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A

AbortException - Exception in edu.illinois.ncsa.datawolf
This class is used to indicate a tool has aborted it's execution.
AbortException(String) - Constructor for exception edu.illinois.ncsa.datawolf.AbortException
Constructs a new exception with the specified detail message.
AbortException(String, Throwable) - Constructor for exception edu.illinois.ncsa.datawolf.AbortException
Constructs a new exception with the specified detail message and cause.
AbstractBean - Class in edu.illinois.ncsa.domain
 
AbstractBean() - Constructor for class edu.illinois.ncsa.domain.AbstractBean
 
AbstractClowderDao<T,ID extends Serializable> - Class in edu.illinois.ncsa.clowder.dao
Clowder Parent DAO
AbstractClowderDao() - Constructor for class edu.illinois.ncsa.clowder.dao.AbstractClowderDao
 
AbstractIncoreDao<T,ID extends Serializable> - Class in edu.illinois.ncsa.incore.dao
 
AbstractIncoreDao() - Constructor for class edu.illinois.ncsa.incore.dao.AbstractIncoreDao
 
AbstractJPADao<T,ID extends Serializable> - Class in edu.illinois.ncsa.jpa.dao
 
AbstractJPADao(Provider<EntityManager>) - Constructor for class edu.illinois.ncsa.jpa.dao.AbstractJPADao
 
AccessType - Class in edu.illinois.ncsa.gondola.types.service
Java class for access-type complex type.
AccessType() - Constructor for class edu.illinois.ncsa.gondola.types.service.AccessType
 
Account - Class in edu.illinois.ncsa.domain
 
Account() - Constructor for class edu.illinois.ncsa.domain.Account
 
Account.MiniAccount - Class in edu.illinois.ncsa.domain
 
AccountDao - Interface in edu.illinois.ncsa.domain.dao
 
AccountJPADao - Class in edu.illinois.ncsa.jpa.dao
 
AccountJPADao(Provider<EntityManager>) - Constructor for class edu.illinois.ncsa.jpa.dao.AccountJPADao
 
active - Variable in class edu.illinois.ncsa.domain.Account.MiniAccount
 
addBlob(FileDescriptor) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Add the blob to the set of blobs to the workflow tool.
addContributor(Person) - Method in class edu.illinois.ncsa.datawolf.domain.Workflow
Add the contributor to the set of contributors to the workflow.
addContributor(Person) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Add the contributor to the set of contributors to the workflow tool.
addContributor(Person) - Method in class edu.illinois.ncsa.domain.Dataset
Add the contributor to the set of contributors to the artifact.
addExecutor(Executor) - Method in class edu.illinois.ncsa.datawolf.Engine
Add an executor to the list of known executors.
addFileDescriptor(FileDescriptor) - Method in class edu.illinois.ncsa.domain.Dataset
Add the file descriptor to the set of file descriptors to the dataset.
addInput(WorkflowToolData) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Add the data to list of inputs to the workflow tool.
addJarFile(File) - Method in class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
 
addLeadingZeros(Object, int) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.StringUtils
 
addOutput(WorkflowToolData) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Add the data to list of outputs to the workflow tool.
addParameter(WorkflowToolParameter) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Add the parameter from the set of parameters to the workflow tool.
addStep(WorkflowStep) - Method in class edu.illinois.ncsa.datawolf.domain.Workflow
Add the step to the list of steps in the workflow.
addTriggerPackage(String) - Static method in class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
 
addUserInfo(URI, String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.UriUtils
Constructs new uri from old, updating userInfo.
admin - Variable in class edu.illinois.ncsa.domain.Account.MiniAccount
 
always - Variable in class edu.illinois.ncsa.gondola.types.service.InitializeType
 
APOS - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
APOS - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
append - Variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.OutputPipe
 
appendToPrefix(StringBuffer, int, String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.StringUtils
Appends the second String to the indicated prefix of the first.
asXML(AccessType) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
 
asXML(ErrorHandlerType) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
 
asXML(IdListType) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
 
asXML(JobStatusListType) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
 
asXML(JobStatusType) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
 
asXML(JobSubmissionType) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
 
asXML(ParserType) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
 
asXML(ScriptType) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
 
asXML(ServiceType) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
 
AT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
AT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
AuthenticationInterceptor - Class in edu.illinois.ncsa.datawolf.service
 
AuthenticationInterceptor() - Constructor for class edu.illinois.ncsa.datawolf.service.AuthenticationInterceptor
 

B

BeanUtil - Class in edu.illinois.ncsa.domain.util
 
BeanUtil() - Constructor for class edu.illinois.ncsa.domain.util.BeanUtil
 
binaryContent - Variable in class edu.illinois.ncsa.datawolf.executor.java.ResourceEntry
Binary content of the resource.
BIT_DEFAULT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
Default value for bit-wise & and |.
BIT_DEFAULT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
Default value for bit-wise & and |.
BKBKESC - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
BKBKESC - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
BKESC - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
BKESC - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
BOOL - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
Type markers for file read.
BOOL - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
Type markers for file read.
BrownDogResource - Class in edu.illinois.ncsa.datawolf.service
 
BrownDogResource() - Constructor for class edu.illinois.ncsa.datawolf.service.BrownDogResource
 
buffer - Variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.OutputPipe
 
bw - Variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.OutputPipe
 
BYTE - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
BYTE - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
byteStreamTransfer(InputStream, OutputStream, long) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.SshUtils
Reads from input stream and writes to output stream.

C

cancel(String) - Static method in class edu.illinois.ncsa.datawolf.service.client.DataWolfServiceClient
 
cancel(String, List<String>) - Static method in class edu.illinois.ncsa.datawolf.service.client.DataWolfServiceClient
 
cancel(String) - Method in interface edu.illinois.ncsa.gondola.ISubmissionEngine
 
cancel(String) - Method in interface edu.illinois.ncsa.gondola.ISubmissionEngineImpl
 
cancelExecution(String, String) - Method in class edu.illinois.ncsa.datawolf.service.ExecutionsResource
Cancel a execution
cancelQueue - Variable in class edu.illinois.ncsa.gondola.types.service.ServiceType
 
cancelRemoteJob() - Method in class edu.illinois.ncsa.datawolf.executor.hpc.HPCExecutor
 
cancelRemoteJob() - Method in class edu.illinois.ncsa.datawolf.RemoteExecutor
Tries to cancel the job on the remote server.
CANON_EQ - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
CANON_EQ - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
CASE_INSENSITIVE - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
Regex flags
CASE_INSENSITIVE - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
Regex flags
CAT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
CAT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
certificates - Variable in class edu.illinois.ncsa.datawolf.executor.java.ResourceEntry
Certificates (if the resource was loaded from a JAR).
changePath(URI, String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.PathUtils
Changes the path in base to newPath.
CHAR - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
CHAR - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
checkAck(InputStream, StringBuffer) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.SshUtils
Reads from the input stream; checks for status of ACK.
checkException(Throwable, String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.ExceptionUtils
Tries to match the given String by recurring on nested exception messages.
checkException(Throwable, String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.StringUtils
Deprecated.
use ExceptionUtils
checkHpcFeil(String) - Static method in class edu.illinois.ncsa.datawolf.service.client.DataWolfServiceClient
 
checkHpcFile(String, String) - Static method in class edu.illinois.ncsa.datawolf.service.client.DataWolfServiceClient
 
checkHpcFile(String, String) - Method in class edu.illinois.ncsa.datawolf.service.KistiHPCResource
 
checkRemoteJob() - Method in class edu.illinois.ncsa.datawolf.executor.hpc.HPCExecutor
 
checkRemoteJob() - Method in class edu.illinois.ncsa.datawolf.RemoteExecutor
Checks the status of the job on the remote server.
clearReferences() - Method in class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
Clear references.
close() - Method in class edu.illinois.ncsa.datawolf.executor.hpc.ssh.SSHSession
Disconnects.
close() - Method in class edu.illinois.ncsa.datawolf.executor.hpc.util.OutputPipe
Nulls out the buffer.
CLOSP - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
CLOSP - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
CLOSSQ - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
CLOSSQ - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
CLOSV - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
CLOSV - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
ClowderDevModule - Class in edu.illinois.ncsa.clowder
 
ClowderDevModule() - Constructor for class edu.illinois.ncsa.clowder.ClowderDevModule
 
ClowderRedirectStrategy - Class in edu.illinois.ncsa.clowder
Subclasses DefaultRedirectStrategy to provide redirect strategy for HttpPost and HttpDelete overrides default redirect behavior.
ClowderRedirectStrategy() - Constructor for class edu.illinois.ncsa.clowder.ClowderRedirectStrategy
 
ClowderTokenProvider - Class in edu.illinois.ncsa.clowder.impl
 
ClowderTokenProvider() - Constructor for class edu.illinois.ncsa.clowder.impl.ClowderTokenProvider
 
CM - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
CM - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
CO - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
CO - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
codeBase - Variable in class edu.illinois.ncsa.datawolf.executor.java.ResourceEntry
URL of the codebase from where the object was loaded.
commandArgs - Variable in class edu.illinois.ncsa.gondola.types.submission.StatusHandlerType
 
CommandLineExecutor - Class in edu.illinois.ncsa.datawolf.executor.commandline
This executor will allow the user to execute any arbitrary executable.
CommandLineExecutor() - Constructor for class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineExecutor
 
CommandLineImplementation - Class in edu.illinois.ncsa.datawolf.executor.commandline
 
CommandLineImplementation() - Constructor for class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineImplementation
 
CommandLineOption - Class in edu.illinois.ncsa.datawolf.executor.commandline
 
CommandLineOption() - Constructor for class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineOption
 
CommandLineOption.InputOutput - Enum in edu.illinois.ncsa.datawolf.executor.commandline
 
CommandLineOption.Type - Enum in edu.illinois.ncsa.datawolf.executor.commandline
 
commandPath - Variable in class edu.illinois.ncsa.gondola.types.submission.StatusHandlerType
 
COMMENTS - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
COMMENTS - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
concatenate(URI, String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.PathUtils
If the sub path is null, the base is returned; else a new URI with the concatenated path is returned.
configure() - Method in class edu.illinois.ncsa.clowder.ClowderDevModule
 
configure() - Method in class edu.illinois.ncsa.datawolf.service.PersistenceModule
 
configure() - Method in class edu.illinois.ncsa.datawolf.service.ResourcesModule
 
configure() - Method in class edu.illinois.ncsa.jpa.JPADevModule
 
configureServlets() - Method in class edu.illinois.ncsa.datawolf.service.DataWolfServletModule
 
ConnectionType - Class in edu.illinois.ncsa.gondola.types.service
Java class for connection-type complex type.
ConnectionType() - Constructor for class edu.illinois.ncsa.gondola.types.service.ConnectionType
 
content - Variable in class edu.illinois.ncsa.gondola.types.service.ConnectionType
 
content - Variable in class edu.illinois.ncsa.gondola.types.service.DbcpType.Property
 
content - Variable in class edu.illinois.ncsa.gondola.types.submission.LineType
 
content - Variable in class edu.illinois.ncsa.gondola.types.submission.RegexType
 
convert(String, int, int) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.StringUtils
 
COPY_BUFFER_SIZE - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
COPY_BUFFER_SIZE - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
copyFrom(String, String, SSHSession) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.SshUtils
Copy remote to local.
copyTo(String, String, SSHSession) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.SshUtils
Copy local to remote.
count(boolean) - Method in class edu.illinois.ncsa.clowder.dao.AbstractClowderDao
 
count(boolean) - Method in interface edu.illinois.ncsa.domain.dao.IDao
 
count(boolean) - Method in class edu.illinois.ncsa.incore.dao.IncoreDatasetDao
 
count(boolean) - Method in class edu.illinois.ncsa.incore.dao.IncoreFileDescriptorDao
 
count(boolean) - Method in class edu.illinois.ncsa.incore.dao.IncorePersonDao
 
count(boolean) - Method in class edu.illinois.ncsa.jpa.dao.AbstractJPADao
 
countLines(File) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.FileUtils
Counts the number of lines in the file.
createAccessType() - Method in class edu.illinois.ncsa.gondola.types.service.ObjectFactory
Create an instance of AccessType
createAccount(String, String, String) - Method in class edu.illinois.ncsa.datawolf.service.LoginResource
Create a user account by either specifying the email or the personId and a password
createChartImage(File, File) - Method in class edu.illinois.ncsa.datawolf.service.KistiHPCResource
 
createCommandlineImplementation(String, String, String, boolean, List<CommandLineOption>, Map<String, String>) - Static method in class edu.illinois.ncsa.datawolf.service.utils.WorkflowUtil
Create command line implementation based on options, standard out/error logs, environment, etc
createCommandlineOption(CommandLineOption.Type, String, String, String, CommandLineOption.InputOutput, String, boolean) - Static method in class edu.illinois.ncsa.datawolf.service.utils.WorkflowUtil
Create command line option
createConnectionType() - Method in class edu.illinois.ncsa.gondola.types.service.ObjectFactory
Create an instance of ConnectionType
createDAPWorkflow(String, String, String, Person) - Static method in class edu.illinois.ncsa.datawolf.service.utils.WorkflowUtil
 
createDataset(File, String) - Static method in class edu.illinois.ncsa.datawolf.service.client.DataWolfServiceClient
 
createDataset(MultipartFormDataInput) - Method in class edu.illinois.ncsa.datawolf.service.DatasetsResource
Create dataset from zip file.
createDbcpType() - Method in class edu.illinois.ncsa.gondola.types.service.ObjectFactory
Create an instance of DbcpType
createDbcpTypeProperty() - Method in class edu.illinois.ncsa.gondola.types.service.ObjectFactory
Create an instance of DbcpType.Property
createDropType() - Method in class edu.illinois.ncsa.gondola.types.service.ObjectFactory
Create an instance of DropType
createDTSWorkflow(String, String, String, Person) - Static method in class edu.illinois.ncsa.datawolf.service.utils.WorkflowUtil
Creates a workflow representing the DTS extractors ran on a file
createErrorHandlerType() - Method in class edu.illinois.ncsa.gondola.types.submission.ObjectFactory
Create an instance of ErrorHandlerType
createExecution(Submission) - Method in class edu.illinois.ncsa.datawolf.service.ExecutionsResource
Create execution via Submission JSON
createExecution(String, boolean) - Method in class edu.illinois.ncsa.datawolf.service.WorkflowsResource
Create a execution by execution JSON
createExpressionGroupTranslatorType() - Method in class edu.illinois.ncsa.gondola.types.submission.ObjectFactory
Create an instance of ExpressionGroupTranslatorType
createFileDescriptor(File) - Static method in class edu.illinois.ncsa.file.service.client.FileServiceClient
 
createIdList(IdListType) - Method in class edu.illinois.ncsa.gondola.types.submission.ObjectFactory
Create an instance of JAXBElement<IdListType>}
createIdListType() - Method in class edu.illinois.ncsa.gondola.types.submission.ObjectFactory
Create an instance of IdListType
createInitializeType() - Method in class edu.illinois.ncsa.gondola.types.service.ObjectFactory
Create an instance of InitializeType
createJdbcAccess(AccessType) - Method in class edu.illinois.ncsa.gondola.types.service.ObjectFactory
Create an instance of JAXBElement<AccessType>}
createJobErrorHandler(ErrorHandlerType) - Method in class edu.illinois.ncsa.gondola.types.submission.ObjectFactory
Create an instance of JAXBElement<ErrorHandlerType>}
createJobScript(ScriptType) - Method in class edu.illinois.ncsa.gondola.types.submission.ObjectFactory
Create an instance of JAXBElement<ScriptType>}
createJobStatus(JobStatusType) - Method in class edu.illinois.ncsa.gondola.types.submission.ObjectFactory
Create an instance of JAXBElement<JobStatusType>}
createJobStatusList(JobStatusListType) - Method in class edu.illinois.ncsa.gondola.types.submission.ObjectFactory
Create an instance of JAXBElement<JobStatusListType>}
createJobStatusListType() - Method in class edu.illinois.ncsa.gondola.types.submission.ObjectFactory
Create an instance of JobStatusListType
createJobStatusParser(ParserType) - Method in class edu.illinois.ncsa.gondola.types.submission.ObjectFactory
Create an instance of JAXBElement<ParserType>}
createJobStatusType() - Method in class edu.illinois.ncsa.gondola.types.submission.ObjectFactory
Create an instance of JobStatusType
createJobSubmission(JobSubmissionType) - Method in class edu.illinois.ncsa.gondola.types.submission.ObjectFactory
Create an instance of JAXBElement<JobSubmissionType>}
createJobSubmissionType() - Method in class edu.illinois.ncsa.gondola.types.submission.ObjectFactory
Create an instance of JobSubmissionType
createLineType() - Method in class edu.illinois.ncsa.gondola.types.submission.ObjectFactory
Create an instance of LineType
createMyProxyType() - Method in class edu.illinois.ncsa.gondola.types.service.ObjectFactory
Create an instance of MyProxyType
createParserType() - Method in class edu.illinois.ncsa.gondola.types.submission.ObjectFactory
Create an instance of ParserType
createPerson(String, String, String) - Static method in class edu.illinois.ncsa.datawolf.service.client.DataWolfServiceClient
 
createPerson(String, String, String) - Method in class edu.illinois.ncsa.datawolf.service.PersonsResource
 
createPerson(String, String, String) - Static method in class edu.illinois.ncsa.domain.Person
Creates a person given first name, last name and email.
createRegexType() - Method in class edu.illinois.ncsa.gondola.types.submission.ObjectFactory
Create an instance of RegexType
createScriptType() - Method in class edu.illinois.ncsa.gondola.types.submission.ObjectFactory
Create an instance of ScriptType
createServiceConfig(ServiceType) - Method in class edu.illinois.ncsa.gondola.types.service.ObjectFactory
Create an instance of JAXBElement<ServiceType>}
createServiceType() - Method in class edu.illinois.ncsa.gondola.types.service.ObjectFactory
Create an instance of ServiceType
createStatusHandlerType() - Method in class edu.illinois.ncsa.gondola.types.submission.ObjectFactory
Create an instance of StatusHandlerType
createTool(MultipartFormDataInput) - Method in class edu.illinois.ncsa.datawolf.service.WorkflowToolsResource
Create workflow via workflow JSON.
createWorkflow(HttpServletRequest, String, String, String) - Method in class edu.illinois.ncsa.datawolf.service.BrownDogResource
 
createWorkflow(File) - Static method in class edu.illinois.ncsa.datawolf.service.client.DataWolfServiceClient
 
createWorkflow(String, String, Person) - Static method in class edu.illinois.ncsa.datawolf.service.utils.WorkflowUtil
Create an empty workflow
createWorkflow(Workflow) - Method in class edu.illinois.ncsa.datawolf.service.WorkflowsResource
Create a new workflow
createWorkflow(MultipartFormDataInput) - Method in class edu.illinois.ncsa.datawolf.service.WorkflowsResource
Create workflow via workflow JSON.
createWorkflowStep(String, Person, WorkflowTool, Map<String, String>, Map<String, String>, Map<String, String>) - Static method in class edu.illinois.ncsa.datawolf.service.utils.WorkflowUtil
Create workflow step
createWorkflowTool(String, String, String, Person, List<WorkflowToolParameter>, List<WorkflowToolData>, List<WorkflowToolData>, Set<FileDescriptor>, String, String) - Static method in class edu.illinois.ncsa.datawolf.service.utils.WorkflowUtil
Create workflow tool
createWorkflowToolData(String, String, String) - Static method in class edu.illinois.ncsa.datawolf.service.utils.WorkflowUtil
Create workflow tool data
createWorkflowToolParameter(String, String, boolean, WorkflowToolParameter.ParameterType, boolean, String) - Static method in class edu.illinois.ncsa.datawolf.service.utils.WorkflowUtil
Create workflow tool parameter
CREATOR - Static variable in class edu.illinois.ncsa.incore.IncoreDataset
 
CRET - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
CRET - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 

D

DATA - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
DATA - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
DATA_URL - Static variable in class edu.illinois.ncsa.incore.IncoreDataset
 
Dataset - Class in edu.illinois.ncsa.datawolf.executor.java.tool
Definition of a dataset (input/output).
Dataset(String, String, String, String) - Constructor for class edu.illinois.ncsa.datawolf.executor.java.tool.Dataset
Define a dataset that will be used or created by the tool.
Dataset - Class in edu.illinois.ncsa.domain
 
Dataset() - Constructor for class edu.illinois.ncsa.domain.Dataset
 
DATASET_FILE - Static variable in class edu.illinois.ncsa.incore.IncoreDataset
 
DATASET_FILES - Static variable in class edu.illinois.ncsa.incore.IncoreDataset
 
DATASET_ID - Static variable in class edu.illinois.ncsa.incore.IncoreDataset
 
DatasetClowderDao - Class in edu.illinois.ncsa.clowder.dao
 
DatasetClowderDao() - Constructor for class edu.illinois.ncsa.clowder.dao.DatasetClowderDao
 
datasetDao - Variable in class edu.illinois.ncsa.datawolf.Executor
 
DatasetDao - Interface in edu.illinois.ncsa.domain.dao
 
DatasetJPADao - Class in edu.illinois.ncsa.jpa.dao
 
DatasetJPADao(Provider<EntityManager>) - Constructor for class edu.illinois.ncsa.jpa.dao.DatasetJPADao
 
DATASETS_ENDPOINT - Static variable in class edu.illinois.ncsa.incore.IncoreDataset
 
DatasetsResource - Class in edu.illinois.ncsa.datawolf.service
 
DatasetsResource() - Constructor for class edu.illinois.ncsa.datawolf.service.DatasetsResource
 
DatasetUtil - Class in edu.illinois.ncsa.domain.util
 
DatasetUtil() - Constructor for class edu.illinois.ncsa.domain.util.DatasetUtil
 
DataWolfServiceClient - Class in edu.illinois.ncsa.datawolf.service.client
 
DataWolfServiceClient() - Constructor for class edu.illinois.ncsa.datawolf.service.client.DataWolfServiceClient
 
DataWolfServletModule - Class in edu.illinois.ncsa.datawolf.service
 
DataWolfServletModule() - Constructor for class edu.illinois.ncsa.datawolf.service.DataWolfServletModule
 
DataWolfTokenProvider - Class in edu.illinois.ncsa.domain.impl
 
DataWolfTokenProvider() - Constructor for class edu.illinois.ncsa.domain.impl.DataWolfTokenProvider
 
