:2.16.840.1.113883.6.2"); targetCodeSystemIdentifier.setCodingSchemeVersion(200909); Step 4: Name the unique identifier of the source concept: String sourceConceptCodeIdentifier = "C27469"; Step 5: Name the unique identifier of the target concept: String targetConceptCodeIdentifier = "199"; Step 6: Identify or name a new relations container String relationsContainerName = "relations"; Step 7: Name the association String associationType = "SY"; Step 8: call create method to create the association: AssociationSource association = associationAuthoringOp.createAssociation(false, revision, entryState, null, sourceCodeSystemIdentifier, targetCodeSystemIdentifier, sourceConceptCodeIdentifier, targetConceptCodeIdentifier, relationsContainerName, associationType, null);

Update Association Operations

updateAssociationStatus(Revision revision, EntryState entryState, AbsoluteCodingSchemeVersionReference scheme, String relationsContainer, String associationName, String sourceCode, String sourceNamespace, String targetCode, String targetNamespace, String instanceId, String status, boolean isActive)

Description:	Updates Association Status
Input:	org.LexGrid.versions.Revision revision - create a mapping coding scheme if one does not exist org.LexGrid.versions.EntryState entryState - revision data container granular to the versionable class. org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference scheme - Scheme targeted for update. java.lang.String relationsContainerName - relations container identifier java.lang.String associationName - association identifier java.lang.String sourcCode - source concept code java.lang.String sourceNamespace - code system identification java.lang.String targetCode - target concept code java.lang.String targetNamespace - minimum code system identification java.lang.String instanceId - instance identifier for the association java.lang.String status - Status designation can be user defined boolean isActive - flag for Active status
Output:	*boolean* - flag for successful update
Exception:	*org.LexGrid.LexBIG.Exceptions.LBException*
Sample Call:	Step 1: Create Revision Elements: Revision revision = new Revision(); - initalize Revision object revision.setChangeAgent("Mayo Foundation"); - Set the change agent if desired Text changeInstructions = new Text(); - initialize Text Object changeInstructions.setContent("To be applied at next source release"); - Define change instructions if desired. revision.setChangeInstructions(changeInstructions); - Set change instructions revision.setEditOrder(new Long(1)); - Set edit order EntityDescription entityDescription = new EntityDescription(); - Initialize EntityDescription Object entityDescription.setContent("TestCTS2AssociationRevision"); - Set content for this object revision.setEntityDescription(entityDescription); - Set revision entityDescription EntryState entryState = new EntryState(); - Initialize EntryStateObject entryState.setChangeType(ChangeType.MODIFY); - Association is being revised. Set ChangeType to "MODIFY" entryState.setContainingRevision("FirstRevision_12_09_2010"); - Define the revision identifier entryState.setRelativeOrder(new Long(1)); - Set relative order Step 2: Define the scheme for the association update: AbsoluteCodingSchemeVersionReference scheme = new AbsoluteCodingSchemeVersionReference(); scheme.setCodingSchemeURN("http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"); scheme.setCodingSchemeVersion(10.10a); Step 3: Name the unique identifier of the source concept: String sourceCode = "C27469"; Step 4: Define the namespace of the source concept supported for this coding scheme String sourceNamespace = "NCI Thesaurus" Step 5: Name the unique identifier of the target concept: String targetCode = "C27469"; Step 6: Identify or name a new relations container String relationsContainerName = "relations"; Step 7: Define the association String associationName = "Disease_Has_Abnormal_Cell"; Step 8: Identify the instance of this association to be updated. String instanceID = "instance001"; Step 9: Define the new status String status = "PENDING_RETIREMENT"; Step 10: Set isActive flag if necessary boolean isActive = false; Step 11: call create method to create the association: AssociationSource association = associationAuthoringOp.updateAssociationStatus(revision, entryState, scheme, relationsContainerName, associationName, sourceCode, namespace, targetCode, namespace, instanceId, status, isActive);

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