Question: How to share a data library with other users
1
gravatar for alex
4 months ago by
alex40
alex40 wrote:

I'm having some trouble allowing other users of my galaxy to see the files in the data library I imported. They can see the directories but not the files.

  • Tried: Admin > Data Libraries > (my library) > Library Actions > edit permissions

Result: The "Access library role has every user and ever role approved. Still no one but me can see the files. Others can only see the folders.

  • Tried: Admin > Data Libraries > (my library) > (at the bottom) For selected datasets: edit permissions (with more than one folder selected)

403 Forbidden

probably a bug here...

  • Tried: Admin > Data Libraries > (my library) > (at the bottom) For selected datasets: edit permissions (with a single folder selected)

Result: Only a single role (mine) is populated in any the options, as if the other users/roles didn't exist, which means I can't add any of the other users to the "Access" permissions. Why are the other users not showing up in this screen?

Thanks in advance!

data-library • 171 views
ADD COMMENTlink written 4 months ago by alex40
1
gravatar for Martin Čech
4 months ago by
Martin Čech ♦♦ 4.0k
United States
Martin Čech ♦♦ 4.0k wrote:

I think the problem here is twofold: The permissions concept is a bit daunting and you are using the old library interface.

In order to allow users to see shared data they need to have the 'access permission' on the dataset itself. Confusingly the old interface does not provide an option to do that directly. Please try using the new interface under Shared/Data Libraries in the top menu - that one does have a field for changing the dataset's access permissions.

Please let us know if you want more guidance.

ADD COMMENTlink written 4 months ago by Martin Čech ♦♦ 4.0k

Related help: https://galaxyproject.org/data-libraries/

ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson22k

Is there a way to change permissions on a batch of datasets? I believe there are a couple hundred in the data library and I'd rather not change permissions one by one..

ADD REPLYlink written 4 months ago by alex40

If you set the permissions on a library right after it is created, then all datasets added later will inherit the permissions. This is probably the easiest way to do batch (and ongoing) permissions.

This and other best practices are near the bottom of the help link I sent.

ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson22k

I'm not sure what you mean exactly. I created the library recently by importing data from the machine the galaxy instance runs on through the admin interface. Now, I see four permissions possible on the library:

  • Roles that can access the library: Everyone
  • Roles that can manage permissions on this library: Me
  • Roles that can add items to this library: Me
  • Roles that can modify this library: Me

But I want to set "Roles that can access the data in the library" to everyone, but such an option doesn't seem to be present. On each of the datasets, I can grant access to everyone, but I can't do that for all users.

ADD REPLYlink written 4 months ago by alex40

If the library was created with "Roles that can access the library: Everyone", then the datasets added after, the permissions for the datasets are inherited from the permissions of the library, in effect meaning "Roles that can access the library: Everyone".

Is there a different behavior?

ADD REPLYlink modified 4 months ago • written 4 months ago by Jennifer Hillman Jackson22k

Yes. That's right. Is there no corrective action? No way to turn this on after the fact?

ADD REPLYlink written 4 months ago by alex40

The permissions can be modified, but only by individual dataset, and the library must have that particular permission enabled as well.

An individual library can have multiple permissions and datasets within must have at least one of those permissions to be accessible by any users that also have at least one of those same permissions.

So to answer your original question, there is no batch operation to reset dataset permissions after adding datasets to a library. After loading datasets into a library, and those permissions need to be changed, the available change permission operation is per-dataset. Therefore it is much easier to set the library permissions first then add the datasets.

ADD REPLYlink modified 4 months ago • written 4 months ago by Jennifer Hillman Jackson22k
1

Okay. I will re-create the library. Do you think this feature should be added to Galaxy?

ADD REPLYlink written 4 months ago by alex40

I asked that of Martin earlier and while this is a good idea the work to implement the feature is non-trivial. A ticket was made anyway to be considered for a future enhancement, please see: https://github.com/galaxyproject/galaxy/issues/4069

Thanks Alex!

ADD REPLYlink modified 4 months ago • written 4 months ago by Jennifer Hillman Jackson22k
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