DateUtils - Class in edu.illinois.ncsa.datawolf.executor.hpc.util
 
DateUtils() - Constructor for class edu.illinois.ncsa.datawolf.executor.hpc.util.DateUtils
 
daysHoursMinutesToMillis(String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.DateUtils
Computes milliseconds from an expression [dd:][HH:]mm.
DbcpType - Class in edu.illinois.ncsa.gondola.types.service
Java class for dbcp-type complex type.
DbcpType() - Constructor for class edu.illinois.ncsa.gondola.types.service.DbcpType
 
DbcpType.Property - Class in edu.illinois.ncsa.gondola.types.service
Java class for anonymous complex type.
debug() - Static method in class edu.illinois.ncsa.datawolf.LocalExecutor
 
DEFAULT_DATE_FORMAT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
DEFAULT_DATE_FORMAT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
DEFAULT_SSH_PORT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
DEFAULT_SSH_PORT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
delete(T) - Method in class edu.illinois.ncsa.clowder.dao.AbstractClowderDao
 
delete(Dataset) - Method in class edu.illinois.ncsa.clowder.dao.DatasetClowderDao
 
delete(T) - Method in interface edu.illinois.ncsa.domain.dao.IDao
 
delete(String) - Method in interface edu.illinois.ncsa.gondola.ISubmissionEngine
 
delete(String) - Method in interface edu.illinois.ncsa.gondola.ISubmissionEngineImpl
 
delete(Dataset) - Method in class edu.illinois.ncsa.incore.dao.IncoreDatasetDao
 
delete(FileDescriptor) - Method in class edu.illinois.ncsa.incore.dao.IncoreFileDescriptorDao
 
delete(Person) - Method in class edu.illinois.ncsa.incore.dao.IncorePersonDao
 
delete(T) - Method in class edu.illinois.ncsa.jpa.dao.AbstractJPADao
 
deleteAfterSubmit - Variable in class edu.illinois.ncsa.gondola.types.submission.ScriptType
 
deleteAll(String, boolean, SSHSession) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.SshUtils
Calls rm -rf.
deleteAll(Long) - Method in interface edu.illinois.ncsa.gondola.ISubmissionEngine
 
deleteAll(Long) - Method in interface edu.illinois.ncsa.gondola.ISubmissionEngineImpl
 
deleteDataset(String) - Method in class edu.illinois.ncsa.datawolf.service.DatasetsResource
Mark dataset as deleted
deleteDataset(String) - Static method in class edu.illinois.ncsa.domain.util.DatasetUtil
 
deleteExecution(String) - Method in class edu.illinois.ncsa.datawolf.service.ExecutionsResource
Delete execution by id
deleteFile(FileDescriptor) - Method in class edu.illinois.ncsa.clowder.impl.FileStorageClowder
 
deleteFile(FileDescriptor, Person) - Method in class edu.illinois.ncsa.clowder.impl.FileStorageClowder
 
deleteFile(String, boolean, SSHSession) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.SshUtils
Calls rm.
deleteFile(String, String) - Method in class edu.illinois.ncsa.datawolf.service.DatasetsResource
get the file with given id
deleteFile(FileDescriptor) - Method in interface edu.illinois.ncsa.domain.FileStorage
Deletes file from storage
deleteFile(FileDescriptor, Person) - Method in interface edu.illinois.ncsa.domain.FileStorage
Deletes file from storage
deleteFile(FileDescriptor, Person) - Method in class edu.illinois.ncsa.domain.impl.FileStorageDisk
 
deleteFile(FileDescriptor) - Method in class edu.illinois.ncsa.domain.impl.FileStorageDisk
 
deleteFile(String) - Method in class edu.illinois.ncsa.file.service.FilesResource
delete the file with given id
deleteFile(FileDescriptor) - Method in class edu.illinois.ncsa.incore.impl.IncoreFileStorage
 
deleteFile(FileDescriptor, Person) - Method in class edu.illinois.ncsa.incore.impl.IncoreFileStorage
 
deletePerson(String) - Method in class edu.illinois.ncsa.datawolf.service.PersonsResource
Delete the person given the specific id.
deleteToken(HttpRequest) - Method in class edu.illinois.ncsa.datawolf.service.LoginResource
 
deleteTool(String) - Method in class edu.illinois.ncsa.datawolf.service.WorkflowToolsResource
Delete the tool given the specific id.
deleteWorkflow(String) - Method in class edu.illinois.ncsa.datawolf.service.WorkflowsResource
Delete a workflow by Id
DESCRIPTION - Static variable in class edu.illinois.ncsa.incore.IncoreDataset
 
destroy(Process, Thread[]) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.SystemUtils
Calls destroy on the process in order to guarantee release of resources in underlying platform.
disable(HttpRequest, String) - Method in class edu.illinois.ncsa.datawolf.service.LoginResource
Delete the account given the specific id.
dispatch(WorkflowToolChangedHandler) - Method in class edu.illinois.ncsa.datawolf.domain.event.WorkflowToolChangedEvent
 
dispatch(WorkflowToolCreatedHandler) - Method in class edu.illinois.ncsa.datawolf.domain.event.WorkflowToolCreatedEvent
 
dispatch(WorkflowToolDeletedHandler) - Method in class edu.illinois.ncsa.datawolf.domain.event.WorkflowToolDeletedEvent
 
dispatch(StepStateChangedHandler) - Method in class edu.illinois.ncsa.datawolf.event.StepStateChangedEvent
 
dispatch(H) - Method in interface edu.illinois.ncsa.domain.event.Event
 
dispatch(ObjectCreatedHandler) - Method in class edu.illinois.ncsa.domain.event.ObjectCreatedEvent
 
dispatch(ObjectRemovedHandler) - Method in class edu.illinois.ncsa.domain.event.ObjectRemovedEvent
 
dispatch(ObjectSelectedHandler) - Method in class edu.illinois.ncsa.domain.event.ObjectSelectedEvent
 
dispatch(ObjectUpdatedHandler) - Method in class edu.illinois.ncsa.domain.event.ObjectUpdatedEvent
 
dispose() - Method in class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
Dispose the class loader.
DisposeClassLoader - Class in edu.illinois.ncsa.datawolf.executor.java
 
DisposeClassLoader() - Constructor for class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
 
DisposeClassLoader(ClassLoader) - Constructor for class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
 
DLESC - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
DLESC - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
DLESCESC - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
DLESCESC - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
doExec(List<String>, String[], File, boolean, StringBuffer, StringBuffer) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.SystemUtils
Execs command directly.
DOL - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
DOL - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
DONE - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
DONE - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
DOT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
DOT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
DOT_SSH - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
DOT_SSH - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
DOT_XML - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
DOT_XML - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
DOTALL - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
DOTALL - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
DOUB - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
DOUB - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
driverClass - Variable in class edu.illinois.ncsa.gondola.types.service.ConnectionType
 
drop - Variable in class edu.illinois.ncsa.gondola.types.service.AccessType
 
DropType - Class in edu.illinois.ncsa.gondola.types.service
Java class for drop-type complex type.
DropType() - Constructor for class edu.illinois.ncsa.gondola.types.service.DropType
 
duplicateName(String, int) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.PathUtils
Constructs a duplicate file name from original plus given number tag.

E

edu.illinois.ncsa.clowder - package edu.illinois.ncsa.clowder
 
edu.illinois.ncsa.clowder.dao - package edu.illinois.ncsa.clowder.dao
 
edu.illinois.ncsa.clowder.impl - package edu.illinois.ncsa.clowder.impl
 
edu.illinois.ncsa.datawolf - package edu.illinois.ncsa.datawolf
 
edu.illinois.ncsa.datawolf.domain - package edu.illinois.ncsa.datawolf.domain
 
edu.illinois.ncsa.datawolf.domain.dao - package edu.illinois.ncsa.datawolf.domain.dao
 
edu.illinois.ncsa.datawolf.domain.event - package edu.illinois.ncsa.datawolf.domain.event
 
edu.illinois.ncsa.datawolf.event - package edu.illinois.ncsa.datawolf.event
 
edu.illinois.ncsa.datawolf.executor.commandline - package edu.illinois.ncsa.datawolf.executor.commandline
 
edu.illinois.ncsa.datawolf.executor.hpc - package edu.illinois.ncsa.datawolf.executor.hpc
 
edu.illinois.ncsa.datawolf.executor.hpc.handlers - package edu.illinois.ncsa.datawolf.executor.hpc.handlers
 
edu.illinois.ncsa.datawolf.executor.hpc.ssh - package edu.illinois.ncsa.datawolf.executor.hpc.ssh
 
edu.illinois.ncsa.datawolf.executor.hpc.util - package edu.illinois.ncsa.datawolf.executor.hpc.util
 
edu.illinois.ncsa.datawolf.executor.java - package edu.illinois.ncsa.datawolf.executor.java
 
edu.illinois.ncsa.datawolf.executor.java.tool - package edu.illinois.ncsa.datawolf.executor.java.tool
 
edu.illinois.ncsa.datawolf.jpa.dao - package edu.illinois.ncsa.datawolf.jpa.dao
 
edu.illinois.ncsa.datawolf.service - package edu.illinois.ncsa.datawolf.service
 
edu.illinois.ncsa.datawolf.service.client - package edu.illinois.ncsa.datawolf.service.client
 
edu.illinois.ncsa.datawolf.service.utils - package edu.illinois.ncsa.datawolf.service.utils
 
edu.illinois.ncsa.datawolf.tool.example - package edu.illinois.ncsa.datawolf.tool.example
 
edu.illinois.ncsa.domain - package edu.illinois.ncsa.domain
 
edu.illinois.ncsa.domain.dao - package edu.illinois.ncsa.domain.dao
 
edu.illinois.ncsa.domain.event - package edu.illinois.ncsa.domain.event
 
edu.illinois.ncsa.domain.impl - package edu.illinois.ncsa.domain.impl
 
edu.illinois.ncsa.domain.jackson - package edu.illinois.ncsa.domain.jackson
 
edu.illinois.ncsa.domain.util - package edu.illinois.ncsa.domain.util
 
edu.illinois.ncsa.file.service - package edu.illinois.ncsa.file.service
 
edu.illinois.ncsa.file.service.client - package edu.illinois.ncsa.file.service.client
 
edu.illinois.ncsa.gondola - package edu.illinois.ncsa.gondola
 
edu.illinois.ncsa.gondola.types.service - package edu.illinois.ncsa.gondola.types.service
 
edu.illinois.ncsa.gondola.types.submission - package edu.illinois.ncsa.gondola.types.submission
 
edu.illinois.ncsa.gondola.utils - package edu.illinois.ncsa.gondola.utils
 
edu.illinois.ncsa.incore - package edu.illinois.ncsa.incore
 
edu.illinois.ncsa.incore.dao - package edu.illinois.ncsa.incore.dao
 
edu.illinois.ncsa.incore.impl - package edu.illinois.ncsa.incore.impl
 
edu.illinois.ncsa.jpa - package edu.illinois.ncsa.jpa
 
edu.illinois.ncsa.jpa.dao - package edu.illinois.ncsa.jpa.dao
 
EMPTY_DATASET - Static variable in class edu.illinois.ncsa.datawolf.domain.Execution
Marker for non existing dataset due to errrors.
Engine - Class in edu.illinois.ncsa.datawolf
Engine that is responsible for executing the steps.
Engine() - Constructor for class edu.illinois.ncsa.datawolf.Engine
Create the engine with a single worker.
ensureUri(String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.UriUtils
SDH 01/06/09: In following with the revelations of isUri, this method also needs to be check out.
ENTITY_ID - Static variable in class edu.illinois.ncsa.incore.IncoreDataset
 
enumerateAncestorsExcludeSelf(URI) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.PathUtils
 
EOF - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
EOF - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
EQ - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
EQ - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
equals(Object) - Method in class edu.illinois.ncsa.domain.AbstractBean
Compares two objects with each other.
equals(Object) - Method in class edu.illinois.ncsa.domain.Account
 
equals(Object) - Method in class edu.illinois.ncsa.domain.Person
 
error - Variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.OutputPipe
 
ErrorHandlerType - Class in edu.illinois.ncsa.gondola.types.submission
Java class for error-handler-type complex type.
ErrorHandlerType() - Constructor for class edu.illinois.ncsa.gondola.types.submission.ErrorHandlerType
 
Event<H extends EventHandler> - Interface in edu.illinois.ncsa.domain.event
 
Event.Type<H> - Class in edu.illinois.ncsa.domain.event
 
EventHandler - Interface in edu.illinois.ncsa.domain.event
 
ExceptionUtils - Class in edu.illinois.ncsa.datawolf.executor.hpc.util
 
ExceptionUtils() - Constructor for class edu.illinois.ncsa.datawolf.executor.hpc.util.ExceptionUtils
 
exec(SSHSession, String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.SshUtils
Execs process without reading output stream, but throws exception if error stream has been written to.
exec(SSHSession, String, OutputStream, OutputStream) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.SshUtils
Executes a single command using the given session; does not disconnect session.
exec(SSHSession, String, StringBuffer, StringBuffer) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.SshUtils
Execs process, reading output stream into the string buffer; throws exception if error stream has been written to.
execute(Execution) - Method in class edu.illinois.ncsa.datawolf.Engine
Submit the all the steps in the workflow to the engine to be executed.
execute(Execution, String...) - Method in class edu.illinois.ncsa.datawolf.Engine
Submit the step to the engine to be executed.
execute(Execution, WorkflowStep...) - Method in class edu.illinois.ncsa.datawolf.Engine
Submit the step to the engine to be executed.
execute(File) - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineExecutor
 
execute(File) - Method in class edu.illinois.ncsa.datawolf.executor.java.JavaExecutor
 
execute() - Method in interface edu.illinois.ncsa.datawolf.executor.java.tool.JavaTool
Execute the tool.
execute(File) - Method in class edu.illinois.ncsa.datawolf.LocalExecutor
This will run the tool specified.
execute() - Method in class edu.illinois.ncsa.datawolf.tool.example.ShiftCharsTool
 
execute - Variable in class edu.illinois.ncsa.gondola.types.service.InitializeType
 
Execution - Class in edu.illinois.ncsa.datawolf.domain
 
Execution() - Constructor for class edu.illinois.ncsa.datawolf.domain.Execution
Create a new instance of the execution.
Execution.State - Enum in edu.illinois.ncsa.datawolf.domain
 
ExecutionDao - Interface in edu.illinois.ncsa.datawolf.domain.dao
 
executionDao - Variable in class edu.illinois.ncsa.datawolf.Executor
 
ExecutionJPADao - Class in edu.illinois.ncsa.datawolf.jpa.dao
 
ExecutionJPADao(Provider<EntityManager>) - Constructor for class edu.illinois.ncsa.datawolf.jpa.dao.ExecutionJPADao
 
ExecutionsResource - Class in edu.illinois.ncsa.datawolf.service
 
ExecutionsResource() - Constructor for class edu.illinois.ncsa.datawolf.service.ExecutionsResource
 
Executor - Class in edu.illinois.ncsa.datawolf
 
Executor() - Constructor for class edu.illinois.ncsa.datawolf.Executor
 
EXECUTOR_NAME - Static variable in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineExecutor
 
EXECUTOR_NAME - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.HPCExecutor
 
EXECUTOR_NAME - Static variable in class edu.illinois.ncsa.datawolf.executor.java.JavaExecutor
 
ExecutorsResource - Class in edu.illinois.ncsa.datawolf.service
 
ExecutorsResource() - Constructor for class edu.illinois.ncsa.datawolf.service.ExecutorsResource
 
exists(ID) - Method in class edu.illinois.ncsa.clowder.dao.AbstractClowderDao
 
exists(String, SSHSession) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.SshUtils
Checks for existence of path.
exists(ID) - Method in interface edu.illinois.ncsa.domain.dao.IDao
 
exists(String) - Method in class edu.illinois.ncsa.incore.dao.IncoreDatasetDao
 
exists(String) - Method in class edu.illinois.ncsa.incore.dao.IncoreFileDescriptorDao
 
exists(String) - Method in class edu.illinois.ncsa.incore.dao.IncorePersonDao
 
exists(ID) - Method in class edu.illinois.ncsa.jpa.dao.AbstractJPADao
 
exportDataset(File, String) - Static method in class edu.illinois.ncsa.datawolf.ImportExport
Exports the given dataset to a zip file.
exportExecution(File, String) - Static method in class edu.illinois.ncsa.datawolf.ImportExport
Exports the given execution to a zip file.
exportLogfile(File, String) - Static method in class edu.illinois.ncsa.datawolf.ImportExport
Exports the given logfile to a textfile.
exportStep(File, String, String) - Static method in class edu.illinois.ncsa.datawolf.ImportExport
Exports the given step to a zip file.
exportTool(File, String) - Static method in class edu.illinois.ncsa.datawolf.ImportExport
Exports the given tool to a zip file.
exportWorkflow(File, String) - Static method in class edu.illinois.ncsa.datawolf.ImportExport
Exports the given workflow to a zip file.
expression - Variable in class edu.illinois.ncsa.gondola.types.submission.ParserType
 
ExpressionGroupTranslatorType - Class in edu.illinois.ncsa.gondola.types.submission
Java class for expression-group-translator-type complex type.
ExpressionGroupTranslatorType() - Constructor for class edu.illinois.ncsa.gondola.types.submission.ExpressionGroupTranslatorType
 
extractSymlink(String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.PathUtils
Presumes listLine follows standard UNIX formatting, with 'l' as first character on line, and symlink indicated by '->'.

F

FailedException - Exception in edu.illinois.ncsa.datawolf
This class is used to indicate a tool has failed it's execution.
FailedException(String) - Constructor for exception edu.illinois.ncsa.datawolf.FailedException
Constructs a new exception with the specified detail message.
FailedException(String, Throwable) - Constructor for exception edu.illinois.ncsa.datawolf.FailedException
Constructs a new exception with the specified detail message and cause.
FILE_BLOB - Static variable in class edu.illinois.ncsa.incore.IncoreDataset
 
FileDescriptor - Class in edu.illinois.ncsa.domain
 
FileDescriptor() - Constructor for class edu.illinois.ncsa.domain.FileDescriptor
 
FileDescriptorClowderDao - Class in edu.illinois.ncsa.clowder.dao
 
FileDescriptorClowderDao() - Constructor for class edu.illinois.ncsa.clowder.dao.FileDescriptorClowderDao
 
fileDescriptorDao - Variable in class edu.illinois.ncsa.datawolf.Executor
 
FileDescriptorDao - Interface in edu.illinois.ncsa.domain.dao
 
FileDescriptorJPADao - Class in edu.illinois.ncsa.jpa.dao
 
FILENAME - Static variable in class edu.illinois.ncsa.incore.IncoreDataset
 
FILES_ENDPOINT - Static variable in class edu.illinois.ncsa.incore.IncoreDataset
 
FileServiceClient - Class in edu.illinois.ncsa.file.service.client
 
FileServiceClient() - Constructor for class edu.illinois.ncsa.file.service.client.FileServiceClient
 
FilesResource - Class in edu.illinois.ncsa.file.service
 
FilesResource() - Constructor for class edu.illinois.ncsa.file.service.FilesResource
 
fileStorage - Variable in class edu.illinois.ncsa.datawolf.Executor
 
FileStorage - Interface in edu.illinois.ncsa.domain
This interface allows files to be saved, read and deleted for different storage implementations.
FileStorageClowder - Class in edu.illinois.ncsa.clowder.impl
 
FileStorageClowder() - Constructor for class edu.illinois.ncsa.clowder.impl.FileStorageClowder
 
FileStorageDisk - Class in edu.illinois.ncsa.domain.impl
Stores files on disk.
FileStorageDisk() - Constructor for class edu.illinois.ncsa.domain.impl.FileStorageDisk
 
