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Posted to dev@taverna.apache.org by Menaka Madushanka <me...@gmail.com> on 2015/06/10 00:48:58 UTC
Taverna language command line tool - progress
Hi all,
Here is my progress so far....
--> Implemented the command line prototype
--> implemented the conversion tools (.t2flow -> .wfbundle / .t2flow ->
.structure / .wfbundle -> .structure)
--> Implemented the inspection tools (servicetypes / processornames)
I had some problems with converting workflow files into wfdesc.ttl format
which fails when writing the bundle.
Also the wfdesc dependency is also seems like not working because I got
some errors in the pom file of wfdesc module.
I want to know that, does taverna has the capability of converting
.structure files into .wfbundle format?
Now I'm working on implementing the json and robundle conversion tools.
I'll commit the code to the repository.
Also, the pull request that I have sent is not merged yet. I need to know
are there any modifications that I want to make.
Thank you very much.
Menaka
--
Menaka Madushanka Jayawardena
Faculty of Engineering, <http://www.pdn.ac.lk/eng>
University of Peradeniyaya.
LinkedIn <http://lk.linkedin.com/in/menakajayawardena>
Re: Taverna language command line tool - progress
Posted by Stian Soiland-Reyes <st...@apache.org>.
Menaka, I updated
https://github.com/stain/scufl2-iwir/
to work with Apache Taverna Language 0.15.1-incubating-SNAPSHOT.
and deployed as a snapshot to
http://www.mygrid.org.uk/maven/snapshot-repository
I also deployed the latest iwirTool.jar to
http://www.mygrid.org.uk/maven/repository/
Something like this should now work:
https://gist.github.com/stain/8d1e0f43d56a57313230
Then you can see if you have support for
"application/vnd.shiwa.iwir+xml" from WorkflowBundleIO.
On 19 June 2015 at 15:57, Stian Soiland-Reyes <st...@apache.org> wrote:
>
> No - scufl2-iwir just lives as that experimental prototype in github.
> My apologies for exposing you to outdated research-grade software..
> :-/
>
> It is my own code, so I'll clarify its own license. It would probably
> need to live outside Apache as otherwise I would need to file a
> Software Grant for it.
>
>
> I am also having second thoughts about scufl2-iwir because of the
> dependency I didn't think about.. are you able to see if it truly
> needs that dependency, or did I just use it out of lazyness? (Most of
> that code was written during a presentation of IWIR :)
>
> I'm trying to update it now to have a look. So perhaps the best is if
> you could move the iwir/ code to a separate branch that you leave out
> of the pull request?
>
>
> Perhaps you could also investigate if there would be an easy way to
> make the command line tool pluggable for additional formats with
> reader/writers, so that a scufl2-iwir.jar and friends can just be
> dropped into a lib/ folder at install? That might not work well with
> a single shaded JAR, though.
>
> On 16 June 2015 at 16:46, Menaka Madushanka <me...@gmail.com> wrote:
> > Hi Stian,
> >
> >> If you get any specific errors with the current wfdesc, raise them in
> >> Jira and ping me.
> >
> >
> > All the errors that I get are because of the Sesame/ Elmo binding problem I
> > think.
> >
> >>
> >> ArtifactTransferException: Failure to transfer
> >> org.openrdf.sesame:sesame-model:jar:2.2.4 from
> >> http://repository.springsource.com/maven/bundles/release was cached in the
> >> local repository, resolution will not be reattempted until the update
> >> interval of com.springsource.repository.bundles.release has elapsed or
> >> updates are forced. Original error: Could not transfer artifact
> >> org.openrdf.sesame:sesame-model:jar:2.2.4 from/to
> >> com.springsource.repository.bundles.release
> >> (http://repository.springsource.com/maven/bundles/release): The operation
> >> was cancelled.
> >
> >
> > There are 23 these messages. So that, I could not build the module.
> >
> > Then the IWIR format....
> > https://github.com/stain/scufl2-iwir
> >
> > Are there any maven dependency for this?
> > Or do I need to overwrite the writers and readers as is the repo?
> >
> > Cheers
> > Menaka
> >
> >
> > On 11 June 2015 at 21:03, Stian Soiland-Reyes <st...@apache.org> wrote:
> >>
> >> This is great progress! Almost too fast..! :))
> >>
> >> I see at
> >> https://github.com/menaka121/incubator-taverna-language/commits/master
> >> you are on board with commit early, commit often!
