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From Menaka Madushanka <menaka12...@gmail.com>
Subject Re: Taverna Language Command Line tool - convert command doc
Date Tue, 30 Jun 2015 14:43:59 GMT
Yes Gale,
I'm thinking on taking them as a reference. For the best, I have some much
better doc from you. :-) :-)

Thank you very much.
Menaka

On 30 June 2015 at 20:09, Gale Naylor <galen@noventussolutions.com> wrote:

> Hi Menaka,
>
> Sounds great! Do you plan to use your blog to prepare the documentation?
>
> Feel free to use anything I've prepared if it helps. And if I can do
> any more before I go on vacation, I will let you know.
>
> Thanks,
>
> Gale
>
> On Tue, Jun 30, 2015 at 7:32 AM, Menaka Madushanka
> <menaka12350@gmail.com> wrote:
> > Hi Gale,
> >
> > The tool is almost done I think. The functionalities,
> > conversion,
> > validation,
> > inspection and
> > statistics
> >
> > are done.
> >
> > So what remaining is, completing the documentation.
> > I'll be able to finish it before 10 July hopefully. :-)
> >
> >
> >
> > On 30 June 2015 at 19:43, Gale Naylor <galen@noventussolutions.com>
> wrote:
> >
> >> Hi Menaka,
> >>
> >> Thank you. I appreciate your feedback, and I'd like to help however I
> can.
> >>
> >> When do you expect to finish your project and documentation?
> >>
> >> I'll be on vacation from July 1 through July 10, but I'll try to stay in
> >> touch.
> >>
> >> Thanks,
> >>
> >> Gale
> >>
> >> On Mon, Jun 29, 2015 at 11:23 AM, Menaka Madushanka
> >> <menaka12350@gmail.com> wrote:
> >> > Hello Gale,
> >> > Great work. :-)
> >> >
> >> > I did notice the mygrid pages said the information was out of date.
> >> >>
> >> > Yes. I also faced the same condition when I was starting the project.
> The
> >> > documentation will be updated very soon as the project releases. :-)
> >> >
> >> > I am to write the full complete documentation for the command line
> tool.
> >> > I'll appreciate your support for it. :-)
> >> >
> >> > Cheers.
> >> > Menaka
> >> >
> >> > On 29 June 2015 at 22:10, Gale Naylor <galen@noventussolutions.com>
> >> wrote:
> >> >
> >> >> Hi Menaka,
> >> >>
> >> >> >I found this doc in
> >> >> >http://dev.mygrid.org.uk/wiki/display/developer/SCUFL2+API
> >> >>
> >> >> Thanks for the link. I also found this mygrid link:
> >> >>
> http://dev.mygrid.org.uk/wiki/display/developer/Taverna+Workflow+Bundle
> >> ,
> >> >> which is very clear about the .wfbundle file extension.
> >> >>
> >> >> I did notice the mygrid pages said the information was out of date.
> >> >> So, I also looked at the taverna incubator documentation, and the
> >> >> incubator SCUFL API page pointed me to a github page for the latest
> >> >> information. I found the github SCUFL examples to be helpful:
> >> >>
> >> >>
> >>
> https://github.com/apache/incubator-taverna-language/tree/master/taverna-scufl2-examples
> >> >> .
> >> >> In the readme file, the t2flowtowfbundle tool describes the
> conversion
> >> >> of a .t2flow file to a SCUFL2 .wfbundle.
> >> >>
> >> >> Although I did find one example of a ".scufl2 bundle"
> >> >> (
> http://dev.mygrid.org.uk/wiki/display/developer/2011-02+Scufl2+status
> >> >> ), most of the references indicate the correct file extension is
> >> >> .wfbundle. So, I removed the .scufl2 references from my mapping
> table.
> >> >> Please let me know if I missed something here.
> >> >>
> >> >> I also updated the table to reflect the .wfbundle --> .json and
> >> >> .wfbundle --> .iwir mappings.
> >> >>
> >> >> Thanks!
> >> >>
> >> >> Gale
> >> >>
> >> >> On Sat, Jun 27, 2015 at 1:38 PM, Menaka Madushanka
> >> >> <menaka12350@gmail.com> wrote:
> >> >> > Hi Gale,
> >> >> >
> >> >> > So, .wfbundles can be converted to .json and .iwir formats as well
> as
> >> >> >> .structure?
> >> >> >
> >> >> >
> >> >> > Yes.
> >> >> >
> >> >> > Is it true that .wfbundle is the *bundle* format of Taverna 3
> >> >> >> (taverna-sculf2-wfbundle)
> >> >> >> and scufl2 is the *workflow* format of Taverna 3
> >> (taverna-scufl2-api)?
