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Open Grid Scheduler package for BASE 1.1: 2017-05-10
A B C D E F G H I J L M N O P Q R S T U V W X 

A

AbortJobIfTransactionFails - Class in net.sf.basedb.opengrid
When a job has been submitted to the cluster the job-id and other information has to be registered in BASE.
AbortJobIfTransactionFails(JobIdentifier) - Constructor for class net.sf.basedb.opengrid.AbortJobIfTransactionFails
 
AbstractFileTransfer - Class in net.sf.basedb.opengrid.filetransfer
Abstract base implementation that is suitable when implementing both file upload and download.
AbstractFileTransfer(String) - Constructor for class net.sf.basedb.opengrid.filetransfer.AbstractFileTransfer
 
AbstractHost<T extends AbstractSession<?>> - Class in net.sf.basedb.opengrid
An abstract host that can be reached via SSH.
AbstractHost(ConnectionInfo) - Constructor for class net.sf.basedb.opengrid.AbstractHost
 
AbstractLockable<T extends AbstractLockable<T>> - Class in net.sf.basedb.opengrid.config
Handles locking and validation of configuration settings.
AbstractLockable() - Constructor for class net.sf.basedb.opengrid.config.AbstractLockable
 
AbstractSession<T extends AbstractHost<?>> - Class in net.sf.basedb.opengrid
Represents an open SSH session to a remote host.
AbstractSession(T, SSHClient) - Constructor for class net.sf.basedb.opengrid.AbstractSession
Session are typically created from RemoteHost.connect(int).
AbstractSession.CloseResourceOutputStream - Class in net.sf.basedb.opengrid
Wrapper around the outputstream so that we can close the related resource when the stream is closed.
AbstractSession.UploadSourceWrapper - Class in net.sf.basedb.opengrid
Wraps an UploadSource implementation with a LocalSourceFile implementation so that the file data can be sent to the remote server with SSHj.
addFile(UploadSource) - Method in class net.sf.basedb.opengrid.JobDefinition
 
addFile(UploadSource, FilePermission) - Method in class net.sf.basedb.opengrid.JobDefinition
Register a file that should be uploaded to the cluster as part of this job.
addNode(NodeConfig) - Method in class net.sf.basedb.opengrid.config.ClusterConfig
Add the name of a node in the cluster.
address - Variable in class net.sf.basedb.opengrid.config.ConnectionInfo
 
appendQsubOptionsToScript(StringBuilder, Set<String>) - Method in class net.sf.basedb.opengrid.config.JobConfig
Add all qsub options in this configuration to the script.
asJobScript(String, String) - Method in class net.sf.basedb.opengrid.JobDefinition
Generate a script for this job that fits what 'qsub' expects.
asJSONObject(JSONOptions) - Method in class net.sf.basedb.opengrid.CmdResult
Get the information in this result as a JSON object.
asJSONObject(JSONOptions) - Method in class net.sf.basedb.opengrid.config.ClusterConfig
Get the configuration information as a JSON object.
asJSONObject(JSONOptions) - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Get the configuration information as a JSON object.
asJSONObject(JSONOptions) - Method in class net.sf.basedb.opengrid.config.NodeConfig
Get the configuration information as a JSON object.
asJSONObject(JSONOptions) - Method in class net.sf.basedb.opengrid.OpenGridCluster
Get the configuration information for this cluster as a JSON object.
asJSONObject(JSONOptions) - Method in class net.sf.basedb.opengrid.OpenGridCluster.Info
Get the information as a JSON object.
asyncJobAbort(JobIdentifier) - Method in class net.sf.basedb.opengrid.service.OpenGridService
Register a job that should be aborted.
asyncJobStatusUpdate(JobIdentifier) - Method in class net.sf.basedb.opengrid.service.OpenGridService
Register a status update request for a job.
asyncJobStatusUpdate(JobIdentifier, JobStatusUpdater) - Method in class net.sf.basedb.opengrid.service.OpenGridService
Register a status update request for a job that is is not an Open Grid job.

B

BaseFileDownloadTarget - Class in net.sf.basedb.opengrid.filetransfer
Download target implementation for storing a file from a remote server to the BASE filesystem.
BaseFileDownloadTarget(File) - Constructor for class net.sf.basedb.opengrid.filetransfer.BaseFileDownloadTarget
Create a new download target that references the given file in BASE.
BaseFileUploadSource - Class in net.sf.basedb.opengrid.filetransfer
Upload source implementation for uploading a BASE file to a remote server.
BaseFileUploadSource(File) - Constructor for class net.sf.basedb.opengrid.filetransfer.BaseFileUploadSource
Create a new upload source that references the given file in BASE.
baseJob - Variable in class net.sf.basedb.opengrid.JobDefinition
 
baseJobId - Variable in class net.sf.basedb.opengrid.JobIdentifier
 
basePriorityToOpenGridPriority(Integer) - Static method in class net.sf.basedb.opengrid.config.JobConfig
Convert a BASE job priority value to an Open Grid job priority value. 1-4 → 1024 -- 1 5 or missing → 0 6-10 → -1 -- -1023
bgProcesses - Variable in class net.sf.basedb.opengrid.ScriptBuilder
 
bkgr(String) - Method in class net.sf.basedb.opengrid.ScriptBuilder
Adds a command that is executed in the background.
bkgr(String...) - Method in class net.sf.basedb.opengrid.ScriptBuilder
Adds a batch of commands that are executed in the background.
ByteArrayDownloadTarget - Class in net.sf.basedb.opengrid.filetransfer
Download target implementation for getting the remote file as a byte array.
ByteArrayDownloadTarget(String) - Constructor for class net.sf.basedb.opengrid.filetransfer.ByteArrayDownloadTarget
Create a new byte array download target with "unlimited" size.
ByteArrayUploadSource - Class in net.sf.basedb.opengrid.filetransfer
Upload source implementation for uploading the contents of a string to a file on a remote server.
ByteArrayUploadSource(String, byte[]) - Constructor for class net.sf.basedb.opengrid.filetransfer.ByteArrayUploadSource
Create a new source file from a byte[].

C

call(OpenGridSession, Job, JobStatus) - Method in class net.sf.basedb.opengrid.service.OpenGridService.JobCompletionInvoker
Call the extensions for the given job.
checkLocked(String) - Method in class net.sf.basedb.opengrid.config.AbstractLockable
Check the locked status and throw an IllegalStateException if this instance has been locked.
checkPermission(DbControl) - Static method in class net.sf.basedb.opengrid.servlet.ServletUtil
Checks if the currently logged in user has permission to manage Open Grid Clusters (=WRITE permission for the extension system).
checkValid(boolean) - Method in class net.sf.basedb.opengrid.config.AbstractLockable
Check if the configuration settings are valid.
checkValid(boolean) - Method in class net.sf.basedb.opengrid.config.ClusterConfig
Job folder and date command are required.
checkValid(boolean) - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Address, fingerprint and user are required.
checkValid(boolean) - Method in class net.sf.basedb.opengrid.config.JobConfig
The priority must be between -1023 and +1024.
checkValid(boolean) - Method in class net.sf.basedb.opengrid.config.NodeConfig
Name is required.
checkValidFilename(String) - Static method in class net.sf.basedb.opengrid.OpenGrid
Checks that a value is allowed as a file/directory name.
chmod() - Method in class net.sf.basedb.opengrid.filetransfer.FilePermission
Get the octal permission representation to set in 'chmod' command.
ci - Variable in class net.sf.basedb.opengrid.AbstractHost
 
close() - Method in class net.sf.basedb.opengrid.AbstractSession
 
close() - Method in class net.sf.basedb.opengrid.AbstractSession.CloseResourceOutputStream
 
close(Closeable) - Static method in class net.sf.basedb.opengrid.OpenGrid
Exception-safe method for closing closeable object.
CloseResourceOutputStream(OutputStream, Closeable) - Constructor for class net.sf.basedb.opengrid.AbstractSession.CloseResourceOutputStream
 
