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Posted to dev@taverna.apache.org by Денис Карякин <sa...@gmail.com> on 2015/03/01 15:56:37 UTC
[GSOC 2015] Taverna: Databundle viewer for web
Hello, my name is Denis, I'm very interested in your project to develop web
viewer for Taverna. I found it here:
https://issues.apache.org/jira/browse/COMDEV-121
I have questions about user story:
"User navigates to inputs/outputs" - this means user can upload input
data?And then get output data?
So, as I understand, user can upload workflow file, then upload input data.
All this data will be sended to Taverna Server, and after processing user
can upload output data.
Or, maybe, needed to do visualization how workflow works and which data
have been processing?
Briefly about me:
I get a master's degree at the Saratov State University
I am in Russia, Saratov, UTC + 3
This is my first participation in GSOC.
I am currently working at the university, developing learning management
system.
I started work with Ruby on Rails two years ago, so i have medium work
experience with this framework. Also, i used Bootstrap, jQuery, etc.
In university I also used C++, Java and PHP.
I also very interesting in bioinformatic, i visited the Bioinformatic
summer school (http://bioinformaticsinstitute.ru/summer2014) and took part
in the work on a small scientific task.
This is my Github profile https://github.com/Samhane
Re: [GSOC 2015] Taverna: Databundle viewer for web
Posted by Stian Soiland-Reyes <st...@apache.org>.
Yes, MIT license is very well.
Pretty much anything open source works as a dependency for the Apache
Software Foundation - except GPL/LGPL.
We as a project should help the GSOC student with any licensing
questions - but I think the student can decide the framework as we are
not requiring any direct integration.
There's obviously already the Taverna Player portal which can do
RUNNING of workflows - so it COULD be interesting to do an integration
here - but I would rely that to a second phase of the project as a
generic DataBundle viewer is more interesting independent of a Taverna
Server installation.
Taverna Player:
https://github.com/myGrid/taverna-player
http://github.com/myGrid/taverna-player-portal
You may notice that most of these web-based Taverna things are not
part of the current incubator code base at
http://taverna.incubator.apache.org/code/
.. but Rob Haines is one of our Apache Taverna committers and these
are fully owned by University of Manchester and so could be covered by
the same Software Grant and moved to Apache. I think we didn't want to
move it in at the same bulk as we had plenty to do with just importing
the Java code :)
On 2 March 2015 at 11:02, Ian Dunlop <ia...@manchester.ac.uk> wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA512
>
> Hello,
>
> I don't think it matters that Ruby is not part of Apache. Any code
> written for this project would be part of the Apache Taverna project,
> not the framework itself. However, I'm not really an expert on
> licenses. For example, Bootstrap is licensed under MIT. Does it matter
> to Apache that an Apache project uses it?
> Anyway, the mentors have most experience with RoR, Java & Ember which
> is why they are mentioned since they are the easiest (at the moment)
> for the Taverna project to support beyond the timescales of GSoC.
> Doesn't mean we aren't open to suggestions though.
>
> Cheers,
>
> Ian
>
> On 01/03/2015 18:04, Alan Williams wrote:
>> On 01-Mar-15 15:31, Mark Fortner wrote:
>>> Looking at the issue, wouldn't Grails or jruby on rails be a
>>> better fit, given that most of the existing codebase is in java?
>>
>> I think that the only relevant code would be that to look inside a
>> Taverna databundle. Although there is Java code for that inside
>> the Taverna Language package, there is a Ruby library for the
>> research object bundles at
>> https://github.com/myGrid/ruby-ro-bundle.git .
>>
>> So Java or Ruby would probably be OK - though as you say, Java
>> would fit in with the majority of the code, and the Ruby library is
>> not in Apache (yet?)
>>
>>> Mark
>>
>> Alan
>>
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--
Stian Soiland-Reyes
Apache Taverna (incubating)
http://orcid.org/0000-0001-9842-9718
Re: [GSOC 2015] Taverna: Databundle viewer for web
Posted by Ian Dunlop <ia...@manchester.ac.uk>.
