Index

A B C D E F G H I J L M N O P Q R S T U V W X 
All Classes|All Packages

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.
appendQsubOptionsToScript(ScriptBuilder, Set<String>) - Method in class net.sf.basedb.opengrid.config.JobConfig
Add all qsub options in this configuration to the script.
appendSbatchOptionsToScript(StringBuilder, Set<String>) - Method in class net.sf.basedb.opengrid.config.JobConfig
Add all sbatch options in this configuration to the script.
appendSbatchOptionsToScript(ScriptBuilder, Set<String>) - Method in class net.sf.basedb.opengrid.config.JobConfig
Add all sbatch options in this configuration to the script.
asJobScript(String, String) - Method in class net.sf.basedb.opengrid.JobDefinition
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.
autoConvertOptions - Variable in class net.sf.basedb.opengrid.config.JobConfig
 
autoConvertOptions() - Method in class net.sf.basedb.opengrid.config.JobConfig
 
autoIndent - Variable in class net.sf.basedb.opengrid.ScriptBuilder
 
autoUnindent - Variable in class net.sf.basedb.opengrid.ScriptBuilder
 

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
batchConfig - Variable in class net.sf.basedb.opengrid.config.JobConfig
 
batchConfig - Variable in class net.sf.basedb.opengrid.JobDefinition
 
BatchConfig - Class in net.sf.basedb.opengrid.config
Configuration settings related to a batch of jobs that are about to be submitted to the cluster at more or less the same time.
BatchConfig() - Constructor for class net.sf.basedb.opengrid.config.BatchConfig
Creates a default batch configuration with a delay interval of 30 seconds and no initial delay.
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.
cancelJob(OpenGridSession, JobIdentifier) - Method in interface net.sf.basedb.opengrid.engine.ClusterEngine
Tell the cluster that a running or waiting job should be cancelled.
cancelJob(OpenGridSession, JobIdentifier) - Method in class net.sf.basedb.opengrid.engine.DirectEngine
 
cancelJob(OpenGridSession, JobIdentifier) - Method in class net.sf.basedb.opengrid.engine.OpenGridEngine
 
cancelJob(OpenGridSession, JobIdentifier) - Method in class net.sf.basedb.opengrid.engine.SlurmEngine
 
checkIndent(String, Collection<String>, int) - Method in class net.sf.basedb.opengrid.ScriptBuilder
If cmd starts with one of the given keys, apply delta to the indentation level and create a new indent-string.
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.BatchConfig
Check that the initial and delay interval are >=0.
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 and 'nice' must be between -2147483645 and +2147483645.
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 cluster.
ClusterConfig() - Constructor for class net.sf.basedb.opengrid.config.ClusterConfig
ClusterConfig(ClusterType) - Constructor for class net.sf.basedb.opengrid.config.ClusterConfig
Create new cluster configuration for the given cluster type.
ClusterEngine - Interface in net.sf.basedb.opengrid.engine
Internal interface to be implemented once for each type of cluster.
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
 
ClusterType - Enum in net.sf.basedb.opengrid.config
Enumeration with cluster types that are supported by this plugin.
ClusterType() - Constructor for enum net.sf.basedb.opengrid.config.ClusterType
 
ClusterTypeFilter - Class in net.sf.basedb.opengrid.filter
Filter implementation that can be used to return clusters of a given type.
ClusterTypeFilter(ClusterType) - Constructor for class net.sf.basedb.opengrid.filter.ClusterTypeFilter
 
