Re: Taverna Language Command Line tool - convert command doc

[Gale Naylor <ga...@noventussolutions.com>]

Hi Menaka,

I read your stats blog post; it looks good.  I am not very familiar
with workflows, so I'm not sure I can comment a lot on your examples,
but I did list some things that appeared to me to be inconsistent.

Also, I think it would be good to make at least a couple of different
sections and identify them with a larger, bold font, like you did in
the Convert command blog post. In the taverna-sculf2-api Readme file
(on github), they show "Usage" as a section:
https://github.com/apache/incubator-taverna-language/tree/master/taverna-scufl2-api.
That might be a good idea. Then, if you use a smaller (but still bold)
font for the Verbose Mode sub-section and Normal Mode sub-section,
that will help the reader navigate your documentation. You could then
take out the second instance of "Verbose Mode" (between the two
verbose examples) like you did in the Normal Mode examples. Then, I
would also create a third sub-section called "Save Results to a Log
File" and below that put your example. The formatting you used in your
Convert command blog post worked well.

A few other things:

Apache Taverna Language Command line tool – Workflow Statistics

    -- Capitalize the first "API," hyphenate "scufl2-api" to match the
module name, and write "whatever" as one word: "The Taverna Language
API (sculf2-api) has several methods to set and retrieve those
resources whenever needed."
    -- Instead of " The command line tool is capable of listing those
resources which a workflow file has." How about "The command line tool
is also capable of listing workflow file resources."
    -- In the options section, you say "Save results in a log file"
(using "in") and in your example you say "Save results to a log file"
(using "to"). You might consider making those consistent.
    -- In your verbose Hello World example, near the end did you mean
to say " | |--> Input Ports" after "|--> Number of Output Ports = 1,"
rather than "Output Ports"?
    -- In your verbose Workflow1 example, in your Data Links section,
you say " |--> DataLink parameters=>input" and then " |--> DataLink
output=>parameters." Should these statements both be formatted the
same and match the last item? Specifically, should they all end in
"==>input"?  Or is there a reason for them to be different?

That's all I can see!

Gale

On Tue, Jun 30, 2015 at 2:03 PM, Menaka Madushanka
<me...@gmail.com> wrote:
> Hello Gale,
> Great feed back. :-)
> I did the modifications and now it looks great and clean....
>
> In statistics blog I did not add explanations much but examples. So that it
> will be easy for you. :-)
> Thank you very much for the great help you are giving me.....!!!
> Please let me know if there anything that I could do and/ or need some
> clarifications.
>
> Thank you very much
> Menaka
>
> On 1 July 2015 at 01:54, Gale Naylor <ga...@noventussolutions.com> wrote:
>
>> Hi Menaka,
>>
>> The changes look great! But I missed one: You should add a "The" in
>> front of the inspection, validation, and statistics sentence, so it
>> reads: "The following file types are supported for inspection,
>> validation and statistics." (with a period at the end.) :-)
>>
>> I will take a look at your statistics blog post. Meanwhile, below are
>> some comments for the Conversion Documentation blog post. Of course,
>> let me know if I misunderstood anything you are trying to say.
>>
>> Apache Taverna Language Command line - Conversion Documentation
>>
>>         Paragraph 1
>>           --  Use "provides" instead of "gives" and "converting and
>> managing" instead of "convert and manage": "The Apache Taverna
>> Language provides a set of APIs for converting and managing workflow
>> bundles and Research Object bundles."
>>
>> Paragraph 3
>>           -- Add "are:": "The basic functionalities of the tool are:"
>>
>> In the Conversion section
>>           --  Use "also has" instead of "is also have": "The tool also
>> has the capability of converting bundles of several formats into
>> Research Object bundles."
>>           --  Use "Refer to" instead of "Refer": " Refer to the
>> following blog for more information about converting bundle formats."
>>
>> In the Example usage section
>>           --  Use "The user" instead of "User": "The user can specify
>> the way that the conversion should be done."
>>
>> In the Recursive conversion section
>>           --  Use "the tool" and "the specified output format": " In
>> recursive conversion mode, the tool can convert .t2flow or .wfbundle
>> files in the given directory into the specified output format."
>>           -- I think you may have a typographical error: "out put"
>> instead of "output" -- it should be "The output will be...
>> /home/username/ ..."
>>
>> In the Non-recursive conversion section
>>           --  Use "The user" instead of "User" and "need" instead of
>> "needed": "The user can use this mode to convert a specific workflow
>> into the format they need." (Or, even better would be to say, "The
>> user can use this mode to convert a specific work flow into the
>> required format."
>>           --  Instead of "Here all the files that want to be converted
>> must specify separately as space separated values." I think it would
>> be better to say: "All files to be converted must be listed as
>> space-separated values."
>>           -- The sentence that describes where files will be saved if
>> there is no specified output directory is a difficult one to write. I
>> had to think about it. Rather than saying "The converted files will be
>> saved in converted folder in each parent folder which contain the
>> input file." What if you said "The converted files will be saved in
>> the /converted folder in the input file's parent directory."? (And use
>> the "/" in front of converted to stress that it is a folder name?)
>>           -- You need a comma after "Also." And use "are to be saved"
>> instead of "to be saved": "Also, users can specify the directory where
>> the converted files are to be saved."
>>           -- In your footnote, "out put" should be one word: "output":
>> "*The tool can only manage one output file format at a time."
>>
>> Happy documenting!
>>
>> Gale
>>
>> On Tue, Jun 30, 2015 at 8:52 AM, Menaka Madushanka
>> <me...@gmail.com> wrote:
>> > Thank you very much Gale.
>> > I did the modifications. :-)
>> > Actually, unless you give me this feedback, it would mislead the readers.
>> > I'm very grateful for correcting me. :-)
>> >
>> > I just wrote the documentation for statistics.
>> >
>> https://menakamadushanka.wordpress.com/2015/06/30/apache-taverna-language-command-line-tool-workflow-statistics/
>> >
>> > Cheers
>> > Menaka
>> >
>> > On 30 June 2015 at 20:53, Gale Naylor <ga...@noventussolutions.com>
>> wrote:
>> >
>> >> 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
>> >> <me...@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 <ga...@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
>> >> >> <me...@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
>> >> >> >> <me...@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
>> >> >> >> >> <me...@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
>> >> >> >> >> >> <me...@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
>> >> >> >> >> >> >> <me...@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
>> >> >> >> >> >> >> >>> <me...@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
>> >> >> >> >> >> >> >>> >> > <me...@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
>> >> >> >> >> >> >> >>> >> > >> <me...@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
>> >> >> >> >> >> >> >>> >> > >> > <ga...@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
>> >> >> >> >> >> >> >>> >> > >> >> <me...@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>
>> >>
>> >>
>> >
>> >
>> > --
>> > Menaka Madushanka Jayawardena
>> > Faculty of Engineering, <http://www.pdn.ac.lk/eng>
>> > University of Peradeniyaya.
>> > LinkedIn <http://lk.linkedin.com/in/menakajayawardena>
>>
>>
>
>
> --
> Menaka Madushanka Jayawardena
> Faculty of Engineering, <http://www.pdn.ac.lk/eng>
> University of Peradeniyaya.
> LinkedIn <http://lk.linkedin.com/in/menakajayawardena>

Re: Taverna Language Command Line tool - convert command doc

[Gale Naylor <ga...@noventussolutions.com>]

Hello Menaka,

I'm glad I was able to help! You are very welcome.

Gale
On Jul 1, 2015 11:24 PM, "Menaka Madushanka" <me...@gmail.com> wrote:

> Hello Gale,
> I really appreciate your grate support.
> I learnt a lot from you. Also I edited my blogs.
> These are not for any submission but to track the progress and for future
> use (completing the full documentation).
> But I noticed there were so many errors as I'm new to documentation and
> blogging. :-)
> However by now I was able to correct those errors with your kind support.
> Thank you very much Gale. :-)
> I hope that I could write the final documentation more successfully with
> the support that you have given me....
>
> Thank you very much for the effort, time and every thing that you spent for
> me.....
> Have a very nice vacation. :-)
>
> Cheers
> Menaka Madushanka
>
> On 1 July 2015 at 07:25, Gale Naylor <ga...@noventussolutions.com> wrote:
>
> > Hi Menaka,
> >
> > You are doing an excellent job on the documentation. I'm sorry for
> > bombarding you with feedback, but I wanted to help as much as possible
> > before I go on vacation.
> >
> > As I was reviewing your blog posts, I noticed that not all of the
> > words in the titles are capitalized as they should be.
> >
> > Also, is your initial post part of your deliverable documentation, or
> > has it been replaced by your later blog posts?
> >
> > Just a couple of things in the research object post:
> >
> > Taverna Language Command line tool – Conversion Documentation – Research
> > objects
> >
> >     -- Use "the" in front of "following bundle formats" and use "into"
> > instead of "in to": "The Apache Taverna Language is capable of
> > converting the following bundle formats into Research Object bundles."
> >     -- Use "development: instead of "development process": "The
> > conversion capability for other formats is still in development."
> >     -- Use "is" instead of "in": "***The support for recursive
> > conversion or selecting the output file directory is not yet
> > included."
> >
> > Thanks!
> >
> > Gale
> >
> >
> > On Tue, Jun 30, 2015 at 6:08 PM, Gale Naylor
> > <ga...@noventussolutions.com> wrote:
> > > Hi Menaka,
> > >
> > > I looked at your validation documentation and I realized I have a
> > > question: If the validate command is run with no options, what
> > > happens? In other words, if you choose not to write the validation
> > > results to a log file, what does the command do? Write the results to
> > > the terminal? Does this need to be explained. (I guess I have the same
> > > question about the stats command.)
> > >
> > > Same comment as with stats documentation about adding sections with
> > > larger, and bold fonts to help with readability.
> > >
> > > Here are some additional comments:
> > >
> > > Apache Taverna Language Command line documentation – Validation
> > >
> > >     -- Use "examining" rather than "examine": "The validation is done
> > > by examining the following factors/ problems."
> > >     -- Use API instead of api, and use "consisting" instead of
> > > "consist: "The API returns a validation report consisting of problems
> > > that exist in the workflow."
> > >     -- Instead of "type of the problem" use either "problem category"
> > > or "category of problem" and I suggest using "listed" instead of the
> > > first "shown": "If there are problems, those problems are listed under
> > > the problem category shown above."
> > >     -- After "The command line tool can execute this validation
> > > process" how about saying " and tell the user if the workflow has
> > > errors/ problems and what they are." So the complete sentence would
> > > be: "The command line tool can execute this validation process and
> > > tell the user if the workflow has errors/ problems and what they are."
> > >     -- Even though you only have one option, I would still put the
> > > option on the next line, like you did in the Stats documentation.
> > >     -- Also, if it's possible it would be good to standardize the
> > > documentation to say either "Supported options" or "Options." You can
> > > use option(s) -- with the "s" in parentheses -- to mean it could be
> > > one option or more than one option.
> > >     -- In the Usage section, you use [args]: "$tavlang validate
> > > [options][args] input_files." In the convert and research objects
> > > posts you use [arguments], and in stats you didn't list arguments at
> > > all, yet it looks to me like the command structure is similar. It
> > > would be good to be consistent and use either [args] or [arguments].
> > >     -- In the stats post you say "Supported file formats: .t2flow and
> > > .wfbundle" using "and" and in the validate post you say "Supported
> > > input file formats:- .t2flow/ .wfbundle" using "/". Would it be
> > > possible to make these the same?
> > >     -- At the end of your "example with options", how about this
> > > instead: "The output file contains the detailed report, including a
> > > list of the workflow problems."
> > >
> > > Good job on all the documentation!
> > >
> > > Gale
> > >
> > > On Tue, Jun 30, 2015 at 5:25 PM, Gale Naylor
> > > <ga...@noventussolutions.com> wrote:
> > >> Hi Menaka,
> > >>
> > >> I read your stats blog post; it looks good.  I am not very familiar
> > >> with workflows, so I'm not sure I can comment a lot on your examples,
> > >> but I did list some things that appeared to me to be inconsistent.
> > >>
> > >> Also, I think it would be good to make at least a couple of different
> > >> sections and identify them with a larger, bold font, like you did in
> > >> the Convert command blog post. In the taverna-sculf2-api Readme file
> > >> (on github), they show "Usage" as a section:
> > >>
> >
> https://github.com/apache/incubator-taverna-language/tree/master/taverna-scufl2-api
> > .
> > >> That might be a good idea. Then, if you use a smaller (but still bold)
> > >> font for the Verbose Mode sub-section and Normal Mode sub-section,
> > >> that will help the reader navigate your documentation. You could then
> > >> take out the second instance of "Verbose Mode" (between the two
> > >> verbose examples) like you did in the Normal Mode examples. Then, I
> > >> would also create a third sub-section called "Save Results to a Log
> > >> File" and below that put your example. The formatting you used in your
> > >> Convert command blog post worked well.
> > >>
> > >> A few other things:
> > >>
> > >> Apache Taverna Language Command line tool – Workflow Statistics
> > >>
> > >>     -- Capitalize the first "API," hyphenate "scufl2-api" to match the
> > >> module name, and write "whatever" as one word: "The Taverna Language
> > >> API (sculf2-api) has several methods to set and retrieve those
> > >> resources whenever needed."
> > >>     -- Instead of " The command line tool is capable of listing those
> > >> resources which a workflow file has." How about "The command line tool
> > >> is also capable of listing workflow file resources."
> > >>     -- In the options section, you say "Save results in a log file"
> > >> (using "in") and in your example you say "Save results to a log file"
> > >> (using "to"). You might consider making those consistent.
> > >>     -- In your verbose Hello World example, near the end did you mean
> > >> to say " | |--> Input Ports" after "|--> Number of Output Ports = 1,"
> > >> rather than "Output Ports"?
> > >>     -- In your verbose Workflow1 example, in your Data Links section,
> > >> you say " |--> DataLink parameters=>input" and then " |--> DataLink
> > >> output=>parameters." Should these statements both be formatted the
> > >> same and match the last item? Specifically, should they all end in
> > >> "==>input"?  Or is there a reason for them to be different?
> > >>
> > >> That's all I can see!
> > >>
> > >> Gale
> > >>
> > >> On Tue, Jun 30, 2015 at 2:03 PM, Menaka Madushanka
> > >> <me...@gmail.com> wrote:
> > >>> Hello Gale,
> > >>> Great feed back. :-)
> > >>> I did the modifications and now it looks great and clean....
> > >>>
> > >>> In statistics blog I did not add explanations much but examples. So
> > that it
> > >>> will be easy for you. :-)
> > >>> Thank you very much for the great help you are giving me.....!!!
> > >>> Please let me know if there anything that I could do and/ or need
> some
> > >>> clarifications.
> > >>>
> > >>> Thank you very much
> > >>> Menaka
> > >>>
> > >>> On 1 July 2015 at 01:54, Gale Naylor <ga...@noventussolutions.com>
> > wrote:
> > >>>
> > >>>> Hi Menaka,
> > >>>>
> > >>>> The changes look great! But I missed one: You should add a "The" in
> > >>>> front of the inspection, validation, and statistics sentence, so it
> > >>>> reads: "The following file types are supported for inspection,
> > >>>> validation and statistics." (with a period at the end.) :-)
> > >>>>
> > >>>> I will take a look at your statistics blog post. Meanwhile, below
> are
> > >>>> some comments for the Conversion Documentation blog post. Of course,
> > >>>> let me know if I misunderstood anything you are trying to say.
> > >>>>
> > >>>> Apache Taverna Language Command line - Conversion Documentation
> > >>>>
> > >>>>         Paragraph 1
> > >>>>           --  Use "provides" instead of "gives" and "converting and
> > >>>> managing" instead of "convert and manage": "The Apache Taverna
> > >>>> Language provides a set of APIs for converting and managing workflow
> > >>>> bundles and Research Object bundles."
> > >>>>
> > >>>> Paragraph 3
> > >>>>           -- Add "are:": "The basic functionalities of the tool
> are:"
> > >>>>
> > >>>> In the Conversion section
> > >>>>           --  Use "also has" instead of "is also have": "The tool
> also
> > >>>> has the capability of converting bundles of several formats into
> > >>>> Research Object bundles."
> > >>>>           --  Use "Refer to" instead of "Refer": " Refer to the
> > >>>> following blog for more information about converting bundle
> formats."
> > >>>>
> > >>>> In the Example usage section
> > >>>>           --  Use "The user" instead of "User": "The user can
> specify
> > >>>> the way that the conversion should be done."
> > >>>>
> > >>>> In the Recursive conversion section
> > >>>>           --  Use "the tool" and "the specified output format": " In
> > >>>> recursive conversion mode, the tool can convert .t2flow or .wfbundle
> > >>>> files in the given directory into the specified output format."
> > >>>>           -- I think you may have a typographical error: "out put"
> > >>>> instead of "output" -- it should be "The output will be...
> > >>>> /home/username/ ..."
> > >>>>
> > >>>> In the Non-recursive conversion section
> > >>>>           --  Use "The user" instead of "User" and "need" instead of
> > >>>> "needed": "The user can use this mode to convert a specific workflow
> > >>>> into the format they need." (Or, even better would be to say, "The
> > >>>> user can use this mode to convert a specific work flow into the
> > >>>> required format."
> > >>>>           --  Instead of "Here all the files that want to be
> converted
> > >>>> must specify separately as space separated values." I think it would
> > >>>> be better to say: "All files to be converted must be listed as
> > >>>> space-separated values."
> > >>>>           -- The sentence that describes where files will be saved
> if
> > >>>> there is no specified output directory is a difficult one to write.
> I
> > >>>> had to think about it. Rather than saying "The converted files will
> be
> > >>>> saved in converted folder in each parent folder which contain the
> > >>>> input file." What if you said "The converted files will be saved in
> > >>>> the /converted folder in the input file's parent directory."? (And
> use
> > >>>> the "/" in front of converted to stress that it is a folder name?)
> > >>>>           -- You need a comma after "Also." And use "are to be
> saved"
> > >>>> instead of "to be saved": "Also, users can specify the directory
> where
> > >>>> the converted files are to be saved."
> > >>>>           -- In your footnote, "out put" should be one word:
> "output":
> > >>>> "*The tool can only manage one output file format at a time."
> > >>>>
> > >>>> Happy documenting!
> > >>>>
> > >>>> Gale
> > >>>>
> > >>>> On Tue, Jun 30, 2015 at 8:52 AM, Menaka Madushanka
> > >>>> <me...@gmail.com> wrote:
> > >>>> > Thank you very much Gale.
> > >>>> > I did the modifications. :-)
> > >>>> > Actually, unless you give me this feedback, it would mislead the
> > readers.
> > >>>> > I'm very grateful for correcting me. :-)
> > >>>> >
> > >>>> > I just wrote the documentation for statistics.
> > >>>> >
> > >>>>
> >
> https://menakamadushanka.wordpress.com/2015/06/30/apache-taverna-language-command-line-tool-workflow-statistics/
> > >>>> >
> > >>>> > Cheers
> > >>>> > Menaka
> > >>>> >
> > >>>> > On 30 June 2015 at 20:53, Gale Naylor <
> galen@noventussolutions.com>
> > >>>> wrote:
> > >>>> >
> > >>>> >> 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
> > >>>> >> <me...@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
> > >>>> >> >> <me...@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
> > >>>> >> >> >> <me...@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
> > >>>> >> >> >> >> <me...@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
> > >>>> >> >> >> >> >> <me...@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
> > >>>> >> >> >> >> >> >> <me...@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
> > >>>> >> >> >> >> >> >> >>> <me...@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
> > >>>> >> >> >> >> >> >> >>> >> > <me...@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
> > >>>> >> >> >> >> >> >> >>> >> > >> <me...@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
> > >>>> >> >> >> >> >> >> >>> >> > >> > <ga...@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
> > >>>> >> >> >> >> >> >> >>> >> > >> >> <me...@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>
> > >>>> >>
> > >>>> >>
> > >>>> >
> > >>>> >
> > >>>> > --
> > >>>> > 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>
>

Re: Taverna Language Command Line tool - convert command doc

[Menaka Madushanka <me...@gmail.com>]

Hello Gale,
I really appreciate your grate support.
I learnt a lot from you. Also I edited my blogs.
These are not for any submission but to track the progress and for future
use (completing the full documentation).
But I noticed there were so many errors as I'm new to documentation and
blogging. :-)
However by now I was able to correct those errors with your kind support.
Thank you very much Gale. :-)
I hope that I could write the final documentation more successfully with
the support that you have given me....