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Hello,
I don't think it matters that Ruby is not part of Apache. Any code
written for this project would be part of the Apache Taverna project,
not the framework itself. However, I'm not really an expert on
licenses. For example, Bootstrap is licensed under MIT. Does it matter
to Apache that an Apache project uses it?
Anyway, the mentors have most experience with RoR, Java & Ember which
is why they are mentioned since they are the easiest (at the moment)
for the Taverna project to support beyond the timescales of GSoC.
Doesn't mean we aren't open to suggestions though.
Cheers,
Ian
On 01/03/2015 18:04, Alan Williams wrote:
> On 01-Mar-15 15:31, Mark Fortner wrote:
>> Looking at the issue, wouldn't Grails or jruby on rails be a
>> better fit, given that most of the existing codebase is in java?
>
> I think that the only relevant code would be that to look inside a
> Taverna databundle. Although there is Java code for that inside
> the Taverna Language package, there is a Ruby library for the
> research object bundles at
> https://github.com/myGrid/ruby-ro-bundle.git .
>
> So Java or Ruby would probably be OK - though as you say, Java
> would fit in with the majority of the code, and the Ruby library is
> not in Apache (yet?)
>
>> Mark
>
> Alan
>
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Re: [GSOC 2015] Taverna: Databundle viewer for web
Posted by Alan Williams <al...@googlemail.com>.
On 01-Mar-15 15:31, Mark Fortner wrote:
> Looking at the issue, wouldn't Grails or jruby on rails be a better fit,
> given that most of the existing codebase is in java?
I think that the only relevant code would be that to look inside a
Taverna databundle. Although there is Java code for that inside the
Taverna Language package, there is a Ruby library for the research
object bundles at https://github.com/myGrid/ruby-ro-bundle.git .
So Java or Ruby would probably be OK - though as you say, Java would fit
in with the majority of the code, and the Ruby library is not in Apache
(yet?)
> Mark
Alan
Re: [GSOC 2015] Taverna: Databundle viewer for web
Posted by Stian Soiland-Reyes <st...@apache.org>.
Hi, thanks for noting your interest! I think this could be a great
GSOC project for a student with your background.
I think the student should be free to choose implementation
language(s). The format is basically a JSON inside a ZIP file - and as
this project was intending to mainly just do parsing/display you can
do it however you want.
See
https://w3id.org/bundle
for the specifications. Note that Workflow Runs don't contain all of
this metadata.
In the first instance you could just show a simple folder view of the
ZIP file - this works fairly OK for inputs and outputs, but falls
apart for intermediate values which just have a UUID-based filename,
and lists, which could become deeply nested in some workflows.
As pointed out we already have RO Bundle APIs for Java and Ruby which
could help you decide:
https://github.com/apache/incubator-taverna-language/tree/master/taverna-databundle
https://github.com/myGrid/ruby-ro-bundle
In a client/server architecture I would myself probably have a simple
server that simply expose the individual bits of the ZIP file as a
resource, and do most of the heavy work in Javascript. (Unzipping the
whole thing in Javascript is probably not a good idea).
On 1 March 2015 at 15:59, Денис Карякин <sa...@gmail.com> wrote:
> I think Jruby with rails is ok, but why Grails?
> Pivotal will close funding for Groovy and Grails, maybe framework will be
> unsupported
>
>
> 2015-03-01 18:31 GMT+03:00 Mark Fortner <ph...@gmail.com>:
>
>> Looking at the issue, wouldn't Grails or jruby on rails be a better fit,
>> given that most of the existing codebase is in java?
>>
>> Mark
>> On Mar 1, 2015 6:59 AM, "Денис Карякин" <sa...@gmail.com> wrote:
>>
>> > Hello, my name is Denis, I'm very interested in your project to develop
>> web
>> > viewer for Taverna. I found it here:
>> > https://issues.apache.org/jira/browse/COMDEV-121
>> >
>> > I have questions about user story:
>> > "User navigates to inputs/outputs" - this means user can upload input
>> > data?And then get output data?
>> > So, as I understand, user can upload workflow file, then upload input
>> data.
>> > All this data will be sended to Taverna Server, and after processing user
>> > can upload output data.
>> > Or, maybe, needed to do visualization how workflow works and which data
>> > have been processing?
