You are viewing a plain text version of this content. The canonical link for it is here.
Posted to dev@taverna.apache.org by Stian Soiland-Reyes <st...@apache.org> on 2016/02/01 11:23:38 UTC
Re: Snapshot issue when releasing taverna language
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 <me...@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 <Ga...@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 <Ga...@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" <ia...@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
Re: Snapshot issue when releasing taverna language
Posted by Menaka Madushanka <me...@gmail.com>.
Hi Gale,
'\n' used to add a new line.
So it wold like,
List of files to be converted.
Give the list of files to be converted without -i/-o and the converted
files will be saved in to /converted folder in the same dir.
Cheers
On 2 February 2016 at 00:01, Gale Naylor <Ga...@noventussolutions.com>
wrote:
> I created a couple of pull requests to make minor changes to the tavlang
> readme file and to CommandLineTool.java. In the Java file, line 197 says
> "List of files to be converted.\n " I'm not sure what the ".\n" means. Is
> this correct? The rest of the descriptions all look good to me. @stain, I
> can't check the help files directly at this time.
>
> Also, is iwir support still in the tavlang tool? (Sorry, if I missed this
> somewhere else. I've been, and still am, pretty sick.)
>
> Gale
>
>
>
> On Mon, Feb 1, 2016 at 6:48 AM alaninmcr <al...@googlemail.com> wrote:
>
> > On 01/02/2016 12:35, Menaka Madushanka wrote:
> > > Hello,
> > > I get this error when building tavlang tool....
> > >
> > > [ERROR] Failed to execute goal
> > > org.apache.maven.plugins:maven-javadoc-plugin:2.9:jar (attach-javadocs)
> > on
> > > project taverna-language-commandline: MavenReportException: Error while
> > > creating archive:
> > > [ERROR] Exit code: 1 - javadoc: error - invalid flag: -Xdoclint:none
> > > [ERROR]
> > > [ERROR] Command line was: /usr/lib/jvm/java-7-oracle/jre/../bin/javadoc
> > > @options @packages
> >
> > Is that option only available in Java 8?
> >
> > Alan
> >
>
--
Menaka Madushanka Jayawardena
Faculty of Engineering, <http://www.pdn.ac.lk/eng>
University of Peradeniyaya.
LinkedIn <http://lk.linkedin.com/in/menakajayawardena>
Re: Snapshot issue when releasing taverna language
Posted by Gale Naylor <Ga...@noventussolutions.com>.
I removed the instances of iwir in the tavlang tool readme (and created a
pull request), but I don't want to touch the actual java code. There are
several instances of iwir in tavlang/CommandLineTool.java:
REMOVE iwir INSTANCES?
(1) Line 98 - @Option(name = "--iwir", ...)
(2) Line 116/117 - else if (isIwir) / return"iwir";
(3) Line 232 - } else if(Filetype.isIwir || ...
On Tue, Feb 2, 2016 at 4:47 PM Stian Soiland-Reyes <st...@apache.org> wrote:
> I just disabled the iwir-dependency and the myGrid repository from
> tavlang.. as I found out that the LGPL iwirTool dependency it uses
> does not exist in Maven Central either, so there was not much point in
> releasing scufl2-iwir to Central.
>
>
> I guess some kind of feature request for tavlang would be to be able
> to "drop in" such libraries? I guess this doesn't work too well with a
> shaded JAR though (modifying -classpath).
>
> On 1 February 2016 at 18:31, Gale Naylor <Ga...@noventussolutions.com>
> wrote:
> > I created a couple of pull requests to make minor changes to the tavlang
> > readme file and to CommandLineTool.java. In the Java file, line 197 says
> > "List of files to be converted.\n " I'm not sure what the ".\n" means. Is
> > this correct? The rest of the descriptions all look good to me. @stain, I
> > can't check the help files directly at this time.
> >
> > Also, is iwir support still in the tavlang tool? (Sorry, if I missed this
> > somewhere else. I've been, and still am, pretty sick.)
> >
> > Gale
> >
> >
> >
> > On Mon, Feb 1, 2016 at 6:48 AM alaninmcr <al...@googlemail.com>
> wrote:
> >
> >> On 01/02/2016 12:35, Menaka Madushanka wrote:
> >> > Hello,
> >> > I get this error when building tavlang tool....
