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A

addCapability(Capability) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Adds either outputs or inputs for the specified capability to this ResultSpecification.
addConfigurationParameter(ConfigurationParameter) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Adds a configuration parameter to the metadata for this AnalysisEngineDescriptor.
addDelegate(String, boolean, NameValue...) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Add a delegate analysis engine descriptor to this engine using the descriptor provided.
addDelegate(LeoDelegate) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Add the provided LeoAEDescriptor as a delegate to this AnalysisEngine.
addFeature(String, String, String) - Method in class gov.va.vinci.leo.descriptors.TypeDescriptionBuilder
 
addFeature(String, String, String, String, Boolean) - Method in class gov.va.vinci.leo.descriptors.TypeDescriptionBuilder
 
addFilters(String...) - Method in class gov.va.vinci.leo.cr.BaseLeoCollectionReader
Add the list of textFilters classes from a String list.
addFilters(TextFilter...) - Method in class gov.va.vinci.leo.cr.BaseLeoCollectionReader
Add one or more text filters to the list of filters to be applied to the document text before adding to the CAS.
addLeoTypeSystemDescription(LeoTypeSystemDescription) - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Add the type system provided to the type system of the annotator.
addOutputAnnotation(String, JCas, int, int) - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Create an output annotation, and add it to the cas.
addOutputAnnotation(String, JCas, int, int, Map<String, Object>) - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Create an output annotation, and add it to the cas.
addParameter(Parameter, Parameter[]) - Static method in class gov.va.vinci.leo.tools.LeoUtils
Add the parameter p to the array of parameters.
addParameterSetting(String, boolean, boolean, String) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Add a new parameter.
addParameterSetting(String, boolean, boolean, String, Object) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Add a new parameter and optionally set an initial value.
addParameterSetting(String, String) - Method in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
Add a new parameter to the descriptor.
addResourceConfiguration(ResourceManagerConfiguration) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Add the external resources specified by the provided ResourceManagerConfiguration object.
addResultToCache(Serializable, Serializable) - Method in class gov.va.vinci.leo.ae.LeoCachingAnnotator
Add a key/value to the cache.
addServerToServiceQueue(String, String, String, int) - Method in class gov.va.vinci.leo.tools.JamService
A web service that add a server to an existing service queue.
addType(String, String, String) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Add a new type to the TypeSystem with the Name and SuperType name provided.
addType(TypeDescription) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Add an Annotation Type to the TypeSystem.
addType(String, String, String) - Method in class gov.va.vinci.leo.descriptors.LeoTypeSystemDescription
Add an Annotation Type to the TypeSystem with the name and supertype name provided.
addType(TypeDescription) - Method in class gov.va.vinci.leo.descriptors.LeoTypeSystemDescription
Add an Annotation Type to the TypeSystem from the TypeDescription provided.
addTypeSystemDescription(LeoTypeSystemDescription) - Method in class gov.va.vinci.leo.ae.ExternalAnnotator
Add the type system provided to the existing type system of this annotator.
addTypeSystemDescription(LeoTypeSystemDescription) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Append the TypeSystem contained in a LeoTypeSystemDescription object to the TypeSystem contained in this Analysis Engine.
addTypeSystemDescription(TypeSystemDescription) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Append an existing TypeSystem to the existing TypeSystem contained in this Analysis Engine.
addTypeSystemDescription(TypeSystemDescription) - Method in class gov.va.vinci.leo.descriptors.LeoTypeSystemDescription
Append the TypeSystem provided to the existing Type System.
addTypeSystemDescription(LeoTypeSystemDescription) - Method in class gov.va.vinci.leo.descriptors.LeoTypeSystemDescription
Add the TypeSystem provided to the existing Type System.
addUABListener(UimaAsBaseCallbackListener) - Method in class gov.va.vinci.leo.Client
Set a reference to the UABCallbackListener object for handling service events.
AggregateEngineFactory - Class in gov.va.vinci.leo.descriptors
Generates elements related to UIMA Aggregate Analysis engines.
AggregateEngineFactory() - Constructor for class gov.va.vinci.leo.descriptors.AggregateEngineFactory
 
AnalysisEngineFactory - Class in gov.va.vinci.leo.descriptors
Generate AnalysisEngineDescription objects with factory methods.
AnalysisEngineFactory() - Constructor for class gov.va.vinci.leo.descriptors.AnalysisEngineFactory
 
analysisEngineSection(TransformerHandler, boolean) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Generate the XML for the analysisEngine section of the deployment descriptor.
analysisEngineSection(TransformerHandler, boolean) - Method in interface gov.va.vinci.leo.descriptors.LeoDelegate
Produce the Analysis Engine section for the Deployment Descriptor XML.
analysisEngineSection(TransformerHandler, boolean) - Method in class gov.va.vinci.leo.descriptors.LeoPearDescriptor
 
analysisEngineSection(TransformerHandler, boolean) - Method in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
Produce the Analysis Engine section for the Deployment Descriptor XML.
annotate(JCas) - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
This method is called by the LeoBaseAnnotator process method if the CAS meets the filter requirements and either has not input types defined or else contains one or more instances of the input types.
annotationTypeFilter - Variable in class gov.va.vinci.leo.listener.BaseListener
the annotation types to filter on.
AsciiFilter - Class in gov.va.vinci.leo.tools
Replace non ASCII-8 characters with ASCII-8 characters.
AsciiFilter() - Constructor for class gov.va.vinci.leo.tools.AsciiFilter
 
AsciiService - Class in gov.va.vinci.leo.tools
Utility class to convert to ASCII characters that are non-ascii.
AsciiService() - Constructor for class gov.va.vinci.leo.tools.AsciiService
 
AutoCompile - Class in gov.va.vinci.leo.tools
Compile Java files.
AutoCompile() - Constructor for class gov.va.vinci.leo.tools.AutoCompile
 

B

BaseCsvListener - Class in gov.va.vinci.leo.listener
Base gov.va.vinci.leo.listener for creating CSV output.
BaseCsvListener(File) - Constructor for class gov.va.vinci.leo.listener.BaseCsvListener
Constructor with File parameter.
BaseCsvListener(OutputStream) - Constructor for class gov.va.vinci.leo.listener.BaseCsvListener
Constructor with an OutputStream parameter.
BaseCsvListener(Writer) - Constructor for class gov.va.vinci.leo.listener.BaseCsvListener
Constructor with a Writer parameter.
BaseDatabaseCollectionReader - Class in gov.va.vinci.leo.cr
Retrieves rows from a database and returns them one at a time for extending readers to handle.
BaseDatabaseCollectionReader() - Constructor for class gov.va.vinci.leo.cr.BaseDatabaseCollectionReader
Default constructor used during UIMA initialization.
BaseDatabaseCollectionReader(DatabaseConnectionInformation) - Constructor for class gov.va.vinci.leo.cr.BaseDatabaseCollectionReader
Initialize the connection information from the DatabaseConnectionInformation object.
BaseDatabaseCollectionReader(String, String, String, String) - Constructor for class gov.va.vinci.leo.cr.BaseDatabaseCollectionReader
Initialize the connection information to the parameters provided.
BaseDatabaseListener - Class in gov.va.vinci.leo.listener
Base class for inserting data into a database as a UIMA AS Listener

To use this class, you must extend it, and implement List getRows(CAS).
BaseDatabaseListener(DatabaseConnectionInformation, String, String, List<DatabaseField>) - Constructor for class gov.va.vinci.leo.listener.BaseDatabaseListener
Constructor for using a fieldList.
BaseDatabaseListener(DatabaseConnectionInformation, String) - Constructor for class gov.va.vinci.leo.listener.BaseDatabaseListener
Base gov.va.vinci.leo.listener.
BaseFileCollectionReader - Class in gov.va.vinci.leo.cr
Get a list of the files in a directory and return them one at a time.
BaseFileCollectionReader() - Constructor for class gov.va.vinci.leo.cr.BaseFileCollectionReader
Default constructor used during UIMA initialization.
BaseFileCollectionReader(File, boolean) - Constructor for class gov.va.vinci.leo.cr.BaseFileCollectionReader
Constructor that sets the input directory to be searched and the recurse flag that controls whether or not the reader will descend in to subdirectories.
BaseLeoCollectionReader - Class in gov.va.vinci.leo.cr
Provides the CollectionReader interface object to the UIMA framework for implementations of SubReaders.
BaseLeoCollectionReader() - Constructor for class gov.va.vinci.leo.cr.BaseLeoCollectionReader
 
BaseListener - Class in gov.va.vinci.leo.listener
BaseListener class that other listeners can extend from to add default functionality commonly used.
BaseListener() - Constructor for class gov.va.vinci.leo.listener.BaseListener
Default Constructor.
baseQuery - Variable in class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
Query template that will be filled in with min and max values for each batch .
batch - Variable in class gov.va.vinci.leo.listener.BaseDatabaseListener
List for holding a batch until pageSize is reached and the batch is committed.
BatchDatabaseCollectionReader - Class in gov.va.vinci.leo.cr
Database CollectionReader that pulls the data in batches of a configurable size.
BatchDatabaseCollectionReader() - Constructor for class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
Default constructor used during UIMA initialization.
BatchDatabaseCollectionReader(DatabaseConnectionInformation, DataQueryInformation, int, int, int) - Constructor for class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
Initialize the reader using the database connection and query information provided, including the size of each batch and optionally the number of random batches to execute.
BatchDatabaseCollectionReader(String, String, String, String, String, String, String, int, int, int) - Constructor for class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
Initialize the reader using the provided connection and query information, including the size of each batch and optionally the number of random batches to execute.
batchSize - Variable in class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
Size of each batch to pull.
batchSize - Variable in class gov.va.vinci.leo.listener.BaseDatabaseListener
Batch size before doing a commit.
bindExternalResources(AnalysisEngineDescription, ResourceCreationSpecifier) - Static method in class gov.va.vinci.leo.descriptors.AggregateEngineFactory
Bind external resources from the primitive spec to the aggregate AnalysisEngineDescription.
BROKER_URL - Static variable in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor.Param
Broker URL where the remote service is being managed.
BROKERURL_DEFAULT - Static variable in class gov.va.vinci.leo.tools.LeoProperties
Default value for the Broker URL.
buildCSVWriter() - Method in class gov.va.vinci.leo.tools.CSVWriterBuilder
 

C

cacheManager - Variable in class gov.va.vinci.leo.ae.LeoCachingAnnotator
Cache manager for getting a cache.
CasTools - Class in gov.va.vinci.leo.tools
Collection of handy methods for CAS information, handling.
CasTools() - Constructor for class gov.va.vinci.leo.tools.CasTools
 
checkForError(CAS, EntityProcessStatus) - Method in class gov.va.vinci.leo.listener.BaseListener
Check for an error in the return status of the processed CAS.
Client - Class in gov.va.vinci.leo
Initialize and execute a pipeline via the client API for UIMA AS which has been created via the Service object.
Client(UimaAsBaseCallbackListener...) - Constructor for class gov.va.vinci.leo.Client
Default Constructor, will try to load properties from file located at conf/leo.properties.
Client(String, UimaAsBaseCallbackListener...) - Constructor for class gov.va.vinci.leo.Client
Constructor with properties file input for client execution context.
Client(String, LeoCollectionReaderInterface, UimaAsBaseCallbackListener...) - Constructor for class gov.va.vinci.leo.Client
Constructor with properties file input for client execution context, a collection reader for input, and option listeners.
Client.LeoEngine - Class in gov.va.vinci.leo
Extends the Base engine in order to expose the listeners in a getter.
close() - Method in class gov.va.vinci.leo.cr.BaseLeoCollectionReader
 
collectionProcessComplete() - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
 
collectionProcessComplete(EntityProcessStatus) - Method in class gov.va.vinci.leo.listener.BaseCsvListener
 
collectionProcessComplete(EntityProcessStatus) - Method in class gov.va.vinci.leo.listener.BaseDatabaseListener
 
collectionProcessComplete(EntityProcessStatus) - Method in class gov.va.vinci.leo.listener.BaseListener
 
collectionProcessComplete(EntityProcessStatus) - Method in class gov.va.vinci.leo.listener.SimpleXmiListener
 
collectionReader - Variable in class gov.va.vinci.leo.Client
Collection reader used for reading documents in and sending them to the service.
CommandLineClient - Class in gov.va.vinci.leo
An example UIMA AS Client that takes command line arguments for its configuration.
CommandLineClient(String[]) - Constructor for class gov.va.vinci.leo.CommandLineClient
 
CommandLineClient(File, File, File[]) - Constructor for class gov.va.vinci.leo.CommandLineClient
Initialize the client using groovy config files for the client, reader, and one or more listeners.
compileFiles(File[], String) - Static method in class gov.va.vinci.leo.tools.AutoCompile
Compile the files in the list.
ConfigurationParameterImpl - Class in gov.va.vinci.leo.tools
Extends the ConfigurationParameter_impl class to provide a constructor that allows the user to set required fields from the constructor.
ConfigurationParameterImpl() - Constructor for class gov.va.vinci.leo.tools.ConfigurationParameterImpl
Default constructor.
ConfigurationParameterImpl(String, String, String, boolean, boolean, String[]) - Constructor for class gov.va.vinci.leo.tools.ConfigurationParameterImpl
Initialize the configuration parameter with the input values provided, rather than using setters only.
ConfigurationParameterUtils - Class in gov.va.vinci.leo.descriptors
Created by thomasginter on 3/10/16.
ConfigurationParameterUtils() - Constructor for class gov.va.vinci.leo.descriptors.ConfigurationParameterUtils
 
conn - Variable in class gov.va.vinci.leo.listener.BaseDatabaseListener
The database connection.
connect(String, String, String, String) - Method in class gov.va.vinci.leo.tools.db.LeoDataSource
Connect to the database.
containsAnnotationInList(JCas, String[], boolean) - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Checks the CAS for instances of the annotation types in the list.
CPC_TIMEOUT - Static variable in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor.Param
Collection Process Complete timeout.
create() - Static method in class gov.va.vinci.leo.descriptors.TypeDescriptionBuilder
Create a new builder.
create(String, String, String) - Static method in class gov.va.vinci.leo.descriptors.TypeDescriptionBuilder
Create a new builder.
createAggregateDescription(String, List<String>, boolean) - Static method in class gov.va.vinci.leo.descriptors.AggregateEngineFactory
Create an AnalysisEngineDescriptor that represents and aggregate analysis engine from a name and a list of primitive engines.
createAggregateDescription(List<LeoDelegate>, String) - Static method in class gov.va.vinci.leo.descriptors.AggregateEngineFactory
Create an aggregate descriptor from a list of LeoAEDescriptor objects.
createAggregateDescription(List<LeoDelegate>, FlowControllerDescription, String) - Static method in class gov.va.vinci.leo.descriptors.AggregateEngineFactory
Create an aggregate descriptor from a list of LeoAEDescriptor objects.
createAggregateDescription(String, List<ResourceSpecifier>) - Static method in class gov.va.vinci.leo.descriptors.AggregateEngineFactory
Create an AnalysisEngineDescription from a name and a list of ResourceCreationSpecifiers each one representing a primitive Analysis engine, CasConsumer, or FlowController.
createCache() - Method in class gov.va.vinci.leo.ae.LeoCachingAnnotator
Create the cache to be used for storing results.
createCreateStatement(String, String, List<DatabaseField>) - Method in class gov.va.vinci.leo.listener.BaseDatabaseListener
Protected method to build a create table statement.
createJmxServerXml(String, String, String, int) - Method in class gov.va.vinci.leo.tools.JamService
Creates the XML request used by other methods when calling the web service.
createMetaDataObject(URL) - Static method in class gov.va.vinci.leo.descriptors.MetaDataObjectFactory
Create a TypeSystemDescription from a URL which points to a Descriptor File.
createMetaDataObject(String) - Static method in class gov.va.vinci.leo.descriptors.MetaDataObjectFactory
Create a MetaDataObject from the path to a Descriptor File.
createMetaDataObject(File) - Static method in class gov.va.vinci.leo.descriptors.MetaDataObjectFactory
Return a ResourceSpecifier from a File object provided.
createPreparedStatementSQL(String, String, List<DatabaseField>) - Method in class gov.va.vinci.leo.listener.BaseDatabaseListener
Creates an insert sql statement for the list of fields.
createResourceSpecifier(URL) - Static method in class gov.va.vinci.leo.descriptors.ResourceSpecifierFactory
Create a ResourceSpecifier from a URL which points to a Descriptor File.
createResourceSpecifier(String) - Static method in class gov.va.vinci.leo.descriptors.ResourceSpecifierFactory
Create a ResourceSpecifier from the path to a Descriptor File.
createResourceSpecifier(File) - Static method in class gov.va.vinci.leo.descriptors.ResourceSpecifierFactory
Return a ResourceSpecifier from a File object provided.
createTable(String, boolean, String) - Method in class gov.va.vinci.leo.listener.BaseDatabaseListener
Creates the table structure.
createTable(boolean, String, String, Map<String, String>) - Method in class gov.va.vinci.leo.listener.BaseDatabaseListener
Creates the table structure.
createTable(boolean, String, String, List<DatabaseField>) - Method in class gov.va.vinci.leo.listener.BaseDatabaseListener
Creates the table structure.
createURL(String) - Static method in class gov.va.vinci.leo.tools.LeoUtils
Computes the absolute URL for this import, using the relative location or name, whichever is specified by this import object.
CSI - Class in gov.va.vinci.leo.types
Updated by JCasGen Wed Jan 25 11:01:45 MST 2012 XML source: null
CSI() - Constructor for class gov.va.vinci.leo.types.CSI
Never called.
CSI(int, TOP_Type) - Constructor for class gov.va.vinci.leo.types.CSI
Internal - constructor used by generator
CSI(JCas) - Constructor for class gov.va.vinci.leo.types.CSI
 
