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From Stian Soiland-Reyes <st...@apache.org>
Subject Re: Snapshot issue when releasing taverna language
Date Mon, 01 Feb 2016 10:23:38 GMT
Thanks for the fixes, Menaka, applied :)

(I did the git pull as it said in the automated git email)



Gale, perhaps you could have a look if the tavlang help screens are
now OK? Feel free to fix anything missed :)

It should work fine to build just the taverna-language-commandline module within
https://git-wip-us.apache.org/repos/asf/incubator-taverna-language.git -
or you can download the latest JAR from
https://builds.apache.org/user/stain/my-views/view/taverna/job/incubator-taverna-language/lastSuccessfulBuild/org.apache.taverna.language$taverna-language-commandline/
and run it with java -jar

e.g.

stain@biggie:~/src/taverna/incubator-taverna-language/taverna-language-commandline/target$
java -jar taverna-language-commandline-0.15.1-incubating-SNAPSHOT.jar
help
usage: tavlang <command> [<args>]

The most commonly used tavlang commands are:
    convert    Convert the given workflow
    help       Display help information about Tvarna
    inspect    Inspect the given workflow and show the results on the terminal
    stats      Shows the workflow statistics
    validate   validate the given workflow
    version    Show version informantion

See 'tavlang help <command>' for more information on a specific command.


Menaka and others - perhaps we should rename the module from
"taverna-language-commandline" to taverna-tavlang ?  Might reduce the
confusion against the taverna-commandline..
Raised as https://issues.apache.org/jira/browse/TAVERNA-889

