Not controversial at all ;) different sub-groups of the galaxy community
just have different needs. I'm in one of those that needs this, but I
likewise agree with the devs that a "password" field is not an optimal
I've proposed something a while back which might achieve what you need,
but it is a long ways (~1-2 months on my current calendar) from
implementation which I realise isn't very helpful right now. (If there
are people who are motivated for this idea, I would be happy to work
with them on this. I'm more interested in the functionality than I am in
any credit for implementing it ;) )
I'm proposing a framework for "Credentials for Remote Services" as this
is a pretty generic problem. The gist of it is:
* There are tools which need user provided credentials for talking to
* The tool should be able to register that it would like all
credentials under a certain namespace (e.g. a tool in my apollo
suite would want all credentials under the "apollo" path). E.g. in a
o The command block uses something like "<command>my_script.sh
o The inputs contains something like '<input><input
o And perhaps somewhere else in the tool we have
'<credentials><input type="text" label="Service Username"
/><input type="text" label="Service Password"/></credentials>
o Galaxy, upon seeing the credentials block, would expose a user
configuration setting, allowing the user to register as many
services as they want with this form for entering credentials.
o The tool, upon looking through the user's configured credentials
in Galaxy, would allow the user to select which credentials they
wish to use.
I am not tackling the encryption portion too heavily, credentials would
be encrypted with the galaxy id_secret going into the database (and
probably salted as well), and then exposed as environment variables orso
when the job is constructed. Anything past that is increasingly less
important for me, any sys admin running Galaxy has access to do much
more malicious things anyway.
There are a couple of specifics I still need to work out (mostly syntax
things for how tools should declare these variables, and how they should
consume them) but I think this would be a much more generic option and
allow for more exciting things in the future. This is what I envision
people selecting in the UI.
On 28. juli 2016 10:53, Katherine Beaulieu wrote:
> Hi Everyone,
> I know this is sort of a controversial topic so I will try to tread
> lightly. It seems that for a couple of years the idea of a password
> parameter for Galaxy tools has come up a lot but has also been
> rejected a lot although I believe there is a lot of merit to it. I
> have found at least two other times where people have tried to
> implement this and it was rejected, but there must have been a reason
> why they needed that parameter. My situation currently is that I have
> created two tools in Galaxy which communicate with another software
> called iRODS which needs authentication from the user. In my own
> department, there is another tool that was created which needed
> authentication from the user but the developer had to create some
> other workaround for this problem.
> In terms of the work I have done for this so far, I have been working
> off the latest release version of Galaxy. I have implemented the field
> so that it is obfuscated in the tool form view as well as on the tool
> info page. I will next be looking into storing the parameter in an
> environment variable so it doesn't get passed through the command line
> and encrypting the password before it enters the database. Speaking
> with a co-worker of mine, we discussed the possibility of implementing
> two option, irreversible encryption of the password as it gets entered
> into the database but then making the tool not workflow compatible, or
> using regular encryption and making the tool workflow compatible. I
> look forward to hearing your opinions and ideas.
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Center for Phage Technology
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