CSI_Type - Class in gov.va.vinci.leo.types
Updated by JCasGen Wed Jan 25 11:01:46 MST 2012
CSI_Type(JCas, Type) - Constructor for class gov.va.vinci.leo.types.CSI_Type
initialize variables to correspond with Cas Type and Features
CSVWriterBuilder - Class in gov.va.vinci.leo.tools
Created by thomasginter on 3/15/16.
CSVWriterBuilder(Writer) - Constructor for class gov.va.vinci.leo.tools.CSVWriterBuilder
Constructs CSVWriter using a comma for the separator.
currentBatch - Variable in class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
Current batch number we are executing.
currentBatch - Variable in class gov.va.vinci.leo.cr.SQLServerPagedDatabaseCollectionReader
Current batch number we are executing.

D

DatabaseCollectionReader - Class in gov.va.vinci.leo.cr
CollectionReader that executes a SQL query one time to pull the needed data from the database.
DatabaseCollectionReader() - Constructor for class gov.va.vinci.leo.cr.DatabaseCollectionReader
Default constructor used during UIMA initialization.
DatabaseCollectionReader(DatabaseConnectionInformation, DataQueryInformation) - Constructor for class gov.va.vinci.leo.cr.DatabaseCollectionReader
Initialize with the database connection and query information.
DatabaseCollectionReader(DatabaseConnectionInformation, String, String, String) - Constructor for class gov.va.vinci.leo.cr.DatabaseCollectionReader
Initialize with the database connection and query information.
DatabaseCollectionReader(String, String, String, String, String, String, String) - Constructor for class gov.va.vinci.leo.cr.DatabaseCollectionReader
Initialize with the database connection and query information.
databaseConnectionInformation - Variable in class gov.va.vinci.leo.listener.BaseDatabaseListener
The database connection information.
DatabaseConnectionInformation - Class in gov.va.vinci.leo.model
Holds information needed to make a connection to a database.
DatabaseConnectionInformation(String, String, String, String) - Constructor for class gov.va.vinci.leo.model.DatabaseConnectionInformation
Constructor.
DatabaseConnectionInformation(String, String, String, String, String) - Constructor for class gov.va.vinci.leo.model.DatabaseConnectionInformation
Constructor.
DatabaseField - Class in gov.va.vinci.leo.listener
Pojo for holding a database field name and type.
DatabaseField(String, String) - Constructor for class gov.va.vinci.leo.listener.DatabaseField
Constructor
dataManager - Variable in class gov.va.vinci.leo.cr.BaseDatabaseCollectionReader
DataManager that performs the query and returns the results.
DataManager - Class in gov.va.vinci.leo.tools.db
Handle the database connection, query, and result set.
DataManager(String, String, String, String) - Constructor for class gov.va.vinci.leo.tools.db.DataManager
Constructor.
DataManager(DatabaseConnectionInformation) - Constructor for class gov.va.vinci.leo.tools.db.DataManager
Constructor with database connection information.
DataManager(DataSource) - Constructor for class gov.va.vinci.leo.tools.db.DataManager
Initialize the DataManager with a DataSource object.
DataQueryInformation - Class in gov.va.vinci.leo.model
Holds query information for processing.
DataQueryInformation(String, String, String) - Constructor for class gov.va.vinci.leo.model.DataQueryInformation
Constructor with all fields required.
DEFAULT_BEAN_NAME - Static variable in interface gov.va.vinci.leo.tools.JetmPerformanceMBean
 
DEFAULT_NUMBER_INSTANCES - Static variable in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Default number of replication instances for this AnalysisEngine.
defaultClientConfig() - Method in class gov.va.vinci.leo.CommandLineClient
The default client config file.
defaultCollectionReaderConfig() - Method in class gov.va.vinci.leo.CommandLineClient
The default collection reader config file.
defaultListenerConfig() - Method in class gov.va.vinci.leo.CommandLineClient
The default listener config files.
deleteOnExit - Variable in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
If TRUE then delete the generated descriptor file once the program exits, defaults to TRUE.
deleteOnExit - Variable in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
If TRUE then delete the generated descriptor file once the program exits, defaults to TRUE.
deploy(ArrayList<String>, boolean) - Method in class gov.va.vinci.leo.Service
Create a deployment descriptor and initialize the mAppCtx and mUAEngine objects then call deploy to deploy the service.
deploy(List<LeoAEDescriptor>) - Method in class gov.va.vinci.leo.Service
Initialize a service pipeline by first generating an aggregate descriptor from a list of LeoAEDescriptor objects.
deploy(LeoTypeSystemDescription, LeoAnnotator...) - Method in class gov.va.vinci.leo.Service
Initialize a pipeline by generating the aggregate descriptor file from the list of LeoAnnotator objects then deploy it in the UIMA-AS framework.
deploy(LeoTypeSystemDescription, int, LeoAnnotator...) - Method in class gov.va.vinci.leo.Service
Initialize a pipeline by generating the aggregate descriptor file from the list of LeoAnnotator objects then deploy it in the UIMA-AS framework.
deploy(List<LeoAnnotator>, int, LeoTypeSystemDescription) - Method in class gov.va.vinci.leo.Service
Initialize a pipeline by generating the aggregate descriptor file from the list of LeoAnnotator objects then deploy it in the UIMA-AS framework.
deploy(AnalysisEngineDescription) - Method in class gov.va.vinci.leo.Service
Use the AnalysisEngineDescription as input for the deployment descriptor that is generated.
deploy(LeoAEDescriptor) - Method in class gov.va.vinci.leo.Service
Initialize the Deployment Descriptor for the service using the provided LeoAEDescriptor object as the Top Descriptor.
deploy(LeoDeployDescriptor) - Method in class gov.va.vinci.leo.Service
Initialize the service using the provided LeoDeployDescriptor object as the basis of the deployment information gov.va.vinci.leo.model.
deploy() - Method in class gov.va.vinci.leo.Service
Initialize the mAppCtx and mUAEngine objects then deploy the service.
DeployDescriptorFactory - Class in gov.va.vinci.leo.descriptors
Generate a Deployment Descriptor.
DeployDescriptorFactory(String, Map<String, String>) - Constructor for class gov.va.vinci.leo.descriptors.DeployDescriptorFactory
Constructor for DeployDescriptorFactory to serialize a deploymentDescriptor based on the settings contained in the descriptorMap provided.
DeployDescriptorWriter - Interface in gov.va.vinci.leo.descriptors
Interface that defines common methods for the implementation of a writer that serializes deployment descriptors into files.
deploymentSectionXML(TransformerHandler) - Method in class gov.va.vinci.leo.descriptors.LeoDeployDescriptor
Serialize the deployment section.
descriptor - Variable in class gov.va.vinci.leo.ae.ExternalAnnotator
External descriptor imported to LeoAnnotator for use in the SimplePipeline representation.
descriptor - Variable in class gov.va.vinci.leo.ae.LeoPearAnnotator
 
descriptor - Variable in class gov.va.vinci.leo.ae.LeoRemoteAnnotator
Descriptor representing the remote annotator.
descriptorLocator - Variable in class gov.va.vinci.leo.descriptors.LeoPearDescriptor
 
deserialize(JsonElement, Type, JsonDeserializationContext) - Method in class gov.va.vinci.leo.tools.LeoInheritanceGsonAdapter
Gson invokes this call-back method during deserialization when it encounters a field of the specified type.
disableServiceQueue(String) - Method in class gov.va.vinci.leo.tools.JamService
Disable monitoring of a service queue.
docInfo - Variable in class gov.va.vinci.leo.listener.BaseListener
CSI annotation for the document being processed in an entityProcessComplete event.
doesServiceQueueExist(String, String) - Method in class gov.va.vinci.leo.tools.JamService
Given a queue name, determine if it already exists.
doHttpCall(HttpMethod) - Method in class gov.va.vinci.leo.tools.JamService
Does the HTTP call and returns the response body as a string, or throws and HttpException.
driver - Variable in class gov.va.vinci.leo.cr.BaseDatabaseCollectionReader
Driver to be used for the database connection.

E

enableServiceQueue(String) - Method in class gov.va.vinci.leo.tools.JamService
Enable monitoring on an existing service queue.
ENDPOINT - Static variable in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor.Param
Input Queue for the remote service.
ENDPOINT_DEFAULT - Static variable in class gov.va.vinci.leo.tools.LeoProperties
Default value for the Endpoint Queue Name, Queue name should be unique for each application.
entityProcessComplete(CAS, EntityProcessStatus) - Method in class gov.va.vinci.leo.listener.BaseCsvListener
Called with a completely processed CAS.
entityProcessComplete(CAS, EntityProcessStatus) - Method in class gov.va.vinci.leo.listener.BaseDatabaseListener
 
entityProcessComplete(CAS, EntityProcessStatus) - Method in class gov.va.vinci.leo.listener.BaseListener
 
entityProcessComplete(CAS, EntityProcessStatus) - Method in class gov.va.vinci.leo.listener.SimpleXmiListener
 
entityProcessError() - Method in class gov.va.vinci.leo.listener.BaseListener
Return true if an exception was received from the service when the entityProcessComplete event was thrown.
ESAPIValidationType - Enum in gov.va.vinci.leo.tools
Types of ESAPI validation
escapechar - Variable in class gov.va.vinci.leo.tools.CSVWriterBuilder
 
excludeTypesFilter - Variable in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Optional, only process a CAS if it does not include instances of one of the types in this list.
exitOnError - Variable in class gov.va.vinci.leo.listener.BaseListener
Flag to indicate whether or not entityProcessComplete processing should terminate when exceptions are received from the service.
ExternalAnnotator - Class in gov.va.vinci.leo.ae
This annotator is used to import external implementations of annotators by descriptor or directly from the object binary.
ExternalAnnotator(String, String) - Constructor for class gov.va.vinci.leo.ae.ExternalAnnotator
Constructor that creates a blank AnalysisEngineDescriptor object with the name provided.
ExternalAnnotator(String, boolean, NameValue...) - Constructor for class gov.va.vinci.leo.ae.ExternalAnnotator
Create this annotator by importing an external descriptor.
ExternalAnnotator(String, boolean, int, NameValue...) - Constructor for class gov.va.vinci.leo.ae.ExternalAnnotator
Create this annotator by importing an external descriptor.
ExternalCollectionReader - Class in gov.va.vinci.leo.cr
Import a third party CollectionReader from a descriptor or an already initialized CollectionReader object.
ExternalCollectionReader(CollectionReader_ImplBase) - Constructor for class gov.va.vinci.leo.cr.ExternalCollectionReader
Initialize with a pre-created CollectionReader object.
ExternalCollectionReader(String) - Constructor for class gov.va.vinci.leo.cr.ExternalCollectionReader
Set the reader from the path to the descriptor.
ExternalCollectionReader(File) - Constructor for class gov.va.vinci.leo.cr.ExternalCollectionReader
Set the reader from the CollectionReader referenced in the File object specified.
extractPearFile(File, File, boolean, boolean) - Static method in class gov.va.vinci.leo.tools.LeoUtils
Extracts the contents of a PEAR file to the directory specified, optionally performs a verification step.

F

featOkTst - Static variable in class gov.va.vinci.leo.types.CSI_Type
 
FeatureNameType - Class in gov.va.vinci.leo.model
A pojo for holding a feature name and UIMA type.
FeatureNameType(String, String) - Constructor for class gov.va.vinci.leo.model.FeatureNameType
Constructor.
FIELD_NAME - Static variable in annotation type gov.va.vinci.leo.descriptors.LeoConfigurationParameter
The default name value if one is not set.
FileCollectionReader - Class in gov.va.vinci.leo.cr
Get a list of the files in a directory and return them one at a time.
FileCollectionReader() - Constructor for class gov.va.vinci.leo.cr.FileCollectionReader
Default constructor used during UIMA initialization.
FileCollectionReader(File, boolean) - Constructor for class gov.va.vinci.leo.cr.FileCollectionReader
Constructor that takes an input directory path and recurse flag as inputs.
fileExtensionString - Static variable in class gov.va.vinci.leo.cr.FileCollectionReader
Default file extension string.
fileExtenstionString - Static variable in class gov.va.vinci.leo.cr.XmiFileCollectionReader
The default file name extension to filter on.
filenameFilter - Variable in class gov.va.vinci.leo.cr.BaseFileCollectionReader
Filters out the files found by filename extension.
fileNameFilterJSON - Variable in class gov.va.vinci.leo.cr.BaseFileCollectionReader
JSON representation of the filename filter used to pass this object to the CollectionReader descriptor for initialization.
fileNameFilterName - Variable in class gov.va.vinci.leo.cr.BaseFileCollectionReader
Class name of the file name filter this reader is using.
filter(String) - Method in class gov.va.vinci.leo.tools.AsciiFilter
 
filter(InputStream) - Method in class gov.va.vinci.leo.tools.AsciiFilter
Create a new String with non-ascii chars replaced with ascii equivalents where applicable, otherwise replaces invalid char with '_'.
filter(InputStream, String) - Method in class gov.va.vinci.leo.tools.AsciiFilter
 
filter(String) - Method in interface gov.va.vinci.leo.tools.TextFilter
Creates a new String from the input String with invalid characters replaced with valid characters.
filter(InputStream) - Method in interface gov.va.vinci.leo.tools.TextFilter
Create a new String from the text found in the input stream replacing invalid characters with valid characters.
filter(InputStream, String) - Method in interface gov.va.vinci.leo.tools.TextFilter
Create a new String from the text found in the input stream replacing invalid characters with valid characters.
filter(String) - Method in class gov.va.vinci.leo.tools.XmlFilter
 
filter(InputStream) - Method in class gov.va.vinci.leo.tools.XmlFilter
 
filter(InputStream, String) - Method in class gov.va.vinci.leo.tools.XmlFilter
 
filters - Variable in class gov.va.vinci.leo.cr.BaseLeoCollectionReader
List of filters to be applied to the text before adding to the CAS as document text.
filterText(String, List<TextFilter>) - Static method in class gov.va.vinci.leo.tools.LeoUtils
Return a String that has applied the list of filters to the input string.
finalize() - Method in class gov.va.vinci.leo.Client
 
findFiles(File) - Method in class gov.va.vinci.leo.cr.BaseFileCollectionReader
Find the list of files that meet the requirements.
firstOffset - Variable in class gov.va.vinci.leo.cr.SQLServerPagedDatabaseCollectionReader
the first row to start with.

