tag	95d73e54d5cfa2083b78552c38726b4360209139
tagger	Stian Soiland-Reyes <stian@soiland-reyes.com>	Tue Nov 19 16:59:15 2013 +0000
object	9e1de4dcbf67b7cfaabc7b61c6fa7920b66d3428

commit	9e1de4dcbf67b7cfaabc7b61c6fa7920b66d3428	[log] [tgz]
author	Stian Soiland-Reyes <stian@soiland-reyes.com>	Tue Nov 19 16:59:12 2013 +0000
committer	Stian Soiland-Reyes <stian@soiland-reyes.com>	Tue Nov 19 16:59:12 2013 +0000
tree	223598eef8e2b00571b7685d13c04432e7fdcfe0
parent	5c532204dfd3108127ad67f49d67f35c64945636 [diff]

tree: 223598eef8e2b00571b7685d13c04432e7fdcfe0

README.md

Taverna PROV support

This is a plugin for the Taverna Workbench and Taverna Command Line which allows export of the provenance of a workflow run according to the proposed PROV-O standard.

Source code and license

This plugin is distributed under the GNU Lesser General Public License 2.1 (LGPL). The source code for this plugin is available at https://github.com/wf4ever/taverna-prov

Installation for Taverna workbench

Installation of an released version of this plugin does not require compilation, but uses Taverna's plugin mechanism.

You need:

To install:

Start Taverna workbench
In the menu, click Advanced -> Updates and plugins
If Taverna does not say “An update is available” , click Find updates
To install the required 2.4.1 patches, click Update for each of:
- External tool service
- Service catalogue
- Services
- Workbench
Note: Click OK in the warning message about restart; you do not need to restart Taverna for each of these as we'll do that in the end
Click Find new plugins, then Add update site and fill in:
- Site name: Taverna PROV
- Site URL: http://wf4ever.github.com/taverna-prov/
Click OK
Under Taverna PROV, tick to select Taverna PROV plugin 1.x
Click Install
Click Close
Exit and Restart Taverna workbench

Usage in workbench

In order for PROV export to be possible from the Taverna Workbench, click Preferences from the File or Taverna menu, then go to the Preferences for Data and Provenance. Ensure that Provenance capture is enabled. (This is the default in 2.4).

If you would like Taverna to keep the provenance data between runs of the workbench (in order to export at a later time), then you need to also untick to disable In memory storage; note however that this may slow down executions of some workflows.

Open and run a workflow to export provenance for. As a quick example, try the very simple helloanyone.t2flow from myExperiment (included in the example/ folder of this source code).

Exporting PROV from Taverna is done similar to the export of OPM and Janus provenance.

The difference is that you need to click Save provenance (PROV), and in the file dialogue give the name of what will become a folder, rather than a single file.

In short:

Click Results perspective
Select a run on the left
Click Show workflow results button (in case you are viewing intermediates)
Click Save all values
Ensure all ports are ticked
Click Save Provenance (PROV)
Browse and type the name of a folder for the results (which will be created)
Click OK
The provenance and results values should have been saved to the requested folder.

Installation for Taverna Command line tool

Installation for the Taverna command line tool is slightly manual as it has no GUI for installing plugins.

These instructions assumes a Linux environment, but the plugin should work also on Windows or OS X. Note that the Taverna home directory has a different locations on those operating systems, replace $HOME/.taverna-cmd-2.4.0 for the equivalent path. (Note that the command line tool has a separate home directory from the workbench)

To install, extract the separate download Taverna command line tool 2.4 to a folder of your choice.

(Optionally, Linux): Make execution shortcut in $HOME/bin

stain@ralph-ubuntu:~/software/taverna-commandline-2.4.0$ chmod 755 executeworkflow.sh 

stain@ralph-ubuntu:~/software/taverna-commandline-2.4.0$ mkdir ~/bin 
mkdir: cannot create directory `/home/stain/bin': File exists

stain@ralph-ubuntu:~/software/taverna-commandline-2.4.0$ cd ~/bin

stain@ralph-ubuntu:~/bin$ ln -s ~/software/taverna-commandline-2.4.0/executeworkflow.sh executeworkflow

stain@ralph-ubuntu:~/bin$ . ~/.profile

stain@ralph-ubuntu:~/bin$ type executeworkflow
executeworkflow is hashed (/home/stain/bin/executeworkflow)

