John Chilton
65e5c8e825
Modify url_for in history_contents.py.
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No clue why - but this randomly fails on main. Will keep looking into it - but it wasn't really giving the pretty URL I wanted anyway (though it was working and this still works due to backward compatbility on this route).
2014-06-11 12:37:24 -05:00
Dannon Baker
a4550e1786
History Contents API: Import url_for from galaxy.web like the other controllers, instead of galaxy.web.base.controller.
2014-06-11 12:24:05 -04:00
Dannon Baker
905bd92cdc
Correct tools handling of tool.handle_input -- this doesn't always return a successful job.
2014-06-11 11:39:21 -04:00
Dannon Baker
e3b635cd2e
Set tabular CHUNK_SIZE to ~10kb
2014-06-10 19:24:00 -04:00
Dannon Baker
a71add8ea1
Pack scripts.
2014-06-10 16:41:53 -04:00
John Chilton
f74142688b
Allow injection of high-level helper utility into dynamic destination rules.
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Helper currently has methods methods for determining users recent usage - job count and sum of job runtime - filterable by user_email, job creation and update time, destination id, job states (only 'ok' job state would make sense for runtime - only way Galaxy has that data). Goal here is to allow dynamic destination to assign higher priorities to users who have not used Galaxy recently.
Example usage here : https://gist.github.com/jmchilton/a1b4f0bd3ce7189c0caf .
2014-06-10 15:01:38 -05:00
Dave Bouvier
dd82de6cd1
Additional fixes for urllib2's 3xx redirects not handling POST requests. This changeset handles httpd proxies that redirect to a secure port before delivering the request to Paste.
2014-06-10 11:11:32 -04:00
Greg Von Kuster
08702be139
Fixes for the Tool Shed API POST and PUT requests that were broken when attempting to handle urllib2 not handling 307 redirects. The initial attempt at handling the urllib2 weakness made a call to urllib2.get_url() which turns POST requests into GET requests as a side-effect.
2014-06-10 10:33:48 -04:00
John Chilton
d35562df06
Merged in jmchilton/galaxy-central-fork-1 (pull request #407 )
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Hide concept of job resources in workflows interface, scrub tool state when extracting workflows.
2014-06-09 20:15:37 -05:00
John Chilton
b8edfb8274
More verbose and defensive exception handling when responding to LWR job updates.
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Handler becoming non-responsive in some cases - this may fix it or there may be a race condition somewhere when caching status messages.
2014-06-09 16:58:10 -05:00
Dannon Baker
ed94d528d8
Detail why the 307 redirect tracking attempt in tool_shed/scripts/api/common.py does not work.
2014-06-09 17:02:27 -04:00
Dave Bouvier
e547936b70
Use the same capitalization for eggs.require as is present in the egg's name. This resolves the install and test buildbot's failure on step 4, delete empty directories.
2014-06-09 14:37:36 -04:00
John Chilton
01ab20646d
Hide concept of job resources in workflows interface, scrupt tool state when extracting workflows.
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Workflows describe abstract computational flow - not how to run the job - so I think it makes sense to not include the state of resource parameters in the workflow. Ideally, the option to override the defaults would always be available at runtime - this is not there currently but I think it is better to have a lower utility core functionality that is correct and can be supported than having something currently maximally functional but may be difficult/impossible to support in the future.
Also now auto-fill of job resource defaults produces no warnings (improves UX when rerunning job with previously didn't have resource parameters or if job resource types change over time).
2014-06-09 13:36:17 -05:00
John Chilton
d3c7c012a1
Merged in jmchilton/galaxy-central-fork-1 (pull request #405 )
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Tool shed refactoring toward use outside Galaxy app.
2014-06-09 11:01:47 -05:00
John Chilton
3b630d082e
More robust path handling for remotely generated metadata.
2014-06-09 10:51:54 -05:00
Dannon Baker
c5bd808d27
merge.
2014-06-09 11:23:14 -04:00
Dannon Baker
b4e52547f1
Add admin_users_list to the toolshed's config.
2014-06-09 11:22:53 -04:00
Greg Von Kuster
8f53cc1c3e
Fix the various step handler function calls to the env manager's get_env_shell_file_paths_from_setup_environment_elem function.
2014-06-09 11:20:49 -04:00
Dave Bouvier
af815ee1bf
Merge bugfix from stable.
2014-06-09 11:15:45 -04:00
Dave Bouvier
d1d9f568ca
Fix step handling for setup of perl and ruby environments.
2014-06-09 11:11:24 -04:00
Dannon Baker
82ca2fcc77
Swap require_admin decorator and trans.user_is_amdin to use the newer correctly filtered admin_users_list in app.config
2014-06-09 10:42:33 -04:00
Dannon Baker
f2a711be12
Add correctly prefiltered admin_users_list to app.config and use it for remote auth.
