Commit Graph
76 Commits
Author SHA1 Message Date
Eric Rasche 27cf4baac6 Refactored more variables out 2014-10-18 18:38:04 -04:00
Eric Rasche bcaa7d9ef9 Removed 'galaxy defaults' 2014-10-18 18:38:04 -04:00
Eric Rasche 743b7d06c2 Bugfix and remove no longer used imports 2014-10-18 18:38:04 -04:00
Eric Rasche 4cff8c3409 Removed more unused code 2014-10-18 18:38:04 -04:00
Eric Rasche 69a98d5c51 moved JS into template 2014-10-18 18:38:04 -04:00
Eric Rasche 5fd45775f2 More static variables gone 2014-10-18 18:38:04 -04:00
Eric Rasche 49950e0fff Moved URL writing into ie.mako 2014-10-18 18:38:04 -04:00
Eric Rasche 07bdd60e7a Reverted change used during testing 2014-10-18 18:38:04 -04:00
Eric Rasche ab5504547b Moved more configuration into ie base module 2014-10-18 18:38:04 -04:00
Eric Rasche 8c8ec8aa68 Added hex gen stmt 2014-10-18 18:38:04 -04:00
Eric Rasche a4dd555ea3 More progress refactoring 2014-10-18 18:38:04 -04:00
Eric Rasche 183da2abc0 Moved more functions over 2014-10-18 18:38:04 -04:00
Eric Rasche 9201ccdd27 First function refactored
This looks like it will definitely work, could be the start of a base IE template
2014-10-18 18:38:04 -04:00
Bjoern Gruening 336f2bc6c3 simplify code 2014-10-18 18:38:04 -04:00
Eric Rasche 7a30335a6b Typo/bug fixes 2014-10-18 18:38:04 -04:00
Eric Rasche 827cce2a67 Move notebook generation to more sensible place 2014-10-18 18:38:04 -04:00
Eric Rasche 91562ed2d0 Random seeding no longer necessary 2014-10-18 18:38:04 -04:00
Eric Rasche 866c1b51a1 Move functions to more appropriate code section 2014-10-18 18:38:04 -04:00
Eric Rasche f25e51e678 Building on b366b0c and eb1c487, cleanup js-var stuff 2014-10-18 18:38:04 -04:00
Eric Rasche 2443e1adda Exchanged conf calls for static variables 2014-10-18 18:38:04 -04:00
Eric Rasche fc1f466c21 Added js-bool function 2014-10-18 18:38:04 -04:00
Eric Rasche 52f878f507 Changed login URLs
The current login URL automatically redirects. Lest bad things happen, and we make extraneous
requests, we just login at the "/login" route without the automatic redirect
2014-10-18 18:38:04 -04:00
Eric Rasche eeea31047a Refactor password generation 2014-10-18 18:38:04 -04:00
Eric Rasche 123a8e94ea Simplification due to tying to galaxy release 2014-10-18 18:38:04 -04:00
Eric Rasche 901ca52aec Refactor to function which will eventually be API call 2014-10-18 18:38:04 -04:00
Eric Rasche e980278b45 Refactor to function 2014-10-18 18:38:04 -04:00
Eric Rasche faf5afe320 Seed more randomly
Originally this was intended to make sure re-clicking a dataset would open the same port+IE, however
that's not a supported behaviour and there's no reason to keep that functionality around.
2014-10-18 18:38:04 -04:00
Eric Rasche d5f141b7eb plugin_path now available
As of https://bitbucket.org/galaxy/galaxy-central/commits/ddc9a669d53aa259d38efc882c890503444daaf5
2014-10-18 18:38:04 -04:00
Eric Rasche 1173909ee9 Refactor into function 2014-10-18 18:38:04 -04:00
Eric Rasche d977726642 added comment 2014-10-18 18:38:04 -04:00
Eric Rasche 9e47db52bc Unused variable 2014-10-18 18:38:04 -04:00
Eric Rasche ffd3b10d5e Added CORS required parameter to conf 2014-10-18 18:38:04 -04:00
Eric Rasche 64bff1a7f5 Fixes #15 2014-10-18 18:38:04 -04:00
Eric Rasche c72cc47fdb Finished work on spinning
- Removed a statically set port during testing
 - Made variables local so we can be sure they aren't being mis-used
 - Removed sleep
 - New parameters needed in notebook load call
 - Added main div to use for images/etc. Probably not necessary.
2014-10-18 18:38:04 -04:00
Eric Rasche fb9cf86ceb JS refactor 2014-10-18 18:38:04 -04:00
Eric Rasche 43304a2325 Modified error message to be more human-friendly
Many people will be intially overwhelmed by the stack trace they see within galaxy in
the even of a missing API key. Hopefully, hopefully, they'll be able to read the bold
portion at the bottom with instructions on generating one. It's mostly a measure to
decrease support tickets/requests
2014-10-18 18:38:04 -04:00
Eric Rasche d32e61eca0 Moved docker delay to conf variable
Users may want to modify this variable, so I've moved it to the conf file.
2014-10-18 18:38:04 -04:00
John Chilton 048834a4a2 Use get_api_key() to fetch Galaxy API key...
This is a more appropriate abstraction layer to work at and provides the added benefit of auto-generating the key if it doesn't exist.
2014-10-18 18:38:04 -04:00
John Chilton 2cd37cc658 Use plugin_path to improve path logic...
Added in Galaxy commit https://bitbucket.org/galaxy/galaxy-central/commits/ddc9a669d53aa259d38efc882c890503444daaf5. Added it to Galaxy cleanup the code and this is the result - oh well :) - it is at least more techically correct.
2014-10-18 18:38:04 -04:00
Eric Rasche b4d641b013 Added documentation for each error message, fixed typo
Wiki pages were added for each of the error messages with a Cause and Solution.
This should be helpful to end users deploying our software
2014-10-18 18:38:04 -04:00
John Chilton ea6bc7be5d Bugfix: Do not hard code 'main' as Galaxy server name.
Determine correct server name corresponding to at least a web request at runtime.
2014-10-18 18:38:04 -04:00
Eric Rasche f8ad738b90 Fixes #7 2014-10-18 18:38:04 -04:00
Eric Rasche 88ce41f0de Fixes #6 2014-10-18 18:38:04 -04:00
Eric Rasche de2c843c06 Bumped timeout
I've found in opera that copy+paste doesn't work, so I have to drag and drop. Additionally, we need
the user to have time to read and comprehend what we're telling them before this notification
disappears forever.

