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10377 Commits
Author SHA1 Message Date
Eric Rasche 4705409d38 Expose all API keys to admins under REMOTE_USER 
This is the default setting for non-remote-user setups, this commit
adjusts the middleware to behave as expected.

Issue raised in http://dev.list.galaxyproject.org/User-API-keys-with-External-LDAP-authentication-disabled-td4668052.html
 2015-10-08 10:22:41 -05:00
Daniel Blankenberg 092fc17ec0 Merge pull request #846 from jmchilton/ucsc_cleanup 
UCSC Tool Cleanup
 2015-10-05 17:05:56 -04:00
Martin Cech 753bb9de0f Merge pull request #839 from jmchilton/text_file_busy 
Attempt to fix "Text file busy" errors (testing and production)
 2015-10-05 14:57:16 -04:00
John Chilton 1aebbc3f68 Remove likely broken UCSC proxy and associated tools. 
Unused for many, many years and likely no longer works.
 2015-10-05 15:55:21 +01:00
Nicola Soranzo 54410d7d70 Use eggs.require() instead of pkg_resources in lib/galaxy/datatypes/ . 
Fix https://github.com/galaxyproject/galaxy/issues/809#issuecomment-145107037 .
 2015-10-05 12:03:36 +01:00
John Chilton b75175f18d Centralize logic for writing job scripts. 
Runners were using various permissions, some didn't close file handles, etc....

In addition, run sync after script is written to avoid "Text file busy" problems in all job script scenerios.
 2015-10-05 11:02:14 +01:00
John Chilton 4e35ff04a1 More improved file handling for job code. 
Another stab in the dark that won't actually fix the testing issues with Docker.
 2015-10-05 09:44:26 +01:00
Dannon Baker 02962ae646 Merge pull request #830 from jmchilton/local_close 
Improved file handling in local runner.
 2015-10-02 11:08:29 -04:00
John Chilton b3a3756424 Merge pull request #821 from dannon/statsd 
Request timing middleware via statsd
 2015-10-02 15:57:37 +01:00
John Chilton 8af833cb34 Fix a potentially problematic file operation. 
It might be causing intermittent test failures when running this code in Docker containers, we are unsure.
 2015-10-02 11:05:55 +01:00
Dannon Baker 5592422d01 Merge pull request #826 from guerler/fix_select_000 
Fix default value for optional select fields
 2015-10-01 16:08:02 -04:00
guerler 8cc27b45d0 Fix default value for optional select fields 2015-10-01 15:23:06 -04:00
Dannon Baker de82b1236d Merge branch 'master' into dev 2015-10-01 12:38:44 -04:00
Martin Cech c133078b60 Merge pull request #822 from jmchilton/db_test_fix 
Fix db initialization when galaxy.ini doesn't exist.
 2015-10-01 12:03:08 -04:00
Dannon Baker 3fa7844956 Opt for failing instead of continuing to run Galaxy if statsd middleware is configured but module is not available. 2015-10-01 11:44:23 -04:00
Dannon Baker 72330cc316 'Fix' for unit tests. 2015-10-01 11:32:55 -04:00
Dannon Baker c6794e62c5 In lieu of rolling an egg, just test for statsd when middleware is wrapped. 2015-10-01 11:19:44 -04:00
Dannon Baker fc69247d50 Fix default statsd port. 2015-10-01 10:50:48 -04:00
John Chilton 6592a14089 Fix db initialization when galaxy.ini doesn't exist. 2015-10-01 12:02:13 +01:00
Dannon Baker 52a51af4ed Fix middleware application message. 2015-09-30 16:01:18 -04:00
Dannon Baker 6ee9a08cf2 Merge pull request #786 from guerler/tool_form_003 
Remove tool form mako, reduce tool runner, fix job resubmission options
 2015-09-30 13:57:25 -04:00
Dannon Baker 1b841a9aa4 Tweak docstring 2015-09-30 13:25:09 -04:00
Dannon Baker e710c46f24 Fix namespacing of events 2015-09-30 13:16:25 -04:00
carlfeberhard 1a13efe488 API, Datasets: fix returned tuple from creating_job; normalize id encoding, parens, naming; move both rerunnable and creating_job into datasets.py to allow (future?) use by lddas and ldas 2015-09-30 11:57:40 -04:00
Dannon Baker 9aee212225 Merge pull request #770 from nsoranzo/dev 
flake8 lib/galaxy/webapps/tool_shed/model/migrate/versions/ .
 2015-09-30 10:28:00 -04:00
Dannon Baker 56734878e7 Statsd middleware for request timing. 2015-09-30 10:23:26 -04:00
guerler 6d00f38f0a Merge branch 'dev' of https://github.com/galaxyproject/galaxy into tool_form_003 
Conflicts:
	client/galaxy/scripts/mvc/tools/tools-form.js
	static/maps/mvc/tools/tools-form.js.map
	static/scripts/mvc/tools/tools-form.js
 2015-09-29 15:55:59 -04:00
Martin Cech 76fcde3274 Merge pull request #811 from dannon/prt_fix 
[15.07] Fix change_password (destination for password reset link) to work w/ …
 2015-09-29 14:54:02 -04:00
Daniel Blankenberg 6406276146 Merge pull request #806 from martenson/data-lib-work 
UI and API for data library folders management
 2015-09-29 14:15:11 -04:00
Daniel Blankenberg 531875753d Merge pull request #812 from dannon/prt_email_tweak 
Tweak password reset email template to truly be plain text.
 2015-09-29 14:04:09 -04:00
Daniel Blankenberg 75cc56793c Merge pull request #813 from jmchilton/tool_loading 
Small tweaks to tool loading.
 2015-09-29 14:03:37 -04:00
Nate Coraor 90dc2b1093 Merge branch 'release_15.07' into dev 2015-09-29 13:55:22 -04:00
Dannon Baker 90f63a401b Tweak password reset email template to truly be plain text. 2015-09-29 11:37:20 -04:00
Dannon Baker 8a30d3add4 Fix change_password (destination for password reset link) to work w/ require_login 2015-09-29 11:27:38 -04:00
John Chilton de2bb5771b Remove unused code. 2015-09-29 13:57:15 +01:00
John Chilton ac18cbe978 Improved "special" tool loading. 
Instead of writing out the tools on startup (a more expensive operation than reading), just read the existing files in. Add new abstraction to the tool panel to reduce some otherwise duplicated code.

