Index (ncboproxy-api 1.0-SNAPSHOT API)

A B C D E F G H I J L M N O P Q R S T V
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

AbstractOutputGeneratorDispatcher - Class in io.github.agroportal.ncboproxy.output: This abstract class implements all the operations for output generator dispatchers, the only responsibility of subclasses is to register generators with their respective trigger terms in their constructors
AbstractOutputGeneratorDispatcher() - Constructor for class io.github.agroportal.ncboproxy.output.AbstractOutputGeneratorDispatcher
AbstractServletHandler - Class in io.github.agroportal.ncboproxy: Handles handler registrations and overrides for ServletHandler implementing classes, please use the following three private methods: registerParameterHandler, registerResponsePostProcessor, registerOutputGenerator
AbstractServletHandler(ParameterHandlerRegistry, ResponsePostProcessorRegistry, OutputGeneratorDispatcher) - Constructor for class io.github.agroportal.ncboproxy.AbstractServletHandler
ACRONYM_PATTERN - Static variable in interface io.github.agroportal.ncboproxy.ServletHandler
add(NCBOOutputModel) - Method in class io.github.agroportal.ncboproxy.model.NCBOCollectionImpl
addAll(Collection<? extends NCBOOutputModel>) - Method in class io.github.agroportal.ncboproxy.model.NCBOCollectionImpl
addCustomHeader(String, String) - Method in class io.github.agroportal.ncboproxy.output.NCBOProxyOutput
addCustomHeader(String, String) - Method in interface io.github.agroportal.ncboproxy.output.ProxyOutput
annotatorError(JsonArray) - Static method in interface io.github.agroportal.ncboproxy.model.NCBOOutputModel
annotatorError(String, int) - Static method in interface io.github.agroportal.ncboproxy.model.NCBOOutputModel
APIContext - Interface in io.github.agroportal.ncboproxy
APIContextImpl - Class in io.github.agroportal.ncboproxy
APIContextImpl(String, String, String, String, String) - Constructor for class io.github.agroportal.ncboproxy.APIContextImpl
APIContextImpl(Properties, HttpServletRequest) - Constructor for class io.github.agroportal.ncboproxy.APIContextImpl
APIKEY_CONFIGURATION_KEY - Static variable in interface io.github.agroportal.ncboproxy.APIContext
APPLICATION_BRAT - Static variable in class io.github.agroportal.ncboproxy.output.MimeTypes
APPLICATION_JSON - Static variable in class io.github.agroportal.ncboproxy.output.MimeTypes
apply(NCBOOutputModel, Map<String, String>) - Method in class io.github.agroportal.ncboproxy.postprocessors.NCBOProxyResponsePostProcessorRegistry
apply(NCBOOutputModel, Map<String, String>) - Method in interface io.github.agroportal.ncboproxy.postprocessors.ResponsePostProcessor: Perform the post-annotation
apply(String, NCBOOutputModel, Map<String, String>) - Method in class io.github.agroportal.ncboproxy.output.AbstractOutputGeneratorDispatcher
apply(String, NCBOOutputModel, Map<String, String>) - Method in interface io.github.agroportal.ncboproxy.output.OutputGeneratorDispatcher: Generate the output with the appropriate generator associated with the generatorTrigger.
apply(Optional<NCBOOutputModel>, Map<String, String>) - Method in class io.github.agroportal.ncboproxy.output.AbstractOutputGeneratorDispatcher
apply(Optional<NCBOOutputModel>, Map<String, String>) - Method in class io.github.agroportal.ncboproxy.output.ErrorOutputGenerator
apply(Optional<NCBOOutputModel>, Map<String, String>) - Method in class io.github.agroportal.ncboproxy.output.JSONOutputGenerator
apply(Optional<NCBOOutputModel>, Map<String, String>) - Method in interface io.github.agroportal.ncboproxy.output.OutputGenerator: Generates the output from the list of annotations as defined by the annotation model API
apply(T, U, V) - Method in interface io.github.agroportal.ncboproxy.util.TriFunction
areMandatoryConstraintsSatisfied(Map<String, List<String>>) - Method in class io.github.agroportal.ncboproxy.parameters.NCBOProxyParameterHandlerRegistry
areMandatoryConstraintsSatisfied(Map<String, List<String>>) - Method in interface io.github.agroportal.ncboproxy.parameters.ParameterHandlerRegistry: Determines if all mandatory parameter handlers are present in the query parameters
areParameterConstraintsMet(Map<String, List<String>>) - Method in class io.github.agroportal.ncboproxy.AbstractServletHandler
areParameterConstraintsMet(Map<String, List<String>>) - Method in interface io.github.agroportal.ncboproxy.ServletHandler: Determine whether all parameters in mandatory registered parameter handlers are met
asBoolean() - Method in interface io.github.agroportal.ncboproxy.model.JSONValue
asCollection() - Method in class io.github.agroportal.ncboproxy.model.NCBOCollectionImpl
asCollection() - Method in interface io.github.agroportal.ncboproxy.model.NCBOOutputModel
asError() - Method in interface io.github.agroportal.ncboproxy.model.NCBOOutputModel
asInteger() - Method in interface io.github.agroportal.ncboproxy.model.JSONValue
asObject() - Method in class io.github.agroportal.ncboproxy.model.JSONLDObjectImpl
asObject() - Method in interface io.github.agroportal.ncboproxy.model.NCBOOutputModel
asPaginatedCollection() - Method in interface io.github.agroportal.ncboproxy.model.NCBOOutputModel
asPaginatedCollection() - Method in class io.github.agroportal.ncboproxy.model.NCBOPaginatedCollectionImpl
asString() - Method in interface io.github.agroportal.ncboproxy.model.JSONValue
asStringStream() - Method in interface io.github.agroportal.ncboproxy.model.NCBOCollection
asValue() - Method in interface io.github.agroportal.ncboproxy.model.NCBOOutputModel