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.
CmdResult.DateResult - Class in net.sf.basedb.opengrid
An implementation that parses the 'stdout' to a date if the exit code is 0.
CmdResult.StdioResult - Class in net.sf.basedb.opengrid
An implementation that set the result to 'stdout' if the exit code is 0, and to 'stderr' if not.
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.
connected - Variable in class net.sf.basedb.opengrid.filter.IsConnectedFilter
 
connected - Variable in class net.sf.basedb.opengrid.OpenGridCluster.Info
 
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 via SSH to the cluster.
ConnectionInfo() - Constructor for class net.sf.basedb.opengrid.config.ConnectionInfo
Create a new connection information 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.
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.
context - Variable in class net.sf.basedb.opengrid.service.OpenGridService.JobCompletionInvoker
 
convertQsubToSbatchOptions() - Method in class net.sf.basedb.opengrid.config.JobConfig
Convert options set for 'qsub' (Open Grid) to options for 'sbatch' (Slurm).
convertSbatchToQsubOptions() - Method in class net.sf.basedb.opengrid.config.JobConfig
Convert options set for 'sbatch' (Slurm) to options for 'qsub' (Open Grid).
COUNTER - Static variable in class net.sf.basedb.opengrid.JobDefinition
 
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.
createEngine() - Method in enum net.sf.basedb.opengrid.config.ClusterType
Create a new engine instance to use for cluster-specific operations.
createFileKeyProvider(Config, String, String, String) - Method in class net.sf.basedb.opengrid.AbstractHost
Create and initialize a private key provider.
createJobScript(JobDefinition, String, String) - Method in class net.sf.basedb.opengrid.engine.DirectEngine
Generates a script that executes the job script.
createJobScript(JobDefinition, String, String) - Method in class net.sf.basedb.opengrid.engine.OpenGridEngine
Generates a script that executes the job script.
createJobScript(JobDefinition, String, String) - Method in class net.sf.basedb.opengrid.engine.SlurmEngine
Generates a script that executes the job script.
createJobSubmission(OpenGridSession, JobDefinition, String, String) - Method in interface net.sf.basedb.opengrid.engine.ClusterEngine
Create a job submission for executing a job on the cluster.
createJobSubmission(OpenGridSession, JobDefinition, String, String) - Method in class net.sf.basedb.opengrid.engine.DirectEngine
 
createJobSubmission(OpenGridSession, JobDefinition, String, String) - Method in class net.sf.basedb.opengrid.engine.OpenGridEngine
 
createJobSubmission(OpenGridSession, JobDefinition, String, String) - Method in class net.sf.basedb.opengrid.engine.SlurmEngine
 
createOptionsFile(OpenGridSession, JobDefinition, String, String) - Method in class net.sf.basedb.opengrid.engine.DirectEngine
 
createQsubScript(JobDefinition, String, String) - Method in class net.sf.basedb.opengrid.engine.OpenGridEngine
Generates a script that can be submitted with 'qsub' to the Open Grid Cluster.
createSbatchScript(JobDefinition, String, String) - Method in class net.sf.basedb.opengrid.engine.SlurmEngine
Generates a script that can be submitted with 'sbatch' to slurm.

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
 
dateFormat - Variable in class net.sf.basedb.opengrid.CmdResult.DateResult
 
DateResult(String) - Constructor for class net.sf.basedb.opengrid.CmdResult.DateResult
Create a date result using the default date format.
DateResult(String, DateFormatter) - Constructor for class net.sf.basedb.opengrid.CmdResult.DateResult
Create a date result using a custom date format.
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 and no batch configuration.
DEFAULT - Static variable in class net.sf.basedb.opengrid.json.JSONOptions
Use default options.
delayInterval - Variable in class net.sf.basedb.opengrid.config.BatchConfig
 
DF - Static variable in class net.sf.basedb.opengrid.JobDefinition
 
DIRECT - net.sf.basedb.opengrid.config.ClusterType
The "cluster" doesn't have an manager, but jobs are started immediately when submitted.
DirectEngine - Class in net.sf.basedb.opengrid.engine
Engine implementation for servers without a job manager.
DirectEngine() - Constructor for class net.sf.basedb.opengrid.engine.DirectEngine
 