G

generate(String, String) - Static method in class gov.va.vinci.leo.tools.GenerateDescriptors
A utility for generating Descriptors and Type Descriptors for an annotator.
generateAED(String, boolean) - Static method in class gov.va.vinci.leo.descriptors.AnalysisEngineFactory
Create an AnalysisEngineFactory object from a string descriptor.
generateAED() - Static method in class gov.va.vinci.leo.descriptors.AnalysisEngineFactory
Create a blank AnalysisEngineDescription object.
generateAED(String, String) - Static method in class gov.va.vinci.leo.descriptors.AnalysisEngineFactory
Create an AnalysisEngineDescription object with the name provided.
generateCollectionReaderDescription() - Method in class gov.va.vinci.leo.cr.BaseLeoCollectionReader
Generate a new CollectionReaderDescription from the CollectionReader parameters and values.
GenerateDescriptors - Class in gov.va.vinci.leo.tools
A utility for generating Descriptors and Type Descriptors for an annotator.
GenerateDescriptors() - Constructor for class gov.va.vinci.leo.tools.GenerateDescriptors
 
generateRemoteAEDescriptor() - Static method in class gov.va.vinci.leo.descriptors.RemoteEngineFactory
Create a CustomResourceSpecifier that represents a remote AE service.
generateRemoteAEDescriptor(String, boolean) - Static method in class gov.va.vinci.leo.descriptors.RemoteEngineFactory
Create a CustomResourceSpecifier from a descriptor xml file.
generateTypeSystemDescription(String, boolean) - Static method in class gov.va.vinci.leo.descriptors.TypeSystemFactory
Create an TypeFactory object from a string descriptor.
generateTypeSystemDescription() - Static method in class gov.va.vinci.leo.descriptors.TypeSystemFactory
Creates a Default TypeSystemDescription object and returns it.
genTypeSystemJava(String, String) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Generate the java source files for the TypeSystem of this AnalysisEngine, then compile them.
GET_META_TIMEOUT - Static variable in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor.Param
Initialize timeout in ms.
getAEDescriptor() - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Return an AnalysisEngineDescription object reference for this model.
getAggregateDescriptorFile() - Method in class gov.va.vinci.leo.Service
Get the aggregate descriptor file path.
getAggregateDescriptorFile() - Method in class gov.va.vinci.leo.tools.LeoProperties
File path to the aggregate descriptor.
getAnalysisEngineDescription() - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Get a reference to the core AnalysisEngineDescription object that this LeoAEDescriptor uses.
getAnnotationListForType(JCas, String) - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Given a cas and type, return all of the annotations in the cas for that type.
getAnnotationTypeFilter() - Method in class gov.va.vinci.leo.listener.BaseListener
gets the list of annotation types to be filtered on.
getASCII7Map() - Static method in class gov.va.vinci.leo.tools.AsciiService
This map is focused on correcting OCR mistakes, so the mappings are performed by visual similarity.
getASCII8Map() - Static method in class gov.va.vinci.leo.tools.AsciiService
Get the ascii 8 map.
getBatchSize() - Method in class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
Get the batch size.
getBatchSize() - Method in class gov.va.vinci.leo.listener.BaseDatabaseListener
Get the batch size for the number of records to accumulate before executing the batch.
getBrokerURL() - Method in class gov.va.vinci.leo.descriptors.LeoDeployDescriptor
get the broker url for this deployment descriptor.
getBrokerURL() - Method in class gov.va.vinci.leo.tools.LeoProperties
Get the broker url.
getCache() - Method in class gov.va.vinci.leo.ae.LeoCachingAnnotator
Get the cache.
getCacheName() - Method in class gov.va.vinci.leo.ae.LeoCachingAnnotator
Returns the ehcache name for this annotator.
getCapabilites() - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Get the capabilities for this Analysis Engine from its metadata.
getCasPoolSize() - Method in class gov.va.vinci.leo.descriptors.LeoDeployDescriptor
Get the cas pool size for this deployment.
getCasPoolSize() - Method in class gov.va.vinci.leo.tools.LeoProperties
get the cas pool size.
getCCTimeout() - Method in class gov.va.vinci.leo.tools.LeoProperties
Get the CCTimeout.
getClient() - Method in class gov.va.vinci.leo.tools.JamService
Return the HttpClient used for communication, or null if one has not been set/created yet.
getCollecting() - Method in class gov.va.vinci.leo.tools.JetmPerformance
 
getCollecting() - Method in interface gov.va.vinci.leo.tools.JetmPerformanceMBean
Return true if the monitor is currently collecting, or else false.
getCollectionSize() - Method in class gov.va.vinci.leo.cr.BaseFileCollectionReader
Return the number of documents in the set.
getColumnIndex(String) - Method in class gov.va.vinci.leo.tools.db.LeoArrayListHandler
Get the index of the column name provided from the last query handled.
getColumnNames() - Method in class gov.va.vinci.leo.tools.db.LeoArrayListHandler
Get the set of column names from the last query handled.
getComponentName(Parameter[], String...) - Static method in class gov.va.vinci.leo.descriptors.AggregateEngineFactory
Pull the component name from the list of parameters.
getConnection() - Method in class gov.va.vinci.leo.tools.db.LeoDataSource
Attempts to establish a connection with the data source that this DataSource object represents.
getConnection(String, String) - Method in class gov.va.vinci.leo.tools.db.LeoDataSource
Attempts to establish a connection with the data source that this DataSource object represents.
getCSITypeSystemDescription() - Static method in class gov.va.vinci.leo.types.TypeLibrarian
Get the standard CSI TypeSystem Description used within most leo projects.
getCurrentIndex() - Method in class gov.va.vinci.leo.cr.BaseFileCollectionReader
 
getData(String) - Method in class gov.va.vinci.leo.cr.BaseDatabaseCollectionReader
Executes the query and saves the results internally to a List of Object[] to be retrieved when getNext() is called.
getData(String) - Method in class gov.va.vinci.leo.cr.DatabaseCollectionReader
Executes the query and saves the results internally to a List of Object[] to be retrieved when getNext() is called.
getDataManager() - Method in class gov.va.vinci.leo.cr.BaseDatabaseCollectionReader
Get the data manager to run queries with.
getDelegate(String) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Get a LeoAEDescriptor for a delegate engine with the name provided.
getDelegateNames() - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Return the names of the delegates found in aggregate descriptors.
getDelegates() - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Get the set of delegate engines for this aggregate if it exists.
getDeploymentDescriptorFile() - Method in class gov.va.vinci.leo.tools.LeoProperties
The deployment descriptor file path and name.
getDescription() - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Gets the description of this Resource.
getDescription() - Method in class gov.va.vinci.leo.descriptors.LeoDeployDescriptor
Get the description of this deployment descriptor.
getDescriptor() - Method in class gov.va.vinci.leo.ae.ExternalAnnotator
 
getDescriptor() - Method in interface gov.va.vinci.leo.ae.LeoAnnotator
Return the Descriptor for this AnalysisEngine or RemoteAnalysisEngine.
getDescriptor() - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Generate a descriptor from this annotator object.
getDescriptor() - Method in class gov.va.vinci.leo.ae.LeoPearAnnotator
 
getDescriptor() - Method in class gov.va.vinci.leo.ae.LeoRemoteAnnotator
Return the Descriptor for this AnalysisEngine or RemoteAnalysisEngine.
getDescriptorDirectory() - Method in class gov.va.vinci.leo.tools.LeoProperties
Get the path to the directory where descriptors will be generated.
getDescriptorLocator() - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
 
getDescriptorLocator() - Method in interface gov.va.vinci.leo.descriptors.LeoDelegate
 
getDescriptorLocator() - Method in class gov.va.vinci.leo.descriptors.LeoPearDescriptor
 
getDescriptorLocator() - Method in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
 
getDescriptorLocator() - Method in class gov.va.vinci.leo.descriptors.LeoTypeSystemDescription
Return the path to the temp XML file for this TypeSystemDescription, null if no path has been generated.
getDriver() - Method in class gov.va.vinci.leo.cr.BaseDatabaseCollectionReader
Get the Driver text string.
getDriver() - Method in class gov.va.vinci.leo.model.DatabaseConnectionInformation
Get database driver classname.
getEncoding() - Method in class gov.va.vinci.leo.cr.BaseFileCollectionReader
Return the encoding format that this CollectionReader will use for the source data.
getEndpoint() - Method in class gov.va.vinci.leo.descriptors.LeoDeployDescriptor
Get the endpoint for this deployment descriptor.
getEndpoint() - Method in class gov.va.vinci.leo.tools.LeoProperties
get the endpoint.
getEscapechar() - Method in class gov.va.vinci.leo.listener.BaseCsvListener
Get the escape character.
getEscapechar() - Method in class gov.va.vinci.leo.tools.CSVWriterBuilder
 
getExcludeTypesFilter() - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Get the exclude types list.
getFilenameFilter() - Method in class gov.va.vinci.leo.cr.BaseFileCollectionReader
Get the filename filter that will be used to filter files found in the input directory.
getFileURI(File) - Static method in class gov.va.vinci.leo.tools.LeoUtils
Return a URI string locator for the File object provided.
getFilters() - Method in class gov.va.vinci.leo.cr.BaseLeoCollectionReader
Return the list of filters for this reader.
getFirstOffset() - Method in class gov.va.vinci.leo.cr.SQLServerPagedDatabaseCollectionReader
Get the first row offset.
getFSGenerator() - Method in class gov.va.vinci.leo.types.CSI_Type
 
getFSHeapSize() - Method in class gov.va.vinci.leo.tools.LeoProperties
Get FS Heap Size.
getHandler() - Method in class gov.va.vinci.leo.tools.db.DataManager
Return a reference to the LeoArrayListHandler which manages query execution and results.
getHeaderManipulationSafeString(Object) - Static method in class gov.va.vinci.leo.tools.LeoUtils
returns a Header-Manipulation safe string using a "WhiteList" approach.
getHeaders() - Method in class gov.va.vinci.leo.listener.BaseCsvListener
Returns the string list of the headers for a row.
getHeaders() - Method in class gov.va.vinci.leo.listener.SimpleCsvListener
 
getID() - Method in class gov.va.vinci.leo.types.CSI
getter for ID - gets ID number of the Analyte being analyzed
getID(int) - Method in class gov.va.vinci.leo.types.CSI_Type
 
getIdColumn() - Method in class gov.va.vinci.leo.cr.DatabaseCollectionReader
Get the ID Column name.
getIdColumn() - Method in class gov.va.vinci.leo.model.DataQueryInformation
Get the id column index, 0 based.
getImplementationName() - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Retrieves the name of this ResourceCreationSpecifier's implementation.
getIncludeTypesFilter() - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Return the types filter array of type names.
getInitialFsHeapSize() - Method in class gov.va.vinci.leo.descriptors.LeoDeployDescriptor
get the initial fs heap size for this deployment.
getInitTimeout() - Method in class gov.va.vinci.leo.tools.LeoProperties
Get the init timeout.
getInputDirectory() - Method in class gov.va.vinci.leo.cr.BaseFileCollectionReader
Return the input directory this reader will search for files.
getInputQueueName() - Method in class gov.va.vinci.leo.tools.LeoProperties
Get the input queue name.
getInputType() - Method in class gov.va.vinci.leo.listener.BaseListener
Get the array of input type names this listener will use.
getInputTypes() - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Get the input types list this annotator will use.
getInputTypesList(CAS) - Method in class gov.va.vinci.leo.listener.BaseListener
 
getJamJmxPort() - Method in class gov.va.vinci.leo.tools.LeoProperties
If registering with JAM, this is the port the local JMX Server will listen on.
getJamQueryIntervalInSeconds() - Method in class gov.va.vinci.leo.tools.LeoProperties
Get the JAM Query Interval in seconds.
getJamServerBaseUrl() - Method in class gov.va.vinci.leo.tools.JamService
Get the JAM server base url.
getJamServerBaseUrl() - Method in class gov.va.vinci.leo.tools.LeoProperties
Get the Jam Server Base URL.
getLastResetDate() - Method in class gov.va.vinci.leo.tools.JetmPerformance
 
getLastResetDate() - Method in interface gov.va.vinci.leo.tools.JetmPerformanceMBean
Date of the last rest of the monitor, or null if no reset has occured.
getLeoAEDescriptor() - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Generate a descriptor from this annotator object.
getLeoCollectionReader() - Method in class gov.va.vinci.leo.Client
Get the collection reader for this client.
getLeoTypeSystemDescription() - Method in class gov.va.vinci.leo.ae.ExternalAnnotator
Return the type system description for this annotator.
getLeoTypeSystemDescription() - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Return the type system description for this annotator.
getLeoTypeSystemDescription() - Method in interface gov.va.vinci.leo.pipeline.PipelineInterface
The full type description for this pipeline.
getLineEnd() - Method in class gov.va.vinci.leo.listener.BaseCsvListener
Get the line ending string.
getLineEnd() - Method in class gov.va.vinci.leo.tools.CSVWriterBuilder
 
getListeners() - Method in class gov.va.vinci.leo.Client
Get the list of listeners that have been registered with the client.
getListeners() - Method in class gov.va.vinci.leo.Client.LeoEngine
Return all listeners for this engine.
getListeners(File...) - Static method in class gov.va.vinci.leo.CommandLineClient
Parse the groovy config files, and return the listener objects that are defined in them.
getLocator() - Method in class gov.va.vinci.leo.types.CSI
getter for Locator - gets File path or query information to allow us to find this record again.
getLocator(int) - Method in class gov.va.vinci.leo.types.CSI_Type
 
getLoginTimeout() - Method in class gov.va.vinci.leo.tools.db.LeoDataSource
Gets the maximum time in seconds that this data source can wait while attempting to connect to a database.
getLogWriter() - Method in class gov.va.vinci.leo.tools.db.LeoDataSource
Retrieves the log writer for this DataSource object.
getMaxNumberOfInstances() - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
 
getMaxOffset() - Method in class gov.va.vinci.leo.cr.SQLServerPagedDatabaseCollectionReader
Get the max offset.
getMaxRecordNumber() - Method in class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
Return the maximum row number.
getMinRecordNumber() - Method in class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
Return the minumum row number.
getModifiesCas() - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Gets whether this component will modify the CAS.
getName() - Method in class gov.va.vinci.leo.ae.ExternalAnnotator
Get the name of this annotator.
getName() - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Get the name of this annotator.
getName() - Method in class gov.va.vinci.leo.ae.LeoPearAnnotator
 
getName() - Method in class gov.va.vinci.leo.ae.LeoRemoteAnnotator
Get the name of this annotator.
getName() - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Gets the name of this Resource.
getName() - Method in interface gov.va.vinci.leo.descriptors.LeoDelegate
Get the name of this delegate.
getName() - Method in class gov.va.vinci.leo.descriptors.LeoDeployDescriptor
Return the name of this Deployment.
getName() - Method in class gov.va.vinci.leo.descriptors.LeoPearDescriptor
 
getName() - Method in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
Get the name of this delegate or null if no name has been set.
getName() - Method in class gov.va.vinci.leo.listener.DatabaseField
Return the name of this database field.
getName() - Method in class gov.va.vinci.leo.model.FeatureNameType
Get the name of the feature.
getName() - Method in class gov.va.vinci.leo.model.NameValue
Get name.
getNext(CAS) - Method in class gov.va.vinci.leo.cr.BaseDatabaseCollectionReader
 
