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# Taverna-Provenance-Extractor v1.0
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# Taverna-Provenance-Extractor v1.3
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Link to the official website: ``http://www.ifs.tuwien.ac.at/dp/process/projects/tavernaExtractor.html``
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Link to the official website: ``http://www.ifs.tuwien.ac.at/dp/process/projects/tavernaExtractor.html``
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Link to the repository ``https://opensourceprojects.eu/p/timbus/context-population/extractors/taverna-extractor``
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Link to the repository ``https://opensourceprojects.eu/p/timbus/context-population/extractors/taverna-extractor``
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## USING THE STANDALONE CLI
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## USING THE STANDALONE CLI
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The standalone CLI version encapsulates two different features:
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The standalone CLI version encapsulates two different features:
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* Feature A: Converts a Taverna 2.4 worfklow to an Archimate model.
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* Feature A: Converts a Taverna 2.4 worfklow to an Archimate model.
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* Feature B: Accesses provenance data captured during a Taverna 2.4 workflow run,
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* Feature B: Updates a OWL with DROID information gathered from the provenance data of a certain workflow execution
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applies DROID on that capturing (to identify used file formats in the workflow) and generates
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a CSV report (including e.g., file formats). Extends an existing Domain Specific Ontology (DSO)
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with file format information identified by DROID.
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### Interacting with the standalone CLI version
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### Interacting with the standalone CLI version
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A => -i,--inputFile <arg> ...specifies the taverna t2flow (input) file. \path\to\taverna\input.t2flow
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-i,--inputFile <arg> ...specifies the taverna t2flow (input) file. \path\to\taverna\input.t2flow
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-o,--outputFile <arg> ...specifies the archimate (output) file. \path\to\archimate\output.archimate
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-o,--outputFile <arg> ...specifies the archimate (output) file. \path\to\archimate\output.archimate
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-p,--provenance <\path\to\copy\provenance-trace> ...fetching provenance information from a workflow execution
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B1 => -d,--droid <arg> ...\path\where\to\save\droidOutputFile
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-ont,--ontology-file <\path\to\myOntology.owl> ...ontology file
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B2 => -cr,--report <arg> ...\path\where\droidOutputFile\is\located
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-r,--reportFile <\path\to\DroidCSVreport.csv> ...DROID report file
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B3 => -ont,--ontology-file <arg> ...ontology to extend. \path\to\ontology
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-r,--reportFile <arg> ...generated DROID CSV report.
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(general) -v, verbose ...enable verbose mode
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(optional) -v, verbose ...enable verbose mode
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### Sample usage
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### Sample usage
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[A] Convert a Taverna Workflow to an Archimate Model:
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[A] Convert a Taverna Workflow to an Archimate Model:
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INPUT: Taverna 2.4/2.5 workflow model
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OUTPUT: Process model of the workflow accoring to Archimate Specification
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java -jar TavernaExtractor.jar -i \path\to\TavernvaWorkflowInputFile.t2flow -o \path\to\ArchimateOutputFile.archimate
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java -jar TavernaExtractor.jar -i \path\to\TavernvaWorkflowInputFile.t2flow -o \path\to\ArchimateOutputFile.archimate
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[B] Extract including file formats from Workflow and identify them with DROID. In the following the 3 necessray steps are presented:
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[B1] Fetch provenance information for a specific workflow run:
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ATTENTION: Due to its DROID dependencies, make sure you are executing the TavernaExtractor.jar in the respective directory!!
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INPUT: directory where to store the fetched provenance information
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OUTPUT: fetched provenance data
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[B1] Running DROID identififaction on collected Taverna Workflow Run data:
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INPUT: path to file which gets created.
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java -jar TavernaExtractor.jar -p \path\to\store\workflow\provenance\data\for\DROID\identification
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OUTPUT: file containing DROID identification information in a none readable form.
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java -jar TavernaExtractor.jar -d path\to\myDroidFile.droid
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Sample Output:
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===== [ID] | [Workflow Name (Timestamp)] ===== | 2 entries found.
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[1] MusicClassificationExperiment (2013-09-25 13:11:42.488)
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[2] MusicClassificationExperiment (2013-09-23 10:44:43.839)
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Your choice: //Enter an ID to process
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[B2] Generate a CSV report out of a DROID profile: (CSV report is stored in the same directory as the *.droid input file)
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INPUT: file from step [B1].
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OUTPUT: file in CSV format containing DROID information in a readable form.
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java -jar TavernaExtractor.jar -cr path\to\myDroidFile.droid
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[B3] Extend existing ontology with information about the used file formats in the workflow run:
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[B2] Extend existing ontology with information about the used file formats in the workflow run:
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INPUT1: existing OWL file, which should be extended.
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INPUT1: existing OWL file, which should be extended.
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INPUT2: file from step [B2].
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INPUT2: DROID generated CSV report.
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OUTPUT: updates OWL file from INPUT1.
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OUTPUT: updates OWL file from INPUT1.
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java -jar TavernaExtractor.jar -ont \path\to\myOntology.owl -r \path\to\myDroidCSVreportFile.droid.csv
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java -jar TavernaExtractor.jar -ont \path\to\myOntology.owl -r \path\to\myDroidCSVreportFile.droid.csv
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### Build and Execution
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### Build and Execution
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6. Run the executable with ``'java -jar TavernaExtractor.jar <args>'``.
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6. Run the executable with ``'java -jar TavernaExtractor.jar <args>'``.
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### Runtime Dependencies
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### Runtime Dependencies
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* JRE 1.7+
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* JRE 1.7+
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* Apache Ant 1.9+ for building
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* Apache Maven 2+ (for building)
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* DOT (comes with Graphviz)
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* DOT (comes with Graphviz)
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## USING THE OSGi TIMBUS testbed BUNDLE
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## USING THE OSGi TIMBUS testbed BUNDLE
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The OSGi bundle can be accessed at ``http://testbed.timbusproject.net:3001/``
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The OSGi bundle can be accessed at ``http://testbed.timbusproject.net:3001/``
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