DirectEngine.ProcessJobStatus - Class in net.sf.basedb.opengrid.engine
Job status information for direct jobs.
DirectEngine.StatusCmd - Class in net.sf.basedb.opengrid.engine
Implementation for getting information about a running or finished job.
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
EIGHT - net.sf.basedb.opengrid.config.JobConfig.Priority
 
enable(JSONOption) - Method in class net.sf.basedb.opengrid.json.JSONOptions
Enable the given option.
endTime - Variable in class net.sf.basedb.opengrid.JobStatus
 
engine - Variable in class net.sf.basedb.opengrid.OpenGridSession
 
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
 
evaluate(OpenGridCluster) - Method in class net.sf.basedb.opengrid.filter.ClusterTypeFilter
 
evaluate(OpenGridCluster) - Method in class net.sf.basedb.opengrid.filter.IsConnectedFilter
 
evaluate(OpenGridCluster) - Method in class net.sf.basedb.opengrid.filter.UsernameFilter
 
exception - Variable in class net.sf.basedb.opengrid.CmdResult
 
EXECUTABLE_FILES - Static variable in class net.sf.basedb.opengrid.JobDefinition.UploadSourceWithPermission
File endings that should automatially be executable when uploaded.
execute(C, int) - Method in class net.sf.basedb.opengrid.AbstractSession
Execute a command on the remote host and store the results in the CmdResult instance.
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.
executeNow(JobDefinition, String, int) - Method in class net.sf.basedb.opengrid.OpenGridSession
Execute a command on a node in the cluster with support for uploading files before the command is executed.
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
 
export(String, String) - Method in class net.sf.basedb.opengrid.ScriptBuilder
Add an exported variable declaration to the script: export key="value".
ext - Variable in class net.sf.basedb.opengrid.service.OpenGridService
 
ext - Variable in class net.sf.basedb.opengrid.service.OpenGridServiceFactory.OpenGridServiceControllerAction
 

F

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
 
findExistingAlgorithms(String, int) - Method in class net.sf.basedb.opengrid.Sha256Verifier
 
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
 
FIVE - net.sf.basedb.opengrid.config.JobConfig.Priority
 
FOUR - net.sf.basedb.opengrid.config.JobConfig.Priority
 

G

getActions(InvokationContext<? super ServiceControllerAction>) - Method in class net.sf.basedb.opengrid.service.OpenGridServiceFactory
 
getActions(InvokationContext<? super ButtonAction>) - Method in class net.sf.basedb.opengrid.service.OpenGridServiceConfigureFactory
 
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 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
getBatchConfig() - Method in class net.sf.basedb.opengrid.config.JobConfig
 
getBatchConfig() - Method in class net.sf.basedb.opengrid.JobDefinition
Get the batch configuration settings.
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(Collection<JobAgent>) - Method in class net.sf.basedb.opengrid.service.OpenGridService
 
getClusters(Collection<JobAgent>, Filter<OpenGridCluster>) - 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.
getClusters(DbControl, Collection<Include>) - Method in class net.sf.basedb.opengrid.service.OpenGridService
 
getClusters(DbControl, Collection<Include>, Filter<OpenGridCluster>) - Method in class net.sf.basedb.opengrid.service.OpenGridService
Get all clusters that the logged in user is allowed to use.
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
Deprecated.
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
 
getDelayForNextJob() - Method in class net.sf.basedb.opengrid.config.BatchConfig
Helper method that get the start time for the next job and calculates the delay in seconds from the current time.
getDelayInterval() - Method in class net.sf.basedb.opengrid.config.BatchConfig
 
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
Deprecated.
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 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.
getHardTimeout(int) - Method in class net.sf.basedb.opengrid.CmdResult
Calculate a hard timeout for the command that depends on the given soft timeout.
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.
getInitialDelay() - Method in class net.sf.basedb.opengrid.config.BatchConfig
 
