Open Source Projects Europe

# Taverna-Provenance-Extractor v1.0

Link to the repository ``https://opensourceprojects.eu/p/timbus/context-population/extractors/taverna-extractor``

This program comes in two flavors:

* Standalone CLI

* OSGi Bundle

## USING THE STANDALONE CLI 

The standalone CLI version encapsulates two different features:

* Feature A: Converts a Taverna 2.4 worfklow to an Archimate model.

* Feature B: Accesses provenance data captured during a Taverna 2.4 workflow run, 

  applies DROID on that capturing (to identify used file formats in the workflow) and generates 

  a CSV report (including e.g., file formats). Extends an existing Domain Specific Ontology (DSO) 

  with file format information identified by DROID.

### Interacting with the standalone CLI version

  A   =>  -i,--inputFile <arg>      ...specifies the taverna t2flow (input) file. \path\to\taverna\input.t2flow

          -o,--outputFile <arg>     ...specifies the archimate (output) file. \path\to\archimate\output.archimate

  B1  =>  -d,--droid <arg>       ...\path\where\to\save\droidOutputFile   

  B2  =>  -cr,--report <arg>      ...\path\where\droidOutputFile\is\located                                   

  B3  =>  -ont,--ontology-file <arg>  ...ontology to extend. \path\to\ontology

          -r,--reportFile <arg>       ...generated DROID CSV report.

  (general)   -v, verbose     ...enable verbose mode

### Sample usage

[A] Convert a Taverna Workflow to an Archimate Model:

  java -jar TavernaExtractor.jar -i \path\to\TavernvaWorkflowInputFile.t2flow -o \path\to\ArchimateOutputFile.archimate 

[B] Extract including file formats from Workflow and identify them with DROID. In the following the 3 necessray steps are presented:

    ATTENTION: Due to its DROID dependencies, make sure you are executing the TavernaExtractor.jar in the respective directory!!

[B1] Running DROID identififaction on collected Taverna Workflow Run data:

     INPUT: path to file which gets created.

     OUTPUT: file containing DROID identification information in a none readable form.

  java -jar TavernaExtractor.jar -d path\to\myDroidFile.droid

  Sample Output:

  ===== [ID] | [Workflow Name (Timestamp)] ===== | 2 entries found.

  [1] MusicClassificationExperiment (2013-09-25 13:11:42.488)

  [2] MusicClassificationExperiment (2013-09-23 10:44:43.839)

  Your choice:  //Enter an ID to process

[B2] Generate a CSV report out of a DROID profile: (CSV report is stored in the same directory as the *.droid input file)

     INPUT: file from step [B1].

     OUTPUT: file in CSV format containing DROID information in a readable form.

  java -jar TavernaExtractor.jar -cr path\to\myDroidFile.droid

[B3] Extend existing ontology with information about the used file formats in the workflow run:

     INPUT1: existing OWL file, which should be extended.

     INPUT2: file from step [B2].

     OUTPUT: updates OWL file from INPUT1.

  java -jar TavernaExtractor.jar -ont \path\to\myOntology.owl -r \path\to\myDroidCSVreportFile.droid.csv

### Build and Execution

1. Clone the current project from ``https://opensourceprojects.eu/p/timbus/context-population/extractors/taverna-extractor``.

2. Change in the checked-out directory.

3. Adapt the ``TavernaExtractor.properties`` file.

4. Use maven (``mvn package -DskipTests=true -Pstandalone``) to package the program. 

5. Change to the 'target' directory.

6. Run the executable with ``'java -jar TavernaExtractor.jar <args>'``.

### Runtime Dependencies

## USING THE OSGi TIMBUS testbed BUNDLE 

The OSGi bundle can be accessed at ``http://testbed.timbusproject.net:3001/``

It encapsulates following feature: Converts a Taverna 2.4/2.5 worfklow to an Archimate model regarding specification 2.1.

### Mandatory Parameters

* fqdn ... IP of the remote address (e.g. ``134.191.240.68``)

* port ... Port of the remote machine (e.g. ``10026``)

* user ... Username Credentials (e.g. ``timbus``)

* password ... Password Credentials (e.g. ``timbus``)

* inputFileName ... Path to the Taverna workflow input file (e.g. ``/home/timbus/Documents/imagemagick_wf.t2flow``)

* archimateOutputPath ... Path to the generated output file (e.g. ``/home/timbus/Documents/imagemagick.contextmodel.archimate``)

* tavernaHome ... Path to Taverna Home directory (e.g. ``/home/timbus/.taverna-2.4.0``)

### Build

The bundle can also be build using maven ``mvn package -DskipTests=true -POSGi``