CLUSTER_INFO - Static variable in class net.sf.basedb.opengrid.json.JSONOption
Include the Open Grid cluster information from OpenGridCluster.getClusterInfo() when calling OpenGridCluster.asJSONObject(JSONOptions).
ClusterConfig - Class in net.sf.basedb.opengrid.config
Configuration settings related to the Open Grid cluster.
ClusterConfig() - Constructor for class net.sf.basedb.opengrid.config.ClusterConfig
 
clusterId - Variable in class net.sf.basedb.opengrid.JobIdentifier
 
clusterJobId - Variable in class net.sf.basedb.opengrid.JobIdentifier
 
clusters - Variable in class net.sf.basedb.opengrid.config.XmlConfig
 
clusters - Variable in class net.sf.basedb.opengrid.service.OpenGridService
 
cmd - Variable in class net.sf.basedb.opengrid.CmdResult
 
cmd - Variable in class net.sf.basedb.opengrid.JobDefinition
 
cmd(String) - Method in class net.sf.basedb.opengrid.ScriptBuilder
Run a command.
CmdResult<R> - Class in net.sf.basedb.opengrid
Holds the result from executing a single command on a cluster.
CmdResult(String) - Constructor for class net.sf.basedb.opengrid.CmdResult
Creates a new result instance.
CmdResult(CmdResult<?>) - Constructor for class net.sf.basedb.opengrid.CmdResult
Clone a cmd result instance except for the result field.
comment(String) - Method in class net.sf.basedb.opengrid.ScriptBuilder
Adds a comment to the script.
config - Variable in class net.sf.basedb.opengrid.JobDefinition
 
config - Variable in class net.sf.basedb.opengrid.OpenGridCluster
 
connect(int) - Method in class net.sf.basedb.opengrid.AbstractHost
Connect to the cluster.
connect(int) - Method in class net.sf.basedb.opengrid.OpenGridCluster
Connect to the cluster.
connect(int) - Method in class net.sf.basedb.opengrid.RemoteHost
Connect to the remote host.
CONNECTION_PASSWORD - Static variable in class net.sf.basedb.opengrid.json.JSONOption
Returns the connection password when calling ConnectionInfo.asJSONObject(JSONOptions).
ConnectionInfo - Class in net.sf.basedb.opengrid.config
Informatation such as the address, port, SSH fingerprint and login information that is needed to connect to a Open Grid Cluster via SSH.
ConnectionInfo() - Constructor for class net.sf.basedb.opengrid.config.ConnectionInfo
Create a new connection information instance.
ConnectionInfo(ConnectionInfo) - Constructor for class net.sf.basedb.opengrid.config.ConnectionInfo
Create a new connection information instance and clone the connection information from the given instance.
ConnectionInfo(FileServer) - Constructor for class net.sf.basedb.opengrid.config.ConnectionInfo
Create a new connection information and use the information in the file server for configuration.
context - Variable in class net.sf.basedb.opengrid.service.OpenGridService.JobCompletionInvoker
 
created - Variable in class net.sf.basedb.opengrid.OpenGridCluster.Info
 
created() - Method in class net.sf.basedb.opengrid.OpenGridCluster.Info
The timestamp when this information was created.

D

data - Variable in class net.sf.basedb.opengrid.filetransfer.ByteArrayDownloadTarget
 
data - Variable in class net.sf.basedb.opengrid.filetransfer.ByteArrayUploadSource
 
DATE_CMD - Static variable in class net.sf.basedb.opengrid.config.ClusterConfig
Convert date string from the date command into Date objects.
dateCommand - Variable in class net.sf.basedb.opengrid.config.ClusterConfig
 
dc - Variable in class net.sf.basedb.opengrid.json.JSONOptions
 
debug - Variable in class net.sf.basedb.opengrid.JobDefinition
 
DEFAULT - Static variable in class net.sf.basedb.opengrid.config.JobConfig
A (locked) configuration instance with default settings.
DEFAULT - Static variable in class net.sf.basedb.opengrid.json.JSONOptions
Use default options.
disable(JSONOption) - Method in class net.sf.basedb.opengrid.json.JSONOptions
Disable the given option.
doGet(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.opengrid.servlet.OpenGridServlet
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.opengrid.servlet.OpenGridServlet
 
downloadFile(String, DownloadTarget) - Method in class net.sf.basedb.opengrid.AbstractSession
Download a remote file to a local destination.
DownloadTarget - Interface in net.sf.basedb.opengrid.filetransfer
Represents a local file or resource that is the target for a file that is about to be downloaded from a remote server.

E

echo(String) - Method in class net.sf.basedb.opengrid.ScriptBuilder
Echo the given text to stdout
enable(JSONOption) - Method in class net.sf.basedb.opengrid.json.JSONOptions
Enable the given option.
endTime - Variable in class net.sf.basedb.opengrid.JobStatus
 
equals(Object) - Method in class net.sf.basedb.opengrid.filetransfer.FilePermission
 
equals(Object) - Method in class net.sf.basedb.opengrid.JobIdentifier
Equality is based on the cluster id and job id only.
error - Variable in class net.sf.basedb.opengrid.OpenGridCluster.Info
 
exception - Variable in class net.sf.basedb.opengrid.CmdResult
 
execute(String, int) - Method in class net.sf.basedb.opengrid.AbstractSession
 
EXECUTE - Static variable in class net.sf.basedb.opengrid.filetransfer.FilePermission
Execute permissions = 1.
executeCmd(String, int) - Method in class net.sf.basedb.opengrid.AbstractSession
Execute a command on the remote host.
executeOnNode(String, String, int) - Method in class net.sf.basedb.opengrid.OpenGridSession
Execute a command on a node in the cluster.
exitCode - Variable in class net.sf.basedb.opengrid.JobStatus
 
exitStatus - Variable in class net.sf.basedb.opengrid.CmdResult
 
ext - Variable in class net.sf.basedb.opengrid.service.OpenGridService
 
ext - Variable in class net.sf.basedb.opengrid.service.OpenGridServiceFactory.OpenGridServiceControllerAction
 

F

failImmediately - Variable in class net.sf.basedb.opengrid.config.JobConfig
 
file - Variable in class net.sf.basedb.opengrid.filetransfer.BaseFileDownloadTarget
 
file - Variable in class net.sf.basedb.opengrid.filetransfer.BaseFileUploadSource
 
FileMetaData - Class in net.sf.basedb.opengrid.filetransfer
Class for holding and collecting metadata about a remote or local file.
FileMetaData() - Constructor for class net.sf.basedb.opengrid.filetransfer.FileMetaData
 
FilePermission - Class in net.sf.basedb.opengrid.filetransfer
Represents the permission code for a file on a UNIX file system.
FilePermission(int, int, int) - Constructor for class net.sf.basedb.opengrid.filetransfer.FilePermission
Create a new set of permissions for the owner, group and all other users.
filesToUpload - Variable in class net.sf.basedb.opengrid.JobDefinition
 
fingerprint - Variable in class net.sf.basedb.opengrid.config.ConnectionInfo
 
fingerprint - Variable in class net.sf.basedb.opengrid.Sha256Verifier
 
FINGERPRINT_PATTERN - Static variable in class net.sf.basedb.opengrid.SshUtil
Deprecated.
fingerPrintType - Variable in class net.sf.basedb.opengrid.config.ConnectionInfo
 

