taverna-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Gale Naylor <ga...@noventussolutions.com>
Subject Re: Taverna Language Command Line tool - convert command doc
Date Fri, 03 Jul 2015 04:29:09 GMT
Hi Stian,

Yes, when I get home from vacation (July 10-11), I will look at this
information more carefully and have a go at adding it to the website. I
will let you know if I have any questions.

Thank you,

Gale
On Jul 2, 2015 4:52 PM, "Stian Soiland-Reyes" <stain@apache.org> wrote:

> Hi, Gale, thanks for your effort on documenting tavlang - as it's
> being developed!
>
> Do you think you could have a go at adding this to the website in
> MarkDown/HTML format..? See
>
>
> https://github.com/apache/incubator-taverna-site/tree/trunk/content/documentation/scufl2
> which is the source for
> http://taverna.incubator.apache.org/documentation/scufl2/
>
> (perhaps /scufl2  in the URL should be renamed to /language ?)
>
>
>
>
>
> .wfbundle workflows is a kind of earlier form of RO Bundle, but
> predates their formal specification and does not use the
> taverna-robundle API. So they were meant to be updated to also be full
> RO Bundles - basically having a JSON manifest instead/in addition to
> the XML one.  So it should at some point be possible to convert them.
> Perhaps a prototype converter could just copy over the files
> internally between the UCFPackage and the Bundle and thus update the
> new manifest?
>
>
>
> The code that does the wfbundle writing:
>
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-wfbundle/src/main/java/org/apache/taverna/scufl2/rdfxml/RDFXMLWriter.java
> and reading:
>
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-wfbundle/src/main/java/org/apache/taverna/scufl2/rdfxml/RDFXMLReader.java
>
> So this relies on the UCF support from:
>
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-ucfpackage/src/main/java/org/apache/taverna/scufl2/ucfpackage/UCFPackage.java
> .. which is basically a proxy for manipulating a ZIP file and its manifest.
>
>
> But this should ideally be updated to use the RO Bundle API from:
>
> https://github.com/apache/incubator-taverna-language/tree/master/taverna-robundle
>
>
> and thus have proper support for linking the annotation/ files to
> their corresponding workflow elements, rather than having to parse
> them all to find the right one.
>
> as the UCFPackage types are used throughout the wfbundle writer
> changing this would take a bit of effort.. or just wrapping it from
> UCFPackage. Here's an earlier attempt:
>
>
> https://github.com/apache/incubator-taverna-language/blob/ucfpackage-robundle/taverna-scufl2-ucfpackage/src/main/java/org/apache/taverna/scufl2/ucfpackage/UCFPackage.java
>
> (Note: That branch has test errors)
>
>
> As you see it calls the writeAsODFManifest(); which writes out the
> classic META-INF/manifest.xml for backwards compatibility. This is
> permitted by our spec - but violating a NOT RECOMMENDED ("e.g. Know
> what you are doing"):
> https://w3id.org/bundle#manifest-xml
>
> On 26 June 2015 at 19:54, Menaka Madushanka <menaka12350@gmail.com> wrote:
> > Hi Gale,
> > I'm really appreciate your feedback on my blogs. I'm very new and there
> > could be some flows. Thank you very much for showing them. :-)
> >
> > 1) Yes, the types of bundle formats that can be converted are listed in
> > this blog.
> >
> https://menakamadushanka.wordpress.com/2015/06/20/taverna-language-command-line-tool-conversion-documentation-research-objects/
> > The bundles are not workflows.
> >
> > 2) No. It seems like the way I have wrote it somewhat misleading.....
> > Actually scufl2 workflows are not Bundles. Those are two different APIs.
> > I'll update the blog. :-)
> >
> > 3).Yes, my mistake. Neither .t2flow nor wfbundle could be converted into
> > robundle.
> >
> > 4). Yes Gale. That modification should be done. Other wise it looks like
> > any format could be converted into Robundle. I'll update my blog too.
> >
> > Are there any more facts that need clarification about the blogs please
> ask
> > me. :)
> >
> > Thank you very much Gale.