> >> >
> >> > [ERROR] Failed to execute goal
> >> > org.apache.maven.plugins:maven-javadoc-plugin:2.9:jar
> (attach-javadocs)
> >> on
> >> > project taverna-language-commandline: MavenReportException: Error
> while
> >> > creating archive:
> >> > [ERROR] Exit code: 1 - javadoc: error - invalid flag: -Xdoclint:none
> >> > [ERROR]
> >> > [ERROR] Command line was:
> /usr/lib/jvm/java-7-oracle/jre/../bin/javadoc
> >> > @options @packages
> >>
> >> Is that option only available in Java 8?
> >>
> >> Alan
> >>
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/0000-0001-9842-9718
>
Re: Snapshot issue when releasing taverna language
Posted by Stian Soiland-Reyes <st...@apache.org>.
I just disabled the iwir-dependency and the myGrid repository from
tavlang.. as I found out that the LGPL iwirTool dependency it uses
does not exist in Maven Central either, so there was not much point in
releasing scufl2-iwir to Central.
I guess some kind of feature request for tavlang would be to be able
to "drop in" such libraries? I guess this doesn't work too well with a
shaded JAR though (modifying -classpath).
On 1 February 2016 at 18:31, Gale Naylor <Ga...@noventussolutions.com> wrote:
> I created a couple of pull requests to make minor changes to the tavlang
> readme file and to CommandLineTool.java. In the Java file, line 197 says
> "List of files to be converted.\n " I'm not sure what the ".\n" means. Is
> this correct? The rest of the descriptions all look good to me. @stain, I
> can't check the help files directly at this time.
>
> Also, is iwir support still in the tavlang tool? (Sorry, if I missed this
> somewhere else. I've been, and still am, pretty sick.)
>
> Gale
>
>
>
> On Mon, Feb 1, 2016 at 6:48 AM alaninmcr <al...@googlemail.com> wrote:
>
>> On 01/02/2016 12:35, Menaka Madushanka wrote:
>> > Hello,
>> > I get this error when building tavlang tool....
>> >
>> > [ERROR] Failed to execute goal
>> > org.apache.maven.plugins:maven-javadoc-plugin:2.9:jar (attach-javadocs)
>> on
>> > project taverna-language-commandline: MavenReportException: Error while
>> > creating archive:
>> > [ERROR] Exit code: 1 - javadoc: error - invalid flag: -Xdoclint:none
>> > [ERROR]
>> > [ERROR] Command line was: /usr/lib/jvm/java-7-oracle/jre/../bin/javadoc
>> > @options @packages
>>
>> Is that option only available in Java 8?
>>
>> Alan
>>
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718
Re: Snapshot issue when releasing taverna language
Posted by Gale Naylor <Ga...@noventussolutions.com>.
I created a couple of pull requests to make minor changes to the tavlang
readme file and to CommandLineTool.java. In the Java file, line 197 says
"List of files to be converted.\n " I'm not sure what the ".\n" means. Is
this correct? The rest of the descriptions all look good to me. @stain, I
can't check the help files directly at this time.
Also, is iwir support still in the tavlang tool? (Sorry, if I missed this
somewhere else. I've been, and still am, pretty sick.)
Gale
On Mon, Feb 1, 2016 at 6:48 AM alaninmcr <al...@googlemail.com> wrote:
> On 01/02/2016 12:35, Menaka Madushanka wrote:
> > Hello,
> > I get this error when building tavlang tool....
> >
> > [ERROR] Failed to execute goal
> > org.apache.maven.plugins:maven-javadoc-plugin:2.9:jar (attach-javadocs)
> on
> > project taverna-language-commandline: MavenReportException: Error while
> > creating archive:
> > [ERROR] Exit code: 1 - javadoc: error - invalid flag: -Xdoclint:none
> > [ERROR]
> > [ERROR] Command line was: /usr/lib/jvm/java-7-oracle/jre/../bin/javadoc
> > @options @packages
>
> Is that option only available in Java 8?
>
> Alan
>
Re: Snapshot issue when releasing taverna language
Posted by alaninmcr <al...@googlemail.com>.
On 01/02/2016 12:35, Menaka Madushanka wrote:
> Hello,
> I get this error when building tavlang tool....
>
> [ERROR] Failed to execute goal
> org.apache.maven.plugins:maven-javadoc-plugin:2.9:jar (attach-javadocs) on
> project taverna-language-commandline: MavenReportException: Error while
> creating archive:
> [ERROR] Exit code: 1 - javadoc: error - invalid flag: -Xdoclint:none
> [ERROR]
> [ERROR] Command line was: /usr/lib/jvm/java-7-oracle/jre/../bin/javadoc
> @options @packages
Is that option only available in Java 8?
Alan
Re: Snapshot issue when releasing taverna language
Posted by Stian Soiland-Reyes <st...@apache.org>.