FileUtils - Class in edu.illinois.ncsa.datawolf.executor.hpc.util
Wrapper static methods for doing reads and writes using RandomAccessFile object.
filter(String) - Method in class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
Filter classes.
findAll() - Method in class edu.illinois.ncsa.clowder.dao.AbstractClowderDao
 
findAll(int, int) - Method in class edu.illinois.ncsa.clowder.dao.AbstractClowderDao
 
findAll() - Method in class edu.illinois.ncsa.clowder.dao.DatasetClowderDao
 
findAll(int, int) - Method in class edu.illinois.ncsa.clowder.dao.DatasetClowderDao
 
findAll() - Method in interface edu.illinois.ncsa.domain.dao.IDao
 
findAll(int, int) - Method in interface edu.illinois.ncsa.domain.dao.IDao
 
findAll() - Method in class edu.illinois.ncsa.incore.dao.IncoreDatasetDao
 
findAll(int, int) - Method in class edu.illinois.ncsa.incore.dao.IncoreDatasetDao
 
findAll() - Method in class edu.illinois.ncsa.incore.dao.IncoreFileDescriptorDao
 
findAll(int, int) - Method in class edu.illinois.ncsa.incore.dao.IncoreFileDescriptorDao
 
findAll() - Method in class edu.illinois.ncsa.incore.dao.IncorePersonDao
 
findAll(int, int) - Method in class edu.illinois.ncsa.incore.dao.IncorePersonDao
 
findAll(int, int) - Method in class edu.illinois.ncsa.jpa.dao.AbstractJPADao
 
findAll() - Method in class edu.illinois.ncsa.jpa.dao.AbstractJPADao
 
findByCreatorEmail(String) - Method in class edu.illinois.ncsa.clowder.dao.DatasetClowderDao
 
findByCreatorEmail(String, int, int) - Method in class edu.illinois.ncsa.clowder.dao.DatasetClowderDao
 
findByCreatorEmail(String, String, String) - Method in interface edu.illinois.ncsa.datawolf.domain.dao.ExecutionDao
 
findByCreatorEmail(String, int, int, String, String) - Method in interface edu.illinois.ncsa.datawolf.domain.dao.ExecutionDao
 
findByCreatorEmail(String) - Method in interface edu.illinois.ncsa.datawolf.domain.dao.WorkflowDao
 
findByCreatorEmail(String) - Method in interface edu.illinois.ncsa.datawolf.domain.dao.WorkflowToolDao
 
findByCreatorEmail(String, String, String) - Method in class edu.illinois.ncsa.datawolf.jpa.dao.ExecutionJPADao
 
findByCreatorEmail(String, int, int, String, String) - Method in class edu.illinois.ncsa.datawolf.jpa.dao.ExecutionJPADao
 
findByCreatorEmail(String) - Method in class edu.illinois.ncsa.datawolf.jpa.dao.WorkflowJPADao
 
findByCreatorEmail(String) - Method in class edu.illinois.ncsa.datawolf.jpa.dao.WorkflowToolJPADao
 
findByCreatorEmail(String) - Method in interface edu.illinois.ncsa.domain.dao.DatasetDao
 
findByCreatorEmail(String, int, int) - Method in interface edu.illinois.ncsa.domain.dao.DatasetDao
 
findByCreatorEmail(String) - Method in class edu.illinois.ncsa.incore.dao.IncoreDatasetDao
 
findByCreatorEmail(String, int, int) - Method in class edu.illinois.ncsa.incore.dao.IncoreDatasetDao
 
findByCreatorEmail(String) - Method in class edu.illinois.ncsa.jpa.dao.DatasetJPADao
 
findByCreatorEmail(String, int, int) - Method in class edu.illinois.ncsa.jpa.dao.DatasetJPADao
 
findByCreatorEmailAndDeleted(String, boolean) - Method in class edu.illinois.ncsa.clowder.dao.DatasetClowderDao
 
findByCreatorEmailAndDeleted(String, boolean, int, int) - Method in class edu.illinois.ncsa.clowder.dao.DatasetClowderDao
 
findByCreatorEmailAndDeleted(String, boolean, String, String) - Method in interface edu.illinois.ncsa.datawolf.domain.dao.ExecutionDao
 
findByCreatorEmailAndDeleted(String, boolean, int, int, String, String) - Method in interface edu.illinois.ncsa.datawolf.domain.dao.ExecutionDao
 
findByCreatorEmailAndDeleted(String, boolean) - Method in interface edu.illinois.ncsa.datawolf.domain.dao.WorkflowDao
 
findByCreatorEmailAndDeleted(String, boolean) - Method in interface edu.illinois.ncsa.datawolf.domain.dao.WorkflowToolDao
 
findByCreatorEmailAndDeleted(String, boolean, String, String) - Method in class edu.illinois.ncsa.datawolf.jpa.dao.ExecutionJPADao
 
findByCreatorEmailAndDeleted(String, boolean, int, int, String, String) - Method in class edu.illinois.ncsa.datawolf.jpa.dao.ExecutionJPADao
 
findByCreatorEmailAndDeleted(String, boolean) - Method in class edu.illinois.ncsa.datawolf.jpa.dao.WorkflowJPADao
 
findByCreatorEmailAndDeleted(String, boolean) - Method in class edu.illinois.ncsa.datawolf.jpa.dao.WorkflowToolJPADao
 
findByCreatorEmailAndDeleted(String, boolean) - Method in interface edu.illinois.ncsa.domain.dao.DatasetDao
 
findByCreatorEmailAndDeleted(String, boolean, int, int) - Method in interface edu.illinois.ncsa.domain.dao.DatasetDao
 
findByCreatorEmailAndDeleted(String, boolean) - Method in class edu.illinois.ncsa.incore.dao.IncoreDatasetDao
 
findByCreatorEmailAndDeleted(String, boolean, int, int) - Method in class edu.illinois.ncsa.incore.dao.IncoreDatasetDao
 
findByCreatorEmailAndDeleted(String, boolean) - Method in class edu.illinois.ncsa.jpa.dao.DatasetJPADao
 
findByCreatorEmailAndDeleted(String, boolean, int, int) - Method in class edu.illinois.ncsa.jpa.dao.DatasetJPADao
 
findByCreatorEmailAndTitleLike(String, String) - Method in class edu.illinois.ncsa.clowder.dao.DatasetClowderDao
 
findByCreatorEmailAndTitleLike(String, String, int, int) - Method in class edu.illinois.ncsa.clowder.dao.DatasetClowderDao
 
findByCreatorEmailAndTitleLike(String, String) - Method in interface edu.illinois.ncsa.domain.dao.DatasetDao
 
findByCreatorEmailAndTitleLike(String, String, int, int) - Method in interface edu.illinois.ncsa.domain.dao.DatasetDao
 
findByCreatorEmailAndTitleLike(String, String) - Method in class edu.illinois.ncsa.incore.dao.IncoreDatasetDao
 
findByCreatorEmailAndTitleLike(String, String, int, int) - Method in class edu.illinois.ncsa.incore.dao.IncoreDatasetDao
 
findByCreatorEmailAndTitleLike(String, String) - Method in class edu.illinois.ncsa.jpa.dao.DatasetJPADao
 
findByCreatorEmailAndTitleLike(String, String, int, int) - Method in class edu.illinois.ncsa.jpa.dao.DatasetJPADao
 
findByCreatorEmailAndTitleLikeAndDeleted(String, String, boolean) - Method in class edu.illinois.ncsa.clowder.dao.DatasetClowderDao
 
findByCreatorEmailAndTitleLikeAndDeleted(String, String, boolean, int, int) - Method in class edu.illinois.ncsa.clowder.dao.DatasetClowderDao
 
findByCreatorEmailAndTitleLikeAndDeleted(String, String, boolean) - Method in interface edu.illinois.ncsa.domain.dao.DatasetDao
 
findByCreatorEmailAndTitleLikeAndDeleted(String, String, boolean, int, int) - Method in interface edu.illinois.ncsa.domain.dao.DatasetDao
 
findByCreatorEmailAndTitleLikeAndDeleted(String, String, boolean) - Method in class edu.illinois.ncsa.incore.dao.IncoreDatasetDao
 
findByCreatorEmailAndTitleLikeAndDeleted(String, String, boolean, int, int) - Method in class edu.illinois.ncsa.incore.dao.IncoreDatasetDao
 
findByCreatorEmailAndTitleLikeAndDeleted(String, String, boolean) - Method in class edu.illinois.ncsa.jpa.dao.DatasetJPADao
 
findByCreatorEmailAndTitleLikeAndDeleted(String, String, boolean, int, int) - Method in class edu.illinois.ncsa.jpa.dao.DatasetJPADao
 
findByDeleted(boolean) - Method in class edu.illinois.ncsa.clowder.dao.DatasetClowderDao
 
findByDeleted(boolean, int, int) - Method in class edu.illinois.ncsa.clowder.dao.DatasetClowderDao
 
findByDeleted(boolean) - Method in class edu.illinois.ncsa.clowder.dao.PersonClowderDao
 
findByDeleted(boolean) - Method in interface edu.illinois.ncsa.datawolf.domain.dao.ExecutionDao
 
findByDeleted(boolean, int, int) - Method in interface edu.illinois.ncsa.datawolf.domain.dao.ExecutionDao
 
findByDeleted(boolean) - Method in interface edu.illinois.ncsa.datawolf.domain.dao.WorkflowDao
 
findByDeleted(boolean) - Method in interface edu.illinois.ncsa.datawolf.domain.dao.WorkflowToolDao
 
findByDeleted(boolean) - Method in class edu.illinois.ncsa.datawolf.jpa.dao.ExecutionJPADao
 
findByDeleted(boolean, int, int) - Method in class edu.illinois.ncsa.datawolf.jpa.dao.ExecutionJPADao
 
findByDeleted(boolean) - Method in class edu.illinois.ncsa.datawolf.jpa.dao.WorkflowJPADao
 
findByDeleted(boolean) - Method in class edu.illinois.ncsa.datawolf.jpa.dao.WorkflowToolJPADao
 
findByDeleted(boolean) - Method in interface edu.illinois.ncsa.domain.dao.DatasetDao
 
findByDeleted(boolean, int, int) - Method in interface edu.illinois.ncsa.domain.dao.DatasetDao
 
findByDeleted(boolean) - Method in interface edu.illinois.ncsa.domain.dao.PersonDao
 
findByDeleted(boolean) - Method in class edu.illinois.ncsa.incore.dao.IncoreDatasetDao
 
findByDeleted(boolean, int, int) - Method in class edu.illinois.ncsa.incore.dao.IncoreDatasetDao
 
findByDeleted(boolean) - Method in class edu.illinois.ncsa.incore.dao.IncorePersonDao
 
findByDeleted(boolean) - Method in class edu.illinois.ncsa.jpa.dao.DatasetJPADao
 
findByDeleted(boolean, int, int) - Method in class edu.illinois.ncsa.jpa.dao.DatasetJPADao
 
findByDeleted(boolean) - Method in class edu.illinois.ncsa.jpa.dao.PersonJPADao
 
findByEmail(String) - Method in class edu.illinois.ncsa.clowder.dao.PersonClowderDao
 
findByEmail(String) - Method in interface edu.illinois.ncsa.domain.dao.PersonDao
 
findByEmail(String) - Method in class edu.illinois.ncsa.incore.dao.IncorePersonDao
 
findByEmail(String) - Method in class edu.illinois.ncsa.jpa.dao.PersonJPADao
 
findByExecutionId(String) - Method in interface edu.illinois.ncsa.datawolf.domain.dao.HPCJobInfoDao
 
findByExecutionId(String) - Method in interface edu.illinois.ncsa.datawolf.domain.dao.LogFileDao
 
findByExecutionId(String) - Method in class edu.illinois.ncsa.datawolf.jpa.dao.HPCJobInfoJPADao
 
findByExecutionId(String) - Method in class edu.illinois.ncsa.datawolf.jpa.dao.LogFileJPADao
 
findByExecutionIdAndStepId(String, String) - Method in interface edu.illinois.ncsa.datawolf.domain.dao.LogFileDao
 
findByExecutionIdAndStepId(String, String) - Method in class edu.illinois.ncsa.datawolf.jpa.dao.LogFileJPADao
 
findByTitleLike(String) - Method in class edu.illinois.ncsa.clowder.dao.DatasetClowderDao
 
findByTitleLike(String, int, int) - Method in class edu.illinois.ncsa.clowder.dao.DatasetClowderDao
 
findByTitleLike(String) - Method in interface edu.illinois.ncsa.domain.dao.DatasetDao
 
findByTitleLike(String, int, int) - Method in interface edu.illinois.ncsa.domain.dao.DatasetDao
 
findByTitleLike(String) - Method in class edu.illinois.ncsa.incore.dao.IncoreDatasetDao
 
findByTitleLike(String, int, int) - Method in class edu.illinois.ncsa.incore.dao.IncoreDatasetDao
 
findByTitleLike(String) - Method in class edu.illinois.ncsa.jpa.dao.DatasetJPADao
 
findByTitleLike(String, int, int) - Method in class edu.illinois.ncsa.jpa.dao.DatasetJPADao
 
findByTitleLikeAndDeleted(String, boolean) - Method in class edu.illinois.ncsa.clowder.dao.DatasetClowderDao
 
findByTitleLikeAndDeleted(String, boolean, int, int) - Method in class edu.illinois.ncsa.clowder.dao.DatasetClowderDao
 
findByTitleLikeAndDeleted(String, boolean) - Method in interface edu.illinois.ncsa.domain.dao.DatasetDao
 
findByTitleLikeAndDeleted(String, boolean, int, int) - Method in interface edu.illinois.ncsa.domain.dao.DatasetDao
 
findByTitleLikeAndDeleted(String, boolean) - Method in class edu.illinois.ncsa.incore.dao.IncoreDatasetDao
 
findByTitleLikeAndDeleted(String, boolean, int, int) - Method in class edu.illinois.ncsa.incore.dao.IncoreDatasetDao
 
findByTitleLikeAndDeleted(String, boolean) - Method in class edu.illinois.ncsa.jpa.dao.DatasetJPADao
 
findByTitleLikeAndDeleted(String, boolean, int, int) - Method in class edu.illinois.ncsa.jpa.dao.DatasetJPADao
 
findByToken(String) - Method in interface edu.illinois.ncsa.domain.dao.AccountDao
 
findByToken(String) - Method in class edu.illinois.ncsa.jpa.dao.AccountJPADao
 
findByUserid(String) - Method in interface edu.illinois.ncsa.domain.dao.AccountDao
 
findByUserid(String) - Method in class edu.illinois.ncsa.jpa.dao.AccountJPADao
 
findByWorkflowId(String) - Method in interface edu.illinois.ncsa.datawolf.domain.dao.ExecutionDao
 
findByWorkflowId(String, int, int) - Method in interface edu.illinois.ncsa.datawolf.domain.dao.ExecutionDao
 
findByWorkflowId(String) - Method in class edu.illinois.ncsa.datawolf.jpa.dao.ExecutionJPADao
 
findByWorkflowId(String, int, int) - Method in class edu.illinois.ncsa.datawolf.jpa.dao.ExecutionJPADao
 
findByWorkflowIdAndDeleted(String, boolean) - Method in interface edu.illinois.ncsa.datawolf.domain.dao.ExecutionDao
 
findByWorkflowIdAndDeleted(String, boolean, int, int) - Method in interface edu.illinois.ncsa.datawolf.domain.dao.ExecutionDao
 
findByWorkflowIdAndDeleted(String, boolean) - Method in class edu.illinois.ncsa.datawolf.jpa.dao.ExecutionJPADao
 
findByWorkflowIdAndDeleted(String, boolean, int, int) - Method in class edu.illinois.ncsa.datawolf.jpa.dao.ExecutionJPADao
 
findClass(String) - Method in class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
Find the specified class in our local repositories, if possible.
findClassInternal(String) - Method in class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
Find specified class in local repositories.
findCommonPrefix(URI, URI) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.PathUtils
Tries to determine the path from root to the nearest common ancestor of the two uri paths, if any.
findExecutor(String) - Method in class edu.illinois.ncsa.datawolf.Engine
Find an executor that fits the given name.
findJavaTools(MultipartFormDataInput) - Method in class edu.illinois.ncsa.datawolf.service.ExecutorsResource
Discovers available JavaTools included in set of Jar files
findLoadedClass0(String) - Method in class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
Finds the class with the given name if it has previously been loaded and cached by this class loader, and return the Class object.
findLoadedResource(String) - Method in class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
Finds the resource with the given name if it has previously been loaded and cached by this class loader, and return an input stream to the resource data.
findOne(ID) - Method in class edu.illinois.ncsa.clowder.dao.AbstractClowderDao
 
findOne(String) - Method in class edu.illinois.ncsa.clowder.dao.DatasetClowderDao
 
findOne(String) - Method in class edu.illinois.ncsa.clowder.dao.PersonClowderDao
 
findOne(ID) - Method in interface edu.illinois.ncsa.domain.dao.IDao
 
findOne(String) - Method in class edu.illinois.ncsa.incore.dao.IncoreDatasetDao
 
findOne(String) - Method in class edu.illinois.ncsa.incore.dao.IncoreFileDescriptorDao
 
findOne(String) - Method in class edu.illinois.ncsa.incore.dao.IncorePersonDao
 
findOne(ID) - Method in class edu.illinois.ncsa.jpa.dao.AbstractJPADao
 
findResource(String) - Method in class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
Find the specified resource in our local repository, and return a URL refering to it, or null if this resource cannot be found.
findResourceInternal(String, String) - Method in class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
Find specified resource in local repositories.
findResources(String) - Method in class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
Return an enumeration of URLs representing all of the resources with the given name.
flags - Variable in class edu.illinois.ncsa.gondola.types.submission.RegexType
 
FLOT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
FLOT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
flush() - Method in class edu.illinois.ncsa.datawolf.executor.hpc.util.OutputPipe
If log is true, logs the current buffer as info; if file exists, writes it to file and flushes.
flushLog() - Method in class edu.illinois.ncsa.datawolf.Executor
 
fout - Variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.OutputPipe
 
from - Variable in class edu.illinois.ncsa.gondola.types.submission.ExpressionGroupTranslatorType
 
fromValue(String) - Static method in enum edu.illinois.ncsa.gondola.types.submission.JobStateType
 

G

getAllFileDescriptors(int, int) - Method in class edu.illinois.ncsa.file.service.FilesResource
get all file-descriptors
getBean(Class<T>) - Static method in class edu.illinois.ncsa.domain.Persistence
 
getBeanType() - Method in class edu.illinois.ncsa.domain.event.ObjectCreatedHandler
 
getBeanType() - Method in class edu.illinois.ncsa.domain.event.ObjectRemovedHandler
 
getBeanType() - Method in class edu.illinois.ncsa.domain.event.ObjectSelectedHandler
 
getBeanType() - Method in class edu.illinois.ncsa.domain.event.ObjectUpdatedHandler
 
getBlobs() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Return the set of blobs associated with the workflow too.
getCancelQueue() - Method in class edu.illinois.ncsa.gondola.types.service.ServiceType
Gets the value of the cancelQueue property.
getCaptureStdErr() - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineImplementation
 
getCaptureStdErr() - Method in class edu.illinois.ncsa.datawolf.executor.hpc.HPCToolImplementation
 
getCaptureStdOut() - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineImplementation
 
getCaptureStdOut() - Method in class edu.illinois.ncsa.datawolf.executor.hpc.HPCToolImplementation
 
getChecksumValue(String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.FileUtils
Checksum using java.util.zip.
getCommandArgs() - Method in class edu.illinois.ncsa.gondola.types.submission.StatusHandlerType
Gets the value of the commandArgs property.
getCommandLineOptions() - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineImplementation
 
getCommandLineOptions() - Method in class edu.illinois.ncsa.datawolf.executor.hpc.HPCToolImplementation
 
getCommandPath() - Method in class edu.illinois.ncsa.gondola.types.submission.StatusHandlerType
Gets the value of the commandPath property.
getContent() - Method in class edu.illinois.ncsa.gondola.types.service.ConnectionType
Gets the value of the content property.
getContent() - Method in class edu.illinois.ncsa.gondola.types.service.DbcpType.Property
Gets the value of the content property.
getContent() - Method in class edu.illinois.ncsa.gondola.types.submission.LineType
Gets the value of the content property.
getContent() - Method in class edu.illinois.ncsa.gondola.types.submission.RegexType
Gets the value of the content property.
getContributors() - Method in class edu.illinois.ncsa.datawolf.domain.Workflow
Return the set of PersonBeans that represents those that are contributors to the workflow.
getContributors() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Return the set of PersonBeans that represents those that are contributors to the workflow tool.
getContributors() - Method in class edu.illinois.ncsa.domain.Dataset
Return the set of PersonBeans that represents those that are contributors to the artifact.
getCreated() - Method in class edu.illinois.ncsa.datawolf.domain.Workflow
Return the date when the workflow was created.
getCreateDate() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowStep
Return the date when the workflow step was created.
getCreator() - Method in class edu.illinois.ncsa.datawolf.domain.Execution
Return the PersonBean that is the creator of the execution
getCreator() - Method in class edu.illinois.ncsa.datawolf.domain.Workflow
Return the PersonBean that is the creator of the workflow
getCreator() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowStep
Return the PersonBean that is the creator of the workflow
getCreator() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Return the PersonBean that is the creator of the workflow tool
getCreator() - Method in class edu.illinois.ncsa.domain.Dataset
Return the PersonBean that is the creator of the artifact
getCreatorId() - Method in class edu.illinois.ncsa.datawolf.domain.Submission
Return the id of the creator of the execution
getDapDatasets(List<String>, String, String, Person) - Static method in class edu.illinois.ncsa.datawolf.service.utils.WorkflowUtil
 
getDAPLogFile(String, String, String) - Static method in class edu.illinois.ncsa.datawolf.service.utils.WorkflowUtil
 
getDAPScript() - Static method in class edu.illinois.ncsa.datawolf.service.utils.WorkflowUtil
Create DataWolf tool shell script for calling SoftwareServers
getDataId() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolData
Return the id of the workflow tool data.
getDataset(String) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
Returns the value for a specific dataset.
getDataset(String) - Method in class edu.illinois.ncsa.datawolf.domain.Submission
Returns the value for a specific dataset.
getDataset(String) - Static method in class edu.illinois.ncsa.datawolf.service.client.DataWolfServiceClient
 
getDataset(String) - Method in class edu.illinois.ncsa.datawolf.service.DatasetsResource
Get a dataset by Id
getDataset(JsonObject, Person) - Static method in class edu.illinois.ncsa.incore.IncoreDataset
 
getDatasets() - Method in class edu.illinois.ncsa.datawolf.domain.Execution
 
getDatasets() - Method in class edu.illinois.ncsa.datawolf.domain.Submission
Returns a map fof all datasets to be used as inputs.
getDatasets(int, int, String, String, boolean) - Method in class edu.illinois.ncsa.datawolf.service.DatasetsResource
Get all datasets
getDatasets(int, int) - Method in class edu.illinois.ncsa.datawolf.service.LogFilesResource
Get all logfiles
getDatasetZip(String) - Method in class edu.illinois.ncsa.datawolf.service.DatasetsResource
Get a dataset in zip with all other files by Id
getDataURL() - Method in class edu.illinois.ncsa.domain.FileDescriptor
 
getDate() - Method in class edu.illinois.ncsa.datawolf.domain.Execution
Return the date when the execution was created.
getDate() - Method in class edu.illinois.ncsa.datawolf.domain.LogFile
Returns the date of when this log message was creaed.
getDate() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Return the date when the workflow tool was created.
getDate(long) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.DateUtils
Uses current system time if millis < 0.
getDate() - Method in class edu.illinois.ncsa.domain.Dataset
Return the date when the artifact was created.
getDateFromDateString(String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.DateUtils
Converts date-time String into Date object using the default formatter.
getDateFromDateString(String, String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.DateUtils
Converts date-time String into Date object using the default formatter.
getDateFromTimeString(String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.DateUtils
Uses current system time if timeString is null.
getDateString(Date) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.DateUtils
Converts Date object to String representation using the default formatter.
getDateString(Date, String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.DateUtils
Converts Date object to String representation using the given format string.
getDateString(long) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.DateUtils
Converts millisecond value to (default) formatted date string.
getDateString(long, DateFormat) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.DateUtils
 
getDateString(long, String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.DateUtils
 
getDaysBetween(Calendar, Calendar) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.DateUtils
Calculates the number of days between two calendar days in a manner which is independent of the Calendar type used.
getDefaultDAOs() - Method in class edu.illinois.ncsa.datawolf.service.PersistenceModule
 