Thank you very much for the effort, time and every thing that you spent for
me.....
Have a very nice vacation. :-)

Cheers
Menaka Madushanka

On 1 July 2015 at 07:25, Gale Naylor <ga...@noventussolutions.com> wrote:

> Hi Menaka,
>
> You are doing an excellent job on the documentation. I'm sorry for
> bombarding you with feedback, but I wanted to help as much as possible
> before I go on vacation.
>
> As I was reviewing your blog posts, I noticed that not all of the
> words in the titles are capitalized as they should be.
>
> Also, is your initial post part of your deliverable documentation, or
> has it been replaced by your later blog posts?
>
> Just a couple of things in the research object post:
>
> Taverna Language Command line tool – Conversion Documentation – Research
> objects
>
>     -- Use "the" in front of "following bundle formats" and use "into"
> instead of "in to": "The Apache Taverna Language is capable of
> converting the following bundle formats into Research Object bundles."
>     -- Use "development: instead of "development process": "The
> conversion capability for other formats is still in development."
>     -- Use "is" instead of "in": "***The support for recursive
> conversion or selecting the output file directory is not yet
> included."
>
> Thanks!
>
> Gale
>
>
> On Tue, Jun 30, 2015 at 6:08 PM, Gale Naylor
> <ga...@noventussolutions.com> wrote:
> > Hi Menaka,
> >
> > I looked at your validation documentation and I realized I have a
> > question: If the validate command is run with no options, what
> > happens? In other words, if you choose not to write the validation
> > results to a log file, what does the command do? Write the results to
> > the terminal? Does this need to be explained. (I guess I have the same
> > question about the stats command.)
> >
> > Same comment as with stats documentation about adding sections with
> > larger, and bold fonts to help with readability.
> >
> > Here are some additional comments:
> >
> > Apache Taverna Language Command line documentation – Validation
> >
> >     -- Use "examining" rather than "examine": "The validation is done
> > by examining the following factors/ problems."
> >     -- Use API instead of api, and use "consisting" instead of
> > "consist: "The API returns a validation report consisting of problems
> > that exist in the workflow."
> >     -- Instead of "type of the problem" use either "problem category"
> > or "category of problem" and I suggest using "listed" instead of the
> > first "shown": "If there are problems, those problems are listed under
> > the problem category shown above."
> >     -- After "The command line tool can execute this validation
> > process" how about saying " and tell the user if the workflow has
> > errors/ problems and what they are." So the complete sentence would
> > be: "The command line tool can execute this validation process and
> > tell the user if the workflow has errors/ problems and what they are."
> >     -- Even though you only have one option, I would still put the
> > option on the next line, like you did in the Stats documentation.
> >     -- Also, if it's possible it would be good to standardize the
> > documentation to say either "Supported options" or "Options." You can
> > use option(s) -- with the "s" in parentheses -- to mean it could be
> > one option or more than one option.
> >     -- In the Usage section, you use [args]: "$tavlang validate
> > [options][args] input_files." In the convert and research objects
> > posts you use [arguments], and in stats you didn't list arguments at
> > all, yet it looks to me like the command structure is similar. It
> > would be good to be consistent and use either [args] or [arguments].
> >     -- In the stats post you say "Supported file formats: .t2flow and
> > .wfbundle" using "and" and in the validate post you say "Supported
> > input file formats:- .t2flow/ .wfbundle" using "/". Would it be
> > possible to make these the same?
> >     -- At the end of your "example with options", how about this
> > instead: "The output file contains the detailed report, including a
> > list of the workflow problems."
> >
> > Good job on all the documentation!
> >
> > Gale
> >
> > On Tue, Jun 30, 2015 at 5:25 PM, Gale Naylor
> > <ga...@noventussolutions.com> wrote:
> >> Hi Menaka,
> >>
> >> I read your stats blog post; it looks good.  I am not very familiar
> >> with workflows, so I'm not sure I can comment a lot on your examples,
> >> but I did list some things that appeared to me to be inconsistent.
> >>
> >> Also, I think it would be good to make at least a couple of different
> >> sections and identify them with a larger, bold font, like you did in
> >> the Convert command blog post. In the taverna-sculf2-api Readme file
> >> (on github), they show "Usage" as a section:
> >>
> https://github.com/apache/incubator-taverna-language/tree/master/taverna-scufl2-api
> .
> >> That might be a good idea. Then, if you use a smaller (but still bold)
> >> font for the Verbose Mode sub-section and Normal Mode sub-section,
> >> that will help the reader navigate your documentation. You could then
> >> take out the second instance of "Verbose Mode" (between the two
> >> verbose examples) like you did in the Normal Mode examples. Then, I
> >> would also create a third sub-section called "Save Results to a Log
> >> File" and below that put your example. The formatting you used in your
> >> Convert command blog post worked well.
> >>
> >> A few other things:
> >>
> >> Apache Taverna Language Command line tool – Workflow Statistics
> >>
> >>     -- Capitalize the first "API," hyphenate "scufl2-api" to match the
> >> module name, and write "whatever" as one word: "The Taverna Language
> >> API (sculf2-api) has several methods to set and retrieve those
> >> resources whenever needed."
> >>     -- Instead of " The command line tool is capable of listing those
> >> resources which a workflow file has." How about "The command line tool
> >> is also capable of listing workflow file resources."
> >>     -- In the options section, you say "Save results in a log file"
> >> (using "in") and in your example you say "Save results to a log file"
> >> (using "to"). You might consider making those consistent.
> >>     -- In your verbose Hello World example, near the end did you mean
> >> to say " | |--> Input Ports" after "|--> Number of Output Ports = 1,"
> >> rather than "Output Ports"?
> >>     -- In your verbose Workflow1 example, in your Data Links section,
> >> you say " |--> DataLink parameters=>input" and then " |--> DataLink
> >> output=>parameters." Should these statements both be formatted the
> >> same and match the last item? Specifically, should they all end in
> >> "==>input"?  Or is there a reason for them to be different?
> >>
> >> That's all I can see!
> >>
> >> Gale
> >>
> >> On Tue, Jun 30, 2015 at 2:03 PM, Menaka Madushanka
> >> <me...@gmail.com> wrote:
> >>> Hello Gale,
> >>> Great feed back. :-)
> >>> I did the modifications and now it looks great and clean....
> >>>
> >>> In statistics blog I did not add explanations much but examples. So
> that it
> >>> will be easy for you. :-)
> >>> Thank you very much for the great help you are giving me.....!!!
> >>> Please let me know if there anything that I could do and/ or need some
> >>> clarifications.
> >>>
> >>> Thank you very much
> >>> Menaka
> >>>
> >>> On 1 July 2015 at 01:54, Gale Naylor <ga...@noventussolutions.com>
> wrote:
> >>>
> >>>> Hi Menaka,
> >>>>
> >>>> The changes look great! But I missed one: You should add a "The" in
> >>>> front of the inspection, validation, and statistics sentence, so it
> >>>> reads: "The following file types are supported for inspection,
> >>>> validation and statistics." (with a period at the end.) :-)
> >>>>
> >>>> I will take a look at your statistics blog post. Meanwhile, below are
> >>>> some comments for the Conversion Documentation blog post. Of course,
> >>>> let me know if I misunderstood anything you are trying to say.
> >>>>
> >>>> Apache Taverna Language Command line - Conversion Documentation
> >>>>
> >>>>         Paragraph 1
> >>>>           --  Use "provides" instead of "gives" and "converting and
> >>>> managing" instead of "convert and manage": "The Apache Taverna
> >>>> Language provides a set of APIs for converting and managing workflow
> >>>> bundles and Research Object bundles."
> >>>>
> >>>> Paragraph 3
> >>>>           -- Add "are:": "The basic functionalities of the tool are:"
> >>>>
> >>>> In the Conversion section
> >>>>           --  Use "also has" instead of "is also have": "The tool also
> >>>> has the capability of converting bundles of several formats into
> >>>> Research Object bundles."
> >>>>           --  Use "Refer to" instead of "Refer": " Refer to the
> >>>> following blog for more information about converting bundle formats."
> >>>>
> >>>> In the Example usage section
> >>>>           --  Use "The user" instead of "User": "The user can specify
> >>>> the way that the conversion should be done."
> >>>>
> >>>> In the Recursive conversion section
> >>>>           --  Use "the tool" and "the specified output format": " In
> >>>> recursive conversion mode, the tool can convert .t2flow or .wfbundle
> >>>> files in the given directory into the specified output format."
> >>>>           -- I think you may have a typographical error: "out put"
> >>>> instead of "output" -- it should be "The output will be...
> >>>> /home/username/ ..."
> >>>>
> >>>> In the Non-recursive conversion section
> >>>>           --  Use "The user" instead of "User" and "need" instead of
> >>>> "needed": "The user can use this mode to convert a specific workflow
> >>>> into the format they need." (Or, even better would be to say, "The
> >>>> user can use this mode to convert a specific work flow into the
> >>>> required format."
> >>>>           --  Instead of "Here all the files that want to be converted
> >>>> must specify separately as space separated values." I think it would
> >>>> be better to say: "All files to be converted must be listed as
> >>>> space-separated values."
> >>>>           -- The sentence that describes where files will be saved if
> >>>> there is no specified output directory is a difficult one to write. I
> >>>> had to think about it. Rather than saying "The converted files will be
> >>>> saved in converted folder in each parent folder which contain the
> >>>> input file." What if you said "The converted files will be saved in
> >>>> the /converted folder in the input file's parent directory."? (And use
> >>>> the "/" in front of converted to stress that it is a folder name?)
> >>>>           -- You need a comma after "Also." And use "are to be saved"
> >>>> instead of "to be saved": "Also, users can specify the directory where
> >>>> the converted files are to be saved."
> >>>>           -- In your footnote, "out put" should be one word: "output":
> >>>> "*The tool can only manage one output file format at a time."
> >>>>
> >>>> Happy documenting!
> >>>>
> >>>> Gale
> >>>>
> >>>> On Tue, Jun 30, 2015 at 8:52 AM, Menaka Madushanka
> >>>> <me...@gmail.com> wrote:
> >>>> > Thank you very much Gale.
> >>>> > I did the modifications. :-)
> >>>> > Actually, unless you give me this feedback, it would mislead the
> readers.
> >>>> > I'm very grateful for correcting me. :-)
> >>>> >
> >>>> > I just wrote the documentation for statistics.
> >>>> >
> >>>>
> https://menakamadushanka.wordpress.com/2015/06/30/apache-taverna-language-command-line-tool-workflow-statistics/
> >>>> >
> >>>> > Cheers
> >>>> > Menaka
> >>>> >
> >>>> > On 30 June 2015 at 20:53, Gale Naylor <ga...@noventussolutions.com>
> >>>> wrote:
> >>>> >
> >>>> >> 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
> >>>> >> <me...@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
> >>>> >> >> <me...@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
> >>>> >> >> >> <me...@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
> >>>> >> >> >> >> <me...@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
> >>>> >> >> >> >> >> <me...@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
> >>>> >> >> >> >> >> >> <me...@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
> >>>> >> >> >> >> >> >> >>> <me...@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
> >>>> >> >> >> >> >> >> >>> >> > <me...@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
> >>>> >> >> >> >> >> >> >>> >> > >> <me...@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
> >>>> >> >> >> >> >> >> >>> >> > >> > <ga...@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
> >>>> >> >> >> >> >> >> >>> >> > >> >> <me...@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>
> >>>> >>
> >>>> >>
> >>>> >
> >>>> >
> >>>> > --
> >>>> > 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>