> >>
> >> Would you be able to change your git config to provide your full name
> >> instead of "menaka121"?
> >>
> >> git config --global user.name "Menaka Madushanka"
> >>
> >>
> >> I was about to accept the pull request, but see you have introduced a
> >> different package name:
> >>
> >> org.apache.tavlang.commandline
> >>
> >> but we only use
> >> org.apache.taverna.*
> >>
> >> as 'tavlang' is not a top level Apache project. (Strictly speaking
> >> Apache Taverna is not even a top level project!)
> >>
> >> Could you change the Java package it to:
> >>
> >> org.apache.taverna.tavlang ? I don't think we need "commandline" in
> >> the package as well, if we agree on "tavlang" as the command.
> >>
> >>
> >>
> >>
> >> The wfdesc module is currently disabled as it depends on old
> >> Sesame/Elmo bindings that are no longer available from a regular Maven
> >> repository. You can build it yourself from taverna-scufl2-wfdesc -
> >> which relies on my mirror at
> >> http://repository.mygrid.org.uk/artifactory/aduna/
> >>
> >> If you get any specific errors with the current wfdesc, raise them in
> >> Jira and ping me. There could be some Java 8 compatibility issue for
> >> all I know.
> >>
> >>
> >> I have a branch which tries to switch wfdesc module to use much simpler
> >> APIs
> >> (although more verbose) of Apache Jena, but it is still not quite
> >> finished as the style of
> >> invoking is a bit different without Elmo and is in a bit of
> >> compiler-error-state -
> >> see
> >> https://github.com/apache/incubator-taverna-language/tree/wfdesc-jena
> >>
> >>
> >>
> >> What is .structure files? Do you mean
> >> text/vnd.taverna.scufl2.structure? Yes, they can be used both for
> >> read and write and should have enough info for execution - although
> >> reading is perhaps not as interesting as they are mainly intended for
> >> quick debugging (e.g. output from your --inspect). and don't have a
> >> proper grammar or parser - it's just using Scanner and keywords.
> >
> >
> >
> >
> > --
> > Menaka Madushanka Jayawardena
> > Faculty of Engineering,
> > University of Peradeniyaya.
> > LinkedIn
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/0000-0001-9842-9718
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718
Re: Taverna language command line tool - progress
Posted by Menaka Madushanka <me...@gmail.com>.
Hi Stian,
I removed the iwir from the new_features branch. I thought it was official
and I'm sorry for it.
I have some problems with ro bundle conversion. There is no example of
showing the conversion of other bundle types in to ro bundle. As in
ro-combined archive, is the same method could used for other formats?
And as an extended proposal the implementing of validation and statistics
commands is also considered. I checked out the api for validation
http://taverna.incubator.apache.org/javadoc/taverna-language/org/apache/taverna/scufl2/validation/package-summary.html
but I was unable to get a better understanding about it. And for
statistics, what are the methods that can be used? Can we processornames
and servicetypes tools which are in inspection section, for this?
So far I was engaged in writing some blogs because I thought they would be
helpful for every one.
Cheers
Menaka
On 19 June 2015 at 20:27, Stian Soiland-Reyes <st...@apache.org> wrote:
> No - scufl2-iwir just lives as that experimental prototype in github.
> My apologies for exposing you to outdated research-grade software..
> :-/
>
> It is my own code, so I'll clarify its own license. It would probably
> need to live outside Apache as otherwise I would need to file a
> Software Grant for it.
>
>
> I am also having second thoughts about scufl2-iwir because of the
> dependency I didn't think about.. are you able to see if it truly
> needs that dependency, or did I just use it out of lazyness? (Most of
> that code was written during a presentation of IWIR :)
>
> I'm trying to update it now to have a look. So perhaps the best is if
> you could move the iwir/ code to a separate branch that you leave out
> of the pull request?
>
>
> Perhaps you could also investigate if there would be an easy way to
> make the command line tool pluggable for additional formats with
> reader/writers, so that a scufl2-iwir.jar and friends can just be
> dropped into a lib/ folder at install? That might not work well with
> a single shaded JAR, though.
>
> On 16 June 2015 at 16:46, Menaka Madushanka <me...@gmail.com> wrote:
> > Hi Stian,
> >
> >> If you get any specific errors with the current wfdesc, raise them in
> >> Jira and ping me.
> >
> >
> > All the errors that I get are because of the Sesame/ Elmo binding
> problem I
> > think.
