Direct access to data via URL?

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Adam Ginsburg

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Oct 7, 2014, 7:26:55 AM10/7/14
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Hi, I'm about to publish a paper and I want to distribute a script to
reproduce the analysis along with the paper.   In order to do this, I
need to provide the users with direct access to the data files.
However, as far as I can tell, all of my data are behind a 'terms of
use' wall that prevents direct download.  Is there any way around this
restriction?

Thanks,
Adam

Mercè Crosas

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Oct 7, 2014, 9:43:30 AM10/7/14
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Adam,

In the current version of the Harvard Dataverse, the default terms of use for downloading data cannot be removed. This is changing in Dataverse 4.0, where by default the data you publish to Dataverse will be assign an "open data" licenses (such as CC0), and only if you want, you will be able to add terms of use or additional restrictions. Also, the download API will deal better with terms of use, in the case terms of use are added to the datasets.

However, I'll discuss with the development team what's the best way, before 4.0., for you to use the API so you can access the data directly, avoiding the terms of use (if you agree to the terms of use ahead of time). We'll get back to you on this.

Finally, as general information about referencing the data in a reproducibility study, note that the Dataverse follows the Data Citation Principles, endorsed by a large number of international organizations. The principles support to reference the data with the formal data citation (generated by Dataverse, in this case), which contains proper attribution and a persistent identifier. The url of the data citation should link to a "landing page" where you can fin the data file(s), plus metadata and documentation to the data which are usually relevant to fully understand the dataset. We'd like to propose that the metadata of the data citation includes the urls to access directly the data. Hopefully, this will all be standardized in the near future.

Best,
Merce



Mercè Crosas, Ph.D.
Director of Data Science, IQSS
Harvard University

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Thomas Leeper

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Oct 8, 2014, 5:55:30 AM10/8/14
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Adam, this is not possible. As far as I can tell (from playing around with it in various ways) there's no way to circumvent the Terms of Use. You could probably setup Selenium web driver to do this, but I haven't given it a try yet. And that's a lot of overhead for a simple data download.

Mercè, this will be a great change! I've been looking forward to it ever since I started working with the API.

On Tuesday, October 7, 2014 3:43:30 PM UTC+2, Merce wrote:
Adam,

In the current version of the Harvard Dataverse, the default terms of use for downloading data cannot be removed. This is changing in Dataverse 4.0, where by default the data you publish to Dataverse will be assign an "open data" licenses (such as CC0), and only if you want, you will be able to add terms of use or additional restrictions. Also, the download API will deal better with terms of use, in the case terms of use are added to the datasets.

However, I'll discuss with the development team what's the best way, before 4.0., for you to use the API so you can access the data directly, avoiding the terms of use (if you agree to the terms of use ahead of time). We'll get back to you on this.

Finally, as general information about referencing the data in a reproducibility study, note that the Dataverse follows the Data Citation Principles, endorsed by a large number of international organizations. The principles support to reference the data with the formal data citation (generated by Dataverse, in this case), which contains proper attribution and a persistent identifier. The url of the data citation should link to a "landing page" where you can fin the data file(s), plus metadata and documentation to the data which are usually relevant to fully understand the dataset. We'd like to propose that the metadata of the data citation includes the urls to access directly the data. Hopefully, this will all be standardized in the near future.

Best,
Merce



Mercè Crosas, Ph.D.
Director of Data Science, IQSS
Harvard University

On Tue, Oct 7, 2014 at 7:26 AM, Adam Ginsburg <kefl...@gmail.com> wrote:
Hi, I'm about to publish a paper and I want to distribute a script to
reproduce the analysis along with the paper.   In order to do this, I
need to provide the users with direct access to the data files.
However, as far as I can tell, all of my data are behind a 'terms of
use' wall that prevents direct download.  Is there any way around this
restriction?

Thanks,
Adam

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Philip Durbin

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Oct 8, 2014, 9:11:11 AM10/8/14
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"Why can't I use the API to download something I just uploaded via the API?" is a common question that (as Merce indicates) we plan to address in Dataverse 4.0.

The Dataverse Data Deposit API is based on SWORDv2 and section 6.4 of that specification ("Retrieving the content") has not yet been implemented because we need to figure out these issue around Terms Of Use. Here's a related ticket to keep an eye on: https://github.com/IQSS/dataverse/issues/183

Please REST assured (heh) that this business of downloading files via API is on our minds! We want to make it easy for developers to integrate with Dataverse!