B

BioportalRestAPIRequestGenerator - Class in io.github.agroportal.ncboproxy.model.retrieval: Provides static methods to process url used by servlet servlets
BioportalRESTRequest - Class in io.github.agroportal.ncboproxy.model.retrieval

C

clear() - Method in class io.github.agroportal.ncboproxy.model.NCBOCollectionImpl
clear() - Method in class io.github.agroportal.ncboproxy.postprocessors.NCBOProxyResponsePostProcessorRegistry
clear() - Method in interface io.github.agroportal.ncboproxy.postprocessors.ResponsePostProcessorRegistry: Remove all registered post-processors
contains(Object) - Method in class io.github.agroportal.ncboproxy.model.NCBOCollectionImpl
containsAll(Collection<?>) - Method in class io.github.agroportal.ncboproxy.model.NCBOCollectionImpl
CONTEXT - Static variable in class io.github.agroportal.ncboproxy.model.JSONLDConstants
create() - Static method in interface io.github.agroportal.ncboproxy.model.parser.NCBOOutputParser: Create an instance of the default parser implementation, relies on a Json
create() - Static method in interface io.github.agroportal.ncboproxy.output.OutputGeneratorDispatcher
create() - Static method in interface io.github.agroportal.ncboproxy.parameters.ParameterHandlerRegistry: Creates an instance of the default ParameterHandlerRegistry implementation, currently NCBOProxyParameterHandlerRegistry
create() - Static method in interface io.github.agroportal.ncboproxy.postprocessors.ResponsePostProcessorRegistry
create() - Static method in interface io.github.agroportal.ncboproxy.ServletHandlerDispatcher
create(byte[], String) - Static method in interface io.github.agroportal.ncboproxy.output.ProxyOutput
create(JsonArray) - Static method in interface io.github.agroportal.ncboproxy.model.NCBOCollection
create(JsonObject) - Static method in interface io.github.agroportal.ncboproxy.model.JSONLDLink
create(JsonObject) - Static method in interface io.github.agroportal.ncboproxy.model.JSONLDObject
create(JsonObject, APIContext) - Static method in interface io.github.agroportal.ncboproxy.model.NCBOPaginatedCollection
create(JsonValue) - Static method in interface io.github.agroportal.ncboproxy.model.JSONValue
create(String, String) - Static method in interface io.github.agroportal.ncboproxy.output.ProxyOutput
create(String, String, String) - Static method in interface io.github.agroportal.ncboproxy.model.JSONLDLink
create(Properties, HttpServletRequest) - Static method in interface io.github.agroportal.ncboproxy.APIContext
createGETRequestGenerator(APIContext, Map<String, List<String>>, Map<String, String>, String) - Static method in interface io.github.agroportal.ncboproxy.model.retrieval.RequestGenerator
createHEADRequestGenerator(APIContext, Map<String, List<String>>, Map<String, String>, String) - Static method in interface io.github.agroportal.ncboproxy.model.retrieval.RequestGenerator
createPOSTRequestGenerator(APIContext, Map<String, List<String>>, Map<String, String>, String) - Static method in interface io.github.agroportal.ncboproxy.model.retrieval.RequestGenerator
createRequest() - Method in class io.github.agroportal.ncboproxy.model.retrieval.BioportalRestAPIRequestGenerator
createRequest() - Method in interface io.github.agroportal.ncboproxy.model.retrieval.RequestGenerator