Re: Taverna Language Command Line tool - convert command doc

[Gale Naylor <ga...@noventussolutions.com>]

It's been my pleasure to help, Stian. I will be happy to provide feedback
on the Taverna pages and README files. Thank you for the links. I will read
them more carefully when I get home from vacation (July10-11).

Gale
On Jul 2, 2015 5:08 PM, "Stian Soiland-Reyes" <st...@apache.org> wrote:

> Thank you Gale, for all your brilliant feedback and helping Menaka!
> This is true community effort!
>
> Good documentation can is more important than good code - specially to
> help newcomers to a project.
>
> So any feedback about any of the Taverna pages or README files are
> appreciated; feel free to suggest an edit of web pages [1], or raise a
> bug [2].
>
>
>
> [1] http://taverna.incubator.apache.org/community/edit
> [2] https://issues.apache.org/jira/browse/TAVERNA/component/12326819
>
>
> On 1 July 2015 at 02:55, Gale Naylor <ga...@noventussolutions.com> wrote:
> > Hi Menaka,
> >
> > You are doing an excellent job on the documentation. I'm sorry for
> > bombarding you with feedback, but I wanted to help as much as possible
> > before I go on vacation.
> >
> > As I was reviewing your blog posts, I noticed that not all of the
> > words in the titles are capitalized as they should be.
> >
> > Also, is your initial post part of your deliverable documentation, or
> > has it been replaced by your later blog posts?
> >
> > Just a couple of things in the research object post:
> >
> > Taverna Language Command line tool – Conversion Documentation – Research
> objects
> >
> >     -- Use "the" in front of "following bundle formats" and use "into"
> > instead of "in to": "The Apache Taverna Language is capable of
> > converting the following bundle formats into Research Object bundles."
> >     -- Use "development: instead of "development process": "The
> > conversion capability for other formats is still in development."
> >     -- Use "is" instead of "in": "***The support for recursive
> > conversion or selecting the output file directory is not yet
> > included."
> >
> > Thanks!
> >
> > Gale
> >
> >
> > On Tue, Jun 30, 2015 at 6:08 PM, Gale Naylor
> > <ga...@noventussolutions.com> wrote:
> >> Hi Menaka,
> >>
> >> I looked at your validation documentation and I realized I have a
> >> question: If the validate command is run with no options, what
> >> happens? In other words, if you choose not to write the validation
> >> results to a log file, what does the command do? Write the results to
> >> the terminal? Does this need to be explained. (I guess I have the same
> >> question about the stats command.)
> >>
> >> Same comment as with stats documentation about adding sections with
> >> larger, and bold fonts to help with readability.
> >>
> >> Here are some additional comments:
> >>
> >> Apache Taverna Language Command line documentation – Validation
> >>
> >>     -- Use "examining" rather than "examine": "The validation is done
> >> by examining the following factors/ problems."
> >>     -- Use API instead of api, and use "consisting" instead of
> >> "consist: "The API returns a validation report consisting of problems
> >> that exist in the workflow."
> >>     -- Instead of "type of the problem" use either "problem category"
> >> or "category of problem" and I suggest using "listed" instead of the
> >> first "shown": "If there are problems, those problems are listed under
> >> the problem category shown above."
> >>     -- After "The command line tool can execute this validation
> >> process" how about saying " and tell the user if the workflow has
> >> errors/ problems and what they are." So the complete sentence would
> >> be: "The command line tool can execute this validation process and
> >> tell the user if the workflow has errors/ problems and what they are."
> >>     -- Even though you only have one option, I would still put the
> >> option on the next line, like you did in the Stats documentation.
> >>     -- Also, if it's possible it would be good to standardize the
> >> documentation to say either "Supported options" or "Options." You can
> >> use option(s) -- with the "s" in parentheses -- to mean it could be
> >> one option or more than one option.
> >>     -- In the Usage section, you use [args]: "$tavlang validate
> >> [options][args] input_files." In the convert and research objects
> >> posts you use [arguments], and in stats you didn't list arguments at
> >> all, yet it looks to me like the command structure is similar. It
> >> would be good to be consistent and use either [args] or [arguments].
> >>     -- In the stats post you say "Supported file formats: .t2flow and
> >> .wfbundle" using "and" and in the validate post you say "Supported
> >> input file formats:- .t2flow/ .wfbundle" using "/". Would it be
> >> possible to make these the same?
> >>     -- At the end of your "example with options", how about this
> >> instead: "The output file contains the detailed report, including a
> >> list of the workflow problems."
> >>
> >> Good job on all the documentation!
> >>
> >> Gale
> >>
> >> On Tue, Jun 30, 2015 at 5:25 PM, Gale Naylor
> >> <ga...@noventussolutions.com> wrote:
> >>> Hi Menaka,
> >>>
> >>> I read your stats blog post; it looks good.  I am not very familiar
> >>> with workflows, so I'm not sure I can comment a lot on your examples,
> >>> but I did list some things that appeared to me to be inconsistent.
> >>>
> >>> Also, I think it would be good to make at least a couple of different
> >>> sections and identify them with a larger, bold font, like you did in
> >>> the Convert command blog post. In the taverna-sculf2-api Readme file
> >>> (on github), they show "Usage" as a section:
> >>>
> https://github.com/apache/incubator-taverna-language/tree/master/taverna-scufl2-api
> .
> >>> That might be a good idea. Then, if you use a smaller (but still bold)
> >>> font for the Verbose Mode sub-section and Normal Mode sub-section,
> >>> that will help the reader navigate your documentation. You could then
> >>> take out the second instance of "Verbose Mode" (between the two
> >>> verbose examples) like you did in the Normal Mode examples. Then, I
> >>> would also create a third sub-section called "Save Results to a Log
> >>> File" and below that put your example. The formatting you used in your
> >>> Convert command blog post worked well.
> >>>
> >>> A few other things:
> >>>
> >>> Apache Taverna Language Command line tool – Workflow Statistics
> >>>
> >>>     -- Capitalize the first "API," hyphenate "scufl2-api" to match the
> >>> module name, and write "whatever" as one word: "The Taverna Language
> >>> API (sculf2-api) has several methods to set and retrieve those
> >>> resources whenever needed."
> >>>     -- Instead of " The command line tool is capable of listing those
> >>> resources which a workflow file has." How about "The command line tool
> >>> is also capable of listing workflow file resources."
> >>>     -- In the options section, you say "Save results in a log file"
> >>> (using "in") and in your example you say "Save results to a log file"
> >>> (using "to"). You might consider making those consistent.
