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Posted to dev@taverna.apache.org by Stian Soiland-Reyes <st...@apache.org> on 2016/06/23 10:43:56 UTC
CWL Browser: File vs Path when parsing *.cwl
Thilina,
Thanks for your latest pull request.
Now I wonder if we could change from using the classic java.util.File
to the more modern java.nio.file.Path here:
https://github.com/apache/incubator-taverna-common-activities/blob/cwl-browse/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java#L47
http://docs.oracle.com/javase/8/docs/api/java/nio/file/Path.html
http://docs.oracle.com/javase/8/docs/api/java/nio/file/Paths.html
http://docs.oracle.com/javase/8/docs/api/java/nio/file/Files.html
(In theory this would also allow you to read a whole Research Object
bundle ZIP file containing many CWL descriptions)
If you combine this with Java 8 lambdas this should also simplify how
you do directory browsing, file name filtering and file opening, e.g.
something like:
try (DirectoryStream<Path> stream = Files.newDirectoryStream(dir,
p -> p.endsWith(".cwl");
)) {
for (Path p : stream) {
...
}
}
Also I see you do callBack.partialResults() with a growing list - it's
not a big problem as duplicates are skipped based on their identifier,
but - you can do result.clear() in-between to just provide the new
partial results. Perhaps we should try this on a large directory (say
150 *.cwl files?) to see if it's fast enough - you could in theory
parse multiple CWL files concurrently (but not too many!) and deliver
them independently.
If you want to play with Java 8 streams and paralellism, perhaps something like:
Stream<Path> s = StreamSupport.stream(stream.spliterator(), true);
s.forEach(this::parseCwlFile) ;
with a new method
void parserCwlFile(Path p);
that does the parsing and adding of its partial results.
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons
http://orcid.org/0000-0001-9842-9718
Re: CWL Browser: File vs Path when parsing *.cwl
Posted by Stian Soiland-Reyes <st...@apache.org>.
Hi!
As always. full links are great..
https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/blob/stream/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java#L50
looks to me like it should work, except for the shared variable
"result" which would not be thread-safe to be accessed by the lambdas
from a parallel stream.
You don't need to keep the List,now you can instead do
callBack.partialResults(Arrays.asList(result));
(or even look at using partialResults together with stream's
.collect()/.reduce() methods - but that might slow down appearance in
the UI)
Instead of e.printStackTrace(); you can do callBack.warning() or callBack.fail()
and then the error should be both logged and shown in the UI.
In general using e.printStackTrace() is a bad idea beyond examples.
In Taverna we (still) use log4j 1, so it's quite easy to do logging.
If there's an exception that you log, then you should also return
right away, so you don't keep getting NullPointerException on the
lines below when the variable didn't get initialized.
Can you reduce catch (Exception e) {} to the actual exception that
could happen?
On 24 June 2016 at 01:25, Thilina Manamgoda <ma...@gmail.com> wrote:
> Hi,
>
> i have tried this and this is the implementation
> https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/tree/stream
> . Any comments on how can i improve it more or change ?.
>
> Can you provide me the instruction to run this plugin inside the Taverna
> workbench. At the moment i test the plugin using tutorial plugin provied in
> the taverna developer tutorial. Also if you can explain how to redirect the
> System.out.println() inside the plugin into Eclipse console would be great.
>
> regards,
> Thilina.
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons
http://orcid.org/0000-0001-9842-9718
Re: CWL Browser: File vs Path when parsing *.cwl
Posted by Thilina Manamgoda <ma...@gmail.com>.
Hi,
I have changed it. How about now :
https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/blob/workbench/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java
i have removed the taverna-activity-test-utils dependency. Although
workbench runs it doesn't recognize CWL Ui plugin. Import service doesn't
contain CWL Service ?
regards,,
Thilina.
On Mon, Jun 27, 2016 at 11:01 PM, Stian Soiland-Reyes <st...@apache.org>
wrote:
> On 27 June 2016 at 18:26, Thilina Manamgoda <ma...@gmail.com> wrote:
> > Hi,
> >
> > "Fix the logging and early return, then it should be ready for a pull
> > request" . I get the logging part what you meant by "early return".
>
> Here:
>
>
> https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/blob/workbench/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java#L62
>
> you can't just print the stacktrace, you also need to return,
> otherwise the variable stream will be null, and the line below doing
> stream.spliterator() will crash.
