├── .gitignore ├── CTS2Profiles.properties ├── D2Refine.zip ├── License.md ├── PrototypeProject ├── AMLPrototypes.mdzip ├── CIMI_RM_v3.0.5.xmi ├── ConstraintProfile.mdzip ├── ReferenceModelProfile.mdzip ├── StructuralReports │ └── AMLPrototypes.docx ├── TerminologyProfile.mdzip ├── XmlPrimitiveTypes.mdzip ├── model_images │ ├── CIMICoreModel.png │ ├── CIMIDataValueTypes.png │ ├── CIMIPartyModel.png │ ├── CIMIPrimitiveTypes.png │ ├── ReferenceArchetypes │ │ ├── Cluster_Archetype.png │ │ ├── Cluster_Definiton.png │ │ ├── ReferenceArchetypeLibrary.png │ │ └── terms.png │ ├── TCGADDAMLModel │ │ ├── DaysToHivDiagnosis_Archetype.png │ │ ├── DaysToHivDiagnosis_Definition.png │ │ ├── DaysToHivDiagnosis_Terms.png │ │ ├── OCGShared_datatypes.png │ │ ├── TCGAOCGSharedCELibrary.png │ │ ├── TCGAReferenceModel.png │ │ ├── Utility_constrained_datatypes.png │ │ └── Utility_datatypes.png │ └── dbGapDDAMLModel │ │ ├── dbGAPArchetypeLibrary.png │ │ ├── pht003255_Archetype.png │ │ ├── pht003255_Definition.png │ │ ├── pht003255_Terms.png │ │ ├── pht123_Archetype.png │ │ ├── pht123_Definition.png │ │ └── pht123_Terms.png └── openEHR_UML.mdzip ├── README.md ├── copyright.md ├── dbGapADLExamples ├── adult_patient.adls ├── adult_patient_withcomments.adls ├── colorectal_cancer.adl └── colorectal_cancer2.adls ├── deploy.sh ├── docs ├── CIMI_RM3.0.4.xsd ├── D2Refine_Functions.owl ├── StandardizedTemplate.xlsx ├── img │ ├── AddCTS2Service.png │ ├── AddCTS2Service2.png │ ├── AddCTS2Service3.png │ ├── CIMIRM305.png │ ├── Create_Project_Granularity.png │ ├── Create_Project_URL.png │ ├── CustomCTS2ServiceDialog.png │ ├── D2Refine.png │ ├── D2RefineArch.png │ ├── D2RefineDetailed.png │ ├── D2RefineVsOntoMatonFavorites.png │ ├── D2Refine_thumbnail.png │ ├── ExportExtensions.png │ ├── ExportMenu.png │ ├── FavoriteRankings.png │ ├── MappingDD2AML.png │ ├── Matches1.png │ ├── Matches2.png │ ├── OpenRefine_URL.png │ ├── Reconcile_Dialog.png │ ├── Reconcile_menu.png │ ├── Reconciliation.png │ ├── Reconciliation2.png │ ├── SearchMatchRequest.png │ ├── SimpleConstraintAML.png │ ├── SimpleConstraint_ADL.png │ ├── TermBindingAML.png │ ├── TermDefADL.png │ ├── TermDefAML.png │ ├── ValueSetADL.png │ ├── ValueSetAML.png │ ├── VariableRangeADL.png │ ├── VariableRangeAML.png │ └── dbGAPDD_Structure.png └── test_workbook.xlsx ├── module ├── MOD-INF │ ├── controller.js │ ├── lib │ │ ├── adl-parser.1.3.0.jar │ │ ├── adlworks.1.0.0.jar │ │ ├── cts2search-1.0-SNAPSHOT.jar │ │ ├── groovy-2.4.7.jar │ │ ├── groovy-ant-2.4.7.jar │ │ ├── groovy-json-2.4.7.jar │ │ ├── jackson-core-asl-1.9.5.jar │ │ ├── jackson-mapper-asl-1.9.5.jar │ │ ├── logback-classic.1.1.3.jar │ │ ├── logback-core.1.1.3.jar │ │ ├── model-am.1.3.0.jar │ │ ├── model-rm-opencimi.1.3.0.jar │ │ ├── model-rm-openehr.1.3.0.jar │ │ └── model-rm.1.3.0.jar │ └── module.properties ├── dialogs │ ├── d2rAbout.html │ ├── d2rAbout.js │ ├── d2rAbout.less │ ├── d2rAddReconService.html │ ├── d2rAddReconService.js │ └── d2rDialogs.less ├── resources │ └── CTS2Profiles.properties ├── scripts │ ├── d2rReconciliation.js │ ├── exporter │ │ └── model-export-menu.js │ ├── extension-bar-menu.js │ └── utils │ │ └── util.js └── styles │ ├── about.less │ ├── d2r-dialogs.less │ ├── d2rAbout.less │ ├── d2refine.less │ └── project-injection.less ├── resources └── CTS2Profiles.properties └── src └── edu └── mayo └── d2refine ├── exporter ├── ADLExporterExtension │ ├── ADLExporter.java │ ├── ADLExporterUtil.java │ └── DDRowVisitor.java ├── impl │ ├── DBGapConstants.java │ └── DBGapTemplate.java └── model │ ├── D2RefineTemplate.java │ ├── DataType.java │ ├── IntegerInterval.java │ ├── Interval.java │ ├── RealInterval.java │ └── StringInterval.java ├── services ├── D2RefineServiceManager.groovy ├── commands │ ├── AbstractReconciliationCommand.groovy │ ├── ReconciliationCommand.groovy │ └── RegistrationCommand.groovy └── reconciliation │ ├── AbstractReconciliationService.groovy │ ├── ReconciliationService.groovy │ ├── 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