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Posted to dev@taverna.apache.org by Denis Karyakin <sa...@gmail.com> on 2015/06/12 19:08:06 UTC
Taverna Databundle Viewer - progress
Hello
Sorry, I'm was a very busy with my graduation work and forgot send updates
in mail list.
I done:
Create new rails application
Set up devise: sign in and sign up + write tests for it
Omniauth authorization with facebook and google + write tests for it
For UI I found Bootstrap theme with the MIT licence.
It's ok to use this theme (https://github.com/almasaeed2010/AdminLTE)?
I has set up continious integration process: after push code on github, all
tests run on Semaphoreci (https://semaphoreci.com/) and if all tests are
success - deploy application to heroku (http://databundle.herokuapp.com/).
I has set up CodeClimate (
https://codeclimate.com/github/Samhane/incubator-taverna-databundle-viewer)
for control code quality and added badges to repository
Also, I have template for uploading files with carrierwave gem.
Also, I write some start documentation for run application
In some files I was added the Apache license header.
There I have a question: need add this header to all files? Or only for
files with some logic, for example controllers, models, specs?
I send pull request on github
Next week I will work by parsing databundle file, first task will be show
input and output.
For this task I need variety examples of databundle files. Where I can find
this?
Re: Taverna Databundle Viewer - progress
Posted by Stian Soiland-Reyes <st...@apache.org>.
On 15 July 2015 at 10:55, alaninmcr <al...@googlemail.com> wrote:
>> How this commits will be merge?
>> In original repository presented commits, which not presented in my
>> repository. Would I need to do pull from original?
> That would be the best way. I think it is just the NOTICE, LICENSE and
> README.md that have been changed.
I think git rebase should work well in this case as the changes should
not conflict with you:
git checkout master # or whatever local branch you have
git checkout -b rebased # just in case it goes wrong
git remote add upstream
https://git-wip-us.apache.org/repos/asf/incubator-taverna-databundle-viewer.git
git fetch upstream
git rebase upstream/master
git checkout master # or whatever local branch you have
git reset --hard rebased
Byt if git rebase goes wrong and you are unable to easily fix it, e.g.
README.md conflicts, then a 'git merge' is probably easier:
git rebase --abort
git checkout master
git branch -D rebased # delete that failed attempt
git merge upstream/master
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718
Re: Taverna Databundle Viewer - progress
Posted by alaninmcr <al...@googlemail.com>.
Hello Denis
I think the request is pulled into the Apache repository OK.
Alan
Re: Taverna Databundle Viewer - progress
Posted by Denis Karyakin <sa...@gmail.com>.
I created it just now)
Pull request can't automatically merge because content(every file) of
commits from "Create Rails application" to "Updated README: simplified
installation instructions" is
already in repository
https://github.com/apache/incubator-taverna-databundle-viewer
In repository only content of commits, not the commits itself
This is because I'm not commiter to the original repository (
https://github.com/apache/incubator-taverna-databundle-viewer)
But how resolve this merge conflicts?)
2015-08-20 18:13 GMT+03:00 alaninmcr <al...@googlemail.com>:
> On 20/08/2015 16:00, Denis Karyakin wrote:
>
>> Hello,
>> I improved test coverage and code quality (by Code Climate metrics)
>>
>> I didn't sent pull request, because github say that this pull request
>> can’t
>> automatically merge
>> And in canceled pull request I saw my commits, content of which already
>> contained in original repository
>>
>
> Hello,
>
> Do you have a pull request to the github repository? I'm confused :)
>
> Alan
>
Re: Taverna Databundle Viewer - progress
Posted by alaninmcr <al...@googlemail.com>.
On 20/08/2015 16:00, Denis Karyakin wrote:
> Hello,
> I improved test coverage and code quality (by Code Climate metrics)
>
> I didn't sent pull request, because github say that this pull request can’t
> automatically merge
> And in canceled pull request I saw my commits, content of which already
> contained in original repository
Hello,
Do you have a pull request to the github repository? I'm confused :)
Alan
Re: Taverna Databundle Viewer - progress
Posted by Denis Karyakin <sa...@gmail.com>.
Hello,
I improved test coverage and code quality (by Code Climate metrics)
I didn't sent pull request, because github say that this pull request can’t
automatically merge
And in canceled pull request I saw my commits, content of which already
contained in original repository
2015-08-19 23:32 GMT+03:00 Denis Karyakin <sa...@gmail.com>:
> Hello,
> I almost finished and checked the project.