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.
getJobScripts() - Method in class net.sf.basedb.opengrid.engine.JobSubmission
List of files that should be uploaded to the work folder that has been created for the job before the job is executed.
getJobStatus(OpenGridSession, JobIdentifier) - Method in interface net.sf.basedb.opengrid.service.JobStatusUpdater
A request for status information about the identified job.
getJobStatusPath(OpenGridSession, String) - Static method in class net.sf.basedb.opengrid.engine.DirectEngine
Get the path to where the status information for a job is saved.
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
 
getMaxNumberInString(String) - Method in class net.sf.basedb.opengrid.config.JobConfig
Get the highest number that can be found in the given string.
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.
getNextStartTime() - Method in class net.sf.basedb.opengrid.config.BatchConfig
Get the start time fo the next job that is scheduled.
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 cluster manager 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 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 primary node.
getPriority() - Method in class net.sf.basedb.opengrid.config.JobConfig
 
getPrivateKey() - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Get the private key to use when connecting to the primary node.
getPrivateKeyFormat() - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Get the format of the private key (null = auto-detect)
getPrivateKeyPassword() - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Get the password for unlocking the private key.
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.
getSbatchOption(String) - Method in class net.sf.basedb.opengrid.config.JobConfig
Get the value of a sbatch option.
getSbatchOptions() - Method in class net.sf.basedb.opengrid.config.JobConfig
Get all options that has been specified for sbatch so far.
getScript(String) - Method in class net.sf.basedb.opengrid.engine.DirectEngine
 
getScript(String) - Method in class net.sf.basedb.opengrid.engine.OpenGridEngine
 
getScript(String) - Method in class net.sf.basedb.opengrid.engine.SlurmEngine
 
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.
getSlurmNice() - Method in class net.sf.basedb.opengrid.config.JobConfig
Get the 'nice' value (used in Slurm) that corresponds to the priority value used in Open Grid.
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.
getStatusIfFinished(OpenGridSession, JobIdentifier, int) - Method in interface net.sf.basedb.opengrid.engine.ClusterEngine
Get information about a job that is expected to have finished.
getStatusIfFinished(OpenGridSession, JobIdentifier, int) - Method in class net.sf.basedb.opengrid.engine.DirectEngine
 
getStatusIfFinished(OpenGridSession, JobIdentifier, int) - Method in class net.sf.basedb.opengrid.engine.OpenGridEngine
 
getStatusIfFinished(OpenGridSession, JobIdentifier, int) - Method in class net.sf.basedb.opengrid.engine.SlurmEngine
 
getStatusInQueue(OpenGridSession, JobIdentifier, int) - Method in interface net.sf.basedb.opengrid.engine.ClusterEngine
Get information about a job that is expected to be waiting in the queue or running.
getStatusInQueue(OpenGridSession, JobIdentifier, int) - Method in class net.sf.basedb.opengrid.engine.DirectEngine
 
getStatusInQueue(OpenGridSession, JobIdentifier, int) - Method in class net.sf.basedb.opengrid.engine.OpenGridEngine
 
getStatusInQueue(OpenGridSession, JobIdentifier, int) - Method in class net.sf.basedb.opengrid.engine.SlurmEngine
 
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.
getSubmitCmd() - Method in class net.sf.basedb.opengrid.engine.JobSubmission
The command that should be executed in order to register the job with 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.
getType() - Method in class net.sf.basedb.opengrid.config.ClusterConfig
 
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 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.engine.OpenGridEngine
 
ignoredSbatchOptions - Static variable in class net.sf.basedb.opengrid.engine.SlurmEngine
 
in - Variable in class net.sf.basedb.opengrid.filetransfer.InputStreamUploadSource
 
inBase - Variable in enum net.sf.basedb.opengrid.config.JobConfig.Priority
 
indentLevel - Variable in class net.sf.basedb.opengrid.ScriptBuilder
 
indentString - Variable in class net.sf.basedb.opengrid.ScriptBuilder
 
info - Variable in class net.sf.basedb.opengrid.OpenGridCluster
 
Info(ClusterConfig, Exception) - Constructor for class net.sf.basedb.opengrid.OpenGridCluster.Info
Constructor to use when connecting to the host fails.
Info(OpenGridSession) - Constructor for class net.sf.basedb.opengrid.OpenGridCluster.Info
 
