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From Gale Naylor <ga...@noventussolutions.com>
Subject Re: Taverna Language Command Line tool - convert command doc
Date Wed, 15 Jul 2015 14:33:33 GMT
Hi Stian,

Thank you for the information!  I will take a look at it and see if I have
any questions.

Gale
On Jul 13, 2015 8:34 AM, "Stian Soiland-Reyes" <stain@apache.org> wrote:

> Thanks!
>
> We have a general contributor guide for the website here:
>
> http://taverna.incubator.apache.org/community/edit
>
>
> Editing the website itself in a fork can be done in the GitHub web
> interface, but to add the diagram to a GitHub pull request (e.g. )
> would probably require you to check out from your fork of
> https://github.com/apache/incubator-taverna-site --
>
> you could also contribute it as an attachment to a Jira bug report:
> https://issues.apache.org/jira/browse/TAVERNA/component/12326819
>
>
> I don't think a single diagram would require a CLA with ASF - your
> contribution should be automatically covered by the #5 in
> http://www.apache.org/licenses/LICENSE-2.0
> - but we might need you to sign a CLA -
> http://www.apache.org/licenses/#clas - before we can accept larger
> contributions.
>
>
>
>
>
> On 3 July 2015 at 05:29, Gale Naylor <galen@noventussolutions.com> wrote:
> > 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
> >>
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/0000-0001-9842-9718
>

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