> >> >> >
> >> >> >
> >> >> > I found this doc in
> >> >> > http://dev.mygrid.org.uk/wiki/display/developer/SCUFL2+API
> >> >> >
> >> >> >  Cheers
> >> >> > Menaka
> >> >> >
> >> >> > On 27 June 2015 at 22:46, Gale Naylor <galen@noventussolutions.com
> >
> >> >> wrote:
> >> >> >
> >> >> >> Hi Menaka,
> >> >> >>
> >> >> >> > According to the documentations provided, SCUFL is an
> experimental
> >> >> >> module.
> >> >> >> > So It has not added to the tool yet.
> >> >> >>
> >> >> >> Okay, I see now. That makes sense. FYI, because I am a visual
> person,
> >> >> >> I took the Taverna
> >> >> >> Language Module information and created a diagram:
> >> >> >>
> >> >> >>
> >> >>
> >>
> https://galenaylor.wordpress.com/2015/06/27/apache-taverna-language-modules-diagram/
> >> >> >>
> >> >> >> > The taverna language is capable of converting .t2flow workflows
> >> into
> >> >> >> > .wfbundle and other formats, and .wfbundles into formats except
> >> >> .t2flow.
> >> >> >>
> >> >> >> So, .wfbundles can be converted to .json and .iwir formats as
> well as
> >> >> >> .structure?
> >> >> >> If so, I will update my table.
> >> >> >>
> >> >> >> > (.t2flow is the format of Taverna 2 and .wfbundle is the format
> of
> >> >> >> Taverna
> >> >> >> > 3)
> >> >> >>
> >> >> >> Is it true that .wfbundle is the *bundle* format of Taverna 3
> >> >> >> (taverna-sculf2-wfbundle)
> >> >> >> and scufl2 is the *workflow* format of Taverna 3
> >> (taverna-scufl2-api)?
> >> >> >>
> >> >> >> > Input file type detection was done to avoid any exceptions when
> >> >> reading
> >> >> >> the
> >> >> >> > wokflow file. ...
> >> >> >> > In new_features2, I removed it because I have entered the wrong
> >> >> logic. I
> >> >> >> > restored it.
> >> >> >>
> >> >> >> Okay, understood.
> >> >> >>
> >> >> >> Thank you!
> >> >> >>
> >> >> >> Gale
> >> >> >>
> >> >> >> On Fri, Jun 26, 2015 at 1:48 PM, Menaka Madushanka
> >> >> >> <menaka12350@gmail.com> wrote:
> >> >> >> > Hi Gale,
> >> >> >> > According to the documentations provided, SCUFL is an
> experimental
> >> >> >> module.
> >> >> >> > So It has not added to the tool yet.
> >> >> >> >
> >> >> >> > I presumed that.scufl2 workflows could be converted to the same
> >> >> >> >> formats as .t2flow workflows, but if that's not correct, let me
> >> know
> >> >> >> >> and I'll fix it.
> >> >> >> >
> >> >> >> > The taverna language is capable of converting .t2flow workflows
> >> into
> >> >> >> > .wfbundle and other formats, and .wfbundles into formats except
> >> >> .t2flow.
> >> >> >> > (.t2flow is the format of Taverna 2 and .wfbundle is the format
> of
> >> >> >> Taverna
> >> >> >> > 3)
> >> >> >> >
> >> >> >> > Also, I was wondering about something you said in one of your
> June
> >> >> >> >> 25th emails ([GitHub] incubator-taverna-language pull request:
> New
> >> >> >> >> features2).
> >> >> >> >> You said "File type detection removed."
> >> >> >> >>
> >> >> >> >> Which file type detection is this? Is this related to Stain's
> June
> >> >> 4th
> >> >> >> >> email, in which he said the input format is auto-guessed by
> >> >> >> >> WorkflowBundleIO? Just wondering, because in my blog I included
> >> this
> >> >> >> >> comment and I wanted to make sure it is still accurate.
> >> >> >> >
> >> >> >> >
> >> >> >> > Input file type detection was done to avoid any exceptions when
> >> >> reading
> >> >> >> the
> >> >> >> > wokflow file. The WorkflowBundleIO can guess the media type and
> >> read
> >> >> the
> >> >> >> > bundle but, the input format could be wrongly entered by the
> user.
> >> We
> >> >> >> can't
> >> >> >> > promise that the user could always do the correct thing. Also in
> >> >> >> recursive
> >> >> >> > conversion, there could be other files also.
> >> >> >> >
> >> >> >> > In new_features2, I removed it because I have entered the wrong
> >> >> logic. I
> >> >> >> > restored it.
> >> >> >> >
> >> >> >> > Thank you
> >> >> >> > Menaka
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> > On 27 June 2015 at 01:54, Gale Naylor <
> galen@noventussolutions.com
> >> >
> >> >> >> wrote:
> >> >> >> >
> >> >> >> >> Hi Menaka,
> >> >> >> >>
> >> >> >> >> A couple more things.