On 31 January 2016 at 16:06, Menaka Madushanka <menaka12350@gmail.com> wrote:
> Hello all,
>
> I corrected the typo issues and removed some unnecessary comments.......
> Thank you very much Gale..!!!
>
> What could we do for the Iwir issue?
>
> I added it because in the Readme.md file of  taverna-scufl2-api
> <https://github.com/apache/incubator-taverna-language/tree/master/taverna-scufl2-api>,
> says about the iwir support.
>
> Cheers
>
> On 30 January 2016 at 01:58, Gale Naylor <GaleN@noventussolutions.com>
> wrote:
>
>> It seems that the iwir capability is already commented out in
>> Scufl2Convert.java? (LInes 185-188) Or am I not reading this right?
>>
>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/tools/convert/Scufl2Convert.java
>>
>> Also, there seem to be some typos in CommandLineTool.java that may be
>> something users can see and, therefore, maybe we should change (see below)?
>>
>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-language-commandline/src/main/java/org/apache/taverna/tavlang/CommandLineTool.java
>>
>> Two instances of bund*el* instead of bund*le*: in description and one
>> Tvarna instead of Taverna.
>>     line 86: @Option(name = "--wfbundle", description = "Convert the
>> workflow file to wfbundel"
>>     line 89: @Option(name = "--robundle", description = "Convert given
>> bundel in to Research Object bundel")
>>     line 178: "Tvarna" should be Taverna --> description = "Display help
>> information about Tvarna"
>>
>> Thanks,
>> Gale
>>
>> On Fri, Jan 29, 2016 at 11:17 AM Gale Naylor <GaleN@noventussolutions.com>
>> wrote:
>>
>> > @stain, when you said maybe scufl2-iwir "should move to
>> >
>> > taverna-extras Github organisations, which we said was for plugins with
>> > LGPL or GPL licences/dependencies," is taverna-extras one of the github
>> > source code repos or something else?
>> >
>> > Also, @stain, if Menaka added IWIR support to the tavtool, does that mean
>> > he is *not* using the iwirTool to provide that support? If so, then can
>> we
>> > leave the iwir capability in the taverna-language-commandline
>> documentation?
>> >
>> > Thanks,
>> > Gale
>> >
>> > On Fri, Jan 29, 2016 at 10:58 AM Gale Naylor <
>> GaleN@noventussolutions.com>
>> > wrote:
>> >
>> >> I am a little confused about the licensing. This Apache webpage seems to
>> >> say that we cannot use anything with an LGPL license:
>> >> http://www.apache.org/legal/resolved.html#category-x. But it's okay if
>> >> the dependency is optional?
>> >>
>> >> Regarding documentation: do we want to remove any mention of iwir
>> >> completely?
>> >>
>> >> Thanks,
>> >>
>> >> Gale
>> >>
>> >> On Fri, Jan 29, 2016 at 7:14 AM Ian Dunlop <ian.dunlop@manchester.ac.uk
>> >
>> >> wrote:
>> >>
>> >>> Hello,
>> >>>
>> >>> I'm just trying to figure out the dependency spaghetti! The scufl2-iwir
>> >>> jar seems to be in the 'tavtool' lib forlder:
>> >>>
>> >>> ls
>> taverna-language-commandline/target/taverna-language-commandline/lib/
>> >>> (...lots of jars)
>> >>>      scufl2-iwir-0.2-20150619.152911-2.jar
>> >>>
>> >>> It is marked as an optional in the taverna-language-commandline pom
>> >>>
>> >>>          <dependency>
>> >>>                 <groupId>no.s11.scufl2</groupId>
>> >>>                 <artifactId>scufl2-iwir</artifactId>
>> >>>                 <version>0.2-SNAPSHOT</version>
>> >>>         <optional>true</optional>
>> >>>     </dependency>
>> >>>
>> >>> I commented the dependency out and there were no problems with mvn
>> clean
>> >>> install plus the jar is no longer in the lib. I'm not 100% clear why
>> >>> this dependency is here anyway, isn't the conversion done by the
>> >>> workflow bundle tool?
>> >>> So, looks like you can remove the dependency from the tavtool although
>> >>> you will probably need some doc updates to point out that iwir is not
>> >>> supported now.
>> >>>
>> >>> Cheers,
>> >>>
>> >>> Ian
>> >>>
>> >>>
>> >>> On 26/01/2016 14:14, Stian Soiland-Reyes wrote:
>> >>> > On 26 Jan 2016 13:45, "Ian Dunlop" <ian.dunlop@manchester.ac.uk>
>> >>> wrote:
>> >>> >>
>> >>> >> Hello,
>> >>> >>
>> >>> >> The scufl2-iwir tool pom
>> >>> >> https://github.com/stain/scufl2-iwir/blob/master/pom.xml lists
an
>> >>> LGPL
>> >>> >> dependency
>> >>> >>
>> >>> >> <groupId>org.shiwa.fgi.iwir</groupId>
>> >>> >> <artifactId>iwirTool</artifactId>
>> >>> >> <version>1.1.11</version>
>> >>> >> <!-- WARNING: LGPL dependency -->
>> >>> >> <!-- See http://sourceforge.net/projects/iwirtool/ -->
>> >>> >>
>> >>> >> Is that a problem for an Apache release?
>> >>> >
>> >>> > Ouch, scufl2-iwir is a dependency Menaka added to tavtool, as one
of
>> >>> the
>> >>> > conversion formats.
>> >>> >
>> >>> > It should not be a problem as long as it is an optional dependency
>> >>> which is
>> >>> > not pulled into use inadvertently. It might be worth checking the
