Commit Graph
85 Commits
Author SHA1 Message Date
Bjoern Gruening e2bf4ccb15 Migrate from <object> to <iframe>. Objects seems to have some bugs in FF32. 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 beb0cb57e9 Possible fix for CORS/cookie issue.
I noticed that the cookie was indeed being set by the POST request. However, that cookie was
essentially ignored in the subsequent requests.

I looked for places to interrupt it, could I just stop after the POST and not execute any redirects.
That did not appear to be an option due to HTTP/XHR spec. After a bit of searching I came up with
this link: http://stackoverflow.com/a/14462615 which seems to solve the issue. Mentioned here:
https://api.jquery.com/jQuery.ajax/
2014-10-18 18:38:04 -04:00
Eric Rasche c185c6e556 Center the spinner 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 8ec2033302 Refactored JS code to wait on page load
See linked SO question in source for information on the type of JS delay loop
we're doing.
2014-10-18 18:38:04 -04:00
Eric Rasche ec2da64444 Removed docker delay with spinning 2014-10-18 18:38:04 -04:00
Eric Rasche 9256fe1c60 Error message is only relevant in specific circumstance, other circumstances are likely more serious errors 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 c296f7883e Removed unnecessary quotes 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 adb7f5eb8f Added SSL option 2014-10-18 18:38:04 -04:00
Bjoern Gruening d8aa2b73da Add "how does it work" section to the readme 2014-10-18 18:38:04 -04:00
Eric Rasche 3718bb1fa3 Fixed URL for easier install 2014-10-18 18:38:04 -04:00
Bjoern Gruening 4b679ae598 Added the initial release date!
Yeah, we are ready to release!
Thanks so much @erasche it is a pleasure to work with you!
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 9142fae801 Updated README with security information 2014-10-18 18:38:04 -04:00
Eric Rasche 62444db82a Accidentally overwrote remote with local changes, reverting 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
Eric Rasche 760bf70359 Added password protection of the notebook 2014-10-18 18:38:04 -04:00
Bjoern Gruening e32f7d1d0f Added the video to the readme file. 2014-10-18 18:38:04 -04:00
Bjoern Gruening 4e1e6cff78 Update README.md
"Next Generation Training" course might be a little bit to much ... ;)
2014-10-18 18:38:04 -04:00
Bjoern Gruening 0ec0413b3b Adopting the help text in the inital welcome Notebook. 2014-10-18 18:38:04 -04:00
Bjoern Gruening f297afd462 Update README.md 2014-10-18 18:38:04 -04:00
Bjoern Gruening e98dd7959f Update README.md 2014-10-18 18:38:04 -04:00
Bjoern Gruening e501e97ddf add image to show the integration of IPython in Galaxy 2014-10-18 18:38:03 -04:00
Bjoern Gruening b0b8b35de4 add some images for better documentation 2014-10-18 18:38:03 -04:00
Bjoern Gruening 97a1a53cf7 Update README.md 2014-10-18 18:38:03 -04:00
Eric Rasche 4f3052fd2b Extracted template into a template file
It was really awful to have that file maintained with the rest of the source code, now it is
separate.
2014-10-18 18:38:03 -04:00
Eric Rasche 27bbce5610 Extracted configuration file
Currently only a few variables, more can be placed here later.
2014-10-18 18:38:03 -04:00
Eric Rasche d96d2fe16e Mentioned nginx 2014-10-18 18:38:03 -04:00
Eric Rasche 9f53d2e94f Updated requirement list 2014-10-18 18:38:03 -04:00
Eric Rasche 5fbf9b884a Added information on template changes required 2014-10-18 18:38:03 -04:00
Eric Rasche c68b15aa04 Todo item completed 2014-10-18 18:38:03 -04:00
Eric Rasche 75d426df52 Added installation information 2014-10-18 18:38:03 -04:00
Eric Rasche 233db5340f Updated text on on template to refer to button colour 2014-10-18 18:38:03 -04:00
Bjoern Gruening 34f7b7d226 remove trailing slash, better save than sorry 2014-10-18 18:38:03 -04:00