> >> >> >> >>
> >> >> >> >> I am trying to organize my understanding of how the conversions
> >> work,
> >> >> >> >> so I wrote a new blog post with a conversion table:
> >> >> >> >>
> >> >> >> >>
> >> >> >>
> >> >>
> >>
> https://galenaylor.wordpress.com/2015/06/26/apache-taverna-language-command-line-conversion-file-type-mapping/
> >> >> >> >>
> >> >> >> >> I presumed that.scufl2 workflows could be converted to the same
> >> >> >> >> formats as .t2flow workflows, but if that's not correct, let me
> >> know
> >> >> >> >> and I'll fix it. Should .scufl (Taverna 1) formats also be
> listed?
> >> >> The
> >> >> >> >> table is my best guess from reading all of the emails, so
> please
> >> let
> >> >> >> >> me know if anything is wrong, or if I missed something.
> >> >> >> >>
> >> >> >> >> Also, I was wondering about something you said in one of your
> June
> >> >> >> >> 25th emails ([GitHub] incubator-taverna-language pull request:
> New
> >> >> >> >> features2).
> >> >> >> >> You said "File type detection removed."
> >> >> >> >>
> >> >> >> >> Which file type detection is this? Is this related to Stain's
> June
> >> >> 4th
> >> >> >> >> email, in which he said the input format is auto-guessed by
> >> >> >> >> WorkflowBundleIO? Just wondering, because in my blog I included
> >> this
> >> >> >> >> comment and I wanted to make sure it is still accurate.
> >> >> >> >>
> >> >> >> >> Thanks!
> >> >> >> >>
> >> >> >> >> Gale
> >> >> >> >>
> >> >> >> >> On Fri, Jun 26, 2015 at 11:55 AM, Menaka Madushanka
> >> >> >> >> <menaka12350@gmail.com> wrote:
> >> >> >> >> > Have a nice weekend too.....!!! :-)
> >> >> >> >> >
> >> >> >> >> > On 27 June 2015 at 00:24, Menaka Madushanka <
> >> menaka12350@gmail.com
> >> >> >
> >> >> >> >> wrote:
> >> >> >> >> >
> >> >> >> >> >> Hi Gale,
> >> >> >> >> >> I'm really appreciate your feedback on my blogs. I'm very
> new
> >> and
> >> >> >> there
> >> >> >> >> >> could be some flows. Thank you very much for showing them.
> :-)
> >> >> >> >> >>
> >> >> >> >> >> 1) Yes, the types of bundle formats that can be converted
> are
> >> >> listed
> >> >> >> in
> >> >> >> >> >> this blog.
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >>
> >> >> >>
> >> >>
> >>
> https://menakamadushanka.wordpress.com/2015/06/20/taverna-language-command-line-tool-conversion-documentation-research-objects/
> >> >> >> >> >> The bundles are not workflows.
> >> >> >> >> >>
> >> >> >> >> >> 2) No. It seems like the way I have wrote it somewhat
> >> >> misleading.....
> >> >> >> >> >> Actually scufl2 workflows are not Bundles. Those are two
> >> different
> >> >> >> APIs.
> >> >> >> >> >> I'll update the blog. :-)
> >> >> >> >> >>
> >> >> >> >> >> 3).Yes, my mistake. Neither .t2flow nor wfbundle could be
> >> >> converted
> >> >> >> into
> >> >> >> >> >> robundle.
> >> >> >> >> >>
> >> >> >> >> >> 4). Yes Gale. That modification should be done. Other wise
> it
> >> >> looks
> >> >> >> like
> >> >> >> >> >> any format could be converted into Robundle. I'll update my
> >> blog
> >> >> too.
> >> >> >> >> >>
> >> >> >> >> >> Are there any more facts that need clarification about the
> >> blogs
> >> >> >> please
> >> >> >> >> >> ask me. :)
> >> >> >> >> >>
> >> >> >> >> >> Thank you very much Gale.
> >> >> >> >> >> Menaka
> >> >> >> >> >>
> >> >> >> >> >> On 27 June 2015 at 00:00, Gale Naylor <
> >> >> galen@noventussolutions.com>
> >> >> >> >> wrote:
> >> >> >> >> >>
> >> >> >> >> >>> Hi Menaka,
> >> >> >> >> >>>
> >> >> >> >> >>> I've been reading and learning more about research objects,
> >> and I
> >> >> >> >> >>> think I understand better what is going on, but I still
> have
> >> some
> >> >> >> >> >>> questions.
> >> >> >> >> >>>
> >> >> >> >> >>> 1) I am curious as to which file types *can* be converted
> to
> >> >> >> .robundle
> >> >> >> >> >>> format? (I must have missed something because I thought
> >> .t2flow
> >> >> and
> >> >> >> >> >>> .wfbundle were the only allowed input file types.)
> >> >> >> >> >>>
> >> >> >> >> >>> 2) In rereading your June 18th blog post, I see you say
> that
> >> the
> >> >> >> >> >>> command line tool is for converting and managing workflow
> >> >> "bundles"
> >> >> >> as
> >> >> >> >> >>> well as research object bundles. Are t2flow files "workflow
> >> >> bundles"
> >> >> >> >> >>> or just "workflows?" Or is there not a practical
> difference?
