Hi,
Taverna 2.5 should be out in the next 2 weeks. Migrating your plugin to
2.5 should not be a problem, it would mainly involve changing version
numbers in pom and plugin files.
Cheers,
Alex
On 04/04/2014 12:47, Sidney Niccolson wrote:
Many thanks for the help, I am now able to implement multiple services
in one plugin. Looking at the Taverna Roadmap there is a Taverna 2.5
workbench under development. When will the workbench be available and
would it be possible to easily migrate the plugin to Taverna 2.5?
Cheers,
Sidney
On Wed, Mar 26, 2014 at 7:04 PM, Stian Soiland-Reyes
<[email protected]
<mailto:[email protected]>> wrote:
aDepending on both x-activity-ui modules (or for the command line,
both x-activity modules) from the same plugin should be sufficient -
you might want to put both activities into the same master project to
achieve this.
Here's an example from a different plugin:
https://github.com/wf4ever/astrotaverna
defines several activities and activity-uis, like
PDL-activity-ui
stilts-activity-ui
and in
https://github.com/wf4ever/astrotaverna/blob/master/astrotaverna-plugin/pom.xml
they are all listed as dependencies:
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>stilts-activity-ui</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>PDL-activity-ui</artifactId>
<version>${project.version}</version>
</dependency>
This would mean they are all be added to the generated plugin file:
http://wf4ever.github.io/astrotaverna/astrotaverna-plugin-1.10.xml
However in your case you would need to manually edit the generated
plugins file to add the <system>true</system> on the additional
dependency (which unfortunately the taverna-maven-plugin does not
support at the moment).
On 26 March 2014 12:23, Sidney Niccolson
<[email protected] <mailto:[email protected]>> wrote:
> Hi,
>
> Thanks for the reply. I managed to have both plugins working by
explicitly
> adding the jersey-bundle dependecy to the plugin pom.xml and
specifying the
> dependency in the upload/download-activity pom.xml. Manually
adding the
> <system>true</system> tag for the jersey-bundle dependency (and
additionally
> jersey multipart dependency for the upload plugin) of the deployed
> plugin.xml solved the issue.
> I have not found a way to have these services (upload/download
activities)
> inside one plugin. How can I develop these activities inside one
single
> plugin instead of two separate plugins?
>
> Cheers,
>
> Sidney
>
>
> On Mon, Mar 24, 2014 at 2:12 PM, Stian Soiland-Reyes
> <[email protected]
<mailto:[email protected]>> wrote:
>>
>> Have you got a stack trace for where
javax/ws/rs/core/MultivaluedMap
>> is not found?
>>
>> It is from the POM file of that class that needs (directly or
>> indirectly) need to depend on the JAR that contains
MultivaluedMap. So
>> let's say jersey-client depends on
javax.ws.rs.core.MultivaluedMap but
>> has not stated so in its POM - then you will get the stack trace
>> above.
>>
>> The difference from running in
TavernaWorkBenchWithExamplePlugin and
>> within Taverna Workbench is that in the first case you get a flat
>> classpath, and so just adding the dependency to the activity's POM
>> file is enough - however within Taverna Workbench's plugin system
>> dependencies are only looked for in depth - so if jersey-client
does
>> not state it needs this, it will not be added.
>>
>>
>> Normally the resolution to this is to either redeploy the
broken POM
>> file to explicitly add the dependency (under a different version
>> number) - or (when you have circular dependencies) to make a
mega-jar
>> that includes all the JARs merged together as a single JAR.
Finally,
>> one solution Taverna supports is to add a 'system' dependency -
this
>> is equivalent to adding the JAR file to lib/ in Taverna's startup
>> folder. It should be the last resort - as it affact any other
part of
>> Taverna that might depend on the library - a system dependency will
>> always 'override' any explicitly declared dependencies - so a
>> potentitally older (or newer) version might appear to those other
>> parts.
>>
>> This really only works for libraries that don't themselves have
>> further dependencies - as the system dependencies are loaded
outside
>> the plugin system - I believe this should work well for you, so
try to
>> add to your plugins.xml file:
>>
>> <dependency>
>> <groupId>javax.ws.rs <http://javax.ws.rs></groupId>
>> <artifactId>javax.ws.rs-api</artifactId>
>> <version>2.0</version>
>> <system>true</system>
>> <dependency>
>>
>> Note that you will probably need to edit and release Taverna's
plugin
>> file manually in order for this to work, as
<system>true</system> is
>> not a standard Maven configuration.
>>
>>
>>
>> On 19 March 2014 17:35, Sidney Niccolson
<[email protected] <mailto:[email protected]>>
>> wrote:
>> > Hi,
>> >
>> > Recently I followed the tutorials on creating plugins for
Taverna 2. I
>> > managed to develop a plugin for uploading large files to a Tomcat
>> > server.