> > Menaka
> >
> > On 27 June 2015 at 00:00, Gale Naylor <galen@noventussolutions.com>
> wrote:
> >
> >> Hi Menaka,
> >>
> >> I've been reading and learning more about research objects, and I
> >> think I understand better what is going on, but I still have some
> >> questions.
> >>
> >> 1) I am curious as to which file types *can* be converted to .robundle
> >> format? (I must have missed something because I thought .t2flow and
> >> .wfbundle were the only allowed input file types.)
> >>
> >> 2) In rereading your June 18th blog post, I see you say that the
> >> command line tool is for converting and managing workflow "bundles" as
> >> well as research object bundles. Are t2flow files "workflow bundles"
> >> or just "workflows?" Or is there not a practical difference?
> >>
> >> 3) I understand now that not all file format conversions are valid.
> >> I'm trying to understand this better. In your June 18th blog post you
> >> say:
> >>
> >> "The conversion function supports converting .t2flow and .wfbundle
> >> formats into following formats:
> >>
> >>     .structure
> >>
> >>     .json
> >>
> >>     .iwir
> >>
> >>     .wfbundle
> >>
> >>     .wfdesc.ttl –> (development in progress)
> >>
> >>     .robundle –> (development in progress)"
> >>
> >> To me, reading this looks like all combinations are valid.
> >>
> >> I'm wondering, can both .t2flow and .wfbundle files be converted to
> >> all file types *except* robundle?
> >>
> >>
> >> 4) I fixed the examples in my blog post.  Should I also change the
> >> --robundle option description to say "Output bundle as .robundle"
> >> instead of "Output workflow as .robundle" ? (Same for .wfbundle
> >> option.)
> >>
> >> Thanks for the feedback and the correct link to the example!
> >>
> >> Have a nice weekend.
> >>
> >> Gale
> >>
> >>
> >>
> >> On Wed, Jun 24, 2015 at 10:52 PM, Menaka Madushanka
> >> <menaka12350@gmail.com> wrote:
> >> > Hi Gale,
> >> > Use this link
> >> >
> >>
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-robundle/src/test/java/org/apache/taverna/robundle/TestExample.java
> >> >
> >> > Cheers
> >> > Menaka
> >> >
> >> > On 25 June 2015 at 05:34, Gale Naylor <galen@noventussolutions.com>
> >> wrote:
> >> >
> >> >> Hi Menaka,
> >> >>
> >> >> Thank you for the feedback and clarifying information. Sorry not to
> >> respond
> >> >> sooner. I am learning about bundles, etc. and reading the link you
> sent.
> >> >>
> >> >> One thing, I'm having trouble getting to the example in the Examples
> of
> >> Use
> >> >> Section: "Example in full is at
> org.apache.taverna.robundle.TestExample"
> >> >>
> >> >> Can you help me? This is what I've done so far:
> >> >>
> >> >> - Clicking on the link gets me the "This is not the web page you are
> >> >> looking
> >> >> for" page. (This is the actual link address:
> >> >>
> >> >>
> >>
> https://github.com/apache/incubator-taverna-language/blob/master/taverna-robundle/src/test/java/org/purl/wf4ever/robundle/TestExample.java
> >> >> )
> >> >>
> >> >> - Entering "org.apache.taverna.robundle.TestExample" also doesn't
> work
> >> for
> >> >> me. I didn't think it would, but I tried anyway.
> >> >>
> >> >> - Searching for "taverna robundle TestExample" on the main Apache.com
> >> page
> >> >> yields no results.
> >> >>
> >> >> I will continue to read and understand the RO Bundle API page, but
I
> >> would
> >> >> like to see the full Test Example, if possible.
> >> >>
> >> >> Thanks!