G

getActions(InvokationContext<? super ButtonAction>) - Method in class net.sf.basedb.opengrid.service.OpenGridServiceConfigureFactory
 
getActions(InvokationContext<? super ServiceControllerAction>) - Method in class net.sf.basedb.opengrid.service.OpenGridServiceFactory
 
getActions(InvokationContext<? super SignalHandler>) - Method in class net.sf.basedb.opengrid.service.OpenGridSignalHandlerFactory
 
getAddress() - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Get the internet address of the Open Grid Cluster primary node.
getBaseJob() - Method in class net.sf.basedb.opengrid.JobDefinition
Get the BASE job that this job definition is connected with.
getBaseJobId() - Method in class net.sf.basedb.opengrid.JobIdentifier
Get the corresponding job id in BASE.
getBASEPriority() - Method in class net.sf.basedb.opengrid.config.JobConfig
getChildren(LocalFileFilter) - Method in class net.sf.basedb.opengrid.AbstractSession.UploadSourceWrapper
No children.
getClusterById(DbControl, String) - Method in class net.sf.basedb.opengrid.service.OpenGridService
Get information about a cluster with known id.
getClusterDate() - Method in class net.sf.basedb.opengrid.OpenGridSession
Get the current date and time of the cluster node.
getClusterId() - Method in class net.sf.basedb.opengrid.JobIdentifier
Get the ID of the cluster the job is located on.
getClusterInfo() - Method in class net.sf.basedb.opengrid.OpenGridCluster
Get information about the Open Grid cluster.
getClusterJobId() - Method in class net.sf.basedb.opengrid.JobIdentifier
Get the (Open Grid Schedulre) ID of the job.
getClusters() - Method in class net.sf.basedb.opengrid.config.XmlConfig
Get all clusters loaded so far.
getClusters(DbControl, Collection<Include>) - Method in class net.sf.basedb.opengrid.service.OpenGridService
Get all clusters that the logged in user is allowed to use.
getClusters(Collection<JobAgent>) - Method in class net.sf.basedb.opengrid.service.OpenGridService
Get a collection with all registered clusters that are either open to all or referencing one of the listed job agents where the logged in user has at least USE permission.
getCmd() - Method in class net.sf.basedb.opengrid.CmdResult
Get the command that was executed.
getCmd() - Method in class net.sf.basedb.opengrid.JobDefinition
 
getConfig() - Method in class net.sf.basedb.opengrid.JobDefinition
Get the configuration settings for this job.
getConfig() - Method in class net.sf.basedb.opengrid.OpenGridCluster
Get configuration settings for this cluster.
getConnectionInfo() - Method in class net.sf.basedb.opengrid.AbstractHost
Get the connection information for this host.
getCreatePrivateFiles() - Method in class net.sf.basedb.opengrid.config.JobConfig
 
getData() - Method in class net.sf.basedb.opengrid.filetransfer.ByteArrayDownloadTarget
Get the downloaded data as a byte array.
getDateCommand() - Method in class net.sf.basedb.opengrid.config.ClusterConfig
Get the command to execute for getting the current date and time from the cluster.
getDbControl() - Method in class net.sf.basedb.opengrid.json.JSONOptions
Get a DbControl which can be used to retreive information from the BASE database.
getDebug() - Method in class net.sf.basedb.opengrid.JobDefinition
 
getDownloadedSize() - Method in class net.sf.basedb.opengrid.filetransfer.ByteArrayDownloadTarget
Get the size of the downloaded data.
getEndDate() - Method in class net.sf.basedb.opengrid.JobStatus
Get the end time as a date.
getEndTime() - Method in class net.sf.basedb.opengrid.JobStatus
Get the time the job ended execution.
getException() - Method in class net.sf.basedb.opengrid.CmdResult
Get the exception that may have caused a failure.
getExitCode() - Method in class net.sf.basedb.opengrid.JobStatus
Get the exit code from the job script.
getExitStatus() - Method in class net.sf.basedb.opengrid.CmdResult
Get the exit status of the command.
getFailImmediately() - Method in class net.sf.basedb.opengrid.config.JobConfig
 
getFilePermission() - Method in class net.sf.basedb.opengrid.JobDefinition.UploadSourceWithPermission
 
getFiles() - Method in class net.sf.basedb.opengrid.JobDefinition
Get all files that should be uploaded to the cluster as part of this job.
getFingerPrint() - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Get the public key SSH fingerprint of the Open Grid Cluster primary node.
getFingerPrintType() - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Get the fingerprint type.
getFingerPrintType(String) - Static method in class net.sf.basedb.opengrid.SshUtil
Check if the given fingerprint is valid and what type it is.
getGroupPermission() - Method in class net.sf.basedb.opengrid.filetransfer.FilePermission
Get the group permission.
getHost() - Method in class net.sf.basedb.opengrid.AbstractSession
Get the host that created this session.
getHostInfo() - Method in class net.sf.basedb.opengrid.OpenGridCluster.Info
Get the cached result of the call to OpenGridSession.getHostInfo().
getHostInfo() - Method in class net.sf.basedb.opengrid.OpenGridSession
Utility method for getting information about the cluster hardware and operating system by executing the ClusterConfig.getHostInfoCommand().
getHostInfoCommand() - Method in class net.sf.basedb.opengrid.config.ClusterConfig
Get the command to execute for getting some information about the hardware and operating system of the host.
getId() - Method in class net.sf.basedb.opengrid.OpenGridCluster
Get the ID of this cluster.
getInputStream() - Method in class net.sf.basedb.opengrid.AbstractSession.UploadSourceWrapper
 
getInputStream() - Method in class net.sf.basedb.opengrid.filetransfer.BaseFileUploadSource
 
getInputStream() - Method in class net.sf.basedb.opengrid.filetransfer.ByteArrayUploadSource
Get the file data.
getInputStream() - Method in class net.sf.basedb.opengrid.filetransfer.InputStreamUploadSource
 
getInputStream() - Method in interface net.sf.basedb.opengrid.filetransfer.UploadSource
Get an input stream for reading the resource data.
getInstance() - Static method in class net.sf.basedb.opengrid.service.OpenGridService
Get the singleton instance of the service.
getJobAgentExternalId() - Method in class net.sf.basedb.opengrid.config.ClusterConfig
Get the External ID of the job agent this cluster should be linked to.
getJobFileAsString(String, String, String) - Method in class net.sf.basedb.opengrid.OpenGridSession
Utility method for downloading a result file from a job as a text file.
getJobFolder() - Method in class net.sf.basedb.opengrid.config.ClusterConfig
Get the path to the primary job folder on the Open Grid cluster.
getJobIdentifier() - Method in class net.sf.basedb.opengrid.JobStatus
Get the identifier for the job.
getJobStatus(OpenGridSession, JobIdentifier) - Method in interface net.sf.basedb.opengrid.service.JobStatusUpdater
A request for status information about the identified job.
getLastAccessedTime() - Method in class net.sf.basedb.opengrid.filetransfer.FileMetaData
Get the timestamp when that the file was last accessed.
getLastAccessTime() - Method in class net.sf.basedb.opengrid.AbstractSession.UploadSourceWrapper
 
getLastModifiedTime() - Method in class net.sf.basedb.opengrid.AbstractSession.UploadSourceWrapper
 
getLastModifiedTime() - Method in class net.sf.basedb.opengrid.filetransfer.FileMetaData
Get the timestamp when the file was last modified.
getLength() - Method in class net.sf.basedb.opengrid.AbstractSession.UploadSourceWrapper
 
getMessage() - Method in class net.sf.basedb.opengrid.JobStatus
Get the progress message of an executing job.
getMetadata() - Method in class net.sf.basedb.opengrid.filetransfer.AbstractFileTransfer
Get metadata about the local file or receive metadata for the remote file.
getMetadata() - Method in interface net.sf.basedb.opengrid.filetransfer.DownloadTarget
Get a metadata instance for collecting information about the remote file.
getMetadata() - Method in class net.sf.basedb.opengrid.filetransfer.InputStreamUploadSource
 
getMetadata() - Method in interface net.sf.basedb.opengrid.filetransfer.UploadSource
Get a metadata instance with information about the local file that is about to be uploaded.
getName() - Method in class net.sf.basedb.opengrid.AbstractSession.UploadSourceWrapper
 
getName() - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Get the display name of the cluster.
getName() - Method in class net.sf.basedb.opengrid.config.NodeConfig
Get the name of the node.
getName() - Method in class net.sf.basedb.opengrid.filetransfer.AbstractFileTransfer
Get the name of the file.
getName() - Method in interface net.sf.basedb.opengrid.filetransfer.DownloadTarget
The name of the local resource.
getName() - Method in class net.sf.basedb.opengrid.filetransfer.InputStreamUploadSource
 
getName() - Method in interface net.sf.basedb.opengrid.filetransfer.UploadSource
The name of the resource.
getName() - Method in class net.sf.basedb.opengrid.JobDefinition
Get the name of this job definition.
getName() - Method in class net.sf.basedb.opengrid.JobStatus
Get the name of the job.
getNodeName() - Method in class net.sf.basedb.opengrid.JobStatus
Get the name of the node in the cluster that the job is/was running on.
getNodes() - Method in class net.sf.basedb.opengrid.config.ClusterConfig
Get all configured nodes.
getOpenGridInfo() - Method in class net.sf.basedb.opengrid.OpenGridCluster.Info
Get the cached result of the call to OpenGridSession.getOpenGridInfo().
getOpenGridInfo() - Method in class net.sf.basedb.opengrid.OpenGridSession
Utility method for getting information about the Open Grid Scheduler software version by executing the ClusterConfig.getOpenGridInfoCommand().
getOpenGridInfoCommand() - Method in class net.sf.basedb.opengrid.config.ClusterConfig
Get the command to execute for getting some information about the Open Grid Scheduler software version.
getOtherPermission() - Method in class net.sf.basedb.opengrid.filetransfer.FilePermission
Get the permission for other users.
getOutputStream() - Method in class net.sf.basedb.opengrid.filetransfer.BaseFileDownloadTarget
 