>
>
>
> > I have added the resource folder and modified class names. But still i
> get
> > the error ? :
> >
> https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/tree/workbench/taverna-cwl-activity-ui/src/resources
>
>
> Try to remove the this taverna-activity-test-utils dependency:
>
>
> https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/blob/workbench/taverna-cwl-activity-ui/pom.xml#L48
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons
> http://orcid.org/0000-0001-9842-9718
>
Re: CWL Browser: File vs Path when parsing *.cwl
Posted by Stian Soiland-Reyes <st...@apache.org>.
On 27 June 2016 at 18:26, Thilina Manamgoda <ma...@gmail.com> wrote:
> Hi,
>
> "Fix the logging and early return, then it should be ready for a pull
> request" . I get the logging part what you meant by "early return".
Here:
https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/blob/workbench/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java#L62
you can't just print the stacktrace, you also need to return,
otherwise the variable stream will be null, and the line below doing
stream.spliterator() will crash.
> I have added the resource folder and modified class names. But still i get
> the error ? :
> https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/tree/workbench/taverna-cwl-activity-ui/src/resources
Try to remove the this taverna-activity-test-utils dependency:
https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/blob/workbench/taverna-cwl-activity-ui/pom.xml#L48
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons
http://orcid.org/0000-0001-9842-9718
Re: CWL Browser: File vs Path when parsing *.cwl
Posted by Thilina Manamgoda <ma...@gmail.com>.
Hi,
"Fix the logging and early return, then it should be ready for a pull
request" . I get the logging part what you meant by "early return".
I have added the resource folder and modified class names. But still i get
the error ? :
https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/tree/workbench/taverna-cwl-activity-ui/src/resources
regards,
Thilina.
On Mon, Jun 27, 2016 at 9:05 PM, Stian Soiland-Reyes <st...@apache.org>
wrote:
> Thilina - I think you forgot to copy over the equivalent of these file
> to incubator-taverna-common-activities:
>
>
> https://github.com/ThilinaManamgoda/exampletool/tree/master/exampletool-activity-ui/src/main/resources/META-INF/services
>
> (ensure you modify the class names)
>
> In Taverna 2 (which the workbench-dev runs) these files are needed so
> that the CWL UI components are discovered by the Workbench.
>
>
> In Taverna 3 these are done in XML files instead, see for instance
>
> https://github.com/apache/incubator-taverna-common-activities/tree/master/taverna-wsdl-activity/src/main/resources/META-INF/spring
>
>
>
> On 24 June 2016 at 20:02, Thilina Manamgoda <ma...@gmail.com> wrote:
> > Hi,
> >
> > i have changed returning result a "Array.asList" like this:
> >
> https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/blob/stream/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java
> >
> >
> > I can't run workbech like this:
> >
> https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/blob/stream/taverna-cwl-activity-ui/src/test/java/org/apache/taverna/cwl/ui/TestWorkBench.java
> > when i try to run it, error "can't connect to database another instance
> is
> > using it" occurs although i am not running another workbench ?
> >
> > How can i use log4j in my implementation ?
> >
> > regards,
> > Thilina.
> >
> >
> > On Fri, Jun 24, 2016 at 7:40 PM, Stian Soiland-Reyes <st...@apache.org>
> > wrote:
> >
> >> On 24 June 2016 at 01:25, Thilina Manamgoda <ma...@gmail.com>
> wrote:
> >> > Can you provide me the instruction to run this plugin inside the
> Taverna
> >> > workbench. At the moment i test the plugin using tutorial plugin
> provied
> >> in
> >> > the taverna developer tutorial. Also if you can explain how to
> redirect
> >> the
> >> > System.out.println() inside the plugin into Eclipse console would be
> >> great.
> >>
> >> To run it with Taverna 2 in Eclipse, it should work to copy and run the
> >> launcher
> >>
> >>
> >>
> https://github.com/ThilinaManamgoda/exampletool/blob/master/exampletool-activity-ui/src/test/java/com/example/exampletool/ui/TavernaWorkbenchWithExamplePlugin.java
> >>
> >> to
> >>
> >> taverna-cwl-activity-ui/src/test/java/
> >>
> >> (perhaps then change its package name)
> >>
> >>
> >>
> >> You already have the workbench-dev dependency block
> >>
> >>
> https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/blob/stream/taverna-cwl-activity-ui/pom.xml#L84
> >>
> >> which should give you a minimal Taverna 2 dev workbench.
> >>
> >> --
> >> Stian Soiland-Reyes
> >> Apache Taverna (incubating), Apache Commons
> >> http://orcid.org/0000-0001-9842-9718
> >>
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons
> http://orcid.org/0000-0001-9842-9718
>
Re: CWL Browser: File vs Path when parsing *.cwl
Posted by Stian Soiland-Reyes <st...@apache.org>.