initialDelay - Variable in class net.sf.basedb.opengrid.config.BatchConfig
 
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.
isConnected() - Method in class net.sf.basedb.opengrid.OpenGridCluster.Info
TRUE if was possible to connect to the cluster, FALSE otherwise.
IsConnectedFilter - Class in net.sf.basedb.opengrid.filter
Filter implementation that can be used to return clusters where the connection is working (or not).
IsConnectedFilter(boolean) - Constructor for class net.sf.basedb.opengrid.filter.IsConnectedFilter
 
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.
isExecutable(String) - Static method in class net.sf.basedb.opengrid.JobDefinition.UploadSourceWithPermission
 
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 or Slurm cluster.
JobConfig() - Constructor for class net.sf.basedb.opengrid.config.JobConfig
Create a new job configuration instance with default settings.
JobConfig(boolean) - Constructor for class net.sf.basedb.opengrid.config.JobConfig
Create a new job configuration instance.
JobConfig(boolean, BatchConfig) - Constructor for class net.sf.basedb.opengrid.config.JobConfig
 
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 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(String, JobConfig, BatchConfig, Job) - Constructor for class net.sf.basedb.opengrid.JobDefinition
Create a job definition with a batch configuration that overrides the default job configuration.
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.engine.DirectEngine.StatusCmd
 
jobId - Variable in class net.sf.basedb.opengrid.engine.OpenGridEngine.QacctCmd
 
jobId - Variable in class net.sf.basedb.opengrid.engine.SlurmEngine.SacctCmd
 
jobId - Variable in class net.sf.basedb.opengrid.engine.SlurmEngine.SqueueCmd
 
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) - 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, 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, 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
 
JobSubmission - Class in net.sf.basedb.opengrid.engine
Represents a job submission for sending a job to the cluster.
JobSubmission() - Constructor for class net.sf.basedb.opengrid.engine.JobSubmission
 
JobSubmission(String, List<UploadSource>) - Constructor for class net.sf.basedb.opengrid.engine.JobSubmission
 
join(ScriptBuilder) - Method in class net.sf.basedb.opengrid.ScriptBuilder
Join the other script with this script.
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.engine.DirectEngine
 
logger - Static variable in class net.sf.basedb.opengrid.engine.OpenGridEngine
 
logger - Static variable in class net.sf.basedb.opengrid.engine.SlurmEngine
 
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.engine - package net.sf.basedb.opengrid.engine
 
net.sf.basedb.opengrid.filetransfer - package net.sf.basedb.opengrid.filetransfer
 
net.sf.basedb.opengrid.filter - package net.sf.basedb.opengrid.filter
 
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
 
nextTime - Variable in class net.sf.basedb.opengrid.config.BatchConfig
 
nice - Variable in class net.sf.basedb.opengrid.config.JobConfig
 
NINE - net.sf.basedb.opengrid.config.JobConfig.Priority
 
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
 
nullVariants - Static variable in class net.sf.basedb.opengrid.engine.SlurmEngine.SlurmJobStatus
The output from 'squeue' and 'sacct' have *several* ways to indicate no information is available.

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
 
ONE - net.sf.basedb.opengrid.config.JobConfig.Priority
 
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
 
OPENGRID - net.sf.basedb.opengrid.config.ClusterType
The cluster is an Open Grid Engine cluster.
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.
OpenGridEngine - Class in net.sf.basedb.opengrid.engine
Cluster engine implementation for Open Grid clusters.
OpenGridEngine() - Constructor for class net.sf.basedb.opengrid.engine.OpenGridEngine
 