> >> >>
> >> >> Gale
> >> >>
> >> >>
> >> >> -----Original Message-----
> >> >> From: Menaka Madushanka [mailto:menaka12350@gmail.com]
> >> >> Sent: Saturday, June 20, 2015 11:09 AM
> >> >> To: dev@taverna.incubator.apache.org
> >> >> Subject: Re: Taverna Language Command Line tool - convert command doc
> >> >>
> >> >> That's cool.....!! :-)
> >> >> Correction:
> >> >>
> >> >>
> >>
> https://galenaylor.wordpress.com/2015/06/19/apache-taverna-language-command-line-convert-examples/
> >> >>
> >> >> > Example 2: Simple conversion, multiple input files, no options
> >> >> >
> >> >> > $tavlang convert –-robundle /someFile1.wfbundle /someFile2.wfbundle
> >> >> >
> >> >> > Converts */someFile1.wfbundle* and */someFile2.wfbundle* into
> >> >> > *.robundle* format and saves the output files to the */converted*
> >> >> > folder in the current working directory.
> >> >> >
> >> >> Taverna language *cannot* convert .wfbundles/.t2flow into robundle
> >> format.
> >> >> Its only for some specific bundle formats. Go through this doc for
> more
> >> >> info.
> >> >>
> >> >>
> >> >>
> >>
> https://github.com/apache/incubator-taverna-language/tree/master/taverna-robundle
> >> >>
> >> >> cheers.
> >> >>
> >> >> On 20 June 2015 at 22:43, Gale Naylor <galen@noventussolutions.com>
> >> wrote:
> >> >>
> >> >> > Thank you for the Wordpress tip, Menaka! I have changed the two
> blog
> >> >> > posts to use the <pre> tag, and it looks great. I also made
a few
> >> >> > refinements.
> >> >> >
> >> >> > Thanks,
> >> >> > Gale
> >> >> >
> >> >> > On Fri, Jun 19, 2015 at 11:54 PM, Menaka Madushanka
> >> >> > <menaka12350@gmail.com> wrote:
> >> >> > > Thank you very much Gale,
> >> >> > >
> >> >> > > I showed the output-format without brackets to indicate it
is
> >> >> > >> required and not optional because it appears to be always
> necessary
> >> >> > >
> >> >> > >
> >> >> > > That would be more accurate I think. I'm very new for
> documentation.
> >> >> > Thank
> >> >> > > you very much.
> >> >> > >
> >> >> > >  I left the -json output file type as having a single dash,
but
> all
> >> >> > >> the other output types have double-dashes. Should I change
the
> json
> >> >> > >> output argument to --json?
> >> >> > >>
> >> >> > > -json should be --json. In my email that was a mistake. So
you
> can
> >> >> > > use
> >> >> > --.
> >> >> > >
> >> >> > > (Wordpress is driving me crazy because it is showing the
> >> >> > > double-dashes
> >> >> > >> as long single dashes, even when I use the monospace
> font-family.
> >> >> > >> Any
> >> >> > >> suggestions?)
> >> >> > >>
> >> >> > >
> >> >> > > Yes, wordpress does what it wants, but not us. :-) Use
> preformatted.
> >> >> > > Not paragraph. Then it would be ok. I updated my blog.
> >> >> > >
> >> >> >
> >> https://menakamadushanka.wordpress.com/2015/06/18/apache-taverna-langu
> >> >> > age-command-line-conversion-documentation/
> >> >> > >
> >> >> > > Thank you very much.
> >> >> > > Menaka
> >> >> > >
> >> >> > > I'll go through your documentations.
> >> >> > >
> >> >> > >
> >> >> > > On 20 June 2015 at 03:43, Gale Naylor <
> galen@noventussolutions.com>
> >> >> > wrote:
> >> >> > >
> >> >> > >> Hi Menaka,
> >> >> > >>
> >> >> > >> Thanks for updating your blog! I have some additional
feedback
> in
> >> >> > >> the form of two blog posts. One has a detailed description
(as I
> >> >> > >> understand it) of the convert command and one has several
> examples,
> >> >> > >> building on the examples in your blog. I hope these will
help
> the
> >> >> > >> discussion of the command structure. Here are the links:
> >> >> > >>
> >> >> > >>
> >> >> > >>
> >> >> >
> >> https://galenaylor.wordpress.com/2015/06/19/apache-taverna-language-co
> >> >> > mmand-line-convert-command/
> >> >> > >>
> >> >> > >>
> >> >> > >>
> >> >> >
> >> https://galenaylor.wordpress.com/2015/06/19/apache-taverna-language-co
> >> >> > mmand-line-convert-examples/
> >> >> > >>
> >> >> > >> Some things to note:
> >> >> > >>
> >> >> > >> (1) l basically used your June 18th post, but a few things
(like
> >> >> > >> the validate command) are from earlier posts/emails.
