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 and Interfaces|All Packages|Constant Field Values|Serialized Form

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

Deprecated.

In 1.4, use OpenGridEngine.createQsubScript(JobDefinition, String, String) instead

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

cleanupTimer - Variable in class net.sf.basedb.opengrid.service.OpenGridService

CleanupTimerTask() - Constructor for class net.sf.basedb.opengrid.service.OpenGridService.CleanupTimerTask

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

Deprecated.

In 1.4, use ClusterConfig(net.sf.basedb.opengrid.config.ClusterType) instead

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 Class in net.sf.basedb.opengrid.config

Enumeration with cluster types that are supported by this plugin.

ClusterType() - Constructor for enum class 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

convertOptionsTo(ClusterType) - Method in class net.sf.basedb.opengrid.config.JobConfig

Convert options to the variant used for the given cluster type.

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 class 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(OpenGridSession, JobDefinition, String, String) - Method in class net.sf.basedb.opengrid.engine.SlurmEngine

Generates a script that can be submitted with 'sbatch' to slurm.

CUSTOM_OPTIONS - Static variable in class net.sf.basedb.opengrid.json.JSONOption

Include the custom configuration options when calling ClusterConfig.asJSONObject(JSONOptions).

customOptions - Variable in class net.sf.basedb.opengrid.config.ClusterConfig

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 - Enum constant in enum class 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 - Enum constant in enum class 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.

exists - Variable in class net.sf.basedb.opengrid.filetransfer.FileMetaData

exists() - Method in class net.sf.basedb.opengrid.filetransfer.FileMetaData

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.

In 1.1, use FileServer.MD5_FINGERPRINT_PATTERN instead

fingerPrintType - Variable in class net.sf.basedb.opengrid.config.ConnectionInfo

FIVE - Enum constant in enum class net.sf.basedb.opengrid.config.JobConfig.Priority

FOUR - Enum constant in enum class 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

Shortcut for calling JobConfig.openGridPriorityToBasePriority(Integer).

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.

getCustomOption(String) - Method in class net.sf.basedb.opengrid.config.ClusterConfig

Get a custom option for the cluster.

getCustomOptions() - Method in class net.sf.basedb.opengrid.config.ClusterConfig

Get all custom option for the cluster.

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.

getJobStatusPath(OpenGridSession, String) - Method in class net.sf.basedb.opengrid.engine.SlurmEngine

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.

getMetadata(String) - Method in class net.sf.basedb.opengrid.AbstractSession

Get metadata about the file on the remote server.

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

ID - Static variable in class net.sf.basedb.opengrid.service.OpenGridService

The ID of the service extension.

ID - Static variable in class net.sf.basedb.opengrid.service.OpenGridSignalHandlerFactory

The ID of the signal handler extension.

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 class 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 class 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

isSacctDisabled(OpenGridSession) - Method in class net.sf.basedb.opengrid.engine.SlurmEngine

Check the flag if 'sacct' is disabled on the cluster.

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 Class 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.engine.SlurmEngine.StatusCmd

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

lastCleanup - Variable in class net.sf.basedb.opengrid.service.OpenGridService

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.OpenGridSession

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_CLEANUP_INTERVAL_DEBUG - Static variable in class net.sf.basedb.opengrid.service.OpenGridService

MIN_CLEANUP_INTERVAL_NORMAL - Static variable in class net.sf.basedb.opengrid.service.OpenGridService

MIN_WAIT_INTERVAL_DEBUG - Static variable in class net.sf.basedb.opengrid.service.OpenGridService

MIN_WAIT_INTERVAL_NORMAL - 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 - Enum constant in enum class 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 - Enum constant in enum class 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 - Enum constant in enum class 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.CleanupTimerTask - Class in net.sf.basedb.opengrid.service

Task for checking current status of jobs that has been sent to the cluster.

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.

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.PendingJobsCmd

parseResult() - Method in class net.sf.basedb.opengrid.engine.SlurmEngine.SacctCmd

parseResult() - Method in class net.sf.basedb.opengrid.engine.SlurmEngine.SqueueCmd

parseResult() - Method in class net.sf.basedb.opengrid.engine.SlurmEngine.StatusCmd

password - Variable in class net.sf.basedb.opengrid.config.ConnectionInfo

pendingJobs - Variable in class net.sf.basedb.opengrid.engine.SlurmEngine

pendingJobs - Variable in class net.sf.basedb.opengrid.engine.SlurmEngine.SqueueCmd

PendingJobsCmd() - Constructor for class net.sf.basedb.opengrid.engine.SlurmEngine.PendingJobsCmd

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 class 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.

processCleanupTasks() - Method in class net.sf.basedb.opengrid.service.OpenGridService

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

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.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, SlurmEngine.PendingJobsCmd) - 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.

readFromStatusFile(String, int) - Method in class net.sf.basedb.opengrid.engine.SlurmEngine.SlurmJobStatus

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.CleanupTimerTask

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

setCustomOption(String, String) - Method in class net.sf.basedb.opengrid.config.ClusterConfig

Set a custom option for the cluster.

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

setExists(boolean) - Method in class net.sf.basedb.opengrid.filetransfer.FileMetaData

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 - Enum constant in enum class 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 - Enum constant in enum class net.sf.basedb.opengrid.config.JobConfig.Priority

size - Variable in class net.sf.basedb.opengrid.filetransfer.FileMetaData

SLURM - Enum constant in enum class 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.PendingJobsCmd - Class in net.sf.basedb.opengrid.engine

Issue an 'squeue' command that get a list of pending jobs sorted in priority order as of this moment.

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.

SlurmEngine.StatusCmd - Class in net.sf.basedb.opengrid.engine

Implementation for getting information about a running or finished 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, SlurmEngine.PendingJobsCmd) - 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(String, JobIdentifier, int) - Constructor for class net.sf.basedb.opengrid.engine.SlurmEngine.StatusCmd

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 - Enum constant in enum class net.sf.basedb.opengrid.config.JobConfig.Priority

THREE - Enum constant in enum class 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.engine.SlurmEngine.StatusCmd

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.OpenGridCluster

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 - Enum constant in enum class 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 class net.sf.basedb.opengrid.config.ClusterType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.sf.basedb.opengrid.config.JobConfig.Priority

Returns the enum constant of this class with the specified name.

values() - Static method in enum class net.sf.basedb.opengrid.config.ClusterType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.sf.basedb.opengrid.config.JobConfig.Priority

Returns an array containing the constants of this enum class, 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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