D

defaultHandler() - Static method in interface io.github.agroportal.ncboproxy.ServletHandler
DefaultNCBOOutputParser - Class in io.github.agroportal.ncboproxy.model.parser
DEPLOYMENT_ROOT - Static variable in interface io.github.agroportal.ncboproxy.APIContext

E

empty() - Static method in interface io.github.agroportal.ncboproxy.model.retrieval.RequestResult
equals(Object) - Method in class io.github.agroportal.ncboproxy.model.JSONLDObjectImpl
error(JsonObject) - Static method in interface io.github.agroportal.ncboproxy.model.NCBOOutputModel
error(String, int) - Static method in interface io.github.agroportal.ncboproxy.model.NCBOOutputModel
ERROR_FORMAT_STRING - Static variable in class io.github.agroportal.ncboproxy.model.NCBOErrorModel
ERROR_STATUS - Static variable in class io.github.agroportal.ncboproxy.model.NCBOErrorModel
errorModel(String) - Static method in interface io.github.agroportal.ncboproxy.output.OutputGenerator
errorOutput(String) - Static method in interface io.github.agroportal.ncboproxy.output.OutputGenerator
ErrorOutputGenerator - Class in io.github.agroportal.ncboproxy.output: Generates an error output in JSON in the same way as Bioportal Annotator
ErrorOutputGenerator() - Constructor for class io.github.agroportal.ncboproxy.output.ErrorOutputGenerator
ERRORS_FORMAT_STRING - Static variable in class io.github.agroportal.ncboproxy.model.NCBOErrorModel
expandFieldFromContext(String) - Method in interface io.github.agroportal.ncboproxy.model.JSONLDObject
expandFieldFromContext(String) - Method in class io.github.agroportal.ncboproxy.model.JSONLDObjectImpl
extractHeaders(HttpServletRequest) - Static method in class io.github.agroportal.ncboproxy.util.ParameterMapper: Extract request headers from an HttpServletRequest object
extractQueryParameters(ServletRequest, String) - Static method in class io.github.agroportal.ncboproxy.util.ParameterMapper: Produce key/value list maps for input query parameters (query string or form data) from a ServletRequest

F

findMatchingHandler(String, Map<String, List<String>>) - Method in interface io.github.agroportal.ncboproxy.ServletHandlerDispatcher
findMatchingPattern(CharSequence, Iterable<String>) - Static method in interface io.github.agroportal.ncboproxy.ServletHandlerDispatcher