> >>>     -- In your verbose Hello World example, near the end did you mean
> >>> to say " | |--> Input Ports" after "|--> Number of Output Ports = 1,"
> >>> rather than "Output Ports"?
> >>>     -- In your verbose Workflow1 example, in your Data Links section,
> >>> you say " |--> DataLink parameters=>input" and then " |--> DataLink
> >>> output=>parameters." Should these statements both be formatted the
> >>> same and match the last item? Specifically, should they all end in
> >>> "==>input"?  Or is there a reason for them to be different?
> >>>
> >>> That's all I can see!
> >>>
> >>> Gale
> >>>
> >>> On Tue, Jun 30, 2015 at 2:03 PM, Menaka Madushanka
> >>> <me...@gmail.com> wrote:
> >>>> Hello Gale,
> >>>> Great feed back. :-)
> >>>> I did the modifications and now it looks great and clean....
> >>>>
> >>>> In statistics blog I did not add explanations much but examples. So
> that it
> >>>> will be easy for you. :-)
> >>>> Thank you very much for the great help you are giving me.....!!!
> >>>> Please let me know if there anything that I could do and/ or need some
> >>>> clarifications.
> >>>>
> >>>> Thank you very much
> >>>> Menaka
> >>>>
> >>>> On 1 July 2015 at 01:54, Gale Naylor <ga...@noventussolutions.com>
> wrote:
> >>>>
> >>>>> Hi Menaka,
> >>>>>
> >>>>> The changes look great! But I missed one: You should add a "The" in
> >>>>> front of the inspection, validation, and statistics sentence, so it
> >>>>> reads: "The following file types are supported for inspection,
> >>>>> validation and statistics." (with a period at the end.) :-)
> >>>>>
> >>>>> I will take a look at your statistics blog post. Meanwhile, below are
> >>>>> some comments for the Conversion Documentation blog post. Of course,
> >>>>> let me know if I misunderstood anything you are trying to say.
> >>>>>
> >>>>> Apache Taverna Language Command line - Conversion Documentation
> >>>>>
> >>>>>         Paragraph 1
> >>>>>           --  Use "provides" instead of "gives" and "converting and
> >>>>> managing" instead of "convert and manage": "The Apache Taverna
> >>>>> Language provides a set of APIs for converting and managing workflow
> >>>>> bundles and Research Object bundles."
> >>>>>
> >>>>> Paragraph 3
> >>>>>           -- Add "are:": "The basic functionalities of the tool are:"
> >>>>>
> >>>>> In the Conversion section
> >>>>>           --  Use "also has" instead of "is also have": "The tool
> also
> >>>>> has the capability of converting bundles of several formats into
> >>>>> Research Object bundles."
> >>>>>           --  Use "Refer to" instead of "Refer": " Refer to the
> >>>>> following blog for more information about converting bundle formats."
> >>>>>
> >>>>> In the Example usage section
> >>>>>           --  Use "The user" instead of "User": "The user can specify
> >>>>> the way that the conversion should be done."
> >>>>>
> >>>>> In the Recursive conversion section
> >>>>>           --  Use "the tool" and "the specified output format": " In
> >>>>> recursive conversion mode, the tool can convert .t2flow or .wfbundle
> >>>>> files in the given directory into the specified output format."
> >>>>>           -- I think you may have a typographical error: "out put"
> >>>>> instead of "output" -- it should be "The output will be...
> >>>>> /home/username/ ..."
> >>>>>
> >>>>> In the Non-recursive conversion section
> >>>>>           --  Use "The user" instead of "User" and "need" instead of
> >>>>> "needed": "The user can use this mode to convert a specific workflow
> >>>>> into the format they need." (Or, even better would be to say, "The
> >>>>> user can use this mode to convert a specific work flow into the
> >>>>> required format."
> >>>>>           --  Instead of "Here all the files that want to be
> converted
> >>>>> must specify separately as space separated values." I think it would
> >>>>> be better to say: "All files to be converted must be listed as
> >>>>> space-separated values."
> >>>>>           -- The sentence that describes where files will be saved if
> >>>>> there is no specified output directory is a difficult one to write. I
> >>>>> had to think about it. Rather than saying "The converted files will
> be
> >>>>> saved in converted folder in each parent folder which contain the
> >>>>> input file." What if you said "The converted files will be saved in
> >>>>> the /converted folder in the input file's parent directory."? (And
> use
> >>>>> the "/" in front of converted to stress that it is a folder name?)
> >>>>>           -- You need a comma after "Also." And use "are to be saved"
> >>>>> instead of "to be saved": "Also, users can specify the directory
> where
> >>>>> the converted files are to be saved."
> >>>>>           -- In your footnote, "out put" should be one word:
> "output":
> >>>>> "*The tool can only manage one output file format at a time."
> >>>>>
> >>>>> Happy documenting!
> >>>>>
> >>>>> Gale
> >>>>>
> >>>>> On Tue, Jun 30, 2015 at 8:52 AM, Menaka Madushanka
> >>>>> <me...@gmail.com> wrote:
> >>>>> > Thank you very much Gale.
> >>>>> > I did the modifications. :-)
> >>>>> > Actually, unless you give me this feedback, it would mislead the
> readers.
> >>>>> > I'm very grateful for correcting me. :-)
> >>>>> >
> >>>>> > I just wrote the documentation for statistics.
> >>>>> >
> >>>>>
> https://menakamadushanka.wordpress.com/2015/06/30/apache-taverna-language-command-line-tool-workflow-statistics/
> >>>>> >
> >>>>> > Cheers
> >>>>> > Menaka
> >>>>> >
> >>>>> > On 30 June 2015 at 20:53, Gale Naylor <galen@noventussolutions.com
> >
> >>>>> wrote:
> >>>>> >
> >>>>> >> 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
> >>>>> >> <me...@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
> >>>>> >> >> <me...@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
> >>>>> >> >> >> <me...@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
> >>>>> >> >> >> >> <me...@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
> >>>>> >> >> >> >> >> <me...@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
> >>>>> >> >> >> >> >> >> <me...@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
> >>>>> >> >> >> >> >> >> >>> <me...@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
> >>>>> >> >> >> >> >> >> >>> >> > <me...@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
> >>>>> >> >> >> >> >> >> >>> >> > >> <me...@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
> >>>>> >> >> >> >> >> >> >>> >> > >> > <ga...@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
> >>>>> >> >> >> >> >> >> >>> >> > >> >> <me...@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>
> >>>>> >>
> >>>>> >>
> >>>>> >
> >>>>> >
> >>>>> > --
> >>>>> > Menaka Madushanka Jayawardena
> >>>>> > Faculty of Engineering, <http://www.pdn.ac.lk/eng>
> >>>>> > University of Peradeniyaya.
> >>>>> > LinkedIn <http://lk.linkedin.com/in/menakajayawardena>
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>> --
> >>>> Menaka Madushanka Jayawardena
> >>>> Faculty of Engineering, <http://www.pdn.ac.lk/eng>
> >>>> University of Peradeniyaya.
> >>>> LinkedIn <http://lk.linkedin.com/in/menakajayawardena>
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/0000-0001-9842-9718
>