> >
> >>
> >> ArtifactTransferException: Failure to transfer
> >> org.openrdf.sesame:sesame-model:jar:2.2.4 from
> >> http://repository.springsource.com/maven/bundles/release was cached in
> the
> >> local repository, resolution will not be reattempted until the update
> >> interval of com.springsource.repository.bundles.release has elapsed or
> >> updates are forced. Original error: Could not transfer artifact
> >> org.openrdf.sesame:sesame-model:jar:2.2.4 from/to
> >> com.springsource.repository.bundles.release
> >> (http://repository.springsource.com/maven/bundles/release): The
> operation
> >> was cancelled.
> >
> >
> > There are 23 these messages. So that, I could not build the module.
> >
> > Then the IWIR format....
> > https://github.com/stain/scufl2-iwir
> >
> > Are there any maven dependency for this?
> > Or do I need to overwrite the writers and readers as is the repo?
> >
> > Cheers
> > Menaka
> >
> >
> > On 11 June 2015 at 21:03, Stian Soiland-Reyes <st...@apache.org> wrote:
> >>
> >> This is great progress! Almost too fast..! :))
> >>
> >> I see at
> >> https://github.com/menaka121/incubator-taverna-language/commits/master
> >> you are on board with commit early, commit often!
> >>
> >> Would you be able to change your git config to provide your full name
> >> instead of "menaka121"?
> >>
> >> git config --global user.name "Menaka Madushanka"
> >>
> >>
> >> I was about to accept the pull request, but see you have introduced a
> >> different package name:
> >>
> >> org.apache.tavlang.commandline
> >>
> >> but we only use
> >> org.apache.taverna.*
> >>
> >> as 'tavlang' is not a top level Apache project. (Strictly speaking
> >> Apache Taverna is not even a top level project!)
> >>
> >> Could you change the Java package it to:
> >>
> >> org.apache.taverna.tavlang ? I don't think we need "commandline" in
> >> the package as well, if we agree on "tavlang" as the command.
> >>
> >>
> >>
> >>
> >> The wfdesc module is currently disabled as it depends on old
> >> Sesame/Elmo bindings that are no longer available from a regular Maven
> >> repository. You can build it yourself from taverna-scufl2-wfdesc -
> >> which relies on my mirror at
> >> http://repository.mygrid.org.uk/artifactory/aduna/
> >>
> >> If you get any specific errors with the current wfdesc, raise them in
> >> Jira and ping me. There could be some Java 8 compatibility issue for
> >> all I know.
> >>
> >>
> >> I have a branch which tries to switch wfdesc module to use much simpler
> >> APIs
> >> (although more verbose) of Apache Jena, but it is still not quite
> >> finished as the style of
> >> invoking is a bit different without Elmo and is in a bit of
> >> compiler-error-state -
> >> see
> >> https://github.com/apache/incubator-taverna-language/tree/wfdesc-jena
> >>
> >>
> >>
> >> What is .structure files? Do you mean
> >> text/vnd.taverna.scufl2.structure? Yes, they can be used both for
> >> read and write and should have enough info for execution - although
> >> reading is perhaps not as interesting as they are mainly intended for
> >> quick debugging (e.g. output from your --inspect). and don't have a
> >> proper grammar or parser - it's just using Scanner and keywords.
> >
> >
> >
> >
> > --
> > Menaka Madushanka Jayawardena
> > Faculty of Engineering,
> > University of Peradeniyaya.
> > LinkedIn
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/0000-0001-9842-9718
>
--
Menaka Madushanka Jayawardena
Faculty of Engineering, <http://www.pdn.ac.lk/eng>
University of Peradeniyaya.
LinkedIn <http://lk.linkedin.com/in/menakajayawardena>
Re: Taverna language command line tool - progress
Posted by Stian Soiland-Reyes <st...@apache.org>.
No - scufl2-iwir just lives as that experimental prototype in github.
My apologies for exposing you to outdated research-grade software..
:-/
It is my own code, so I'll clarify its own license. It would probably
need to live outside Apache as otherwise I would need to file a
Software Grant for it.
I am also having second thoughts about scufl2-iwir because of the
dependency I didn't think about.. are you able to see if it truly
needs that dependency, or did I just use it out of lazyness? (Most of
that code was written during a presentation of IWIR :)
I'm trying to update it now to have a look. So perhaps the best is if
you could move the iwir/ code to a separate branch that you leave out
of the pull request?