G

getApiKey() - Method in interface io.github.agroportal.ncboproxy.APIContext
getApiKey() - Method in class io.github.agroportal.ncboproxy.APIContextImpl
getBinaryContent() - Method in class io.github.agroportal.ncboproxy.output.NCBOProxyOutput
getBinaryContent() - Method in interface io.github.agroportal.ncboproxy.output.ProxyOutput
getBooleanValue(String) - Method in interface io.github.agroportal.ncboproxy.model.JSONLDObject
getBooleanValue(String) - Method in class io.github.agroportal.ncboproxy.model.JSONLDObjectImpl
getCode() - Method in interface io.github.agroportal.ncboproxy.model.retrieval.RequestResult
getCollection(String) - Method in interface io.github.agroportal.ncboproxy.model.JSONLDObject
getCollection(String) - Method in class io.github.agroportal.ncboproxy.model.JSONLDObjectImpl
getCurrentPageNumber() - Method in interface io.github.agroportal.ncboproxy.model.NCBOPaginatedCollection
getCurrentPageNumber() - Method in class io.github.agroportal.ncboproxy.model.NCBOPaginatedCollectionImpl
getDeploymentRoot() - Method in interface io.github.agroportal.ncboproxy.APIContext
getDeploymentRoot() - Method in class io.github.agroportal.ncboproxy.APIContextImpl
getId() - Method in interface io.github.agroportal.ncboproxy.model.JSONLDObject
getId() - Method in class io.github.agroportal.ncboproxy.model.JSONLDObjectImpl
getIntegerValue(String) - Method in interface io.github.agroportal.ncboproxy.model.JSONLDObject
getIntegerValue(String) - Method in class io.github.agroportal.ncboproxy.model.JSONLDObjectImpl
getIntegerValue(String...) - Method in interface io.github.agroportal.ncboproxy.model.JSONLDObject
getIntegerValue(String...) - Method in class io.github.agroportal.ncboproxy.model.JSONLDObjectImpl
getLinkContext() - Method in interface io.github.agroportal.ncboproxy.model.JSONLDLink
getLinkName() - Method in interface io.github.agroportal.ncboproxy.model.JSONLDLink
getLinks() - Method in interface io.github.agroportal.ncboproxy.model.JSONLDObject
getLinks() - Method in class io.github.agroportal.ncboproxy.model.JSONLDObjectImpl
getLinkValue() - Method in interface io.github.agroportal.ncboproxy.model.JSONLDLink
getMessage() - Method in interface io.github.agroportal.ncboproxy.model.retrieval.RequestResult
getMethod() - Method in interface io.github.agroportal.ncboproxy.APIContext
getMethod() - Method in class io.github.agroportal.ncboproxy.APIContextImpl
getMimeType() - Method in class io.github.agroportal.ncboproxy.output.NCBOProxyOutput
getMimeType() - Method in interface io.github.agroportal.ncboproxy.output.ProxyOutput: Get the mime type of the content
getModelRoot() - Method in class io.github.agroportal.ncboproxy.model.JSONLDObjectImpl
getModelRoot() - Method in class io.github.agroportal.ncboproxy.model.NCBOAnnotatorErrorModel
getModelRoot() - Method in class io.github.agroportal.ncboproxy.model.NCBOCollectionImpl
getModelRoot() - Method in class io.github.agroportal.ncboproxy.model.NCBOErrorModel
getModelRoot() - Method in interface io.github.agroportal.ncboproxy.model.NCBOOutputModel
getNextPage() - Method in interface io.github.agroportal.ncboproxy.model.NCBOPaginatedCollection
getNextPage() - Method in class io.github.agroportal.ncboproxy.model.NCBOPaginatedCollectionImpl
getNumberOfPages() - Method in interface io.github.agroportal.ncboproxy.model.NCBOPaginatedCollection
getNumberOfPages() - Method in class io.github.agroportal.ncboproxy.model.NCBOPaginatedCollectionImpl
getObject(String) - Method in interface io.github.agroportal.ncboproxy.model.JSONLDObject
getObject(String) - Method in class io.github.agroportal.ncboproxy.model.JSONLDObjectImpl
getPreviousPage() - Method in interface io.github.agroportal.ncboproxy.model.NCBOPaginatedCollection
getPreviousPage() - Method in class io.github.agroportal.ncboproxy.model.NCBOPaginatedCollectionImpl
getQueryPathPattern() - Method in interface io.github.agroportal.ncboproxy.ServletHandler
getRestAPIURL() - Method in interface io.github.agroportal.ncboproxy.APIContext
getRestAPIURL() - Method in class io.github.agroportal.ncboproxy.APIContextImpl
getServerEncoding() - Method in interface io.github.agroportal.ncboproxy.APIContext
getServerEncoding() - Method in class io.github.agroportal.ncboproxy.APIContextImpl
getStringContent() - Method in class io.github.agroportal.ncboproxy.output.NCBOProxyOutput
getStringContent() - Method in interface io.github.agroportal.ncboproxy.output.ProxyOutput: The content of the output
getStringValue(String) - Method in interface io.github.agroportal.ncboproxy.model.JSONLDObject
getStringValue(String) - Method in class io.github.agroportal.ncboproxy.model.JSONLDObjectImpl
getStringValue(String...) - Method in interface io.github.agroportal.ncboproxy.model.JSONLDObject: Get first field value that exists and that is not null out of the list supplied in fieldsName
getStringValue(String...) - Method in class io.github.agroportal.ncboproxy.model.JSONLDObjectImpl
getTotalSize() - Method in interface io.github.agroportal.ncboproxy.model.NCBOPaginatedCollection
getTotalSize() - Method in class io.github.agroportal.ncboproxy.model.NCBOPaginatedCollectionImpl

