Inheritance diagram for org.ensembl.hive.BaseRunnable:

Collaboration diagram for org.ensembl.hive.BaseRunnable:

Public Member Functions
void	setFileDescriptors (FileDescriptor inputDescriptor, FileDescriptor outputDescriptor) throws IOException

void	processLifeCycle ()

Static Public Member Functions
static Long	numericParamToLong (Object param)

static String	numericParamToStr (Object param)

Static Public Attributes
static final String	VERSION = "5.0"

Protected Member Functions
Logger	getLog ()

void	runLifeCycle (Job job, boolean executeWrites)

void	init ()

Map< String, Object >	getParamDefaults ()

void	preCleanUp (Job job)

abstract void	fetchInput (Job job)

abstract void	run (Job job)

void	postHealthcheck (Job job)

void	postCleanUp (Job job)

abstract void	writeOutput (Job job)

void	warning (String message, boolean isError)

Map< String, Object >	dataflow (ParamContainer params, Collection< Object > outputIds)

Map< String, Object >	dataflow (ParamContainer params, Collection< Object > outputIds, int branchNameOrCode)

String	workerTempDirectory ()

void	sendMessageAndWait (String event, Object content)

void	sendEventMessage (String event, Object content)

Map< String, Object >	readMessage ()

Map< String, Object >	readMessageAndRespond ()

void	sendOK ()

Static Protected Member Functions
static Map< String, Object >	toMap (Object... o)

Static Protected Attributes
static final Map< String, Object >	DEFAULT_PARAMS = new HashMap<>()

Detailed Description

Base class implementing the runnable lifecycle

Author: dstaines

Definition at line 48 of file BaseRunnable.java.

Member Function Documentation

◆ dataflow() [1/2]

Map<String, Object> org.ensembl.hive.BaseRunnable.dataflow	(	ParamContainer	params,
		Collection< Object >	outputIds
	)

inlineprotected

Dataflows the output_id(s) on a given branch (default 1). Returns whatever the Perl side returns

Parameters

params	The current Parameters structure of job
outputIds	Collection of hashes representing the parameters of the new jobs

Returns: Structure received from the parent

Definition at line 281 of file BaseRunnable.java.

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◆ dataflow() [2/2]

Map<String, Object> org.ensembl.hive.BaseRunnable.dataflow	(	ParamContainer	params,
		Collection< Object >	outputIds,
		int	branchNameOrCode
	)

inlineprotected

Dataflows the output_id(s) on a given branch (default 1). Returns whatever the Perl side returns

Parameters

params	The current Parameters structure of job
outputIds	Collection of hashes representing the parameters of the new jobs
branchNameOrCode	Branch number

Returns: Structure received from the parent

Definition at line 295 of file BaseRunnable.java.

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◆ fetchInput()

abstract void org.ensembl.hive.BaseRunnable.fetchInput ( Job job )

abstractprotected

Reimplemented in org.ensembl.hive.longmult.PartMultiply, org.ensembl.hive.longmult.DigitFactory, org.ensembl.hive.TestRunnable, and org.ensembl.hive.longmult.AddTogether.

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◆ getLog()

Logger org.ensembl.hive.BaseRunnable.getLog ( )

inlineprotected

Definition at line 108 of file BaseRunnable.java.

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◆ getParamDefaults()

Map<String, Object> org.ensembl.hive.BaseRunnable.getParamDefaults ( )

inlineprotected

Reimplemented in org.ensembl.hive.longmult.PartMultiply, org.ensembl.hive.longmult.DigitFactory, org.ensembl.hive.longmult.AddTogether, and org.ensembl.hive.TestRunnable.

Definition at line 242 of file BaseRunnable.java.

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◆ init()

void org.ensembl.hive.BaseRunnable.init ( )

inlineprotected

Definition at line 235 of file BaseRunnable.java.

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◆ numericParamToLong()

static Long org.ensembl.hive.BaseRunnable.numericParamToLong ( Object param )

inlinestatic

Helper method for dealing with numbers that have been passed around through JSON and may be of different types

Parameters

param The source object. Currently only numeric and string types are handled

Returns: A Long with the same representation as

Parameters

Definition at line 429 of file BaseRunnable.java.

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◆ numericParamToStr()

static String org.ensembl.hive.BaseRunnable.numericParamToStr ( Object param )

inlinestatic

Definition at line 445 of file BaseRunnable.java.

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◆ postCleanUp()

void org.ensembl.hive.BaseRunnable.postCleanUp ( Job job )

inlineprotected

Definition at line 256 of file BaseRunnable.java.

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◆ postHealthcheck()

void org.ensembl.hive.BaseRunnable.postHealthcheck ( Job job )

inlineprotected

Definition at line 253 of file BaseRunnable.java.

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◆ preCleanUp()

void org.ensembl.hive.BaseRunnable.preCleanUp ( Job job )

inlineprotected

Definition at line 246 of file BaseRunnable.java.