OpenGridEngine.OpenGridJobStatus - Class in net.sf.basedb.opengrid.engine
Job status information for Open Grid jobs.
OpenGridEngine.QacctCmd - Class in net.sf.basedb.opengrid.engine
Implements the 'qacct' command for getting information about a completed job.
OpenGridEngine.QstatCmd - Class in net.sf.basedb.opengrid.engine
Get job status information from an existing QstatXmlCmd instance.
OpenGridEngine.QstatXmlCmd - Class in net.sf.basedb.opengrid.engine
Execute the 'qstat -xml' command, parse the XML and store the result for future use with QstatCmd.
OpenGridJobStatus(JobIdentifier) - Constructor for class net.sf.basedb.opengrid.engine.OpenGridEngine.OpenGridJobStatus
 
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
openGridPriorityToSlurmNice(Integer) - Static method in class net.sf.basedb.opengrid.config.JobConfig
Convert an Open Grid job priority value to a 'nice' value used in Slurm.
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
 

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parseRequest(HttpServletRequest) - Static method in class net.sf.basedb.opengrid.servlet.ServletUtil
Parse the request as JSON data.
parseResult() - Method in class net.sf.basedb.opengrid.CmdResult.DateResult
 
parseResult() - Method in class net.sf.basedb.opengrid.CmdResult
This method is called after the command has been executed and the exit code, stdout and stderr has been updated.
parseResult() - Method in class net.sf.basedb.opengrid.CmdResult.StdioResult
 
parseResult() - Method in class net.sf.basedb.opengrid.engine.DirectEngine.StatusCmd
 
parseResult() - Method in class net.sf.basedb.opengrid.engine.OpenGridEngine.QacctCmd
 
parseResult() - Method in class net.sf.basedb.opengrid.engine.OpenGridEngine.QstatXmlCmd
 
parseResult() - Method in class net.sf.basedb.opengrid.engine.SlurmEngine.SacctCmd
 
parseResult() - Method in class net.sf.basedb.opengrid.engine.SlurmEngine.SqueueCmd
 
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
 
PRIVATE_KEY - Static variable in class net.sf.basedb.opengrid.json.JSONOption
Returns the private key information (including password) when calling ConnectionInfo.asJSONObject(JSONOptions).
privateKey - Variable in class net.sf.basedb.opengrid.config.ConnectionInfo
 
privateKeyFormat - Variable in class net.sf.basedb.opengrid.config.ConnectionInfo
 
privateKeyPassword - Variable in class net.sf.basedb.opengrid.config.ConnectionInfo
 
processAsyncRequests() - Method in class net.sf.basedb.opengrid.service.OpenGridService
Process async requests since the last time.
ProcessJobStatus(JobIdentifier) - Constructor for class net.sf.basedb.opengrid.engine.DirectEngine.ProcessJobStatus
 
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 a 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.
QacctCmd(JobIdentifier, int) - Constructor for class net.sf.basedb.opengrid.engine.OpenGridEngine.QacctCmd
 
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 a command, parse the result and return the information as a JobStatus object.
QSTAT_DATE - Static variable in class net.sf.basedb.opengrid.JobStatus
Convert date string from "qstat -xml" into Date objects.
QstatCmd(OpenGridEngine.QstatXmlCmd, JobIdentifier, int) - Constructor for class net.sf.basedb.opengrid.engine.OpenGridEngine.QstatCmd
 
qstatXml - Variable in class net.sf.basedb.opengrid.engine.OpenGridEngine
 
QstatXmlCmd() - Constructor for class net.sf.basedb.opengrid.engine.OpenGridEngine.QstatXmlCmd
 
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
 

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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.engine.OpenGridEngine.OpenGridJobStatus
Get information from output from 'qacct -j {job-id}'.
readFromQstatXml(Element, int) - Method in class net.sf.basedb.opengrid.engine.OpenGridEngine.OpenGridJobStatus
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.
readFromSqueueAndSacct(String, int) - Method in class net.sf.basedb.opengrid.engine.SlurmEngine.SlurmJobStatus
Parse the output from 'squeue -o %all -j{id}'.
readFromStatusFile(String, int) - Method in class net.sf.basedb.opengrid.engine.DirectEngine.ProcessJobStatus
Parse information from the STATUS_FILE.
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.
readTextFile(File) - Method in class net.sf.basedb.opengrid.config.XmlConfig
 