Re: Taverna Language Command Line tool - convert command doc

[Stian Soiland-Reyes <st...@apache.org>]

Thank you Gale, for all your brilliant feedback and helping Menaka!
This is true community effort!

Good documentation can is more important than good code - specially to
help newcomers to a project.

So any feedback about any of the Taverna pages or README files are
appreciated; feel free to suggest an edit of web pages [1], or raise a
bug [2].



[1] http://taverna.incubator.apache.org/community/edit
[2] https://issues.apache.org/jira/browse/TAVERNA/component/12326819


On 1 July 2015 at 02:55, Gale Naylor <ga...@noventussolutions.com> wrote:
> Hi Menaka,
>
> You are doing an excellent job on the documentation. I'm sorry for
> bombarding you with feedback, but I wanted to help as much as possible
> before I go on vacation.
>
> As I was reviewing your blog posts, I noticed that not all of the
> words in the titles are capitalized as they should be.
>
> Also, is your initial post part of your deliverable documentation, or
> has it been replaced by your later blog posts?
>
> Just a couple of things in the research object post:
>
> Taverna Language Command line tool – Conversion Documentation – Research objects
>
>     -- Use "the" in front of "following bundle formats" and use "into"
> instead of "in to": "The Apache Taverna Language is capable of
> converting the following bundle formats into Research Object bundles."
>     -- Use "development: instead of "development process": "The
> conversion capability for other formats is still in development."
>     -- Use "is" instead of "in": "***The support for recursive
> conversion or selecting the output file directory is not yet
> included."
>
> Thanks!
>
> Gale
>
>
> On Tue, Jun 30, 2015 at 6:08 PM, Gale Naylor
> <ga...@noventussolutions.com> wrote:
>> Hi Menaka,
>>
>> I looked at your validation documentation and I realized I have a
>> question: If the validate command is run with no options, what
>> happens? In other words, if you choose not to write the validation
>> results to a log file, what does the command do? Write the results to
>> the terminal? Does this need to be explained. (I guess I have the same
>> question about the stats command.)
>>
>> Same comment as with stats documentation about adding sections with
>> larger, and bold fonts to help with readability.
>>
>> Here are some additional comments:
>>
>> Apache Taverna Language Command line documentation – Validation
>>
>>     -- Use "examining" rather than "examine": "The validation is done
>> by examining the following factors/ problems."
>>     -- Use API instead of api, and use "consisting" instead of
>> "consist: "The API returns a validation report consisting of problems
>> that exist in the workflow."
>>     -- Instead of "type of the problem" use either "problem category"
>> or "category of problem" and I suggest using "listed" instead of the
>> first "shown": "If there are problems, those problems are listed under
>> the problem category shown above."
>>     -- After "The command line tool can execute this validation
>> process" how about saying " and tell the user if the workflow has
>> errors/ problems and what they are." So the complete sentence would
>> be: "The command line tool can execute this validation process and
>> tell the user if the workflow has errors/ problems and what they are."
>>     -- Even though you only have one option, I would still put the
>> option on the next line, like you did in the Stats documentation.
>>     -- Also, if it's possible it would be good to standardize the
>> documentation to say either "Supported options" or "Options." You can
>> use option(s) -- with the "s" in parentheses -- to mean it could be
>> one option or more than one option.
>>     -- In the Usage section, you use [args]: "$tavlang validate
>> [options][args] input_files." In the convert and research objects
>> posts you use [arguments], and in stats you didn't list arguments at
>> all, yet it looks to me like the command structure is similar. It
>> would be good to be consistent and use either [args] or [arguments].
>>     -- In the stats post you say "Supported file formats: .t2flow and
>> .wfbundle" using "and" and in the validate post you say "Supported
>> input file formats:- .t2flow/ .wfbundle" using "/". Would it be
>> possible to make these the same?
>>     -- At the end of your "example with options", how about this
>> instead: "The output file contains the detailed report, including a
>> list of the workflow problems."
>>
>> Good job on all the documentation!
>>
>> Gale
>>
>> On Tue, Jun 30, 2015 at 5:25 PM, Gale Naylor
>> <ga...@noventussolutions.com> wrote:
>>> Hi Menaka,
>>>
>>> I read your stats blog post; it looks good.  I am not very familiar
>>> with workflows, so I'm not sure I can comment a lot on your examples,
>>> but I did list some things that appeared to me to be inconsistent.
>>>
>>> Also, I think it would be good to make at least a couple of different
>>> sections and identify them with a larger, bold font, like you did in
>>> the Convert command blog post. In the taverna-sculf2-api Readme file
>>> (on github), they show "Usage" as a section:
>>> https://github.com/apache/incubator-taverna-language/tree/master/taverna-scufl2-api.
>>> That might be a good idea. Then, if you use a smaller (but still bold)
>>> font for the Verbose Mode sub-section and Normal Mode sub-section,
>>> that will help the reader navigate your documentation. You could then
>>> take out the second instance of "Verbose Mode" (between the two
>>> verbose examples) like you did in the Normal Mode examples. Then, I
>>> would also create a third sub-section called "Save Results to a Log
>>> File" and below that put your example. The formatting you used in your
>>> Convert command blog post worked well.
>>>
>>> A few other things:
>>>
>>> Apache Taverna Language Command line tool – Workflow Statistics
>>>
>>>     -- Capitalize the first "API," hyphenate "scufl2-api" to match the
>>> module name, and write "whatever" as one word: "The Taverna Language
>>> API (sculf2-api) has several methods to set and retrieve those
>>> resources whenever needed."
>>>     -- Instead of " The command line tool is capable of listing those
>>> resources which a workflow file has." How about "The command line tool
>>> is also capable of listing workflow file resources."
>>>     -- In the options section, you say "Save results in a log file"
>>> (using "in") and in your example you say "Save results to a log file"
>>> (using "to"). You might consider making those consistent.
>>>     -- In your verbose Hello World example, near the end did you mean
>>> to say " | |--> Input Ports" after "|--> Number of Output Ports = 1,"
>>> rather than "Output Ports"?
>>>     -- In your verbose Workflow1 example, in your Data Links section,
>>> you say " |--> DataLink parameters=>input" and then " |--> DataLink
>>> output=>parameters." Should these statements both be formatted the
>>> same and match the last item? Specifically, should they all end in
>>> "==>input"?  Or is there a reason for them to be different?
>>>
>>> That's all I can see!
>>>
>>> Gale
>>>
>>> On Tue, Jun 30, 2015 at 2:03 PM, Menaka Madushanka
>>> <me...@gmail.com> wrote:
>>>> Hello Gale,
>>>> Great feed back. :-)
>>>> I did the modifications and now it looks great and clean....
>>>>
>>>> In statistics blog I did not add explanations much but examples. So that it
>>>> will be easy for you. :-)
>>>> Thank you very much for the great help you are giving me.....!!!
>>>> Please let me know if there anything that I could do and/ or need some
>>>> clarifications.
>>>>
>>>> Thank you very much
>>>> Menaka
>>>>
>>>> On 1 July 2015 at 01:54, Gale Naylor <ga...@noventussolutions.com> wrote:
>>>>
>>>>> Hi Menaka,
>>>>>
>>>>> The changes look great! But I missed one: You should add a "The" in
>>>>> front of the inspection, validation, and statistics sentence, so it
>>>>> reads: "The following file types are supported for inspection,
>>>>> validation and statistics." (with a period at the end.) :-)
>>>>>
>>>>> I will take a look at your statistics blog post. Meanwhile, below are
>>>>> some comments for the Conversion Documentation blog post. Of course,
>>>>> let me know if I misunderstood anything you are trying to say.
>>>>>
>>>>> Apache Taverna Language Command line - Conversion Documentation
>>>>>
>>>>>         Paragraph 1
>>>>>           --  Use "provides" instead of "gives" and "converting and
>>>>> managing" instead of "convert and manage": "The Apache Taverna
>>>>> Language provides a set of APIs for converting and managing workflow
>>>>> bundles and Research Object bundles."
>>>>>
>>>>> Paragraph 3
>>>>>           -- Add "are:": "The basic functionalities of the tool are:"
>>>>>
>>>>> In the Conversion section
>>>>>           --  Use "also has" instead of "is also have": "The tool also
>>>>> has the capability of converting bundles of several formats into
>>>>> Research Object bundles."
>>>>>           --  Use "Refer to" instead of "Refer": " Refer to the
>>>>> following blog for more information about converting bundle formats."
>>>>>
>>>>> In the Example usage section
>>>>>           --  Use "The user" instead of "User": "The user can specify
>>>>> the way that the conversion should be done."
>>>>>
>>>>> In the Recursive conversion section
>>>>>           --  Use "the tool" and "the specified output format": " In
>>>>> recursive conversion mode, the tool can convert .t2flow or .wfbundle
>>>>> files in the given directory into the specified output format."
>>>>>           -- I think you may have a typographical error: "out put"
>>>>> instead of "output" -- it should be "The output will be...
>>>>> /home/username/ ..."
>>>>>
>>>>> In the Non-recursive conversion section
>>>>>           --  Use "The user" instead of "User" and "need" instead of
>>>>> "needed": "The user can use this mode to convert a specific workflow
>>>>> into the format they need." (Or, even better would be to say, "The
>>>>> user can use this mode to convert a specific work flow into the
>>>>> required format."
>>>>>           --  Instead of "Here all the files that want to be converted
>>>>> must specify separately as space separated values." I think it would
>>>>> be better to say: "All files to be converted must be listed as
>>>>> space-separated values."
>>>>>           -- The sentence that describes where files will be saved if
>>>>> there is no specified output directory is a difficult one to write. I
>>>>> had to think about it. Rather than saying "The converted files will be
>>>>> saved in converted folder in each parent folder which contain the
>>>>> input file." What if you said "The converted files will be saved in
>>>>> the /converted folder in the input file's parent directory."? (And use
>>>>> the "/" in front of converted to stress that it is a folder name?)
>>>>>           -- You need a comma after "Also." And use "are to be saved"
>>>>> instead of "to be saved": "Also, users can specify the directory where
>>>>> the converted files are to be saved."
>>>>>           -- In your footnote, "out put" should be one word: "output":
>>>>> "*The tool can only manage one output file format at a time."
>>>>>
>>>>> Happy documenting!
>>>>>
>>>>> Gale
>>>>>
>>>>> On Tue, Jun 30, 2015 at 8:52 AM, Menaka Madushanka
>>>>> <me...@gmail.com> wrote:
>>>>> > Thank you very much Gale.
>>>>> > I did the modifications. :-)
>>>>> > Actually, unless you give me this feedback, it would mislead the readers.
>>>>> > I'm very grateful for correcting me. :-)
>>>>> >
>>>>> > I just wrote the documentation for statistics.
>>>>> >
>>>>> https://menakamadushanka.wordpress.com/2015/06/30/apache-taverna-language-command-line-tool-workflow-statistics/
>>>>> >
>>>>> > Cheers
>>>>> > Menaka
>>>>> >
>>>>> > On 30 June 2015 at 20:53, Gale Naylor <ga...@noventussolutions.com>
>>>>> wrote:
>>>>> >
>>>>> >> 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
>>>>> >> <me...@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 <ga...@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
>>>>> >> >> <me...@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
>>>>> >> >> >> <me...@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
>>>>> >> >> >> >> <me...@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
>>>>> >> >> >> >> >> <me...@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
>>>>> >> >> >> >> >> >> <me...@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
>>>>> >> >> >> >> >> >> >>> <me...@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
>>>>> >> >> >> >> >> >> >>> >> > <me...@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
>>>>> >> >> >> >> >> >> >>> >> > >> <me...@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
>>>>> >> >> >> >> >> >> >>> >> > >> > <ga...@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
>>>>> >> >> >> >> >> >> >>> >> > >> >> <me...@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>
>>>>> >>
>>>>> >>
>>>>> >
>>>>> >
>>>>> > --
>>>>> > Menaka Madushanka Jayawardena
>>>>> > Faculty of Engineering, <http://www.pdn.ac.lk/eng>
>>>>> > University of Peradeniyaya.
>>>>> > LinkedIn <http://lk.linkedin.com/in/menakajayawardena>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Menaka Madushanka Jayawardena
>>>> Faculty of Engineering, <http://www.pdn.ac.lk/eng>
>>>> University of Peradeniyaya.
>>>> LinkedIn <http://lk.linkedin.com/in/menakajayawardena>



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

Re: Taverna Language Command Line tool - convert command doc

[Gale Naylor <ga...@noventussolutions.com>]

Hi Menaka,

You are doing an excellent job on the documentation. I'm sorry for
bombarding you with feedback, but I wanted to help as much as possible
before I go on vacation.

As I was reviewing your blog posts, I noticed that not all of the
words in the titles are capitalized as they should be.

Also, is your initial post part of your deliverable documentation, or
has it been replaced by your later blog posts?

Just a couple of things in the research object post:

Taverna Language Command line tool – Conversion Documentation – Research objects

    -- Use "the" in front of "following bundle formats" and use "into"
instead of "in to": "The Apache Taverna Language is capable of
converting the following bundle formats into Research Object bundles."
    -- Use "development: instead of "development process": "The
conversion capability for other formats is still in development."
    -- Use "is" instead of "in": "***The support for recursive
conversion or selecting the output file directory is not yet
included."