>
> This is my report for last two weeks:
> Added the Apache licenses in files which don't contained it yet.
> Added comments to Gemfile and in project files.
> Updated GEM_LICENSES.md, renamed to DEPENDENCY_LICENSES.md, because it now
> contains not only gems licenses, but also front-end assets licenses,
> installed with bower.
> Updated and checked UI for every page.
> Updated and wrote a few new tests for the application .
> Removed vendor front-end assets from codebase, added it with bower,
> because with bower I can easy manage front-end assets, for example:
> bootstrap theme used in databundle viewer updated and with bower I easy
> download and use new version. It depend from npm (from node.js), but if
> this application will grow, bower will help to manage javascript and css
> dependencies.
> Added pagination for data_bundles.
> Replaced jsPlumb to d3.js
> Made visualization of workflow run, not great, but showed every steps of
> run. In inputs and outputs you can click and see value on input and output.
>
> Updated README:
> Updated building and install requirements, include information about
> installing bower, setting up AWS S3, and ways to setting environmental
> variables.
> Added section abut usage, in development and production environments.
> Added documentation, wrote some about main classes in application
> Added todo section, with future plans.
>
> Now I have some troubles with AWS S3 and heroku, but you can download
> DataBundle Viewer and use it locally.
>
> I sent pull request to original repository
>
> 2015-08-14 19:29 GMT+03:00 Alan Williams <al...@googlemail.com>:
>
>> On 14-Aug-15 16:54, Denis Karyakin wrote:
>>
>>> Hello,
>>>
>>
>> Hello
>>
>> I updated some issues status and add comments to it.
>>> I think in Monday I will deploy ready to get user feedback DataBundle
>>> viewer and write additional documentation and tests.
>>>
>>
>> We also need to make sure everything is checked in.
>>
>> I choosed js library for show workflow run and now I have only one
>>> trouble:
>>> how to link intermediate files with workflow step? I still research it in
>>> the taverna source codes (taverna language and taverna workbench).
>>>
>>
>> Stian can probably help. You need to be careful about starting new blocks
>> of work. It is more important to get everything checked in and documented
>> even if there are still areas not done.
>>
>> Also I have a question: will the DataBundle viewer integrate with taverna
>>> player portal?
>>>
>> > I think in future it will be great transform databundle viewer from
>> rails
>> > application to gem, what will be included in taverna player
>>
>> In my opinion, yes and no :) It will be great if the viewer is integrated
>> with the portal, but we need to make sure that it is usable outside of the
>> context of the portal.
>>
>> Alan
>>
>
>
Re: Taverna Databundle Viewer - progress
Posted by Denis Karyakin <sa...@gmail.com>.
Hello,
I almost finished and checked the project.
This is my report for last two weeks:
Added the Apache licenses in files which don't contained it yet.
Added comments to Gemfile and in project files.
Updated GEM_LICENSES.md, renamed to DEPENDENCY_LICENSES.md, because it now
contains not only gems licenses, but also front-end assets licenses,
installed with bower.
Updated and checked UI for every page.
Updated and wrote a few new tests for the application .
Removed vendor front-end assets from codebase, added it with bower, because
with bower I can easy manage front-end assets, for example: bootstrap theme
used in databundle viewer updated and with bower I easy download and use
new version. It depend from npm (from node.js), but if this application
will grow, bower will help to manage javascript and css dependencies.
Added pagination for data_bundles.
Replaced jsPlumb to d3.js
Made visualization of workflow run, not great, but showed every steps of
run. In inputs and outputs you can click and see value on input and output.
Updated README:
Updated building and install requirements, include information about
installing bower, setting up AWS S3, and ways to setting environmental
variables.
Added section abut usage, in development and production environments.
Added documentation, wrote some about main classes in application
Added todo section, with future plans.
Now I have some troubles with AWS S3 and heroku, but you can download
DataBundle Viewer and use it locally.
I sent pull request to original repository
2015-08-14 19:29 GMT+03:00 Alan Williams <al...@googlemail.com>:
> On 14-Aug-15 16:54, Denis Karyakin wrote:
>
>> Hello,
>>
>
> Hello
>
> I updated some issues status and add comments to it.
>> I think in Monday I will deploy ready to get user feedback DataBundle
>> viewer and write additional documentation and tests.
>>
>
> We also need to make sure everything is checked in.
