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Hey everyone!
We are working on a project at UC Berkeley to integrate Dataverse with Binder which is a service that automatically hosts dockerized instances of Jupyter notebooks online. This is part of a larger project to aid with research data reproducibility. It seems like the newExternal Tools features would be perfect for what we want to do, but currently it only supports tabular data at the file level. In our usecase, we would want to make an external tool at the dataset level so that our tool could download all of the files in a dataset and use those files to automatically create a docker instance to interact with the data. We already have the ability to automatically setup a docker instance, but we need a way to interface with Dataverse to retrieve the files for that instance.
Are there currently any efforts to expand the capability of External Tools outside of tabular data or anyone who would be willing to try to add some basic integration? Our thoughts are essentially having another 'Explore' button show up in the Dataset view just as it currently does in the view for tabular files.
Thanks,
Sean Dooher, Kevin Yang, and Aaron Culich
UC Berkeley
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The integration of Dataverse with Binder is really exciting! Thanks for sharing it.
I can see that what you are requesting could work well, but I'll let other in the team follow up with details.
Merce
----------Mercè Crosas, Ph.D., Chief Data Science and Technology Officer, IQSS, Harvard University
On Fri, Apr 6, 2018 at 6:42 PM, <sean....@berkeley.edu> wrote:
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Sean
Odum is working on a similar effort for journal verification
We would love to coordinate
Jus let me know when you would like to talk
Jon
Get Outlook for iOS
_____________________________
From: Mercè Crosas <merce....@gmail.com>
Sent: Friday, April 6, 2018 7:03 PM
Subject: Re: [Dataverse-Users] External Tools Dataset Extension
The integration of Dataverse with Binder is really exciting! Thanks for sharing it.
I can see that what you are requesting could work well, but I'll let other in the team follow up with details.
Merce
----------Mercè Crosas, Ph.D., Chief Data Science and Technology Officer, IQSS, Harvard University
On Fri, Apr 6, 2018 at 6:42 PM, <sean....@berkeley.edu> wrote:
Hey everyone!
We are working on a project at UC Berkeley to integrate Dataverse with Binder which is a service that automatically hosts dockerized instances of Jupyter notebooks online. This is part of a larger project to aid with research data reproducibility. It seems like the newExternal Tools features would be perfect for what we want to do, but currently it only supports tabular data at the file level. In our usecase, we would want to make an external tool at the dataset level so that our tool could download all of the files in a dataset and use those files to automatically create a docker instance to interact with the data. We already have the ability to automatically setup a docker instance, but we need a way to interface with Dataverse to retrieve the files for that instance.
Are there currently any efforts to expand the capability of External Tools outside of tabular data or anyone who would be willing to try to add some basic integration? Our thoughts are essentially having another 'Explore' button show up in the Dataset view just as it currently does in the view for tabular files.
Thanks,
Sean Dooher, Kevin Yang, and Aaron Culich
UC Berkeley
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I'm glad to see that this feature has some interest! That Compute feature does seem interesting and while I definitely am going to take a closer look at it, I think in the long term we'll want to use external tool because, like you said, it's much more lightweight. As a kludge, we can probably hard code in a button on that page until the feature is developed for testing purposes at least. We still have a decent amount of work to do in actually implementing the tool itself so it shouldn't block us up for a while yet. I'd love the pointers to those API endpoints you mention as that's exactly what we had in mind for the tool.