getNext(CAS) - Method in class gov.va.vinci.leo.cr.BaseFileCollectionReader
Get the next file to be processed in the pipeline.
getNext(CAS) - Method in class gov.va.vinci.leo.cr.BaseLeoCollectionReader
 
getNext(CAS) - Method in class gov.va.vinci.leo.cr.DatabaseCollectionReader
 
getNext(CAS) - Method in class gov.va.vinci.leo.cr.FileCollectionReader
Get the next file to be processed in the pipeline.
getNext(CAS) - Method in class gov.va.vinci.leo.cr.XmiFileCollectionReader
De-serialize the next XMI file in the collection.
getNextRandomBatchNumber() - Method in class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
Get the next unused random batch number to pull.
getNoteColumn() - Method in class gov.va.vinci.leo.cr.DatabaseCollectionReader
Get the note column name.
getNoteColumn() - Method in class gov.va.vinci.leo.model.DataQueryInformation
Get the note column index, 0 based.
getNumberOfCASesProcessed() - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Get the number of CASes this annotator has processed.
getNumberOfFilteredCASesProcessed() - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Get the number of CASes that were processed once getting through the filter.
getNumberOfInstances() - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
 
getNumInstances() - Method in class gov.va.vinci.leo.ae.ExternalAnnotator
Number of instances of this annotator in the pipeline.
getNumInstances() - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Number of instances of this annotator in the pipeline.
getNumReceived() - Method in class gov.va.vinci.leo.listener.BaseListener
Return the number of CAS objects that were returned by the service.
getNumSent() - Method in class gov.va.vinci.leo.listener.BaseListener
The number of CAS objects sent to the service.
getOutputDir() - Method in class gov.va.vinci.leo.listener.BaseListener
Return the output directory File object for this listener.
getOutputsNewCASes() - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Gets whether this AnalysisEngine may output new CASes.
getOutputType() - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Get the output type name this annotator will use.
getPageQuery(Integer) - Method in class gov.va.vinci.leo.tools.db.SQLServerPagedQuery
Get the query needed to get a specific page of records from the database.
getPageSize() - Method in class gov.va.vinci.leo.cr.SQLServerPagedDatabaseCollectionReader
Get the page size.
getParameter(String, Parameter[]) - Static method in class gov.va.vinci.leo.tools.LeoUtils
Return the Parameter in the array whose name matches the name provided.
getParameterSetting(String) - Method in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
Get the Parameter object from the descriptor with the name provided or null if the parameter is not found in the descriptor.
getParameterTypeFromField(Field, ConfigurationParameter) - Static method in class gov.va.vinci.leo.descriptors.ConfigurationParameterUtils
Get the multivalued and type parameter information from the field object.
getParameterValue(T, String, UimaContext) - Static method in class gov.va.vinci.leo.descriptors.ConfigurationParameterUtils
Return the value set in the configuration for the parameter named.
getParameterValue(String) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Return the value to which the parameter has been set.
getParameterValue(String) - Method in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
Get the value of a parameter in the descriptor, returns null if the name is not found in the parameter list.
getParams(Class<T>) - Static method in class gov.va.vinci.leo.descriptors.ConfigurationParameterUtils
 
getParamsToValuesMap(T) - Static method in class gov.va.vinci.leo.descriptors.ConfigurationParameterUtils
 
getParentLogger() - Method in class gov.va.vinci.leo.tools.db.LeoDataSource
Return the parent Logger of all the Loggers used by this data source.
getPassword() - Method in class gov.va.vinci.leo.cr.BaseDatabaseCollectionReader
Get the database password.
getPassword() - Method in class gov.va.vinci.leo.model.DatabaseConnectionInformation
Get the connection password.
getPerformanceReport() - Method in class gov.va.vinci.leo.Client
Get the performance report stored after the last "run" invocation in this client object.
getPipeline() - Method in interface gov.va.vinci.leo.pipeline.PipelineInterface
Get the full Pipeline.
getProgress() - Method in class gov.va.vinci.leo.cr.BaseDatabaseCollectionReader
Gets information about the number of entities and/or amount of data that has been read from this CollectionReader, and the total amount that remains (if that information is available).
getProgress() - Method in class gov.va.vinci.leo.cr.BaseFileCollectionReader
 
getProgress() - Method in class gov.va.vinci.leo.cr.DatabaseCollectionReader
Gets information about the number of entities and/or amount of data that has been read from this CollectionReader, and the total amount that remains (if that information is available).
getPropertiesKeys() - Method in class gov.va.vinci.leo.types.CSI
getter for PropertiesKeys - gets
getPropertiesKeys(int) - Method in class gov.va.vinci.leo.types.CSI
indexed getter for PropertiesKeys - gets an indexed value -
getPropertiesKeys(int) - Method in class gov.va.vinci.leo.types.CSI_Type
 
getPropertiesKeys(int, int) - Method in class gov.va.vinci.leo.types.CSI_Type
 
getPropertiesValues() - Method in class gov.va.vinci.leo.types.CSI
getter for PropertiesValues - gets
getPropertiesValues(int) - Method in class gov.va.vinci.leo.types.CSI
indexed getter for PropertiesValues - gets an indexed value -
getPropertiesValues(int) - Method in class gov.va.vinci.leo.types.CSI_Type
 
getPropertiesValues(int, int) - Method in class gov.va.vinci.leo.types.CSI_Type
 
getQuery(int) - Method in class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
Does a string substitution on the query, replacing {min} and {max} with the appropriate values for this batch.
getQuery() - Method in class gov.va.vinci.leo.cr.DatabaseCollectionReader
Get the database query used to pull data.
getQuery() - Method in class gov.va.vinci.leo.model.DataQueryInformation
Get the query.
getQuotechar() - Method in class gov.va.vinci.leo.listener.BaseCsvListener
Get the quote character.
getQuotechar() - Method in class gov.va.vinci.leo.tools.CSVWriterBuilder
 
getRandomBatches() - Method in class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
Get the number of random batches, defaults to zero.
getReader(File) - Static method in class gov.va.vinci.leo.CommandLineClient
Parse the groovy config file, and return the reader object.
getReferenceID(JCas) - Static method in class gov.va.vinci.leo.tools.CasTools
Return the document ID based on the CSI or SourceDocumentInformation objects.
getReferenceLocation(JCas) - Method in class gov.va.vinci.leo.listener.BaseListener
Return the document ID based on the CSI or SourceDocumentInformation objects.
getRegisterServiceRequestBody(String, String, int, boolean, boolean) - Method in class gov.va.vinci.leo.tools.JamService
Returns the xml for the registerServiceRequest method.
getRelationshipAnnotationTypeSystemDescription() - Static method in class gov.va.vinci.leo.types.TypeLibrarian
Get the standard RelationshipAnnotation TypeSystem Description used within some leo projects.
getRemoteDescriptor() - Method in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
 
getResourceAsInputStream(String) - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Gets a resource as an input stream.
getResourceFileAsString(String) - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Note: Resource paths are specified via file: and classpath: to determine if the resource should be looked up in the file system or in the classpath.
getResourceSpecifier() - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Return a reference to the internal ResourceSpecifier that is the backend model for the delegate.
getResourceSpecifier() - Method in interface gov.va.vinci.leo.descriptors.LeoDelegate
Return a reference to the internal ResourceSpecifier that is the backend model for the delegate.
getResourceSpecifier() - Method in class gov.va.vinci.leo.descriptors.LeoPearDescriptor
 
getResourceSpecifier() - Method in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
Return a reference to the internal ResourceSpecifier that is the backend model for the delegate.
getResultFromCache(Serializable) - Method in class gov.va.vinci.leo.ae.LeoCachingAnnotator
Look in the cache for input and return the result.
getResultSetMetaData() - Method in class gov.va.vinci.leo.tools.db.DataManager
Return the MetaData from the ResultSet of the query that was last executed.
getResultSetMetaData() - Method in class gov.va.vinci.leo.tools.db.LeoArrayListHandler
Return the ResultSetMetaData from the last query handled.
getRowData() - Method in class gov.va.vinci.leo.types.CSI
getter for RowData - gets
getRowData(int) - Method in class gov.va.vinci.leo.types.CSI
indexed getter for RowData - gets an indexed value -
getRowData(int) - Method in class gov.va.vinci.leo.types.CSI_Type
 
getRowData(int, int) - Method in class gov.va.vinci.leo.types.CSI_Type
 
getRows(CAS) - Method in class gov.va.vinci.leo.listener.BaseCsvListener
Given a cas, return one or more rows of data.
getRows(CAS) - Method in class gov.va.vinci.leo.listener.BaseDatabaseListener
Abstract method: You must implement this method.
getRows(CAS) - Method in class gov.va.vinci.leo.listener.SimpleCsvListener
 
getRuntimeClass() - Static method in class gov.va.vinci.leo.tools.LeoUtils
Determines the currently executing runtime class.
getSeparator() - Method in class gov.va.vinci.leo.listener.BaseCsvListener
Get the separator character.
getSeparator() - Method in class gov.va.vinci.leo.tools.CSVWriterBuilder
 
getServiceName() - Method in class gov.va.vinci.leo.tools.LeoProperties
Get the service name.
getServiceQueueExistRequestBody(String, String) - Method in class gov.va.vinci.leo.tools.JamService
Get the serviceQueueExistRequest body xml.
getServiceTypeSystemDescription(String, String) - Static method in class gov.va.vinci.leo.Client
Calls the service to determine the TypeSystemDescription it is using, and returns it.
getServiceTypeSystemDescription() - Method in class gov.va.vinci.leo.Client
Calls the service to determine the TypeSystemDescription it is using, and returns it.
getServiceTypeSystemDescriptionXml(String, String) - Static method in class gov.va.vinci.leo.Client
Returns the remote service TypeSystemDescription in xml.
getServiceTypeSystemDescriptionXml() - Method in class gov.va.vinci.leo.Client
Returns the remote service TypeSystemDescription in xml.
getStartDate() - Method in class gov.va.vinci.leo.tools.JetmPerformance
 
getStartDate() - Method in interface gov.va.vinci.leo.tools.JetmPerformanceMBean
The date the monitor was started or null if the monitor hasn't been started.
getStarted() - Method in class gov.va.vinci.leo.tools.JetmPerformance
 
getStarted() - Method in interface gov.va.vinci.leo.tools.JetmPerformanceMBean
True if the monitor has been started, false if it has not.
getStaticConfigurationParameters(Class) - Static method in class gov.va.vinci.leo.tools.LeoUtils
Create the set of ConfigurationParameter objects from the Param class of an object.
getTHandler() - Method in class gov.va.vinci.leo.tools.XMLSerializer
Return a pointer to the TransformerHandler object created and managed by the serializer.
getTimeout() - Method in class gov.va.vinci.leo.tools.LeoProperties
Set timeout.
getTimestampDateDotTime() - Static method in class gov.va.vinci.leo.tools.LeoUtils
Return a timestamp in the format of yyyyMMdd.HHmmss.
getTimestampDateUnderscoreTime() - Static method in class gov.va.vinci.leo.tools.LeoUtils
Return a timestamp in the format of yyyyMMdd_HHmmss.
getTopDescriptor() - Method in class gov.va.vinci.leo.descriptors.LeoDeployDescriptor
Get a reference to the top descriptor for this service.
getType(String) - Method in class gov.va.vinci.leo.descriptors.LeoTypeSystemDescription
Return a TypeDescription object with the name provided.
getType() - Method in class gov.va.vinci.leo.listener.DatabaseField
Return the database type for this database field.
getType() - Method in class gov.va.vinci.leo.model.FeatureNameType
Get the UIMA Type of the feature.
getTypeDescription() - Method in class gov.va.vinci.leo.descriptors.TypeDescriptionBuilder
Get the TypeDescription this builder has created.
getTypeIndexID() - Method in class gov.va.vinci.leo.types.CSI
 
getTypes() - Method in class gov.va.vinci.leo.descriptors.LeoTypeSystemDescription
Return the collection of Types in this TypeSystem, if there is no TypeSystem set then returns null.
getTypeSystemDescription() - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
A simple method for getting the hold of current Type System.
getTypeSystemDescription() - Method in class gov.va.vinci.leo.descriptors.LeoTypeSystemDescription
Return a reference to the underlying UIMA TypeSystemDescription.
getTypeSystemDescription(String, FeatureNameType...) - Static method in class gov.va.vinci.leo.types.TypeLibrarian
A method for easily building simple type system descriptions.
getTypeSystemDescriptor() - Method in class gov.va.vinci.leo.listener.SimpleXmiListener
Get the type system or aggregate descriptor File reference that this listener will set in the viewer if launched.
getURL() - Method in class gov.va.vinci.leo.cr.BaseDatabaseCollectionReader
Database connection URL.
getUrl() - Method in class gov.va.vinci.leo.model.DatabaseConnectionInformation
Get the connection URL.
getUsername() - Method in class gov.va.vinci.leo.cr.BaseDatabaseCollectionReader
Return the database username.
getUsername() - Method in class gov.va.vinci.leo.model.DatabaseConnectionInformation
Get the connection username.
getUUID() - Static method in class gov.va.vinci.leo.tools.LeoUtils
Generate a random UUID string.
getValidationAnnotationTypeSystemDescription() - Static method in class gov.va.vinci.leo.types.TypeLibrarian
Get the validation annotation type that Siman/Chex creates.
getValidationQuery() - Method in class gov.va.vinci.leo.model.DatabaseConnectionInformation
Get the validation query for this connection.
getValue() - Method in class gov.va.vinci.leo.model.NameValue
Get the value.
getVersion() - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Sets the version number of this Resource.
gov.va.vinci.leo - package gov.va.vinci.leo
Core Client objects.
gov.va.vinci.leo.ae - package gov.va.vinci.leo.ae
Provides base Annotator classes.
gov.va.vinci.leo.cr - package gov.va.vinci.leo.cr
CollectionReader base classes and implementations are found in this package.
gov.va.vinci.leo.descriptors - package gov.va.vinci.leo.descriptors
Provides factories and classes for type, aggregate, analysis, deployment descriptors, and other descriptors UIMA AS uses.
gov.va.vinci.leo.listener - package gov.va.vinci.leo.listener
Provides common and base listeners usable in leo clients.
gov.va.vinci.leo.model - package gov.va.vinci.leo.model
Provides model POJO objects used in Leo.
gov.va.vinci.leo.pipeline - package gov.va.vinci.leo.pipeline
 
gov.va.vinci.leo.tools - package gov.va.vinci.leo.tools
Service utility classes for descriptor handling and JAM service registration.
gov.va.vinci.leo.tools.db - package gov.va.vinci.leo.tools.db
Database query and results handling objects including implementations of the JdbcScriptRunner and the Apache Commons QueryRunner classes.
gov.va.vinci.leo.types - package gov.va.vinci.leo.types
Provides the CSI type that leo uses from all documents.