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◆ processLifeCycle()

void org.ensembl.hive.BaseRunnable.processLifeCycle ( )

inline

Definition at line 138 of file BaseRunnable.java.

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◆ readMessage()

Map<String, Object> org.ensembl.hive.BaseRunnable.readMessage ( )

inlineprotected

Read a JSON message from the parent

Returns: A Map structure representing the JSON string read from the parent

Definition at line 381 of file BaseRunnable.java.

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◆ readMessageAndRespond()

Map<String, Object> org.ensembl.hive.BaseRunnable.readMessageAndRespond ( )

inlineprotected

Definition at line 394 of file BaseRunnable.java.

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◆ run()

abstract void org.ensembl.hive.BaseRunnable.run ( Job job )

abstractprotected

Reimplemented in org.ensembl.hive.longmult.DigitFactory, org.ensembl.hive.longmult.AddTogether, org.ensembl.hive.longmult.PartMultiply, and org.ensembl.hive.TestRunnable.

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◆ runLifeCycle()

void org.ensembl.hive.BaseRunnable.runLifeCycle	(	Job	job,
		boolean	executeWrites
	)

inlineprotected

Definition at line 213 of file BaseRunnable.java.

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◆ sendEventMessage()

void org.ensembl.hive.BaseRunnable.sendEventMessage	(	String	event,
		Object	content
	)

inlineprotected

Send an event-based message to the parent

Parameters

event	Type of the event
content	Content of the event

Definition at line 348 of file BaseRunnable.java.

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◆ sendMessageAndWait()

void org.ensembl.hive.BaseRunnable.sendMessageAndWait	(	String	event,
		Object	content
	)

inlineprotected

Send a message and wait for OK from the parent

Parameters

event	Type of the event
content	Content of the event

Definition at line 333 of file BaseRunnable.java.

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◆ sendOK()

void org.ensembl.hive.BaseRunnable.sendOK ( )

inlineprotected

Definition at line 400 of file BaseRunnable.java.

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◆ setFileDescriptors()

void org.ensembl.hive.BaseRunnable.setFileDescriptors	(	FileDescriptor	inputDescriptor,
		FileDescriptor	outputDescriptor
	)		throws IOException

inline

Definition at line 132 of file BaseRunnable.java.

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◆ toMap()

static Map<String, Object> org.ensembl.hive.BaseRunnable.toMap ( Object... o )

inlinestaticprotected

Utility method for building a hash from key-value pairs

Parameters

o	A list with an even number of elemements

Returns: A hash that associates its key to its next value in the list

Definition at line 86 of file BaseRunnable.java.

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◆ warning()

void org.ensembl.hive.BaseRunnable.warning	(	String	message,
		boolean	isError
	)

inlineprotected

Store a message in the log_message table with is_error indicating whether the warning is actually an error or not

Parameters

message	The message string
isError	Directly maps to the log_message.is_error columns

Definition at line 268 of file BaseRunnable.java.

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◆ workerTempDirectory()

String org.ensembl.hive.BaseRunnable.workerTempDirectory ( )

inlineprotected

Returns the full path of the temporary directory created by the worker. Runnables can override this to return the name they would like to use

Returns: directory name

Definition at line 318 of file BaseRunnable.java.

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◆ writeOutput()

abstract void org.ensembl.hive.BaseRunnable.writeOutput ( Job job )

abstractprotected

Reimplemented in org.ensembl.hive.longmult.AddTogether, org.ensembl.hive.longmult.PartMultiply, org.ensembl.hive.longmult.DigitFactory, and org.ensembl.hive.TestRunnable.

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Member Data Documentation

◆ DEFAULT_PARAMS

final Map<String, Object> org.ensembl.hive.BaseRunnable.DEFAULT_PARAMS = new HashMap<>()

staticprotected

Definition at line 78 of file BaseRunnable.java.

◆ VERSION

final String org.ensembl.hive.BaseRunnable.VERSION = "5.0"

static

Definition at line 76 of file BaseRunnable.java.

The documentation for this class was generated from the following file:

src/main/java/org/ensembl/hive/BaseRunnable.java

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Static Protected Member Functions

Static Protected Attributes

Detailed Description

Member Function Documentation

◆ dataflow() [1/2]

◆ dataflow() [2/2]

◆ fetchInput()

◆ getLog()

◆ getParamDefaults()

◆ init()

◆ numericParamToLong()

◆ numericParamToStr()

◆ postCleanUp()

◆ postHealthcheck()

◆ preCleanUp()

◆ processLifeCycle()

◆ readMessage()

◆ readMessageAndRespond()

◆ run()

◆ runLifeCycle()

◆ sendEventMessage()

◆ sendMessageAndWait()

◆ sendOK()

◆ setFileDescriptors()

◆ toMap()

◆ warning()

◆ workerTempDirectory()

◆ writeOutput()

Member Data Documentation

◆ DEFAULT_PARAMS

◆ VERSION