>
> I choosed js library for show workflow run and now I have only one trouble:
>> how to link intermediate files with workflow step? I still research it in
>> the taverna source codes (taverna language and taverna workbench).
>>
>
> Stian can probably help. You need to be careful about starting new blocks
> of work. It is more important to get everything checked in and documented
> even if there are still areas not done.
>
> Also I have a question: will the DataBundle viewer integrate with taverna
>> player portal?
>>
> > I think in future it will be great transform databundle viewer from
> rails
> > application to gem, what will be included in taverna player
>
> In my opinion, yes and no :) It will be great if the viewer is integrated
> with the portal, but we need to make sure that it is usable outside of the
> context of the portal.
>
> Alan
>
Re: Taverna Databundle Viewer - progress
Posted by Alan Williams <al...@googlemail.com>.
On 14-Aug-15 16:54, Denis Karyakin wrote:
> Hello,
Hello
> I updated some issues status and add comments to it.
> I think in Monday I will deploy ready to get user feedback DataBundle
> viewer and write additional documentation and tests.
We also need to make sure everything is checked in.
> I choosed js library for show workflow run and now I have only one trouble:
> how to link intermediate files with workflow step? I still research it in
> the taverna source codes (taverna language and taverna workbench).
Stian can probably help. You need to be careful about starting new
blocks of work. It is more important to get everything checked in and
documented even if there are still areas not done.
> Also I have a question: will the DataBundle viewer integrate with taverna
> player portal?
> I think in future it will be great transform databundle viewer from
rails
> application to gem, what will be included in taverna player
In my opinion, yes and no :) It will be great if the viewer is
integrated with the portal, but we need to make sure that it is usable
outside of the context of the portal.
Alan
Re: Taverna Databundle Viewer - progress
Posted by Denis Karyakin <sa...@gmail.com>.
Hello,
I updated some issues status and add comments to it.
I think in Monday I will deploy ready to get user feedback DataBundle
viewer and write additional documentation and tests.
I choosed js library for show workflow run and now I have only one trouble:
how to link intermediate files with workflow step? I still research it in
the taverna source codes (taverna language and taverna workbench).
Also I have a question: will the DataBundle viewer integrate with taverna
player portal?
I think in future it will be great transform databundle viewer from rails
application to gem, what will be included in taverna player
2015-08-07 2:55 GMT+03:00 Denis Karyakin <sa...@gmail.com>:
> 2015-08-05 17:59 GMT+03:00 alaninmcr <al...@googlemail.com>:
>
>> On 04/08/2015 23:31, Denis Karyakin wrote:
>>
>>> Hello,
>>> What I need to do with different commits?
>>>
>>
>> I am uncertain what you are asking. Were the merge conflicts sorted out?
>>
>>
> Hello,
> Maybe I misunderstood work with pull requests to the apache repository.
>
> Repository https://github.com/apache/incubator-taverna-databundle-viewer
> have commits:
> ...
> "Pull from github" ae912ef29fe42b808840c9b4833a21d0e6cae3a9
> "Pull from github" 17edf13a7d3149904467ecd3a5cd3e256d447ec4
> ....
>
> This two commits contain all changes (all files and content in this files)
> from commit
> "Create Rails application" 042ef369762de3019d539a4d8a605e68d5087391
> to commit
> "Removed trailing whitespaces" cac0c307a8a31ac9285f8bf0afb1c1ba4bd6c697
> in my fork https://github.com/Samhane/incubator-taverna-databundle-viewer
>
> So, in repositories are different history and therefore I get many merge
> conflicts when pull from
> https://github.com/apache/incubator-taverna-databundle-viewer.
> Should I merge with
> https://github.com/apache/incubator-taverna-databundle-viewer (as
> upstream repository) and fix all conflicts? Or I should only create pull
> request?
>
>
>> Currently I work with new features in separate git branch. I processed all
>>> workflow files from the Starter Pack and now work by show workflow run
>>> from
>>> input to output step by step
>>>
>>
>> Hello. I think we need to get user feedback. Do you have a server stood
>> up or should I do it?
>>
>
> I have a deployed application on heroku. But before presentation to get
> user feedback I want to finish with draft showing full workflow run
>
>>
>> Alan
>>
>
>
Re: Taverna Databundle Viewer - progress
Posted by Denis Karyakin <sa...@gmail.com>.
2015-08-05 17:59 GMT+03:00 alaninmcr <al...@googlemail.com>:
> On 04/08/2015 23:31, Denis Karyakin wrote:
>
>> Hello,
>> What I need to do with different commits?