> >> >> >> >> >>>
> >> >> >> >> >>> 3) I understand now that not all file format conversions
> are
> >> >> valid.
> >> >> >> >> >>> I'm trying to understand this better. In your June 18th
> blog
> >> post
> >> >> >> you
> >> >> >> >> >>> say:
> >> >> >> >> >>>
> >> >> >> >> >>> "The conversion function supports converting .t2flow and
> >> >> .wfbundle
> >> >> >> >> >>> formats into following formats:
> >> >> >> >> >>>
> >> >> >> >> >>>     .structure
> >> >> >> >> >>>
> >> >> >> >> >>>     .json
> >> >> >> >> >>>
> >> >> >> >> >>>     .iwir
> >> >> >> >> >>>
> >> >> >> >> >>>     .wfbundle
> >> >> >> >> >>>
> >> >> >> >> >>>     .wfdesc.ttl –> (development in progress)
> >> >> >> >> >>>
> >> >> >> >> >>>     .robundle –> (development in progress)"
> >> >> >> >> >>>
> >> >> >> >> >>> To me, reading this looks like all combinations are valid.
> >> >> >> >> >>>
> >> >> >> >> >>> I'm wondering, can both .t2flow and .wfbundle files be
> >> converted
> >> >> to
> >> >> >> >> >>> all file types *except* robundle?
> >> >> >> >> >>>
> >> >> >> >> >>>
> >> >> >> >> >>> 4) I fixed the examples in my blog post.  Should I also
> change
> >> >> the
> >> >> >> >> >>> --robundle option description to say "Output bundle as
> >> .robundle"
> >> >> >> >> >>> instead of "Output workflow as .robundle" ? (Same for
> >> .wfbundle
> >> >> >> >> >>> option.)
> >> >> >> >> >>>
> >> >> >> >> >>> Thanks for the feedback and the correct link to the
> example!
> >> >> >> >> >>>
> >> >> >> >> >>> Have a nice weekend.
> >> >> >> >> >>>
> >> >> >> >> >>> Gale
> >> >> >> >> >>>
> >> >> >> >> >>>
> >> >> >> >> >>>
> >> >> >> >> >>> On Wed, Jun 24, 2015 at 10:52 PM, Menaka Madushanka
> >> >> >> >> >>> <menaka12350@gmail.com> wrote:
> >> >> >> >> >>> > Hi Gale,
> >> >> >> >> >>> > Use this link
> >> >> >> >> >>> >
> >> >> >> >> >>>
> >> >> >> >>
> >> >> >>
> >> >>
> >>
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-robundle/src/test/java/org/apache/taverna/robundle/TestExample.java
> >> >> >> >> >>> >
> >> >> >> >> >>> > Cheers
> >> >> >> >> >>> > Menaka
> >> >> >> >> >>> >
> >> >> >> >> >>> > On 25 June 2015 at 05:34, Gale Naylor <
> >> >> >> galen@noventussolutions.com>
> >> >> >> >> >>> wrote:
> >> >> >> >> >>> >
> >> >> >> >> >>> >> Hi Menaka,
> >> >> >> >> >>> >>
> >> >> >> >> >>> >> Thank you for the feedback and clarifying information.
> >> Sorry
> >> >> not
> >> >> >> to
> >> >> >> >> >>> respond
> >> >> >> >> >>> >> sooner. I am learning about bundles, etc. and reading
> the
> >> link
> >> >> >> you
> >> >> >> >> >>> sent.
> >> >> >> >> >>> >>
> >> >> >> >> >>> >> One thing, I'm having trouble getting to the example in
> the
> >> >> >> Examples
> >> >> >> >> >>> of Use
> >> >> >> >> >>> >> Section: "Example in full is at
> >> >> >> >> >>> org.apache.taverna.robundle.TestExample"
> >> >> >> >> >>> >>
> >> >> >> >> >>> >> Can you help me? This is what I've done so far:
> >> >> >> >> >>> >>
> >> >> >> >> >>> >> - Clicking on the link gets me the "This is not the web
> >> page
> >> >> you
> >> >> >> are
> >> >> >> >> >>> >> looking
> >> >> >> >> >>> >> for" page. (This is the actual link address:
> >> >> >> >> >>> >>
> >> >> >> >> >>> >>
> >> >> >> >> >>>
> >> >> >> >>
> >> >> >>
> >> >>
> >>
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-robundle/src/test/java/org/purl/wf4ever/robundle/TestExample.java
> >> >> >> >> >>> >> )
> >> >> >> >> >>> >>
> >> >> >> >> >>> >> - Entering "org.apache.taverna.robundle.TestExample"
> also
> >> >> doesn't
> >> >> >> >> work
> >> >> >> >> >>> for
> >> >> >> >> >>> >> me. I didn't think it would, but I tried anyway.