getDescription() - Method in class edu.illinois.ncsa.datawolf.domain.Execution
Return the description of the execution.
getDescription() - Method in class edu.illinois.ncsa.datawolf.domain.Submission
Return the description of the execution.
getDescription() - Method in class edu.illinois.ncsa.datawolf.domain.Workflow
Return the description of the workflow.
getDescription() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Return the description of the workflow tool.
getDescription() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolData
Return the description of the workflow tool data.
getDescription() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolParameter
Return the description of the workflow parameter.
getDescription() - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Dataset
Return the description of the dataset.
getDescription() - Method in interface edu.illinois.ncsa.datawolf.executor.java.tool.JavaTool
Long textual description of the tool.
getDescription() - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Parameter
Return the description of the parameter.
getDescription() - Method in class edu.illinois.ncsa.datawolf.tool.example.ShiftCharsTool
 
getDescription() - Method in class edu.illinois.ncsa.domain.Dataset
Return the description of the artifact.
getDriverClass() - Method in class edu.illinois.ncsa.gondola.types.service.ConnectionType
Gets the value of the driverClass property.
getDrop() - Method in class edu.illinois.ncsa.gondola.types.service.AccessType
Gets the value of the drop property.
getDTSShellScript() - Static method in class edu.illinois.ncsa.datawolf.service.utils.WorkflowUtil
Shell script to run DTS extractor
getDTSTools(String, String, String) - Static method in class edu.illinois.ncsa.datawolf.service.utils.WorkflowUtil
Get list of DTS tools
getEmail() - Method in class edu.illinois.ncsa.domain.Person
Gets the email of the person.
getEntityManager() - Method in class edu.illinois.ncsa.jpa.dao.AbstractJPADao
 
getEntityType() - Method in class edu.illinois.ncsa.jpa.dao.AbstractJPADao
 
getEnv() - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineImplementation
 
getEventType() - Method in class edu.illinois.ncsa.datawolf.domain.event.WorkflowToolChangedEvent
 
getEventType() - Method in class edu.illinois.ncsa.datawolf.domain.event.WorkflowToolCreatedEvent
 
getEventType() - Method in class edu.illinois.ncsa.datawolf.domain.event.WorkflowToolDeletedEvent
 
getEventType() - Method in class edu.illinois.ncsa.datawolf.event.StepStateChangedEvent
 
getEventType() - Method in interface edu.illinois.ncsa.domain.event.Event
 
getEventType() - Method in class edu.illinois.ncsa.domain.event.ObjectCreatedEvent
 
getEventType() - Method in class edu.illinois.ncsa.domain.event.ObjectRemovedEvent
 
getEventType() - Method in class edu.illinois.ncsa.domain.event.ObjectSelectedEvent
 
getEventType() - Method in class edu.illinois.ncsa.domain.event.ObjectUpdatedEvent
 
getExecChannel() - Method in class edu.illinois.ncsa.datawolf.executor.hpc.ssh.SSHSession
The main purpose of the SSH connection: to do an exec.
getExecutable() - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineImplementation
 
getExecutable() - Method in class edu.illinois.ncsa.datawolf.executor.hpc.HPCToolImplementation
 
getExecute() - Method in class edu.illinois.ncsa.gondola.types.service.InitializeType
Gets the value of the execute property.
getExecution() - Method in class edu.illinois.ncsa.datawolf.event.StepStateChangedEvent
 
getExecution(String) - Static method in class edu.illinois.ncsa.datawolf.service.client.DataWolfServiceClient
 
getExecution(String) - Method in class edu.illinois.ncsa.datawolf.service.ExecutionsResource
Get a execution by Id
getExecutionId() - Method in class edu.illinois.ncsa.datawolf.domain.HPCJobInfo
Return the execution id assigned by the engine
getExecutionId() - Method in class edu.illinois.ncsa.datawolf.domain.LogFile
 
getExecutionId() - Method in class edu.illinois.ncsa.datawolf.Executor
Returns the id of the execution associated with this executor.
getExecutions(int, int, String, String, String, boolean) - Method in class edu.illinois.ncsa.datawolf.service.ExecutionsResource
Get all executions
getExecutions(String, int, int, boolean) - Method in class edu.illinois.ncsa.datawolf.service.WorkflowsResource
Get all executions by workflow id
getExecutionsByEmail(String) - Static method in class edu.illinois.ncsa.datawolf.service.client.DataWolfServiceClient
 
getExecutionsByEmail(String, int, int) - Static method in class edu.illinois.ncsa.datawolf.service.client.DataWolfServiceClient
 
getExecutor() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Return the executor of the tool
getExecutorName() - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineExecutor
 
getExecutorName() - Method in class edu.illinois.ncsa.datawolf.Executor
Name of the executor.
getExecutorName() - Method in class edu.illinois.ncsa.datawolf.executor.hpc.HPCExecutor
 
getExecutorName() - Method in class edu.illinois.ncsa.datawolf.executor.java.JavaExecutor
 
getExecutors() - Method in class edu.illinois.ncsa.datawolf.Engine
 
getExecutors() - Method in class edu.illinois.ncsa.datawolf.service.ExecutorsResource
Get all available executors
getExpression() - Method in class edu.illinois.ncsa.gondola.types.submission.ParserType
Gets the value of the expression property.
getExtraLocalExecutor() - Method in class edu.illinois.ncsa.datawolf.Engine
The number of additional jobs that can be scheduled on the local executor.
getFile(URL) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.UriUtils
For local file conversion.
getFile(String, String) - Method in class edu.illinois.ncsa.datawolf.service.DatasetsResource
get the file with given id
getFile(String) - Static method in class edu.illinois.ncsa.file.service.client.FileServiceClient
 
getFile(String) - Method in class edu.illinois.ncsa.file.service.FilesResource
get the file with given id
getFileDescriptor(String, String) - Method in class edu.illinois.ncsa.datawolf.service.DatasetsResource
Get a FileDescriptor by dataset-Id and filedescriptor-id
getFileDescriptor(String) - Static method in class edu.illinois.ncsa.file.service.client.FileServiceClient
 
getFileDescriptor(String) - Method in class edu.illinois.ncsa.file.service.FilesResource
get a file-descriptor with given id
getFileDescriptors() - Method in class edu.illinois.ncsa.domain.Dataset
Return the set of file descriptors associated with the dataset.
getFilename() - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineOption
 
getFilename() - Method in class edu.illinois.ncsa.domain.FileDescriptor
If this dataset originated in a filesystem, or is intended to be stored in a filesystem, what filename is/should be used? If not, will return null.
getFirstName() - Method in class edu.illinois.ncsa.domain.Person
Gets the first name of the person.
getFlag() - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineOption
 
getFlags(String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.handlers.JobInfoParser
Translates the string representation of the flags into the corresponding Java int value.
getFlags() - Method in class edu.illinois.ncsa.gondola.types.submission.RegexType
Gets the value of the flags property.
getFolder() - Method in class edu.illinois.ncsa.domain.impl.FileStorageDisk
 
getForm() - Method in class edu.illinois.ncsa.file.service.FilesResource
get a file-descriptor with given id
getFormattedErrorString(String, Throwable) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.ExceptionUtils
 
getFrom() - Method in class edu.illinois.ncsa.gondola.types.submission.ExpressionGroupTranslatorType
Gets the value of the from property.
getGondolaLogFile() - Method in class edu.illinois.ncsa.datawolf.executor.hpc.HPCExecutor
 
getGroup() - Method in class edu.illinois.ncsa.gondola.types.submission.ExpressionGroupTranslatorType
Gets the value of the group property.
getHostCertDir() - Method in class edu.illinois.ncsa.gondola.types.service.MyProxyType
Gets the value of the hostCertDir property.
getHpcFile(String, String) - Method in class edu.illinois.ncsa.datawolf.service.KistiHPCResource
 
getID() - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Dataset
Return the id of the dataset.
getID() - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Parameter
Return the id of the parameter.
getId() - Method in class edu.illinois.ncsa.domain.AbstractBean
Return the id of the bean.
getId() - Method in class edu.illinois.ncsa.gondola.types.submission.IdListType
Gets the value of the id property.
getId() - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Gets the value of the id property.
getImplementation() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Return the implementation of the tool
getInfo() - Method in class edu.illinois.ncsa.datawolf.executor.hpc.ssh.SSHSession
 
getInitialize() - Method in class edu.illinois.ncsa.gondola.types.service.AccessType
Gets the value of the initialize property.
getInitializeQueue() - Method in class edu.illinois.ncsa.gondola.types.service.ServiceType
Gets the value of the initializeQueue property.
getInjector() - Method in class edu.illinois.ncsa.datawolf.service.GuiceContextListener
 
getInput(String) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowStep
Returns a specific input.
getInput(String) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Return the input associated with this id.
getInputOutput() - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineOption
 
getInputs() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowStep
Returns a map of inputs from the workflow step.
getInputs() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Return the collection of datasets that are inputs to the tool.
getInputs() - Method in interface edu.illinois.ncsa.datawolf.executor.java.tool.JavaTool
Retrieve list of inputs for the tool.
getInputs() - Method in class edu.illinois.ncsa.datawolf.tool.example.ShiftCharsTool
 
getInputsToolData() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowStep
Returns a map of id of step's input to the tool's data definition.
getInstanceId() - Method in class edu.illinois.ncsa.gondola.types.submission.JobStatusType
Gets the value of the instanceId property.
getInstanceId() - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Gets the value of the instanceId property.
getJdbcAccess() - Method in class edu.illinois.ncsa.gondola.types.service.ServiceType
Gets the value of the jdbcAccess property.
getJdbcConnection() - Method in class edu.illinois.ncsa.gondola.types.service.AccessType
Gets the value of the jdbcConnection property.
getJdbcDbcp() - Method in class edu.illinois.ncsa.gondola.types.service.AccessType
Gets the value of the jdbcDbcp property.
getJobId() - Method in class edu.illinois.ncsa.datawolf.domain.HPCJobInfo
Return the job id from the scheduler
getJobId() - Method in class edu.illinois.ncsa.gondola.types.submission.JobStatusType
Gets the value of the jobId property.
getJobIdGroup() - Method in class edu.illinois.ncsa.gondola.types.submission.ParserType
Gets the value of the jobIdGroup property.
getJobIdParser() - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Gets the value of the jobIdParser property.
getJobStatus(String) - Method in interface edu.illinois.ncsa.gondola.ISubmissionEngine
 
getJobStatus(IdListType) - Method in interface edu.illinois.ncsa.gondola.ISubmissionEngineImpl
 
getJobStatus() - Method in class edu.illinois.ncsa.gondola.types.submission.JobStatusListType
Gets the value of the jobStatus property.
getKey() - Method in class edu.illinois.ncsa.clowder.dao.AbstractClowderDao
 
getKey(URI) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.UriUtils
 
getKey(String) - Method in class edu.illinois.ncsa.datawolf.service.LoginResource
Gets the key/token associated with a user account
getLastName() - Method in class edu.illinois.ncsa.domain.Person
Gets the last name of the person.
getLCSuffix(String, String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.StringUtils
 
getLevels() - Method in class edu.illinois.ncsa.domain.impl.FileStorageDisk
 
getLine() - Method in class edu.illinois.ncsa.gondola.types.submission.ScriptType
Gets the value of the line property.
getLog() - Method in class edu.illinois.ncsa.datawolf.domain.LogFile
Returns the filedescriptor of the log message.
getLog() - Method in class edu.illinois.ncsa.datawolf.Executor
Return any log information.
getLog() - Method in class edu.illinois.ncsa.datawolf.executor.hpc.HPCToolImplementation
 
getLogFile(String) - Method in class edu.illinois.ncsa.datawolf.service.LogFilesResource
Get a dataset by Id
getLogfiles(String) - Method in class edu.illinois.ncsa.datawolf.service.ExecutionsResource
Get all logfiles belonging to the execution
getLogfiles(String, String) - Method in class edu.illinois.ncsa.datawolf.service.ExecutionsResource
Get the logfile belonging to a single step of the execution
getMaxBatchInsert() - Method in class edu.illinois.ncsa.gondola.types.service.AccessType
Gets the value of the maxBatchInsert property.
getMd5sum() - Method in class edu.illinois.ncsa.domain.FileDescriptor
 
getMd5sumAsBigInteger() - Method in class edu.illinois.ncsa.domain.FileDescriptor
Returns the md5sum as a string of length 32.
getMd5sumAsBytes() - Method in class edu.illinois.ncsa.domain.FileDescriptor
 
getMetadata(String, String, String) - Static method in class edu.illinois.ncsa.datawolf.service.utils.WorkflowUtil
Get metadata for file extraction from api/files/{file-id}/metadata.jsonld
getMetadataJsonLD(String, String, String) - Static method in class edu.illinois.ncsa.datawolf.service.utils.WorkflowUtil
Get metadata for file extraction from api/files/{file-id}/metadata.jsonld
getMimeType() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolData
Return the mime type of the workflow tool data.
getMimeType() - Method in class edu.illinois.ncsa.domain.FileDescriptor
Return the mime type of the artifact.
getMiniAccount() - Method in class edu.illinois.ncsa.domain.Account
 
getMinutesBetween(Calendar, Calendar) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.DateUtils
Calculates the number of minutes between two dates in a manner which is independent of the Calendar type used.
getModules(ServletContext) - Method in class edu.illinois.ncsa.datawolf.service.GuiceContextListener
 
getMyproxySettings() - Method in class edu.illinois.ncsa.gondola.types.service.ServiceType
Gets the value of the myproxySettings property.
getMyproxyUser() - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Gets the value of the myproxyUser property.
getName(URI) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.PathUtils
Derives name from uri.
getName() - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Dataset
Return the name of the dataset.
getName() - Method in interface edu.illinois.ncsa.datawolf.executor.java.tool.JavaTool
Return the name of the tool.
getName() - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Parameter
Return the name of the paraemter.
getName() - Method in class edu.illinois.ncsa.datawolf.tool.example.ShiftCharsTool
 
getName() - Method in class edu.illinois.ncsa.domain.Person
This will return the formatted name.
getName() - Method in class edu.illinois.ncsa.gondola.types.service.DbcpType
Gets the value of the name property.
getName() - Method in class edu.illinois.ncsa.gondola.types.service.DbcpType.Property
Gets the value of the name property.
getNewState() - Method in class edu.illinois.ncsa.datawolf.event.StepStateChangedEvent
 
getNormalizedPath(URI) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.PathUtils
 
getOp() - Method in class edu.illinois.ncsa.gondola.types.submission.ExpressionGroupTranslatorType
Gets the value of the op property.
getOptionId() - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineOption
 
getOptions() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolParameter
Return the list of options for this parameter.
getOptions() - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Parameter
Returns array with all allowable options.
getOutput(String) - Method in class edu.illinois.ncsa.datawolf.domain.Workflow
 
getOutput(String) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowStep
Returns a specific output.
getOutput(String) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Return the output associated with this id.
getOutput(String) - Method in interface edu.illinois.ncsa.datawolf.executor.java.tool.JavaTool
Retrieve a specific output.
getOutput(String) - Method in class edu.illinois.ncsa.datawolf.tool.example.ShiftCharsTool
 
getOutputs() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowStep
Returns a map of outputs from the workflow step.
getOutputs() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Return the collection of datasets that are outputs to the tool.
getOutputs() - Method in interface edu.illinois.ncsa.datawolf.executor.java.tool.JavaTool
Retrieve list of outputs for the tool.
getOutputs() - Method in class edu.illinois.ncsa.datawolf.tool.example.ShiftCharsTool
 
getOutputsToolData() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowStep
Returns a map of id of step's output to the tool's data definition.
getParameter(String) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
Returns the value for a specific parameter.
getParameter(String) - Method in class edu.illinois.ncsa.datawolf.domain.Submission
Returns the value for a specific parameter.
getParameter(String) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowStep
Returns a specific parameter.
getParameter(String) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Return the parameter associated with this id.
getParameterId() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolParameter
Return the id of the workflow parameter.
getParameters() - Method in class edu.illinois.ncsa.datawolf.domain.Execution
 
getParameters() - Method in class edu.illinois.ncsa.datawolf.domain.Submission
Returs the map of all parameters.
getParameters() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowStep
Returns a map of parameters from the workflow step.
getParameters() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Return the collection of parameters of the tool.
getParameters() - Method in interface edu.illinois.ncsa.datawolf.executor.java.tool.JavaTool
Retrieve list of parameters for the tool.
getParameters() - Method in class edu.illinois.ncsa.datawolf.tool.example.ShiftCharsTool
 
getParent(URI) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.PathUtils
Derives parent uri from uri.
getParser() - Method in class edu.illinois.ncsa.gondola.types.submission.StatusHandlerType
Gets the value of the parser property.
getPassphrase() - Method in class edu.illinois.ncsa.datawolf.executor.hpc.ssh.SSHInfo
 
getPassword() - Method in class edu.illinois.ncsa.datawolf.executor.hpc.ssh.SSHInfo
 
getPassword() - Method in class edu.illinois.ncsa.domain.Account
 
getPassword() - Method in class edu.illinois.ncsa.gondola.types.service.ConnectionType
Gets the value of the password property.
getPerson(String) - Method in class edu.illinois.ncsa.datawolf.service.PersonsResource
Get a dataset by Id
getPerson() - Method in class edu.illinois.ncsa.domain.Account
 
getPersonByEmail(String) - Static method in class edu.illinois.ncsa.datawolf.service.client.DataWolfServiceClient
 
getPersons(int, int, String, boolean) - Method in class edu.illinois.ncsa.datawolf.service.PersonsResource
Get all users
getPrefix(String, String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.StringUtils
 
getPreviousVersion() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Return the previous version of the workflow tool.
getProperties() - Method in class edu.illinois.ncsa.datawolf.domain.Execution
 
getProperty(String) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
 
getProperty() - Method in class edu.illinois.ncsa.gondola.types.service.DbcpType
Gets the value of the property property.
getProxyMarginInMins() - Method in class edu.illinois.ncsa.gondola.types.service.MyProxyType
Gets the value of the proxyMarginInMins property.
getProxyRefreshInMins() - Method in class edu.illinois.ncsa.gondola.types.service.MyProxyType
Gets the value of the proxyRefreshInMins property.
getQueueRefreshInSecs() - Method in class edu.illinois.ncsa.gondola.types.service.ServiceType
Gets the value of the queueRefreshInSecs property.
getRandomizedId(String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.StringUtils
Returns an id with a pretty good chance of being unique, by appending to the given prefix the date, host and a random long.
getRandomizedId(String, boolean, boolean, boolean, boolean) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.StringUtils
Returns an id by appending to the given prefix the date, host and a random long.
getRedirect(HttpRequest, HttpResponse, HttpContext) - Method in class edu.illinois.ncsa.clowder.ClowderRedirectStrategy
 
getRelativePath(URI, URI) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.PathUtils
Determines the relative path of the second URI with respect to the first.
getRelativePath(URI, URI, boolean) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.PathUtils
Determines the relative path of the second URI with respect to the first.
getRemoteLog() - Method in class edu.illinois.ncsa.datawolf.executor.hpc.HPCExecutor
 
getRemoteLog() - Method in class edu.illinois.ncsa.datawolf.RemoteExecutor
Checks the remote server for any log messages.
getRequestedDao(Class<T>, String) - Method in class edu.illinois.ncsa.datawolf.service.PersistenceModule
 
getResource(String) - Method in class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
Find the resource with the given name.
getResourceAsStream(String) - Method in class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
Find the resource with the given name, and return an input stream that can be used for reading it.
getScript() - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Gets the value of the script property.
getSelectedBean() - Method in class edu.illinois.ncsa.domain.event.ObjectRemovedEvent
 
getSelectedBean() - Method in class edu.illinois.ncsa.domain.event.ObjectSelectedEvent
 
getSelectedBean() - Method in class edu.illinois.ncsa.domain.event.ObjectUpdatedEvent
 
getSelectedBeans() - Method in class edu.illinois.ncsa.domain.event.ObjectCreatedEvent
 
getSequenceId(String, long) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.StringUtils
Appends a sequence suffix to the base.
getServer() - Method in class edu.illinois.ncsa.clowder.dao.AbstractClowderDao
 
getServer() - Method in class edu.illinois.ncsa.clowder.impl.FileStorageClowder
 
getServer() - Method in class edu.illinois.ncsa.incore.dao.AbstractIncoreDao
IN-CORE Service endpoint
getServerUri() - Method in class edu.illinois.ncsa.gondola.types.service.MyProxyType
Gets the value of the serverUri property.
getServiceUserHome() - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Gets the value of the serviceUserHome property.
getSize() - Method in class edu.illinois.ncsa.domain.FileDescriptor
Returns the size of the blob, this is -2 if there is no blob associated or the size has not been computed.
getSpaces(int) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.StringUtils
 
getSshHome() - Method in class edu.illinois.ncsa.datawolf.executor.hpc.ssh.SSHInfo
 
getStackTrace(Throwable) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.ExceptionUtils
Redirects a stack trace into a String.
getStackTrace(Throwable) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.StringUtils
Deprecated.
use ExceptionUtils
getStandardError() - Method in class edu.illinois.ncsa.datawolf.domain.HPCJobInfo
Return the standard error from the job execution
getStandardOutput() - Method in class edu.illinois.ncsa.datawolf.domain.HPCJobInfo
Return the standard output from the job execution
getState() - Method in class edu.illinois.ncsa.datawolf.Executor
Return current state of the execution.
getState(String) - Static method in class edu.illinois.ncsa.datawolf.service.client.DataWolfServiceClient
 
getState(String) - Method in class edu.illinois.ncsa.datawolf.service.ExecutionsResource
Get the state all steps in an execution
getState() - Method in class edu.illinois.ncsa.gondola.types.submission.JobStatusType
Gets the value of the state property.
getStatusHandler() - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Gets the value of the statusHandler property.
getStatusRefreshInSecs() - Method in class edu.illinois.ncsa.gondola.types.service.ServiceType
Gets the value of the statusRefreshInSecs property.
getStderr() - Method in class edu.illinois.ncsa.datawolf.executor.hpc.handlers.JobInfoParser
 
getStderrError() - Method in class edu.illinois.ncsa.gondola.types.submission.ErrorHandlerType
Gets the value of the stderrError property.
getStderrWarn() - Method in class edu.illinois.ncsa.gondola.types.submission.ErrorHandlerType
Gets the value of the stderrWarn property.
getStdoutError() - Method in class edu.illinois.ncsa.gondola.types.submission.ErrorHandlerType
Gets the value of the stdoutError property.
getStdoutWarn() - Method in class edu.illinois.ncsa.gondola.types.submission.ErrorHandlerType
Gets the value of the stdoutWarn property.
getStep(String) - Method in class edu.illinois.ncsa.datawolf.domain.Workflow
Retrieve a specific step from the workflow.
getStep() - Method in class edu.illinois.ncsa.datawolf.event.StepStateChangedEvent
 