H

handleRequest(Map<String, List<String>>, Map<String, String>, String, APIContext, Map<String, String>) - Method in class io.github.agroportal.ncboproxy.AbstractServletHandler
handleRequest(Map<String, List<String>>, Map<String, String>, String, APIContext, Map<String, String>) - Method in interface io.github.agroportal.ncboproxy.ServletHandler
hashCode() - Method in class io.github.agroportal.ncboproxy.model.JSONLDObjectImpl
HTTP_INTERNAL_APPLICATION_ERROR - Static variable in interface io.github.agroportal.ncboproxy.output.ProxyOutput

I

ID - Static variable in class io.github.agroportal.ncboproxy.model.JSONLDConstants
InvalidFormatException - Exception in io.github.agroportal.ncboproxy: This exception is thrown when the format of the input Bioportal JSON-LD syntax is invalid
InvalidFormatException(String) - Constructor for exception io.github.agroportal.ncboproxy.InvalidFormatException
InvalidParameterException - Exception in io.github.agroportal.ncboproxy.parameters
io.github.agroportal.ncboproxy - package io.github.agroportal.ncboproxy
io.github.agroportal.ncboproxy.model - package io.github.agroportal.ncboproxy.model
io.github.agroportal.ncboproxy.model.parser - package io.github.agroportal.ncboproxy.model.parser
io.github.agroportal.ncboproxy.model.retrieval - package io.github.agroportal.ncboproxy.model.retrieval
io.github.agroportal.ncboproxy.output - package io.github.agroportal.ncboproxy.output
io.github.agroportal.ncboproxy.parameters - package io.github.agroportal.ncboproxy.parameters
io.github.agroportal.ncboproxy.postprocessors - package io.github.agroportal.ncboproxy.postprocessors
io.github.agroportal.ncboproxy.util - package io.github.agroportal.ncboproxy.util
isBinary() - Method in class io.github.agroportal.ncboproxy.output.NCBOProxyOutput
isBinary() - Method in interface io.github.agroportal.ncboproxy.output.ProxyOutput
isBoolean() - Method in interface io.github.agroportal.ncboproxy.model.JSONValue
isCollection() - Method in class io.github.agroportal.ncboproxy.model.NCBOCollectionImpl
isCollection() - Method in interface io.github.agroportal.ncboproxy.model.NCBOOutputModel
isEmpty() - Method in class io.github.agroportal.ncboproxy.model.NCBOCollectionImpl
isError() - Method in class io.github.agroportal.ncboproxy.model.NCBOAnnotatorErrorModel
isError() - Method in class io.github.agroportal.ncboproxy.model.NCBOErrorModel
isError() - Method in interface io.github.agroportal.ncboproxy.model.NCBOOutputModel
isInteger() - Method in interface io.github.agroportal.ncboproxy.model.JSONValue
isObject() - Method in class io.github.agroportal.ncboproxy.model.JSONLDObjectImpl
isObject() - Method in interface io.github.agroportal.ncboproxy.model.NCBOOutputModel
isPaginatedCollection() - Method in interface io.github.agroportal.ncboproxy.model.NCBOOutputModel
isPaginatedCollection() - Method in class io.github.agroportal.ncboproxy.model.NCBOPaginatedCollectionImpl
isString() - Method in interface io.github.agroportal.ncboproxy.model.JSONValue
isValue() - Method in interface io.github.agroportal.ncboproxy.model.JSONValue
isValue() - Method in interface io.github.agroportal.ncboproxy.model.NCBOOutputModel
iterator() - Method in class io.github.agroportal.ncboproxy.model.NCBOCollectionImpl