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

SACCT_COLS - Static variable in class net.sf.basedb.opengrid.engine.SlurmEngine.SacctCmd
Data columns we want to return from 'sacct'.
SacctCmd(JobIdentifier, int) - Constructor for class net.sf.basedb.opengrid.engine.SlurmEngine.SacctCmd
 
sbatchOptions - Variable in class net.sf.basedb.opengrid.config.JobConfig
 
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.
scripts - Variable in class net.sf.basedb.opengrid.engine.JobSubmission
 
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 primary node.
setBatchConfig(BatchConfig) - Method in class net.sf.basedb.opengrid.config.JobConfig
Set the batch configuration to use with this job configuration.
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
Deprecated.
In 1.5, "umask" is no longer included in the generated scripts
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.
setDefaultConfig(ClusterConfig) - Method in interface net.sf.basedb.opengrid.engine.ClusterEngine
Set default configuration parameters on the given configuration object.
setDefaultConfig(ClusterConfig) - Method in class net.sf.basedb.opengrid.engine.DirectEngine
 
setDefaultConfig(ClusterConfig) - Method in class net.sf.basedb.opengrid.engine.OpenGridEngine
 
setDefaultConfig(ClusterConfig) - Method in class net.sf.basedb.opengrid.engine.SlurmEngine
 
setDelayInterval(int) - Method in class net.sf.basedb.opengrid.config.BatchConfig
If multiple jobs are submitted in a batch, instruct the scheduler to defer each job for a short amount of time.
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
Deprecated.
In 1.5, "set -e' is no longer included in the generated scripts automatically
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.
setInitialDelay(int) - Method in class net.sf.basedb.opengrid.config.BatchConfig
Set the delay of the first job that is submitted in a batch.
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 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 cluster manager software version.
setPassword(String) - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Set the password to use for connecting to the primary node.
setPort(int) - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Set the port number to use for connecting to the primary node.
setPriority(Integer) - Method in class net.sf.basedb.opengrid.config.JobConfig
Set the priority of the job.
setPrivateKey(String) - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Set the private key to use for connecting to the primary node.
setPrivateKeyFormat(String) - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Set the format of the private key (null = auto-detect).
setPrivateKeyPassword(String) - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Set the password to use for unlocking the private key.
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
 
setSbatchOption(String, String) - Method in class net.sf.basedb.opengrid.config.JobConfig
Set an option for the 'sbatch' command (Slurm).
setSize(long) - Method in class net.sf.basedb.opengrid.filetransfer.FileMetaData
Set the size of the file that is about to be downloaded.
setSlurmNice(Integer) - Method in class net.sf.basedb.opengrid.config.JobConfig
Set the priority of the job using a Slurm 'nice' value.
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 cluster.
setUser(String) - Method in class net.sf.basedb.opengrid.config.ConnectionInfo
Set the username to use for connecting to the primary node.
SEVEN - net.sf.basedb.opengrid.config.JobConfig.Priority
 
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
 
SIX - net.sf.basedb.opengrid.config.JobConfig.Priority
 
size - Variable in class net.sf.basedb.opengrid.filetransfer.FileMetaData
 
SLURM - net.sf.basedb.opengrid.config.ClusterType
The cluster is a Slurm Workload Manager cluster.
SLURM_DATE - Static variable in class net.sf.basedb.opengrid.engine.SlurmEngine.SlurmJobStatus
Slurm always (I hope) return dates in "yyyy-MM-ddTHH:mm:ss" format.
SlurmEngine - Class in net.sf.basedb.opengrid.engine
Cluster engine implementation for Slurm clusters.
SlurmEngine() - Constructor for class net.sf.basedb.opengrid.engine.SlurmEngine
 