Edit the file plugins/plugin.xml of the unpacked installation, and add this section right before </plugins:plugin> at the end of the file:

<plugin>
    <provider>org.purl.wf4ever</provider>
    <identifier>org.purl.wf4ever.provtaverna.prov-taverna-plugin</identifier>
    <version>1.5</version>
    <name>Taverna PROV plugin</name>
    <description/>
    <enabled>true</enabled>
    <repositories>
        <repository>http://wf4ever.github.com/taverna-prov/</repository>
        <repository>http://repo.aduna-software.org/maven2/releases/</repository>
        <repository>http://uk.maven.org/maven2/</repository>
    </repositories>
    <profile>
        <dependency>
            <groupId>org.purl.wf4ever.provtaverna</groupId>
            <artifactId>prov-taverna-cmdline</artifactId>
            <version>1.5</version>
        </dependency>
    </profile>
    <compatibility>
        <application>
            <version>2.4.0</version>
        </application>
    </compatibility>
</plugin>

You should replace <version>1.5</version> with whatever is the latest version listed on the taverna-prov plugin site.

Start the command line tool without parameters to force downloading of plugins (this might take a few minutes the first time):
```
stain@vmint:~/software/taverna-commandline-2.4.0$ sh executeworkflow.sh 
usage: executeworkflow [options] [workflow]
 -clientserver                           Connect as a client to a derby
                                         server instance.
 -cmdir <directory path>                 Absolute path to a directory
(..)
```
Note that Taverna will copy the content of this file to $HOME/.taverna-cmd-2.4.0/plugins/plugins.xml only on first start, so if you do further edits, you will need to delete the file in $HOME/.taverna-cmd-2.4.0/plugins/.

If you get an error such as:

WARN  2012-07-18 16:44:36,323 (net.sf.taverna.raven.repository.impl.LocalRepository:85) - Could not find artifact org.purl.wf4ever.provtaverna:prov-taverna-cmdline:1.5
net.sf.taverna.raven.repository.ArtifactNotFoundException: Could not find artifact org.purl.wf4ever.provtaverna:prov-taverna-cmdline:1.5: Can't find artifact for: org.purl.wf4ever.provtaverna:prov-taverna-cmdline:1.5
    at net.sf.taverna.raven.repository.impl.LocalRepository.fetch(LocalRepository.java:820)

then check if you need to configure Java for using proxies by modifying the java command line in executeworkflow.sh or executeworkflow.bat.

Modify the script executeworkflow.sh so that the line with raven.launcher.app.main says:

-Draven.launcher.app.main=org.purl.wf4ever.provtaverna.cmdline.ProvCommandLineLauncher \

or for executeworkflow.bat:

set ARGS=%ARGS% -Draven.launcher.app.main=org.purl.wf4ever.provtaverna.cmdline.ProvCommandLineLauncher

Execute without parameters to ensure the modified launcher is working:

stain@vmint:~/software/taverna-commandline-2.4.0$ sh executeworkflow.sh 
usage: executeworkflow [options] [workflow]
 -clientserver                           Connect as a client to a derby
                                         server instance.
 -cmdir <directory path>                 Absolute path to a directory
(..)

If you get this error:
```
Could not find class: org.purl.wf4ever.provtaverna.cmdline.ProvCommandLineLauncher
java.lang.ClassNotFoundException: Could not find org.purl.wf4ever.provtaverna.cmdline.ProvCommandLineLauncher
```
Then check that org.purl.wf4ever is listed in $HOME/.taverna-cmd-2.4.0/plugins/plugins.xml - if not, then delete that file so that it is restored from the installation directory.
(Optional) Copy the downloaded repository content to the installation folder:
```
stain@ralph-ubuntu:~/software/taverna-commandline-2.4.0$ cp -r ~/.taverna-cmd-2.4.0/repository .
```
This is useful if several users will run the same Taverna installation (such as in a Taverna Server installation), or if you are going to repackage the installation, as those users would not need to wait for the initial download of the plugin libraries.

Usage on command line

The Taverna documentation has general information about how to use the Taverna Command line tool.

The Taverna-PROV command line does not support all the output options of the regular Taverna command line, output has to be saved using -outputdir, as the PROV export refers to files in the output directory.

To enable PROV export for the workflow run, add the parameter -provenance, which requires the parameter -embedded or -clientserver.

Note: -embedded allows only one concurrent execution at a time due to database locking. To support multiple concurrent runs, start executeworkflow -startdb separately to start the database server, and use executeworkflow -provenance -clientserver for the workflow executions.