>>
>
> I am uncertain what you are asking. Were the merge conflicts sorted out?
>
>
Hello,
Maybe I misunderstood work with pull requests to the apache repository.
Repository https://github.com/apache/incubator-taverna-databundle-viewer
have commits:
...
"Pull from github" ae912ef29fe42b808840c9b4833a21d0e6cae3a9
"Pull from github" 17edf13a7d3149904467ecd3a5cd3e256d447ec4
....
This two commits contain all changes (all files and content in this files)
from commit
"Create Rails application" 042ef369762de3019d539a4d8a605e68d5087391
to commit
"Removed trailing whitespaces" cac0c307a8a31ac9285f8bf0afb1c1ba4bd6c697
in my fork https://github.com/Samhane/incubator-taverna-databundle-viewer
So, in repositories are different history and therefore I get many merge
conflicts when pull from
https://github.com/apache/incubator-taverna-databundle-viewer.
Should I merge with
https://github.com/apache/incubator-taverna-databundle-viewer (as upstream
repository) and fix all conflicts? Or I should only create pull request?
> Currently I work with new features in separate git branch. I processed all
>> workflow files from the Starter Pack and now work by show workflow run
>> from
>> input to output step by step
>>
>
> Hello. I think we need to get user feedback. Do you have a server stood up
> or should I do it?
>
I have a deployed application on heroku. But before presentation to get
user feedback I want to finish with draft showing full workflow run
>
> Alan
>
Re: Taverna Databundle Viewer - progress
Posted by alaninmcr <al...@googlemail.com>.
On 04/08/2015 23:31, Denis Karyakin wrote:
> Hello,
> What I need to do with different commits?
I am uncertain what you are asking. Were the merge conflicts sorted out?
> Currently I work with new features in separate git branch. I processed all
> workflow files from the Starter Pack and now work by show workflow run from
> input to output step by step
Hello. I think we need to get user feedback. Do you have a server stood
up or should I do it?
Alan
Re: Taverna Databundle Viewer - progress
Posted by Denis Karyakin <sa...@gmail.com>.
Hello,
What I need to do with different commits?
Currently I work with new features in separate git branch. I processed all
workflow files from the Starter Pack and now work by show workflow run from
input to output step by step
2015-07-24 1:02 GMT+03:00 Denis Karyakin <sa...@gmail.com>:
> Hello,
>
> 2015-07-15 12:55 GMT+03:00 alaninmcr <al...@googlemail.com>:
>
>> On 14/07/2015 23:11, Denis Karyakin wrote:
>>
>>> Hello,
>>> This is my report for almost two weeks.
>>>
>>
>> It is OK to do more frequent commits - hint :)
>>
>
> Yes, I will try this...
>
>>
>> I send last commits with new feature
>>> 1) User can upload databundle file
>>> 2) User can navigates to inputs and outputs of databundle file
>>> 3) Store uploaded files to Amazon S3
>>>
>>
>> So does someone need an Amazon account to view databundles?
>
>
> Only owner of installed application need an Amazon account. Users don't
> need an Amazon account.
>
>>
>>
>> 4) Updated routes.rb with licence and removing unused staff
>>> 5) Display errors on log in
>>>
>>> I will run all workflows from the Starter Pack of the myExperiment for
>>> see
>>> diffrent types of inputs and outputs.
>>> Temporarily pages with show databundles contain ugly UI, I search good
>>> way
>>> for show workflow run
>>>
>>
>> There are lots of people here who can help with styling and presentation
>> issues.
>>
>> How this commits will be merge?
>>> In original repository presented commits, which not presented in my
>>> repository. Would I need to do pull from original?
>>>
>>
>> That would be the best way. I think it is just the NOTICE, LICENSE and
>> README.md that have been changed.
>
>
> In repositories some different commits :)
> Two commits (
> https://github.com/apache/incubator-taverna-databundle-viewer/commit/ae912ef29fe42b808840c9b4833a21d0e6cae3a9
> and
> https://github.com/apache/incubator-taverna-databundle-viewer/commit/17edf13a7d3149904467ecd3a5cd3e256d447ec4)
> contain many commits from
> https://github.com/Samhane/incubator-taverna-databundle-viewer.
> At merging I got many merge conflicts.
> What should I do? Fix merge conflicts? Or somehow repair history in
> repository https://github.com/apache/incubator-taverna-databundle-viewer/
> ?