J

JSONLDConstants - Class in io.github.agroportal.ncboproxy.model
JSONLDLink - Interface in io.github.agroportal.ncboproxy.model
JSONLDObject - Interface in io.github.agroportal.ncboproxy.model
JSONLDObjectImpl - Class in io.github.agroportal.ncboproxy.model
JSONOutputGenerator - Class in io.github.agroportal.ncboproxy.output
JSONOutputGenerator() - Constructor for class io.github.agroportal.ncboproxy.output.JSONOutputGenerator
JSONValue - Interface in io.github.agroportal.ncboproxy.model

L

latchToOutputGeneratorDispatcher(OutputGeneratorDispatcher) - Method in class io.github.agroportal.ncboproxy.AbstractServletHandler
latchToOutputGeneratorDispatcher(OutputGeneratorDispatcher) - Method in interface io.github.agroportal.ncboproxy.ServletHandler
latchToParameterHandlerRegistry(ParameterHandlerRegistry) - Method in class io.github.agroportal.ncboproxy.AbstractServletHandler
latchToParameterHandlerRegistry(ParameterHandlerRegistry) - Method in interface io.github.agroportal.ncboproxy.ServletHandler
latchToResponsePostProcessorRegistry(ResponsePostProcessorRegistry) - Method in class io.github.agroportal.ncboproxy.AbstractServletHandler
latchToResponsePostProcessorRegistry(ResponsePostProcessorRegistry) - Method in interface io.github.agroportal.ncboproxy.ServletHandler
logger - Static variable in class io.github.agroportal.ncboproxy.NCBOAPILogger

M

makeFileTransfer(String) - Method in class io.github.agroportal.ncboproxy.output.NCBOProxyOutput
makeFileTransfer(String) - Method in interface io.github.agroportal.ncboproxy.output.ProxyOutput
MimeTypes - Class in io.github.agroportal.ncboproxy.output

N

NCBOAnnotatorErrorModel - Class in io.github.agroportal.ncboproxy.model
NCBOAPILogger - Class in io.github.agroportal.ncboproxy
NCBOAPILogger() - Constructor for class io.github.agroportal.ncboproxy.NCBOAPILogger
NCBOCollection - Interface in io.github.agroportal.ncboproxy.model
NCBOCollectionImpl - Class in io.github.agroportal.ncboproxy.model
NCBOErrorModel - Class in io.github.agroportal.ncboproxy.model
NCBOOutputModel - Interface in io.github.agroportal.ncboproxy.model
NCBOOutputParser - Interface in io.github.agroportal.ncboproxy.model.parser
NCBOPaginatedCollection - Interface in io.github.agroportal.ncboproxy.model
NCBOPaginatedCollectionImpl - Class in io.github.agroportal.ncboproxy.model
NCBOProxyErrorException - Exception in io.github.agroportal.ncboproxy: This is a generic exception encapsulating error messages from an NCBO Bioportal api service
NCBOProxyErrorException(String) - Constructor for exception io.github.agroportal.ncboproxy.NCBOProxyErrorException
NCBOProxyOutput - Class in io.github.agroportal.ncboproxy.output: Default implementation of ProxyOutput
NCBOProxyOutputGeneratorDispatcher - Class in io.github.agroportal.ncboproxy.output
NCBOProxyParameterHandlerRegistry - Class in io.github.agroportal.ncboproxy.parameters
NCBOProxyResponsePostProcessorRegistry - Class in io.github.agroportal.ncboproxy.postprocessors