2014-06-09 10:37:10 -04:00
John Chilton
12b063ece4
Refactor code actually orchistrating installs out of high-level API action.
2014-06-09 09:13:40 -05:00
John Chilton
7a3d8479ab
Refactor install_repository_revision - move all API formatting logic to end of function.
2014-06-09 09:13:40 -05:00
John Chilton
475256a1bf
Break-up big function install_repository_revision in tool_shed_repositories API.
2014-06-09 09:13:40 -05:00
John Chilton
ad42538a1f
Improved exception handling when installing repositories on tool shed comm errors.
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Now 5XX status will be set. More specific errors else where as well.
2014-06-09 09:13:40 -05:00
John Chilton
c89fa6e595
Make helper function for some duplicated code in tool shed repositories API.
2014-06-09 09:13:40 -05:00
John Chilton
c3c4b78915
Add AdminRequiredException to galaxy.exceptions.
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There was a INSUFFICIENT_PERMISSIONS error code - but that seems more for user-land sharable objects.
2014-06-09 09:13:40 -05:00
John Chilton
4b02203384
Refactor common code out of tool shed repositories API...
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... and rework suc.have_shed_tool_conf_for_install to not require trans.
2014-06-09 09:13:40 -05:00
John Chilton
ffd562c922
Rework ToolShedRepositoriesController API controller to use newer API decorator.
2014-06-09 09:13:39 -05:00
John Chilton
ebe264becc
Refactoring toward allowing tool shed installs outside of web threads.
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Continuing work started by Greg, nearly all the helpers called from "install_repository_revision" in tool_shed_repositry API take in app instead of trans.
This was 36 fairly atomic commits that I have rebased into 1 (even for me that is a lot of commits for absolutely no new functionality). One can track the invidual steps and check work here: https://github.com/jmchilton/galaxy-central/compare/tool_shed_hacking .
2014-06-09 09:13:39 -05:00
John Chilton
530265d718
Merge.
2014-06-09 08:32:24 -05:00
John Chilton
069a9f61a1
Tools: MATCH (pair) multi-run datasets by default instead of doing ALL-V-ALL.
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Worried this might be responsible for problems on main. TODO is to make this an optional and explicit like with workflows.
2014-06-09 08:30:40 -05:00
Dannon Baker
5ff2875549
Wrap remote user conditional on multiple lines.
2014-06-09 09:09:45 -04:00
Dannon Baker
eeb946cec9
Slightly simplify remote_user_header access logic.
2014-06-09 08:40:40 -04:00
Dannon Baker
480ea96d90
Cleanup/pep8 of remoteuser middleware.
2014-06-09 08:38:47 -04:00
Dannon Baker
6f9d687269
One more touchup in webframework -- correct raise form and use multiple lines.
2014-06-09 08:35:32 -04:00
Dannon Baker
23b488f7bb
pep8/cleanup. set NERD_tree_1noqa for impossible sqlalchemy lines.
2014-06-09 08:33:25 -04:00
Dannon Baker
5769ea88fa
Fix impersonation when using external authentication. Admins can now impersonate (and then log out of) users when using external auth.
2014-06-09 08:14:18 -04:00
Dannon Baker
a01ccc9f4a
Update user honeypot error message.
2014-06-09 07:58:18 -04:00
Greg Von Kuster
5d56c27f9c
More fixes for handling 307 redirects not being handled nicely by urllib2.urlopen() when the urllib2.Request has data provided.
2014-06-08 08:45:16 -04:00
Dannon Baker
5ccd70ebea
Clarify language in DeleteIntermediateDataset PJA.
2014-06-06 17:12:30 -04:00
Dannon Baker
54a6ebe355
Cleanup, pep8 for postjobactions.
2014-06-06 16:44:47 -04:00
Dannon Baker
4fb8b2d9f0
Initial version of delete intermediate output steps action for workflows.
2014-06-06 16:32:44 -04:00
Dannon Baker
82941fa9f8
Add Workflow.has_outputs_defined to the Workflow model.
2014-06-06 15:36:07 -04:00
Greg Von Kuster
9580a076d5
Fix for getting updates to an installed repository that has a dependency on a Tool dependency definition repository that also has available updates.
2014-06-06 09:45:37 -04:00
John Chilton
2a90811ea3
Another fix for remotely populated metadata FileParameters.
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Requires update to remote LWR as well.
2014-06-05 17:08:24 -05:00
Nate Coraor
41a7637a76
Allow hiding tools from the toolbox config.
2014-06-05 14:46:56 -04:00
John Chilton
036168bdad
Fix working directory used for remote metadata command generation.
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In short - should fix bam outputs for LWR jobs when setting metadata on remote resource. Thanks to @natefoo for tracking down problem.
2014-06-05 11:54:58 -05:00
Dave Bouvier
67718f9d52
Merge bugfix from stable.
2014-06-04 15:15:23 -04:00
John Chilton