raw2nexus taverna 2 workflow using pt-mapreduce

Created: 2013-12-12 08:47:21 Last updated: 2014-06-20 08:41:00

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Workflow to migrate raw to NeXus format data, also does validation and generates a checksum. Utilises the ToMaR tool produced in the SCAPE project

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Workflow Components

Authors (0)

Titles (0)

Descriptions (0)

Dependencies (0)

Inputs (10)

Name	Description
inputdir
outputdir
jarfile
raw2nexus_infile
fido_infile
validator_infile
checksum_infile
split
convert_infile
hadoop_properties

Processors (5)

Name	Type	Description
raw2nexushadoop	externaltool
fidohadoop	externaltool
validatehadoop	externaltool
checksumhadoop	externaltool
converthadoop	externaltool

Beanshells (0)

Outputs (2)

Name	Description
stderr
stdout

Datalinks (40)

Source	Sink
raw2nexus_infile	raw2nexushadoop:infile
inputdir	raw2nexushadoop:inputdir
jarfile	raw2nexushadoop:jarfile
outputdir	raw2nexushadoop:outputdir
split	raw2nexushadoop:split
hadoop_properties	raw2nexushadoop:hadoop_properties
fido_infile	fidohadoop:infile
inputdir	fidohadoop:inputdir
jarfile	fidohadoop:jarfile
outputdir	fidohadoop:outputdir
split	fidohadoop:split
hadoop_properties	fidohadoop:hadoop_properties
validator_infile	validatehadoop:infile
inputdir	validatehadoop:inputdir
jarfile	validatehadoop:jarfile
outputdir	validatehadoop:outputdir
split	validatehadoop:split
hadoop_properties	validatehadoop:hadoop_properties
checksum_infile	checksumhadoop:infile
split	checksumhadoop:split
inputdir	checksumhadoop:inputdir
jarfile	checksumhadoop:jarfile
outputdir	checksumhadoop:outputdir
hadoop_properties	checksumhadoop:hadoop_properties
convert_infile	converthadoop:infile
inputdir	converthadoop:inputdir
jarfile	converthadoop:jarfile
outputdir	converthadoop:outputdir
split	converthadoop:split
hadoop_properties	converthadoop:hadoop_properties
checksumhadoop:STDERR	stderr
converthadoop:STDERR	stderr
fidohadoop:STDERR	stderr
raw2nexushadoop:STDERR	stderr
validatehadoop:STDERR	stderr
checksumhadoop:STDOUT	stdout
converthadoop:STDOUT	stdout
fidohadoop:STDOUT	stdout
validatehadoop:STDOUT	stdout
raw2nexushadoop:STDOUT	stdout

Coordinations (4)

Controller	Target
converthadoop	validatehadoop
validatehadoop	checksumhadoop
raw2nexushadoop	fidohadoop
fidohadoop	converthadoop

Information Workflow Type

Taverna 2

Information Uploader

Alastai...

Information License

All versions of this Workflow are licensed under:

Information Version 3 (of 5)

Information Credits (1)

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Alastairduncan

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Information Statistics

3404 viewings

1318 downloads

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Citations (0)

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Version History

In chronological order:

raw2nexus taverna 2 workflow using pt-mapreduce

Created by Alastairduncan on Thursday 12 December 2013 08:47:19 (UTC)
raw2nexus taverna 2 workflow using pt-mapreduce

Created by Alastairduncan on Thursday 16 January 2014 14:58:50 (UTC)

Revision comment:

Has a conversion process which converts to a reduced xml format for metadata which can then be validated via probatron and a schematron schema. The validation process has also changed from nxvalidate which was not available in the nexus distribution as it was not compiled with xml dependencies
raw2nexus taverna 2 workflow using pt-mapreduce

Created by Alastairduncan on Tuesday 08 April 2014 14:51:14 (UTC)

Last edited by Alastairduncan on Tuesday 08 April 2014 14:53:41 (UTC)

Revision comment:

Now uses ToMaR rather than pt-mapreduce
raw2nexus taverna 2 workflow using pt-mapreduce

Created by Alastairduncan on Tuesday 08 April 2014 15:01:32 (UTC)

Revision comment:

Updated title and Image
raw2nexus taverna 2 workflow using pt-mapreduce

Created by Alastairduncan on Friday 20 June 2014 08:41:00 (UTC)

Revision comment:

Hadoop properties added

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