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Posted to dev@taverna.apache.org by Dmitry <re...@list.ru> on 2014/12/11 12:10:00 UTC
WS Galaxy integration.
Hello everybody.
I am working on a project to integrate Web Services into Galaxy.
As an engine I use a branch of "wsdl-generic" which is based on XML
Schema tree model.
This branch includes a command line invoker:
java -jar wsdl-generic-3.5.0-SNAPSHOT.jar -wsdl
"http://inb.bsc.es/service/NCBIBlastp?wsdl" -operation runNCBIBlastp -in
"/request/sequence/sequence" MKELNDLEKKYNAHIGVYALDTKSGKEVKFNSDKRFAYA
"wsdl-generic" is executable (via manifest "Main-Class").
There are few parameters at the moment:
-wsdl WSDL location URL
-operation the name of the operation
-in a pair of "xpath" and the "value"
-file "xpath" and the file which contains the value
-out "xpath" and the file for the output.
"wsdl-generic" is also used for the WS Galaxy tool generator -
"galaxy-gears"
The generator uses a plain parameters model - the xml tree goes down to
its leafs with simple parameters.
The "xs:string" parameters that have no predefined values may be marked
as a "file" so galaxy tool may link files from its history.
Of course this is not the same as Taverna's command line execution:
http://mail-archives.apache.org/mod_mbox/incubator-taverna-users/201412.mbox/%3C2607C5CD-D7D8-4702-A142-9DFF9CA14BAD%40rostlab.org%3E
Cheers,
Dmitry
Re: WS Galaxy integration.
Posted by Stian Soiland-Reyes <so...@cs.manchester.ac.uk>.
Migration is a bit slow - we're waiting for IP clearance from Manchester to
be signed and sent in by the right lawyers
I have played with the new git structure at
https://github.com/taverna-incubator/ -- but this is done with file copies
and does not preserve the git history.
https://github.com/taverna-incubator/taverna-language is complete in how I
think the structure could be - the rest are just drafts. I think We don't
need to split -api and -impl anymore - considering each repository will
basically have to be made into an Apache Release.
I will redo these and merging in the full history from
https://github.com/taverna/ - so please just keep committing to
https://github.com/taverna/*
If we include the WSDL Generic then we have three releases that are ready
to go almost right away:
* taverna-osgi - quite minimal OSGi extensions
* taverna-language - libaries + command line tool for SCUFL2 and data
bundle
* taverna-wsdl-generic -- now with a command line tool! Yay!
None of these should have any LGPL dependencies -
Sorting out the platform and engine will take a bit more time - mainly due
to pom.xml editing and getting it to build again after moving modules
around - but there are also some dependency licenses to check and resolve:
http://dev.mygrid.org.uk/wiki/display/developer/Third-party+licenses#Third-partylicenses-Unknownlicenses
I guess you should keep existing uk.org.taverna* and net.sf.taverna.*
package names and groupIds until the move to not give the wrong impression.
Changing those are relatively easy after migration.
Just make sure you don't add any LGPL dependencies! :_)
On 11 December 2014 at 11:29, Dmitry <re...@list.ru> wrote:
> Hello Stian,
>
> I am currently debugging the generic branch (along the "galaxy-gears").
> The problem is in "wsdl-activity" and "wsdl-activity-ui" - although I did
> "something" that compile, it is only one working week left in December.
> Again it would be great to put "apache" packages and put the headers.
> How the migration to apache is going?
>
> Dmitry
>
> P.S. it looks like there is no way to attach to the apache mailing list.
>
> On 12/11/2014 12:17 PM, Stian Soiland-Reyes wrote:
>
> Great! Good to see wsdl-generic finally being used in a generic way. :)
>
> I guess this is a good enough reason to keep taverna-wsdl-generic as a
> separate git repository when we import into git.apache.org - it can
> work as a separate product.
>
> I could not find your branch in https://github.com/taverna/taverna-wsdl-generic/
>
> What do you feel is remaining before we can merge your branch into the master?
>
> On 11 December 2014 at 11:10, Dmitry <re...@list.ru> <re...@list.ru> wrote:
>
> Hello everybody.
>
> I am working on a project to integrate Web Services into Galaxy.