> >> >> > >>
> >> >> > >> (2) I showed the output-format without brackets to indicate
it
> is
> >> >> > >> required and not optional because it appears to be always
> >> necessary.
> >> >> > >>
> >> >> > >> (3) The way I understand the overall command structure,
it
> seemed
> >> >> > >> that all options (e.g., the output file directory) should
come
> >> >> > >> before the input-file-list, so that's what I assumed.
> >> >> > >>
> >> >> > >> (4) I left the -json output file type as having a single
dash,
> but
> >> >> > >> all the other output types have double-dashes. Should
I change
> the
> >> >> > >> json output argument to --json?
> >> >> > >>
> >> >> > >> Please let me know if anything is incorrect and I will
change
> it. I
> >> >> > >> realize the command structure is fluid, and I'm happy
to make
> any
> >> >> > >> changes as things evolve.
> >> >> > >>
> >> >> > >> (Wordpress is driving me crazy because it is showing
the
> >> >> > >> double-dashes as long single dashes, even when I use
the
> monospace
> >> >> > >> font-family. Any
> >> >> > >> suggestions?)
> >> >> > >>
> >> >> > >> Thanks,
> >> >> > >>
> >> >> > >> Gale
> >> >> > >>
> >> >> > >> On Fri, Jun 19, 2015 at 10:11 AM, Menaka Madushanka
> >> >> > >> <menaka12350@gmail.com> wrote:
> >> >> > >> > Hi Gale,
> >> >> > >> >
> >> >> > >> > Thank you very much.
> >> >> > >> >
> >> >> > >> > . Can you help me
> >> >> > >> >> understand what you mean when you say the files
will get
> saved
> >> >> > >> >> to the C directory?
> >> >> > >> >
> >> >> > >> > That was a mistake :-). I updated the blog. That
should be
> >> >> > >> > corrected
> >> >> > as
> >> >> > >> > *$tavlang convert –json -r -i /home/usrname/toConvert/
 –>
> >> >> > >> > *Convert
> >> >> > the
> >> >> > >> > files and save them in the …/toConvert/converted/
directory.
> >> >> > >> >
> >> >> > >> > I would appreciate more feedback, modifications
etc. So with
> the
> >> >> > >> > help
> >> >> > of
> >> >> > >> > the community we could come up with a much better
structure.
> >> >> > >> > Cheers
> >> >> > >> > Menaka
> >> >> > >> >
> >> >> > >> > On 19 June 2015 at 22:32, Gale Naylor
> >> >> > >> > <galen@noventussolutions.com>
> >> >> > >> wrote:
> >> >> > >> >
> >> >> > >> >> Hi Menaka,
> >> >> > >> >>
> >> >> > >> >> I am very happy to help, and I understand the
command
> structure
> >> >> > >> >> is a little fluid right now. Thank you for the
blog post; it
> was
> >> >> > >> >> very helpful.
> >> >> > >> >>
> >> >> > >> >> I am a little confused about your recursive
example. Can you
> >> >> > >> >> help me understand what you mean when you say
the files will
> get
> >> >> > >> >> saved to the C directory? Because you show the
output being
> >> saved
> >> >> > >> >> to:
> >> >> > >> >> /home/usrname/toConvert/converted/somefile1.json
> >> >> > >> >>
> >> >> > >> >> This is the example:
> >> >> > >> >> $tavlang convert –json -r -i /home/usrname/toConvert/
 –>
> >> >> > >> >> Convert the files and save them in the C directory.
> >> >> > >> >>
> >> >> > >> >> Thank you!