> >> >> >> >> >>> >>
> >> >> >> >> >>> >> - Searching for "taverna robundle TestExample" on the
> main
> >> >> >> >> Apache.com
> >> >> >> >> >>> page
> >> >> >> >> >>> >> yields no results.
> >> >> >> >> >>> >>
> >> >> >> >> >>> >> I will continue to read and understand the RO Bundle API
> >> page,
> >> >> >> but I
> >> >> >> >> >>> would
> >> >> >> >> >>> >> like to see the full Test Example, if possible.
> >> >> >> >> >>> >>
> >> >> >> >> >>> >> Thanks!
> >> >> >> >> >>> >>
> >> >> >> >> >>> >> Gale
> >> >> >> >> >>> >>
> >> >> >> >> >>> >>
> >> >> >> >> >>> >> -----Original Message-----
> >> >> >> >> >>> >> From: Menaka Madushanka [mailto:menaka12350@gmail.com]
> >> >> >> >> >>> >> Sent: Saturday, June 20, 2015 11:09 AM
> >> >> >> >> >>> >> To: dev@taverna.incubator.apache.org
> >> >> >> >> >>> >> Subject: Re: Taverna Language Command Line tool -
> convert
> >> >> command
> >> >> >> >> doc
> >> >> >> >> >>> >>
> >> >> >> >> >>> >> That's cool.....!! :-)
> >> >> >> >> >>> >> Correction:
> >> >> >> >> >>> >>
> >> >> >> >> >>> >>
> >> >> >> >> >>>
> >> >> >> >>
> >> >> >>
> >> >>
> >>
> https://galenaylor.wordpress.com/2015/06/19/apache-taverna-language-command-line-convert-examples/
> >> >> >> >> >>> >>
> >> >> >> >> >>> >> > Example 2: Simple conversion, multiple input files, no
> >> >> options
> >> >> >> >> >>> >> >
> >> >> >> >> >>> >> > $tavlang convert –-robundle /someFile1.wfbundle
> >> >> >> >> /someFile2.wfbundle
> >> >> >> >> >>> >> >
> >> >> >> >> >>> >> > Converts */someFile1.wfbundle* and
> */someFile2.wfbundle*
> >> >> into
> >> >> >> >> >>> >> > *.robundle* format and saves the output files to the
> >> >> >> */converted*
> >> >> >> >> >>> >> > folder in the current working directory.
> >> >> >> >> >>> >> >
> >> >> >> >> >>> >> Taverna language *cannot* convert .wfbundles/.t2flow
> into
> >> >> >> robundle
> >> >> >> >> >>> format.
> >> >> >> >> >>> >> Its only for some specific bundle formats. Go through
> this
> >> doc
> >> >> >> for
> >> >> >> >> more
> >> >> >> >> >>> >> info.
> >> >> >> >> >>> >>
> >> >> >> >> >>> >>
> >> >> >> >> >>> >>
> >> >> >> >> >>>
> >> >> >> >>
> >> >> >>
> >> >>
> >>
> https://github.com/apache/incubator-taverna-language/tree/master/taverna-robundle
> >> >> >> >> >>> >>
> >> >> >> >> >>> >> cheers.
> >> >> >> >> >>> >>
> >> >> >> >> >>> >> On 20 June 2015 at 22:43, Gale Naylor <
> >> >> >> galen@noventussolutions.com>
> >> >> >> >> >>> wrote:
> >> >> >> >> >>> >>
> >> >> >> >> >>> >> > Thank you for the Wordpress tip, Menaka! I have
> changed
> >> the
> >> >> two
> >> >> >> >> blog
> >> >> >> >> >>> >> > posts to use the <pre> tag, and it looks great. I also
> >> made
> >> >> a
> >> >> >> few
> >> >> >> >> >>> >> > refinements.
> >> >> >> >> >>> >> >
> >> >> >> >> >>> >> > Thanks,
> >> >> >> >> >>> >> > Gale
> >> >> >> >> >>> >> >
> >> >> >> >> >>> >> > On Fri, Jun 19, 2015 at 11:54 PM, Menaka Madushanka
> >> >> >> >> >>> >> > <menaka12350@gmail.com> wrote:
> >> >> >> >> >>> >> > > Thank you very much Gale,
> >> >> >> >> >>> >> > >
> >> >> >> >> >>> >> > > I showed the output-format without brackets to
> indicate
> >> >> it is
> >> >> >> >> >>> >> > >> required and not optional because it appears to be
> >> always
> >> >> >> >> >>> necessary
> >> >> >> >> >>> >> > >
> >> >> >> >> >>> >> > >
> >> >> >> >> >>> >> > > That would be more accurate I think. I'm very new
> for
> >> >> >> >> >>> documentation.
> >> >> >> >> >>> >> > Thank
> >> >> >> >> >>> >> > > you very much.
> >> >> >> >> >>> >> > >
> >> >> >> >> >>> >> > >  I left the -json output file type as having a
> single
> >> >> dash,
> >> >> >> but
> >> >> >> >> all
> >> >> >> >> >>> >> > >> the other output types have double-dashes. Should I
> >> >> change
> >> >> >> the
> >> >> >> >> >>> json
> >> >> >> >> >>> >> > >> output argument to --json?