Thanks!

Gale


On Tue, Jun 30, 2015 at 6:08 PM, Gale Naylor
<ga...@noventussolutions.com> wrote:
> Hi Menaka,
>
> I looked at your validation documentation and I realized I have a
> question: If the validate command is run with no options, what
> happens? In other words, if you choose not to write the validation
> results to a log file, what does the command do? Write the results to
> the terminal? Does this need to be explained. (I guess I have the same
> question about the stats command.)
>
> Same comment as with stats documentation about adding sections with
> larger, and bold fonts to help with readability.
>
> Here are some additional comments:
>
> Apache Taverna Language Command line documentation – Validation
>
>     -- Use "examining" rather than "examine": "The validation is done
> by examining the following factors/ problems."
>     -- Use API instead of api, and use "consisting" instead of
> "consist: "The API returns a validation report consisting of problems
> that exist in the workflow."
>     -- Instead of "type of the problem" use either "problem category"
> or "category of problem" and I suggest using "listed" instead of the
> first "shown": "If there are problems, those problems are listed under
> the problem category shown above."
>     -- After "The command line tool can execute this validation
> process" how about saying " and tell the user if the workflow has
> errors/ problems and what they are." So the complete sentence would
> be: "The command line tool can execute this validation process and
> tell the user if the workflow has errors/ problems and what they are."
>     -- Even though you only have one option, I would still put the
> option on the next line, like you did in the Stats documentation.
>     -- Also, if it's possible it would be good to standardize the
> documentation to say either "Supported options" or "Options." You can
> use option(s) -- with the "s" in parentheses -- to mean it could be
> one option or more than one option.
>     -- In the Usage section, you use [args]: "$tavlang validate
> [options][args] input_files." In the convert and research objects
> posts you use [arguments], and in stats you didn't list arguments at
> all, yet it looks to me like the command structure is similar. It
> would be good to be consistent and use either [args] or [arguments].
>     -- In the stats post you say "Supported file formats: .t2flow and
> .wfbundle" using "and" and in the validate post you say "Supported
> input file formats:- .t2flow/ .wfbundle" using "/". Would it be
> possible to make these the same?
>     -- At the end of your "example with options", how about this
> instead: "The output file contains the detailed report, including a
> list of the workflow problems."
>
> Good job on all the documentation!
>
> Gale
>
> On Tue, Jun 30, 2015 at 5:25 PM, Gale Naylor
> <ga...@noventussolutions.com> wrote:
>> Hi Menaka,
>>
>> I read your stats blog post; it looks good.  I am not very familiar
>> with workflows, so I'm not sure I can comment a lot on your examples,
>> but I did list some things that appeared to me to be inconsistent.
>>
>> Also, I think it would be good to make at least a couple of different
>> sections and identify them with a larger, bold font, like you did in
>> the Convert command blog post. In the taverna-sculf2-api Readme file
>> (on github), they show "Usage" as a section:
>> https://github.com/apache/incubator-taverna-language/tree/master/taverna-scufl2-api.
>> That might be a good idea. Then, if you use a smaller (but still bold)
>> font for the Verbose Mode sub-section and Normal Mode sub-section,
>> that will help the reader navigate your documentation. You could then
>> take out the second instance of "Verbose Mode" (between the two
>> verbose examples) like you did in the Normal Mode examples. Then, I
>> would also create a third sub-section called "Save Results to a Log
>> File" and below that put your example. The formatting you used in your
>> Convert command blog post worked well.
>>
>> A few other things:
>>
>> Apache Taverna Language Command line tool – Workflow Statistics
>>
>>     -- Capitalize the first "API," hyphenate "scufl2-api" to match the
>> module name, and write "whatever" as one word: "The Taverna Language
>> API (sculf2-api) has several methods to set and retrieve those
>> resources whenever needed."
>>     -- Instead of " The command line tool is capable of listing those
>> resources which a workflow file has." How about "The command line tool
>> is also capable of listing workflow file resources."
>>     -- In the options section, you say "Save results in a log file"
>> (using "in") and in your example you say "Save results to a log file"
>> (using "to"). You might consider making those consistent.
>>     -- In your verbose Hello World example, near the end did you mean
>> to say " | |--> Input Ports" after "|--> Number of Output Ports = 1,"
>> rather than "Output Ports"?
>>     -- In your verbose Workflow1 example, in your Data Links section,
>> you say " |--> DataLink parameters=>input" and then " |--> DataLink
>> output=>parameters." Should these statements both be formatted the
>> same and match the last item? Specifically, should they all end in
>> "==>input"?  Or is there a reason for them to be different?
>>
>> That's all I can see!
>>
>> Gale
>>
>> On Tue, Jun 30, 2015 at 2:03 PM, Menaka Madushanka
>> <me...@gmail.com> wrote:
>>> Hello Gale,
>>> Great feed back. :-)
>>> I did the modifications and now it looks great and clean....
>>>
>>> In statistics blog I did not add explanations much but examples. So that it
>>> will be easy for you. :-)
>>> Thank you very much for the great help you are giving me.....!!!
>>> Please let me know if there anything that I could do and/ or need some
>>> clarifications.
>>>
>>> Thank you very much
>>> Menaka
>>>
>>> On 1 July 2015 at 01:54, Gale Naylor <ga...@noventussolutions.com> wrote:
>>>
>>>> Hi Menaka,
>>>>
>>>> The changes look great! But I missed one: You should add a "The" in
>>>> front of the inspection, validation, and statistics sentence, so it
>>>> reads: "The following file types are supported for inspection,
>>>> validation and statistics." (with a period at the end.) :-)
>>>>
>>>> I will take a look at your statistics blog post. Meanwhile, below are
>>>> some comments for the Conversion Documentation blog post. Of course,
>>>> let me know if I misunderstood anything you are trying to say.
>>>>
>>>> Apache Taverna Language Command line - Conversion Documentation
>>>>
>>>>         Paragraph 1
>>>>           --  Use "provides" instead of "gives" and "converting and
>>>> managing" instead of "convert and manage": "The Apache Taverna
>>>> Language provides a set of APIs for converting and managing workflow
>>>> bundles and Research Object bundles."
>>>>
>>>> Paragraph 3
>>>>           -- Add "are:": "The basic functionalities of the tool are:"
>>>>
>>>> In the Conversion section
>>>>           --  Use "also has" instead of "is also have": "The tool also
>>>> has the capability of converting bundles of several formats into
>>>> Research Object bundles."
>>>>           --  Use "Refer to" instead of "Refer": " Refer to the
>>>> following blog for more information about converting bundle formats."
>>>>
>>>> In the Example usage section
>>>>           --  Use "The user" instead of "User": "The user can specify
>>>> the way that the conversion should be done."
>>>>
>>>> In the Recursive conversion section
>>>>           --  Use "the tool" and "the specified output format": " In
>>>> recursive conversion mode, the tool can convert .t2flow or .wfbundle
>>>> files in the given directory into the specified output format."
>>>>           -- I think you may have a typographical error: "out put"
>>>> instead of "output" -- it should be "The output will be...
>>>> /home/username/ ..."
>>>>
>>>> In the Non-recursive conversion section
>>>>           --  Use "The user" instead of "User" and "need" instead of
>>>> "needed": "The user can use this mode to convert a specific workflow
>>>> into the format they need." (Or, even better would be to say, "The
>>>> user can use this mode to convert a specific work flow into the
>>>> required format."
>>>>           --  Instead of "Here all the files that want to be converted
>>>> must specify separately as space separated values." I think it would
>>>> be better to say: "All files to be converted must be listed as
>>>> space-separated values."
>>>>           -- The sentence that describes where files will be saved if
>>>> there is no specified output directory is a difficult one to write. I
>>>> had to think about it. Rather than saying "The converted files will be
>>>> saved in converted folder in each parent folder which contain the
>>>> input file." What if you said "The converted files will be saved in
>>>> the /converted folder in the input file's parent directory."? (And use
>>>> the "/" in front of converted to stress that it is a folder name?)
>>>>           -- You need a comma after "Also." And use "are to be saved"
>>>> instead of "to be saved": "Also, users can specify the directory where
>>>> the converted files are to be saved."
>>>>           -- In your footnote, "out put" should be one word: "output":
>>>> "*The tool can only manage one output file format at a time."
>>>>
>>>> Happy documenting!
>>>>
>>>> Gale
>>>>
>>>> On Tue, Jun 30, 2015 at 8:52 AM, Menaka Madushanka
>>>> <me...@gmail.com> wrote:
>>>> > Thank you very much Gale.
>>>> > I did the modifications. :-)
>>>> > Actually, unless you give me this feedback, it would mislead the readers.
>>>> > I'm very grateful for correcting me. :-)
>>>> >
>>>> > I just wrote the documentation for statistics.
>>>> >
>>>> https://menakamadushanka.wordpress.com/2015/06/30/apache-taverna-language-command-line-tool-workflow-statistics/
>>>> >
>>>> > Cheers
>>>> > Menaka
>>>> >
>>>> > On 30 June 2015 at 20:53, Gale Naylor <ga...@noventussolutions.com>
>>>> wrote:
>>>> >
>>>> >> 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
>>>> >> <me...@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 <ga...@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
>>>> >> >> <me...@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
>>>> >> >> >> <me...@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
>>>> >> >> >> >> <me...@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
>>>> >> >> >> >> >> <me...@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
>>>> >> >> >> >> >> >> <me...@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
>>>> >> >> >> >> >> >> >>> <me...@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
>>>> >> >> >> >> >> >> >>> >> > <me...@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
>>>> >> >> >> >> >> >> >>> >> > >> <me...@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
>>>> >> >> >> >> >> >> >>> >> > >> > <ga...@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
>>>> >> >> >> >> >> >> >>> >> > >> >> <me...@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>
>>>> >>
>>>> >>
>>>> >
>>>> >
>>>> > --
>>>> > Menaka Madushanka Jayawardena
>>>> > Faculty of Engineering, <http://www.pdn.ac.lk/eng>
>>>> > University of Peradeniyaya.
>>>> > LinkedIn <http://lk.linkedin.com/in/menakajayawardena>
>>>>
>>>>
>>>
>>>
>>> --
>>> Menaka Madushanka Jayawardena
>>> Faculty of Engineering, <http://www.pdn.ac.lk/eng>
>>> University of Peradeniyaya.
>>> LinkedIn <http://lk.linkedin.com/in/menakajayawardena>

Re: Taverna Language Command Line tool - convert command doc

[Gale Naylor <ga...@noventussolutions.com>]

Hi Menaka,

I looked at your validation documentation and I realized I have a
question: If the validate command is run with no options, what
happens? In other words, if you choose not to write the validation
results to a log file, what does the command do? Write the results to
the terminal? Does this need to be explained. (I guess I have the same
question about the stats command.)