Thilina - I think you forgot to copy over the equivalent of these file
to incubator-taverna-common-activities:
https://github.com/ThilinaManamgoda/exampletool/tree/master/exampletool-activity-ui/src/main/resources/META-INF/services
(ensure you modify the class names)
In Taverna 2 (which the workbench-dev runs) these files are needed so
that the CWL UI components are discovered by the Workbench.
In Taverna 3 these are done in XML files instead, see for instance
https://github.com/apache/incubator-taverna-common-activities/tree/master/taverna-wsdl-activity/src/main/resources/META-INF/spring
On 24 June 2016 at 20:02, Thilina Manamgoda <ma...@gmail.com> wrote:
> Hi,
>
> i have changed returning result a "Array.asList" like this:
> https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/blob/stream/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java
>
>
> I can't run workbech like this:
> https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/blob/stream/taverna-cwl-activity-ui/src/test/java/org/apache/taverna/cwl/ui/TestWorkBench.java
> when i try to run it, error "can't connect to database another instance is
> using it" occurs although i am not running another workbench ?
>
> How can i use log4j in my implementation ?
>
> regards,
> Thilina.
>
>
> On Fri, Jun 24, 2016 at 7:40 PM, Stian Soiland-Reyes <st...@apache.org>
> wrote:
>
>> On 24 June 2016 at 01:25, Thilina Manamgoda <ma...@gmail.com> wrote:
>> > Can you provide me the instruction to run this plugin inside the Taverna
>> > workbench. At the moment i test the plugin using tutorial plugin provied
>> in
>> > the taverna developer tutorial. Also if you can explain how to redirect
>> the
>> > System.out.println() inside the plugin into Eclipse console would be
>> great.
>>
>> To run it with Taverna 2 in Eclipse, it should work to copy and run the
>> launcher
>>
>>
>> https://github.com/ThilinaManamgoda/exampletool/blob/master/exampletool-activity-ui/src/test/java/com/example/exampletool/ui/TavernaWorkbenchWithExamplePlugin.java
>>
>> to
>>
>> taverna-cwl-activity-ui/src/test/java/
>>
>> (perhaps then change its package name)
>>
>>
>>
>> You already have the workbench-dev dependency block
>>
>> https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/blob/stream/taverna-cwl-activity-ui/pom.xml#L84
>>
>> which should give you a minimal Taverna 2 dev workbench.
>>
>> --
>> Stian Soiland-Reyes
>> Apache Taverna (incubating), Apache Commons
>> http://orcid.org/0000-0001-9842-9718
>>
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons
http://orcid.org/0000-0001-9842-9718
Re: CWL Browser: File vs Path when parsing *.cwl
Posted by Stian Soiland-Reyes <st...@apache.org>.
To use log4j, just instantiate a org.apache.log4j.Logger:
Logger logger = Logger.getLogger(CwlServiceProvider.class); //
whatever class you are in
try {
// ...
} catch (IOException ex) {
logger.warn("Could not shutdown the internet", ex);
return; // we'll have to give up then
}
On 24 June 2016 at 20:02, Thilina Manamgoda <ma...@gmail.com> wrote:
> Hi,
>
> i have changed returning result a "Array.asList" like this:
> https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/blob/stream/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java
>
>
> I can't run workbech like this:
> https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/blob/stream/taverna-cwl-activity-ui/src/test/java/org/apache/taverna/cwl/ui/TestWorkBench.java
> when i try to run it, error "can't connect to database another instance is
> using it" occurs although i am not running another workbench ?
>
> How can i use log4j in my implementation ?
>
> regards,
> Thilina.
>
>
> On Fri, Jun 24, 2016 at 7:40 PM, Stian Soiland-Reyes <st...@apache.org>
> wrote:
>
>> On 24 June 2016 at 01:25, Thilina Manamgoda <ma...@gmail.com> wrote:
>> > Can you provide me the instruction to run this plugin inside the Taverna
>> > workbench. At the moment i test the plugin using tutorial plugin provied
>> in
>> > the taverna developer tutorial. Also if you can explain how to redirect
>> the
>> > System.out.println() inside the plugin into Eclipse console would be
>> great.
>>
>> To run it with Taverna 2 in Eclipse, it should work to copy and run the
>> launcher
>>
>>
>> https://github.com/ThilinaManamgoda/exampletool/blob/master/exampletool-activity-ui/src/test/java/com/example/exampletool/ui/TavernaWorkbenchWithExamplePlugin.java
>>
>> to
>>
>> taverna-cwl-activity-ui/src/test/java/
>>
>> (perhaps then change its package name)
>>
>>
>>
>> You already have the workbench-dev dependency block
>>
>> https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/blob/stream/taverna-cwl-activity-ui/pom.xml#L84
>>
>> which should give you a minimal Taverna 2 dev workbench.
