File | Date | Author | Commit |
---|---|---|---|
META-INF | 2014-11-05 | munterberger | [1b6592] improve user feedback information |
samples | 2014-05-07 | munterberger | [50d445] initial project import from internal SVN |
src | 2014-12-03 | munterberger | [dc6df6] * change Taverna type from Artifact to SystemSo... |
.gitignore | 2014-10-14 | munterberger | [8d1358] merge with current master; minor changes in the... |
ChangeInformation.md | 2014-12-04 | munterberger | [310918] bug fix |
DEPRECATED_build.xml | 2014-11-03 | munterberger | [b8d08d] fixed provenance issues |
README.md | 2014-11-03 | munterberger | [b8d08d] fixed provenance issues |
TavernaExtractor.properties | 2014-12-04 | munterberger | [310918] bug fix |
TavernaToArchiMapping.txt | 2014-06-26 | munterberger | [f9a9cc] improve arguments handing |
pom.xml | 2014-12-04 | munterberger | [310918] bug fix |
Read Me
Taverna-Provenance-Extractor v1.0
Link to the official website: http://www.ifs.tuwien.ac.at/dp/process/projects/tavernaExtractor.html
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
- Clone the current project from
https://opensourceprojects.eu/p/timbus/context-population/extractors/taverna-extractor
. - Change in the checked-out directory.
- Adapt the
TavernaExtractor.properties
file. - Use maven (
mvn package -DskipTests=true -Pstandalone
) to package the program. - Change to the 'target' directory.
- Run the executable with
'java -jar TavernaExtractor.jar <args>'
.
Runtime Dependencies
- JRE 1.7+
- Apache Ant 1.9+ for building
- DOT (comes with Graphviz)
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
SUPPORTED TAVERNA ACTIVITIES
At the moment, the following activitied are supported.
- Beanshell script
- RShell
- Tool innvocation
- Text constant
- WSDL/Rest Services
All other activities will cause an ClassNotFoundException.
To suppress that error, add the stated dependency to the classpath.
In case you have successfully executed the workflow once,
the dependency should be available somewhere in the repository location of the Taverna installation directory.
But keep in mind: That activity won't be processed by the tool correctly!