getStep(String, String) - Method in class edu.illinois.ncsa.datawolf.service.WorkflowsResource
Get a workflow step associated with a workflow
getStepEnd(String) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
Returns the end time of the step with the given id, or null if the step has not ended.
getStepId() - Method in class edu.illinois.ncsa.datawolf.domain.LogFile
 
getStepId() - Method in class edu.illinois.ncsa.datawolf.Executor
Returns the id of the step associated with this executor.
getStepQueued(String) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
Returns the queued time of the step with the given id, or null if the step has not been queued.
getSteps() - Method in class edu.illinois.ncsa.datawolf.domain.Workflow
Retrieve the list of steps of a workflow.
getSteps(String) - Method in class edu.illinois.ncsa.datawolf.Engine
 
getSteps(String) - Method in class edu.illinois.ncsa.datawolf.service.WorkflowsResource
Get steps associated with a workflow
getStepsEnd() - Method in class edu.illinois.ncsa.datawolf.domain.Execution
 
getStepsQueued() - Method in class edu.illinois.ncsa.datawolf.domain.Execution
 
getStepsStart() - Method in class edu.illinois.ncsa.datawolf.domain.Execution
 
getStepStart(String) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
Returns the start time of the step with the given id, or null if the step has not been started.
getStepState(String) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
Returns the state for a specific step.
getStepState() - Method in class edu.illinois.ncsa.datawolf.domain.Execution
 
getSubmissionTemplate(String, String) - Method in class edu.illinois.ncsa.datawolf.service.ExecutionsResource
 
getSubmitErrorHandler() - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Gets the value of the submitErrorHandler property.
getSubmitPath() - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Gets the value of the submitPath property.
getSubmitQueue() - Method in class edu.illinois.ncsa.gondola.types.service.ServiceType
Gets the value of the submitQueue property.
getSuffix(String, String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.StringUtils
 
getTargetUri() - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Gets the value of the targetUri property.
getTargetUser() - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Gets the value of the targetUser property.
getTargetUserHome() - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Gets the value of the targetUserHome property.
getTemplate() - Method in class edu.illinois.ncsa.datawolf.executor.hpc.HPCToolImplementation
 
getTerminatePath() - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Gets the value of the terminatePath property.
getTimeInMillis(long) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.DateUtils
Uses current system time if millis < 0.
getTimeInMillis(String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.DateUtils
Uses current system time if dateTime is null.
getTimeInMillis(String, String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.DateUtils
Uses current system time if dateTime is null.
getTimeout() - Method in class edu.illinois.ncsa.datawolf.Engine
Return the timout the engine will wait when no steps are ready to be executed, or executing before it declares the workflow aborted.
getTitle() - Method in class edu.illinois.ncsa.datawolf.domain.Execution
Return the title of the execution.
getTitle() - Method in class edu.illinois.ncsa.datawolf.domain.Submission
Return the title of the execution.
getTitle() - Method in class edu.illinois.ncsa.datawolf.domain.Workflow
Return the title of the workflow.
getTitle() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowStep
Return the title of the workflow step.
getTitle() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Return the title of the workflow tool.
getTitle() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolData
Return the title of the workflow tool data.
getTitle() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolParameter
Return the title of the workflow parameter.
getTitle() - Method in class edu.illinois.ncsa.domain.Dataset
Return the title of the artifact.
getTo() - Method in class edu.illinois.ncsa.gondola.types.submission.ExpressionGroupTranslatorType
Gets the value of the to property.
getToken(String) - Method in class edu.illinois.ncsa.clowder.dao.AbstractClowderDao
 
getToken(String, String) - Method in class edu.illinois.ncsa.clowder.impl.ClowderTokenProvider
 
getToken(String) - Method in class edu.illinois.ncsa.clowder.impl.FileStorageClowder
 
getToken() - Method in class edu.illinois.ncsa.domain.Account
 
getToken(String, String) - Method in class edu.illinois.ncsa.domain.impl.DataWolfTokenProvider
 
getToken(String, String) - Method in class edu.illinois.ncsa.domain.impl.LDAPTokenProvider
 
getToken(String, String) - Method in interface edu.illinois.ncsa.domain.TokenProvider
 
getTokenArray(String, String[], boolean, boolean) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.StringUtils
 
getTool() - Method in class edu.illinois.ncsa.datawolf.domain.event.WorkflowToolChangedEvent
 
getTool() - Method in class edu.illinois.ncsa.datawolf.domain.event.WorkflowToolCreatedEvent
 
getTool() - Method in class edu.illinois.ncsa.datawolf.domain.event.WorkflowToolDeletedEvent
 
getTool() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowStep
Return the tool for the workflow step.
getToolClassName() - Method in class edu.illinois.ncsa.datawolf.executor.java.JavaToolImplementation
 
getTranslator() - Method in class edu.illinois.ncsa.gondola.types.submission.ParserType
Gets the value of the translator property.
getType() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolParameter
Return the type of the workflow parameter.
getType() - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineOption
 
getType() - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Dataset
Return the type of the dataset.
getType() - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Parameter
Return the type of the parameter.
getType() - Method in class edu.illinois.ncsa.gondola.types.service.AccessType
Gets the value of the type property.
getUpdateQueue() - Method in class edu.illinois.ncsa.gondola.types.service.ServiceType
Gets the value of the updateQueue property.
getUri(String, String, int, String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.UriUtils
Constructs the uri string and creates a URI object.
getUri(String, String, String, int, String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.UriUtils
Constructs the uri string and creates a URI object.
getUri(String, URI) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.UriUtils
Constructs new uri from old, swapping out the old scheme for the new.
getUri(URI, String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.UriUtils
Constructs new uri from old, updating path.
getUri(URL) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.UriUtils
Constructs the uri from the url using protocol, host, port and path.
getURI(File) - Method in class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
Get URL.
getURIName(String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.PathUtils
Path is parsed using '/' as separator.
getURIName(URI) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.PathUtils
Derives name from uri; calls overloaded method.
getURIParent(String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.PathUtils
 
getURL(File, boolean) - Method in class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
Get URL.
getUser() - Method in class edu.illinois.ncsa.datawolf.executor.hpc.ssh.SSHInfo
 
getUser() - Method in class edu.illinois.ncsa.gondola.types.service.ConnectionType
Gets the value of the user property.
getUser(JsonObject) - Static method in class edu.illinois.ncsa.incore.IncoreUser
 
getUserid() - Method in class edu.illinois.ncsa.domain.Account
 
getUsers(HttpRequest) - Method in class edu.illinois.ncsa.datawolf.service.UsersResource
Returns basic user information
getValue() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolParameter
Return the value of the workflow parameter.
getValue() - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineOption
 
getValue() - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Parameter
Return the value of the parameter.
getVersion() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Return the version of the workflow tool.
getVersion() - Method in interface edu.illinois.ncsa.datawolf.executor.java.tool.JavaTool
Return the version number of the tool.
getVersion() - Method in class edu.illinois.ncsa.datawolf.tool.example.ShiftCharsTool
 
getWorkerPool() - Method in class edu.illinois.ncsa.gondola.types.service.ServiceType
Gets the value of the workerPool property.
getWorkers() - Static method in class edu.illinois.ncsa.datawolf.LocalExecutor
 
getWorkflow(String) - Static method in class edu.illinois.ncsa.datawolf.service.client.DataWolfServiceClient
 
getWorkflow(String) - Method in class edu.illinois.ncsa.datawolf.service.WorkflowsResource
Get a workflow by Id
getWorkflowId() - Method in class edu.illinois.ncsa.datawolf.domain.Execution
Return the workflow that was executed.
getWorkflowId() - Method in class edu.illinois.ncsa.datawolf.domain.Submission
Return the workflow that was executed.
getWorkflowJson(String) - Static method in class edu.illinois.ncsa.datawolf.service.client.DataWolfServiceClient
 
getWorkflows(int, int, String, boolean) - Method in class edu.illinois.ncsa.datawolf.service.WorkflowsResource
Get all workflows
getWorkflowTool(String) - Method in class edu.illinois.ncsa.datawolf.service.WorkflowToolsResource
Get a workflow tool by Id
getWorkflowTools(int, int, boolean, String) - Method in class edu.illinois.ncsa.datawolf.service.WorkflowToolsResource
Get all workflow tools
getWorkflowToolZip(String) - Method in class edu.illinois.ncsa.datawolf.service.WorkflowToolsResource
Export a workflow tool by id
getWorkflowZip(String) - Method in class edu.illinois.ncsa.datawolf.service.WorkflowsResource
Get a workflow by Id
getWorkingDir() - Method in class edu.illinois.ncsa.datawolf.domain.HPCJobInfo
Return the working directory for the job on the remote machine
getWorkingDirectory() - Method in class edu.illinois.ncsa.gondola.types.submission.JobStatusType
Gets the value of the workingDirectory property.
getX509Certificate() - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Gets the value of the x509Certificate property.
group - Variable in class edu.illinois.ncsa.gondola.types.submission.ExpressionGroupTranslatorType
 
GT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
GT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
GTGT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
GTGT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
GTLT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
GTLT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
GuiceContextListener - Class in edu.illinois.ncsa.datawolf.service
 
GuiceContextListener() - Constructor for class edu.illinois.ncsa.datawolf.service.GuiceContextListener
 

H

halt() - Method in interface edu.illinois.ncsa.gondola.IStoppable
User-defined method for allowing the run() method (or some other continuous looping process) to exit peacefully.
hasDataset(String) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
 
hasDataset(String) - Method in class edu.illinois.ncsa.datawolf.domain.Submission
 
hashCode() - Method in class edu.illinois.ncsa.domain.AbstractBean
Returns the hashcode of this object, which is the hashcode of the id.
hashCode() - Method in class edu.illinois.ncsa.domain.event.Event.Type
 
hasParameter(String) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
 
hasParameter(String) - Method in class edu.illinois.ncsa.datawolf.domain.Submission
 
hasProperty(String) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
 
hasStep(String, String) - Method in class edu.illinois.ncsa.datawolf.Engine
 
haveSameConnection(URI, URI) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.UriUtils
 
hostCertDir - Variable in class edu.illinois.ncsa.gondola.types.service.MyProxyType
 
HPCExecutor - Class in edu.illinois.ncsa.datawolf.executor.hpc
The HPCExecutor will launch remote jobs based on machine information provided in the XML template.
HPCExecutor() - Constructor for class edu.illinois.ncsa.datawolf.executor.hpc.HPCExecutor
 
HPCJobInfo - Class in edu.illinois.ncsa.datawolf.domain
 
HPCJobInfo() - Constructor for class edu.illinois.ncsa.datawolf.domain.HPCJobInfo
 
HPCJobInfoDao - Interface in edu.illinois.ncsa.datawolf.domain.dao
 
hpcJobInfoDao - Variable in class edu.illinois.ncsa.datawolf.executor.hpc.HPCExecutor
 
HPCJobInfoJPADao - Class in edu.illinois.ncsa.datawolf.jpa.dao
 
HPCJobInfoJPADao(Provider<EntityManager>) - Constructor for class edu.illinois.ncsa.datawolf.jpa.dao.HPCJobInfoJPADao
 
HPCToolImplementation - Class in edu.illinois.ncsa.datawolf.executor.hpc
 
HPCToolImplementation() - Constructor for class edu.illinois.ncsa.datawolf.executor.hpc.HPCToolImplementation
 
HTML_A_HREF_TAG_PATTERN - Static variable in class edu.illinois.ncsa.incore.IncoreDataset
 
HTML_A_TAG_PATTERN - Static variable in class edu.illinois.ncsa.incore.IncoreDataset
 
HYPH - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
HYPH - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 

I

id - Variable in class edu.illinois.ncsa.domain.Account.MiniAccount
 
id - Variable in class edu.illinois.ncsa.gondola.types.submission.IdListType
 
id - Variable in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
 
IDao<T,ID extends Serializable> - Interface in edu.illinois.ncsa.domain.dao
DAO interface for generic operations supported by all DAOs
IdListType - Class in edu.illinois.ncsa.gondola.types.submission
Java class for id-list-type complex type.
IdListType() - Constructor for class edu.illinois.ncsa.gondola.types.submission.IdListType
 
iEQ - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
Logical operations & comparators
iEQ - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
Logical operations & comparators
iEQUALS - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
iEQUALS - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
iGE - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
iGE - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
iGT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
iGT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
iLE - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
iLE - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
iLT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
iLT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
importDataset(File) - Static method in class edu.illinois.ncsa.datawolf.ImportExport
Imports the dataset from the zipfile.
ImportExport - Class in edu.illinois.ncsa.datawolf
 
ImportExport() - Constructor for class edu.illinois.ncsa.datawolf.ImportExport
 
importTool(File) - Static method in class edu.illinois.ncsa.datawolf.ImportExport
Imports the tool from the zipfile.
importWorkflow(File) - Static method in class edu.illinois.ncsa.datawolf.ImportExport
Imports the workflow from the zipfile.
INAME - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
INAME - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
IncoreDataset - Class in edu.illinois.ncsa.incore
 
IncoreDataset() - Constructor for class edu.illinois.ncsa.incore.IncoreDataset
 
IncoreDatasetDao - Class in edu.illinois.ncsa.incore.dao
 
IncoreDatasetDao() - Constructor for class edu.illinois.ncsa.incore.dao.IncoreDatasetDao
 
IncoreFileDescriptorDao - Class in edu.illinois.ncsa.incore.dao
 
IncoreFileDescriptorDao() - Constructor for class edu.illinois.ncsa.incore.dao.IncoreFileDescriptorDao
 
IncoreFileStorage - Class in edu.illinois.ncsa.incore.impl
 
IncoreFileStorage() - Constructor for class edu.illinois.ncsa.incore.impl.IncoreFileStorage
 
IncorePersonDao - Class in edu.illinois.ncsa.incore.dao
 
IncorePersonDao() - Constructor for class edu.illinois.ncsa.incore.dao.IncorePersonDao
 
IncoreUser - Class in edu.illinois.ncsa.incore
 
IncoreUser() - Constructor for class edu.illinois.ncsa.incore.IncoreUser
 
iNE - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
iNE - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
iNEQUALS - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
iNEQUALS - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
initialize - Variable in class edu.illinois.ncsa.gondola.types.service.AccessType
 
initializeQueue - Variable in class edu.illinois.ncsa.gondola.types.service.ServiceType
 
InitializeType - Class in edu.illinois.ncsa.gondola.types.service
Java class for initialize-type complex type.
InitializeType() - Constructor for class edu.illinois.ncsa.gondola.types.service.InitializeType
 
instanceId - Variable in class edu.illinois.ncsa.gondola.types.submission.JobStatusType
 
instanceId - Variable in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
 
INTG - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
INTG - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
isActive() - Method in class edu.illinois.ncsa.domain.Account
Check if user account is active
isAdmin() - Method in class edu.illinois.ncsa.domain.Account
Check if user account is an admin
isAllowEmpty() - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Parameter
Returns true if the parameter can be empty
isAllowNull() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolParameter
Return true if the parameter is allowed to be empty.
isAlways() - Method in class edu.illinois.ncsa.gondola.types.service.InitializeType
Gets the value of the always property.
isBusy() - Static method in class edu.illinois.ncsa.datawolf.LocalExecutor
 
isCommandline() - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineOption
 
isDebug() - Method in class edu.illinois.ncsa.datawolf.Executor
Get debug flag for the executor.
isDeleteAfterSubmit() - Method in class edu.illinois.ncsa.gondola.types.submission.ScriptType
Gets the value of the deleteAfterSubmit property.
isDeleted() - Method in class edu.illinois.ncsa.domain.AbstractBean
Should the bean be assumed to be deleted.
isDirectory(String, SSHSession) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.SshUtils
Checks for existence of directory.
isEnabled() - Method in class edu.illinois.ncsa.datawolf.service.AuthenticationInterceptor
 
isExecutorReady() - Method in class edu.illinois.ncsa.datawolf.Executor
Before a step is executed this will check to see if the executor is ready to run.
isFile(String, SSHSession) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.SshUtils
Checks for existence of file.
isHidden() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolParameter
Returns true if the workflow parameter should not be shown to the user.
isHidden() - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Parameter
Returns true if the parameter should not be shown to the user.
isHierarchicalUri(String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.UriUtils
SDH 01/06/09: This method shouldn't be used.
isJobStopped() - Method in class edu.illinois.ncsa.datawolf.Executor
Returns true if the job is stopped.
isJoinStdOutStdErr() - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineImplementation
 
isLog() - Method in class edu.illinois.ncsa.gondola.types.submission.LineType
Gets the value of the log property.
isOnExit() - Method in class edu.illinois.ncsa.gondola.types.service.DropType
Gets the value of the onExit property.
isRedirectable(String) - Method in class edu.illinois.ncsa.clowder.ClowderRedirectStrategy
 
isResource(URI) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.UriUtils
 
isSplit() - Method in class edu.illinois.ncsa.gondola.types.submission.RegexType
Gets the value of the split property.
isStderr() - Method in class edu.illinois.ncsa.gondola.types.submission.ParserType
Gets the value of the stderr property.
isStoreLog() - Method in class edu.illinois.ncsa.datawolf.Executor
Should the executor store the logfiles generated.
isStoreLogs() - Method in class edu.illinois.ncsa.datawolf.Engine
Returns true if the executors store the logfiles in the database.
isSupportsRelationalConstraints() - Method in class edu.illinois.ncsa.gondola.types.service.AccessType
Gets the value of the supportsRelationalConstraints property.
isTokenValid(String) - Method in class edu.illinois.ncsa.clowder.impl.ClowderTokenProvider
 
isTokenValid(String) - Method in class edu.illinois.ncsa.domain.impl.DataWolfTokenProvider
 
isTokenValid(String) - Method in class edu.illinois.ncsa.domain.impl.LDAPTokenProvider
 
isTokenValid(String) - Method in interface edu.illinois.ncsa.domain.TokenProvider
 
IStoppable - Interface in edu.illinois.ncsa.gondola
Threaded object which needs to be, or can be, shut down.
ISubmissionEngine - Interface in edu.illinois.ncsa.gondola
 
ISubmissionEngineImpl - Interface in edu.illinois.ncsa.gondola
 
IVALUE - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
IVALUE - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 

J

JavaExecutor - Class in edu.illinois.ncsa.datawolf.executor.java
Executor for java tools.
JavaExecutor() - Constructor for class edu.illinois.ncsa.datawolf.executor.java.JavaExecutor
 
JavaTool - Interface in edu.illinois.ncsa.datawolf.executor.java.tool
Definition of a tool for use with DataWolf.
JavaToolImplementation - Class in edu.illinois.ncsa.datawolf.executor.java
 
JavaToolImplementation() - Constructor for class edu.illinois.ncsa.datawolf.executor.java.JavaToolImplementation
 
JAXB - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
JAXB - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
JAXB_SERV_CONTEXT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
JAXB_SERV_CONTEXT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
JAXB_SUBM_CONTEXT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
JAXB_SUBM_CONTEXT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
JAXBUtils - Class in edu.illinois.ncsa.gondola.utils
Convenience methods for handling XML using JAXB.
jdbcAccess - Variable in class edu.illinois.ncsa.gondola.types.service.ServiceType
 
jdbcConnection - Variable in class edu.illinois.ncsa.gondola.types.service.AccessType
 
jdbcDbcp - Variable in class edu.illinois.ncsa.gondola.types.service.AccessType
 
JOB_SCRIPTS - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
JOB_SCRIPTS - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
jobId - Variable in class edu.illinois.ncsa.gondola.types.submission.JobStatusType
 
jobIdGroup - Variable in class edu.illinois.ncsa.gondola.types.submission.ParserType
 
jobIdParser - Variable in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
 
JobInfoParser - Class in edu.illinois.ncsa.datawolf.executor.hpc.handlers
 
JobInfoParser(ParserType) - Constructor for class edu.illinois.ncsa.datawolf.executor.hpc.handlers.JobInfoParser
 
JobStateType - Enum in edu.illinois.ncsa.gondola.types.submission
Java class for job-state-type.
jobStatus - Variable in class edu.illinois.ncsa.gondola.types.submission.JobStatusListType
 
JobStatusListType - Class in edu.illinois.ncsa.gondola.types.submission
Java class for job-status-list-type complex type.
JobStatusListType() - Constructor for class edu.illinois.ncsa.gondola.types.submission.JobStatusListType
 
JobStatusType - Class in edu.illinois.ncsa.gondola.types.submission
Java class for job-status-type complex type.
JobStatusType() - Constructor for class edu.illinois.ncsa.gondola.types.submission.JobStatusType
 
JobSubmissionType - Class in edu.illinois.ncsa.gondola.types.submission
Java class for job-submission-type complex type.
JobSubmissionType() - Constructor for class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
 
join(Thread) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.SystemUtils
Safety feature: checks to make sure the calling thread is not the thread on which the join is called, to avoid deadlock.
JPADevModule - Class in edu.illinois.ncsa.jpa
 
JPADevModule() - Constructor for class edu.illinois.ncsa.jpa.JPADevModule
 
JsonDateSerializer - Class in edu.illinois.ncsa.domain.jackson
 
JsonDateSerializer() - Constructor for class edu.illinois.ncsa.domain.jackson.JsonDateSerializer
 
JSONToObject(String, Class<T>) - Static method in class edu.illinois.ncsa.domain.util.BeanUtil
Converts a JSON string to an actual object.
JSONToObject(InputStream, Class<T>) - Static method in class edu.illinois.ncsa.domain.util.BeanUtil
Converts a JSON inputstream to an actual object.