Phil

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Tom Roche

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Oct 8, 2014, 11:12:25 AM10/8/14
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Adam Ginsburg Tue, 7 Oct 2014 04:26:55 -0700 (PDT) [1]
>> I want to distribute a script to reproduce the analysis along with the paper.

Philip Durbin Wed, 8 Oct 2014 09:11:10 -0400 [2]
>> downloading files via API is on our minds!

Just to clarify: for users of dataverse version < 4 who want to publish instructions for reproduction of results, the instructions should be like

1. tell prospective reproducer how to download data via web UI

2. tell prospective reproducer how/where to interface script(s) and data (e.g., edit properties file to add data filepaths, give data filepaths via commandline)

3. run the script(s)

Or am I missing something?

TIA, Tom Roche <Tom_...@pobox.com>

[1] https://groups.google.com/d/msg/dataverse-community/Uz-_PoyxvY0/QktP9GbRWLYJ
[2] https://groups.google.com/d/msg/dataverse-community/Uz-_PoyxvY0/KDKiDaQT6FcJ

Philip Durbin

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Oct 8, 2014, 11:20:14 AM10/8/14
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Tom, that sounds right. With DVN 3.x one must use the web UI and check a box to agree to Terms Of Use before downloading data. This is how it works from Open Science Framework, for example: https://osf.io/getting-started/#dataverse

Please see Merce's email earlier in this thread for how we're hoping to improve this situation in Dataverse 4.0: https://groups.google.com/d/msg/dataverse-community/Uz-_PoyxvY0/4VKU9TeBS0oJ

Phil

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Adam Ginsburg

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Apr 26, 2015, 9:01:51 AM4/26/15
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Hi all,
    Now that dataverse 4.0 is out, is there an answer to the original question: How can I provide a direct data download link?

    Even if a direct data link is not possible, I'd like to know the best scripted (no human intervention) approach for downloading the data: in order to make my project fully reproducible, I'd like to provide one end-to-end script that downloads and processes the data.

Thanks,
Adam


On Wednesday, October 8, 2014 at 5:20:14 PM UTC+2, Philip Durbin wrote:
Tom, that sounds right. With DVN 3.x one must use the web UI and check a box to agree to Terms Of Use before downloading data. This is how it works from Open Science Framework, for example: https://osf.io/getting-started/#dataverse

Please see Merce's email earlier in this thread for how we're hoping to improve this situation in Dataverse 4.0: https://groups.google.com/d/msg/dataverse-community/Uz-_PoyxvY0/4VKU9TeBS0oJ

Phil
On Wed, Oct 8, 2014 at 11:12 AM, Tom Roche <Tom_...@pobox.com> wrote:

Adam Ginsburg Tue, 7 Oct 2014 04:26:55 -0700 (PDT) [1]
>> I want to distribute a script to reproduce the analysis along with the paper.

Philip Durbin Wed, 8 Oct 2014 09:11:10 -0400 [2]
>> downloading files via API is on our minds!

Just to clarify: for users of dataverse version < 4 who want to publish instructions for reproduction of results, the instructions should be like

1. tell prospective reproducer how to download data via web UI

2. tell prospective reproducer how/where to interface script(s) and data (e.g., edit properties file to add data filepaths, give data filepaths via commandline)

3. run the script(s)

Or am I missing something?

TIA, Tom Roche <Tom_...@pobox.com>

[1] https://groups.google.com/d/msg/dataverse-community/Uz-_PoyxvY0/QktP9GbRWLYJ
[2] https://groups.google.com/d/msg/dataverse-community/Uz-_PoyxvY0/KDKiDaQT6FcJ

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Philip Durbin

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Apr 26, 2015, 11:55:17 AM4/26/15
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Hi Adam!

Thanks for hanging in there for Dataverse 4.0!

The short answer is that it *may* be as easy as this:

curl https://apitest.dataverse.org/api/access/datafile/12?key=6fbb494e-3846-4fd0-9955-2e13bbdd04b1

For details on the new Data Access API, please see http://guides.dataverse.org/en/latest/api/dataaccess.html

Of course, the longer answer is, "it depends!" Obviously, *restricted* files can only be downloaded by people who have been granted access. Files from CC0 datasets can be downloaded more freely.

I'm not sure that we have great documentation on all of this yet but I did reference your specific use case of writing a script not long ago at https://github.com/IQSS/dataverse/issues/1809#issuecomment-88889417

Does this help? I'd suggest playing with the Data Access API and reporting back to us if you're better able to write that script to reproduce your results! Sounds like a great script! Please keep us posted!

