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From Gale Naylor <ga...@noventussolutions.com>
Subject Re: Taverna Language Command Line tool - convert command doc
Date Tue, 30 Jun 2015 14:39:32 GMT
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 I did notice the mygrid pages said the information was out of date.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 I did notice the mygrid pages said the information was out of date.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>

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