Taverna-Provenance-Extractor and Archimate-Converter v1.0

This program encapsulates 2 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.

===== RUNTIME DEPENDENCIES =====

• JRE 1.6+
• Apache Ant 1.9+ for building
• DOT (comes with Graphviz)

===== HOW-TO BUILD AND EXECUTE =====

(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 'ant jar' to build the a runnable jar.
(5) Change to the 'dist' directory.
(6) Run the executable with 'java -jar TavernaExtractor.jar '. DO NOT run the executable from different location, due the 3rd party DROID dependencies!

===== HOW-TO USE =====

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
        -d,--dependencyDir <arg>  ...workflow dependencies directory. [OPTIONAL]

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.

        -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