Thanks,
Sean Dooher
On Friday, April 6, 2018 at 5:08:20 PM UTC-7, Philip Durbin wrote:
PhilThanks!Longer term, we should extend the external tool concept to operate at the dataset level. Please go ahead and open an issue at https://github.com/IQSS/dataverse/issues about this if you are so inclined.If you'd rather stick with external tool, and you might because it's much more lightweight and doesn't require Swift storage or anything, as a kludge you could make every dataset include a file that's tabular just so you'll get the Explore button to show up so you can get the user over to BinderHub. Then from BinderHub you can use the file ID in Dataverse to derive the dataset ID an then proceed to download all the files. I can give you pointers to all the API endpoints you'd need on the Dataverse side to accomplish this. Just let us know which direction you'd like to go.Anyway, it might be something to try. I'd hate for you to be blocked because you need the external tool feature to do more.These settings should give you a "Compute" button at the dataset level. Basically, it's just a link that dumps to another website (an OpenStack environment, for example) with the bucket for your dataset in the URL. I believe you need to be configured for Swift storage for this to work, judging from my faulty memory and what I'm reading at http://guides.dataverse.org/en/4.8.6/installation/config.html#setting-up-computeSean, the external tool feature is new and shiny (I don't think we've even tweeted about the Dataverse 4.8.6 release yet) and you aren't the only one who has expressed interested in having external tools at the dataset level rather than the file (tabular file only right now) level but since you have your own installation of Dataverse (if memory serves), I'm wondering if these two settings are on your radar:Hi all,This is all super exciting and I'm sorry that I missed you at http://irclog.iq.harvard.edu/dataverse/2018-04-06#i_65518 a bit ago. Stupid timezones. ;)
- :ComputeBaseUrl - http://guides.dataverse.org/en/4.8.6/installation/config.html#computebaseurl
- :CloudEnvironmentName - http://guides.dataverse.org/en/4.8.6/installation/config.html#cloudenvironmentnamep.s. In case anyone is wondering, this didn't come out of nowhere. You can check out the "2018-03-09 Meeting with UC Berkeley and Dataverse" notes I took at https://docs.google.com/document/d/12njDDHHfoNdos0By3lKlxYbRWLsAp8Eo-AGpjuBF_rY/edit?usp=sharing and discussion at chatter at https://github.com/jupyterhub/binder/issues/80 and https://github.com/nds-org/ndslabs-dataverse/issues/8#issuecomment-372359052
On Fri, Apr 6, 2018 at 7:08 PM, Jonathan Crabtree <jonc...@gmail.com> wrote:
Sean
Odum is working on a similar effort for journal verification
We would love to coordinate
Jus let me know when you would like to talk
Jon
Get Outlook for iOS
_____________________________
From: Mercè Crosas <merce....@gmail.com>
Sent: Friday, April 6, 2018 7:03 PM
Subject: Re: [Dataverse-Users] External Tools Dataset Extension
The integration of Dataverse with Binder is really exciting! Thanks for sharing it.
I can see that what you are requesting could work well, but I'll let other in the team follow up with details.
Merce
----------Mercè Crosas, Ph.D., Chief Data Science and Technology Officer, IQSS, Harvard University
On Fri, Apr 6, 2018 at 6:42 PM, <sean....@berkeley.edu> wrote:
Hey everyone!
We are working on a project at UC Berkeley to integrate Dataverse with Binder which is a service that automatically hosts dockerized instances of Jupyter notebooks online. This is part of a larger project to aid with research data reproducibility. It seems like the newExternal Tools features would be perfect for what we want to do, but currently it only supports tabular data at the file level. In our usecase, we would want to make an external tool at the dataset level so that our tool could download all of the files in a dataset and use those files to automatically create a docker instance to interact with the data. We already have the ability to automatically setup a docker instance, but we need a way to interface with Dataverse to retrieve the files for that instance.
Are there currently any efforts to expand the capability of External Tools outside of tabular data or anyone who would be willing to try to add some basic integration? Our thoughts are essentially having another 'Explore' button show up in the Dataset view just as it currently does in the view for tabular files.
Thanks,
Sean Dooher, Kevin Yang, and Aaron Culich
UC Berkeley
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--Philip Durbin
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http://www.iq.harvard.edu/people/philip-durbin
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Hi Sean and others,
We (DANS) are also very interested in the possibility to run Jupyter notebooks online bundled to Dataverse datasets. We've actually started this integration on Docker level to get tools running in the separate containers as internal microservices, but support of external tools like Binder sounds very promising. Please keep us in the loop!
Best,
Slava
On Saturday, April 7, 2018 at 12:42:49 AM UTC+2, sean....@berkeley.edu wrote:
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