A C D E G I J L N O R S T U

A

ADMIN_DATA_GROUP - Static variable in class org.eaglei.model.EagleIOntConstants

URI of PropertyGroup instance that is set as the value of the IN_PROPERTY_GROUP annotation for properties that hold administrative data.

C

CORE_FACILITY_CLASS_URI - Static variable in class org.eaglei.model.EagleIOntConstants

URI for the core facility class TODO would really like to move this to EagleITestOntConstants but it is used for generating fake data during execution of production components

D

DATA_COLLECTION_PROPERTY - Static variable in class org.eaglei.model.EagleIOntConstants

URI of PropertyGroup instance that is set as the value of the IN_PROPERTY_GROUP annotation for properties that should be exposed for data collection.

DATA_MODEL_EXCLUDE - Static variable in class org.eaglei.model.EagleIOntConstants

URI of PropertyGroup instance that is set as the value of the IN_PROPERTY_GROUP annotation for properties that should be exposed for data collection.

DIRECT_TYPE_URI - Static variable in class org.eaglei.model.EagleIOntConstants

URI for property that is used to record the direct rdf:type of a resource when the type hierarchy is being materialized.

DISPLAY_ORDER - Static variable in class org.eaglei.model.EagleIOntConstants

URI of the annotation property used to indicate display order for properties and classes.

DOMAIN_CONSTRAINT - Static variable in class org.eaglei.model.EagleIOntConstants

URI of annotation property that is used to specify a list of domain URIs that should take precedence over the domain specification in the ontoloyg model.

E

EAGLE_I_APP_EXT_URI - Static variable in class org.eaglei.model.jena.JenaModelConfig

URI of the eagle-i model root

EAGLE_I_APP_ONT_URI - Static variable in class org.eaglei.model.EagleIOntConstants

Namespace of eagle-i-app-ont.owl ontology.

EAGLE_I_URI - Static variable in class org.eaglei.model.EagleIOntConstants

URI of the eagle-i.owl ontology

EagleIOntConstants - Class in org.eaglei.model

Holds eagle-i ontology constants

EagleIOntConstants() - Constructor for class org.eaglei.model.EagleIOntConstants

eagleiOntModel() - Method in class org.eaglei.model.jena.JenaModelConfig

EagleIOntUtils - Class in org.eaglei.model.jena

Utility methods for accessing common elements of the eagle-i ontology.

EagleIOntUtils() - Constructor for class org.eaglei.model.jena.EagleIOntUtils

EI_PREFERRED_DEFINITION_URI - Static variable in class org.eaglei.model.EagleIOntConstants

URI of the eagle-i preferred definition annotation property

EI_PREFERRED_LABEL - Static variable in class org.eaglei.model.EagleIOntConstants

URI of annotation property that is used to specify eagle-i specific preferred labels

G

generateStackTrace(Deque<String>) - Method in class org.eaglei.model.jena.JenaEIOntModel

getClass(EIURI) - Method in class org.eaglei.model.jena.JenaEIOntModel

getClass(String) - Method in class org.eaglei.model.jena.JenaEIOntModel

getClassAnnotations(List<EIURI>) - Method in class org.eaglei.model.jena.JenaEIOntModel

getClassAnnotations(EIURI) - Method in class org.eaglei.model.jena.JenaEIOntModel

getClassDefinition(EIURI) - Method in class org.eaglei.model.jena.JenaEIOntModel

getClassDefinitions(List<EIURI>) - Method in class org.eaglei.model.jena.JenaEIOntModel

getClassesInGroup(OntModel, String) - Static method in class org.eaglei.model.jena.EagleIOntUtils

Retrieves the classes in the eagle-i ontology that have been designated (via an special annotation property) as belonging to the specified group.

getClassesInGroup(OntModel, List<String>) - Static method in class org.eaglei.model.jena.EagleIOntUtils

getEquivalentClasses(EIURI) - Method in class org.eaglei.model.jena.JenaEIOntModel

getLabels(EIURI) - Method in class org.eaglei.model.jena.JenaEIOntModel

getLiteralsForProperty(Resource, Property, List<String>, List<String>) - Static method in class org.eaglei.model.jena.JenaEIOntModel

getNonResourceBaseClasses() - Method in class org.eaglei.model.jena.JenaEIOntModel

getOntModel() - Method in class org.eaglei.model.jena.JenaEIOntModel

Retrieves the underlying Jena OntModel.

getPreferredLabel(EIURI) - Method in class org.eaglei.model.jena.JenaEIOntModel

getPrefLabelProperties() - Method in class org.eaglei.model.jena.JenaEIOntModel

getProperties(EIURI) - Method in class org.eaglei.model.jena.JenaEIOntModel

getProperties(EIURI, String) - Method in class org.eaglei.model.jena.JenaEIOntModel

Retrieves the properties with the inPropertyGroup annotation set to the given value.