>> >
>> > Briefly about me:
>> > I get a master's degree at the Saratov State University
>> > I am in Russia, Saratov, UTC + 3
>> > This is my first participation in GSOC.
>> > I am currently working at the university, developing learning management
>> > system.
>> > I started work with Ruby on Rails two years ago, so i have medium work
>> > experience with this framework. Also, i used Bootstrap, jQuery, etc.
>> > In university I also used C++, Java and PHP.
>> > I also very interesting in bioinformatic, i visited the Bioinformatic
>> > summer school (http://bioinformaticsinstitute.ru/summer2014) and took
>> part
>> > in the work on a small scientific task.
>> > This is my Github profile https://github.com/Samhane
>> >
>>
--
Stian Soiland-Reyes
Apache Taverna (incubating)
http://orcid.org/0000-0001-9842-9718
Re: [GSOC 2015] Taverna: Databundle viewer for web
Posted by Mark Fortner <ph...@gmail.com>.
They're currently evaluating options from Apache, Eclipse and other
organizations. They'll both survive, the main question is how the leads
developers will be paid.
Mark
On Mar 1, 2015 8:00 AM, "Денис Карякин" <sa...@gmail.com> wrote:
> I think Jruby with rails is ok, but why Grails?
> Pivotal will close funding for Groovy and Grails, maybe framework will be
> unsupported
>
>
> 2015-03-01 18:31 GMT+03:00 Mark Fortner <ph...@gmail.com>:
>
> > Looking at the issue, wouldn't Grails or jruby on rails be a better fit,
> > given that most of the existing codebase is in java?
> >
> > Mark
> > On Mar 1, 2015 6:59 AM, "Денис Карякин" <sa...@gmail.com> wrote:
> >
> > > Hello, my name is Denis, I'm very interested in your project to develop
> > web
> > > viewer for Taverna. I found it here:
> > > https://issues.apache.org/jira/browse/COMDEV-121
> > >
> > > I have questions about user story:
> > > "User navigates to inputs/outputs" - this means user can upload input
> > > data?And then get output data?
> > > So, as I understand, user can upload workflow file, then upload input
> > data.
> > > All this data will be sended to Taverna Server, and after processing
> user
> > > can upload output data.
> > > Or, maybe, needed to do visualization how workflow works and which data
> > > have been processing?
> > >
> > > Briefly about me:
> > > I get a master's degree at the Saratov State University
> > > I am in Russia, Saratov, UTC + 3
> > > This is my first participation in GSOC.
> > > I am currently working at the university, developing learning
> management
> > > system.
> > > I started work with Ruby on Rails two years ago, so i have medium work
> > > experience with this framework. Also, i used Bootstrap, jQuery, etc.
> > > In university I also used C++, Java and PHP.
> > > I also very interesting in bioinformatic, i visited the Bioinformatic
> > > summer school (http://bioinformaticsinstitute.ru/summer2014) and took
> > part
> > > in the work on a small scientific task.
> > > This is my Github profile https://github.com/Samhane
> > >
> >
>
Re: [GSOC 2015] Taverna: Databundle viewer for web
Posted by Денис Карякин <sa...@gmail.com>.
I think Jruby with rails is ok, but why Grails?
Pivotal will close funding for Groovy and Grails, maybe framework will be
unsupported
2015-03-01 18:31 GMT+03:00 Mark Fortner <ph...@gmail.com>:
> Looking at the issue, wouldn't Grails or jruby on rails be a better fit,
> given that most of the existing codebase is in java?
>
> Mark
> On Mar 1, 2015 6:59 AM, "Денис Карякин" <sa...@gmail.com> wrote:
>
> > Hello, my name is Denis, I'm very interested in your project to develop
> web
> > viewer for Taverna. I found it here:
> > https://issues.apache.org/jira/browse/COMDEV-121
> >
> > I have questions about user story:
> > "User navigates to inputs/outputs" - this means user can upload input
> > data?And then get output data?
> > So, as I understand, user can upload workflow file, then upload input
> data.
> > All this data will be sended to Taverna Server, and after processing user
> > can upload output data.
> > Or, maybe, needed to do visualization how workflow works and which data
> > have been processing?
