1:28 a.m.
After uploading my beta status tool to our test toolshed, I tried installing it on another
of our galaxy servers but it wasn't able to find the api endpoint url. Is there a way
to automatically do this within tool forms? I was hoping to avoid hardcoding this as part
of the tool installation process. I'd thought I had it automated:
In tool's form, a dynamic_options param
<param name="api_url" display="radio" type="drill_down"
label="For user with Galaxy API Key"
dynamic_options="vdb_init_tool_user(__trans__)" />
was able to pass "trans" galaxy structure so I got as far as this python:
self.api_url = 'http://' + trans.request.host
... but this yeilds
http://acme.com/
rather than what's needed, the path to a particular installation:
http://acme.com/galaxy/
I couldn't find a way to read the /galaxylab/ setting from the (slightly dated)
universe_wsgi.ini config file - without say reading the file and parsing it. Is there an
__app__.config.prefix or somesuch variable where this info is?
Thanks!
Damion
1:42 a.m.
Well host is probably not enough - it doesn't seem like a good idea to
assume http right? There is the prefix and (trans.request.scheme) that
could be missing. Is trans.request.base what you want? Maybe
trans.request.path_url? It should be possible to recover that from
trans I guess - though I don't know exactly what parts of the request
you need to use.
So this isn't in stable yet - but there is going to be a sanctioned
way for Galaxy deployers to describe what the URL to their Galaxy
instance should be for internal consumption (stuff like docker
containers and Pulsar)
https://bitbucket.org/natefoo/galaxy-central/commits/4348618b4b8dd5f0c6d6....
It will be settable in config/galaxy.ini and accessible via
trans.app.config.galaxy_infrastructure_url. There is a related
attribute trans.app.config.galaxy_infrastructure_url_set which if True
specifies that the deployer actually filled in a value and this is not
Galaxy's best guess at what URL should be used to access it. If it is
false - probably best to fallback to something like trans and the
request if you have it.
Hope this helps some.
-John
On Wed, Oct 22, 2014 at 9:28 PM, Dooley, Damion <Damion.Dooley(a)bccdc.ca> wrote:
After uploading my beta status tool to our test toolshed, I tried
installing it on another of our galaxy servers but it wasn't able to find the api
endpoint url. Is there a way to automatically do this within tool forms? I was hoping to
avoid hardcoding this as part of the tool installation process. I'd thought I had it
automated:
In tool's form, a dynamic_options param
<param name="api_url" display="radio"
type="drill_down" label="For user with Galaxy API Key"
dynamic_options="vdb_init_tool_user(__trans__)" />
was able to pass "trans" galaxy structure so I got as far as this python:
self.api_url = 'http://' + trans.request.host
... but this yeilds
http://acme.com/
rather than what's needed, the path to a particular installation:
http://acme.com/galaxy/
I couldn't find a way to read the /galaxylab/ setting from the (slightly dated)
universe_wsgi.ini config file - without say reading the file and parsing it. Is there an
__app__.config.prefix or somesuch variable where this info is?
Thanks!
Damion
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5:50 p.m.
Hi folks,
It was the universe_wsgi.ini 'prefix' parameter I was needing, though yes,
http/https was an issue too. Good to know that the
trans.app.config.galaxy_infrastructure_url is in the works.
It turns out for now - thanks Eric Raschle - that the trans.request.application_url is the
magic pill, it has the complete url.
self.api_url = trans.request.application_url
Cheers,
Damion
Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease
Control
655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
________________________________________
From: John Chilton [jmchilton(a)gmail.com]
Sent: Wednesday, October 22, 2014 6:42 PM
To: Dooley, Damion
Cc: galaxy-dev(a)lists.bx.psu.edu
Subject: Re: [galaxy-dev] Determining galaxy api path automatically from a tool via
dynamic_options?
Well host is probably not enough - it doesn't seem like a good idea to
assume http right? There is the prefix and (trans.request.scheme) that
could be missing. Is trans.request.base what you want? Maybe
trans.request.path_url? It should be possible to recover that from
trans I guess - though I don't know exactly what parts of the request
you need to use.
So this isn't in stable yet - but there is going to be a sanctioned
way for Galaxy deployers to describe what the URL to their Galaxy
instance should be for internal consumption (stuff like docker
containers and Pulsar)
https://bitbucket.org/natefoo/galaxy-central/commits/4348618b4b8dd5f0c6d6....
It will be settable in config/galaxy.ini and accessible via
trans.app.config.galaxy_infrastructure_url. There is a related
attribute trans.app.config.galaxy_infrastructure_url_set which if True
specifies that the deployer actually filled in a value and this is not
Galaxy's best guess at what URL should be used to access it. If it is
false - probably best to fallback to something like trans and the
request if you have it.
Hope this helps some.
-John
3027
days inactive
3027
days old
galaxy-dev@lists.galaxyproject.org
2 comments
2 participants
participants (2)
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Dooley, Damion -
John Chilton