Perhaps you could also investigate if there would be an easy way to
make the command line tool pluggable for additional formats with
reader/writers, so that a scufl2-iwir.jar and friends can just be
dropped into a lib/ folder at install? That might not work well with
a single shaded JAR, though.
On 16 June 2015 at 16:46, Menaka Madushanka <me...@gmail.com> wrote:
> Hi Stian,
>
>> If you get any specific errors with the current wfdesc, raise them in
>> Jira and ping me.
>
>
> All the errors that I get are because of the Sesame/ Elmo binding problem I
> think.
>
>>
>> ArtifactTransferException: Failure to transfer
>> org.openrdf.sesame:sesame-model:jar:2.2.4 from
>> http://repository.springsource.com/maven/bundles/release was cached in the
>> local repository, resolution will not be reattempted until the update
>> interval of com.springsource.repository.bundles.release has elapsed or
>> updates are forced. Original error: Could not transfer artifact
>> org.openrdf.sesame:sesame-model:jar:2.2.4 from/to
>> com.springsource.repository.bundles.release
>> (http://repository.springsource.com/maven/bundles/release): The operation
>> was cancelled.
>
>
> There are 23 these messages. So that, I could not build the module.
>
> Then the IWIR format....
> https://github.com/stain/scufl2-iwir
>
> Are there any maven dependency for this?
> Or do I need to overwrite the writers and readers as is the repo?
>
> Cheers
> Menaka
>
>
> On 11 June 2015 at 21:03, Stian Soiland-Reyes <st...@apache.org> wrote:
>>
>> This is great progress! Almost too fast..! :))
>>
>> I see at
>> https://github.com/menaka121/incubator-taverna-language/commits/master
>> you are on board with commit early, commit often!
>>
>> Would you be able to change your git config to provide your full name
>> instead of "menaka121"?
>>
>> git config --global user.name "Menaka Madushanka"
>>
>>
>> I was about to accept the pull request, but see you have introduced a
>> different package name:
>>
>> org.apache.tavlang.commandline
>>
>> but we only use
>> org.apache.taverna.*
>>
>> as 'tavlang' is not a top level Apache project. (Strictly speaking
>> Apache Taverna is not even a top level project!)
>>
>> Could you change the Java package it to:
>>
>> org.apache.taverna.tavlang ? I don't think we need "commandline" in
>> the package as well, if we agree on "tavlang" as the command.
>>
>>
>>
>>
>> The wfdesc module is currently disabled as it depends on old
>> Sesame/Elmo bindings that are no longer available from a regular Maven
>> repository. You can build it yourself from taverna-scufl2-wfdesc -
>> which relies on my mirror at
>> http://repository.mygrid.org.uk/artifactory/aduna/
>>
>> If you get any specific errors with the current wfdesc, raise them in
>> Jira and ping me. There could be some Java 8 compatibility issue for
>> all I know.
>>
>>
>> I have a branch which tries to switch wfdesc module to use much simpler
>> APIs
>> (although more verbose) of Apache Jena, but it is still not quite
>> finished as the style of
>> invoking is a bit different without Elmo and is in a bit of
>> compiler-error-state -
>> see
>> https://github.com/apache/incubator-taverna-language/tree/wfdesc-jena
>>
>>
>>
>> What is .structure files? Do you mean
>> text/vnd.taverna.scufl2.structure? Yes, they can be used both for
>> read and write and should have enough info for execution - although
>> reading is perhaps not as interesting as they are mainly intended for
>> quick debugging (e.g. output from your --inspect). and don't have a
>> proper grammar or parser - it's just using Scanner and keywords.
>
>
>
>
> --
> Menaka Madushanka Jayawardena
> Faculty of Engineering,
> University of Peradeniyaya.
> LinkedIn
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718
Re: Taverna language command line tool - progress
Posted by Menaka Madushanka <me...@gmail.com>.
Hi Stian,
If you get any specific errors with the current wfdesc, raise them in
> Jira and ping me.
All the errors that I get are because of the Sesame/ Elmo binding problem I
think.
> ArtifactTransferException: Failure to transfer
> org.openrdf.sesame:sesame-model:jar:2.2.4 from
> http://repository.springsource.com/maven/bundles/release was cached in
> the local repository, resolution will not be reattempted until the update
> interval of com.springsource.repository.bundles.release has elapsed or
> updates are forced. Original error: Could not transfer artifact
> org.openrdf.sesame:sesame-model:jar:2.2.4 from/to
> com.springsource.repository.bundles.release (
> http://repository.springsource.com/maven/bundles/release): The operation
> was cancelled.