K

KistiHPCResource - Class in edu.illinois.ncsa.datawolf.service
 
KistiHPCResource() - Constructor for class edu.illinois.ncsa.datawolf.service.KistiHPCResource
 

L

lastModified - Variable in class edu.illinois.ncsa.datawolf.executor.java.ResourceEntry
The "last modified" time of the origin file at the time this class was loaded, in milliseconds since the epoch.
LDAPTokenProvider - Class in edu.illinois.ncsa.domain.impl
 
LDAPTokenProvider() - Constructor for class edu.illinois.ncsa.domain.impl.LDAPTokenProvider
 
LEN - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
LEN - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
line - Variable in class edu.illinois.ncsa.gondola.types.submission.ScriptType
 
LINE_SEP - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
LINE_SEP - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
LINE_SEP_CHAR - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
LINE_SEP_CHAR - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
LineType - Class in edu.illinois.ncsa.gondola.types.submission
Java class for line-type complex type.
LineType() - Constructor for class edu.illinois.ncsa.gondola.types.submission.LineType
 
LITERAL - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
LITERAL - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
LN - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
LN - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
LNESC - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
LNESC - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
LNSEPESC - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
LNSEPESC - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
loadClass(String) - Method in class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
Load the class with the specified name.
loadClass(String, boolean) - Method in class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
Load the class with the specified name, searching using the following algorithm until it finds and returns the class.
loadedByThisOrChild(Class<? extends Object>) - Method in class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
Determine whether a class was loaded by this class loader or one of its child class loaders.
loadedClass - Variable in class edu.illinois.ncsa.datawolf.executor.java.ResourceEntry
Loaded class.
loaderDir - Variable in class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
Path where resources loaded from JARs will be extracted.
LocalExecutor - Class in edu.illinois.ncsa.datawolf
Abstract class representing a local executor.
LocalExecutor() - Constructor for class edu.illinois.ncsa.datawolf.LocalExecutor
 
LOCATION - Static variable in class edu.illinois.ncsa.incore.IncoreDataset
 
LOG - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
log - Variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.OutputPipe
 
LOG - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
log - Variable in class edu.illinois.ncsa.gondola.types.submission.LineType
 
LogFile - Class in edu.illinois.ncsa.datawolf.domain
A simple class to store the log.
LogFile() - Constructor for class edu.illinois.ncsa.datawolf.domain.LogFile
 
LogFileDao - Interface in edu.illinois.ncsa.datawolf.domain.dao
 
logFileDao - Variable in class edu.illinois.ncsa.datawolf.Executor
 
LogFileJPADao - Class in edu.illinois.ncsa.datawolf.jpa.dao
 
LogFileJPADao(Provider<EntityManager>) - Constructor for class edu.illinois.ncsa.datawolf.jpa.dao.LogFileJPADao
 
LogFilesResource - Class in edu.illinois.ncsa.datawolf.service
 
LogFilesResource() - Constructor for class edu.illinois.ncsa.datawolf.service.LogFilesResource
 
logger - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.OutputPipe
 
login(String, String) - Method in class edu.illinois.ncsa.datawolf.service.LoginResource
Login a user by email and authorization string
LoginResource - Class in edu.illinois.ncsa.datawolf.service
 
LoginResource() - Constructor for class edu.illinois.ncsa.datawolf.service.LoginResource
 
LoginUtil - Class in edu.illinois.ncsa.datawolf.service.utils
 
LoginUtil() - Constructor for class edu.illinois.ncsa.datawolf.service.utils.LoginUtil
 
LONG - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
LONG - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
LOOKING - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
LOOKING - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
LT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
LT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
LTS - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
LTS - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 

M

MAEVIZ_MAPPING - Static variable in class edu.illinois.ncsa.incore.IncoreDataset
 
manifest - Variable in class edu.illinois.ncsa.datawolf.executor.java.ResourceEntry
Manifest (if the resource was loaded from a JAR).
MANY_TO_ONE - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
MANY_TO_ONE - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
MATCHED - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
MATCHED - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
MATCHES - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
Regex filter settings
MATCHES - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
Regex filter settings
MAX_PATTERN_LENGTH - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
MAX_PATTERN_LENGTH - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
MAX_TAG_LENGTH - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
MAX_TAG_LENGTH - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
maxBatchInsert - Variable in class edu.illinois.ncsa.gondola.types.service.AccessType
 
maybeGetSession(URI, String, String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.SshUtils
 
maybeGetSession(URI, String, String) - Method in class edu.illinois.ncsa.datawolf.service.KistiHPCResource
 
MiniAccount(String, String, Person, boolean, boolean) - Constructor for class edu.illinois.ncsa.domain.Account.MiniAccount
 
mkdirs(String, SSHSession) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.SshUtils
Makes directory and all its parents.
MULTILINE - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
MULTILINE - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
mv(String, String, SSHSession) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.SshUtils
For use on same file system instead of copy + delete.
myproxySettings - Variable in class edu.illinois.ncsa.gondola.types.service.ServiceType
 
MyProxyType - Class in edu.illinois.ncsa.gondola.types.service
Java class for my-proxy-type complex type.
MyProxyType() - Constructor for class edu.illinois.ncsa.gondola.types.service.MyProxyType
 
myproxyUser - Variable in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
 

N

NAME - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
NAME - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
name - Variable in class edu.illinois.ncsa.gondola.types.service.DbcpType
 
name - Variable in class edu.illinois.ncsa.gondola.types.service.DbcpType.Property
 
NEWL - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
NEWL - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
nextDuplicateName(String, Map) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.PathUtils
Retrieves the next duplicate id number from the map and modifies the name accordingly.
NMATCHES - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
NMATCHES - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
NonNLSConstants - Class in edu.illinois.ncsa.datawolf.executor.hpc.util
Gathers all internal, unmodifiable string constants into a single place for convenience and in the interest of uncluttered code.
NonNLSConstants() - Constructor for class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
NonNLSConstants - Class in edu.illinois.ncsa.gondola
Gathers all internal, unmodifiable string constants into a single place for convenience and in the interest of uncluttered code.
NonNLSConstants() - Constructor for class edu.illinois.ncsa.gondola.NonNLSConstants
 
normalizeNonAlphanumeric(StringBuffer) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.StringUtils
Normalizes all non-alphanumeric characters to "_".
now() - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.DateUtils
 
nullInstance(Object) - Method in class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
 

O

objectCreated(ObjectCreatedEvent) - Method in class edu.illinois.ncsa.domain.event.ObjectCreatedHandler
 
ObjectCreatedEvent - Class in edu.illinois.ncsa.domain.event
 
ObjectCreatedEvent(AbstractBean) - Constructor for class edu.illinois.ncsa.domain.event.ObjectCreatedEvent
 
ObjectCreatedEvent(List<AbstractBean>) - Constructor for class edu.illinois.ncsa.domain.event.ObjectCreatedEvent
 
ObjectCreatedHandler - Class in edu.illinois.ncsa.domain.event
 
ObjectCreatedHandler() - Constructor for class edu.illinois.ncsa.domain.event.ObjectCreatedHandler
 
ObjectFactory - Class in edu.illinois.ncsa.gondola.types.service
This object contains factory methods for each Java content interface and Java element interface generated in the edu.illinois.ncsa.gondola.types.service package.
ObjectFactory() - Constructor for class edu.illinois.ncsa.gondola.types.service.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: edu.illinois.ncsa.gondola.types.service
ObjectFactory - Class in edu.illinois.ncsa.gondola.types.submission
This object contains factory methods for each Java content interface and Java element interface generated in the edu.illinois.ncsa.gondola.types.submission package.
ObjectFactory() - Constructor for class edu.illinois.ncsa.gondola.types.submission.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: edu.illinois.ncsa.gondola.types.submission
objectRemoved(ObjectRemovedEvent) - Method in class edu.illinois.ncsa.domain.event.ObjectRemovedHandler
 
ObjectRemovedEvent - Class in edu.illinois.ncsa.domain.event
 
ObjectRemovedEvent(AbstractBean) - Constructor for class edu.illinois.ncsa.domain.event.ObjectRemovedEvent
 
ObjectRemovedHandler - Class in edu.illinois.ncsa.domain.event
 
ObjectRemovedHandler() - Constructor for class edu.illinois.ncsa.domain.event.ObjectRemovedHandler
 
objectSelected(ObjectSelectedEvent) - Method in class edu.illinois.ncsa.domain.event.ObjectSelectedHandler
 
ObjectSelectedEvent - Class in edu.illinois.ncsa.domain.event
 
ObjectSelectedEvent(AbstractBean) - Constructor for class edu.illinois.ncsa.domain.event.ObjectSelectedEvent
 
ObjectSelectedHandler - Class in edu.illinois.ncsa.domain.event
 
ObjectSelectedHandler() - Constructor for class edu.illinois.ncsa.domain.event.ObjectSelectedHandler
 
objectToJSON(Object) - Static method in class edu.illinois.ncsa.domain.util.BeanUtil
Convert the object to JSON.
objectToString(Object) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.StringUtils
To restore the object to string method.
objectUpdated(ObjectUpdatedEvent) - Method in class edu.illinois.ncsa.domain.event.ObjectUpdatedHandler
 
ObjectUpdatedEvent - Class in edu.illinois.ncsa.domain.event
 
ObjectUpdatedEvent(AbstractBean) - Constructor for class edu.illinois.ncsa.domain.event.ObjectUpdatedEvent
 
ObjectUpdatedHandler - Class in edu.illinois.ncsa.domain.event
 
ObjectUpdatedHandler() - Constructor for class edu.illinois.ncsa.domain.event.ObjectUpdatedHandler
 
ONE_TO_ONE - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
ONE_TO_ONE - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
onExit - Variable in class edu.illinois.ncsa.gondola.types.service.DropType
 
op - Variable in class edu.illinois.ncsa.gondola.types.submission.ExpressionGroupTranslatorType
 
OPENP - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
OPENP - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
OPENSQ - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
OPENSQ - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
OPENV - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
OPENV - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
OutputPipe - Class in edu.illinois.ncsa.datawolf.executor.hpc.util
General-purpose pipe for capturing data written to an output stream.
OutputPipe() - Constructor for class edu.illinois.ncsa.datawolf.executor.hpc.util.OutputPipe
 

P

Parameter - Class in edu.illinois.ncsa.datawolf.executor.java.tool
Definition of a parameter.
Parameter(String, String, String, Parameter.ParameterType, String) - Constructor for class edu.illinois.ncsa.datawolf.executor.java.tool.Parameter
Define a parameter that will be shown to the user of the tool.
Parameter(String, String, String, Parameter.ParameterType, String, boolean) - Constructor for class edu.illinois.ncsa.datawolf.executor.java.tool.Parameter
Define a parameter that will be shown to the user of the tool, if hidden is not set to true.
Parameter(String, String, String, Parameter.ParameterType, String, boolean, boolean) - Constructor for class edu.illinois.ncsa.datawolf.executor.java.tool.Parameter
Define a parameter that will be shown to the user of the tool, if hidden is not set to true.
Parameter(String, String, String, String, String...) - Constructor for class edu.illinois.ncsa.datawolf.executor.java.tool.Parameter
Define a parameter that will be shown to the user of the tool.
Parameter(String, String, String, String, boolean, String...) - Constructor for class edu.illinois.ncsa.datawolf.executor.java.tool.Parameter
Define a parameter that will be shown to the user of the tool, if hidden is not set to true.
Parameter(String, String, String, String, boolean, boolean, String...) - Constructor for class edu.illinois.ncsa.datawolf.executor.java.tool.Parameter
Define a parameter that will be shown to the user of the tool, if hidden is not set to true.
Parameter.ParameterType - Enum in edu.illinois.ncsa.datawolf.executor.java.tool
 
PARENT_DATASET - Static variable in class edu.illinois.ncsa.incore.IncoreDataset
 
parseCredentials(String) - Static method in class edu.illinois.ncsa.datawolf.service.utils.LoginUtil
 
parseIntoLines(String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.StringUtils
 
parseJobId(String[]) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.handlers.JobInfoParser
 
parseJobId(String[]) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.HPCExecutor
 
parseJobState(String) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.handlers.JobInfoParser
 
parser - Variable in class edu.illinois.ncsa.gondola.types.submission.StatusHandlerType
 
ParserType - Class in edu.illinois.ncsa.gondola.types.submission
Java class for parser-type complex type.
ParserType() - Constructor for class edu.illinois.ncsa.gondola.types.submission.ParserType
 
password - Variable in class edu.illinois.ncsa.gondola.types.service.ConnectionType
 
PATH_SEP - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
PATH_SEP - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
PathUtils - Class in edu.illinois.ncsa.datawolf.executor.hpc.util
Management of file paths.
pauseExecution(String) - Method in class edu.illinois.ncsa.datawolf.service.ExecutionsResource
Pause a execution
PD - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
PD - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
PDRX - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
PDRX - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
Persistence - Class in edu.illinois.ncsa.domain
Provides an instance of the injector where needed.
Persistence() - Constructor for class edu.illinois.ncsa.domain.Persistence
 
PersistenceModule - Class in edu.illinois.ncsa.datawolf.service
Binds Persistence DAOs and available executors
PersistenceModule() - Constructor for class edu.illinois.ncsa.datawolf.service.PersistenceModule
 
person - Variable in class edu.illinois.ncsa.domain.Account.MiniAccount
email of the person.
Person - Class in edu.illinois.ncsa.domain
 
Person() - Constructor for class edu.illinois.ncsa.domain.Person
 
PersonClowderDao - Class in edu.illinois.ncsa.clowder.dao
 
PersonClowderDao() - Constructor for class edu.illinois.ncsa.clowder.dao.PersonClowderDao
 
PersonDao - Interface in edu.illinois.ncsa.domain.dao
 
PersonJPADao - Class in edu.illinois.ncsa.jpa.dao
 
PersonsResource - Class in edu.illinois.ncsa.datawolf.service
 
PersonsResource() - Constructor for class edu.illinois.ncsa.datawolf.service.PersonsResource
 
PIP - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
PIP - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
postWorkflow(File) - Static method in class edu.illinois.ncsa.datawolf.service.client.DataWolfServiceClient
 
preProcess(HttpRequest, ResourceMethodInvoker) - Method in class edu.illinois.ncsa.datawolf.service.AuthenticationInterceptor
 
print(String) - Method in class edu.illinois.ncsa.datawolf.Executor
Append message to the log.
print(String, Object...) - Method in class edu.illinois.ncsa.datawolf.Executor
Append formatted message to the log.
println(String) - Method in class edu.illinois.ncsa.datawolf.Executor
Append message with newline to the log.
println(String, Object...) - Method in class edu.illinois.ncsa.datawolf.Executor
Append formatted message with newline to the log.
println(String, Throwable) - Method in class edu.illinois.ncsa.datawolf.Executor
Append message and stacktrace of throwable to the log.
PRIORITY - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
PRIORITY - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
promptPassphrase(String) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.ssh.SSHInfo
 
promptPassword(String) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.ssh.SSHInfo
 
promptYesNo(String) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.ssh.SSHInfo
 
property - Variable in class edu.illinois.ncsa.gondola.types.service.DbcpType
 
Property() - Constructor for class edu.illinois.ncsa.gondola.types.service.DbcpType.Property
 
proxyMarginInMins - Variable in class edu.illinois.ncsa.gondola.types.service.MyProxyType
 
proxyRefreshInMins - Variable in class edu.illinois.ncsa.gondola.types.service.MyProxyType
 
purgeDataset(String) - Method in class edu.illinois.ncsa.datawolf.service.DatasetsResource
Delete dataset from repository

Q

QM - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
QM - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
QT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
QT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
queueRefreshInSecs - Variable in class edu.illinois.ncsa.gondola.types.service.ServiceType
 

R

random - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.SystemUtils
 
read(File, long, long) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.FileUtils
 
readBytes(File, int, int) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.FileUtils
 
READER_BUFFER_SIZE - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
READER_BUFFER_SIZE - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
readFile(FileDescriptor) - Method in class edu.illinois.ncsa.clowder.impl.FileStorageClowder
 
readFile(FileDescriptor) - Method in interface edu.illinois.ncsa.domain.FileStorage
Read file from storage
readFile(FileDescriptor) - Method in class edu.illinois.ncsa.domain.impl.FileStorageDisk
 
readFile(FileDescriptor) - Method in class edu.illinois.ncsa.incore.impl.IncoreFileStorage
 
readJarFiles(File) - Static method in class edu.illinois.ncsa.datawolf.service.ExecutorsResource
Finds all available JavaTools in set of jar files
readLines(File, long, long, boolean) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.FileUtils
 
readLinesFromEnd(File, long, boolean) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.FileUtils
 
readLinesFromStart(File, long, boolean) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.FileUtils
 
readReply() - Method in class edu.illinois.ncsa.datawolf.executor.hpc.util.OutputPipe
Sets reply to empty after read.
REGDOT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
REGDOT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
RegexType - Class in edu.illinois.ncsa.gondola.types.submission
Java class for regex-type complex type.
RegexType() - Constructor for class edu.illinois.ncsa.gondola.types.submission.RegexType
 
REGPIP - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
REGPIP - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
REMOTE_LINE_SEP - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
REMOTE_LINE_SEP - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
REMOTE_PATH_SEP - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
REMOTE_PATH_SEP - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
RemoteExecutor - Class in edu.illinois.ncsa.datawolf
This executor will run the job on a remote server.
RemoteExecutor() - Constructor for class edu.illinois.ncsa.datawolf.RemoteExecutor
 
removeBlob(FileDescriptor) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Remove the blob from the set of blobs of the worflow tool.
removeContributor(Person) - Method in class edu.illinois.ncsa.datawolf.domain.Workflow
Remove the contributor from the set of contributors to the worflow.
removeContributor(Person) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Remove the contributor from the set of contributors to the worflow tool.
removeContributor(Person) - Method in class edu.illinois.ncsa.domain.Dataset
Remove the contributor from the set of contributors to the dataset.
removeDir(String, SSHSession) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.SshUtils
Calls rmdir.
removeDuplicate(T) - Static method in class edu.illinois.ncsa.domain.util.BeanUtil
Check the object for any objects that have same ID but are different instance.
removeFileDescriptor(FileDescriptor) - Method in class edu.illinois.ncsa.domain.Dataset
Remove the file descriptor from the set of files of the dataset.
removeInput(WorkflowToolData) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Remove the data from list of inputs to the workflow tool.
removeOutput(WorkflowToolData) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Remove the data from list of outputs to the workflow tool.
removeParameter(WorkflowToolParameter) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Remove the parameter from the set of parameters to the workflow tool.
removeUserInfo(URI) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.UriUtils
Constructs new uri from old, removing the userInfo.
reply - Variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.OutputPipe
 
ResourceEntry - Class in edu.illinois.ncsa.datawolf.executor.java
Resource entry.
ResourceEntry() - Constructor for class edu.illinois.ncsa.datawolf.executor.java.ResourceEntry
 
ResourcesModule - Class in edu.illinois.ncsa.datawolf.service
Binds resource files
ResourcesModule() - Constructor for class edu.illinois.ncsa.datawolf.service.ResourcesModule
 
rootCause(Throwable) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.ExceptionUtils
Extracts the root cause.
RT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
RT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
RTESC - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
RTESC - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
run() - Method in class edu.illinois.ncsa.datawolf.LocalExecutor
 
run() - Method in class edu.illinois.ncsa.datawolf.RemoteExecutor
Submit the remote job and keep checking to see what the status of the job is and fetch any remote information.

S

save(T) - Method in class edu.illinois.ncsa.clowder.dao.AbstractClowderDao
 
save(Dataset) - Method in class edu.illinois.ncsa.clowder.dao.DatasetClowderDao
 
save(T) - Method in interface edu.illinois.ncsa.domain.dao.IDao
 
save(Dataset) - Method in class edu.illinois.ncsa.incore.dao.IncoreDatasetDao
 
save(FileDescriptor) - Method in class edu.illinois.ncsa.incore.dao.IncoreFileDescriptorDao
 
save(Person) - Method in class edu.illinois.ncsa.incore.dao.IncorePersonDao
 
save(T) - Method in class edu.illinois.ncsa.jpa.dao.AbstractJPADao
 
sb - Variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.OutputPipe
 
SC - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
SC - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
sCHAR - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
sCHAR - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
SCHEMA - Static variable in class edu.illinois.ncsa.incore.IncoreDataset
 
SCRIPT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
SCRIPT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
script - Variable in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
 
ScriptType - Class in edu.illinois.ncsa.gondola.types.submission
Java class for script-type complex type.
ScriptType() - Constructor for class edu.illinois.ncsa.gondola.types.submission.ScriptType
 
sDOUBLE - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
sDOUBLE - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
serialize(Date, JsonGenerator, SerializerProvider) - Method in class edu.illinois.ncsa.domain.jackson.JsonDateSerializer
 
SERV_XSD - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
SERV_XSD - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
SERVER - Static variable in class edu.illinois.ncsa.datawolf.service.client.DataWolfServiceClient
 
SERVER - Static variable in class edu.illinois.ncsa.file.service.client.FileServiceClient
 
serverUri - Variable in class edu.illinois.ncsa.gondola.types.service.MyProxyType
 