getPropertyDefinition(EIURI) - Method in class org.eaglei.model.jena.JenaEIOntModel

getPropertyDefinitions(List<EIURI>) - Method in class org.eaglei.model.jena.JenaEIOntModel

getSubClasses(EIURI) - Method in class org.eaglei.model.jena.JenaEIOntModel

getSuperClass(EIClass) - Method in class org.eaglei.model.jena.JenaEIOntModel

getSuperClasses(EIURI) - Method in class org.eaglei.model.jena.JenaEIOntModel

getTopLevelClasses() - Method in class org.eaglei.model.jena.JenaEIOntModel

getTypeEntities(EIURI) - Method in class org.eaglei.model.jena.JenaEIOntModel

getVersion() - Method in class org.eaglei.model.jena.JenaEIOntModel

I

IAO_ALTERNATE_TERM_URI - Static variable in class org.eaglei.model.EagleIOntConstants

URI of the IAO alternate term annotation property

IAO_PREFERRED_TERM_URI - Static variable in class org.eaglei.model.EagleIOntConstants

URI of the IAO perferred term annotation property

IN_CLASS_GROUP - Static variable in class org.eaglei.model.EagleIOntConstants

URI of the annotation property used to mark class group.

IN_PROPERTY_GROUP - Static variable in class org.eaglei.model.EagleIOntConstants

URI of the annotation property used to mark class group.

IS_DELETED - Static variable in class org.eaglei.model.EagleIOntConstants

special :isDeleted predicate

isModelClassURI(String) - Method in class org.eaglei.model.jena.JenaEIOntModel

isPropertyInGroup(OntModel, String, String) - Static method in class org.eaglei.model.jena.EagleIOntUtils

Determines if the specified property in the eagle-i ontology has been designated (via an special annotation property) as belonging to the specified group.

isSubClass(EIURI, EIURI) - Method in class org.eaglei.model.jena.JenaEIOntModel

isSubClass(String, String) - Method in class org.eaglei.model.jena.JenaEIOntModel

J

JenaEIOntModel - Class in org.eaglei.model.jena

Exposes the eagle-i ontology using GWT friendly model classes.

JenaEIOntModel(OntModel) - Constructor for class org.eaglei.model.jena.JenaEIOntModel

JenaModelConfig - Class in org.eaglei.model.jena

JenaModelConfig() - Constructor for class org.eaglei.model.jena.JenaModelConfig

jenaOntModel() - Method in class org.eaglei.model.jena.JenaModelConfig

L

LAB_CLASS_URI - Static variable in class org.eaglei.model.EagleIOntConstants

URI for the laboratory class TODO would really like to move this to EagleITestOntConstants but it is used for generating fake data during execution of production components

LOCATED_IN_URI - Static variable in class org.eaglei.model.EagleIOntConstants

URI for the located_in object property

LOCATION_OF_URI - Static variable in class org.eaglei.model.EagleIOntConstants

URI for the location_of object property

logger - Static variable in class org.eaglei.model.jena.JenaEIOntModel

N

NON_RESOURCE_GROUP - Static variable in class org.eaglei.model.EagleIOntConstants

URI of ClassGroup instance that is set as the value of the IN_CLASS_GROUP annotation for classes that are used in the data model, but are not eagle-i resources.

O

OBI_DEFINITION_URI - Static variable in class org.eaglei.model.EagleIOntConstants

URI of the OBI definition annotation property

org.eaglei.model - package org.eaglei.model

org.eaglei.model.jena - package org.eaglei.model.jena

ORGANIZATION_CLASS_URI - Static variable in class org.eaglei.model.EagleIOntConstants

URI for the organization TODO would really like to move this to EagleITestOntConstants but it is used for excluding the organization subtree during certain tests.

R

RANGE_CONSTRAINT - Static variable in class org.eaglei.model.EagleIOntConstants

URI of annotation property that is used to specify a list of range URIs that should take precedence over the range list in the ontology model.

S

SEARCH_FILTER_PROPERTY - Static variable in class org.eaglei.model.EagleIOntConstants

URI of PropertyGroup instance that is set as the value of the IN_PROPERTY_GROUP annotation for properties that should be exposed for data collection.

SERVICE_PROVIDED_BY_URI - Static variable in class org.eaglei.model.EagleIOntConstants

URI for the service_provided_by property

setInstitutionRegistry(InstitutionRegistry) - Method in class org.eaglei.model.jena.JenaEIOntModel

Retrieves the classes in the specified group.

T

TOP_LEVEL_GROUP - Static variable in class org.eaglei.model.EagleIOntConstants

URI of ClassGroup instance that is set as the value of the IN_CLASS_GROUP annotation for classes that are top-level eagle-i resources.

traverseDataModel(List<EIOntModel.Visitor>) - Method in class org.eaglei.model.jena.JenaEIOntModel

U

UNIVERSITY_CLASS_URI - Static variable in class org.eaglei.model.EagleIOntConstants

URI for the university class

USED_BY_URI - Static variable in class org.eaglei.model.EagleIOntConstants

URI for the used_by object property

A C D E G I J L N O R S T U