H

handle(ResultSet) - Method in class gov.va.vinci.leo.tools.db.LeoArrayListHandler
Whole ResultSet handler.
handler - Variable in class gov.va.vinci.leo.tools.db.DataManager
Query results handler.
hasAnnotationsToProcess(CAS) - Method in class gov.va.vinci.leo.listener.BaseListener
See if the cas has any annotations of the input type (if input types are specified).
hasColumn(String) - Method in class gov.va.vinci.leo.tools.db.LeoArrayListHandler
Checks the column names from the last executed query, returns true if the name is found.
hasFilteredAnnotation(JCas) - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
If includeTypesFilter is not set then return true.
hasFilteredAnnotation(CAS) - Method in class gov.va.vinci.leo.listener.BaseListener
See if the CAS has ANY annotations of the types specified in annotationTypeFilter.
hasInputTypesAnnotation(JCas) - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
If the input types list is empty or one or more of the types are found in the CAS then return true, return false otherwise.
hasNext() - Method in class gov.va.vinci.leo.cr.BaseDatabaseCollectionReader
 
hasNext() - Method in class gov.va.vinci.leo.cr.BaseFileCollectionReader
 
hasNext() - Method in class gov.va.vinci.leo.cr.BaseLeoCollectionReader
 
hasNext() - Method in class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
 
hasNext() - Method in class gov.va.vinci.leo.cr.DatabaseCollectionReader
 
hasNext() - Method in class gov.va.vinci.leo.cr.SQLServerPagedDatabaseCollectionReader
 

I

idColumn - Variable in class gov.va.vinci.leo.cr.DatabaseCollectionReader
Zero based index of the ID column in the query.
includeFeatures - Variable in class gov.va.vinci.leo.listener.SimpleCsvListener
Include features on the annotations or not.
includeHeader - Variable in class gov.va.vinci.leo.listener.BaseCsvListener
Include a header row at the start of the output file.
includeTypesFilter - Variable in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Optional, only process CAS if it includes instances of one of the types in the list.
incrementAndGet() - Method in class gov.va.vinci.leo.tools.JetmPerformance.WrappedInteger
 
init(UimaAsBaseCallbackListener...) - Method in class gov.va.vinci.leo.Client
Initialize the client engine and application context.
initializationComplete(EntityProcessStatus) - Method in class gov.va.vinci.leo.listener.BaseCsvListener
Called once client initialization is complete.
initializationComplete(EntityProcessStatus) - Method in class gov.va.vinci.leo.listener.BaseListener
Called once client initialization is complete.
initialize(UimaContext) - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Initialize this annotator.
initialize() - Method in class gov.va.vinci.leo.cr.BaseFileCollectionReader
This method is called during initialization, and does nothing by default.
initialize() - Method in class gov.va.vinci.leo.cr.BaseLeoCollectionReader
This method is called during initialization, and does nothing by default.
initialize() - Method in class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
This method is called during initialization.
initialize() - Method in class gov.va.vinci.leo.cr.SQLServerPagedDatabaseCollectionReader
This method is called during initialization.
initParameterValues(T, UimaContext) - Static method in class gov.va.vinci.leo.descriptors.ConfigurationParameterUtils
 
inputDirectoryPath - Variable in class gov.va.vinci.leo.cr.BaseFileCollectionReader
Path to the input directory.
inputType - Variable in class gov.va.vinci.leo.listener.BaseListener
The list of input types to save to the database.
inputTypes - Variable in class gov.va.vinci.leo.ae.LeoBaseAnnotator
The types of annotations to use as "anchors" or to be processed.
IPADDRESS - Static variable in class gov.va.vinci.leo.tools.LocalhostIPAddress
 
isAggregate() - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
 
isAsync() - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
 
isConsoleOut() - Method in class gov.va.vinci.leo.tools.db.JdbcScriptRunner
If true then results will be written to the console.
isDeleteOnExit() - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Returns TRUE if the generated descriptors will be deleted when the program exits.
isDeleteOnExit() - Method in interface gov.va.vinci.leo.descriptors.LeoDelegate
Returns TRUE if the generated descriptors will be deleted when the program exits.
isDeleteOnExit() - Method in class gov.va.vinci.leo.descriptors.LeoPearDescriptor
 
isDeleteOnExit() - Method in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
Returns TRUE if the generated descriptors will be deleted when the program exits.
isDeleteOnExit() - Method in class gov.va.vinci.leo.tools.LeoProperties
TRUE if generated descriptors will be deleted when the program exits, FALSE otherwise.
isExitOnError() - Method in class gov.va.vinci.leo.listener.BaseListener
If true then the listener will exit the entityProcessComplete event when an error occurs.
isIncludeFeatures() - Method in class gov.va.vinci.leo.listener.SimpleCsvListener
Get the includeFeatures flag value, if true then include feature values in the output.
isIncludeHeader() - Method in class gov.va.vinci.leo.listener.BaseCsvListener
Return the flag value that if true will cause the listener to include a header row, defaults false.
isJamResetStatisticsAfterQuery() - Method in class gov.va.vinci.leo.tools.LeoProperties
Reset statistics after jam query.
isLaunchAnnotationViewer() - Method in class gov.va.vinci.leo.listener.SimpleXmiListener
True if the annotation viewer should be launched after processing is complete, else false.
isLogErrors() - Method in class gov.va.vinci.leo.listener.BaseListener
If true, when the service returns an error status, it is logged via log4j.
isMultipleDeploymentAllowed() - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Gets whether multiple instances of this component can be run in parallel, each receiving a subset of the documents from a collection.
isPrimitive() - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Retrieves whether the AnalysisEngine is primitive (consisting of one annotator), as opposed to aggregate (containing multiple delegate AnalysisEngines).
isRandom - Variable in class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
True if we are pulling random batches.
isUAListenerAdded - Variable in class gov.va.vinci.leo.Client
Flag to let us know if a UAB Listener has been added.
isValidateConnectionEachBatch() - Method in class gov.va.vinci.leo.listener.BaseDatabaseListener
Return true if the connection will be validated when executing each batch.
isWrapperFor(Class<?>) - Method in class gov.va.vinci.leo.tools.db.LeoDataSource
Returns true if this either implements the interface argument or is directly or indirectly a wrapper for an object that does.
itemDescriptions - Variable in class gov.va.vinci.leo.tools.JetmPerformance
 
itemNames - Variable in class gov.va.vinci.leo.tools.JetmPerformance
 
itemTypes - Variable in class gov.va.vinci.leo.tools.JetmPerformance
 

J

JamService - Class in gov.va.vinci.leo.tools
This is part of the Jmx Analytics Monitor package, and allows a client to register with a running JAM instance anywhere on the network using HTTP Web Services.
JamService(String) - Constructor for class gov.va.vinci.leo.tools.JamService
The base url for the JAM server.
javaTypeToUimaType - Static variable in class gov.va.vinci.leo.descriptors.ConfigurationParameterUtils
Map of Java type strings to UIMA configuration parameter types.
jCasGen(String, String) - Method in class gov.va.vinci.leo.descriptors.LeoTypeSystemDescription
Generate the .java files for the types in this TypeSystem then compile them into byte code to the bin directory specified.
JdbcScriptRunner - Class in gov.va.vinci.leo.tools.db
Tool to run database scripts
JdbcScriptRunner(Connection, boolean, boolean) - Constructor for class gov.va.vinci.leo.tools.db.JdbcScriptRunner
Default constructor
JetmPerformance - Class in gov.va.vinci.leo.tools
Management bean interface for an exportable MBean to use JMX.
JetmPerformance() - Constructor for class gov.va.vinci.leo.tools.JetmPerformance
 
JetmPerformance(EtmMonitor) - Constructor for class gov.va.vinci.leo.tools.JetmPerformance
 
JetmPerformance.WrappedInteger - Class in gov.va.vinci.leo.tools
 
JetmPerformanceMBean - Interface in gov.va.vinci.leo.tools
Management bean interface for an exportable MBean to use JMX.

L

lastException - Variable in class gov.va.vinci.leo.listener.BaseListener
Exceptions Received from service via entityProcessComplete event.
launchAnnotationViewer - Variable in class gov.va.vinci.leo.listener.SimpleXmiListener
Flag to launch annotation viewer when processing is complete.
launchAnnotationViewer() - Method in class gov.va.vinci.leo.listener.SimpleXmiListener
Launch the UIMA annotation viewer.
LeoAEDescriptor - Class in gov.va.vinci.leo.descriptors
Allows the user to easily modify and create an AnalysisEngineDescriptor object without needing to directly access the UIMA API.
LeoAEDescriptor() - Constructor for class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Default constructor.
LeoAEDescriptor(String, String) - Constructor for class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Constructor that creates a blank AnalysisEngineDescriptor object with the name provided.
LeoAEDescriptor(String, boolean, NameValue...) - Constructor for class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Create a new description object from the descriptor file provided.
LeoAEDescriptor(List<LeoAEDescriptor>) - Constructor for class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Create a new LeoAEDescriptor object that represents an aggregate from a list of LeoAEDescriptor primitives.
LeoAEDescriptor(AnalysisEngineDescription) - Constructor for class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Use an existing AnalysisEngineDescription object to create a new LeoAEDescriptor.
LeoAnnotator - Interface in gov.va.vinci.leo.ae
Interface for Leo pipeline annotator objects.
LeoArrayListHandler - Class in gov.va.vinci.leo.tools.db
Handles executing the query and processing the result set.
LeoArrayListHandler() - Constructor for class gov.va.vinci.leo.tools.db.LeoArrayListHandler
 
LeoBaseAnnotator - Class in gov.va.vinci.leo.ae
Base annotator class for holding functions that all annotators might take advantage of, such as loading resource files, etc.
LeoBaseAnnotator() - Constructor for class gov.va.vinci.leo.ae.LeoBaseAnnotator
Default constructor for initialization by the UIMA Framework.
LeoBaseAnnotator(String, String...) - Constructor for class gov.va.vinci.leo.ae.LeoBaseAnnotator
Constructor setting the initial values for the inputTypes and outputType parameters.
LeoCachingAnnotator - Class in gov.va.vinci.leo.ae
Base annotator with methods that implement caching via EHCache.
LeoCachingAnnotator() - Constructor for class gov.va.vinci.leo.ae.LeoCachingAnnotator
Default constructor.
LeoCollectionReaderInterface - Interface in gov.va.vinci.leo.cr
Defines the interface for the SuperReader which primarily defines abstract methods that exist in CollectionReader implementation objects.
LeoConfigurationParameter - Annotation Type in gov.va.vinci.leo.descriptors
Marks a class field variable as a configuration parameter.
LeoDataSource - Class in gov.va.vinci.leo.tools.db
DataSource that creates/manages the database connection and returns a reference to the connection object.
LeoDataSource(Connection) - Constructor for class gov.va.vinci.leo.tools.db.LeoDataSource
Initialize the DataSource with the connection object.
LeoDataSource(String, String, String, String) - Constructor for class gov.va.vinci.leo.tools.db.LeoDataSource
Initialize the DataSource with the connection information.
LeoDelegate - Interface in gov.va.vinci.leo.descriptors
Common API interface for Remote and Local Analysis Engine Delegates.
LeoDeployDescriptor - Class in gov.va.vinci.leo.descriptors
Store the metadata for a Deployment Descriptor.
LeoDeployDescriptor(String, boolean) - Constructor for class gov.va.vinci.leo.descriptors.LeoDeployDescriptor
Constructor to start with top descriptor by at filename.
LeoDeployDescriptor(LeoAEDescriptor) - Constructor for class gov.va.vinci.leo.descriptors.LeoDeployDescriptor
Constructor that sets top descriptor initially.
LeoEngine() - Constructor for class gov.va.vinci.leo.Client.LeoEngine
 
LeoInheritanceGsonAdapter<T> - Class in gov.va.vinci.leo.tools
Adds the class type name to the json output so that deserialization will invoke the correct constructor within a class hierarchy.
LeoInheritanceGsonAdapter() - Constructor for class gov.va.vinci.leo.tools.LeoInheritanceGsonAdapter
 
LeoPearAnnotator - Class in gov.va.vinci.leo.ae
Created by tginter on 7/7/17.
LeoPearAnnotator(URI) - Constructor for class gov.va.vinci.leo.ae.LeoPearAnnotator
 
LeoPearAnnotator(LeoPearDescriptor) - Constructor for class gov.va.vinci.leo.ae.LeoPearAnnotator
 
LeoPearDescriptor - Class in gov.va.vinci.leo.descriptors
Created by tginter on 7/6/17.
LeoPearDescriptor(String) - Constructor for class gov.va.vinci.leo.descriptors.LeoPearDescriptor
 
LeoPearDescriptor(File) - Constructor for class gov.va.vinci.leo.descriptors.LeoPearDescriptor
 
LeoPearDescriptor(URI) - Constructor for class gov.va.vinci.leo.descriptors.LeoPearDescriptor
 
LeoProperties - Class in gov.va.vinci.leo.tools
Handles loading Properties from the leo.properties file including setting defaults initially and storing values we expect from that properties file.
LeoProperties() - Constructor for class gov.va.vinci.leo.tools.LeoProperties
 
LeoRemoteAEDescriptor - Class in gov.va.vinci.leo.descriptors
Create and modify remote service analysis engine descriptors in order to include remote services in an aggregate.
LeoRemoteAEDescriptor() - Constructor for class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
Default constructor creates a blank remote service descriptor.
LeoRemoteAEDescriptor(CustomResourceSpecifier) - Constructor for class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
Initialize with the CustomResourceSpecifier that represents a remote service.
LeoRemoteAEDescriptor(String, boolean, NameValue...) - Constructor for class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
Import an XML descriptor and use it as the model.
LeoRemoteAEDescriptor(String, String) - Constructor for class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
Create a remote descriptor with the BrokerURL and Endpoint parameters completed.
LeoRemoteAEDescriptor.Param - Class in gov.va.vinci.leo.descriptors
Default params for remote service descriptors.
LeoRemoteAnnotator - Class in gov.va.vinci.leo.ae
Create an annotator that sends each CAS received to a remote service.
LeoRemoteAnnotator(String, String) - Constructor for class gov.va.vinci.leo.ae.LeoRemoteAnnotator
Create a new LeoRemoteAnnotator with the brokerURL and endPoint variables specified.
LeoRemoteAnnotator(String, String, String) - Constructor for class gov.va.vinci.leo.ae.LeoRemoteAnnotator
Create a new LeoRemoteAnnotator with the brokerURL, endPoint, and annotator name specified.
LeoTypeSystemDescription - Class in gov.va.vinci.leo.descriptors
Stores a type system description gov.va.vinci.leo.model that is used for import and creation of type objects.
LeoTypeSystemDescription(TypeDescription...) - Constructor for class gov.va.vinci.leo.descriptors.LeoTypeSystemDescription
Create an initial, empty TypeSystemDescription.
LeoTypeSystemDescription(TypeSystemDescription) - Constructor for class gov.va.vinci.leo.descriptors.LeoTypeSystemDescription
Set the initial underlying TypeSystemDescription to the object reference provided.
LeoTypeSystemDescription(String, boolean) - Constructor for class gov.va.vinci.leo.descriptors.LeoTypeSystemDescription
Import the TypeSystemDescription from the descriptor provided either by name or by path.
LeoTypeSystemDescription(String, String, String) - Constructor for class gov.va.vinci.leo.descriptors.LeoTypeSystemDescription
Create a new TypeSystem then add a type object with the name (aType), description, and name of the super type.
LeoUtils - Class in gov.va.vinci.leo.tools
Commonly used functions.
LeoUtils() - Constructor for class gov.va.vinci.leo.tools.LeoUtils
 
lineEnd - Variable in class gov.va.vinci.leo.tools.CSVWriterBuilder
 
listFiles(File, FileFilter, boolean) - Static method in class gov.va.vinci.leo.tools.LeoUtils
Return a list of File Objects in a directory.
loadConfigFile(String, String...) - Static method in class gov.va.vinci.leo.tools.LeoUtils
Load the config file(s).
loadDefaults() - Method in class gov.va.vinci.leo.tools.LeoProperties
Load default values for required parameters.
loadJMXAgent(int) - Method in class gov.va.vinci.leo.tools.JamService
Load the JMX Agent for gathering statistics via JMX on this running service.
loadProperties(Properties) - Method in class gov.va.vinci.leo.tools.LeoProperties
Load the properties from a properties object.
loadprops(String) - Method in class gov.va.vinci.leo.tools.LeoProperties
Load the properties file specified by the user.
loadprops() - Method in class gov.va.vinci.leo.tools.LeoProperties
Load the properties from the properties file that will be used for execution.
LocalhostIPAddress - Class in gov.va.vinci.leo.tools
 
LocalhostIPAddress() - Constructor for class gov.va.vinci.leo.tools.LocalhostIPAddress
 
LOG - Static variable in class gov.va.vinci.leo.Client
Logger object.
LOG - Variable in class gov.va.vinci.leo.cr.BaseFileCollectionReader
Logger for class.
LOG - Static variable in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Logging object of output.
log - Static variable in class gov.va.vinci.leo.descriptors.LeoTypeSystemDescription
Logging object of output.
LOG - Variable in class gov.va.vinci.leo.listener.BaseDatabaseListener
Logging object of output.
LOG - Variable in class gov.va.vinci.leo.listener.BaseListener
Logging object of output.
log - Static variable in class gov.va.vinci.leo.listener.SimpleXmiListener
Logging object of output.
LOG - Static variable in class gov.va.vinci.leo.tools.CasTools
Class log.
LOG - Static variable in class gov.va.vinci.leo.tools.LeoProperties
Logging object of output.
logErrors - Variable in class gov.va.vinci.leo.listener.BaseListener
If true, the base listener will log errors via log4j.
logger - Static variable in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Logger object for messaging.
LOGGER - Static variable in class gov.va.vinci.leo.Service
Logger for this class.
LOGGER - Static variable in class gov.va.vinci.leo.tools.JamService
Logger for this class.
LOGGER - Static variable in class gov.va.vinci.leo.tools.LocalhostIPAddress
Logger for this class.