ServiceType - Class in edu.illinois.ncsa.gondola.types.service
Java class for service-type complex type.
ServiceType() - Constructor for class edu.illinois.ncsa.gondola.types.service.ServiceType
 
serviceUserHome - Variable in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
 
setActive(boolean) - Method in class edu.illinois.ncsa.domain.Account
Set the user account as active
setAdmin(boolean) - Method in class edu.illinois.ncsa.domain.Account
Set the administrative privileges of the account
setAllowEmpty(boolean) - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Parameter
Set to true if the parameter should not be shown to the user.
setAllowNull(boolean) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolParameter
Sets whether or not the workflow parameter can be empty.
setAlways(Boolean) - Method in class edu.illinois.ncsa.gondola.types.service.InitializeType
Sets the value of the always property.
setAppend(boolean) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.util.OutputPipe
 
setBlobs(Set<FileDescriptor>) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Set the set of blobs associated with the workflow tool.
setBuffer(boolean) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.util.OutputPipe
 
setCancelQueue(int) - Method in class edu.illinois.ncsa.gondola.types.service.ServiceType
Sets the value of the cancelQueue property.
setCaptureStdErr(String) - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineImplementation
 
setCaptureStdErr(String) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.HPCToolImplementation
 
setCaptureStdOut(String) - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineImplementation
 
setCaptureStdOut(String) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.HPCToolImplementation
 
setCommandArgs(String) - Method in class edu.illinois.ncsa.gondola.types.submission.StatusHandlerType
Sets the value of the commandArgs property.
setCommandline(boolean) - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineOption
 
setCommandLineOptions(List<CommandLineOption>) - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineImplementation
 
setCommandLineOptions(List<CommandLineOption>) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.HPCToolImplementation
 
setCommandPath(String) - Method in class edu.illinois.ncsa.gondola.types.submission.StatusHandlerType
Sets the value of the commandPath property.
setContent(String) - Method in class edu.illinois.ncsa.gondola.types.service.ConnectionType
Sets the value of the content property.
setContent(String) - Method in class edu.illinois.ncsa.gondola.types.service.DbcpType.Property
Sets the value of the content property.
setContent(String) - Method in class edu.illinois.ncsa.gondola.types.submission.LineType
Sets the value of the content property.
setContent(String) - Method in class edu.illinois.ncsa.gondola.types.submission.RegexType
Sets the value of the content property.
setContributors(List<Person>) - Method in class edu.illinois.ncsa.datawolf.domain.Workflow
Set the set of PersonBeans that represents those that contributed to the workflow.
setContributors(Set<Person>) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Set the set of PersonBeans that represents those that contributed to the workflow tool.
setContributors(List<Person>) - Method in class edu.illinois.ncsa.domain.Dataset
Set the set of PersonBeans that represents those that contributed to the artifact.
setCreated(Date) - Method in class edu.illinois.ncsa.datawolf.domain.Workflow
Sets the date when the workflow was created.
setCreateDate(Date) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowStep
Sets the date when the workflow step was created.
setCreator(Person) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
Sets the PersonBean that represents the creator of the execution.
setCreator(Person) - Method in class edu.illinois.ncsa.datawolf.domain.Workflow
Sets the PersonBean that represents the creator of the workflow.
setCreator(Person) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowStep
Sets the PersonBean that represents the creator of the workflow.
setCreator(Person) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Sets the PersonBean that represents the creator of the workflow tool.
setCreator(Person) - Method in class edu.illinois.ncsa.domain.Dataset
Sets the PersonBean that represents the creator of the artifact.
setCreatorId(String) - Method in class edu.illinois.ncsa.datawolf.domain.Submission
Sets the the id that represents the creator of the execution.
setDataId(String) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolData
Sets the id of the workflow tool data
setDataset(String, String) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
Sets the dataset associated with that specific uuid.
setDataset(String, String) - Method in class edu.illinois.ncsa.datawolf.domain.Submission
Sets the dataset associated with that specific uuid.
setDatasets(Map<String, String>) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
 
setDatasets(Map<String, String>) - Method in class edu.illinois.ncsa.datawolf.domain.Submission
 
setDataURL(String) - Method in class edu.illinois.ncsa.domain.FileDescriptor
 
setDate(Date) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
Sets the date when the execution was created.
setDate(Date) - Method in class edu.illinois.ncsa.datawolf.domain.LogFile
Sets the date of the log message.
setDate(Date) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Sets the date when the workflow tool was created.
setDate(Date) - Method in class edu.illinois.ncsa.domain.Dataset
Sets the date when the artifact was created.
setDebug(boolean) - Method in class edu.illinois.ncsa.datawolf.Executor
Set executor debug flag.
setDeleteAfterSubmit(Boolean) - Method in class edu.illinois.ncsa.gondola.types.submission.ScriptType
Sets the value of the deleteAfterSubmit property.
setDeleted(boolean) - Method in class edu.illinois.ncsa.domain.AbstractBean
Should the bean be assumed to be deleted.
setDescription(String) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
Sets the description of the execution
setDescription(String) - Method in class edu.illinois.ncsa.datawolf.domain.Submission
Sets the description of the execution
setDescription(String) - Method in class edu.illinois.ncsa.datawolf.domain.Workflow
Sets the description of the workflow
setDescription(String) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Sets the description of the workflow tool
setDescription(String) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolData
Sets the description of the workflow tool data
setDescription(String) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolParameter
Sets the description of the workflow parameter.
setDescription(String) - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Dataset
Set the description of the dataset.
setDescription(String) - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Parameter
Set the description of the parameter.
setDescription(String) - Method in class edu.illinois.ncsa.domain.Dataset
Sets the description of the artifact
setDriverClass(String) - Method in class edu.illinois.ncsa.gondola.types.service.ConnectionType
Sets the value of the driverClass property.
setDrop(DropType) - Method in class edu.illinois.ncsa.gondola.types.service.AccessType
Sets the value of the drop property.
setEmail(String) - Method in class edu.illinois.ncsa.domain.Person
Sets the email of the person.
setEnabled(boolean) - Method in class edu.illinois.ncsa.datawolf.service.AuthenticationInterceptor
 
setEnv(Map<String, String>) - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineImplementation
 
setError(boolean) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.util.OutputPipe
 
setExecutable(String) - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineImplementation
 
setExecutable(String) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.HPCToolImplementation
 
setExecutionId(String) - Method in class edu.illinois.ncsa.datawolf.domain.HPCJobInfo
Sets the execution id assigned by the engine for the workflow
setExecutionId(String) - Method in class edu.illinois.ncsa.datawolf.domain.LogFile
 
setExecutor(String) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Sets the executor of the tool.
setExecutors(Set<Executor>) - Method in class edu.illinois.ncsa.datawolf.Engine
 
setExpression(RegexType) - Method in class edu.illinois.ncsa.gondola.types.submission.ParserType
Sets the value of the expression property.
setExtraLocalExecutor(int) - Method in class edu.illinois.ncsa.datawolf.Engine
Sets the number of additional jobs that can be scheduled.
setFile(File) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.util.OutputPipe
 
setFileDescriptors(List<FileDescriptor>) - Method in class edu.illinois.ncsa.domain.Dataset
Set the set of file descriptors associated with the dataset.
setFilename(String) - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineOption
 
setFilename(String) - Method in class edu.illinois.ncsa.domain.FileDescriptor
If this dataset originated in a filesystem, or is intended to be stored in a filesystem, what filename is/should be used? If not, set to null.
setFirstName(String) - Method in class edu.illinois.ncsa.domain.Person
Sets the first name of the person.
setFlag(String) - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineOption
 
setFlags(String) - Method in class edu.illinois.ncsa.gondola.types.submission.RegexType
Sets the value of the flags property.
setFolder(String) - Method in class edu.illinois.ncsa.domain.impl.FileStorageDisk
 
setFrom(String) - Method in class edu.illinois.ncsa.gondola.types.submission.ExpressionGroupTranslatorType
Sets the value of the from property.
setGroup(Integer) - Method in class edu.illinois.ncsa.gondola.types.submission.ExpressionGroupTranslatorType
Sets the value of the group property.
setHidden(boolean) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolParameter
Sets whether or not the workflow parameter should be shown to the user.
setHidden(boolean) - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Parameter
Set to true if the parameter should not be shown to the user.
setHostCertDir(String) - Method in class edu.illinois.ncsa.gondola.types.service.MyProxyType
Sets the value of the hostCertDir property.
setID(String) - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Dataset
Set the id of the dataset.
setID(String) - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Parameter
Set the id of the parameter.
setId(String) - Method in class edu.illinois.ncsa.domain.AbstractBean
Sets the id of the bean.
setId(String) - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Sets the value of the id property.
setImplementation(String) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Sets the implementation of the tool.
setInfo(SSHInfo) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.ssh.SSHSession
 
setInitialize(InitializeType) - Method in class edu.illinois.ncsa.gondola.types.service.AccessType
Sets the value of the initialize property.
setInitializeQueue(int) - Method in class edu.illinois.ncsa.gondola.types.service.ServiceType
Sets the value of the initializeQueue property.
setInjector(Injector) - Static method in class edu.illinois.ncsa.domain.Persistence
 
setInput(WorkflowToolData, String) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowStep
Maps the input of the tool to a specific output generated in another step.
setInput(String, String) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowStep
Maps the input of the tool to a specific output generated in another step.
setInput(String, InputStream) - Method in interface edu.illinois.ncsa.datawolf.executor.java.tool.JavaTool
Set a specific input.
setInput(String, InputStream) - Method in class edu.illinois.ncsa.datawolf.tool.example.ShiftCharsTool
 
setInputOutput(CommandLineOption.InputOutput) - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineOption
 
setInputs(Map<String, String>) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowStep
 
setInputs(List<WorkflowToolData>) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Set the list of datasets that make up the inputs to the tool.
setInstanceId(String) - Method in class edu.illinois.ncsa.gondola.types.submission.JobStatusType
Sets the value of the instanceId property.
setInstanceId(String) - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Sets the value of the instanceId property.
setJdbcAccess(AccessType) - Method in class edu.illinois.ncsa.gondola.types.service.ServiceType
Sets the value of the jdbcAccess property.
setJdbcConnection(ConnectionType) - Method in class edu.illinois.ncsa.gondola.types.service.AccessType
Sets the value of the jdbcConnection property.
setJdbcDbcp(DbcpType) - Method in class edu.illinois.ncsa.gondola.types.service.AccessType
Sets the value of the jdbcDbcp property.
setJobId(String) - Method in class edu.illinois.ncsa.datawolf.domain.HPCJobInfo
Sets the job id assigned by the scheduler
setJobId(String) - Method in class edu.illinois.ncsa.gondola.types.submission.JobStatusType
Sets the value of the jobId property.
setJobIdGroup(int) - Method in class edu.illinois.ncsa.gondola.types.submission.ParserType
Sets the value of the jobIdGroup property.
setJobIdParser(ParserType) - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Sets the value of the jobIdParser property.
setJobInformation(Execution, WorkflowStep) - Method in class edu.illinois.ncsa.datawolf.Executor
Set the job information for this executor.
setJoinStdOutStdErr(boolean) - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineImplementation
 
setLastName(String) - Method in class edu.illinois.ncsa.domain.Person
Sets the last name of the person.
setLevels(int) - Method in class edu.illinois.ncsa.domain.impl.FileStorageDisk
 
setLocalExecutorThreads(int) - Method in class edu.illinois.ncsa.datawolf.Engine
 
setLog(FileDescriptor) - Method in class edu.illinois.ncsa.datawolf.domain.LogFile
Sets the filedescriptor of the log message.
setLog(String) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.HPCToolImplementation
 
setLog(boolean) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.util.OutputPipe
 
setLog(String) - Method in class edu.illinois.ncsa.datawolf.Executor
Sets the log to the message.
setLog(Boolean) - Method in class edu.illinois.ncsa.gondola.types.submission.LineType
Sets the value of the log property.
setMaxBatchInsert(Integer) - Method in class edu.illinois.ncsa.gondola.types.service.AccessType
Sets the value of the maxBatchInsert property.
setMd5sum(String) - Method in class edu.illinois.ncsa.domain.FileDescriptor
 
setMd5sum(byte[]) - Method in class edu.illinois.ncsa.domain.FileDescriptor
 
setMd5sum(BigInteger) - Method in class edu.illinois.ncsa.domain.FileDescriptor
 
setMimeType(String) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolData
Sets the mime type of the workflow tool data
setMimeType(String) - Method in class edu.illinois.ncsa.domain.FileDescriptor
Sets the mime type of the artifact
setMyproxySettings(MyProxyType) - Method in class edu.illinois.ncsa.gondola.types.service.ServiceType
Sets the value of the myproxySettings property.
setMyproxyUser(String) - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Sets the value of the myproxyUser property.
setName(String) - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Dataset
Set the name of the dataset.
setName(String) - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Parameter
Set the name of the parameter.
setName(String, String) - Method in class edu.illinois.ncsa.domain.Person
Single function to set both first and last name of the person.
setName(String) - Method in class edu.illinois.ncsa.gondola.types.service.DbcpType.Property
Sets the value of the name property.
setName(String) - Method in class edu.illinois.ncsa.gondola.types.service.DbcpType
Sets the value of the name property.
setOnExit(Boolean) - Method in class edu.illinois.ncsa.gondola.types.service.DropType
Sets the value of the onExit property.
setOp(String) - Method in class edu.illinois.ncsa.gondola.types.submission.ExpressionGroupTranslatorType
Sets the value of the op property.
setOptionId(String) - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineOption
 
setOptions(List<String>) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolParameter
Sets the list of options this parameter can be.
setOptions(String...) - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Parameter
Sets an array with all allowable options.
setOutputs(Map<String, String>) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowStep
 
setOutputs(List<WorkflowToolData>) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Set the list of datasets that make up the outputs to the tool.
setParameter(String, String) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
Sets the value for the specific parameter.
setParameter(String, String) - Method in class edu.illinois.ncsa.datawolf.domain.Submission
Sets the value for the specific parameter.
setParameter(String, String) - Method in interface edu.illinois.ncsa.datawolf.executor.java.tool.JavaTool
Set a specific parameter.
setParameter(String, String) - Method in class edu.illinois.ncsa.datawolf.tool.example.ShiftCharsTool
 
setParameterId(String) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolParameter
Sets the id of the workflow parameter.
setParameters(Map<String, String>) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
 
setParameters(Map<String, String>) - Method in class edu.illinois.ncsa.datawolf.domain.Submission
 
setParameters(Map<String, String>) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowStep
 
setParameters(List<WorkflowToolParameter>) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Sets the collection of parameters of the tool.
setParser(ParserType) - Method in class edu.illinois.ncsa.gondola.types.submission.StatusHandlerType
Sets the value of the parser property.
setPassword(String) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.ssh.SSHInfo
 
setPassword(String) - Method in class edu.illinois.ncsa.domain.Account
 
setPassword(String) - Method in class edu.illinois.ncsa.gondola.types.service.ConnectionType
Sets the value of the password property.
setPerson(Person) - Method in class edu.illinois.ncsa.domain.Account
 
setPreviousVersion(WorkflowTool) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Sets the previous version of the workflow tool.
setProperties(Map<String, String>) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
 
setProperty(String, String) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
 
setProxyMarginInMins(int) - Method in class edu.illinois.ncsa.gondola.types.service.MyProxyType
Sets the value of the proxyMarginInMins property.
setProxyRefreshInMins(int) - Method in class edu.illinois.ncsa.gondola.types.service.MyProxyType
Sets the value of the proxyRefreshInMins property.
setQueueRefreshInSecs(int) - Method in class edu.illinois.ncsa.gondola.types.service.ServiceType
Sets the value of the queueRefreshInSecs property.
setScript(ScriptType) - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Sets the value of the script property.
setServerUri(String) - Method in class edu.illinois.ncsa.gondola.types.service.MyProxyType
Sets the value of the serverUri property.
setServiceUserHome(String) - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Sets the value of the serviceUserHome property.
setSize(long) - Method in class edu.illinois.ncsa.domain.FileDescriptor
Sets the size of the blob, this can be set to -2 if there is no blob associated with this dataset.
setSplit(Boolean) - Method in class edu.illinois.ncsa.gondola.types.submission.RegexType
Sets the value of the split property.
setSshHome(File) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.ssh.SSHInfo
 
setStandardError(String) - Method in class edu.illinois.ncsa.datawolf.domain.HPCJobInfo
Sets the standard error for the job execution
setStandardOutput(String) - Method in class edu.illinois.ncsa.datawolf.domain.HPCJobInfo
Sets the standard output from the job execution
setState(Execution.State) - Method in class edu.illinois.ncsa.datawolf.Executor
Sets the state of the job.
setState(JobStateType) - Method in class edu.illinois.ncsa.gondola.types.submission.JobStatusType
Sets the value of the state property.
setStatusHandler(StatusHandlerType) - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Sets the value of the statusHandler property.
setStatusRefreshInSecs(int) - Method in class edu.illinois.ncsa.gondola.types.service.ServiceType
Sets the value of the statusRefreshInSecs property.
setStderr(Boolean) - Method in class edu.illinois.ncsa.gondola.types.submission.ParserType
Sets the value of the stderr property.
setStepEnd(String) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
Sets the the the end time of the given step with the id to now().
setStepEnd(String, Long) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
 
setStepId(String) - Method in class edu.illinois.ncsa.datawolf.domain.LogFile
 
setStepQueued(String) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
Sets the the the queued time of the given step with the id to now().
setStepQueued(String, Long) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
 
setSteps(List<WorkflowStep>) - Method in class edu.illinois.ncsa.datawolf.domain.Workflow
Set the list of steps of a workflow.
setStepsEnd(Map<String, Long>) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
 
setStepsQueued(Map<String, Long>) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
 
setStepsStart(Map<String, Long>) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
 
setStepStart(String) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
Sets the the the start time of the given step with the id to now().
setStepStart(String, Long) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
 
setStepState(String, Execution.State) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
Sets the state of the specific step in the workflow.
setStepState(Map<String, Execution.State>) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
 
setStoreLog(boolean) - Method in class edu.illinois.ncsa.datawolf.Executor
Should the logfiles be stored in the database.
setStoreLogs(boolean) - Method in class edu.illinois.ncsa.datawolf.Engine
Should the logfiles be stored in the database.
setSubmitErrorHandler(ErrorHandlerType) - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Sets the value of the submitErrorHandler property.
setSubmitPath(String) - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Sets the value of the submitPath property.
setSubmitQueue(int) - Method in class edu.illinois.ncsa.gondola.types.service.ServiceType
Sets the value of the submitQueue property.
setSupportsRelationalConstraints(Boolean) - Method in class edu.illinois.ncsa.gondola.types.service.AccessType
Sets the value of the supportsRelationalConstraints property.
setTargetUri(String) - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Sets the value of the targetUri property.
setTargetUser(String) - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Sets the value of the targetUser property.
setTargetUserHome(String) - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Sets the value of the targetUserHome property.
setTempFolder(File) - Method in interface edu.illinois.ncsa.datawolf.executor.java.tool.JavaTool
Sets the temp folder.
setTempFolder(File) - Method in class edu.illinois.ncsa.datawolf.tool.example.ShiftCharsTool
 
setTemplate(String) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.HPCToolImplementation
 
setTerminatePath(String) - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Sets the value of the terminatePath property.
setTimeout(int) - Method in class edu.illinois.ncsa.datawolf.Engine
Sets the timeout for a workflow in seconds.
setTitle(String) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
Sets the title of the execution
setTitle(String) - Method in class edu.illinois.ncsa.datawolf.domain.Submission
Sets the title of the execution
setTitle(String) - Method in class edu.illinois.ncsa.datawolf.domain.Workflow
Sets the title of the workflow
setTitle(String) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowStep
Sets the title of the workflow step.
setTitle(String) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Sets the title of the workflow tool
setTitle(String) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolData
Sets the title of the workflow tool data
setTitle(String) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolParameter
Sets the title of the workflow parameter.
setTitle(String) - Method in class edu.illinois.ncsa.domain.Dataset
Sets the title of the artifact
setTo(JobStateType) - Method in class edu.illinois.ncsa.gondola.types.submission.ExpressionGroupTranslatorType
Sets the value of the to property.
setToken(String) - Method in class edu.illinois.ncsa.domain.Account
Associate a token with a user account
setTool(WorkflowTool) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowStep
Sets the tool for the workflow step.
setToolClassName(String) - Method in class edu.illinois.ncsa.datawolf.executor.java.JavaToolImplementation
 
setToTime(Calendar, int, int) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.DateUtils
 
setToTime(Date, int, int) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.DateUtils
 
setType(WorkflowToolParameter.ParameterType) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolParameter
Sets the type of the workflow parameter.
setType(String) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolParameter
Deprecated.
see setType(ParameterType type)
setType(CommandLineOption.Type) - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineOption
 
setType(String) - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Dataset
Set the type of the dataset.
setType(Parameter.ParameterType) - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Parameter
Set the type of the parameter.
setType(String) - Method in class edu.illinois.ncsa.gondola.types.service.AccessType
Sets the value of the type property.
setUpdateQueue(int) - Method in class edu.illinois.ncsa.gondola.types.service.ServiceType
Sets the value of the updateQueue property.
setUser(String) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.ssh.SSHInfo
 
setUser(String) - Method in class edu.illinois.ncsa.gondola.types.service.ConnectionType
Sets the value of the user property.
setUserid(String) - Method in class edu.illinois.ncsa.domain.Account
 
setValue(String) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolParameter
Sets the value of the workflow parameter.
setValue(String) - Method in class edu.illinois.ncsa.datawolf.executor.commandline.CommandLineOption
 
setValue(String) - Method in class edu.illinois.ncsa.datawolf.executor.java.tool.Parameter
Set the value of the parameter.
setVersion(String) - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Sets the version of the workflow tool.
setWorkDir(File) - Method in class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
Change the work directory.
setWorkerPool(int) - Method in class edu.illinois.ncsa.gondola.types.service.ServiceType
Sets the value of the workerPool property.
setWorkers(int) - Static method in class edu.illinois.ncsa.datawolf.LocalExecutor
 
setWorkflow(Workflow) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
Sets the workflow that is executed.
setWorkflowId(String) - Method in class edu.illinois.ncsa.datawolf.domain.Execution
 
setWorkflowId(String) - Method in class edu.illinois.ncsa.datawolf.domain.Submission
Sets the workflow that is executed.
setWorkingDir(String) - Method in class edu.illinois.ncsa.datawolf.domain.HPCJobInfo
Sets the working directory for the job on the remote machine
setWorkingDirectory(String) - Method in class edu.illinois.ncsa.gondola.types.submission.JobStatusType
Sets the value of the workingDirectory property.
setX509Certificate(String) - Method in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
Sets the value of the x509Certificate property.
sFLOAT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
sFLOAT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
ShiftCharsTool - Class in edu.illinois.ncsa.datawolf.tool.example
Simple test java tool.
ShiftCharsTool() - Constructor for class edu.illinois.ncsa.datawolf.tool.example.ShiftCharsTool
 
showMessage(String) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.ssh.SSHInfo
 
SHRT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
SHRT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
sINT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
sINT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
sLONG - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
sLONG - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
source - Variable in class edu.illinois.ncsa.datawolf.executor.java.ResourceEntry
URL source from where the object was loaded.
SP - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
SP - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
SP_EQ_SP - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
SP_EQ_SP - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
SPESC - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
SPESC - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
split - Variable in class edu.illinois.ncsa.gondola.types.submission.RegexType
 
SSH - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
SSH - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
SSHInfo - Class in edu.illinois.ncsa.datawolf.executor.hpc.ssh
 
SSHInfo() - Constructor for class edu.illinois.ncsa.datawolf.executor.hpc.ssh.SSHInfo
 