getOutputStream() - Method in class net.sf.basedb.opengrid.filetransfer.ByteArrayDownloadTarget
 
getOutputStream() - Method in interface net.sf.basedb.opengrid.filetransfer.DownloadTarget
Get an ouput stream for writing the file data to the local resource.
getOutputStream() - Method in class net.sf.basedb.opengrid.filetransfer.OutputStreamDownloadTarget
 
getOutputStream() - Method in class net.sf.basedb.opengrid.filetransfer.ServletResponseDownloadTarget
 
getPassword() - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Get the password to use when connecting to the Open Grid Cluster primary node.
getPermissions() - Method in class net.sf.basedb.opengrid.AbstractSession.UploadSourceWrapper
 
getPermissions() - Method in class net.sf.basedb.opengrid.filetransfer.FilePermission
Get the combined permissions.
getPort() - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Get the port number to use for connecting to the Open Grid Cluster primary node.
getPriority() - Method in class net.sf.basedb.opengrid.config.JobConfig
 
getProgress() - Method in class net.sf.basedb.opengrid.JobStatus
Get the progress in percent of an executing job.
getQsubOption(String) - Method in class net.sf.basedb.opengrid.config.JobConfig
Get the value of a qsub option.
getQsubOptions() - Method in class net.sf.basedb.opengrid.config.JobConfig
Get all options that has been specified for qsub so far.
getRemoteInputStream(String, FileMetaData) - Method in class net.sf.basedb.opengrid.AbstractSession
 
getRemoteOutputStream(String, boolean, FileMetaData, FilePermission) - Method in class net.sf.basedb.opengrid.AbstractSession
 
getResult() - Method in class net.sf.basedb.opengrid.CmdResult
Get the result that was parsed from the command output.
getSession(JobIdentifier, Map<String, OpenGridSession>) - Method in class net.sf.basedb.opengrid.service.OpenGridService
Get an existing session from the cache or create a new connection if it doesn't exists.
getSessionControl(ServletRequest) - Static method in class net.sf.basedb.opengrid.servlet.ServletUtil
Get an existing session control and check that a user is logged in.
getSFTPClient() - Method in class net.sf.basedb.opengrid.AbstractSession
 
getSignalUri(JobIdentifier) - Static method in class net.sf.basedb.opengrid.service.OpenGridSignalHandlerFactory
Generate a signal URI that is used to send signals to a given job on a cluster.
getSize() - Method in class net.sf.basedb.opengrid.filetransfer.FileMetaData
The number of bytes of the resource or 0 if not known.
getStartDate() - Method in class net.sf.basedb.opengrid.JobStatus
Get the start time as a date.
getStartTime() - Method in class net.sf.basedb.opengrid.JobStatus
Get the time the job started to execute on one of the cluster nodes.
getStatus() - Method in class net.sf.basedb.opengrid.JobStatus
Get the status of the job.
getStderr() - Method in class net.sf.basedb.opengrid.CmdResult
Get the text written to standard error stream from the command.
getStdout() - Method in class net.sf.basedb.opengrid.CmdResult
Get the text written to the standard output stream from the command.
getString(String) - Method in class net.sf.basedb.opengrid.filetransfer.ByteArrayDownloadTarget
Get the downloaded data as a string.
getSubmissionDate() - Method in class net.sf.basedb.opengrid.JobStatus
Get the submission time as a date.
getSubmissionTime() - Method in class net.sf.basedb.opengrid.JobStatus
Get the time the job was submitted to the cluster.
getSupportedSignals() - Method in class net.sf.basedb.opengrid.service.OpenGridSignalHandlerFactory.OpenGridSignalHandler
 
getTimeAdjustment() - Method in class net.sf.basedb.opengrid.OpenGridCluster.Info
Get the cached result of the call to OpenGridSession.getTimeAdjustment().
getTimeAdjustment() - Method in class net.sf.basedb.opengrid.OpenGridSession
Get the time different in seconds between the BASE server and the remote host.
getTmpFolder(boolean) - Method in class net.sf.basedb.opengrid.config.ClusterConfig
Get the path to a temporary folder that a job can use for storing temporary data.
getTmpFolder(String, boolean) - Method in class net.sf.basedb.opengrid.OpenGridCluster
Get the tmp folder for a job with the given name.
getUploadSource() - Method in class net.sf.basedb.opengrid.JobDefinition.UploadSourceWithPermission
 
getUser() - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Get the username to use when connecting to the Open Grid Cluster primary node.
getUserPermission() - Method in class net.sf.basedb.opengrid.filetransfer.FilePermission
Get the user (owner) permission.
getWorkFolder(String) - Method in class net.sf.basedb.opengrid.OpenGridCluster
Get the work folder for a job with the given name.
group - Variable in class net.sf.basedb.opengrid.filetransfer.FilePermission
 

H

handleSignal(Signal) - Method in class net.sf.basedb.opengrid.service.OpenGridSignalHandlerFactory.OpenGridSignalHandler
 
hashCode() - Method in class net.sf.basedb.opengrid.filetransfer.FilePermission
 
hashCode() - Method in class net.sf.basedb.opengrid.JobIdentifier
 
hostInfo - Variable in class net.sf.basedb.opengrid.OpenGridCluster.Info
 
hostInfoCommand - Variable in class net.sf.basedb.opengrid.config.ClusterConfig
 

I

id - Variable in class net.sf.basedb.opengrid.OpenGridCluster
 
ignoredQsubOptions - Static variable in class net.sf.basedb.opengrid.JobDefinition
 
in - Variable in class net.sf.basedb.opengrid.filetransfer.InputStreamUploadSource
 
inBase - Variable in enum net.sf.basedb.opengrid.config.JobConfig.Priority
 
info - Variable in class net.sf.basedb.opengrid.OpenGridCluster
 
Info(OpenGridSession) - Constructor for class net.sf.basedb.opengrid.OpenGridCluster.Info
 
initMetadata(FileMetaData) - Method in class net.sf.basedb.opengrid.filetransfer.AbstractFileTransfer
Subclasses that are implementing the UploadSource interface should override this method and initialize the metadata instance with information about the loca file.
initMetadata(FileMetaData) - Method in class net.sf.basedb.opengrid.filetransfer.BaseFileUploadSource
 
initMetadata(FileMetaData) - Method in class net.sf.basedb.opengrid.filetransfer.ByteArrayUploadSource
 
inOpenGrid - Variable in enum net.sf.basedb.opengrid.config.JobConfig.Priority
 
InputStreamUploadSource - Class in net.sf.basedb.opengrid.filetransfer
Generic upload source implementation that simply wraps an existing input stream.
InputStreamUploadSource(String, InputStream) - Constructor for class net.sf.basedb.opengrid.filetransfer.InputStreamUploadSource
Create a new upload source from the existing input stream.
InputStreamUploadSource(String, InputStream, FileMetaData) - Constructor for class net.sf.basedb.opengrid.filetransfer.InputStreamUploadSource
Create a new upload source from the existing input stream and file metadata.
instance - Static variable in class net.sf.basedb.opengrid.service.OpenGridService
 
internalConnect(int) - Method in class net.sf.basedb.opengrid.AbstractHost
 
invoker - Variable in class net.sf.basedb.opengrid.service.OpenGridService.JobCompletionInvoker
 
isAlive() - Method in class net.sf.basedb.opengrid.JobStatus
Utility method for checking if the status of this job is "alive": eg. null, WAITING or EXECUTING
isClosed() - Method in class net.sf.basedb.opengrid.AbstractSession
Check if the session has been closed or not.
isDefined(String) - Method in class net.sf.basedb.opengrid.service.OpenGridService
Check if a cluster with the given id has been defined and registered with this service.
isDirectory() - Method in class net.sf.basedb.opengrid.AbstractSession.UploadSourceWrapper
 
isEnabled(JSONOption) - Method in class net.sf.basedb.opengrid.json.JSONOptions
Checks if the given option has been enabled.
isFile() - Method in class net.sf.basedb.opengrid.AbstractSession.UploadSourceWrapper
We only support files.
isLocked() - Method in class net.sf.basedb.opengrid.config.AbstractLockable
Is this instance locked for modifications?
isRunning - Variable in class net.sf.basedb.opengrid.service.OpenGridService
 
isRunning() - Method in class net.sf.basedb.opengrid.service.OpenGridService
Is the Open Grid service running or not?
isRunning() - Method in class net.sf.basedb.opengrid.service.OpenGridServiceFactory.OpenGridServiceControllerAction
 
isValid() - Method in class net.sf.basedb.opengrid.config.AbstractLockable
Check if this configuration is valid or not.