> >
> > Briefly about me:
> > I get a master's degree at the Saratov State University
> > I am in Russia, Saratov, UTC + 3
> > This is my first participation in GSOC.
> > I am currently working at the university, developing learning management
> > system.
> > I started work with Ruby on Rails two years ago, so i have medium work
> > experience with this framework. Also, i used Bootstrap, jQuery, etc.
> > In university I also used C++, Java and PHP.
> > I also very interesting in bioinformatic, i visited the Bioinformatic
> > summer school (http://bioinformaticsinstitute.ru/summer2014) and took
> part
> > in the work on a small scientific task.
> > This is my Github profile https://github.com/Samhane
> >
>
Re: [GSOC 2015] Taverna: Databundle viewer for web
Posted by Mark Fortner <ph...@gmail.com>.
Looking at the issue, wouldn't Grails or jruby on rails be a better fit,
given that most of the existing codebase is in java?
Mark
On Mar 1, 2015 6:59 AM, "Денис Карякин" <sa...@gmail.com> wrote:
> Hello, my name is Denis, I'm very interested in your project to develop web
> viewer for Taverna. I found it here:
> https://issues.apache.org/jira/browse/COMDEV-121
>
> I have questions about user story:
> "User navigates to inputs/outputs" - this means user can upload input
> data?And then get output data?
> So, as I understand, user can upload workflow file, then upload input data.
> All this data will be sended to Taverna Server, and after processing user
> can upload output data.
> Or, maybe, needed to do visualization how workflow works and which data
> have been processing?
>
> Briefly about me:
> I get a master's degree at the Saratov State University
> I am in Russia, Saratov, UTC + 3
> This is my first participation in GSOC.
> I am currently working at the university, developing learning management
> system.
> I started work with Ruby on Rails two years ago, so i have medium work
> experience with this framework. Also, i used Bootstrap, jQuery, etc.
> In university I also used C++, Java and PHP.
> I also very interesting in bioinformatic, i visited the Bioinformatic
> summer school (http://bioinformaticsinstitute.ru/summer2014) and took part
> in the work on a small scientific task.
> This is my Github profile https://github.com/Samhane
>
Re: [GSOC 2015] Taverna: Databundle viewer for web
Posted by Alan Williams <al...@googlemail.com>.
On 01-Mar-15 14:56, Денис Карякин wrote:
> Hello, my name is Denis, I'm very interested in your project to develop web
> viewer for Taverna. I found it here:
> https://issues.apache.org/jira/browse/COMDEV-121
>
> I have questions about user story:
> "User navigates to inputs/outputs" - this means user can upload input
> data?And then get output data?
> So, as I understand, user can upload workflow file, then upload input data.
> All this data will be sended to Taverna Server, and after processing user
> can upload output data.
> Or, maybe, needed to do visualization how workflow works and which data
> have been processing?
My understanding is that the server mentioned in (1) to (5) is not a
Taverna server but the server on which the web-based presentation system
is hosted.
Taverna Server is only relevant because a Taverna Server, once a
workflow has been run, creates a single file that contains all the
information about that workflow run, It is that single file that is
uploaded to the presentation server.
I will not edit the issue as it is probably better if Stian or Ian
change it, as I may be wrong in my interpretation of the issue. I have
put my suggestion in a comment.
[snip]
Alan
Re: [GSOC 2015] Taverna: Databundle viewer for web
Posted by Денис Карякин <sa...@gmail.com>.
Thank you very much for reviewing proposal. I fixed mistakes and added some
information about me and about description and scheduling
2015-03-25 12:38 GMT+03:00 alaninmcr <al...@googlemail.com>:
> On 24/03/2015 22:27, Денис Карякин wrote:
>
>> Hello, I successfully upgrade taverna-player-portal to 4.2.0 rails(
>> https://github.com/Samhane/taverna-player-portal/commits/rails-4).
>> Also, I updated taverna-player(
>> https://github.com/Samhane/taverna-player/commits/rails4) for successfull
>> working with taverna-player-portal, but getting errors in tests,
>> associated
>> with problem in encoding. After resolving this errors and updating to new
>> rails 4.2.1, I planning to create pull request to original taverna-player
>> and taverna-player-portal repositories.