O

ONTOLOGIES_API_URI - Static variable in interface io.github.agroportal.ncboproxy.APIContext
OutputGenerator - Interface in io.github.agroportal.ncboproxy.output: Specification of an OutputGenerator that produces a String output from an annotation model
OutputGeneratorDispatcher - Interface in io.github.agroportal.ncboproxy.output: Dispatches the output generation to the right output generator depending on the generator trigger

P

ParameterHandler - Interface in io.github.agroportal.ncboproxy.parameters: Handler for a parameter passed to the Proxy Servlet.
ParameterHandlerRegistry - Interface in io.github.agroportal.ncboproxy.parameters
ParameterMapper - Class in io.github.agroportal.ncboproxy.util
parse(RequestResult, APIContext) - Method in class io.github.agroportal.ncboproxy.model.parser.DefaultNCBOOutputParser
parse(RequestResult, APIContext) - Method in interface io.github.agroportal.ncboproxy.model.parser.NCBOOutputParser: Parse the output JSON-LD from the response of the original REST API and generate a corresponding NCBOOutputModel
polymorphicOverride(OutputGeneratorDispatcher) - Method in class io.github.agroportal.ncboproxy.output.AbstractOutputGeneratorDispatcher
polymorphicOverride(OutputGeneratorDispatcher) - Method in interface io.github.agroportal.ncboproxy.output.OutputGeneratorDispatcher: This OutputGeneratorDispatcher registers all its output generators in outputGeneratorDispatcher, output generators for already registered output formats are overridden.
polymorphicOverride(ParameterHandlerRegistry) - Method in class io.github.agroportal.ncboproxy.parameters.NCBOProxyParameterHandlerRegistry
polymorphicOverride(ParameterHandlerRegistry) - Method in interface io.github.agroportal.ncboproxy.parameters.ParameterHandlerRegistry: Override existing parameter handlers registered in otherParameterHandlerRegistry
polymorphicOverride(ResponsePostProcessorRegistry) - Method in class io.github.agroportal.ncboproxy.postprocessors.NCBOProxyResponsePostProcessorRegistry
polymorphicOverride(ResponsePostProcessorRegistry) - Method in interface io.github.agroportal.ncboproxy.postprocessors.ResponsePostProcessorRegistry
prettyError(NCBOOutputModel) - Static method in interface io.github.agroportal.ncboproxy.output.OutputGenerator
processParameter(Map<String, List<String>>, Map<String, String>, String, ServletHandler) - Method in interface io.github.agroportal.ncboproxy.parameters.ParameterHandler: Callback that handles the parameter.
processParameters(Map<String, List<String>>, Map<String, String>, String, ServletHandler) - Method in class io.github.agroportal.ncboproxy.parameters.NCBOProxyParameterHandlerRegistry
processParameters(Map<String, List<String>>, Map<String, String>, String, ServletHandler) - Method in interface io.github.agroportal.ncboproxy.parameters.ParameterHandlerRegistry: Process parameters and trigger matching parameter handlers
ProxyOutput - Interface in io.github.agroportal.ncboproxy.output: This interface specifies the output of the annotator
PUBLIC_VIEWING_RESTRICTIONS_VALUE - Static variable in class io.github.agroportal.ncboproxy.output.NCBOProxyOutput

Q

query(RequestGenerator) - Static method in class io.github.agroportal.ncboproxy.model.retrieval.BioportalRESTRequest
query(String) - Static method in class io.github.agroportal.ncboproxy.model.retrieval.BioportalRESTRequest
query(String, APIContext) - Static method in class io.github.agroportal.ncboproxy.model.retrieval.BioportalRESTRequest