Despite the fact that this is technically a configuration bug on the sys admin's part, for a future
release, we should switch to a different type of notification, probably like a banner with an X that
they can close once they're done reading it. That way we know it'll be there as long as they need it
to be.
2014-10-18 18:38:04 -04:00
Bjoern Gruening 58061f6504 replace toastr.css with the Galaxy one 2014-10-18 18:38:04 -04:00
Bjoern Gruening 75441ad142 Release sugar! Hope you like it @erasche. 2014-10-18 18:38:04 -04:00
Bjoern Gruening 4eaba38f2e =?UTF-8?q?In=20FF=20the=20<object>=20attriute=20needs=20to=20be?= =?UTF-8?q?=20from=20type=20'data'=20and=20not=20'src'.=0AChrome=20seems?= =?UTF-8?q?=20to=20be=20happy=20with=20'src'.=20This=20commit=20changes=20?= =?UTF-8?q?it=20back=20to=20'data'.?= 2014-10-18 18:38:04 -04:00
Eric Rasche 0e8289d47f Better failover in all situations
Previously in a specific situation (apache_urls = False and password_auth = True), we saw that users
would see a blank screen rather than an informative error message. This should not happen under any
circumstances.

This has been replaced with logic to handle the failure modes in as sane of a way as possible. If
the above situation is true, we provide the users with their random password and a login box. If any
other bad situation occurs, we pass the error message along to them.

Additionally a new variable "password_auth" has been introduced, describing whether or not passwords
should be used to authenticate users (mostly auto-magically) against their notebooks.

Because we have control over this docker image, it is possible we can handle that specific case
above by convincing ipython to set a content-origin header allowing the galaxy host to make the JS
login request.
2014-10-18 18:38:04 -04:00
Eric Rasche ef1c20f8d0 Replaced iframe with embed for aesthetics
Now whenever a notebook is loaded we first do a POST to the notebook login URL with the correct
authentication details. This logs us in and stores a cookie for us. Once this is done, (and we know
we were successful) we add the embed/object elements to the body of the page, which the browser then
loads.
2014-10-18 18:38:04 -04:00
Eric Rasche 3a212cd6c2 Completely working login system 2014-10-18 18:38:04 -04:00