>>
>
> That is great. Thanks
>
> Also, I started upgrade SEEK to Rails 4 :) But, it project has many
>> dependencies and I first need to upgrade it dependencies.
>> I think I'll do it after some time.
>>
>
> There is no need to upgrade SEEK.
>
> Also, i wrote proposal for databundle viewer. I would like to thank
>> someone
>> for feedback in this proposal :)
>> https://docs.google.com/document/d/1wiEMMBCmPCVlFgvVz7Rux-
>> Y7IXX3LOJRSuoiBpRhLtc/edit?usp=sharing
>>
>
> I will read the proposal and comment.
>
> Alan
>
Re: [GSOC 2015] Taverna: Databundle viewer for web
Posted by alaninmcr <al...@googlemail.com>.
On 24/03/2015 22:27, Денис Карякин wrote:
> Hello, I successfully upgrade taverna-player-portal to 4.2.0 rails(
> https://github.com/Samhane/taverna-player-portal/commits/rails-4).
> Also, I updated taverna-player(
> https://github.com/Samhane/taverna-player/commits/rails4) for successfull
> working with taverna-player-portal, but getting errors in tests, associated
> with problem in encoding. After resolving this errors and updating to new
> rails 4.2.1, I planning to create pull request to original taverna-player
> and taverna-player-portal repositories.
That is great. Thanks
> Also, I started upgrade SEEK to Rails 4 :) But, it project has many
> dependencies and I first need to upgrade it dependencies.
> I think I'll do it after some time.
There is no need to upgrade SEEK.
> Also, i wrote proposal for databundle viewer. I would like to thank someone
> for feedback in this proposal :)
> https://docs.google.com/document/d/1wiEMMBCmPCVlFgvVz7Rux-Y7IXX3LOJRSuoiBpRhLtc/edit?usp=sharing
I will read the proposal and comment.
Alan
Re: [GSOC 2015] Taverna: Databundle viewer for web
Posted by Денис Карякин <sa...@gmail.com>.
Hello, I successfully upgrade taverna-player-portal to 4.2.0 rails(
https://github.com/Samhane/taverna-player-portal/commits/rails-4).
Also, I updated taverna-player(
https://github.com/Samhane/taverna-player/commits/rails4) for successfull
working with taverna-player-portal, but getting errors in tests, associated
with problem in encoding. After resolving this errors and updating to new
rails 4.2.1, I planning to create pull request to original taverna-player
and taverna-player-portal repositories.
Also, I started upgrade SEEK to Rails 4 :) But, it project has many
dependencies and I first need to upgrade it dependencies.
I think I'll do it after some time.
Also, i wrote proposal for databundle viewer. I would like to thank someone
for feedback in this proposal :)
https://docs.google.com/document/d/1wiEMMBCmPCVlFgvVz7Rux-Y7IXX3LOJRSuoiBpRhLtc/edit?usp=sharing
2015-03-04 23:24 GMT+03:00 Alan Williams <al...@googlemail.com>:
> On 04-Mar-15 19:51, Денис Карякин wrote:
>
>> I installed Taverna Server, and play with taverna-player-portal.
>>
>
> Great. In theory, you do not need to understand the Taverna Server or
> player as you will just read the databundle. However, it is excellent that
> you are looking at these.
>
> I think Ruby on Rails will be a good choise for Databundle viewer, because
>> already exists ro-bundle and taverna-player gems, written in Ruby.
>> Maybe create viewer as a gem, like taverna-player?
>>
>
> It may be good to have Gem to do much of the processing. However, I think
> you would still need something to do the presentation system - so you can
> have a website that the user uses.
>
> And what with Taverna Online? This project proprietary software?
>>
>
> Yes. Taverna Online is proprietary software. It may be able to generate a
> Databundle for you as it runs the workflows on a server. I do not think it
> is immediately relevant to you.
>
> My brief proposal plan:
>> 1) Upload file with using carrierwave (
>> https://github.com/carrierwaveuploader/carrierwave), parse it on the
>> backend(with using ruby-ro-bundle) and send data to frontend.
>> For backend use RoR, for frontend ember.js or backbone.
>>
>
> I think this needs a diagram :) By "frontend" I guess you mean the user's
> browser.
