Dannon Baker
4dc04e1472
Fix a few instances of incorrect (deprecated) use of value instead of identity testing in xml parsing.
2015-02-08 11:16:14 -05:00
John Chilton
0e582719fe
Fix running tool tests for recent control reworking.
2015-02-07 19:32:16 -05:00
John Chilton
9e0d530c0c
Rework control queue setup to work in non-web contexts.
...
Namely in the new lib/galaxy/main.py. I think this break down of the code makes more sense also since control queues aren't inheriently something web-y so lib/galaxy/app.py makes more sense for configuring them. Dannon feel free to reorganize if you dislike this particular organization - I just wanted to make sure lib/galaxy/main.py could share in the new stuff.
2015-02-07 19:32:16 -05:00
Carl Eberhard
0547725d03
Fix to 8c71422: add the file
2015-02-06 13:56:31 -05:00
Carl Eberhard
242f2634cf
API, configuration: expand exposed settings to include those needed by the masthead in galaxy.masthead.mako, add serializers for config
2015-02-06 13:38:53 -05:00
Daniel Blankenberg
1155ead7ff
Fix for SelectToolParameters that utilize dynamic options and that make use of __trans__ failing at get_legal_values().
2015-02-06 11:56:54 -05:00
Dannon Baker
f4ec978d9e
Relocate uwsgi test to the beginning of config, since this might affect other config options down the road.
2015-02-06 11:40:47 -05:00
Dannon Baker
f457c09f07
Adjust generated queue names to match with new postfork manipulation of config.server_name
2015-02-06 11:33:33 -05:00
Dannon Baker
7adff59c5f
Force postfork unique servername on uwsgi workers in the format of 'servername.workername'. Use this for correctly routing messages.
2015-02-06 11:05:06 -05:00
Dannon Baker
5eff5db70d
Minor formatting of routes in buildapp.py
2015-02-06 10:55:15 -05:00
Dannon Baker
2fed958e86
The other half of d89864b9f5daaec89dfda0ad5772a13aed72536b.
2015-02-06 09:00:12 -05:00
Dannon Baker
9f826acff7
Merge.
2015-02-06 08:56:03 -05:00
Dannon Baker
c973726bb1
Postfork (under uwsgi at least -- otherwise just the last bit before webapp returns) magic for kicking off workers (and potentially other things)
2015-02-06 08:55:50 -05:00
John Chilton
ba825fc553
Fix reports webapp for MySQL.
...
Big thanks for Eric Enns and Fernandez Edgar for contributing patches to the galaxy-dev list.
2015-02-05 21:27:53 -05:00
John Chilton
09c88b119c
PEP-8 fixes for reports controllers and app.
2015-02-05 21:27:53 -05:00
Dannon Baker
17d3311f3a
Minor pep8'ing in lib/galaxy/config.py
2015-02-05 19:16:19 -05:00
Dannon Baker
269cab275f
Remove TODO about moving uwsgi test since I did it.
2015-02-05 19:15:10 -05:00
Dannon Baker
c3004f7af1
Relocate is_uwsgi to app.config (determined at configuration time via import).
2015-02-05 19:13:59 -05:00
Dannon Baker
7b8dac532e
Merge.
2015-02-05 18:55:20 -05:00
Dannon Baker
a5c151ead8
Add reference to the webapp to galaxy.app
2015-02-05 18:35:43 -05:00
Carl Eberhard
d31335fbcf
Fix to 3abf1c3: pass app to super
2015-02-05 17:36:26 -05:00
Carl Eberhard
23991f5e1b
Managers, users: add filters for later admin use, quota serializers, and a fallback anonymous user serialization; DatasetAssociations & HDAs: add filters
2015-02-05 16:55:23 -05:00
Aysam Guerler
a251de996a
ToolForm: Update version selection, use underscores for internal parameters
2015-02-05 13:34:51 -05:00
John Chilton
ab2bfa88b8
Bugfix for bugfix d3b1f6b.
...
d3b1f6b fix the GUI (in an obsecure use) but broke fairly typical uses of the API.
2015-02-05 13:32:56 -05:00
John Chilton
5956c42d2c
Improved error message if things don't match up when recovering workflows.
...
Ideally this shouldn't really happen - but this should help if it does.
2015-02-05 12:27:46 -05:00
John Chilton
afed259b39
Fix scheduling_manager.py for unknown attribute reference.
...
Not sure if this was a poor rebasing or a copy and paste error.
2015-02-05 12:27:46 -05:00
John Chilton
5a1336f7de
Workflow scheduling delay fix.
...
There were problems if all three of these conditions were met - 1) workflow from GUI, 2) workflow evaluation delayed, and 3) a delayed step was connected to a input dataset. This fixes these workflows.