I think it is caused by this:
https://github.com/apache/incubator-taverna-language/blob/master/pom.xml#L48
https://issues.apache.org/jira/browse/TAVERNA-867
https://issues.apache.org/jira/browse/TAVERNA-869
Does it work with Java 8?
On 1 February 2016 at 12:35, Menaka Madushanka <me...@gmail.com> wrote:
> Hello,
> I get this error when building tavlang tool....
>
> [ERROR] Failed to execute goal
> org.apache.maven.plugins:maven-javadoc-plugin:2.9:jar (attach-javadocs) on
> project taverna-language-commandline: MavenReportException: Error while
> creating archive:
> [ERROR] Exit code: 1 - javadoc: error - invalid flag: -Xdoclint:none
> [ERROR]
> [ERROR] Command line was: /usr/lib/jvm/java-7-oracle/jre/../bin/javadoc
> @options @packages
> [ERROR]
> [ERROR] Refer to the generated Javadoc files in
> '/media/menaka/7567da6f-cbe0-4f3e-9277-7ff83266e516/incubator-taverna-language/taverna-language-commandline/target/apidocs'
> dir.
> [ERROR] -> [Help 1]
> [ERROR]
> [ERROR] To see the full stack trace of the errors, re-run Maven with the -e
> switch.
> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
> [ERROR]
> [ERROR] For more information about the errors and possible solutions,
> please read the following articles:
> [ERROR] [Help 1]
> http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
>
>
> Has anyone got this error before?
>
>
> On 1 February 2016 at 17:06, Menaka Madushanka <me...@gmail.com>
> wrote:
>
>> I'll change the module name as suggested.
>>
>> Cheers
>>
>> On 1 February 2016 at 15:53, Stian Soiland-Reyes <st...@apache.org> wrote:
>>
>>> 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 <me...@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 <Ga...@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" <ia...@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
>>>
>>
>>
>>
>> --
>> Menaka Madushanka Jayawardena
>> Faculty of Engineering, <http://www.pdn.ac.lk/eng>
>> University of Peradeniyaya.
>> LinkedIn <http://lk.linkedin.com/in/menakajayawardena>
>>
>
>
>
> --
> 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
Re: Snapshot issue when releasing taverna language
Posted by Menaka Madushanka <me...@gmail.com>.
Hello,
I get this error when building tavlang tool....
[ERROR] Failed to execute goal
org.apache.maven.plugins:maven-javadoc-plugin:2.9:jar (attach-javadocs) on
project taverna-language-commandline: MavenReportException: Error while
creating archive:
[ERROR] Exit code: 1 - javadoc: error - invalid flag: -Xdoclint:none
[ERROR]
[ERROR] Command line was: /usr/lib/jvm/java-7-oracle/jre/../bin/javadoc
@options @packages
[ERROR]
[ERROR] Refer to the generated Javadoc files in
'/media/menaka/7567da6f-cbe0-4f3e-9277-7ff83266e516/incubator-taverna-language/taverna-language-commandline/target/apidocs'
dir.
[ERROR] -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e
switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions,
please read the following articles:
[ERROR] [Help 1]
http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
Has anyone got this error before?
On 1 February 2016 at 17:06, Menaka Madushanka <me...@gmail.com>
wrote:
> I'll change the module name as suggested.
>
> Cheers
>
> On 1 February 2016 at 15:53, Stian Soiland-Reyes <st...@apache.org> wrote:
>
>> 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 <me...@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 <Ga...@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" <ia...@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
>>
>
>
>
> --
> Menaka Madushanka Jayawardena
> Faculty of Engineering, <http://www.pdn.ac.lk/eng>
> University of Peradeniyaya.
> LinkedIn <http://lk.linkedin.com/in/menakajayawardena>
>
--
Menaka Madushanka Jayawardena
Faculty of Engineering, <http://www.pdn.ac.lk/eng>
University of Peradeniyaya.
LinkedIn <http://lk.linkedin.com/in/menakajayawardena>
Re: Snapshot issue when releasing taverna language
Posted by Menaka Madushanka <me...@gmail.com>.
I'll change the module name as suggested.
Cheers
On 1 February 2016 at 15:53, Stian Soiland-Reyes <st...@apache.org> wrote:
> 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 <me...@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 <Ga...@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" <ia...@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
>
--
Menaka Madushanka Jayawardena
Faculty of Engineering, <http://www.pdn.ac.lk/eng>
University of Peradeniyaya.
LinkedIn <http://lk.linkedin.com/in/menakajayawardena>