> >> >> >> >> >>> >> > >>
> >> >> >> >> >>> >> > > -json should be --json. In my email that was a
> >> mistake. So
> >> >> >> you
> >> >> >> >> can
> >> >> >> >> >>> >> > > use
> >> >> >> >> >>> >> > --.
> >> >> >> >> >>> >> > >
> >> >> >> >> >>> >> > > (Wordpress is driving me crazy because it is showing
> >> the
> >> >> >> >> >>> >> > > double-dashes
> >> >> >> >> >>> >> > >> as long single dashes, even when I use the
> monospace
> >> >> >> >> font-family.
> >> >> >> >> >>> >> > >> Any
> >> >> >> >> >>> >> > >> suggestions?)
> >> >> >> >> >>> >> > >>
> >> >> >> >> >>> >> > >
> >> >> >> >> >>> >> > > Yes, wordpress does what it wants, but not us. :-)
> Use
> >> >> >> >> >>> preformatted.
> >> >> >> >> >>> >> > > Not paragraph. Then it would be ok. I updated my
> blog.
> >> >> >> >> >>> >> > >
> >> >> >> >> >>> >> >
> >> >> >> >> >>>
> >> >> >>
> >> https://menakamadushanka.wordpress.com/2015/06/18/apache-taverna-langu
> >> >> >> >> >>> >> > age-command-line-conversion-documentation/
> >> >> >> >> >>> >> > >
> >> >> >> >> >>> >> > > Thank you very much.
> >> >> >> >> >>> >> > > Menaka
> >> >> >> >> >>> >> > >
> >> >> >> >> >>> >> > > I'll go through your documentations.
> >> >> >> >> >>> >> > >
> >> >> >> >> >>> >> > >
> >> >> >> >> >>> >> > > On 20 June 2015 at 03:43, Gale Naylor <
> >> >> >> >> galen@noventussolutions.com
> >> >> >> >> >>> >
> >> >> >> >> >>> >> > wrote:
> >> >> >> >> >>> >> > >
> >> >> >> >> >>> >> > >> Hi Menaka,
> >> >> >> >> >>> >> > >>
> >> >> >> >> >>> >> > >> Thanks for updating your blog! I have some
> additional
> >> >> >> feedback
> >> >> >> >> in
> >> >> >> >> >>> >> > >> the form of two blog posts. One has a detailed
> >> >> description
> >> >> >> (as
> >> >> >> >> I
> >> >> >> >> >>> >> > >> understand it) of the convert command and one has
> >> several
> >> >> >> >> >>> examples,
> >> >> >> >> >>> >> > >> building on the examples in your blog. I hope these
> >> will
> >> >> >> help
> >> >> >> >> the
> >> >> >> >> >>> >> > >> discussion of the command structure. Here are the
> >> links:
> >> >> >> >> >>> >> > >>
> >> >> >> >> >>> >> > >>
> >> >> >> >> >>> >> > >>
> >> >> >> >> >>> >> >
> >> >> >> >> >>>
> >> >> >>
> >> https://galenaylor.wordpress.com/2015/06/19/apache-taverna-language-co
> >> >> >> >> >>> >> > mmand-line-convert-command/
> >> >> >> >> >>> >> > >>
> >> >> >> >> >>> >> > >>
> >> >> >> >> >>> >> > >>
> >> >> >> >> >>> >> >
> >> >> >> >> >>>
> >> >> >>
> >> https://galenaylor.wordpress.com/2015/06/19/apache-taverna-language-co
> >> >> >> >> >>> >> > mmand-line-convert-examples/
> >> >> >> >> >>> >> > >>
> >> >> >> >> >>> >> > >> Some things to note:
> >> >> >> >> >>> >> > >>
> >> >> >> >> >>> >> > >> (1) l basically used your June 18th post, but a few
> >> >> things
> >> >> >> >> (like
> >> >> >> >> >>> >> > >> the validate command) are from earlier
> posts/emails.
> >> >> >> >> >>> >> > >>
> >> >> >> >> >>> >> > >> (2) I showed the output-format without brackets to
> >> >> indicate
> >> >> >> it
> >> >> >> >> is
> >> >> >> >> >>> >> > >> required and not optional because it appears to be
> >> always
> >> >> >> >> >>> necessary.
> >> >> >> >> >>> >> > >>
> >> >> >> >> >>> >> > >> (3) The way I understand the overall command
> >> structure,
> >> >> it
> >> >> >> >> seemed
> >> >> >> >> >>> >> > >> that all options (e.g., the output file directory)
> >> should
> >> >> >> come
> >> >> >> >> >>> >> > >> before the input-file-list, so that's what I
> assumed.