>> > The server contains a REST service developed with the Jersey
API, where
>> > the
>> > post method is used for uploading.The Taverna plugin contains
user-side
>> > (client) code which is directly dependent on jersey-client,
jersey-core,
>> > jersey-multipart, mimepull. I got the following questions/notes
>> > regarding
>> > the plugin:
>> >
>> > 1: When invoking the service (plugin) the following error occurs:
>> > java.lang.NoClassDefFoundError:
javax/ws/rs/core/MultivaluedMap. This
>> > seems
>> > to be an indirect dependency used by Jersey. I do not
understand why
>> > this
>> > class is not available even though the jersey-core package
contains this
>> > specific class. Looking at the
/home/user/.taverna-2.4.0/repository/
>> > folder
>> > on the client side I am able to see the packages specified in the
>> > pom.xml of
>> > the Maven plugin project. I also added the javax-ws.rs-api as an
>> > dependency
>> > to the pom.xml but this does not solve the issue.
>> >
>> > 2: Running the TavernaWorkBenchWithExamplePlugin.java does
not give the
>> > NoClassDefFoundError and works perfectly.
>> >
>> > 3: I developed another plugin for downloading large files
successfully.
>> > This
>> > service is dependent on jersey-client. I added the
jersey-bundle which
>> > contains the jersey-client package as a dependency to the
pom.xml. This
>> > dependency seems enough to make the download plugin work.
>> >
>> > 4:Regarding the previous notes I am not able to solve this
dependency
>> > issue
>> > for the upload plugin. Am I missing additional dependencies
or else why
>> > is
>> > Taverna not able to locate the MultiValuedMap class ? The
attachment of
>> > this
>> > mail contains the pom.xml of the Uploader-activity. I also
tried adding
>> > the
>> > same dependencies in the pom.xml of the parent project
(Uploader) but to
>> > no
>> > avail.
>> >
>> > Cheers,
>> >
>> > Sidney
>> >
>> >
>> >
>> >
>> >
------------------------------------------------------------------------------
>> > Learn Graph Databases - Download FREE O'Reilly Book
>> > "Graph Databases" is the definitive new guide to graph
databases and
>> > their
>> > applications. Written by three acclaimed leaders in the field,
>> > this first edition is now available. Download your free book
today!
>> > http://p.sf.net/sfu/13534_NeoTech
>> > _______________________________________________
>> > taverna-hackers mailing list
>> > [email protected]
<mailto:[email protected]>
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>> > Developers Guide: http://www.taverna.org.uk/developers/
>>
>>
>>
>> --
>> Stian Soiland-Reyes, myGrid team
>> School of Computer Science
>> The University of Manchester
>> http://soiland-reyes.com/stian/work/
http://orcid.org/0000-0001-9842-9718
>>
>>
>>
------------------------------------------------------------------------------
>> Learn Graph Databases - Download FREE O'Reilly Book
>> "Graph Databases" is the definitive new guide to graph
databases and their
>> applications. Written by three acclaimed leaders in the field,
>> this first edition is now available. Download your free book today!
>> http://p.sf.net/sfu/13534_NeoTech
>> _______________________________________________
>> taverna-hackers mailing list
>> [email protected]
<mailto:[email protected]>
>> Web site: http://www.taverna.org.uk
>> Mailing lists: http://www.taverna.org.uk/about/contact-us/
>> Developers Guide: http://www.taverna.org.uk/developers/
>
>
>
>
------------------------------------------------------------------------------
> Learn Graph Databases - Download FREE O'Reilly Book
> "Graph Databases" is the definitive new guide to graph databases
and their
> applications. Written by three acclaimed leaders in the field,
> this first edition is now available. Download your free book today!
> http://p.sf.net/sfu/13534_NeoTech
> _______________________________________________
> taverna-hackers mailing list
> [email protected]
<mailto:[email protected]>
> Web site: http://www.taverna.org.uk
> Mailing lists: http://www.taverna.org.uk/about/contact-us/
> Developers Guide: http://www.taverna.org.uk/developers/
--
Stian Soiland-Reyes, myGrid team
School of Computer Science
The University of Manchester
http://soiland-reyes.com/stian/work/
http://orcid.org/0000-0001-9842-9718
------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases
and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech
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Web site: http://www.taverna.org.uk
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taverna-hackers mailing list
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Developers Guide: http://www.taverna.org.uk/developers/
--
. . . . . . . . . . . . . . . . . . . . .
Dr Aleksandra Nenadic
myGrid project
School of Computer Science
University of Manchester
E-mail: [email protected]
Web: http://www.cs.man.ac.uk/~nenadic
Office: +44 (0)161 275 0672
. . . . . . . . . . . . . . . . . . . . .
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