There are 23 these messages. So that, I could not build the module.
Then the IWIR format....
https://github.com/stain/scufl2-iwir
Are there any maven dependency for this?
Or do I need to overwrite the writers and readers as is the repo?
Cheers
Menaka
On 11 June 2015 at 21:03, Stian Soiland-Reyes <st...@apache.org> wrote:
> This is great progress! Almost too fast..! :))
>
> I see at
> https://github.com/menaka121/incubator-taverna-language/commits/master
> you are on board with commit early, commit often!
>
> Would you be able to change your git config to provide your full name
> instead of "menaka121"?
>
> git config --global user.name "Menaka Madushanka"
>
>
> I was about to accept the pull request, but see you have introduced a
> different package name:
>
> org.apache.tavlang.commandline
>
> but we only use
> org.apache.taverna.*
>
> as 'tavlang' is not a top level Apache project. (Strictly speaking
> Apache Taverna is not even a top level project!)
>
> Could you change the Java package it to:
>
> org.apache.taverna.tavlang ? I don't think we need "commandline" in
> the package as well, if we agree on "tavlang" as the command.
>
>
>
>
> The wfdesc module is currently disabled as it depends on old
> Sesame/Elmo bindings that are no longer available from a regular Maven
> repository. You can build it yourself from taverna-scufl2-wfdesc -
> which relies on my mirror at
> http://repository.mygrid.org.uk/artifactory/aduna/
>
> If you get any specific errors with the current wfdesc, raise them in
> Jira and ping me. There could be some Java 8 compatibility issue for
> all I know.
>
>
> I have a branch which tries to switch wfdesc module to use much simpler
> APIs
> (although more verbose) of Apache Jena, but it is still not quite
> finished as the style of
> invoking is a bit different without Elmo and is in a bit of
> compiler-error-state -
> see
> https://github.com/apache/incubator-taverna-language/tree/wfdesc-jena
>
>
>
> What is .structure files? Do you mean
> text/vnd.taverna.scufl2.structure? Yes, they can be used both for
> read and write and should have enough info for execution - although
> reading is perhaps not as interesting as they are mainly intended for
> quick debugging (e.g. output from your --inspect). and don't have a
> proper grammar or parser - it's just using Scanner and keywords.
>
--
Menaka Madushanka Jayawardena
Faculty of Engineering, <http://www.pdn.ac.lk/eng>
University of Peradeniyaya.
LinkedIn <http://lk.linkedin.com/in/menakajayawardena>
Re: Taverna language command line tool - progress
Posted by Stian Soiland-Reyes <st...@apache.org>.
This is great progress! Almost too fast..! :))
I see at https://github.com/menaka121/incubator-taverna-language/commits/master
you are on board with commit early, commit often!
Would you be able to change your git config to provide your full name
instead of "menaka121"?
git config --global user.name "Menaka Madushanka"
I was about to accept the pull request, but see you have introduced a
different package name:
org.apache.tavlang.commandline
but we only use
org.apache.taverna.*
as 'tavlang' is not a top level Apache project. (Strictly speaking
Apache Taverna is not even a top level project!)
Could you change the Java package it to:
org.apache.taverna.tavlang ? I don't think we need "commandline" in
the package as well, if we agree on "tavlang" as the command.
The wfdesc module is currently disabled as it depends on old
Sesame/Elmo bindings that are no longer available from a regular Maven
repository. You can build it yourself from taverna-scufl2-wfdesc -
which relies on my mirror at
http://repository.mygrid.org.uk/artifactory/aduna/
If you get any specific errors with the current wfdesc, raise them in
Jira and ping me. There could be some Java 8 compatibility issue for
all I know.
I have a branch which tries to switch wfdesc module to use much simpler APIs
(although more verbose) of Apache Jena, but it is still not quite
finished as the style of
invoking is a bit different without Elmo and is in a bit of
compiler-error-state -
see
https://github.com/apache/incubator-taverna-language/tree/wfdesc-jena
What is .structure files? Do you mean
text/vnd.taverna.scufl2.structure? Yes, they can be used both for
read and write and should have enough info for execution - although
reading is perhaps not as interesting as they are mainly intended for
quick debugging (e.g. output from your --inspect). and don't have a
proper grammar or parser - it's just using Scanner and keywords.