>
>
Re: Taverna Databundle Viewer - progress
Posted by Denis Karyakin <sa...@gmail.com>.
Hello,
2015-07-15 12:55 GMT+03:00 alaninmcr <al...@googlemail.com>:
> On 14/07/2015 23:11, Denis Karyakin wrote:
>
>> Hello,
>> This is my report for almost two weeks.
>>
>
> It is OK to do more frequent commits - hint :)
>
Yes, I will try this...
>
> I send last commits with new feature
>> 1) User can upload databundle file
>> 2) User can navigates to inputs and outputs of databundle file
>> 3) Store uploaded files to Amazon S3
>>
>
> So does someone need an Amazon account to view databundles?
Only owner of installed application need an Amazon account. Users don't
need an Amazon account.
>
>
> 4) Updated routes.rb with licence and removing unused staff
>> 5) Display errors on log in
>>
>> I will run all workflows from the Starter Pack of the myExperiment for see
>> diffrent types of inputs and outputs.
>> Temporarily pages with show databundles contain ugly UI, I search good way
>> for show workflow run
>>
>
> There are lots of people here who can help with styling and presentation
> issues.
>
> How this commits will be merge?
>> In original repository presented commits, which not presented in my
>> repository. Would I need to do pull from original?
>>
>
> That would be the best way. I think it is just the NOTICE, LICENSE and
> README.md that have been changed.
In repositories some different commits :)
Two commits (
https://github.com/apache/incubator-taverna-databundle-viewer/commit/ae912ef29fe42b808840c9b4833a21d0e6cae3a9
and
https://github.com/apache/incubator-taverna-databundle-viewer/commit/17edf13a7d3149904467ecd3a5cd3e256d447ec4)
contain many commits from
https://github.com/Samhane/incubator-taverna-databundle-viewer.
At merging I got many merge conflicts.
What should I do? Fix merge conflicts? Or somehow repair history in
repository https://github.com/apache/incubator-taverna-databundle-viewer/ ?
Re: Taverna Databundle Viewer - progress
Posted by alaninmcr <al...@googlemail.com>.
On 14/07/2015 23:11, Denis Karyakin wrote:
> Hello,
> This is my report for almost two weeks.
It is OK to do more frequent commits - hint :)
> I send last commits with new feature
> 1) User can upload databundle file
> 2) User can navigates to inputs and outputs of databundle file
> 3) Store uploaded files to Amazon S3
So does someone need an Amazon account to view databundles?
> 4) Updated routes.rb with licence and removing unused staff
> 5) Display errors on log in
>
> I will run all workflows from the Starter Pack of the myExperiment for see
> diffrent types of inputs and outputs.
> Temporarily pages with show databundles contain ugly UI, I search good way
> for show workflow run
There are lots of people here who can help with styling and presentation
issues.
> How this commits will be merge?
> In original repository presented commits, which not presented in my
> repository. Would I need to do pull from original?
That would be the best way. I think it is just the NOTICE, LICENSE and
README.md that have been changed.
Alan
Re: Taverna Databundle Viewer - progress
Posted by Denis Karyakin <sa...@gmail.com>.
Hello,
This is my report for almost two weeks.
I send last commits with new features:
1) User can upload databundle file
2) User can navigates to inputs and outputs of databundle file
3) Store uploaded files to Amazon S3
4) Updated routes.rb with licence and removing unused staff
5) Display errors on log in
I will run all workflows from the Starter Pack of the myExperiment for see
diffrent types of inputs and outputs.
Temporarily pages with show databundles contain ugly UI, I search good way
for show workflow run
How this commits will be merge?
In original repository presented commits, which not presented in my
repository. Would I need to do pull from original?
2015-06-27 1:14 GMT+03:00 Alan Williams <al...@googlemail.com>:
> On 26-Jun-15 23:13, Denis Karyakin wrote:
>
>> Yes, I did it! :)
>> I have downloaded results from runs page of taverna-player-portal earlier.
>> But this results were received by taverna-player-portal by url
>> /runs/{id}/wd/out.
>> Now I get results with /runs/{id}/run-bundle url. It's valid ro-bundle
>> file, I checked with gem ruby-ro-bundle.
>> I think, later need to add this functionality (get run-bundle file) to
>> taverna-player-portal.
>>
>
> Yay! Happy dance :-D Well done.