> >> >> >> >> >>> >> > >>
> >> >> >> >> >>> >> > >> (4) I left the -json output file type as having a
> >> single
> >> >> >> dash,
> >> >> >> >> but
> >> >> >> >> >>> >> > >> all the other output types have double-dashes.
> Should
> >> I
> >> >> >> change
> >> >> >> >> the
> >> >> >> >> >>> >> > >> json output argument to --json?
> >> >> >> >> >>> >> > >>
> >> >> >> >> >>> >> > >> Please let me know if anything is incorrect and I
> will
> >> >> >> change
> >> >> >> >> it.
> >> >> >> >> >>> I
> >> >> >> >> >>> >> > >> realize the command structure is fluid, and I'm
> happy
> >> to
> >> >> >> make
> >> >> >> >> any
> >> >> >> >> >>> >> > >> changes as things evolve.
> >> >> >> >> >>> >> > >>
> >> >> >> >> >>> >> > >> (Wordpress is driving me crazy because it is
> showing
> >> the
> >> >> >> >> >>> >> > >> double-dashes as long single dashes, even when I
> use
> >> the
> >> >> >> >> monospace
> >> >> >> >> >>> >> > >> font-family. Any
> >> >> >> >> >>> >> > >> suggestions?)
> >> >> >> >> >>> >> > >>
> >> >> >> >> >>> >> > >> Thanks,
> >> >> >> >> >>> >> > >>
> >> >> >> >> >>> >> > >> Gale
> >> >> >> >> >>> >> > >>
> >> >> >> >> >>> >> > >> On Fri, Jun 19, 2015 at 10:11 AM, Menaka Madushanka
> >> >> >> >> >>> >> > >> <menaka12350@gmail.com> wrote:
> >> >> >> >> >>> >> > >> > Hi Gale,
> >> >> >> >> >>> >> > >> >
> >> >> >> >> >>> >> > >> > Thank you very much.
> >> >> >> >> >>> >> > >> >
> >> >> >> >> >>> >> > >> > . Can you help me
> >> >> >> >> >>> >> > >> >> understand what you mean when you say the files
> >> will
> >> >> get
> >> >> >> >> saved
> >> >> >> >> >>> >> > >> >> to the C directory?
> >> >> >> >> >>> >> > >> >
> >> >> >> >> >>> >> > >> > That was a mistake :-). I updated the blog. That
> >> >> should be
> >> >> >> >> >>> >> > >> > corrected
> >> >> >> >> >>> >> > as
> >> >> >> >> >>> >> > >> > *$tavlang convert –json -r -i
> >> >> /home/usrname/toConvert/  –>
> >> >> >> >> >>> >> > >> > *Convert
> >> >> >> >> >>> >> > the
> >> >> >> >> >>> >> > >> > files and save them in the …/toConvert/converted/
> >> >> >> directory.
> >> >> >> >> >>> >> > >> >
> >> >> >> >> >>> >> > >> > I would appreciate more feedback, modifications
> >> etc. So
> >> >> >> with
> >> >> >> >> the
> >> >> >> >> >>> >> > >> > help
> >> >> >> >> >>> >> > of
> >> >> >> >> >>> >> > >> > the community we could come up with a much better
> >> >> >> structure.
> >> >> >> >> >>> >> > >> > Cheers
> >> >> >> >> >>> >> > >> > Menaka
> >> >> >> >> >>> >> > >> >
> >> >> >> >> >>> >> > >> > On 19 June 2015 at 22:32, Gale Naylor
> >> >> >> >> >>> >> > >> > <galen@noventussolutions.com>
> >> >> >> >> >>> >> > >> wrote:
> >> >> >> >> >>> >> > >> >
> >> >> >> >> >>> >> > >> >> Hi Menaka,
> >> >> >> >> >>> >> > >> >>
> >> >> >> >> >>> >> > >> >> I am very happy to help, and I understand the
> >> command
> >> >> >> >> structure
> >> >> >> >> >>> >> > >> >> is a little fluid right now. Thank you for the
> blog
> >> >> >> post; it
> >> >> >> >> >>> was
> >> >> >> >> >>> >> > >> >> very helpful.
> >> >> >> >> >>> >> > >> >>
> >> >> >> >> >>> >> > >> >> I am a little confused about your recursive
> >> example.
> >> >> Can
> >> >> >> you
> >> >> >> >> >>> >> > >> >> help me understand what you mean when you say
> the
> >> >> files
> >> >> >> will
> >> >> >> >> >>> get
> >> >> >> >> >>> >> > >> >> saved to the C directory? Because you show the
> >> output
> >> >> >> being
> >> >> >> >> >>> saved
> >> >> >> >> >>> >> > >> >> to:
> >> >> >> >> >>> >> > >> >> /home/usrname/toConvert/converted/somefile1.json
> >> >> >> >> >>> >> > >> >>
> >> >> >> >> >>> >> > >> >> This is the example:
> >> >> >> >> >>> >> > >> >> $tavlang convert –json -r -i
> >> >> /home/usrname/toConvert/  –>
> >> >> >> >> >>> >> > >> >> Convert the files and save them in the C
> directory.