> As an engine I use a branch of "wsdl-generic" which is based on XML Schema
> tree model.
> This branch includes a command line invoker:
>
> java -jar wsdl-generic-3.5.0-SNAPSHOT.jar -wsdl"http://inb.bsc.es/service/NCBIBlastp?wsdl" <http://inb.bsc.es/service/NCBIBlastp?wsdl> -operation runNCBIBlastp -in
> "/request/sequence/sequence" MKELNDLEKKYNAHIGVYALDTKSGKEVKFNSDKRFAYA
>
> "wsdl-generic" is executable (via manifest "Main-Class").
>
> There are few parameters at the moment:
>
> -wsdl WSDL location URL
> -operation the name of the operation
> -in a pair of "xpath" and the "value"
> -file "xpath" and the file which contains the value
> -out "xpath" and the file for the output.
>
> "wsdl-generic" is also used for the WS Galaxy tool generator -
> "galaxy-gears"
>
> The generator uses a plain parameters model - the xml tree goes down to its
> leafs with simple parameters.
> The "xs:string" parameters that have no predefined values may be marked as a
> "file" so galaxy tool may link files from its history.
>
> Of course this is not the same as Taverna's command line execution:http://mail-archives.apache.org/mod_mbox/incubator-taverna-users/201412.mbox/%3C2607C5CD-D7D8-4702-A142-9DFF9CA14BAD%40rostlab.org%3E
>
> Cheers,
>
> Dmitry
>
>
>
>
>
>
--
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
Re: WS Galaxy integration.
Posted by alaninmcr <al...@googlemail.com>.
On 11/12/2014 11:29, Dmitry wrote:
> Hello Stian,
>
[snip]
> How the migration to apache is going?
In addition to what Stian described, there is a new
https://github.com/taverna-extras for code that although it can be made
T3 compatible will never (as far as can be predicted) go into Apache
because of license restrictions.
> Dmitry
Alan
Re: WS Galaxy integration.
Posted by Dmitry <re...@list.ru>.
Hello Stian,
I am currently debugging the generic branch (along the "galaxy-gears").
The problem is in "wsdl-activity" and "wsdl-activity-ui" - although I
did "something" that compile, it is only one working week left in
December. Again it would be great to put "apache" packages and put the
headers.
How the migration to apache is going?
Dmitry
P.S. it looks like there is no way to attach to the apache mailing list.
On 12/11/2014 12:17 PM, Stian Soiland-Reyes wrote:
> Great! Good to see wsdl-generic finally being used in a generic way. :)
>
> I guess this is a good enough reason to keep taverna-wsdl-generic as a
> separate git repository when we import into git.apache.org - it can
> work as a separate product.
>
> I could not find your branch in https://github.com/taverna/taverna-wsdl-generic/
>
> What do you feel is remaining before we can merge your branch into the master?
>
> On 11 December 2014 at 11:10, Dmitry <re...@list.ru> wrote:
>> Hello everybody.
>>
>> I am working on a project to integrate Web Services into Galaxy.
>> As an engine I use a branch of "wsdl-generic" which is based on XML Schema
>> tree model.
>> This branch includes a command line invoker:
>>
>> java -jar wsdl-generic-3.5.0-SNAPSHOT.jar -wsdl
>> "http://inb.bsc.es/service/NCBIBlastp?wsdl" -operation runNCBIBlastp -in
>> "/request/sequence/sequence" MKELNDLEKKYNAHIGVYALDTKSGKEVKFNSDKRFAYA
>>
>> "wsdl-generic" is executable (via manifest "Main-Class").
>>
>> There are few parameters at the moment:
>>
>> -wsdl WSDL location URL
>> -operation the name of the operation
>> -in a pair of "xpath" and the "value"
>> -file "xpath" and the file which contains the value
>> -out "xpath" and the file for the output.
>>
>> "wsdl-generic" is also used for the WS Galaxy tool generator -
>> "galaxy-gears"
>>
>> The generator uses a plain parameters model - the xml tree goes down to its
>> leafs with simple parameters.
>> The "xs:string" parameters that have no predefined values may be marked as a
>> "file" so galaxy tool may link files from its history.
