Dummy example of looping

Created: 2010-01-27 15:52:50 Last updated: 2013-10-08 11:24:47

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Example of looping over asynchronous services. The dummy beanshell scripts represents the operations of an asynchronous submit-status-results style service, such as EBI's InterProScan and NCBI Blast.

createJob creates a temporary file with the content "0". Filename retuirned as a "job ID".

checkStatus reads the job, and return state "RUNNING" as long as the content is less than 10, increasing the number for each call. (As no actual job is being run)

getResults reads the file content, with the condition 'Run after checkStatus'.

In Details->Advanced for checkStatus you can check the loop condition for checkStatus, which says it will loop as long as the output 'state' is equal to 'RUNNING' - with a 0.5s delay.

Thus when executing this workflow, checkStatus will be called repeatedly, and finally the 'result' should be '10' and 'state' should be 'COMPLETE'.

See http://www.mygrid.org.uk/dev/wiki/display/scrap/Looping+in+Taverna+2.1 for details

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Descriptions (1)

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Inputs (0)

Processors (3)

Name	Type	Description
createJob	beanshell	Script import java.nio.file.; import java.nio.file.attribute.; attrs = new FileAttribute[0]; file = Files.createTempFile("example", "looping", attrs); value = "0".getBytes("ASCII"); options = new OpenOption[0]; Files.write(file, value, options); jobId = file.toString();
checkStatus	beanshell	Script import java.nio.file.; import java.nio.file.attribute.; import java.nio.charset.Charset; options = new OpenOption[0]; file = Paths.get(jobId, new String[0]); utf8 = Charset.forName("UTF-8"); value = Files.readAllLines(file, utf8).get(0); value = Integer.parseInt(value); if (value < 10) { state = "RUNNING"; // Increment for next time around value = value + 1; bytes = Integer.toString(value).getBytes("UTF-8"); Files.write(file, bytes, options); } else { state = "COMPLETE"; }
getResults	beanshell	Script import java.nio.file.; import java.nio.file.attribute.; import java.nio.charset.Charset; file = Paths.get(jobId, new String[0]); utf8 = Charset.forName("UTF-8"); value = Files.readAllLines(file, utf8).get(0);

Beanshells (3)

Name	Inputs	Outputs
createJob		jobId value
checkStatus	jobId	state
getResults	jobId	value

Outputs (4)

Name	Description
jobId
initial_value
state
result

Datalinks (6)

Source	Sink
createJob:jobId	checkStatus:jobId
createJob:jobId	getResults:jobId
createJob:jobId	jobId
createJob:value	initial_value
checkStatus:state	state
getResults:value	result

Coordinations (1)

Controller	Target
checkStatus	getResults

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Taverna 2

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Stian Soiland-Reyes

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Version History

In chronological order:

Example of looping using dummy services

Created by Stian Soiland-Reyes on Wednesday 27 January 2010 14:13:55 (UTC)

Last edited by Stian Soiland-Reyes on Wednesday 27 January 2010 15:53:43 (UTC)
Dummy example of looping

Created by Stian Soiland-Reyes on Wednesday 27 January 2010 15:52:50 (UTC)

Last edited by Stian Soiland-Reyes on Wednesday 27 January 2010 15:56:11 (UTC)

Revision comment:

Modified checkStatus() scripts to no longer have intValue as a separate variable
Dummy example of looping

Created by Stian Soiland-Reyes on Tuesday 08 October 2013 11:24:47 (UTC)

Revision comment:

A Java 7 version using java.nio.Files