Example:

stain@ralph-ubuntu:~/src/taverna-prov/example$ executeworkflow -embedded \
  -provenance -outputdir hello -inputvalue name fred helloanyone.t2flow 

Outputs will be saved to the directory: /home/stain/src/taverna-prov/example/hello

stain@ralph-ubuntu:~/src/taverna-prov/example$ ls hello
greeting  workflowrun.prov.ttl

Structure of exported provenance

The folder selected will contain each of the selected input and output ports. Ports with multiple values are stored as a folder with numbered outputs, starting from 0. Values representing errors have extension .err.

In you will find the file workflowrun.prov.ttl which contains the PROV-O export of the workflow run (including nested workflows) in RDF Turtle format.

Intermediate values are stored in the intermediates/ folder.

Example listing:

stain@vmint ~/src/taverna-prov/example/helloanyone $ ls .
greeting.txt  intermediates  name.txt  workflowrun.prov.ttl

stain@vmint ~/src/taverna-prov/example/helloanyone $ ls intermediates/*
def2e58b-50e2-4949-9980-fd310166621a.txt

stain@vmint:~/src/taverna-prov/example/helloanyone$ cat greeting.txt ; echo
Hello, World!

stain@vmint ~/src/taverna-prov/example/helloanyone $ cat intermediates/de/def2e58b-50e2-4949-9980-fd310166621a.txt  ; echo
Hello, 

stain@vmint ~/src/taverna-prov/example/helloanyone $ head -n 17 workflowrun.prov.ttl
# @base <file:/C:/Users/stain/Desktop/fred/soup/workflowrun.prov.ttl> .
@prefix cnt: <http://www.w3.org/2011/content#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix doap: <http://usefulinc.com/ns/doap#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix scufl2: <http://ns.taverna.org.uk/2010/scufl2#> .
@prefix tavernaprov: <http://ns.taverna.org.uk/2012/tavernaprov/> .
@prefix wfdesc: <http://purl.org/wf4ever/wfdesc#> .
@prefix wfprov: <http://purl.org/wf4ever/wfprov#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix : <#> .

:taverna-prov-export rdfs:label "taverna-prov export of workflow run provenance" ;
    prov:qualifiedAssociation _:node17rnpj0m5x1 ;
    prov:startedAtTime "2013-05-29T10:23:43.074+01:00"^^xsd:dateTime ;

This source includes an example provenance folder and example provenance graph from running a simple hello world workflow.

Querying

Example SPARQL query from test.sparql:

stain@vmint:~/src/taverna-prov/example/helloanyone$ cat ../test.sparql 
PREFIX prov: <http://www.w3.org/ns/prov#> 
PREFIX wfprov: <http://purl.org/wf4ever/wfprov#> 
PREFIX tavernaprov: <http://ns.taverna.org.uk/2012/tavernaprov/>

SELECT DISTINCT ?name ?plan ?ended
WHERE {
    ?greeting tavernaprov:content <greeting.txt> .
    ?greeting prov:wasGeneratedBy ?concatenate .
    ?concatenate prov:endedAtTime ?ended ;
        prov:qualifiedAssociation [
            prov:hadPlan ?plan
    ] ;
        wfprov:wasPartOfWorkflowRun ?run .
    ?concatenate wfprov:usedInput ?string2 .
    ?string2 tavernaprov:content ?name .
}

Query using rdfproc (apt-get install redland-utils):

stain@vmint:~/src/taverna-prov/example/helloanyone$ rdfproc test parse workflowrun.prov.ttl turtle
rdfproc: Parsing URI file:///home/stain/src/taverna-prov/example/helloanyone/workflowrun.prov.ttl with turtle parser

stain@vmint ~/src/taverna-prov/example/helloanyone $ rdfproc test query sparql - "$(cat ../test.sparql)" 
rdfproc: Warning - URI file:///home/stain/src/taverna-prov/example/helloanyone/:1: Variable run was bound but is unused in the query
rdfproc: Query returned bindings results:
result: [name=<file:///home/stain/src/taverna-prov/example/helloanyone/name.txt>, plan=<http://ns.taverna.org.uk/2010/workflowBundle/01348671-5aaa-4cc2-84cc-477329b70b0d/workflow/Hello_Anyone/processor/Concatenate_two_strings/>, ended="2013-05-29T10:22:09.961+01:00"^^<http://www.w3.org/2001/XMLSchema#dateTime>]
result: [name=<file:///home/stain/src/taverna-prov/example/helloanyone/intermediates/de/def2e58b-50e2-4949-9980-fd310166621a.txt>, plan=<http://ns.taverna.org.uk/2010/workflowBundle/01348671-5aaa-4cc2-84cc-477329b70b0d/workflow/Hello_Anyone/processor/Concatenate_two_strings/>, ended="2013-05-29T10:22:09.961+01:00"^^<http://www.w3.org/2001/XMLSchema#dateTime>]
rdfproc: Query returned 2 results