J

job - Variable in class net.sf.basedb.opengrid.service.OpenGridSignalHandlerFactory.OpenGridSignalHandler
 
JOBAGENT_INFO - Static variable in class net.sf.basedb.opengrid.json.JSONOption
Inlcude job agent information from the BASE database when calling ClusterConfig.asJSONObject(JSONOptions).
jobAgentExternalId - Variable in class net.sf.basedb.opengrid.config.ClusterConfig
 
jobCompleted(SessionControl, OpenGridSession, Job, JobStatus) - Method in interface net.sf.basedb.opengrid.service.JobCompletionHandler
Called when the job has been completed (successful or failed).
JobCompletionHandler - Interface in net.sf.basedb.opengrid.service
Callback interface when a job has been completed on an Open Grid cluster.
JobCompletionInvoker(SessionControl) - Constructor for class net.sf.basedb.opengrid.service.OpenGridService.JobCompletionInvoker
 
JobConfig - Class in net.sf.basedb.opengrid.config
Configuration settings related to a job definition that is about to be run on an Open Grid cluster.
JobConfig() - Constructor for class net.sf.basedb.opengrid.config.JobConfig
Create a new job configuration instance with default settings.
JobConfig.Priority - Enum in net.sf.basedb.opengrid.config
Used for converting between Open Grid priority values and BASE priority values.
JobDefinition - Class in net.sf.basedb.opengrid
Define a job that should be submitted to the Open Grid cluster.
JobDefinition(String, JobConfig) - Constructor for class net.sf.basedb.opengrid.JobDefinition
Create a new job definition that is not connected to a BASE job item.
JobDefinition(String, JobConfig, Job) - Constructor for class net.sf.basedb.opengrid.JobDefinition
Create a new job definition that is connected to a BASE job.
JobDefinition.UploadSourceWithPermission - Class in net.sf.basedb.opengrid
Class for storing a file and a permission as one entity.
jobFolder - Variable in class net.sf.basedb.opengrid.config.ClusterConfig
 
jobId - Variable in class net.sf.basedb.opengrid.AbortJobIfTransactionFails
 
jobId - Variable in class net.sf.basedb.opengrid.JobStatus
 
JobIdentifier - Class in net.sf.basedb.opengrid
Represents an identifier for a job on an Open Grid Scheduler cluster.
JobIdentifier(String, String, int) - Constructor for class net.sf.basedb.opengrid.JobIdentifier
Creates a job identifier for a job on a cluster that has a known job in BASE.
JobIdentifier(String, String) - Constructor for class net.sf.basedb.opengrid.JobIdentifier
Creates a job identifier for a job on a cluster that has no known job in BASE.
JobIdentifier(String, String, Job) - Constructor for class net.sf.basedb.opengrid.JobIdentifier
Creates a job identifier for a job on a cluster that has a known job in BASE.
JobStatus - Class in net.sf.basedb.opengrid
Class for keeping track of the status of jobs submitted to an Open Grid cluster.
JobStatus(JobIdentifier) - Constructor for class net.sf.basedb.opengrid.JobStatus
 
jobStatusTimer - Variable in class net.sf.basedb.opengrid.service.OpenGridService
 
JobStatusTimerTask() - Constructor for class net.sf.basedb.opengrid.service.OpenGridService.JobStatusTimerTask
 
JobStatusUpdater - Interface in net.sf.basedb.opengrid.service
Defines an interface for hooking non-grid jobs into the async feature of status updates made by OpenGridService.
jobsToAbort - Variable in class net.sf.basedb.opengrid.service.OpenGridService
 
jobsToUpdate - Variable in class net.sf.basedb.opengrid.service.OpenGridService
 
JSONOption - Class in net.sf.basedb.opengrid.json
Define individual options that can be enabled when returning data in JSON format.
JSONOption(String) - Constructor for class net.sf.basedb.opengrid.json.JSONOption
 
JSONOptions - Class in net.sf.basedb.opengrid.json
Options for converting other information to JSON data.
JSONOptions() - Constructor for class net.sf.basedb.opengrid.json.JSONOptions
Create a new options instance.
JSONOptions(DbControl) - Constructor for class net.sf.basedb.opengrid.json.JSONOptions
Create a new options instance with the possibility to access the BASE database.

L

lastAccessed - Variable in class net.sf.basedb.opengrid.filetransfer.FileMetaData
 
lastJobStatusUpdate - Variable in class net.sf.basedb.opengrid.service.OpenGridService
 
lastModified - Variable in class net.sf.basedb.opengrid.filetransfer.FileMetaData
 
length() - Method in class net.sf.basedb.opengrid.ScriptBuilder
Get the current length of the script.
limit - Variable in class net.sf.basedb.opengrid.filetransfer.ByteArrayDownloadTarget
 
localTimeAdjustment - Variable in class net.sf.basedb.opengrid.OpenGridSession
 
lock() - Method in class net.sf.basedb.opengrid.config.AbstractLockable
Lock this instance for future modifications.
locked - Variable in class net.sf.basedb.opengrid.config.AbstractLockable
 
logFolder - Variable in class net.sf.basedb.opengrid.ScriptBuilder
 
logger - Static variable in class net.sf.basedb.opengrid.AbortJobIfTransactionFails
 
logger - Static variable in class net.sf.basedb.opengrid.AbstractHost
 
logger - Static variable in class net.sf.basedb.opengrid.AbstractSession
 
logger - Static variable in class net.sf.basedb.opengrid.config.XmlConfig
 
logger - Static variable in class net.sf.basedb.opengrid.OpenGrid
 
logger - Static variable in class net.sf.basedb.opengrid.OpenGridCluster
 
logger - Static variable in class net.sf.basedb.opengrid.OpenGridSession
 
logger - Static variable in class net.sf.basedb.opengrid.RemoteHost
 
logger - Static variable in class net.sf.basedb.opengrid.service.OpenGridService
 
logger - Static variable in class net.sf.basedb.opengrid.service.OpenGridSignalHandlerFactory
 

M

message - Variable in class net.sf.basedb.opengrid.JobStatus
 
metadata - Variable in class net.sf.basedb.opengrid.AbstractSession.UploadSourceWrapper
 
metadata - Variable in class net.sf.basedb.opengrid.filetransfer.AbstractFileTransfer
 
metadata - Variable in class net.sf.basedb.opengrid.filetransfer.InputStreamUploadSource
 
MIN_WAIT_INTERVAL - Static variable in class net.sf.basedb.opengrid.service.OpenGridService
 
mkdirs(FilePermission, String...) - Method in class net.sf.basedb.opengrid.AbstractSession
Create directories on the remote server if they do not already exists.

