[Bioc-devel] Web App for SSH keys

[Obenchain, Valerie]

On 04/19/2018 06:29 PM, Leonardo Collado Torres wrote:

Hi Valerie,

Thanks for the reply and the doc changes ^^. I added a few short replies below.

Best,
Leo

On Thu, Apr 19, 2018 at 4:49 PM, Obenchain, Valerie
<Valerie.Obenchain at roswellpark.org><mailto:Valerie.Obenchain at roswellpark.org> wrote:


Hi Leo,

Great feedback, thanks.

On 04/19/2018 08:04 AM, Leonardo Collado Torres wrote:

This looks great Valerie, congrats to all of those involved in making
the web app! I hope that it leads to less questions/confusion.

Here are some minor comments, mostly about including some links/docs.

* Under the which packages we have access to, I noticed that it's not
showing the experimental data packages. I guess that's because they
are not in git yet (right?).


All software, data experiment and workflow packages are in git. You should
be able to see all associated with your account. One of the goals of the app
was to make package access more transparent which could help explain why a
`push` or `fetch` failed. We match your email to the username we have in the
gitolite packages.conf file. When I search packages.conf I see your username
on these packages:

~/git.bioconductor.org/admin/gitolite-admin >grep -B 1
'master.*collado-torres' conf/packages.conf
repo packages/sva
    RW master = j.leek l.collado-torres
--
repo packages/derfinder
    RW master = l.collado-torres
--
repo packages/derfinderHelper
    RW master = l.collado-torres
--
repo packages/derfinderPlot
    RW master = l.collado-torres
--
repo packages/regionReport
    RW master = l.collado-torres
--
repo packages/recount
    RW master = l.collado-torres
--
repo packages/recountWorkflow
    RW master = l.collado-torres


If there is a package missing that you should have access to let us know.
Also let me know if this differs from the list you saw when you were logged
in.



This matches what I saw when I logged in. The only data package I've
contributed to Bioc is derfinderData. We haven't had to make any
changes to it in a long time as you can see at
https://github.com/leekgroup/derfinderData. I don't know if that
played a role in the package not showing up on m list. My email is
there on the DESCRIPTION file though
https://github.com/leekgroup/derfinderData/blob/master/DESCRIPTION#L7.

You're right, not all experimental data packages show up in this list because they aren't all in the packages.conf config file. The reason is historical. When we first started the experimental data packages we viewed them as static or at least changing very little. SVN write access wasn't given unless the maintainer explicitly requested it. When we transitioned from SVN to Git, only packages with write access by a specific maintainer were transferred to the config file.

After the next release we'll go through the data packages and make sure they're all in packages.conf with write access by the maintainer in DESCRIPTION.









* Under add an ssh key, the second option mentions "username.keys
files in your GitHub account". I hadn't heard about this before. Is
that file made automatically by editing
https://github.com/settings/keys? If there's a website that describes
this in more detail, I suggest including a link to it.


Yes, this is the standard keys file and is edited through github account
settings.

A link has been added to the github HOWTO page:

https://help.github.com/articles/adding-a-new-ssh-key-to-your-github-account/



I like the change, it's much clearer!




* I've seen several emails where Nitesh and others ask developers to
check their SSH key using ssh -T git at git.bioconductor.org<mailto:git at git.bioconductor.org>, so maybe
adding a reminder there would be good. Actually, maybe just include a
link to http://bioconductor.org/developers/how-to/git/faq/ from this
new site. By the way, that last link is not directly available from
http://bioconductor.org/developers/ (I think), I had to go to
http://bioconductor.org/developers/how-to/git/ then "See other
frequently asked questions."


I've added a link to the FAQ.



Nice! By the way, I just noticed a typo on
http://bioconductor.org/developers/how-to/git/faq/ bullet 17:

git clone git at git.bioconductor.org:packagse/<mailto:git at git.bioconductor.org:packagse/><myPackage>

packagse -> packages

Fixed (may take 20 minutes to propagate).








Since the FAQ is specific to version control it probably still belongs under
developers -> Git Source Control. Maybe we could change the title from 'See
other frequently asked questions' to just 'FAQ' or something more obvious.




Ok! To me it's really the "Git / ssh Bioc FAQ".

I'll pass that on, thanks.

Val








* Typo: "Which packages do I have acces to?" --> access


Fixed.


Valerie




Best,
Leo

On Wed, Apr 18, 2018 at 12:53 PM, Obenchain, Valerie
<Valerie.Obenchain at roswellpark.org><mailto:Valerie.Obenchain at roswellpark.org> wrote:

My last email didn't make it through to the list - trying again ...


The Web App for managing SSH keys is now available at

  https://git.bioconductor.org/BiocCredentials/

Accounts have been created for all package maintainers. Note the central
identifier, i.e., how you login is your email. This email was taken from the
DESCRIPTION of your package or the Google Sheet if you registered a key
there.

When you first visit the App you'll need to activate your account. An
activation link will be sent to your email. Once your account is activated
you can login. Trying to login without activation will lead to an error.

Let us know if you have any questions or problems.


This email message may contain legally privileged and/or confidential
information.  If you are not the intended recipient(s), or the employee or
agent responsible for the delivery of this message to the intended
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