SlurmEngine.SacctCmd - Class in net.sf.basedb.opengrid.engine
Implements the 'sacct' command for getting information about a completed job.
SlurmEngine.SlurmJobStatus - Class in net.sf.basedb.opengrid.engine
Job status information for Slurm jobs.
SlurmEngine.SqueueCmd - Class in net.sf.basedb.opengrid.engine
Implements the 'squeue' command for getting information about a waiting or running job.
SlurmJobStatus(JobIdentifier) - Constructor for class net.sf.basedb.opengrid.engine.SlurmEngine.SlurmJobStatus
 
slurmNiceToOpenGridPriority(Integer) - Static method in class net.sf.basedb.opengrid.config.JobConfig
Convert a Slurm nice value to Open Grid priority.
source - Variable in class net.sf.basedb.opengrid.AbstractSession.UploadSourceWrapper
 
SqueueCmd(JobIdentifier, int) - Constructor for class net.sf.basedb.opengrid.engine.SlurmEngine.SqueueCmd
 
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() - Method in class net.sf.basedb.opengrid.service.OpenGridServiceFactory.OpenGridServiceControllerAction
 
start(SessionControl, Extension<ServiceControllerAction>) - Method in class net.sf.basedb.opengrid.service.OpenGridService
Start the service if it is not running.
startTime - Variable in class net.sf.basedb.opengrid.JobStatus
 
STARTTIME_DATE - Static variable in class net.sf.basedb.opengrid.engine.OpenGridEngine
Format to use for the -a parameter that contols the earliest start time for a job: YYMMDDhhmm.SS Example: 2204081145.51
status - Variable in class net.sf.basedb.opengrid.JobStatus
 
StatusCmd(OpenGridSession, JobIdentifier, int) - Constructor for class net.sf.basedb.opengrid.engine.DirectEngine.StatusCmd
 
stderr - Variable in class net.sf.basedb.opengrid.CmdResult
 
StdioResult(String) - Constructor for class net.sf.basedb.opengrid.CmdResult.StdioResult
 
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
 
submitCmd - Variable in class net.sf.basedb.opengrid.engine.JobSubmission
 
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

TEN - net.sf.basedb.opengrid.config.JobConfig.Priority
 
THREE - net.sf.basedb.opengrid.config.JobConfig.Priority
 
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.engine.DirectEngine.StatusCmd
 
timeAdjustment - Variable in class net.sf.basedb.opengrid.engine.OpenGridEngine.QacctCmd
 
timeAdjustment - Variable in class net.sf.basedb.opengrid.engine.SlurmEngine.SacctCmd
 
timeAdjustment - Variable in class net.sf.basedb.opengrid.engine.SlurmEngine.SqueueCmd
 
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
 
toUploadSource(String) - Method in class net.sf.basedb.opengrid.ScriptBuilder
Get an upload source representation for uploading the script to a remote server.
tryConnect(JobIdentifier) - Method in class net.sf.basedb.opengrid.service.OpenGridService
Try to connect to the cluster referenced by the job identifier.
TWO - net.sf.basedb.opengrid.config.JobConfig.Priority
 
type - Variable in class net.sf.basedb.opengrid.config.ClusterConfig
 
type - Variable in class net.sf.basedb.opengrid.filter.ClusterTypeFilter
 

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.
username - Variable in class net.sf.basedb.opengrid.filter.UsernameFilter
 
UsernameFilter - Class in net.sf.basedb.opengrid.filter
Filter implementation that can be used to return clusters connected to by a specified user.
UsernameFilter(String) - Constructor for class net.sf.basedb.opengrid.filter.UsernameFilter
 

V

valid - Variable in class net.sf.basedb.opengrid.config.AbstractLockable
 
valueOf(String) - Static method in enum net.sf.basedb.opengrid.config.ClusterType
Returns the enum constant of this type with the specified name.
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.ClusterType
Returns an array containing the constants of this enum type, in the order they are declared.
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.
var(String, String) - Method in class net.sf.basedb.opengrid.ScriptBuilder
Add an variable declaration to the script: key="value".
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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