> >> >> > >> >>
> >> >> > >> >> Gale
> >> >> > >> >>
> >> >> > >> >> B
> >> >> > >> >>
> >> >> > >> >> On Fri, Jun 19, 2015 at 2:15 AM, Menaka Madushanka
> >> >> > >> >> <menaka12350@gmail.com> wrote:
> >> >> > >> >> > Hi Gale,
> >> >> > >> >> > I extremely appreciate your help. Thank
you very much. :-)
> >> >> > >> >> >
> >> >> > >> >> > 1) Is this still the basic structure of
the command:
> tavlang
> >> >> > convert
> >> >> > >> >> >> [options] <output format> <input
files>? Am I wrong in
> >> >> > >> >> >> thinking
> >> >> > that
> >> >> > >> the
> >> >> > >> >> >> output formats are handled as options?
> >> >> > >> >> >
> >> >> > >> >> >
> >> >> > >> >> > Yes there is a little difference in the
structure of
> commands
> >> >> > >> >> > now
> >> >> > and
> >> >> > >> >> then.
> >> >> > >> >> > So for the moment the command structure
is like this.
> >> >> > >> >> >
> >> >> > >> >> > $tavlang convert [--out-put format] [options]
[arguments]
> >> >> > >> >> >
> >> >> > >> >> >
> >> >> > >> >> > 2) Are -r and -i ever used independently?
If so, under what
> >> >> > >> >> circumstances?
> >> >> > >> >> >
> >> >> > >> >> > No. In recursive case the input will be
a directory
> containing
> >> >> > >> .t2flow of
> >> >> > >> >> > .wfbundle files. The output dir is optional
for both
> recursive
> >> >> > >> >> > and
> >> >> > non
> >> >> > >> >> > recursive cases.
> >> >> > >> >> >
> >> >> > >> >> > I created a blog about the conversion command.
> >> >> > >> >> >
> >> >> > >> >>
> >> >> > >>
> >> >> >
> >> https://menakamadushanka.wordpress.com/2015/06/18/apache-taverna-langu
> >> >> > age-command-line-conversion-documentation/
> >> >> > >> >> >
> >> >> > >> >> > If you have some suggestions, please inform.
> >> >> > >> >> >
> >> >> > >> >> > Thank you very much!
> >> >> > >> >> >
> >> >> > >> >> > Regards
> >> >> > >> >> > Menaka
> >> >> > >> >> >
> >> >> > >> >> > --
> >> >> > >> >> > Menaka Madushanka Jayawardena
> >> >> > >> >> > Faculty of Engineering, <http://www.pdn.ac.lk/eng>
> University
> >> >> > >> >> > of Peradeniyaya.
> >> >> > >> >> > LinkedIn <http://lk.linkedin.com/in/menakajayawardena>
> >> >> > >> >>
> >> >> > >> >
> >> >> > >> >
> >> >> > >> >
> >> >> > >> > --
> >> >> > >> > Menaka Madushanka Jayawardena
> >> >> > >> > Faculty of Engineering, <http://www.pdn.ac.lk/eng>
> University of
> >> >> > >> > Peradeniyaya.
> >> >> > >> > LinkedIn <http://lk.linkedin.com/in/menakajayawardena>
> >> >> > >>
> >> >> > >
> >> >> > >
> >> >> > >
> >> >> > > --
> >> >> > > Menaka Madushanka Jayawardena
> >> >> > > Faculty of Engineering, <http://www.pdn.ac.lk/eng>
University of
> >> >> > > Peradeniyaya.
> >> >> > > LinkedIn <http://lk.linkedin.com/in/menakajayawardena>
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Menaka Madushanka Jayawardena
> >> >> Faculty of Engineering, <http://www.pdn.ac.lk/eng> University
of
> >> >> Peradeniyaya.
> >> >> LinkedIn <http://lk.linkedin.com/in/menakajayawardena>
> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > Menaka Madushanka Jayawardena
> >> > Faculty of Engineering, <http://www.pdn.ac.lk/eng>
> >> > University of Peradeniyaya.
> >> > LinkedIn <http://lk.linkedin.com/in/menakajayawardena>
> >>
> >
> >
> >
> > --
> > Menaka Madushanka Jayawardena
> > Faculty of Engineering, <http://www.pdn.ac.lk/eng>
> > University of Peradeniyaya.
> > LinkedIn <http://lk.linkedin.com/in/menakajayawardena>
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/0000-0001-9842-9718
>

Mime
  • Unnamed multipart/alternative (inline, None, 0 bytes)
View raw message