N

name - Variable in class net.sf.basedb.opengrid.config.ConnectionInfo
 
name - Variable in class net.sf.basedb.opengrid.config.NodeConfig
 
name - Variable in class net.sf.basedb.opengrid.filetransfer.AbstractFileTransfer
 
name - Variable in class net.sf.basedb.opengrid.filetransfer.InputStreamUploadSource
 
name - Variable in class net.sf.basedb.opengrid.JobDefinition
 
name - Variable in class net.sf.basedb.opengrid.JobStatus
 
name - Variable in class net.sf.basedb.opengrid.json.JSONOption
 
net.sf.basedb.opengrid - package net.sf.basedb.opengrid
 
net.sf.basedb.opengrid.config - package net.sf.basedb.opengrid.config
 
net.sf.basedb.opengrid.filetransfer - package net.sf.basedb.opengrid.filetransfer
 
net.sf.basedb.opengrid.json - package net.sf.basedb.opengrid.json
 
net.sf.basedb.opengrid.service - package net.sf.basedb.opengrid.service
 
net.sf.basedb.opengrid.servlet - package net.sf.basedb.opengrid.servlet
 
newLine() - Method in class net.sf.basedb.opengrid.ScriptBuilder
Adds an empty line.
nextBgPid - Variable in class net.sf.basedb.opengrid.ScriptBuilder
 
NODE_INFO - Static variable in class net.sf.basedb.opengrid.json.JSONOption
Inlcude the node information when calling ClusterConfig.asJSONObject(JSONOptions).
NodeConfig - Class in net.sf.basedb.opengrid.config
Configuration settings related to a single node in the cluster.
NodeConfig() - Constructor for class net.sf.basedb.opengrid.config.NodeConfig
 
nodeName - Variable in class net.sf.basedb.opengrid.JobStatus
 
nodes - Variable in class net.sf.basedb.opengrid.config.ClusterConfig
 
NONE - Static variable in class net.sf.basedb.opengrid.filetransfer.FilePermission
No permissions = 0;
nonGridJobsToUpdate - Variable in class net.sf.basedb.opengrid.service.OpenGridService
 

O

ogsInfo - Variable in class net.sf.basedb.opengrid.OpenGridCluster.Info
 
ogsInfoCommand - Variable in class net.sf.basedb.opengrid.config.ClusterConfig
 
onAfterCommit() - Method in class net.sf.basedb.opengrid.AbortJobIfTransactionFails
 
onBeforeCommit() - Method in class net.sf.basedb.opengrid.AbortJobIfTransactionFails
 
onRollback() - Method in class net.sf.basedb.opengrid.AbortJobIfTransactionFails
 
OpenGrid - Class in net.sf.basedb.opengrid
Global constants and utility functions for the Open Grid Scheduler service package.
OpenGrid() - Constructor for class net.sf.basedb.opengrid.OpenGrid
 
OpenGridCluster - Class in net.sf.basedb.opengrid
Represents a single Open Grid Scheduler cluster together with login information for accessing it via SSH.
OpenGridCluster(ConnectionInfo, ClusterConfig) - Constructor for class net.sf.basedb.opengrid.OpenGridCluster
Creates a new Open Grid Cluster instance.
OpenGridCluster.Info - Class in net.sf.basedb.opengrid
Holds information about the Open Grid cluster together with a timestamp for caching purposes.
openGridPriorityToBasePriority(Integer) - Static method in class net.sf.basedb.opengrid.config.JobConfig
Convert an Open Grid job priority value to a BASE job priority value. 1024 -- 1 → 1 -- 4 0 or missing → 5 -1 -- -1023 → 6 -- 10
OpenGridService - Class in net.sf.basedb.opengrid.service
Service class for asynchronous communication with Open Grid Scheduler clusters.
OpenGridService() - Constructor for class net.sf.basedb.opengrid.service.OpenGridService
 
OpenGridService.JobCompletionInvoker - Class in net.sf.basedb.opengrid.service
 
OpenGridService.JobStatusTimerTask - Class in net.sf.basedb.opengrid.service
Task for checking current status of jobs that has been sent to the cluster.
OpenGridServiceConfigureFactory - Class in net.sf.basedb.opengrid.service
Action factory that creates a "Configure" button in the "Action" column for the Open Grid service.
OpenGridServiceConfigureFactory() - Constructor for class net.sf.basedb.opengrid.service.OpenGridServiceConfigureFactory
 
OpenGridServiceControllerAction(SessionControl, Extension) - Constructor for class net.sf.basedb.opengrid.service.OpenGridServiceFactory.OpenGridServiceControllerAction
 
OpenGridServiceFactory - Class in net.sf.basedb.opengrid.service
Action factory and service controller for the OpenGridService.
OpenGridServiceFactory() - Constructor for class net.sf.basedb.opengrid.service.OpenGridServiceFactory
 
OpenGridServiceFactory.OpenGridServiceControllerAction - Class in net.sf.basedb.opengrid.service
 
OpenGridServlet - Class in net.sf.basedb.opengrid.servlet
Get information about Open Grid Scheduler hosts.
OpenGridServlet() - Constructor for class net.sf.basedb.opengrid.servlet.OpenGridServlet
 
OpenGridSession - Class in net.sf.basedb.opengrid
An open session to an Open Grid cluster.
OpenGridSession(OpenGridCluster, SSHClient) - Constructor for class net.sf.basedb.opengrid.OpenGridSession
Session are typically created from OpenGridCluster.connect(int).
OpenGridSignalHandler(URI, Job, Collection<Signal>) - Constructor for class net.sf.basedb.opengrid.service.OpenGridSignalHandlerFactory.OpenGridSignalHandler
 
OpenGridSignalHandlerFactory - Class in net.sf.basedb.opengrid.service
Signal handler implementation for Open Grid Scheduler clusters.
OpenGridSignalHandlerFactory() - Constructor for class net.sf.basedb.opengrid.service.OpenGridSignalHandlerFactory
 
OpenGridSignalHandlerFactory.OpenGridSignalHandler - Class in net.sf.basedb.opengrid.service
Signal handler implementation.
options - Variable in class net.sf.basedb.opengrid.json.JSONOptions
 
other - Variable in class net.sf.basedb.opengrid.filetransfer.FilePermission
 
out - Variable in class net.sf.basedb.opengrid.filetransfer.OutputStreamDownloadTarget
 
out - Variable in class net.sf.basedb.opengrid.filetransfer.ServletResponseDownloadTarget
 
OutputStreamDownloadTarget - Class in net.sf.basedb.opengrid.filetransfer
Generic download target implementation that simply wraps an existing output stream.
OutputStreamDownloadTarget(String, OutputStream) - Constructor for class net.sf.basedb.opengrid.filetransfer.OutputStreamDownloadTarget
 

P

parseRequest(HttpServletRequest) - Static method in class net.sf.basedb.opengrid.servlet.ServletUtil
Parse the request as JSON data.
password - Variable in class net.sf.basedb.opengrid.config.ConnectionInfo
 
permission - Variable in class net.sf.basedb.opengrid.AbstractSession.UploadSourceWrapper
 
permission - Variable in class net.sf.basedb.opengrid.JobDefinition.UploadSourceWithPermission
 
port - Variable in class net.sf.basedb.opengrid.config.ConnectionInfo
 
prepareContext(InvokationContext<? super ServiceControllerAction>) - Method in class net.sf.basedb.opengrid.service.OpenGridServiceFactory
 
prepareContext(InvokationContext<? super SignalHandler>) - Method in class net.sf.basedb.opengrid.service.OpenGridSignalHandlerFactory
If the signal schema is "ogx" this factory should handle it.
priority - Variable in class net.sf.basedb.opengrid.config.JobConfig
 
Priority(int, int) - Constructor for enum net.sf.basedb.opengrid.config.JobConfig.Priority
 
privateFiles - Variable in class net.sf.basedb.opengrid.config.JobConfig
 
processAsyncRequests() - Method in class net.sf.basedb.opengrid.service.OpenGridService
Process async requests since the last time.
progress - Variable in class net.sf.basedb.opengrid.JobStatus
 
progress(int, String) - Method in class net.sf.basedb.opengrid.ScriptBuilder
Update the progress file.
providesAtimeMtime() - Method in class net.sf.basedb.opengrid.AbstractSession.UploadSourceWrapper
 