> >> >> >> >> >>> >> > >> >>
> >> >> >> >> >>> >> > >> >> Thank you!
> >> >> >> >> >>> >> > >> >>
> >> >> >> >> >>> >> > >> >> Gale
> >> >> >> >> >>> >> > >> >>
> >> >> >> >> >>> >> > >> >> B
> >> >> >> >> >>> >> > >> >>
> >> >> >> >> >>> >> > >> >> On Fri, Jun 19, 2015 at 2:15 AM, Menaka
> Madushanka
> >> >> >> >> >>> >> > >> >> <menaka12350@gmail.com> wrote:
> >> >> >> >> >>> >> > >> >> > Hi Gale,
> >> >> >> >> >>> >> > >> >> > I extremely appreciate your help. Thank you
> very
> >> >> much.
> >> >> >> :-)
> >> >> >> >> >>> >> > >> >> >
> >> >> >> >> >>> >> > >> >> > 1) Is this still the basic structure of the
> >> command:
> >> >> >> >> tavlang
> >> >> >> >> >>> >> > convert
> >> >> >> >> >>> >> > >> >> >> [options] <output format> <input files>? Am I
> >> >> wrong in
> >> >> >> >> >>> >> > >> >> >> thinking
> >> >> >> >> >>> >> > that
> >> >> >> >> >>> >> > >> the
> >> >> >> >> >>> >> > >> >> >> output formats are handled as options?
> >> >> >> >> >>> >> > >> >> >
> >> >> >> >> >>> >> > >> >> >
> >> >> >> >> >>> >> > >> >> > Yes there is a little difference in the
> >> structure of
> >> >> >> >> commands
> >> >> >> >> >>> >> > >> >> > now
> >> >> >> >> >>> >> > and
> >> >> >> >> >>> >> > >> >> then.
> >> >> >> >> >>> >> > >> >> > So for the moment the command structure is
> like
> >> >> this.
> >> >> >> >> >>> >> > >> >> >
> >> >> >> >> >>> >> > >> >> > $tavlang convert [--out-put format] [options]
> >> >> >> [arguments]
> >> >> >> >> >>> >> > >> >> >
> >> >> >> >> >>> >> > >> >> >
> >> >> >> >> >>> >> > >> >> > 2) Are -r and -i ever used independently? If
> so,
> >> >> under
> >> >> >> >> what
> >> >> >> >> >>> >> > >> >> circumstances?
> >> >> >> >> >>> >> > >> >> >
> >> >> >> >> >>> >> > >> >> > No. In recursive case the input will be a
> >> directory
> >> >> >> >> >>> containing
> >> >> >> >> >>> >> > >> .t2flow of
> >> >> >> >> >>> >> > >> >> > .wfbundle files. The output dir is optional
> for
> >> both
> >> >> >> >> >>> recursive
> >> >> >> >> >>> >> > >> >> > and
> >> >> >> >> >>> >> > non
> >> >> >> >> >>> >> > >> >> > recursive cases.
> >> >> >> >> >>> >> > >> >> >
> >> >> >> >> >>> >> > >> >> > I created a blog about the conversion command.
> >> >> >> >> >>> >> > >> >> >
> >> >> >> >> >>> >> > >> >>
> >> >> >> >> >>> >> > >>
> >> >> >> >> >>> >> >
> >> >> >> >> >>>
> >> >> >>
> >> https://menakamadushanka.wordpress.com/2015/06/18/apache-taverna-langu
> >> >> >> >> >>> >> > age-command-line-conversion-documentation/
> >> >> >> >> >>> >> > >> >> >
> >> >> >> >> >>> >> > >> >> > If you have some suggestions, please inform.
> >> >> >> >> >>> >> > >> >> >
> >> >> >> >> >>> >> > >> >> > Thank you very much!
> >> >> >> >> >>> >> > >> >> >
> >> >> >> >> >>> >> > >> >> > Regards
> >> >> >> >> >>> >> > >> >> > Menaka
> >> >> >> >> >>> >> > >> >> >
> >> >> >> >> >>> >> > >> >> > --
> >> >> >> >> >>> >> > >> >> > 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>
> >> >> >> >> >>> >> > >>
> >> >> >> >> >>> >> > >
> >> >> >> >> >>> >> > >
> >> >> >> >> >>> >> > >
> >> >> >> >> >>> >> > > --
> >> >> >> >> >>> >> > > 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>
> >> >> >> >> >>> >>
> >> >> >> >> >>> >
> >> >> >> >> >>> >
> >> >> >> >> >>> >
> >> >> >> >> >>> > --
> >> >> >> >> >>> > 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>
> >> >> >> >> >>
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> > --
> >> >> >> >> > 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>
> >> >> >>
> >> >> >
> >> >> >
> >> >> >
> >> >> > --
> >> >> > 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>
> >>
> >
> >
> >
> > --
> > 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>

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