>
> Alan
>
>
>
Re: Taverna Databundle Viewer - progress
Posted by Alan Williams <al...@googlemail.com>.
On 26-Jun-15 23:13, Denis Karyakin wrote:
> Yes, I did it! :)
> I have downloaded results from runs page of taverna-player-portal earlier.
> But this results were received by taverna-player-portal by url
> /runs/{id}/wd/out.
> Now I get results with /runs/{id}/run-bundle url. It's valid ro-bundle
> file, I checked with gem ruby-ro-bundle.
> I think, later need to add this functionality (get run-bundle file) to
> taverna-player-portal.
Yay! Happy dance :-D Well done.
Alan
Re: Taverna Databundle Viewer - progress
Posted by Denis Karyakin <sa...@gmail.com>.
Yes, I did it! :)
I have downloaded results from runs page of taverna-player-portal earlier.
But this results were received by taverna-player-portal by url
/runs/{id}/wd/out.
Now I get results with /runs/{id}/run-bundle url. It's valid ro-bundle
file, I checked with gem ruby-ro-bundle.
I think, later need to add this functionality (get run-bundle file) to
taverna-player-portal.
2015-06-26 14:01 GMT+03:00 alaninmcr <al...@googlemail.com>:
> On 25/06/2015 23:47, Denis Karyakin wrote:
>
>> Yes, I missed restful url, sorry)
>>
>> I didn't find how to set provenance parameter because t2-server gem
>> version
>> 1.0.0 didn't use provenance. After upgrade t2-server to 1.3.0 I find how
>> to
>> set up provenance. This upgrade I sent in pull request to
>> taverna-player-portal.
>>
>> After creating workflow run in taverna server I have sent put request by
>> using T2Server::Run#generate_provenance. In wireshark I see this request:
>> PUT
>>
>> /taverna-2.5.4/rest/runs/f844a875-e1c5-42c4-96ea-9e58073b9994/generate-provenance
>> HTTP/1.1\r\n
>> with true parameter.
>>
>> But taverna server returned again zip archive with only outputs..
>>
>
> I am a bit confused. On heater, I created a run, set generate provenance
> to true, set the run to Operating, waited and then fetched the run bundle.
>
> Can you try with a very simple workflow such as that from
> http://www.myexperiment.org/workflows/2648.html ?
>
> Alan
>
>
Re: Taverna Databundle Viewer - progress
Posted by alaninmcr <al...@googlemail.com>.
On 25/06/2015 23:47, Denis Karyakin wrote:
> Yes, I missed restful url, sorry)
>
> I didn't find how to set provenance parameter because t2-server gem version
> 1.0.0 didn't use provenance. After upgrade t2-server to 1.3.0 I find how to
> set up provenance. This upgrade I sent in pull request to
> taverna-player-portal.
>
> After creating workflow run in taverna server I have sent put request by
> using T2Server::Run#generate_provenance. In wireshark I see this request:
> PUT
> /taverna-2.5.4/rest/runs/f844a875-e1c5-42c4-96ea-9e58073b9994/generate-provenance
> HTTP/1.1\r\n
> with true parameter.
>
> But taverna server returned again zip archive with only outputs..
I am a bit confused. On heater, I created a run, set generate provenance
to true, set the run to Operating, waited and then fetched the run bundle.
Can you try with a very simple workflow such as that from
http://www.myexperiment.org/workflows/2648.html ?
Alan
Re: Taverna Databundle Viewer - progress
Posted by Denis Karyakin <sa...@gmail.com>.
Yes, I missed restful url, sorry)
I didn't find how to set provenance parameter because t2-server gem version
1.0.0 didn't use provenance. After upgrade t2-server to 1.3.0 I find how to
set up provenance. This upgrade I sent in pull request to
taverna-player-portal.
After creating workflow run in taverna server I have sent put request by
using T2Server::Run#generate_provenance. In wireshark I see this request:
PUT
/taverna-2.5.4/rest/runs/f844a875-e1c5-42c4-96ea-9e58073b9994/generate-provenance
HTTP/1.1\r\n
with true parameter.
But taverna server returned again zip archive with only outputs..
2015-06-24 11:26 GMT+03:00 Alan Williams <al...@googlemail.com>:
> On 24-Jun-15 01:11, Denis Karyakin wrote:
>
>> No, I didn't set generate-provenance earlier.
>> I tried to set it in taverna_server.rb:
>> in block TavernaPlayer.setup do |config|
>> config.server_connection[:generate_provenance] = true
>> but this has no effect.