>>
>> --
>> Stian Soiland-Reyes
>> Apache Taverna (incubating), Apache Commons
>> http://orcid.org/0000-0001-9842-9718
>>
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons
http://orcid.org/0000-0001-9842-9718
Re: CWL Browser: File vs Path when parsing *.cwl
Posted by Stian Soiland-Reyes <st...@apache.org>.
Yes, remove the <dependency> on taverna-activity-test-utils - this brings in
taverna=reference-impl from Taverna 3 which says
stain@biggiebuntu:~/src/taverna$ grep -r
org.apache.taverna.platform.spring.ArtifactSupportNamespaceHandler .
./incubator-taverna-engine/taverna-reference-impl/src/main/resources/META-INF/spring.handlers:http\://taverna.sf.net/schema/artifact-support=org.apache.taverna.platform.spring.ArtifactSupportNamespaceHandler
... but no such class exists anymore in T3 - it was used to support
Taverna 2 "Raven" extensions.
https://github.com/apache/incubator-taverna-engine/blob/dc2f51d12be58d1dc35b8a0d090c1cfea360ecfe/reference-impl/src/main/java/net/sf/taverna/platform/spring/ArtifactSupportNamespaceHandler.java
I've deleted the spring.handlers file from taverna-reference-impl
As this error didn't show up in the command line run I don't think
it's a problem for the current RC - but worth keeping in mind if the
Taverna 3 workbench causes the same error.
On 27 June 2016 at 16:19, Stian Soiland-Reyes <st...@apache.org> wrote:
> On 24 June 2016 at 20:02, Thilina Manamgoda <ma...@gmail.com> wrote:
>> i have changed returning result a "Array.asList" like this:
>> https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/blob/stream/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java
>
> Looks good.
>
> Fix the logging and early return, then it should be ready for a pull request.
>
>
>> I can't run workbech like this:
>> https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/blob/stream/taverna-cwl-activity-ui/src/test/java/org/apache/taverna/cwl/ui/TestWorkBench.java
>> when i try to run it, error "can't connect to database another instance is
>> using it" occurs although i am not running another workbench ?
>
> Uhu, yes, I got that as well when trying to launch from your
> repository.. I think it is caused by version 2 and version 3
> dependencies fighting a bit over their initialization.
>
> stain@biggiebuntu:~/.taverna-2.5.0-dev/logs$ tail taverna-2.5.0-dev.log
> ERROR 2016-06-27 16:18:28,935
> (net.sf.taverna.t2.workbench.reference.config.DataManagementHelper:165)
> - org.springframework.beans.factory.parsing.BeanDefinitionParsingException:
> Configuration problem: Failed to import bean definitions from relative
> location [context-parts/dao_hibernate.xml]
> Offending resource: class path resource
> [hibernateReferenceServiceContext.xml]; nested exception is
> org.springframework.beans.factory.BeanDefinitionStoreException:
> Unexpected exception parsing XML document from class path resource
> [context-parts/dao_hibernate.xml]; nested exception is
> org.springframework.beans.FatalBeanException: NamespaceHandler class
> [org.apache.taverna.platform.spring.ArtifactSupportNamespaceHandler]
> for namespace [http://taverna.sf.net/schema/artifact-support] not
> found; nested exception is java.lang.ClassNotFoundException:
> org.apache.taverna.platform.spring.ArtifactSupportNamespaceHandler
>
> I'll see if there is a way to add a Maven <exclusion> to help this.
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons
> http://orcid.org/0000-0001-9842-9718
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons
http://orcid.org/0000-0001-9842-9718
Re: CWL Browser: File vs Path when parsing *.cwl
Posted by Stian Soiland-Reyes <st...@apache.org>.
On 24 June 2016 at 20:02, Thilina Manamgoda <ma...@gmail.com> wrote:
> i have changed returning result a "Array.asList" like this:
> https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/blob/stream/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java
Looks good.
Fix the logging and early return, then it should be ready for a pull request.
> I can't run workbech like this:
> https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/blob/stream/taverna-cwl-activity-ui/src/test/java/org/apache/taverna/cwl/ui/TestWorkBench.java
> when i try to run it, error "can't connect to database another instance is
> using it" occurs although i am not running another workbench ?