M

mAEDescriptor - Variable in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
AnalysisEngineDescription reference object.
mAggregateDescriptorFile - Variable in class gov.va.vinci.leo.tools.LeoProperties
File path to the aggregate descriptor.
main(String[]) - Static method in class gov.va.vinci.leo.CommandLineClient
Main method for java execution.
main(String[]) - Static method in class gov.va.vinci.leo.tools.GenerateDescriptors
Main method for running from the command line.
mAppCtx - Variable in class gov.va.vinci.leo.Client
Application execution map used primarily by the client.
mAppCtx - Variable in class gov.va.vinci.leo.Service
Application execution map used primarily by the client.
maxOffset - Variable in class gov.va.vinci.leo.cr.SQLServerPagedDatabaseCollectionReader
The maximum record offset to get.
maxRecordNumber - Variable in class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
Max record ID.
mBrokerURL - Variable in class gov.va.vinci.leo.tools.LeoProperties
Broker URL for the remote service.
mCasPoolSize - Variable in class gov.va.vinci.leo.tools.LeoProperties
CAS pool size determines the max number of requests that can be outstanding.
mCCTimeout - Variable in class gov.va.vinci.leo.tools.LeoProperties
CAS complete timeout in seconds.
mColumnNames - Variable in class gov.va.vinci.leo.tools.db.LeoArrayListHandler
Map of column name to index location in the result set.
mConn - Variable in class gov.va.vinci.leo.tools.db.LeoDataSource
Database connection object.
mDelegateNames - Variable in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Names of the delegate engines for aggregates only.
mDelegates - Variable in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Delegate AnalysisEngineDescriptors for aggregates only.
mDeleteOnExit - Variable in class gov.va.vinci.leo.tools.LeoProperties
Should the generated XML descriptors be deleted on program exit? Default is true.
mDeploymentDescriptorFile - Variable in class gov.va.vinci.leo.tools.LeoProperties
File path to the deployment descriptor for the AS service that will be deployed.
mDescriptorDirectory - Variable in class gov.va.vinci.leo.tools.LeoProperties
The path to the directory where descriptors will be generated.
mDescriptorLocator - Variable in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
The locator for this descriptor.
mDescriptorLocator - Variable in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
Location of the XML representation of this descriptor.
mDriver - Variable in class gov.va.vinci.leo.tools.db.LeoDataSource
JDBC driver class name.
mEncoding - Variable in class gov.va.vinci.leo.cr.BaseFileCollectionReader
Encoding type for the files being read in.
mEndpoint - Variable in class gov.va.vinci.leo.tools.LeoProperties
Endpoint or Input Queue Name for the service.
MetaDataObjectFactory - Class in gov.va.vinci.leo.descriptors
Allows creating Metadata object and access methods to parse TypeSystemDescription XMLs.
MetaDataObjectFactory() - Constructor for class gov.va.vinci.leo.descriptors.MetaDataObjectFactory
 
metrics(boolean) - Method in class gov.va.vinci.leo.tools.JetmPerformance
Return the current JETM performance metrics.
metrics(boolean) - Method in interface gov.va.vinci.leo.tools.JetmPerformanceMBean
Return the current JETM performance metrics.
mFileCollection - Variable in class gov.va.vinci.leo.cr.BaseFileCollectionReader
Array of File objects being processed.
mFileIndex - Variable in class gov.va.vinci.leo.cr.BaseFileCollectionReader
Index of the next file to be processed.
mFlowConstraints - Variable in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Flow constraints for aggregates not using a fixed flow.
mFSHeapSize - Variable in class gov.va.vinci.leo.tools.LeoProperties
FS heap size in bytes of each CAS in the pool.
mInDir - Variable in class gov.va.vinci.leo.cr.BaseFileCollectionReader
Input Directory File object to be searched for available files.
mInitTimeout - Variable in class gov.va.vinci.leo.tools.LeoProperties
Initialization timeout period in seconds.
minRecordNumber - Variable in class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
Min record ID.
mIsAsync - Variable in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
For an aggregate engine deployment will this aggregate be executed asynchronously, if false (default) then the engine will be executed and scaled as a unit, if true then the delegate engines will each be scaled individually.
mJamJmxPort - Variable in class gov.va.vinci.leo.tools.LeoProperties
If registering with JAM, this is the port the local JMX Server will listen on.
mJamQueryIntervalInSeconds - Variable in class gov.va.vinci.leo.tools.LeoProperties
If registering with JAM, what is the monitor query interval in seconds.
mJamResetStatisticsAfterQuery - Variable in class gov.va.vinci.leo.tools.LeoProperties
If registering with JAM, should statistics be reset after each gather? Default is true.
mJamServerBaseUrl - Variable in class gov.va.vinci.leo.tools.LeoProperties
The base url for the Jam (JMX Analytics Monitoring) server if available.
mNumberOfInstances - Variable in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
The number of instances of this Engine to execute in parellel on the service.
mOutputDir - Variable in class gov.va.vinci.leo.listener.BaseListener
Output Directory for this gov.va.vinci.leo.listener output if required.
mPropertiesFile - Variable in class gov.va.vinci.leo.tools.LeoProperties
Name and location of the properties file.
mRecordList - Variable in class gov.va.vinci.leo.cr.BaseDatabaseCollectionReader
List of Records that were returned by the query.
mRecurse - Variable in class gov.va.vinci.leo.cr.BaseFileCollectionReader
Recurse flag we will search recursively in sub-directories if true.
mRemoteDescriptor - Variable in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
Resource specifier reference object.
mResultSetMetaData - Variable in class gov.va.vinci.leo.tools.db.LeoArrayListHandler
Metadata from the ResultSet passed into the handle method.
mRowIndex - Variable in class gov.va.vinci.leo.cr.BaseDatabaseCollectionReader
Index of the current analyte being processed, -1 if the query has not yet been executed.
mServiceName - Variable in class gov.va.vinci.leo.tools.LeoProperties
Name of the service for deployment.
mTimeout - Variable in class gov.va.vinci.leo.tools.LeoProperties
Timeout period in seconds.
mUAEngine - Variable in class gov.va.vinci.leo.Client
UIMA Asynchronous Engine object used to deploy the server and later to init and run the client side of the service also.
mUAEngine - Variable in class gov.va.vinci.leo.Service
UIMA Asynchronous Engine object used to deploy the server and later to init and run the client side of the service also.
mUrl - Variable in class gov.va.vinci.leo.tools.db.LeoDataSource
JDBC database connection URL.

N

name - Variable in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Optional, Name of the annotator to be set in the descriptor.
name - Variable in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
Parameter object where the name is stored.
name - Variable in class gov.va.vinci.leo.model.NameValue
The name of the parameter to set.
NameValue - Class in gov.va.vinci.leo.model
Stores name, value pair.
NameValue(String, Object) - Constructor for class gov.va.vinci.leo.model.NameValue
Constructor with initial name and value input arguments.
noteColumn - Variable in class gov.va.vinci.leo.cr.DatabaseCollectionReader
Zero based index of the note column in the query.
numberOfCASesProcessed - Variable in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Counter for the number of CASes this annotator has processed.
numberOfFilteredCASesProcessed - Variable in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Counter for the number of CASes that made it past the filter for processing.
numInstances - Variable in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Number of replication instances for this annotator.
numReceived - Variable in class gov.va.vinci.leo.listener.BaseListener
Number of CAS objects returned from the pipeline.
numSent - Variable in class gov.va.vinci.leo.listener.BaseListener
Number of CAS objects sent to the service for processing.

O

onBeforeMessageSend(UimaASProcessStatus) - Method in class gov.va.vinci.leo.listener.BaseListener
Called before sending a CAS to the pipeline, If we were timing each CAS individually this is where we would want to capture individual start times.
outputType - Variable in class gov.va.vinci.leo.ae.LeoBaseAnnotator
The output type that will be created for each matching window.

P

pageSize - Variable in class gov.va.vinci.leo.cr.SQLServerPagedDatabaseCollectionReader
Size of each batch to pull.
Param() - Constructor for class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor.Param
 
parseMappingString(String) - Static method in class gov.va.vinci.leo.tools.LeoUtils
Convert the JSON formatted string into a Map of Strings.
password - Variable in class gov.va.vinci.leo.cr.BaseDatabaseCollectionReader
Password for this database.
performanceReport - Variable in class gov.va.vinci.leo.Client
Holds performance report data from the engine after processing is complete.
PipelineInterface - Interface in gov.va.vinci.leo.pipeline
Defines the API for returning a pipeline and the associated type system.
preparedStatementSQL - Variable in class gov.va.vinci.leo.listener.BaseDatabaseListener
The insert statement sql.
previousReferenceId - Variable in class gov.va.vinci.leo.listener.BaseListener
Use to work around a bug in 2.4.2 where UIMA calls the onBeforeMessageSend one extra time on the last document.
printUsage() - Static method in class gov.va.vinci.leo.CommandLineClient
Print the command line usage statement to the console and exit.
process(JCas) - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Called once by the UIMA Framework for each document being analyzed (each CAS instance).
processBatch() - Method in class gov.va.vinci.leo.listener.BaseDatabaseListener
This is called when a batch is ready to be send to the database.
produceCollectionReader() - Method in class gov.va.vinci.leo.cr.BaseLeoCollectionReader
Generate a new CollectionReaderDescription from the current reader and reader parameters.
produceCollectionReader() - Method in class gov.va.vinci.leo.cr.ExternalCollectionReader
Generate the UIMA Collection reader with resources.
produceCollectionReader() - Method in interface gov.va.vinci.leo.cr.LeoCollectionReaderInterface
Generate the UIMA CollectionReader with resources.
PROPERTIES_DEFAULT - Static variable in class gov.va.vinci.leo.tools.LeoProperties
Default value for the Properties File path.
ps - Variable in class gov.va.vinci.leo.listener.BaseDatabaseListener
The prepared statement for inserting a record.

Q

query - Variable in class gov.va.vinci.leo.cr.DatabaseCollectionReader
Query to be used to get the data.
query(String) - Method in class gov.va.vinci.leo.tools.db.DataManager
Execute a SQL query against the database and capture the ResultSet.
query(String, Object...) - Method in class gov.va.vinci.leo.tools.db.DataManager
Execute a SQL query against the database and capture the ResultSet.
quotechar - Variable in class gov.va.vinci.leo.tools.CSVWriterBuilder
 

R

randomBatches - Variable in class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
Number of random batches to pull.
reader - Variable in class gov.va.vinci.leo.cr.ExternalCollectionReader
Reference to the external CollectionReader object that will do the real work of getting the data.
referenceID - Variable in class gov.va.vinci.leo.listener.BaseListener
ID of the document received in an entityProcessComplete event.
registerJetm() - Static method in class gov.va.vinci.leo.tools.JetmPerformance
Registers JETM with the MBeanServer in the JVM.
registerServiceQueue(String, String, int, boolean, boolean) - Method in class gov.va.vinci.leo.tools.JamService
Registers a new service queue in Jam.
registerWithJam() - Method in class gov.va.vinci.leo.Service
Call the appropriate JAM web services to register this service with jam.
RemoteEngineFactory - Class in gov.va.vinci.leo.descriptors
Generate a CustomResourceSpecifier that describes a remote service to be included in the pipeline.
RemoteEngineFactory() - Constructor for class gov.va.vinci.leo.descriptors.RemoteEngineFactory
 
removeServerFromServiceQueue(String, String, String, int) - Method in class gov.va.vinci.leo.tools.JamService
Remove a host/port from a service queue.
removeServiceQueue(String) - Method in class gov.va.vinci.leo.tools.JamService
Removes a service queue, and all related hosts and monitoring jobs.
resetMetrics() - Method in class gov.va.vinci.leo.tools.JetmPerformance
Resets JETM metrics immediately.
resetMetrics() - Method in interface gov.va.vinci.leo.tools.JetmPerformanceMBean
Resets JETM metrics immediately.
resetNumberOfCASesProcessed() - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Set the number of CASes this annotator has processed.
resetNumberOfFilteredCASesProcessed() - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Reset the number of filtered CASes processed.
resourceSpecifier - Variable in class gov.va.vinci.leo.descriptors.LeoPearDescriptor
 
ResourceSpecifierFactory - Class in gov.va.vinci.leo.descriptors
Factory for create UIMA resources.
ResourceSpecifierFactory() - Constructor for class gov.va.vinci.leo.descriptors.ResourceSpecifierFactory
 
run(UimaAsBaseCallbackListener...) - Method in class gov.va.vinci.leo.Client
Run with the collection reader that is already set in the client.
run(LeoCollectionReaderInterface, UimaAsBaseCallbackListener...) - Method in class gov.va.vinci.leo.Client
Execute the AS pipeline using the LeoCollectionReaderInterface object.
run(InputStream, UimaAsBaseCallbackListener...) - Method in class gov.va.vinci.leo.Client
Run the pipeline on one document at a time using the document text provided.
run(String, UimaAsBaseCallbackListener...) - Method in class gov.va.vinci.leo.Client
Run the pipeline on one document at a time using the document text provided.
run(CAS, UimaAsBaseCallbackListener...) - Method in class gov.va.vinci.leo.Client
Run the pipeline on a single CAS object.
runClient() - Method in class gov.va.vinci.leo.CommandLineClient
Actual run method that configures and runs the client.
runGather(String, String) - Method in class gov.va.vinci.leo.tools.JamService
Given a queuename and broker, do an immediate gather of stats.
runScript(Reader) - Method in class gov.va.vinci.leo.tools.db.JdbcScriptRunner
Runs an SQL script (read in using the Reader parameter)