>
> Need to save uploaded file for next usage?
>>
>
> That will get you into the area of user accounts, user separation,
> sharing, deletion of files etc. I think Rob is best to advise on this.
>
> And how big size of bundle file?
>>
>
> Stian (and Donal?) can answer that.
>
> 2) Show structure of file on frontend with js and bootstrap
>> What data may contain bundle file? Graphics, images, text, anything else?
>>
>
> Lists (of lists of lists ...). Error documents.
>
> What i need to do now?
>> For showing competence in rails, maybe to do something with
>> taverna-payer-portal?
>> For example, add build status images or upgrade rails to 4.2, or something
>> else?
>>
>
> Upgrading it to Rails 4.2 would be brilliant. I am looking at upgrading
> SEEK (https://github.com/seek4science/seek) to Rails 4 :)
>
> Alan
>
Re: [GSOC 2015] Taverna: Databundle viewer for web
Posted by Alan Williams <al...@googlemail.com>.
On 04-Mar-15 19:51, Денис Карякин wrote:
> I installed Taverna Server, and play with taverna-player-portal.
Great. In theory, you do not need to understand the Taverna Server or
player as you will just read the databundle. However, it is excellent
that you are looking at these.
> I think Ruby on Rails will be a good choise for Databundle viewer, because
> already exists ro-bundle and taverna-player gems, written in Ruby.
> Maybe create viewer as a gem, like taverna-player?
It may be good to have Gem to do much of the processing. However, I
think you would still need something to do the presentation system - so
you can have a website that the user uses.
> And what with Taverna Online? This project proprietary software?
Yes. Taverna Online is proprietary software. It may be able to generate
a Databundle for you as it runs the workflows on a server. I do not
think it is immediately relevant to you.
> My brief proposal plan:
> 1) Upload file with using carrierwave (
> https://github.com/carrierwaveuploader/carrierwave), parse it on the
> backend(with using ruby-ro-bundle) and send data to frontend.
> For backend use RoR, for frontend ember.js or backbone.
I think this needs a diagram :) By "frontend" I guess you mean the
user's browser.
> Need to save uploaded file for next usage?
That will get you into the area of user accounts, user separation,
sharing, deletion of files etc. I think Rob is best to advise on this.
> And how big size of bundle file?
Stian (and Donal?) can answer that.
> 2) Show structure of file on frontend with js and bootstrap
> What data may contain bundle file? Graphics, images, text, anything else?
Lists (of lists of lists ...). Error documents.
> What i need to do now?
> For showing competence in rails, maybe to do something with
> taverna-payer-portal?
> For example, add build status images or upgrade rails to 4.2, or something
> else?
Upgrading it to Rails 4.2 would be brilliant. I am looking at upgrading
SEEK (https://github.com/seek4science/seek) to Rails 4 :)
Alan
Re: [GSOC 2015] Taverna: Databundle viewer for web
Posted by Денис Карякин <sa...@gmail.com>.
I installed Taverna Server, and play with taverna-player-portal.
I think Ruby on Rails will be a good choise for Databundle viewer, because
already exists ro-bundle and taverna-player gems, written in Ruby.
Maybe create viewer as a gem, like taverna-player?
And what with Taverna Online? This project proprietary software?
My brief proposal plan:
1) Upload file with using carrierwave (
https://github.com/carrierwaveuploader/carrierwave), parse it on the
backend(with using ruby-ro-bundle) and send data to frontend.
For backend use RoR, for frontend ember.js or backbone.
Need to save uploaded file for next usage? And how big size of bundle file?
2) Show structure of file on frontend with js and bootstrap
What data may contain bundle file? Graphics, images, text, anything else?
What i need to do now?
For showing competence in rails, maybe to do something with
taverna-payer-portal?
For example, add build status images or upgrade rails to 4.2, or something
else?
2015-03-02 16:30 GMT+03:00 Stian Soiland-Reyes <st...@apache.org>:
> ..apologies for the confusing text.. we put it together a bit quickly.
> You actually found it in the bug tracker the next day!