Q

qacct(JobIdentifier, boolean) - Method in class net.sf.basedb.opengrid.OpenGridSession
Issue an 'qacct -j' command to find out information about a job that has ended.
QACCT_DATE - Static variable in class net.sf.basedb.opengrid.JobStatus
Convert date string from "qacct -j <id>" into Date objects.
qdel(JobIdentifier) - Method in class net.sf.basedb.opengrid.OpenGridSession
Abort the job with the specified job id.
qstat(JobIdentifier, boolean) - Method in class net.sf.basedb.opengrid.OpenGridSession
Issue an 'qstat -xml' command, parse the result and return the information as a JobStatus object.
qstat() - Method in class net.sf.basedb.opengrid.OpenGridSession
Execute the 'qstat -xml' command, parse the XML and store it in the cache.
QSTAT_DATE - Static variable in class net.sf.basedb.opengrid.JobStatus
Convert date string from "qstat -xml" into Date objects.
qstatXml - Variable in class net.sf.basedb.opengrid.OpenGridSession
 
qsub(DbControl, List<JobDefinition>) - Method in class net.sf.basedb.opengrid.OpenGridSession
Submit jobs to the cluster.
qsubOptions - Variable in class net.sf.basedb.opengrid.config.JobConfig
 

R

READ - Static variable in class net.sf.basedb.opengrid.filetransfer.FilePermission
Read permissions = 4.
readFile(String, FileMetaData) - Method in class net.sf.basedb.opengrid.AbstractSession
Read from a file on the remote server.
readFromProgress(String) - Method in class net.sf.basedb.opengrid.JobStatus
Parse the data from the 'progress' file which is fomatted as <percent-value> <message>.
readFromQacct(String, int) - Method in class net.sf.basedb.opengrid.JobStatus
Get information from output from 'qacct -j <job-id>'.
readFromQstatXml(Element, int) - Method in class net.sf.basedb.opengrid.JobStatus
Get information from XML element generated by 'qstat -xml'.
readFromResource(String) - Method in class net.sf.basedb.opengrid.config.XmlConfig
Read cluster configuration from a resource on the class path.
readProgress(JobStatus) - Method in class net.sf.basedb.opengrid.OpenGridSession
Read the 'progress' information for the job and update job status instance.
readStderr(JobStatus) - Method in class net.sf.basedb.opengrid.OpenGridSession
Read the 'stderr' file and update the message in the job status instance.
remote - Variable in class net.sf.basedb.opengrid.AbstractSession
 
RemoteHost - Class in net.sf.basedb.opengrid
A regular remote host that we can connect to via SSH.
RemoteHost(ConnectionInfo) - Constructor for class net.sf.basedb.opengrid.RemoteHost
Create a new remote host instance.
RemoteSession - Class in net.sf.basedb.opengrid
A remote session to a RemoteHost.
RemoteSession(RemoteHost, SSHClient) - Constructor for class net.sf.basedb.opengrid.RemoteSession
Session are typically created from RemoteHost.connect(int).
resource - Variable in class net.sf.basedb.opengrid.AbstractSession.CloseResourceOutputStream
 
resp - Variable in class net.sf.basedb.opengrid.filetransfer.ServletResponseDownloadTarget
 
result - Variable in class net.sf.basedb.opengrid.CmdResult
 
rootSc - Variable in class net.sf.basedb.opengrid.service.OpenGridService.JobCompletionInvoker
 
rootSc - Variable in class net.sf.basedb.opengrid.service.OpenGridService
 
run() - Method in class net.sf.basedb.opengrid.service.OpenGridService.JobStatusTimerTask
 

S

sc - Variable in class net.sf.basedb.opengrid.service.OpenGridServiceFactory.OpenGridServiceControllerAction
 
script - Variable in class net.sf.basedb.opengrid.ScriptBuilder
 
ScriptBuilder - Class in net.sf.basedb.opengrid
Utility class for generating shell scripts.
ScriptBuilder() - Constructor for class net.sf.basedb.opengrid.ScriptBuilder
Create a new script builder using the working folder for log and progress information.
ScriptBuilder(String) - Constructor for class net.sf.basedb.opengrid.ScriptBuilder
Create a new script builder for a generic script.
serialVersionUID - Static variable in class net.sf.basedb.opengrid.servlet.OpenGridServlet
 
ServletResponseDownloadTarget - Class in net.sf.basedb.opengrid.filetransfer
Download target implementation that forwards the downloaded remote file to the servlet response output stream.
ServletResponseDownloadTarget(HttpServletResponse, String) - Constructor for class net.sf.basedb.opengrid.filetransfer.ServletResponseDownloadTarget
 
ServletUtil - Class in net.sf.basedb.opengrid.servlet
Utility functions for servlets.
ServletUtil() - Constructor for class net.sf.basedb.opengrid.servlet.ServletUtil
 
setAddress(String) - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Set the internet address to the Open Grid Cluster primary node.
setCmd(String) - Method in class net.sf.basedb.opengrid.JobDefinition
Set the command/bash script to execute as part of this job.
setCreatePrivateFiles(boolean) - Method in class net.sf.basedb.opengrid.config.JobConfig
Set this option to automatically include a "umask" command that makes all files created by the job script private (eg, umask u=rwx,g=,o=) This is on by default.
setDateCommand(String) - Method in class net.sf.basedb.opengrid.config.ClusterConfig
Set the command that should be executed to get the current date and time from the cluster.
setDebug(boolean) - Method in class net.sf.basedb.opengrid.JobDefinition
Set the debug flag.
setEndTime(long) - Method in class net.sf.basedb.opengrid.JobStatus
 
setErrorOnBaseJob(JobIdentifier, String) - Method in class net.sf.basedb.opengrid.service.OpenGridService
Set ERROR status on a BASE job.
setException(Exception) - Method in class net.sf.basedb.opengrid.CmdResult
 
setExitCode(int) - Method in class net.sf.basedb.opengrid.JobStatus
 
setExitStatus(int) - Method in class net.sf.basedb.opengrid.CmdResult
 
setFailImmediately(boolean) - Method in class net.sf.basedb.opengrid.config.JobConfig
Set this option if the job script should exit as soon as an error is encountered.
setFingerPrint(String) - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Set the public key fingerprint for the host so we can verify that the connection is made to the exepected SSH server.
setHostInfoCommand(String) - Method in class net.sf.basedb.opengrid.config.ClusterConfig
Set the command that should be executed to get some information about the hardware and operating system of the host.
setJobAgentExternalId(String) - Method in class net.sf.basedb.opengrid.config.ClusterConfig
Set the External ID of the job agent this cluster should be linked to.
setJobFolder(String) - Method in class net.sf.basedb.opengrid.config.ClusterConfig
Set the path to the primary job folder on the Open Grid cluster.
setJsonResponseHeaders(HttpServletResponse) - Static method in class net.sf.basedb.opengrid.servlet.ServletUtil
Set proper response headers for returning a JSON response.
setLastAccessedTime(long) - Method in class net.sf.basedb.opengrid.filetransfer.FileMetaData
Set the date and time the file was last accessed.
setLastModifiedTime(long) - Method in class net.sf.basedb.opengrid.filetransfer.FileMetaData
Set the date and time the file was last modified.
setMessage(String) - Method in class net.sf.basedb.opengrid.JobStatus
 
setName(String) - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Set the display name of the cluster.
setName(String) - Method in class net.sf.basedb.opengrid.config.NodeConfig
Set the name of the node.
setName(String) - Method in class net.sf.basedb.opengrid.JobStatus
 
setNodeName(String) - Method in class net.sf.basedb.opengrid.JobStatus
 
setOpenGridInfoCommand(String) - Method in class net.sf.basedb.opengrid.config.ClusterConfig
Set the command that should be executed to get some information about the Open Grid Scheduler software version.
setPassword(String) - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Set the password to use for connecting to the Open Grid Cluster primary node.
setPort(int) - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Set the port number to use for connecting to the Open Grid Cluster primary node.
setPriority(Integer) - Method in class net.sf.basedb.opengrid.config.JobConfig
Set the priority of the job.
setProgress(int) - Method in class net.sf.basedb.opengrid.JobStatus
 
setProgressOnBaseJob(JobIdentifier, int, String) - Method in class net.sf.basedb.opengrid.service.OpenGridService
Update the progress status on a BASE job.
setQsubOption(String, String) - Method in class net.sf.basedb.opengrid.config.JobConfig
Set an option for the 'qsub' command.
setResult(R) - Method in class net.sf.basedb.opengrid.CmdResult
 
setSize(long) - Method in class net.sf.basedb.opengrid.filetransfer.FileMetaData
Set the size of the file that is about to be downloaded.
setStartTime(long) - Method in class net.sf.basedb.opengrid.JobStatus
 
setStatus(Job.Status) - Method in class net.sf.basedb.opengrid.JobStatus
 
setStderr(String) - Method in class net.sf.basedb.opengrid.CmdResult
 
setStdout(String) - Method in class net.sf.basedb.opengrid.CmdResult
 
setSubmissionTime(long) - Method in class net.sf.basedb.opengrid.JobStatus
 
setSubmitted(long, String) - Method in class net.sf.basedb.opengrid.JobStatus
Called after a job has been been successfully submitted to the cluster.
setTmpFolder(String, boolean) - Method in class net.sf.basedb.opengrid.config.ClusterConfig
Set the path to the temporary job folder on the Open Grid cluster.
setUser(String) - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Set the username to use for connecting to the Open Grid Cluster primary node.
sftp - Variable in class net.sf.basedb.opengrid.AbstractSession
 