S

safeClose(InputStream) - Static method in class gov.va.vinci.leo.tools.StreamUtils
 
safeClose(OutputStream) - Static method in class gov.va.vinci.leo.tools.StreamUtils
 
secureRandom - Static variable in class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
Generates the random batch number if random batches are indicated.
separator - Variable in class gov.va.vinci.leo.tools.CSVWriterBuilder
 
serialize() - Method in class gov.va.vinci.leo.descriptors.DeployDescriptorFactory
Create a deployment descriptor file from the map data.
serialize() - Method in interface gov.va.vinci.leo.descriptors.DeployDescriptorWriter
Serialize the deployment descriptor to a file.
serialize(T, Type, JsonSerializationContext) - Method in class gov.va.vinci.leo.tools.LeoInheritanceGsonAdapter
Gson invokes this call-back method during serialization when it encounters a field of the specified type.
Service - Class in gov.va.vinci.leo
This object will deploy a UIMA AS server from the list of primitive descriptor files provided by the caller.
Service() - Constructor for class gov.va.vinci.leo.Service
Default constructor loads the application execution variables from the properties file.
Service(Map<String, Object>) - Constructor for class gov.va.vinci.leo.Service
Loads the application execution variables from the map.
Service(String) - Constructor for class gov.va.vinci.leo.Service
Constructor which first sets a new properties file then calls the default constructor to load the properties.
serviceSectionXML(TransformerHandler) - Method in class gov.va.vinci.leo.descriptors.LeoDeployDescriptor
Serialize the service section.
setAEDescriptor(AnalysisEngineDescription) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Assign the AnalysisEngineDescription model for this LeoAEDescriptor object.
setAggregateDescriptorFile(String) - Method in class gov.va.vinci.leo.tools.LeoProperties
Set the file path to the aggregate descriptor.
setAllowedValues(AllowedValue[]) - Method in class gov.va.vinci.leo.descriptors.TypeDescriptionBuilder
Set the allowed values in this type description.
setAnalysisEngineDescription(String, boolean) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Generate the AnalysisEngineDescription object from the descriptor file and set it as the internal gov.va.vinci.leo.model for this LeoAEDescriptor.
setAnalysisEngineDescription(AnalysisEngineDescription) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Set the AnalysisEngineDescription object that will be the core gov.va.vinci.leo.model for this LeoAEDescriptor.
setAnnotationTypeFilter(String...) - Method in class gov.va.vinci.leo.listener.BaseListener
Sets a list of annotation types.
setBatchSize(int) - Method in class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
Set the batch size.
setBatchSize(int) - Method in class gov.va.vinci.leo.listener.BaseDatabaseListener
Set the batch size for the number of records to accumulate before executing the batch.
setBrokerURL(String) - Method in class gov.va.vinci.leo.descriptors.LeoDeployDescriptor
Set the broker url for this deployment descriptor.
setBrokerURL(String) - Method in class gov.va.vinci.leo.tools.LeoProperties
set the broker url.
setCasPoolSize(int) - Method in class gov.va.vinci.leo.descriptors.LeoDeployDescriptor
Set the cas pool size for this deployment.
setCasPoolSize(Integer) - Method in class gov.va.vinci.leo.tools.LeoProperties
Set the size of the CAS pool.
setCCTimeout(Integer) - Method in class gov.va.vinci.leo.tools.LeoProperties
CAS complete timeout in seconds.
setClient(HttpClient) - Method in class gov.va.vinci.leo.tools.JamService
Set the HttpClient to use for communication.
setClientProperties(Client) - Method in class gov.va.vinci.leo.CommandLineClient
Set the client properties, such as brokerURL, from a pre-loaded groovy config file.
setConsoleOut(boolean) - Method in class gov.va.vinci.leo.tools.db.JdbcScriptRunner
Set the console output flag.
setDeleteOnExit(boolean) - Method in class gov.va.vinci.leo.tools.LeoProperties
Set the flag to TRUE if generated descriptors should be deleted on program exit.
setDelimiter(String, boolean) - Method in class gov.va.vinci.leo.tools.db.JdbcScriptRunner
 
setDeploymentDescriptorFile(String) - Method in class gov.va.vinci.leo.tools.LeoProperties
Set the existing Deployment Descriptor file to use.
setDescription(String) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Sets the description of this Resource.
setDescription(String) - Method in class gov.va.vinci.leo.descriptors.LeoDeployDescriptor
Set the description for this deployment descriptor.
setDescription(String) - Method in class gov.va.vinci.leo.descriptors.TypeDescriptionBuilder
Set a description for this type description.
setDescriptor(LeoPearDescriptor) - Method in class gov.va.vinci.leo.ae.LeoPearAnnotator
 
setDescriptorDirectory(String) - Method in class gov.va.vinci.leo.tools.LeoProperties
Set the directory path where generated descriptors will be generated.
setDescriptorLocator(URI) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Set the location where the descriptor should be generated.
setDescriptorLocator(URI) - Method in interface gov.va.vinci.leo.descriptors.LeoDelegate
Set the location where the descriptor should be generated.
setDescriptorLocator(URI) - Method in class gov.va.vinci.leo.descriptors.LeoPearDescriptor
 
setDescriptorLocator(URI) - Method in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
Set the location where the descriptor should be generated.
setDriver(String) - Method in class gov.va.vinci.leo.cr.BaseDatabaseCollectionReader
Set the driver name for this reader.
setDriver(String) - Method in class gov.va.vinci.leo.model.DatabaseConnectionInformation
Set database driver classname.
setEncoding(String) - Method in class gov.va.vinci.leo.cr.BaseFileCollectionReader
Set the file encoding from the encoding string provided.
setEndpoint(String) - Method in class gov.va.vinci.leo.descriptors.LeoDeployDescriptor
Set the endpoint for this deployment descriptor.
setEndpoint(String) - Method in class gov.va.vinci.leo.tools.LeoProperties
Set the "InputQueueName" for this service.
setErrorLogWriter(PrintWriter) - Method in class gov.va.vinci.leo.tools.db.JdbcScriptRunner
Setter for errorLogWriter property
setEscapechar(char) - Method in class gov.va.vinci.leo.listener.BaseCsvListener
Set the escape character.
setEscapechar(char) - Method in class gov.va.vinci.leo.tools.CSVWriterBuilder
 
setExcludeTypesFilter(String...) - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Set the list of exclude types.
setExitOnError(boolean) - Method in class gov.va.vinci.leo.listener.BaseListener
Set the flag that if true will cause the entityProcessComplete method to return when an error occurs.
setFeatures(FeatureDescription[]) - Method in class gov.va.vinci.leo.descriptors.TypeDescriptionBuilder
Set the feature descriptions for this type description.
setFilenameFilter(FilenameFilter) - Method in class gov.va.vinci.leo.cr.BaseFileCollectionReader
Set the FilenameFilter that this object will use to filter the files found in the input directory.
setFirstOffset(int) - Method in class gov.va.vinci.leo.cr.SQLServerPagedDatabaseCollectionReader
Set the first row offset.
setFSHeapSize(int) - Method in class gov.va.vinci.leo.tools.LeoProperties
Size of the FS heap in bytes of each CAS in the pool.
setID(String) - Method in class gov.va.vinci.leo.types.CSI
setter for ID - sets ID number of the Analyte being analyzed
setID(int, String) - Method in class gov.va.vinci.leo.types.CSI_Type
 
setIdColumn(String) - Method in class gov.va.vinci.leo.cr.DatabaseCollectionReader
Set the ID column to be used.
setIdColumn(String) - Method in class gov.va.vinci.leo.model.DataQueryInformation
Set the id column index, 0 based.
setImplementationName(String) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Sets the name of this ResourceCreationSpecifier's implementation.
setIncludeFeatures(boolean) - Method in class gov.va.vinci.leo.listener.SimpleCsvListener
Set the includeFeatures flag value, if true then include feature values in the output.
setIncludeHeader(boolean) - Method in class gov.va.vinci.leo.listener.BaseCsvListener
Set the boolean flag that if true will cause the listener to include a header row.
setIncludeTypesFilter(String...) - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Set one or more types to filter on.
setInitialFsHeapSize(int) - Method in class gov.va.vinci.leo.descriptors.LeoDeployDescriptor
set the initial fs heap size for this deployment.
setInitTimeout(int) - Method in class gov.va.vinci.leo.tools.LeoProperties
Initialization timeout period in seconds.
setInputDirectory(File) - Method in class gov.va.vinci.leo.cr.BaseFileCollectionReader
Set the inputDirectory for this FileSubReader object.
setInputQueueName(String) - Method in class gov.va.vinci.leo.tools.LeoProperties
Set the "InputQueueName" for this service.
setInputType(String...) - Method in class gov.va.vinci.leo.listener.BaseListener
Set the array of input type names.
setInputTypes(String...) - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Set the input types list.
setIsAsync(boolean) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Set the async flag for an aggregate deployment only, see the isAsync method for more information about flag usage.
setIsDeleteOnExit(boolean) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Set the flag to TRUE if generated descriptors should be deleted when the program exits, FALSE to persist them.
setIsDeleteOnExit(boolean) - Method in interface gov.va.vinci.leo.descriptors.LeoDelegate
Set the flag to TRUE if generated descriptors should be deleted when the program exits, FALSE to persist them.
setIsDeleteOnExit(boolean) - Method in class gov.va.vinci.leo.descriptors.LeoPearDescriptor
 
setIsDeleteOnExit(boolean) - Method in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
Set the flag to TRUE if generated descriptors should be deleted when the program exits, FALSE to persist them.
setJamJmxPort(Integer) - Method in class gov.va.vinci.leo.tools.LeoProperties
If registering with JAM, this is the port the local JMX Server will listen on.
setJamQueryIntervalInSeconds(Integer) - Method in class gov.va.vinci.leo.tools.LeoProperties
If registering with JAM, the monitor query interval in seconds.
setJamResetStatisticsAfterQuery(Boolean) - Method in class gov.va.vinci.leo.tools.LeoProperties
If registering with JAM, should statistics be reset after each gather? Default is true.
setJamServerBaseUrl(String) - Method in class gov.va.vinci.leo.tools.JamService
Set the JAM server base url.
setJamServerBaseUrl(String) - Method in class gov.va.vinci.leo.tools.LeoProperties
The base URL for the JAM (JMX Analytics Monitoring) server if available.
setLaunchAnnotationViewer(boolean) - Method in class gov.va.vinci.leo.listener.SimpleXmiListener
Set the value of launch annotation viewer.
setLeoCollectionReader(LeoCollectionReaderInterface) - Method in class gov.va.vinci.leo.Client
Set the collection reader for this client.
setLeoTypeSystemDescription(LeoTypeSystemDescription) - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Set the type system for this annotator.
setLineEnd(String) - Method in class gov.va.vinci.leo.listener.BaseCsvListener
Set the line ending.
setLineEnd(String) - Method in class gov.va.vinci.leo.tools.CSVWriterBuilder
 
setLocator(String) - Method in class gov.va.vinci.leo.types.CSI
setter for Locator - sets File path or query information to allow us to find this record again.
setLocator(int, String) - Method in class gov.va.vinci.leo.types.CSI_Type
 
setLogErrors(boolean) - Method in class gov.va.vinci.leo.listener.BaseListener
Set whether or not to log errors to log4j.
setLoginTimeout(int) - Method in class gov.va.vinci.leo.tools.db.LeoDataSource
Sets the maximum time in seconds that this data source will wait while attempting to connect to a database.
setLogWriter(PrintWriter) - Method in class gov.va.vinci.leo.tools.db.JdbcScriptRunner
Setter for logWriter property
setLogWriter(PrintWriter) - Method in class gov.va.vinci.leo.tools.db.LeoDataSource
Sets the log writer for this DataSource object to the given java.io.PrintWriter object.
setMaxOffset(int) - Method in class gov.va.vinci.leo.cr.SQLServerPagedDatabaseCollectionReader
Set the max offset.
setMaxRecordNumber(int) - Method in class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
Set the maximum row number.
setMinRecordNumber(int) - Method in class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
Set the minimum row number.
setModifiesCas(boolean) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Sets whether this component will modify the CAS.
setMultipleDeploymentAllowed(boolean) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Sets whether multiple instances of this component can be run in parallel, each receiving a subset of the documents from a collection.
setName(String) - Method in class gov.va.vinci.leo.ae.ExternalAnnotator
Set the name of this annotator.
setName(String) - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Set the name of this annotator.
setName(String) - Method in class gov.va.vinci.leo.ae.LeoPearAnnotator
 
setName(String) - Method in class gov.va.vinci.leo.ae.LeoRemoteAnnotator
Set the name of this annotator.
setName(String) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Sets the name of this Resource.
setName(String) - Method in interface gov.va.vinci.leo.descriptors.LeoDelegate
Set the name of this delegate, return a reference to the delegate type object in each implementation.
setName(String) - Method in class gov.va.vinci.leo.descriptors.LeoDeployDescriptor
Set the name of the Deployment.
setName(String) - Method in class gov.va.vinci.leo.descriptors.LeoPearDescriptor
 
setName(String) - Method in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
Set the name of this remote service, return a reference to the delegate type object in each implementation.
setName(String) - Method in class gov.va.vinci.leo.descriptors.TypeDescriptionBuilder
Set a name for this type description.
setName(String) - Method in class gov.va.vinci.leo.model.FeatureNameType
Set the name of the feature.
setName(String) - Method in class gov.va.vinci.leo.model.NameValue
Set name.
setNoteColumn(String) - Method in class gov.va.vinci.leo.cr.DatabaseCollectionReader
Set the note column name.
setNoteColumn(String) - Method in class gov.va.vinci.leo.model.DataQueryInformation
Set the note column index, 0 based.
setNumberOfInstances(int) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
 
setNumInstances(int) - Method in class gov.va.vinci.leo.ae.ExternalAnnotator
Set the number of instances of this annotator in the pipeline.
setNumInstances(int) - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Set the number of instances of this annotator in the pipeline.
setOutputDir(File) - Method in class gov.va.vinci.leo.listener.BaseListener
Set the output directory for this listener.
setOutputProperty(String, String) - Method in class gov.va.vinci.leo.tools.XMLSerializer
Allow the user to specify arbitrary properties for output.
setOutputsNewCASes(boolean) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Sets whether this AnalysisEngine may output new CASes.
setOutputStream(String) - Method in class gov.va.vinci.leo.tools.XMLSerializer
Set the OutputStream for this serializer from a String file name.
setOutputStream(File) - Method in class gov.va.vinci.leo.tools.XMLSerializer
Set the OutputStream for this serializer from a File Handle.
setOutputStream(OutputStream) - Method in class gov.va.vinci.leo.tools.XMLSerializer
Set the OutputStream for this serializer.
setOutputType(String) - Method in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Set the output type name.
setPageSize(int) - Method in class gov.va.vinci.leo.cr.SQLServerPagedDatabaseCollectionReader
Set the page size.
setParameterSetting(String, Object) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Set the parameter with the name to the value.
setParameterSetting(NameValue) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Set a parameter from a NameValue object.
setParameterSetting(String, String) - Method in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
Set the remote parameter setting.
setParameterSetting(NameValue) - Method in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
Set the remote service parameter from the NameValue pair information provided.
setParameterSetting(Parameter) - Method in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
Set the remote service parameter from the Parameter name and value information.
setPassword(String) - Method in class gov.va.vinci.leo.cr.BaseDatabaseCollectionReader
Set the database password.
setPassword(String) - Method in class gov.va.vinci.leo.model.DatabaseConnectionInformation
Set the connection password.
setPropertiesKeys(StringArray) - Method in class gov.va.vinci.leo.types.CSI
setter for PropertiesKeys - sets
setPropertiesKeys(int, String) - Method in class gov.va.vinci.leo.types.CSI
indexed setter for PropertiesKeys - sets an indexed value -
setPropertiesKeys(int, int) - Method in class gov.va.vinci.leo.types.CSI_Type
 
setPropertiesKeys(int, int, String) - Method in class gov.va.vinci.leo.types.CSI_Type
 
setPropertiesValues(StringArray) - Method in class gov.va.vinci.leo.types.CSI
setter for PropertiesValues - sets
setPropertiesValues(int, String) - Method in class gov.va.vinci.leo.types.CSI
indexed setter for PropertiesValues - sets an indexed value -
setPropertiesValues(int, int) - Method in class gov.va.vinci.leo.types.CSI_Type
 
setPropertiesValues(int, int, String) - Method in class gov.va.vinci.leo.types.CSI_Type
 
setQuery(String) - Method in class gov.va.vinci.leo.cr.DatabaseCollectionReader
Set the database query used to pull data.
setQuery(String) - Method in class gov.va.vinci.leo.model.DataQueryInformation
Set the query.
setQuotechar(char) - Method in class gov.va.vinci.leo.listener.BaseCsvListener
Set the quote character.
setQuotechar(char) - Method in class gov.va.vinci.leo.tools.CSVWriterBuilder
 