>
>
> We were thinking mainly as an independent viewer of past results -
> exactly how those runs were made should not be important, as you can
> create DataBundles from the workbench, command line and server. The
> data bundles could also be shared on websites like myExperiment.org
> and Dropbox - and be attached as supplementary material to published
> papers.
>
> Obviously an integration with say the Taverna Player code (Ruby on
> Rails plugin for executing through taverna server) could also be
> interesting - but I was thinking to mainly focus on the viewer aspect
> rather than prepare-for-run aspect (which we have some support for
> already in Taverna Player).
>
> If this becomes useful we can try to host the DataBundle Viewer
> somewhere as a general service - similar to Python Notebook Viewer in
> a way.
>
>
>
> On 1 March 2015 at 14:56, Денис Карякин <sa...@gmail.com> wrote:
> > Hello, my name is Denis, I'm very interested in your project to develop
> web
> > viewer for Taverna. I found it here:
> > https://issues.apache.org/jira/browse/COMDEV-121
> >
> > I have questions about user story:
> > "User navigates to inputs/outputs" - this means user can upload input
> > data?And then get output data?
> > So, as I understand, user can upload workflow file, then upload input
> data.
> > All this data will be sended to Taverna Server, and after processing user
> > can upload output data.
> > Or, maybe, needed to do visualization how workflow works and which data
> > have been processing?
> >
> > Briefly about me:
> > I get a master's degree at the Saratov State University
> > I am in Russia, Saratov, UTC + 3
> > This is my first participation in GSOC.
> > I am currently working at the university, developing learning management
> > system.
> > I started work with Ruby on Rails two years ago, so i have medium work
> > experience with this framework. Also, i used Bootstrap, jQuery, etc.
> > In university I also used C++, Java and PHP.
> > I also very interesting in bioinformatic, i visited the Bioinformatic
> > summer school (http://bioinformaticsinstitute.ru/summer2014) and took
> part
> > in the work on a small scientific task.
> > This is my Github profile https://github.com/Samhane
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating)
> http://orcid.org/0000-0001-9842-9718
>
Re: [GSOC 2015] Taverna: Databundle viewer for web
Posted by Stian Soiland-Reyes <st...@apache.org>.
..apologies for the confusing text.. we put it together a bit quickly.
You actually found it in the bug tracker the next day!
We were thinking mainly as an independent viewer of past results -
exactly how those runs were made should not be important, as you can
create DataBundles from the workbench, command line and server. The
data bundles could also be shared on websites like myExperiment.org
and Dropbox - and be attached as supplementary material to published
papers.
Obviously an integration with say the Taverna Player code (Ruby on
Rails plugin for executing through taverna server) could also be
interesting - but I was thinking to mainly focus on the viewer aspect
rather than prepare-for-run aspect (which we have some support for
already in Taverna Player).
If this becomes useful we can try to host the DataBundle Viewer
somewhere as a general service - similar to Python Notebook Viewer in
a way.
On 1 March 2015 at 14:56, Денис Карякин <sa...@gmail.com> wrote:
> Hello, my name is Denis, I'm very interested in your project to develop web
> viewer for Taverna. I found it here:
> https://issues.apache.org/jira/browse/COMDEV-121
>
> I have questions about user story:
> "User navigates to inputs/outputs" - this means user can upload input
> data?And then get output data?
> So, as I understand, user can upload workflow file, then upload input data.
> All this data will be sended to Taverna Server, and after processing user
> can upload output data.
> Or, maybe, needed to do visualization how workflow works and which data
> have been processing?
>
> Briefly about me:
> I get a master's degree at the Saratov State University
> I am in Russia, Saratov, UTC + 3
> This is my first participation in GSOC.
> I am currently working at the university, developing learning management
> system.
> I started work with Ruby on Rails two years ago, so i have medium work
> experience with this framework. Also, i used Bootstrap, jQuery, etc.
> In university I also used C++, Java and PHP.
> I also very interesting in bioinformatic, i visited the Bioinformatic
> summer school (http://bioinformaticsinstitute.ru/summer2014) and took part
> in the work on a small scientific task.
> This is my Github profile https://github.com/Samhane
--
Stian Soiland-Reyes
Apache Taverna (incubating)
http://orcid.org/0000-0001-9842-9718