Uhu, yes, I got that as well when trying to launch from your
repository.. I think it is caused by version 2 and version 3
dependencies fighting a bit over their initialization.
stain@biggiebuntu:~/.taverna-2.5.0-dev/logs$ tail taverna-2.5.0-dev.log
ERROR 2016-06-27 16:18:28,935
(net.sf.taverna.t2.workbench.reference.config.DataManagementHelper:165)
- org.springframework.beans.factory.parsing.BeanDefinitionParsingException:
Configuration problem: Failed to import bean definitions from relative
location [context-parts/dao_hibernate.xml]
Offending resource: class path resource
[hibernateReferenceServiceContext.xml]; nested exception is
org.springframework.beans.factory.BeanDefinitionStoreException:
Unexpected exception parsing XML document from class path resource
[context-parts/dao_hibernate.xml]; nested exception is
org.springframework.beans.FatalBeanException: NamespaceHandler class
[org.apache.taverna.platform.spring.ArtifactSupportNamespaceHandler]
for namespace [http://taverna.sf.net/schema/artifact-support] not
found; nested exception is java.lang.ClassNotFoundException:
org.apache.taverna.platform.spring.ArtifactSupportNamespaceHandler
I'll see if there is a way to add a Maven <exclusion> to help this.
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons
http://orcid.org/0000-0001-9842-9718
Re: CWL Browser: File vs Path when parsing *.cwl
Posted by Thilina Manamgoda <ma...@gmail.com>.
Hi,
i have changed returning result a "Array.asList" like this:
https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/blob/stream/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java
I can't run workbech like this:
https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/blob/stream/taverna-cwl-activity-ui/src/test/java/org/apache/taverna/cwl/ui/TestWorkBench.java
when i try to run it, error "can't connect to database another instance is
using it" occurs although i am not running another workbench ?
How can i use log4j in my implementation ?
regards,
Thilina.
On Fri, Jun 24, 2016 at 7:40 PM, Stian Soiland-Reyes <st...@apache.org>
wrote:
> On 24 June 2016 at 01:25, Thilina Manamgoda <ma...@gmail.com> wrote:
> > Can you provide me the instruction to run this plugin inside the Taverna
> > workbench. At the moment i test the plugin using tutorial plugin provied
> in
> > the taverna developer tutorial. Also if you can explain how to redirect
> the
> > System.out.println() inside the plugin into Eclipse console would be
> great.
>
> To run it with Taverna 2 in Eclipse, it should work to copy and run the
> launcher
>
>
> https://github.com/ThilinaManamgoda/exampletool/blob/master/exampletool-activity-ui/src/test/java/com/example/exampletool/ui/TavernaWorkbenchWithExamplePlugin.java
>
> to
>
> taverna-cwl-activity-ui/src/test/java/
>
> (perhaps then change its package name)
>
>
>
> You already have the workbench-dev dependency block
>
> https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/blob/stream/taverna-cwl-activity-ui/pom.xml#L84
>
> which should give you a minimal Taverna 2 dev workbench.
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons
> http://orcid.org/0000-0001-9842-9718
>
Re: CWL Browser: File vs Path when parsing *.cwl
Posted by Stian Soiland-Reyes <st...@apache.org>.
On 24 June 2016 at 01:25, Thilina Manamgoda <ma...@gmail.com> wrote:
> Can you provide me the instruction to run this plugin inside the Taverna
> workbench. At the moment i test the plugin using tutorial plugin provied in
> the taverna developer tutorial. Also if you can explain how to redirect the
> System.out.println() inside the plugin into Eclipse console would be great.
To run it with Taverna 2 in Eclipse, it should work to copy and run the launcher
https://github.com/ThilinaManamgoda/exampletool/blob/master/exampletool-activity-ui/src/test/java/com/example/exampletool/ui/TavernaWorkbenchWithExamplePlugin.java
to
taverna-cwl-activity-ui/src/test/java/
(perhaps then change its package name)
You already have the workbench-dev dependency block
https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/blob/stream/taverna-cwl-activity-ui/pom.xml#L84
which should give you a minimal Taverna 2 dev workbench.
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons
http://orcid.org/0000-0001-9842-9718
Re: CWL Browser: File vs Path when parsing *.cwl
Posted by Thilina Manamgoda <ma...@gmail.com>.
Hi,
i have tried this and this is the implementation
https://github.com/ThilinaManamgoda/incubator-taverna-common-activities/tree/stream
. Any comments on how can i improve it more or change ?.
Can you provide me the instruction to run this plugin inside the Taverna
workbench. At the moment i test the plugin using tutorial plugin provied in
the taverna developer tutorial. Also if you can explain how to redirect the
System.out.println() inside the plugin into Eclipse console would be great.
regards,
Thilina.