2015-02-05 12:27:46 -05:00
John Chilton
85eb1fed9f
Fix workflow schedulers to fallback onto sample like other config files.
2015-02-05 12:27:46 -05:00
Aysam Guerler
840176e543
Workflow: Fix text and boolean parameter handling, simplify module update
2015-02-05 10:08:45 -05:00
Dannon Baker
2de2e340a2
pep8, cleanup in galaxy/buildapp
2015-02-05 09:45:15 -05:00
Dannon Baker
e25ea889b2
Prevent uwsgi from ever loading static middleware -- it can serve static files directly with appropriate routes in its config (see wiki).
2015-02-05 09:35:36 -05:00
Nate Coraor
caa8cd0a56
Minor bug fixes for main.py (webless Galaxy entry point).
2015-02-04 23:40:59 -05:00
Daniel Blankenberg
0ed4ee779b
Allow reloading External Display applications without restarting Galaxy.
2015-02-04 16:12:03 -05:00
Dannon Baker
0bcfe09fa2
Merged in dan/galaxy-central-prs (pull request #659 )
...
In API, when removing or refreshing a data table, send the reload signal to the worker queue. Change return values of reload and delete to be the new table contents, instead of the only-internally-useful 'version'.
2015-02-04 12:45:56 -05:00
Dannon Baker
f7c030718f
pep8 webapp.py.
2015-02-04 11:08:25 -05:00
Dannon Baker
75ccacd6e3
Update commentary per previous commit re: API request handling.
2015-02-04 11:07:58 -05:00
Dannon Baker
45caf23933
Handle timeout correctly for API requests. There's still the issue of clients potentially not understanding this, and of course the @web.json requests.
2015-02-04 11:06:53 -05:00
Dannon Baker
05ba490f7c
Initial version of session_timeout. Still needs client side work to handle API/web.json requests better but that turned out to be a large project -- see TODOs for more details.
2015-02-04 10:33:07 -05:00
Daniel Blankenberg
3039743782
In API, when removing or refreshing a data table, send the reload signal to the worker queue. Change return values of reload and delete to be the new table contents, instead of the only-internally-useful 'version'.
2015-02-04 10:02:20 -05:00
Aysam Guerler
889dc5a68f
ToolForm: Add optional tool state format
2015-02-03 23:40:36 -05:00
Dannon Baker
d88586be03
Add requires to ensure repoze is on the path (should resolve issue seen on Test but nowhere else that I know of).
2015-02-03 13:25:42 -05:00
Carl Eberhard
462ade7aa4
Core, authentication: set status code of trans._authenticate_api errors to 403 in _future_expose_api, some readability changes
2015-02-03 12:47:02 -05:00
John Chilton
1f0c450952
API endpoint for reloading tool data tables (from Bjoern).
...
The endpoint isn't "RESTful" IMO - but it does match what we are doing for tools - so it is consistent which is more important.
2015-02-03 12:44:39 -05:00
John Chilton
ca18ff517d
Small cleanup to lib/galaxy/tools/evaluation.py.
...
Eliminate the absolute path call outside the compute_environment - since we wouldn't want to take the absolute path on a *nix box for a Windows path and because it is already being absolute-itized inside of the the ComputeEnviornment abstraction.
Eliminate TODO comment that has already been TODONE.
2015-02-03 12:22:57 -05:00
John Chilton
b56bd85b6a
Expose $__tool_directory__ to tools.
...
Repeatedly one wants to do things like create symbolic links and then call a helper script - the 'interpreter' tag doesn't allow shell commands before calling a helper script so they could not be used in this fashion. The previous pattern for doing this was then to use the ToolShed only 'set_environment' requirement tag. These were onerous to setup and the resulting tools were no longer portable to non-ToolShed installed contexts - I believe this variant is more robust and elegant.
More information https://trello.com/c/0pgF5PBQ and here https://trello.com/c/XK5SqE1i .
2015-02-03 10:29:34 -05:00
Carl Eberhard
16828184ad
Fix to 8e5b9ca: implement _future_expose_api_anonymous_and_sessionless to allow endpoints to be access without user or session (fixes access to api/authenticate)
2015-02-02 18:57:54 -05:00
Carl Eberhard
f1eff6f022
API, folders & folder_contents: use _future_expose_api on NotImplemented routes
2015-02-02 18:01:44 -05:00
Carl Eberhard
b4c34f1517
API, users: use _future_expose_api and minor clean up
2015-02-02 17:48:31 -05:00
Carl Eberhard
5e39759b27
Core, startup: add deprecation log.warn if using 'pack_scripts' option
2015-02-02 17:09:12 -05:00
Carl Eberhard
91beddc6f9
API, tags & annotations: use _future_expose_api and minor clean up
2015-02-02 17:08:17 -05:00
Dannon Baker