Same comment as with stats documentation about adding sections with
larger, and bold fonts to help with readability.

Here are some additional comments:

Apache Taverna Language Command line documentation – Validation

    -- Use "examining" rather than "examine": "The validation is done
by examining the following factors/ problems."
    -- Use API instead of api, and use "consisting" instead of
"consist: "The API returns a validation report consisting of problems
that exist in the workflow."
    -- Instead of "type of the problem" use either "problem category"
or "category of problem" and I suggest using "listed" instead of the
first "shown": "If there are problems, those problems are listed under
the problem category shown above."
    -- After "The command line tool can execute this validation
process" how about saying " and tell the user if the workflow has
errors/ problems and what they are." So the complete sentence would
be: "The command line tool can execute this validation process and
tell the user if the workflow has errors/ problems and what they are."
    -- Even though you only have one option, I would still put the
option on the next line, like you did in the Stats documentation.
    -- Also, if it's possible it would be good to standardize the
documentation to say either "Supported options" or "Options." You can
use option(s) -- with the "s" in parentheses -- to mean it could be
one option or more than one option.
    -- In the Usage section, you use [args]: "$tavlang validate
[options][args] input_files." In the convert and research objects
posts you use [arguments], and in stats you didn't list arguments at
all, yet it looks to me like the command structure is similar. It
would be good to be consistent and use either [args] or [arguments].
    -- In the stats post you say "Supported file formats: .t2flow and
.wfbundle" using "and" and in the validate post you say "Supported
input file formats:- .t2flow/ .wfbundle" using "/". Would it be
possible to make these the same?
    -- At the end of your "example with options", how about this
instead: "The output file contains the detailed report, including a
list of the workflow problems."

Good job on all the documentation!

Gale

On Tue, Jun 30, 2015 at 5:25 PM, Gale Naylor
<ga...@noventussolutions.com> wrote:
> Hi Menaka,
>
> I read your stats blog post; it looks good.  I am not very familiar
> with workflows, so I'm not sure I can comment a lot on your examples,
> but I did list some things that appeared to me to be inconsistent.
>
> Also, I think it would be good to make at least a couple of different
> sections and identify them with a larger, bold font, like you did in
> the Convert command blog post. In the taverna-sculf2-api Readme file
> (on github), they show "Usage" as a section:
> https://github.com/apache/incubator-taverna-language/tree/master/taverna-scufl2-api.
> That might be a good idea. Then, if you use a smaller (but still bold)
> font for the Verbose Mode sub-section and Normal Mode sub-section,
> that will help the reader navigate your documentation. You could then
> take out the second instance of "Verbose Mode" (between the two
> verbose examples) like you did in the Normal Mode examples. Then, I
> would also create a third sub-section called "Save Results to a Log
> File" and below that put your example. The formatting you used in your
> Convert command blog post worked well.
>
> A few other things:
>
> Apache Taverna Language Command line tool – Workflow Statistics
>
>     -- Capitalize the first "API," hyphenate "scufl2-api" to match the
> module name, and write "whatever" as one word: "The Taverna Language
> API (sculf2-api) has several methods to set and retrieve those
> resources whenever needed."
>     -- Instead of " The command line tool is capable of listing those
> resources which a workflow file has." How about "The command line tool
> is also capable of listing workflow file resources."
>     -- In the options section, you say "Save results in a log file"
> (using "in") and in your example you say "Save results to a log file"
> (using "to"). You might consider making those consistent.
>     -- In your verbose Hello World example, near the end did you mean
> to say " | |--> Input Ports" after "|--> Number of Output Ports = 1,"
> rather than "Output Ports"?
>     -- In your verbose Workflow1 example, in your Data Links section,
> you say " |--> DataLink parameters=>input" and then " |--> DataLink
> output=>parameters." Should these statements both be formatted the
> same and match the last item? Specifically, should they all end in
> "==>input"?  Or is there a reason for them to be different?
>
> That's all I can see!
>
> Gale
>
> On Tue, Jun 30, 2015 at 2:03 PM, Menaka Madushanka
> <me...@gmail.com> wrote:
>> Hello Gale,
>> Great feed back. :-)
>> I did the modifications and now it looks great and clean....
>>
>> In statistics blog I did not add explanations much but examples. So that it
>> will be easy for you. :-)
>> Thank you very much for the great help you are giving me.....!!!
>> Please let me know if there anything that I could do and/ or need some
>> clarifications.
>>
>> Thank you very much
>> Menaka
>>
>> On 1 July 2015 at 01:54, Gale Naylor <ga...@noventussolutions.com> wrote:
>>
>>> Hi Menaka,
>>>
>>> The changes look great! But I missed one: You should add a "The" in
>>> front of the inspection, validation, and statistics sentence, so it
>>> reads: "The following file types are supported for inspection,
>>> validation and statistics." (with a period at the end.) :-)
>>>
>>> I will take a look at your statistics blog post. Meanwhile, below are
>>> some comments for the Conversion Documentation blog post. Of course,
>>> let me know if I misunderstood anything you are trying to say.
>>>
>>> Apache Taverna Language Command line - Conversion Documentation
>>>
>>>         Paragraph 1
>>>           --  Use "provides" instead of "gives" and "converting and
>>> managing" instead of "convert and manage": "The Apache Taverna
>>> Language provides a set of APIs for converting and managing workflow
>>> bundles and Research Object bundles."
>>>
>>> Paragraph 3
>>>           -- Add "are:": "The basic functionalities of the tool are:"
>>>
>>> In the Conversion section
>>>           --  Use "also has" instead of "is also have": "The tool also
>>> has the capability of converting bundles of several formats into
>>> Research Object bundles."
>>>           --  Use "Refer to" instead of "Refer": " Refer to the
>>> following blog for more information about converting bundle formats."
>>>
>>> In the Example usage section
>>>           --  Use "The user" instead of "User": "The user can specify
>>> the way that the conversion should be done."
>>>
>>> In the Recursive conversion section
>>>           --  Use "the tool" and "the specified output format": " In
>>> recursive conversion mode, the tool can convert .t2flow or .wfbundle
>>> files in the given directory into the specified output format."
>>>           -- I think you may have a typographical error: "out put"
>>> instead of "output" -- it should be "The output will be...
>>> /home/username/ ..."
>>>
>>> In the Non-recursive conversion section
>>>           --  Use "The user" instead of "User" and "need" instead of
>>> "needed": "The user can use this mode to convert a specific workflow
>>> into the format they need." (Or, even better would be to say, "The
>>> user can use this mode to convert a specific work flow into the
>>> required format."
>>>           --  Instead of "Here all the files that want to be converted
>>> must specify separately as space separated values." I think it would
>>> be better to say: "All files to be converted must be listed as
>>> space-separated values."
>>>           -- The sentence that describes where files will be saved if
>>> there is no specified output directory is a difficult one to write. I
>>> had to think about it. Rather than saying "The converted files will be
>>> saved in converted folder in each parent folder which contain the
>>> input file." What if you said "The converted files will be saved in
>>> the /converted folder in the input file's parent directory."? (And use
>>> the "/" in front of converted to stress that it is a folder name?)
>>>           -- You need a comma after "Also." And use "are to be saved"
>>> instead of "to be saved": "Also, users can specify the directory where
>>> the converted files are to be saved."
>>>           -- In your footnote, "out put" should be one word: "output":
>>> "*The tool can only manage one output file format at a time."
>>>
>>> Happy documenting!
>>>
>>> Gale
>>>
>>> On Tue, Jun 30, 2015 at 8:52 AM, Menaka Madushanka
>>> <me...@gmail.com> wrote:
>>> > Thank you very much Gale.
>>> > I did the modifications. :-)
>>> > Actually, unless you give me this feedback, it would mislead the readers.
>>> > I'm very grateful for correcting me. :-)
>>> >
>>> > I just wrote the documentation for statistics.
>>> >
>>> https://menakamadushanka.wordpress.com/2015/06/30/apache-taverna-language-command-line-tool-workflow-statistics/
>>> >
>>> > Cheers
>>> > Menaka
>>> >
>>> > On 30 June 2015 at 20:53, Gale Naylor <ga...@noventussolutions.com>
>>> wrote:
>>> >
>>> >> 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
>>> >> <me...@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 <ga...@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
>>> >> >> <me...@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
>>> >> >> >> <me...@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
>>> >> >> >> >> <me...@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
>>> >> >> >> >> >> <me...@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
>>> >> >> >> >> >> >> <me...@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
>>> >> >> >> >> >> >> >>> <me...@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
>>> >> >> >> >> >> >> >>> >> > <me...@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
>>> >> >> >> >> >> >> >>> >> > >> <me...@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
>>> >> >> >> >> >> >> >>> >> > >> > <ga...@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
>>> >> >> >> >> >> >> >>> >> > >> >> <me...@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>
>>> >>
>>> >>
>>> >
>>> >
>>> > --
>>> > 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>