Sha256Verifier - Class in net.sf.basedb.opengrid
Verify the connection to a remote host using SHA-256 hash of the servers public key.
Sha256Verifier(String) - Constructor for class net.sf.basedb.opengrid.Sha256Verifier
 
signalURI - Variable in class net.sf.basedb.opengrid.service.OpenGridSignalHandlerFactory.OpenGridSignalHandler
 
size - Variable in class net.sf.basedb.opengrid.filetransfer.FileMetaData
 
source - Variable in class net.sf.basedb.opengrid.AbstractSession.UploadSourceWrapper
 
ssh - Variable in class net.sf.basedb.opengrid.AbstractSession
 
SSH_CONFIG - Static variable in class net.sf.basedb.opengrid.SshUtil
Default configuration for SSH connections.
SshUtil - Class in net.sf.basedb.opengrid
Interal class with utility functions for SSH connections.
SshUtil() - Constructor for class net.sf.basedb.opengrid.SshUtil
 
start(SessionControl, Extension<ServiceControllerAction>) - Method in class net.sf.basedb.opengrid.service.OpenGridService
Start the service if it is not running.
start() - Method in class net.sf.basedb.opengrid.service.OpenGridServiceFactory.OpenGridServiceControllerAction
 
startTime - Variable in class net.sf.basedb.opengrid.JobStatus
 
status - Variable in class net.sf.basedb.opengrid.JobStatus
 
stderr - Variable in class net.sf.basedb.opengrid.CmdResult
 
stdout - Variable in class net.sf.basedb.opengrid.CmdResult
 
stop() - Method in class net.sf.basedb.opengrid.service.OpenGridService
Stop the service if it is running.
stop() - Method in class net.sf.basedb.opengrid.service.OpenGridServiceFactory.OpenGridServiceControllerAction
 
stopInternal() - Method in class net.sf.basedb.opengrid.service.OpenGridService
 
StringUploadSource - Class in net.sf.basedb.opengrid.filetransfer
Upload source implementation for uploading the contents of a string to a file on a remote server.
StringUploadSource(String, String) - Constructor for class net.sf.basedb.opengrid.filetransfer.StringUploadSource
Create a new source file from a string of data.
submissionTime - Variable in class net.sf.basedb.opengrid.JobStatus
 
SUPPORTED_SIGNALS - Static variable in class net.sf.basedb.opengrid.service.OpenGridSignalHandlerFactory
All supported signals by this signal handler.
supportedSignals - Variable in class net.sf.basedb.opengrid.service.OpenGridSignalHandlerFactory.OpenGridSignalHandler
 
supports(Signal) - Method in class net.sf.basedb.opengrid.service.OpenGridSignalHandlerFactory.OpenGridSignalHandler
 
systemSc - Variable in class net.sf.basedb.opengrid.service.OpenGridService
 

T

throwExceptionIfNonZeroExitStatus() - Method in class net.sf.basedb.opengrid.CmdResult
Throws an exception if the exist status is not 0.
time(String) - Method in class net.sf.basedb.opengrid.ScriptBuilder
Append the current time (hour:minute:second) and comment into the 'time.log' file in the log folder.
timeAdjustment - Variable in class net.sf.basedb.opengrid.OpenGridCluster.Info
 
tmpFolder - Variable in class net.sf.basedb.opengrid.config.ClusterConfig
 
tmpFolderDebug - Variable in class net.sf.basedb.opengrid.config.ClusterConfig
 
toString() - Method in class net.sf.basedb.opengrid.AbstractHost
 
toString() - Method in class net.sf.basedb.opengrid.CmdResult
 
toString() - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
 
toString() - Method in class net.sf.basedb.opengrid.JobIdentifier
 
toString() - Method in class net.sf.basedb.opengrid.JobStatus
 
toString() - Method in class net.sf.basedb.opengrid.json.JSONOption
 
toString() - Method in class net.sf.basedb.opengrid.ScriptBuilder
Get the generated script.
toString() - Method in class net.sf.basedb.opengrid.service.OpenGridServiceFactory.OpenGridServiceControllerAction
 
tryConnect(JobIdentifier) - Method in class net.sf.basedb.opengrid.service.OpenGridService
Try to connect to the cluster referenced by the job identifier.

U

umask() - Method in class net.sf.basedb.opengrid.filetransfer.FilePermission
Get the octal permission representation to set in 'umask' command.
unknownJobs - Variable in class net.sf.basedb.opengrid.service.OpenGridService
 
updateJobStatusInBase(JobStatus, OpenGridSession, OpenGridService.JobCompletionInvoker) - Method in class net.sf.basedb.opengrid.service.OpenGridService
 
upload - Variable in class net.sf.basedb.opengrid.JobDefinition.UploadSourceWithPermission
 
uploadFile(UploadSource, String, FilePermission) - Method in class net.sf.basedb.opengrid.AbstractSession
Upload a file with SFTP.
UploadSource - Interface in net.sf.basedb.opengrid.filetransfer
Represents a local file or resource that can be uploaded as a file to a remote server.
UploadSourceWithPermission(UploadSource, FilePermission) - Constructor for class net.sf.basedb.opengrid.JobDefinition.UploadSourceWithPermission
 
UploadSourceWrapper(UploadSource, FilePermission) - Constructor for class net.sf.basedb.opengrid.AbstractSession.UploadSourceWrapper
 
user - Variable in class net.sf.basedb.opengrid.config.ConnectionInfo
 
user - Variable in class net.sf.basedb.opengrid.filetransfer.FilePermission
 
USER_RW - Static variable in class net.sf.basedb.opengrid.filetransfer.FilePermission
Predefined set of permission giving the owner READ+WRITE permission and no permissions to other users.
USER_RW_ALL_R - Static variable in class net.sf.basedb.opengrid.filetransfer.FilePermission
Predefined set of permission giving the owner READ+WRITE permission and READ permissions to other users.
USER_RW_GROUP_R - Static variable in class net.sf.basedb.opengrid.filetransfer.FilePermission
Predefined set of permission giving the owner READ+WRITE permission, the group READ permission and no permissions to other users.
USER_RWX - Static variable in class net.sf.basedb.opengrid.filetransfer.FilePermission
Predefined set of permission giving the owner READ+WRITE+EXECUTE permission and no permissions to other users.

V

valid - Variable in class net.sf.basedb.opengrid.config.AbstractLockable
 
valueOf(String) - Static method in enum net.sf.basedb.opengrid.config.JobConfig.Priority
Returns the enum constant of this type with the specified name.
values() - Static method in enum net.sf.basedb.opengrid.config.JobConfig.Priority
Returns an array containing the constants of this enum type, in the order they are declared.
verify(String, int, PublicKey) - Method in class net.sf.basedb.opengrid.Sha256Verifier
 
VERSION - Static variable in class net.sf.basedb.opengrid.OpenGrid
The current version of this package.

W

waitForProcess(String) - Method in class net.sf.basedb.opengrid.ScriptBuilder
Wait for the given process to end.
WRITE - Static variable in class net.sf.basedb.opengrid.filetransfer.FilePermission
Write permissions = 2.
writeFile(String, boolean, FileMetaData, FilePermission) - Method in class net.sf.basedb.opengrid.AbstractSession
Write to a file on the remote server.

X

XmlConfig - Class in net.sf.basedb.opengrid.config
Helper class for reading cluster configuration settings from an XML file.
XmlConfig() - Constructor for class net.sf.basedb.opengrid.config.XmlConfig
Create a new configuration instance.
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Open Grid Scheduler package for BASE 1.1: 2017-05-10