Thanks!

Phil


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August Muench

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May 7, 2015, 9:30:26 AM5/7/15
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I hate to be a spoilsport, but I don't think that is exactly what we had in mind. I know I was thinking of something more restful.

 - gus
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Mercè Crosas

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May 7, 2015, 9:44:16 AM5/7/15
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Gus and others,

Do you mean that the API to download open data (that is, CC0 waiver, no terms of use and no restricted files) should not need a key? My understanding is that we are, at least for now, protecting the application from receiving (and not be able to handle) a huge number of large data downloads at once. But I can see that this might not be the best solution to accomplish this. What do you suggest instead?


Mercè Crosas, Ph.D.
Director of Data Science, IQSS
Harvard University

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August Muench

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May 7, 2015, 9:52:18 AM5/7/15
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Ah, my bad -- I see it is restful with a key. My eyes just glossed over a file called "12".  

The headers come back clean too:


HTTP/1.1 200 OK                                                                 

Date: Thu, 07 May 2015 13:50:51 GMT

Set-Cookie: JSESSIONID=ea4a63b58f9d2e4aba6e9ef55767; Path=/; Secure; HttpOnly

Access-Control-Allow-Origin: *

Content-disposition: attachment; filename="trees.png"

Content-Type: image/png; name="trees.png"

Content-Length: 8361

Connection: close

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Mercè Crosas

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May 7, 2015, 9:54:33 AM5/7/15
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Great, thanks for clarifying!



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Philip Durbin

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May 7, 2015, 10:10:15 AM5/7/15
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So you're all set, Gus? I hope so. We're certainly not done with these APIs! Everyone is invited to join http://community.dataverse.org/community-groups/api.html

Thanks for testing!

Phil

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Adam Ginsburg

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Jun 6, 2015, 2:46:39 PM6/6/15
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In case anyone comes to this thread: the question was asked again and answered here:
and that answer worked for me.

August Muench

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Jul 27, 2015, 11:27:21 AM7/27/15
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So Adam...

You are happy using the SWORD api to get a list of file #'s and file names and then working that out off line to provide direct links to your files? I'm writing up some author instructions right now for using 3rd party repositories in AAS articles and this is utterly baffling to explain this compared to Zenodo, which uses restful real file names to resolve to files. 

To be clear, if one is building an application around a Dataverse dataset, then the SWORD API seems like an awesome solution. But if all you (the dataset author) want to do is reuse the direct link to a file in another place this(*) is a huge, huge barrier. 

But maybe I need another astronomer's perspective here on what is and isn't useful about file level links. 

 - Gus

(*): calling a file named trees.png "https://apitest.dataverse.org/api/access/datafile/12" instead of something human readable. 

Philip Durbin

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Jul 27, 2015, 11:43:42 AM7/27/15
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Gus, when you say the Zenodo API uses real file names do you mean names like "12345678-9abc-def1-2345-6789abcdef12"?

That's what I'm seeing at http://zenodo.org/dev#restapi-res-files

Here's the curl example from that page:

Or are you saying you can use a file name like "readme"? If so, can you please point to where they say this in the Zenodo API docs?

Thanks! We aren't trying to baffle you! :)

Phil

p.s. For what it's worth recently I was thinking about how it's still sort of tricky to find file IDs in Dataverse: https://github.com/IQSS/dataverse/issues/1837#issuecomment-121736332


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August Muench

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Jul 27, 2015, 11:51:47 AM7/27/15
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Hi Phil:

No, that isn't what I said/meant. I didn't say Zenodo API's used real filenames. I said Zenodo uses real file level links to users without using the API to get to them:



Like that.

 - Gus

Adam Ginsburg

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Jul 27, 2015, 12:03:19 PM7/27/15
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You are happy using the SWORD api to get a list of file #'s and file names and then working that out off line to provide direct links to your files? I'm writing up some author instructions right now for using 3rd party repositories in AAS articles and this is utterly baffling to explain this compared to Zenodo, which uses restful real file names to resolve to files. 

To be clear, if one is building an application around a Dataverse dataset, then the SWORD API seems like an awesome solution. But if all you (the dataset author) want to do is reuse the direct link to a file in another place this(*) is a huge, huge barrier. 


Gus: No, you're right, I want file-level links without API access.  I still have to use dropbox links for some data sets if I want some of my lazier colleagues to download the files.
 

Philip Durbin

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Jul 27, 2015, 12:31:40 PM7/27/15
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Thanks, Gus, I think I understand what you mean now.