>>
>
> It isn't part of the server connection information. It has to be set for
> each run.
>
> Also, with this option, file will be return in RDF Turtle format or RO
>> Bundle format?
>>
>
> Stian or Donal will be able to answer.
>
> Alan
>
Re: Taverna Databundle Viewer - progress
Posted by Alan Williams <al...@googlemail.com>.
On 24-Jun-15 01:11, Denis Karyakin wrote:
> No, I didn't set generate-provenance earlier.
> I tried to set it in taverna_server.rb:
> in block TavernaPlayer.setup do |config|
> config.server_connection[:generate_provenance] = true
> but this has no effect.
It isn't part of the server connection information. It has to be set for
each run.
> Also, with this option, file will be return in RDF Turtle format or RO
> Bundle format?
Stian or Donal will be able to answer.
Alan
Re: Taverna Databundle Viewer - progress
Posted by Denis Karyakin <sa...@gmail.com>.
No, I didn't set generate-provenance earlier.
I tried to set it in taverna_server.rb:
in block TavernaPlayer.setup do |config|
config.server_connection[:generate_provenance] = true
but this has no effect.
Also, with this option, file will be return in RDF Turtle format or RO
Bundle format?
2015-06-23 15:16 GMT+03:00 alaninmcr <al...@googlemail.com>:
> On 23/06/2015 13:02, Denis Karyakin wrote:
>
>> Hello,
>>
>
> Hello Denis
>
> How I can get robundle file from Taverna Server? After run workflow I get
>> zip archive only with outputs.
>>
>
> What options are you setting when you create the workflow run? Did you put
> true to /runs/{id}/generate-provenance ? It defaults to false.
>
> Alan
>
Re: Taverna Databundle Viewer - progress
Posted by alaninmcr <al...@googlemail.com>.
On 23/06/2015 13:02, Denis Karyakin wrote:
> Hello,
Hello Denis
> How I can get robundle file from Taverna Server? After run workflow I get
> zip archive only with outputs.
What options are you setting when you create the workflow run? Did you
put true to /runs/{id}/generate-provenance ? It defaults to false.
Alan
Re: Taverna Databundle Viewer - progress
Posted by Denis Karyakin <sa...@gmail.com>.
Hello,
How I can get robundle file from Taverna Server? After run workflow I get
zip archive only with outputs.
>From taverna player portal I can get full info about workflow run. Maybe
some convert this information in robundle file? Or I can use taverna player
API, without uploading file with result of workflow run?
2015-06-15 16:10 GMT+03:00 Denis Karyakin <sa...@gmail.com>:
> Thank you, I will use this gem
>
> 2015-06-12 20:56 GMT+03:00 Robert Haines <ro...@manchester.ac.uk>:
>
>> Hi Denis,
>>
>> <snip>
>>
>> Next week I will work by parsing databundle file, first task will be
>>> show input and output.
>>>
>>
>> Are databundles research objects underneath? If so then the ro-bundle gem
>> may do what you need, or could be extended, for parsing:
>>
>> https://rubygems.org/gems/ro-bundle
>>
>> Cheers,
>> Rob
>>
>>
>> For this task I need variety examples of
>>> databundle files. Where I can find this?
>>>
>>>
>
Re: Taverna Databundle Viewer - progress
Posted by Denis Karyakin <sa...@gmail.com>.
Thank you, I will use this gem
2015-06-12 20:56 GMT+03:00 Robert Haines <ro...@manchester.ac.uk>:
> Hi Denis,
>
> <snip>
>
> Next week I will work by parsing databundle file, first task will be
>> show input and output.
>>
>
> Are databundles research objects underneath? If so then the ro-bundle gem
> may do what you need, or could be extended, for parsing:
>
> https://rubygems.org/gems/ro-bundle
>
> Cheers,
> Rob
>
>
> For this task I need variety examples of
>> databundle files. Where I can find this?
>>
>>
Re: Taverna Databundle Viewer - progress
Posted by Robert Haines <ro...@manchester.ac.uk>.
Hi Denis,
<snip>
> Next week I will work by parsing databundle file, first task will be
> show input and output.
Are databundles research objects underneath? If so then the ro-bundle
gem may do what you need, or could be extended, for parsing:
https://rubygems.org/gems/ro-bundle
Cheers,
Rob
> For this task I need variety examples of
> databundle files. Where I can find this?
>