>>
>> Of course this is not the same as Taverna's command line execution:
>> http://mail-archives.apache.org/mod_mbox/incubator-taverna-users/201412.mbox/%3C2607C5CD-D7D8-4702-A142-9DFF9CA14BAD%40rostlab.org%3E
>>
>> Cheers,
>>
>> Dmitry
>>
>>
>
>
Re: WS Galaxy integration.
Posted by Stian Soiland-Reyes <so...@cs.manchester.ac.uk>.
Great! Good to see wsdl-generic finally being used in a generic way. :)
I guess this is a good enough reason to keep taverna-wsdl-generic as a
separate git repository when we import into git.apache.org - it can
work as a separate product.
I could not find your branch in https://github.com/taverna/taverna-wsdl-generic/
What do you feel is remaining before we can merge your branch into the master?
On 11 December 2014 at 11:10, Dmitry <re...@list.ru> wrote:
> Hello everybody.
>
> I am working on a project to integrate Web Services into Galaxy.
> As an engine I use a branch of "wsdl-generic" which is based on XML Schema
> tree model.
> This branch includes a command line invoker:
>
> java -jar wsdl-generic-3.5.0-SNAPSHOT.jar -wsdl
> "http://inb.bsc.es/service/NCBIBlastp?wsdl" -operation runNCBIBlastp -in
> "/request/sequence/sequence" MKELNDLEKKYNAHIGVYALDTKSGKEVKFNSDKRFAYA
>
> "wsdl-generic" is executable (via manifest "Main-Class").
>
> There are few parameters at the moment:
>
> -wsdl WSDL location URL
> -operation the name of the operation
> -in a pair of "xpath" and the "value"
> -file "xpath" and the file which contains the value
> -out "xpath" and the file for the output.
>
> "wsdl-generic" is also used for the WS Galaxy tool generator -
> "galaxy-gears"
>
> The generator uses a plain parameters model - the xml tree goes down to its
> leafs with simple parameters.
> The "xs:string" parameters that have no predefined values may be marked as a
> "file" so galaxy tool may link files from its history.
>
> Of course this is not the same as Taverna's command line execution:
> http://mail-archives.apache.org/mod_mbox/incubator-taverna-users/201412.mbox/%3C2607C5CD-D7D8-4702-A142-9DFF9CA14BAD%40rostlab.org%3E
>
> Cheers,
>
> Dmitry
>
>
--
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
Re: WS Galaxy integration.
Posted by alaninmcr <al...@googlemail.com>.
On 11/12/2014 12:26, Dmitry wrote:
> No.
>
> There is no such a thing in WSDL, I mean that this is only a pattern of
> operations usage.
> I am not sure if it is possible to do in Galaxy's tool XML descriptor
> (there is only "command line" command there).
> It's possible to create 2 tools descriptions and link them in Galaxy
> (one for submit and another for polling).
Yes. The problem that others (I think from Georgia, US) had was that
users of Galaxy want to be able to include "what the calls do" in their
workflow not the calls themselves.
> Dmitry
Alan
Re: WS Galaxy integration.
Posted by Dmitry <re...@list.ru>.
No.
There is no such a thing in WSDL, I mean that this is only a pattern of
operations usage.
I am not sure if it is possible to do in Galaxy's tool XML descriptor
(there is only "command line" command there).
It's possible to create 2 tools descriptions and link them in Galaxy
(one for submit and another for polling).
Dmitry
On 12/11/2014 12:48 PM, alaninmcr wrote:
> On 11/12/2014 11:10, Dmitry wrote:
>> Hello everybody.
>>
>> I am working on a project to integrate Web Services into Galaxy.
>
>
> This is probably out-of-scope, but are you dealing with WSDL service
> sets that require polling with job ids ?
>
>> Cheers,
>>
>> Dmitry
>
> Alan
> .
>
Re: WS Galaxy integration.
Posted by alaninmcr <al...@googlemail.com>.
On 11/12/2014 11:10, Dmitry wrote:
> Hello everybody.
>
> I am working on a project to integrate Web Services into Galaxy.
This is probably out-of-scope, but are you dealing with WSDL service
sets that require polling with job ids ?
> Cheers,
>
> Dmitry
Alan