>> >>> tavtool
>> >>> > lib folder after compilation if it does so.
>> >>> >
>> >>> > As I was not sure at the time (plus this was experimental) I put
the
>> >>> IWIR
>> >>> > support in a separate repository. Perhaps this should move to
>> >>> > taverna-extras Github organisations, which we said was for plugins
>> with
>> >>> > LGPL or GPL licences/dependencies.
>> >>> >
>> >>> > Do we need this ependency to compile (e.g. release) or can
>> scufl2-iwir
>> >>> > dependency be commented out / moved to a Maven profile?
>> >>> >
>> >>> > I guess this is a bit of spaghetti leftover :/ as scufl2-iwir is
a
>> >>> plugin
>> >>> > for scufl2-api to deal with the IWIR format, but Menaka added IWIR
>> >>> support
>> >>> > to the tavtool, and both are part of taverna-language while
>> >>> scufl2-iwir is
>> >>> > outside Apache Taverna.
>> >>> >
>> >>> > I am not sure why this dependency is SNAPSHOT though, I can try
to
>> >>> release
>> >>> > it, and to a better repository (Central?)
>> >>> >
>> >>> > Really the scufl2 command line tool might need a pluggable structure
>> so
>> >>> > third-party plugins (even if that third party in this case is me!)
>> can
>> >>> be
>> >>> > dropped into say the lib folder rather than by editing the pom.xml
>> >>> >
>> >>> >>
>> >>> >> Cheers,
>> >>> >>
>> >>> >> Ian
>> >>> >>
>> >>> >> On 26/01/2016 12:15, Ian Dunlop wrote:
>> >>> >>> Hello,
>> >>> >>>
>> >>> >>> Looks like https://github.com/stain/scufl2-iwir needs to
be
>> released
>> >>> >>> without SNAPSHOT version. The SNAPSHOT is available from
the mygrid
>> >>> repo
>> >>> >>>
>> >>> >
>> >>>
>> http://repository.mygrid.org.uk/artifactory/mygrid-snapshots/no/s11/scufl2/scufl2-iwir/0.2-SNAPSHOT/
>> >>> >>>
>> >>> >>> Cheers,
>> >>> >>>
>> >>> >>> Ian
>> >>> >>>
>> >>> >>> On 26/01/2016 12:09, Ian Dunlop wrote:
>> >>> >>>> Hello,
>> >>> >>>>
>> >>> >>>> Yes it is in
>> >>> >>>>
>> >>> >
>> >>>
>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-language-commandline/pom.xml
>> >>> >>>> which (IIRC) is the module that menaka built for GSOC.
I think the
>> >>> last
>> >>> >>>> release did not include this module -
>> >>> >>>>
>> >>> >
>> >>>
>> https://github.com/apache/incubator-taverna-language/commit/349460af1447cd04bfea59b047a99ab85652c185
>> >>> > .
>> >>> >>>>
>> >>> >>>> <dependency>
>> >>> >>>>      <groupId>no.s11.scufl2</groupId>
>> >>> >>>>      <artifactId>scufl2-iwir</artifactId>
>> >>> >>>>      <version>0.2-SNAPSHOT</version>
>> >>> >>>>      <optional>true</optional>
>> >>> >>>> </dependency>
>> >>> >>>>
>> >>> >>>> So it looks like we need to get the no.s11.scufl2:scufl2-iwir
>> >>> > dependency
>> >>> >>>> deployed 'properly'
>> >>> >>>>
>> >>> >>>> Cheers,
>> >>> >>>>
>> >>> >>>> Ian
>> >>> >>>>
>> >>> >>>> On 25/01/2016 17:27, Andy Seaborne wrote:
>> >>> >>>>> On 25/01/16 16:37, Ian Dunlop wrote:
>> >>> >>>>>> Hello
>> >>> >>>>>>
>> >>> >>>>>> Pasted from IRC chat!
>> >>> >>>>>>
>> >>> >>>>>> "Was going to try a taverna-language release
but mvn
>> >>> release:prepare
>> >>> >>>>>> asked if I wanted to resolve some SNAPSHOT
dependencies
>> >>> >>>>>> [15:42] <IanD_> I said no which resulted
in: [ERROR] Failed to
>> >>> > execute
>> >>> >>>>>> goal org.apache.maven.plugins:maven-release-plugin:2.5.2:prepare
>> >>> >>>>>> (default-cli) on project taverna-language:
Can't release project
>> >>> due
>> >>> > to
>> >>> >>>>>> non released dependencies : [ERROR]
>> >>> >>>>>> no.s11.scufl2:scufl2-iwir:jar:0.2-SNAPSHOT:compile
>> >>> >>>>>> [15:43] <IanD_> [ERROR] in project 'Apache
Taverna Language
>> >>> > Commandline'
>> >>> >>>>>>
>> >>> >
>> >>>
>> (org.apache.taverna.language:taverna-language-commandline:jar:0.15.1-incubating-SNAPSHOT)"
>> >>> >>>>>>
>> >>> >>>>>>
>> >>> >>>>>> Any ideas?
>> >>> >>>>>> Cheers,
>> >>> >>>>>>
>> >>> >>>>>> Ian
>> >>> >>>>>>
>> >>> >>>>>
>> >>> >>>>> One reason this can happen is when, somewhere,
a module depends
>> on
>> >>> a
>> >>> >>>>> SNAPSHOT and it's getting that SNAPSHOT from the
repo, not as
>> part
>> >>> of
>> >>> >>>>> the build.
>> >>> >>>>>
>> >>> >>>>>     Andy
>> >>> >>>>>
>> >>> >>>>>
>> >>> >>>>>
>> >>> >>>>
>> >>> >>>
>> >>> >>
>> >>> >> --
>> >>> >> Ian Dunlop, eScience Lab
>> >>> >> School of Computer Science
>> >>> >> The University of Manchester
>> >>> >> http://orcid.org/0000-0001-7066-3350
>> >>> >
>> >>>
>> >>> --
>> >>> Ian Dunlop, eScience Lab
>> >>> School of Computer Science
>> >>> The University of Manchester
>> >>> http://orcid.org/0000-0001-7066-3350
>> >>>
>> >>
>>
>
>
>
> --
> Menaka Madushanka Jayawardena
> Faculty of Engineering, <http://www.pdn.ac.lk/eng>
> University of Peradeniyaya.
> LinkedIn <http://lk.linkedin.com/in/menakajayawardena>



-- 
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718

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