setRandomBatches(int) - Method in class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
Set the number of random batches.
setRecurseFlag(boolean) - Method in class gov.va.vinci.leo.cr.BaseFileCollectionReader
Set the recurse flag for this property.
setRowData(StringArray) - Method in class gov.va.vinci.leo.types.CSI
setter for RowData - sets
setRowData(int, String) - Method in class gov.va.vinci.leo.types.CSI
indexed setter for RowData - sets an indexed value -
setRowData(int, int) - Method in class gov.va.vinci.leo.types.CSI_Type
 
setRowData(int, int, String) - Method in class gov.va.vinci.leo.types.CSI_Type
 
setSeparator(char) - Method in class gov.va.vinci.leo.listener.BaseCsvListener
Set the separator character.
setSeparator(char) - Method in class gov.va.vinci.leo.tools.CSVWriterBuilder
 
setServiceName(String) - Method in class gov.va.vinci.leo.tools.LeoProperties
Optional, name of the service to deploy.
setSupertypeName(String) - Method in class gov.va.vinci.leo.descriptors.TypeDescriptionBuilder
Set a super type for this type description.
setTimeout(int) - Method in class gov.va.vinci.leo.tools.LeoProperties
Timeout period in seconds.
setTopDescriptor(String, boolean) - Method in class gov.va.vinci.leo.descriptors.LeoDeployDescriptor
Set the top descriptor for this deployment by importing the descriptor by name or value.
setTopDescriptor(LeoAEDescriptor) - Method in class gov.va.vinci.leo.descriptors.LeoDeployDescriptor
Set the top descriptor for this deployment to the LeoAEDescriptor object provided.
setType(String) - Method in class gov.va.vinci.leo.model.FeatureNameType
Set the UIMA Type of the feature.
setTypeSystemDescription(LeoTypeSystemDescription) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
This method sets the type system description for this analysis engine to the TypeSystem provided.
setTypeSystemDescription(TypeSystemDescription) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Set the type system description for this analysis engine to the TypeSystem provided.
setTypeSystemDescriptor(File) - Method in class gov.va.vinci.leo.listener.SimpleXmiListener
Set the type system descriptor File reference that this listener will set in the viewer if launched.
setTypeSystemDescriptor(LeoTypeSystemDescription) - Method in class gov.va.vinci.leo.listener.SimpleXmiListener
Set the type system description this listener will serialize into the output directory.
setURL(String) - Method in class gov.va.vinci.leo.cr.BaseDatabaseCollectionReader
Set the driver URL.
setUrl(String) - Method in class gov.va.vinci.leo.model.DatabaseConnectionInformation
Set the connection URL.
setUsername(String) - Method in class gov.va.vinci.leo.cr.BaseDatabaseCollectionReader
Set the database username.
setUsername(String) - Method in class gov.va.vinci.leo.model.DatabaseConnectionInformation
set the connection username.
setValidateConnectionEachBatch(boolean) - Method in class gov.va.vinci.leo.listener.BaseDatabaseListener
Set the flag that if true will cause the connection to be validated when executing each batch.
setValidationQuery(String) - Method in class gov.va.vinci.leo.model.DatabaseConnectionInformation
Set the validation query for this connection.
setValue(Object) - Method in class gov.va.vinci.leo.model.NameValue
Set the value.
setVersion(String) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Sets the version number of this Resource.
setWriter(Writer) - Method in class gov.va.vinci.leo.tools.XMLSerializer
Set the Writer object for this serializer.
SimpleCsvListener - Class in gov.va.vinci.leo.listener
Note: This is a very simple gov.va.vinci.leo.listener to output one type of annotation and, optionally, its features.
SimpleCsvListener(File) - Constructor for class gov.va.vinci.leo.listener.SimpleCsvListener
Constructor with File parameter.
SimpleCsvListener(OutputStream) - Constructor for class gov.va.vinci.leo.listener.SimpleCsvListener
Constructor with an OutputStream parameter.
SimpleCsvListener(Writer) - Constructor for class gov.va.vinci.leo.listener.SimpleCsvListener
Constructor with a Writer parameter.
SimpleXmiListener - Class in gov.va.vinci.leo.listener
Store processed CAS objects in XMI files then launch the AnnotationViewer once collection processing is complete.
SimpleXmiListener(File) - Constructor for class gov.va.vinci.leo.listener.SimpleXmiListener
Constructor with output directory input.
SQLServerPagedDatabaseCollectionReader - Class in gov.va.vinci.leo.cr
Database CollectionReader that pulls the data in pages of a configurable size from SQL Server.
SQLServerPagedDatabaseCollectionReader() - Constructor for class gov.va.vinci.leo.cr.SQLServerPagedDatabaseCollectionReader
Default constructor used during UIMA initialization.
SQLServerPagedDatabaseCollectionReader(DatabaseConnectionInformation, DataQueryInformation, int) - Constructor for class gov.va.vinci.leo.cr.SQLServerPagedDatabaseCollectionReader
Initialize the reader using the database connection and query information provided, including the size of each batch and optionally the number of random batches to execute.
SQLServerPagedDatabaseCollectionReader(DatabaseConnectionInformation, DataQueryInformation, int, int) - Constructor for class gov.va.vinci.leo.cr.SQLServerPagedDatabaseCollectionReader
Initialize the reader using the database connection and query information provided, including the size of each batch and optionally the number of random batches to execute.
SQLServerPagedDatabaseCollectionReader(String, String, String, String, String, String, String, int) - Constructor for class gov.va.vinci.leo.cr.SQLServerPagedDatabaseCollectionReader
Initialize the reader using the provided connection and query information, including the size of each batch and optionally the number of random batches to execute.
SQLServerPagedDatabaseCollectionReader(String, String, String, String, String, String, String, int, int) - Constructor for class gov.va.vinci.leo.cr.SQLServerPagedDatabaseCollectionReader
Initialize the reader using the provided connection and query information, including the size of each batch and optionally the number of random batches to execute.
SQLServerPagedDatabaseCollectionReader(String, String, String, String, String, String, String, int, int, int) - Constructor for class gov.va.vinci.leo.cr.SQLServerPagedDatabaseCollectionReader
Initialize the reader using the provided connection and query information, including the size of each batch and optionally the number of random batches to execute.
sqlServerPagedQuery - Variable in class gov.va.vinci.leo.cr.SQLServerPagedDatabaseCollectionReader
The SQLServerPageQuery that creates the query for the specific page of records needed at any given time.
SQLServerPagedQuery - Class in gov.va.vinci.leo.tools.db
Helper class for paging through SQL Server records.
SQLServerPagedQuery(String, Integer) - Constructor for class gov.va.vinci.leo.tools.db.SQLServerPagedQuery
Constructor
SQLServerPagedQuery(String, Integer, Integer) - Constructor for class gov.va.vinci.leo.tools.db.SQLServerPagedQuery
Constructor
SQLServerPagedQuery(String, Integer, Integer, Integer) - Constructor for class gov.va.vinci.leo.tools.db.SQLServerPagedQuery
Constructor
StreamUtils - Class in gov.va.vinci.leo.tools
 
StreamUtils() - Constructor for class gov.va.vinci.leo.tools.StreamUtils
 
StringException - Exception in gov.va.vinci.leo.tools
 
StringException() - Constructor for exception gov.va.vinci.leo.tools.StringException
The default constructor.
StringException(String) - Constructor for exception gov.va.vinci.leo.tools.StringException
Constructor with pattern.

T

TextFilter - Interface in gov.va.vinci.leo.tools
Defines methods that provide filter functionality for text.
textFilters - Variable in class gov.va.vinci.leo.cr.BaseLeoCollectionReader
 
TIMEOUT - Static variable in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor.Param
Process CAS timeout in ms.
toASCII7(String) - Static method in class gov.va.vinci.leo.tools.AsciiService
Creates a new string, substituting ASCII-7 characters for all non-ASCII-7 characters in the argument string.
toASCII8(String) - Static method in class gov.va.vinci.leo.tools.AsciiService
Creates a new string, substituting ASCII-7 characters for all non-ASCII-8 characters in the argument string.
toString() - Method in exception gov.va.vinci.leo.tools.StringException
 
toString() - Method in exception gov.va.vinci.leo.tools.XMLException
 
totalNumberOfBatches - Variable in class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
Total number of batches available to be executed in the table.
toXML(String) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Write the descriptor out to a temp XML file with the name provided as filename.
toXML() - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Write the descriptor file out based on the locator information in the object.
toXML() - Method in interface gov.va.vinci.leo.descriptors.LeoDelegate
Write the descriptor file out based on the locator information in the object.
toXML(String) - Method in interface gov.va.vinci.leo.descriptors.LeoDelegate
Write the descriptor out to a temp XML file with the name provided as the base filename.
toXML(String) - Method in class gov.va.vinci.leo.descriptors.LeoDeployDescriptor
Serialize this Deployment Descriptor to a file at the name and path provided.
toXML(OutputStream) - Method in class gov.va.vinci.leo.descriptors.LeoDeployDescriptor
Serialize the deployment descriptor to xml using the output stream provided.
toXML() - Method in class gov.va.vinci.leo.descriptors.LeoPearDescriptor
 
toXML(String) - Method in class gov.va.vinci.leo.descriptors.LeoPearDescriptor
 
toXML() - Method in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
 
toXML(String) - Method in class gov.va.vinci.leo.descriptors.LeoRemoteAEDescriptor
 
toXML(String) - Method in class gov.va.vinci.leo.descriptors.LeoTypeSystemDescription
Serialize the TypeSystemDescription to xml using the path and filename provided.
toXml10(String) - Static method in class gov.va.vinci.leo.tools.XmlFilter
Return a copy of the input string with non XML-1.0 characters replaced by spaces.
type - Static variable in class gov.va.vinci.leo.types.CSI
 
TYPE_DESCRIPTION_NAME - Static variable in class gov.va.vinci.leo.listener.SimpleXmiListener
Name of the type system description which this listener will serialize if the typeSystemDescriptor is set.
TypeDescriptionBuilder - Class in gov.va.vinci.leo.descriptors
Improve the Type building system in UIMA with a builder.
typeDescriptionFile - Variable in class gov.va.vinci.leo.listener.SimpleXmiListener
File pointer to the serialized type description.
typeIndexID - Static variable in class gov.va.vinci.leo.types.CSI
 
typeIndexID - Static variable in class gov.va.vinci.leo.types.CSI_Type
 
TypeLibrarian - Class in gov.va.vinci.leo.types
Static methods to help with Type creation and other methods.
TypeLibrarian() - Constructor for class gov.va.vinci.leo.types.TypeLibrarian
 
typeSystemDescription - Variable in class gov.va.vinci.leo.ae.LeoBaseAnnotator
Type system for this annotator, defaults to an empty type system.
typeSystemDescriptor - Variable in class gov.va.vinci.leo.listener.SimpleXmiListener
Path to the type system descriptor or aggregate descriptor file for the service.
TypeSystemFactory - Class in gov.va.vinci.leo.descriptors
Generate TypeSystemDescription objects from imported descriptors or as new objects without arguments.
TypeSystemFactory() - Constructor for class gov.va.vinci.leo.descriptors.TypeSystemFactory
 

U

uiamAsContainerId - Variable in class gov.va.vinci.leo.Service
When a service is deployed, UIMA assigns it a unique container id to be used for undeploying.
undeploy() - Method in class gov.va.vinci.leo.Service
Undeploys a running service from the UIMA AS engine.
unwrap(Class<T>) - Method in class gov.va.vinci.leo.tools.db.LeoDataSource
Returns an object that implements the given interface to allow access to non-standard methods, or standard methods not exposed by the proxy.
url - Variable in class gov.va.vinci.leo.cr.BaseDatabaseCollectionReader
Connection URL for the database to be accessed.
usedBatches - Variable in class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
Store the batch numbers already visited when executing random batches.
username - Variable in class gov.va.vinci.leo.cr.BaseDatabaseCollectionReader
Username for this database.

V

validateConnection() - Method in class gov.va.vinci.leo.listener.BaseDatabaseListener
Method to validate the connection is not null, and if specified, run the validation query against the database.
validateConnectionEachBatch - Variable in class gov.va.vinci.leo.listener.BaseDatabaseListener
If true, the connection is validated before committing each batch.
validateData() - Method in class gov.va.vinci.leo.Client
Validate the required data for client execution.
validateParams(int, int, int) - Method in class gov.va.vinci.leo.cr.BatchDatabaseCollectionReader
Validate the parameters that will initialize this object.
validateParams(String, String, String) - Method in class gov.va.vinci.leo.cr.DatabaseCollectionReader
Validate the parameters for the DatabaseCollectionReader to ensure that none of the required arguments are missing or invalid.
validParamType(String) - Method in class gov.va.vinci.leo.descriptors.LeoAEDescriptor
Test the Parameter Type string to make sure it is not null or empty and it is one of the defined type constants defined in the ConfigurationParameter interface.
value - Variable in class gov.va.vinci.leo.model.NameValue
The value to which the parameter will be set.
valueOf(String) - Static method in enum gov.va.vinci.leo.tools.ESAPIValidationType
Returns the enum constant of this type with the specified name.
values() - Static method in enum gov.va.vinci.leo.tools.ESAPIValidationType
Returns an array containing the constants of this enum type, in the order they are declared.

W

WrappedInteger(int) - Constructor for class gov.va.vinci.leo.tools.JetmPerformance.WrappedInteger
 
writeHeaders() - Method in class gov.va.vinci.leo.listener.BaseCsvListener
Write out headers to the writerBuilder for this gov.va.vinci.leo.listener.
writer - Variable in class gov.va.vinci.leo.listener.BaseCsvListener
CSVWriter that will format and write the output.
writer - Variable in class gov.va.vinci.leo.tools.CSVWriterBuilder
 
writerBuilder - Variable in class gov.va.vinci.leo.listener.BaseCsvListener
CSVWriterBuilder used to create the CSVWriter.

X

XmiFileCollectionReader - Class in gov.va.vinci.leo.cr
Get a list of the XMI files in a directory and populate the CAS when getNext(Cas) is called on the reader.
XmiFileCollectionReader() - Constructor for class gov.va.vinci.leo.cr.XmiFileCollectionReader
Default constructor used during UIMA initialization.
XmiFileCollectionReader(File, boolean) - Constructor for class gov.va.vinci.leo.cr.XmiFileCollectionReader
Constructor that sets the inputDirectory and recurse flag.
XMLException - Exception in gov.va.vinci.leo.tools
 
XMLException(String) - Constructor for exception gov.va.vinci.leo.tools.XMLException
The user constructor.
XMLException() - Constructor for exception gov.va.vinci.leo.tools.XMLException
The default Constructor.
XmlFilter - Class in gov.va.vinci.leo.tools
Replace non XML-1.0 characters with spaces.
XmlFilter() - Constructor for class gov.va.vinci.leo.tools.XmlFilter
 
XMLSerializer - Class in gov.va.vinci.leo.tools
Use SAX to serialize XML data out to a file.
XMLSerializer() - Constructor for class gov.va.vinci.leo.tools.XMLSerializer
Default Constructor, setup basic XML output properties such as Encoding, Method, and Indent.
XMLSerializer(String) - Constructor for class gov.va.vinci.leo.tools.XMLSerializer
Constructor with file path input paramter, uses the path to setup the output stream.
XMLSerializer(File) - Constructor for class gov.va.vinci.leo.tools.XMLSerializer
Constructor with File Handle input.
XMLSerializer(OutputStream) - Constructor for class gov.va.vinci.leo.tools.XMLSerializer
Constructor with outputStream input.
XMLSerializer(Writer) - Constructor for class gov.va.vinci.leo.tools.XMLSerializer
Constructor with Writer input.
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