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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 15:23:50 GMT
Hi Menaka,

I'm so glad I could help. You've done a nice job on your blog posts.
If you don't mind, I can suggest some slight wording changes that I
believe will make your meanings more clear. For example:

Apache Taverna Language Command Line Tool – Supported functions and file types
        Paragraph 1
          --  Capitalize Taverna and Language: "The Apache Taverna
Language is still …"
          --  Use "Currently" instead of "By now": "Currently the tool
supports…"
        Paragraph 2
          --  Add "The" to the beginning of the sentence: "The
following file types are supported..."
          -- I noticed you use .scufl2 in this blogpost, but .t2flow
in the next blogpost.

Please let me know if this kind of feedback would be helpful.

Thanks,

Gale

On Tue, Jun 30, 2015 at 7:43 AM, Menaka Madushanka
<menaka12350@gmail.com> wrote:
> 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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