If everyone would take a look at this issue I just created I would appreciate it:

Hovering mouse over Download button does not reveal the URL of the file and the URL does not contain the file name - https://github.com/IQSS/dataverse/issues/2416

Please feel free to leave comments if this isn't want you mean! :)

Phil



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August Muench

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Jul 27, 2015, 12:37:36 PM7/27/15
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Thanks. To be clear, I tried various free text searches on github Dataverse issues to see if this already existed before reviving this thread. :-) 

I'll comment there and follow along. 

 - g

Azadeh Hashemi

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Aug 24, 2016, 5:48:25 PM8/24/16
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Hey Phil,

I didn't get it. 
I want to download my files via a script.

Is it possible to make a account and give it the direct access permission to files?
I mean may have access to the files in my script like '[BASEURL]/dvn/api/download/{databaseID}'? (Obviousley, plus the auth info)


--
Azadeh


On Wednesday, October 8, 2014 at 8:20:14 AM UTC-7, Philip Durbin wrote:
Tom, that sounds right. With DVN 3.x one must use the web UI and check a box to agree to Terms Of Use before downloading data. This is how it works from Open Science Framework, for example: https://osf.io/getting-started/#dataverse

Please see Merce's email earlier in this thread for how we're hoping to improve this situation in Dataverse 4.0: https://groups.google.com/d/msg/dataverse-community/Uz-_PoyxvY0/4VKU9TeBS0oJ

Phil
On Wed, Oct 8, 2014 at 11:12 AM, Tom Roche <Tom_...@pobox.com> wrote:

Adam Ginsburg Tue, 7 Oct 2014 04:26:55 -0700 (PDT) [1]
>> I want to distribute a script to reproduce the analysis along with the paper.

Philip Durbin Wed, 8 Oct 2014 09:11:10 -0400 [2]
>> downloading files via API is on our minds!

Just to clarify: for users of dataverse version < 4 who want to publish instructions for reproduction of results, the instructions should be like

1. tell prospective reproducer how to download data via web UI

2. tell prospective reproducer how/where to interface script(s) and data (e.g., edit properties file to add data filepaths, give data filepaths via commandline)

3. run the script(s)

Or am I missing something?

TIA, Tom Roche <Tom_...@pobox.com>

[1] https://groups.google.com/d/msg/dataverse-community/Uz-_PoyxvY0/QktP9GbRWLYJ
[2] https://groups.google.com/d/msg/dataverse-community/Uz-_PoyxvY0/KDKiDaQT6FcJ

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danny...@g.harvard.edu

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Aug 25, 2016, 10:27:12 AM8/25/16
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Hey Azadeh,

I believe this is possible. There's some discussion about this here:


There's also a script linked that may be helpful to you:

https://github.com/IQSS/dataverse/commit/812424a

In regards to the permissioning, would an API token work for you? You can set up a token following the instructions here:


Let me know if you have any questions!

- Danny

Hashemi, Azadeh

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Aug 25, 2016, 1:01:01 PM8/25/16
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Hey Danny,

 

Thank you for your reply. Before I try these methods I just want to make sure, do they work on Dataverse v3.6?

 

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danny...@g.harvard.edu

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Aug 26, 2016, 10:09:29 AM8/26/16
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Hey Azadeh,

I took a look through the 3.6 guides and found the URL format for downloads as well as some other information for APIs:


Let me check around a bit. Dataverse 3.6 predates me! :)

- Danny




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Thomas J. Leeper

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Aug 26, 2016, 10:12:28 AM8/26/16
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More likely than not, direct file download will not work in Dataverse
< v4.0 because of terms of use restrictions (at least at the Harvard
Dataverse; or any Dataverse that was setup similarly). You'll just get
an error message instead.

This is handled much better in Dataverse >= 4.0.

-Thomas

Thomas J. Leeper
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Azadeh Hashemi

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Aug 26, 2016, 5:05:55 PM8/26/16
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Thanks everyone.

Danny it doesn't work like that and as Thomas said I'm afraid there is no way. I have to think about upgrading. BTW, please let me know if you find one.

Thanks,
Azadeh
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Philip Durbin

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Sep 1, 2016, 10:12:26 AM9/1/16
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I agree with Thomas. Downloading files programmatically was not well supported in DVN 3.x. This is something we fixed in the Dataverse 4 rewrite (credit to Leonid). See the "Data Access" API docs for details: http://guides.dataverse.org/en/4.5/api/dataaccess.html

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