SSHInfo(URI) - Constructor for class edu.illinois.ncsa.datawolf.executor.hpc.ssh.SSHInfo
 
sSHORT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
sSHORT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
SSHSession - Class in edu.illinois.ncsa.datawolf.executor.hpc.ssh
Manages the JSch Session object by checking for connection and trying to reconnect whenever a channel is retrieved.
SSHSession(Session) - Constructor for class edu.illinois.ncsa.datawolf.executor.hpc.ssh.SSHSession
 
SSHSession(URI) - Constructor for class edu.illinois.ncsa.datawolf.executor.hpc.ssh.SSHSession
 
SSHSession(URI, SSHInfo) - Constructor for class edu.illinois.ncsa.datawolf.executor.hpc.ssh.SSHSession
 
SshUtils - Class in edu.illinois.ncsa.datawolf.executor.hpc.util
Methods associated with Ssh (= jcraft.JSch implementation).
startExecution(String) - Static method in class edu.illinois.ncsa.datawolf.service.client.DataWolfServiceClient
 
startExecution(String) - Method in class edu.illinois.ncsa.datawolf.service.ExecutionsResource
Start a execution
startJob() - Method in class edu.illinois.ncsa.datawolf.Executor
The job is ready to be executed.
startJob() - Method in class edu.illinois.ncsa.datawolf.LocalExecutor
 
startJob() - Method in class edu.illinois.ncsa.datawolf.RemoteExecutor
 
state - Variable in class edu.illinois.ncsa.gondola.types.submission.JobStatusType
 
statusHandler - Variable in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
 
StatusHandlerType - Class in edu.illinois.ncsa.gondola.types.submission
Java class for status-handler-type complex type.
StatusHandlerType() - Constructor for class edu.illinois.ncsa.gondola.types.submission.StatusHandlerType
 
statusRefreshInSecs - Variable in class edu.illinois.ncsa.gondola.types.service.ServiceType
 
stderr - Variable in class edu.illinois.ncsa.gondola.types.submission.ParserType
 
stderrError - Variable in class edu.illinois.ncsa.gondola.types.submission.ErrorHandlerType
 
stderrWarn - Variable in class edu.illinois.ncsa.gondola.types.submission.ErrorHandlerType
 
stdoutError - Variable in class edu.illinois.ncsa.gondola.types.submission.ErrorHandlerType
 
stdoutWarn - Variable in class edu.illinois.ncsa.gondola.types.submission.ErrorHandlerType
 
stepStateChange(StepStateChangedEvent) - Method in interface edu.illinois.ncsa.datawolf.event.StepStateChangedHandler
 
StepStateChangedEvent - Class in edu.illinois.ncsa.datawolf.event
 
StepStateChangedEvent(WorkflowStep, Execution, Execution.State) - Constructor for class edu.illinois.ncsa.datawolf.event.StepStateChangedEvent
 
StepStateChangedHandler - Interface in edu.illinois.ncsa.datawolf.event
 
stop(String, String...) - Method in class edu.illinois.ncsa.datawolf.Engine
Stops a particular step from being executed, and removes it from the list.
stop(String) - Method in class edu.illinois.ncsa.datawolf.Engine
Stops all steps in a execution from being executed, and removes it from the list.
stopAll() - Method in class edu.illinois.ncsa.datawolf.Engine
Stop all steps from executing.
stopJob() - Method in class edu.illinois.ncsa.datawolf.executor.java.JavaExecutor
 
stopJob() - Method in class edu.illinois.ncsa.datawolf.Executor
The job should be stopped.
stopJob() - Method in class edu.illinois.ncsa.datawolf.LocalExecutor
 
stopJob() - Method in class edu.illinois.ncsa.datawolf.RemoteExecutor
 
storeFile(InputStream) - Method in class edu.illinois.ncsa.clowder.impl.FileStorageClowder
 
storeFile(String, InputStream, Person, Dataset) - Method in class edu.illinois.ncsa.clowder.impl.FileStorageClowder
 
storeFile(String, InputStream) - Method in class edu.illinois.ncsa.clowder.impl.FileStorageClowder
 
storeFile(FileDescriptor, InputStream) - Method in class edu.illinois.ncsa.clowder.impl.FileStorageClowder
 
storeFile(FileDescriptor, String, InputStream) - Method in class edu.illinois.ncsa.clowder.impl.FileStorageClowder
 
storeFile(String, String, InputStream) - Method in class edu.illinois.ncsa.clowder.impl.FileStorageClowder
 
storeFile(String, String, InputStream, Person, Dataset) - Method in class edu.illinois.ncsa.clowder.impl.FileStorageClowder
 
storeFile(InputStream) - Method in interface edu.illinois.ncsa.domain.FileStorage
Store file in file storage system
storeFile(String, InputStream) - Method in interface edu.illinois.ncsa.domain.FileStorage
Store file in file storage system
storeFile(String, InputStream, Person, Dataset) - Method in interface edu.illinois.ncsa.domain.FileStorage
Store file in file storage system
storeFile(FileDescriptor, InputStream) - Method in interface edu.illinois.ncsa.domain.FileStorage
Store file in file storage system
storeFile(String, String, InputStream) - Method in interface edu.illinois.ncsa.domain.FileStorage
Store file in file storage system
storeFile(String, String, InputStream, Person, Dataset) - Method in interface edu.illinois.ncsa.domain.FileStorage
Store file in file storage system
storeFile(InputStream) - Method in class edu.illinois.ncsa.domain.impl.FileStorageDisk
 
storeFile(String, InputStream, Person, Dataset) - Method in class edu.illinois.ncsa.domain.impl.FileStorageDisk
 
storeFile(String, InputStream) - Method in class edu.illinois.ncsa.domain.impl.FileStorageDisk
 
storeFile(FileDescriptor, InputStream) - Method in class edu.illinois.ncsa.domain.impl.FileStorageDisk
 
storeFile(String, String, InputStream) - Method in class edu.illinois.ncsa.domain.impl.FileStorageDisk
 
storeFile(String, String, InputStream, Person, Dataset) - Method in class edu.illinois.ncsa.domain.impl.FileStorageDisk
 
storeFile(String, String, InputStream, Dataset) - Method in class edu.illinois.ncsa.domain.impl.FileStorageDisk
 
storeFile(InputStream) - Method in class edu.illinois.ncsa.incore.impl.IncoreFileStorage
 
storeFile(String, InputStream) - Method in class edu.illinois.ncsa.incore.impl.IncoreFileStorage
 
storeFile(String, InputStream, Person, Dataset) - Method in class edu.illinois.ncsa.incore.impl.IncoreFileStorage
 
storeFile(FileDescriptor, InputStream) - Method in class edu.illinois.ncsa.incore.impl.IncoreFileStorage
 
storeFile(String, String, InputStream) - Method in class edu.illinois.ncsa.incore.impl.IncoreFileStorage
 
storeFile(String, String, InputStream, Person, Dataset) - Method in class edu.illinois.ncsa.incore.impl.IncoreFileStorage
 
STREAM_BUFFER_SIZE - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
STREAM_BUFFER_SIZE - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
streamConsumer(InputStreamReader, boolean, StringBuffer) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.SystemUtils
Creates thread which consumes the stream by reading and appending to buffer
stringToDecimal(String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.StringUtils
 
StringUtils - Class in edu.illinois.ncsa.datawolf.executor.hpc.util
Convenience wrappers around some Java String functionality.
SUBM_XSD - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
SUBM_XSD - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
Submission - Class in edu.illinois.ncsa.datawolf.domain
Used for submission of a workflow to the datawolf service.
Submission() - Constructor for class edu.illinois.ncsa.datawolf.domain.Submission
Create a new instance of the execution.
SubmissionDao - Interface in edu.illinois.ncsa.datawolf.domain.dao
 
SubmissionJPADao - Class in edu.illinois.ncsa.datawolf.jpa.dao
 
SubmissionJPADao(Provider<EntityManager>) - Constructor for class edu.illinois.ncsa.datawolf.jpa.dao.SubmissionJPADao
 
submit(Submission) - Static method in class edu.illinois.ncsa.datawolf.service.client.DataWolfServiceClient
 
submit(String) - Method in interface edu.illinois.ncsa.gondola.ISubmissionEngine
 
submit(JobSubmissionType) - Method in interface edu.illinois.ncsa.gondola.ISubmissionEngineImpl
 
submitErrorHandler - Variable in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
 
submitPath - Variable in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
 
submitQueue - Variable in class edu.illinois.ncsa.gondola.types.service.ServiceType
 
submitRemoteJob(File) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.HPCExecutor
 
submitRemoteJob(File) - Method in class edu.illinois.ncsa.datawolf.RemoteExecutor
Submit the job to the remote server.
supportsRelationalConstraints - Variable in class edu.illinois.ncsa.gondola.types.service.AccessType
 
sync(File) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.FileUtils
 
SystemUtils - Class in edu.illinois.ncsa.datawolf.executor.hpc.util
 
SystemUtils() - Constructor for class edu.illinois.ncsa.datawolf.executor.hpc.util.SystemUtils
 

T

TAB - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
TAB - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
TAG_SUPPORTS_RC - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
TAG_SUPPORTS_RC - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
targetUri - Variable in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
 
targetUser - Variable in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
 
targetUserHome - Variable in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
 
TBESC - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
TBESC - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
TBESCESC - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
TBESCESC - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
terminatePath - Variable in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
 
TEXT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
TEXT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
TITLE - Static variable in class edu.illinois.ncsa.incore.IncoreDataset
 
TMP_DIR - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
TMP_DIR - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
to - Variable in class edu.illinois.ncsa.gondola.types.submission.ExpressionGroupTranslatorType
 
tokenize(String, String[], boolean, boolean) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.StringUtils
Moves through the chain of delimiters in order until one of the tokens is not found in the remainder of the string.
TokenProvider - Interface in edu.illinois.ncsa.domain
 
toolChanged(WorkflowToolChangedEvent) - Method in interface edu.illinois.ncsa.datawolf.domain.event.WorkflowToolChangedHandler
 
toolCreated(WorkflowToolCreatedEvent) - Method in interface edu.illinois.ncsa.datawolf.domain.event.WorkflowToolCreatedHandler
 
toolDeleted(WorkflowToolDeletedEvent) - Method in interface edu.illinois.ncsa.datawolf.domain.event.WorkflowToolDeletedHandler
 
toString() - Method in class edu.illinois.ncsa.datawolf.domain.Workflow
 
toString() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowTool
 
toString() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolData
 
toString() - Method in class edu.illinois.ncsa.datawolf.domain.WorkflowToolParameter
 
toString() - Method in class edu.illinois.ncsa.domain.Dataset
 
toString() - Method in class edu.illinois.ncsa.domain.FileDescriptor
 
toString() - Method in class edu.illinois.ncsa.domain.Person
 
touch(String, SSHSession, long) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.SshUtils
Calls touch -m -t.
translator - Variable in class edu.illinois.ncsa.gondola.types.submission.ParserType
 
TYPE - Static variable in class edu.illinois.ncsa.datawolf.domain.event.WorkflowToolChangedEvent
 
TYPE - Static variable in class edu.illinois.ncsa.datawolf.domain.event.WorkflowToolCreatedEvent
 
TYPE - Static variable in class edu.illinois.ncsa.datawolf.domain.event.WorkflowToolDeletedEvent
 
TYPE - Static variable in class edu.illinois.ncsa.datawolf.event.StepStateChangedEvent
 
TYPE - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
Type() - Constructor for class edu.illinois.ncsa.domain.event.Event.Type
 
TYPE - Static variable in class edu.illinois.ncsa.domain.event.ObjectCreatedEvent
 
TYPE - Static variable in class edu.illinois.ncsa.domain.event.ObjectRemovedEvent
 
TYPE - Static variable in class edu.illinois.ncsa.domain.event.ObjectSelectedEvent
 
TYPE - Static variable in class edu.illinois.ncsa.domain.event.ObjectUpdatedEvent
 
TYPE - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
type - Variable in class edu.illinois.ncsa.gondola.types.service.AccessType
 
TYPE - Static variable in class edu.illinois.ncsa.incore.IncoreDataset
 

U

UBYT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
UBYT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
UNDEFINED - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
UNDEFINED - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
UNICODE_CASE - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
UNICODE_CASE - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
UNIX_LINES - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
UNIX_LINES - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
unmarshalErrorHandler(String) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
 
unmarshalIdList(String) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
Delegates to #getJAXBElement(String).
unmarshalIdList(URL) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
Delegates to JAXBUtils.unmarshalIdList(String), #getXML(url)
unmarshalJdbcAccess(String) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
Delegates to #getJAXBElement(String).
unmarshalJdbcAccess(URL) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
Delegates to JAXBUtils.unmarshalJdbcAccess(String), #getXML(url)
unmarshalJobScript(String) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
 
unmarshalJobStatus(String) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
Delegates to #getJAXBElement(String).
unmarshalJobStatus(URL) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
Delegates to JAXBUtils.unmarshalJobStatus(String), #getXML(url)
unmarshalJobStatusList(String) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
Delegates to #getJAXBElement(String).
unmarshalJobStatusList(URL) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
Delegates to JAXBUtils.unmarshalJobStatusList(String), #getXML(url)
unmarshalJobSubmission(String) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
Delegates to #getJAXBElement(String).
unmarshalJobSubmission(URL) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
Delegates to JAXBUtils.unmarshalJobSubmission(String), #getXML(url)
unmarshalParser(String) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
 
unmarshalService(String) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
Delegates to #getJAXBElement(String).
unmarshalService(URL) - Static method in class edu.illinois.ncsa.gondola.utils.JAXBUtils
Delegates to JAXBUtils.unmarshalIdList(String), #getXML(url)
UNMATCHED - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
UNMATCHED - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
updateAccount(HttpRequest, String) - Method in class edu.illinois.ncsa.datawolf.service.LoginResource
Enable/Disable user accounts
updateAccountPassword(String, String) - Method in class edu.illinois.ncsa.datawolf.service.LoginResource
 
updateJobScript(ScriptType, Map<String, String>, List<String>, String) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.HPCExecutor
 
updateQueue - Variable in class edu.illinois.ncsa.gondola.types.service.ServiceType
 
updateWorkflow(Workflow) - Method in class edu.illinois.ncsa.datawolf.service.WorkflowsResource
Update workflow by id
uploadFile(MultipartFormDataInput) - Method in class edu.illinois.ncsa.file.service.FilesResource
upload a file
UriUtils - Class in edu.illinois.ncsa.datawolf.executor.hpc.util
Static auxiliary methods for dealing with java.net.URI.
user - Variable in class edu.illinois.ncsa.gondola.types.service.ConnectionType
 
userid - Variable in class edu.illinois.ncsa.domain.Account.MiniAccount
userid of the person, often email address.
USERS_ENDPOINT - Static variable in class edu.illinois.ncsa.incore.IncoreUser
 
UsersResource - Class in edu.illinois.ncsa.datawolf.service
 
UsersResource() - Constructor for class edu.illinois.ncsa.datawolf.service.UsersResource
 
USHT - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
USHT - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
UTFC - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
UTFC - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
UUID - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
UUID - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 

V

validate(String) - Method in class edu.illinois.ncsa.datawolf.executor.java.DisposeClassLoader
Validate a classname.
VALUE - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
VALUE - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
value() - Method in enum edu.illinois.ncsa.gondola.types.submission.JobStateType
 
valueOf(String) - Static method in enum edu.illinois.ncsa.datawolf.domain.Execution.State
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.illinois.ncsa.datawolf.domain.WorkflowToolParameter.ParameterType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.illinois.ncsa.datawolf.executor.commandline.CommandLineOption.InputOutput
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.illinois.ncsa.datawolf.executor.commandline.CommandLineOption.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.illinois.ncsa.datawolf.executor.java.tool.Parameter.ParameterType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.illinois.ncsa.gondola.types.submission.JobStateType
Returns the enum constant of this type with the specified name.
values() - Static method in enum edu.illinois.ncsa.datawolf.domain.Execution.State
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.illinois.ncsa.datawolf.domain.WorkflowToolParameter.ParameterType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.illinois.ncsa.datawolf.executor.commandline.CommandLineOption.InputOutput
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.illinois.ncsa.datawolf.executor.commandline.CommandLineOption.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.illinois.ncsa.datawolf.executor.java.tool.Parameter.ParameterType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.illinois.ncsa.gondola.types.submission.JobStateType
Returns an array containing the constants of this enum type, in the order they are declared.

W

withInjector(Injector) - Method in class edu.illinois.ncsa.datawolf.service.GuiceContextListener
 
work - Variable in class edu.illinois.ncsa.datawolf.Executor
 
workerPool - Variable in class edu.illinois.ncsa.gondola.types.service.ServiceType
 
Workflow - Class in edu.illinois.ncsa.datawolf.domain
 
Workflow() - Constructor for class edu.illinois.ncsa.datawolf.domain.Workflow
Create a new instance of the workflow.
WorkflowDao - Interface in edu.illinois.ncsa.datawolf.domain.dao
 
WorkflowJPADao - Class in edu.illinois.ncsa.datawolf.jpa.dao
 
WorkflowJPADao(Provider<EntityManager>) - Constructor for class edu.illinois.ncsa.datawolf.jpa.dao.WorkflowJPADao
 
WorkflowsResource - Class in edu.illinois.ncsa.datawolf.service
 
WorkflowsResource() - Constructor for class edu.illinois.ncsa.datawolf.service.WorkflowsResource
 
WorkflowStep - Class in edu.illinois.ncsa.datawolf.domain
 
WorkflowStep() - Constructor for class edu.illinois.ncsa.datawolf.domain.WorkflowStep
Create a new instance of the workflow step.
WorkflowStepDao - Interface in edu.illinois.ncsa.datawolf.domain.dao
 
workflowStepDao - Variable in class edu.illinois.ncsa.datawolf.Executor
 
WorkflowStepJPADao - Class in edu.illinois.ncsa.datawolf.jpa.dao
 
WorkflowStepJPADao(Provider<EntityManager>) - Constructor for class edu.illinois.ncsa.datawolf.jpa.dao.WorkflowStepJPADao
 
WorkflowTool - Class in edu.illinois.ncsa.datawolf.domain
 
WorkflowTool() - Constructor for class edu.illinois.ncsa.datawolf.domain.WorkflowTool
Create a new instance of the workflow tool.
WorkflowToolChangedEvent - Class in edu.illinois.ncsa.datawolf.domain.event
 
WorkflowToolChangedEvent(WorkflowTool) - Constructor for class edu.illinois.ncsa.datawolf.domain.event.WorkflowToolChangedEvent
 
WorkflowToolChangedHandler - Interface in edu.illinois.ncsa.datawolf.domain.event
 
WorkflowToolCreatedEvent - Class in edu.illinois.ncsa.datawolf.domain.event
 
WorkflowToolCreatedEvent(WorkflowTool) - Constructor for class edu.illinois.ncsa.datawolf.domain.event.WorkflowToolCreatedEvent
 
WorkflowToolCreatedHandler - Interface in edu.illinois.ncsa.datawolf.domain.event
 
WorkflowToolDao - Interface in edu.illinois.ncsa.datawolf.domain.dao
 
WorkflowToolData - Class in edu.illinois.ncsa.datawolf.domain
 
WorkflowToolData() - Constructor for class edu.illinois.ncsa.datawolf.domain.WorkflowToolData
Create a new instance of the workflow tool.
WorkflowToolDataDao - Interface in edu.illinois.ncsa.datawolf.domain.dao
 
WorkflowToolDataJPADao - Class in edu.illinois.ncsa.datawolf.jpa.dao
 
WorkflowToolDataJPADao(Provider<EntityManager>) - Constructor for class edu.illinois.ncsa.datawolf.jpa.dao.WorkflowToolDataJPADao
 
WorkflowToolDeletedEvent - Class in edu.illinois.ncsa.datawolf.domain.event
 
WorkflowToolDeletedEvent(WorkflowTool) - Constructor for class edu.illinois.ncsa.datawolf.domain.event.WorkflowToolDeletedEvent
 
WorkflowToolDeletedHandler - Interface in edu.illinois.ncsa.datawolf.domain.event
 
WorkflowToolJPADao - Class in edu.illinois.ncsa.datawolf.jpa.dao
 
WorkflowToolJPADao(Provider<EntityManager>) - Constructor for class edu.illinois.ncsa.datawolf.jpa.dao.WorkflowToolJPADao
 
WorkflowToolParameter - Class in edu.illinois.ncsa.datawolf.domain
 
WorkflowToolParameter() - Constructor for class edu.illinois.ncsa.datawolf.domain.WorkflowToolParameter
Create a new instance of the workflow parameter.
WorkflowToolParameter.ParameterType - Enum in edu.illinois.ncsa.datawolf.domain
 
WorkflowToolParameterDao - Interface in edu.illinois.ncsa.datawolf.domain.dao
 
WorkflowToolParameterJPADao - Class in edu.illinois.ncsa.datawolf.jpa.dao
 
WorkflowToolParameterJPADao(Provider<EntityManager>) - Constructor for class edu.illinois.ncsa.datawolf.jpa.dao.WorkflowToolParameterJPADao
 
WorkflowToolsResource - Class in edu.illinois.ncsa.datawolf.service
 
WorkflowToolsResource() - Constructor for class edu.illinois.ncsa.datawolf.service.WorkflowToolsResource
 
WorkflowUtil - Class in edu.illinois.ncsa.datawolf.service.utils
 
WorkflowUtil() - Constructor for class edu.illinois.ncsa.datawolf.service.utils.WorkflowUtil
 
workingDirectory - Variable in class edu.illinois.ncsa.gondola.types.submission.JobStatusType
 
write(int) - Method in class edu.illinois.ncsa.datawolf.executor.hpc.util.OutputPipe
Appends to string buffer.
writeBinary(File, List, boolean, String) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.FileUtils
 
writeBytes(File, byte[], boolean) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.FileUtils
 
writeLines(File, List, boolean) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.FileUtils
 
writeLines(File, List, boolean, boolean) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.FileUtils
 
writeLines(File, String[], boolean, boolean) - Static method in class edu.illinois.ncsa.datawolf.executor.hpc.util.FileUtils
 
WSPC - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
WSPC - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 

X

x509Certificate - Variable in class edu.illinois.ncsa.gondola.types.submission.JobSubmissionType
 
XMLSchema - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
XMLSchema - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 

Z

ZEROSTR - Static variable in class edu.illinois.ncsa.datawolf.executor.hpc.util.NonNLSConstants
 
ZEROSTR - Static variable in class edu.illinois.ncsa.gondola.NonNLSConstants
 
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