R

registerGenerator(String, OutputGenerator) - Method in class io.github.agroportal.ncboproxy.output.AbstractOutputGeneratorDispatcher
registerGenerator(String, OutputGenerator) - Method in interface io.github.agroportal.ncboproxy.output.OutputGeneratorDispatcher: Register an OutputGenerator for a given generatorTrigger
registerOutputGenerator(String, OutputGenerator) - Method in class io.github.agroportal.ncboproxy.AbstractServletHandler
registerOutputGenerator(String, OutputGenerator) - Method in interface io.github.agroportal.ncboproxy.ServletHandler
registerParameterHandler(String, ParameterHandler, boolean) - Method in class io.github.agroportal.ncboproxy.AbstractServletHandler
registerParameterHandler(String, ParameterHandler, boolean) - Method in class io.github.agroportal.ncboproxy.parameters.NCBOProxyParameterHandlerRegistry
registerParameterHandler(String, ParameterHandler, boolean) - Method in interface io.github.agroportal.ncboproxy.parameters.ParameterHandlerRegistry: Register a parameter handler for a given parameter name, that may be optional or mandatory
registerParameterHandler(String, ParameterHandler, boolean, String...) - Method in class io.github.agroportal.ncboproxy.AbstractServletHandler
registerParameterHandler(String, ParameterHandler, boolean, String...) - Method in class io.github.agroportal.ncboproxy.parameters.NCBOProxyParameterHandlerRegistry
registerParameterHandler(String, ParameterHandler, boolean, String...) - Method in interface io.github.agroportal.ncboproxy.parameters.ParameterHandlerRegistry: Register a parameter handler for a given parameter name, that may be optional or mandatory
registerPostProcessor(ResponsePostProcessor) - Method in class io.github.agroportal.ncboproxy.AbstractServletHandler
registerPostProcessor(ResponsePostProcessor) - Method in class io.github.agroportal.ncboproxy.postprocessors.NCBOProxyResponsePostProcessorRegistry
registerPostProcessor(ResponsePostProcessor) - Method in interface io.github.agroportal.ncboproxy.postprocessors.ResponsePostProcessorRegistry: Register a ResponsePostProcessor
registerServletHandler(ServletHandler) - Method in interface io.github.agroportal.ncboproxy.ServletHandlerDispatcher
remove(Object) - Method in class io.github.agroportal.ncboproxy.model.NCBOCollectionImpl
removeAll(Collection<?>) - Method in class io.github.agroportal.ncboproxy.model.NCBOCollectionImpl
RequestGenerator - Interface in io.github.agroportal.ncboproxy.model.retrieval
RequestResult - Interface in io.github.agroportal.ncboproxy.model.retrieval
ResponsePostProcessor - Interface in io.github.agroportal.ncboproxy.postprocessors: Appends annotations to an existing Bioportal Annotation Model.
ResponsePostProcessorRegistry - Interface in io.github.agroportal.ncboproxy.postprocessors: Specification of a registry for ResponsePostProcessor components that allows registering and chain-applying the post processors.
retainAll(Collection<?>) - Method in class io.github.agroportal.ncboproxy.model.NCBOCollectionImpl

S

SERVER_ENCODING - Static variable in interface io.github.agroportal.ncboproxy.APIContext
ServletHandler - Interface in io.github.agroportal.ncboproxy
ServletHandlerDispatcher - Interface in io.github.agroportal.ncboproxy
size() - Method in class io.github.agroportal.ncboproxy.model.NCBOCollectionImpl
SUBMISSION_ID_PATTERN - Static variable in interface io.github.agroportal.ncboproxy.ServletHandler

T

toArray() - Method in class io.github.agroportal.ncboproxy.model.NCBOCollectionImpl
toArray(T[]) - Method in class io.github.agroportal.ncboproxy.model.NCBOCollectionImpl
toPrettyString() - Method in interface io.github.agroportal.ncboproxy.model.NCBOOutputModel
transferCustomHeadersToResponse(HttpServletResponse) - Method in class io.github.agroportal.ncboproxy.output.NCBOProxyOutput
transferCustomHeadersToResponse(HttpServletResponse) - Method in interface io.github.agroportal.ncboproxy.output.ProxyOutput
TriFunction<T,U,V,R> - Interface in io.github.agroportal.ncboproxy.util

V

VALUE - Static variable in class io.github.agroportal.ncboproxy.model.JSONLDConstants

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