This shows how both name.txt and intermediates/de/def...txt are the origins of greeting.txt.

Troubleshooting

If the Save Provenance (PROV) button is not listed, then the plugin was most likely not installed correctly.

Check that:

You installed all the 2.4.1 updates (duplicate icons in toolbar indicates no)
You restarted Taverna after installation
Taverna can access the Internet; check proxy settings
The plugin and its dependences downloaded correctly
- Check the logs/ in the Taverna home directory for any error messages relating to PROV or Sesame
- To force a new download of plugin, delete repository/ from the above folder (not the installation folder) and restart Taverna
- To start clean and reinstall the plugin, delete everything from the Taverna home directory and restart Taverna
Check your Java version with java -version
Reinstall Taverna
Contact myGrid for support support@mygrid.org.uk

TODO

Include workflow definition as t2flow and wfdesc
Save as RO bundle (single ZIP file)

Building

Note - you do not normally need to build from source code, installation from the above plugin site is the preferred way to install this plugin.

You need:

Java JDK 1.6 or newer (Tested with OpenJDK 1.7.0_03)
- Note: Do not use the OpenJDK 1.6 (default in Ubuntu), as this is buggy with GUI and File operations, both used by Taverna workbench.
Maven 2.2 or newer (Tested with Maven 3.0.4)

To compile, run mvn clean install

On first run this will download various open-source third-party libraries from Maven repositories, including required modules of Taverna 2.4. These JARs, and the compiled JARs from this source code, are installed into $HOME/.m2/repository/ by default. Depending on your network connection, this first run might take about 5 minutes to complete.

Example compilation:

stain@vmint:~/src/taverna-prov$ mvn clean install
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] Taverna PROV
[INFO] Taverna PROV W3 Provenance ontology Elmo bindings
[INFO] Taverna PROV export
[INFO] Taverna PROV activity UI bindings
[INFO] Taverna PROV plugin
[INFO] PROV Taverna command line
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Taverna PROV 2.0.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
(..)
Downloading: http://www.mygrid.org.uk/maven/repository/net/sf/taverna/t2/taverna-workbench/workbench-dev/2.4.0/workbench-dev-2.4.0.pom
Downloaded: http://www.mygrid.org.uk/maven/repository/net/sf/taverna/t2/taverna-workbench/workbench-dev/2.4.0/workbench-dev-2.4.0.pom (3 KB at 5.4 KB/sec)
(..)
[INFO] Installing /home/stain/src/taverna-prov/prov-taverna-cmdline/target/prov-taverna-cmdline-2.0.0-SNAPSHOT-tests.jar to /home/stain/.m2/repository/org/purl/wf4ever/provtaverna/prov-taverna-cmdline/2.0.0-SNAPSHOT/prov-taverna-cmdline-2.0.0-SNAPSHOT-tests.jar
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] Taverna PROV ...................................... SUCCESS [4.109s]
[INFO] Taverna PROV W3 Provenance ontology Elmo bindings . SUCCESS [1.55.270s]
[INFO] Taverna PROV export ............................... SUCCESS [45.873s]
[INFO] Taverna PROV activity UI bindings ................. SUCCESS [1.56.572s]
[INFO] Taverna PROV plugin ............................... SUCCESS [15.028s]
[INFO] PROV Taverna command line ......................... SUCCESS [1:12.093s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 5:54.000s
[INFO] Finished at: Wed Jul 18 12:08:13 BST 2012
[INFO] Final Memory: 72M/274M
[INFO] ------------------------------------------------------------------------

WARNING:

Building currently fails for unknown reasons that may indicate a bug in our dependency Alibaba or in our OWL ontologies:

 [java] C:\Users\stain\AppData\Local\Temp\OWLCompiler777760187968267646\rdf\IsNil.java:5: error: cannot find symbol
 [java] import owl.NamedIndividual;
 [java]           ^
 [java]   symbol:   class NamedIndividual
 [java]   location: package owl
 [java] C:\Users\stain\AppData\Local\Temp\OWLCompiler777760187968267646\rdf\IsNil.java:12: error: cannot find symbol
 [java] public interface IsNil extends Resource, NamedIndividual {
 [java]                                          ^
 [java]   symbol: class NamedIndividual
 ...
 [java] 5 errors
 [java] Exception in thread "main" org.openrdf.repository.object.exceptions.ObjectCompileException: Could not compile
 [java]     at org.openrdf.repository.object.compiler.source.JavaCompiler.compile(JavaCompiler.java:80)
 [java]     at org.openrdf.repository.object.compiler.OWLCompiler.compile(OWLCompiler.java:384)
 [java]     at org.openrdf.repository.object.compiler.OWLCompiler.createJar(OWLCompiler.java:353)
 [java]     at org.openrdf.repository.object.compiler.Compiler.main(Compiler.java:167)

Note that to work with Taverna's plugin system, the build is specific for a particular Taverna version. To build this plugin for a different version of Taverna, modify the <properties> section of pom.xml to match the Maven module versions for the specific Taverna release.

In order for Taverna to find your install of the plugin rather than download from the official plugin site, you will need to manually edit plugins/plugins.xml of the Taverna home directory (run Taverna once to create the file) to include this section right before the final </plugins:plugins>.

NOTE: If you have already installed the official plugin, first Remove it from within Taverna. To check, look for org.purl.wf4ever.provtaverna in plugins/plugins.xml.

     <plugin>
        <provider>org.purl.wf4ever</provider>
        <identifier>org.purl.wf4ever.provtaverna.prov-taverna-plugin</identifier>
        <version>2.0.0-SNAPSHOT</version>
        <name>Taverna PROV plugin</name>
        <description/>
        <enabled>true</enabled>
        <repositories>
            <repository>file:///home/johndoe/.m2/repository/</repository>
            <repository>http://www.mygrid.org.uk/maven/repository/</repository>
            <repository>http://uk.maven.org/maven2/</repository>
            <repository>http://repo.aduna-software.org/maven2/releases/</repository>
            <repository>http://repo.aduna-software.org/maven2/snapshots/</repository>
            <repository>http://repo.aduna-software.org/maven2/ext/</repository>
            <repository>http://repository.aduna-software.org/maven2/</repository>
            <repository>http://repository.aduna-software.org/maven2-snapshots/</repository>
            <repository>http://people.apache.org/repo/m2-snapshot-repository/</repository>
            <repository>http://nexus.codehaus.org/snapshots/</repository>
            <repository>http://repository.jboss.org/maven2/</repository>
        </repositories>
        <profile>
            <dependency>
                <groupId>org.purl.wf4ever.provtaverna</groupId>
                <artifactId>prov-taverna-ui</artifactId>
                <version>2.0.0-SNAPSHOT</version>
            </dependency>
            <dependency>
                <groupId>junit</groupId>
                <artifactId>junit</artifactId>
                <version>4.8.2</version>
            </dependency>
        </profile>
        <compatibility>
            <application>
                <version>2.4.0</version>
            </application>
        </compatibility>
    </plugin>

Modify the line:

    <repository>file:///home/johndoe/.m2/repository/</repository>

to match your $HOME/.m2/repository. On Windows this path should look like:

    <repository>file:///C:/Users/johndoe/.m2/repository/</repository>

Take care that the <version> of the <plugin> and prov-taverna-ui matches the <version> specified in the pom.xml of this source code (typically 1.x-SNAPSHOT).
If you are building for a different Taverna, check that the <application><version> matches the Taverna version (compare with the existing plugins)
Start Taverna Workbench.

You only need to do this plugin installation once - if you later recompile the source code without changing the version numbers, next start of Taverna will use the newer JARs from mvn clean install as Taverna will prefer accessing $HOME/.m2/repository. You might however need to delete the repository/org/purl/wf4ever folder of the Taverna home directory if Taverna has downloaded the SNAPSHOT versions from the myGrid repository instead (for instance because you used the wrong <repository> path or did not update <version>).

To make the plugin installation system-side (ie. multiple UNIX users or to make a customized Taverna distribution), copy plugins/ and repository with overwrite onto the Taverna installation directory. (See Installation for Taverna Command Line above)