Testing:

The following two API tests should cover the modified behavior, they verify that metadata is still detectable and that history import and export still works.

```
./run_tests.sh -api test/api/test_histories.py:HistoriesApiTestCase.test_import_export
./run_tests.sh -with_framework_test_tools -api test/api/test_tools.py:ToolsTestCase.test_rdata_not_decompressed
```
 2015-09-29 13:57:15 +01:00
Martin Cech e9f12d3b5b move dict formatting call from api controller to manager 2015-09-28 15:27:29 -04:00
Nate Coraor 6fef4465ae [Pulsar] Resubmit AMQP acknowledgement messages to the correct queue 
when consuming more than one. Also, only start one acknowledgement
manager thread rather than one per consumer.
 2015-09-28 15:07:07 -04:00
Martin Cech f778a3864c :bird:👀 and some docs 2015-09-28 12:42:56 -04:00
Martin Cech b77c28cd77 flake8 fix 2015-09-28 11:50:05 -04:00
Martin Cech 10c915bb62 Merge branch 'dev' into data-lib-work 
Conflicts:
	static/maps/mvc/library/library-foldertoolbar-view.js.map
	static/scripts/mvc/library/library-foldertoolbar-view.js

also re-grunted
 2015-09-28 11:40:35 -04:00
Martin Cech 796f803df0 provide UI to delete and udelete lib folders; slight refactor 2015-09-28 11:38:35 -04:00
John Chilton d3b53544df Fix framework test failures. 
Some other fix caused the yaml example tool to load in the framework and api tests again after a long regression, this in turn caused a more recent regression to pop out in the framework test suite. This fixes that, thanks for the heads up @martenson.
 2015-09-28 12:37:57 +01:00
guerler f5a6e25ebd Reinsert data_source tool execution into tool runner controller (requires separate PR) 2015-09-28 00:33:09 -04:00
Dannon Baker 6d5ee0b6c8 Merge branch 'master' into dev 2015-09-25 13:41:10 -04:00
Dannon Baker 1a17dbb68d Merge pull request #798 from blankenberg/tool_error_fixes 
[15.07] Fix for not respecting tool errors when trying to execute tools
 2015-09-25 13:39:17 -04:00
Nicola Soranzo e006745508 Merge branch 'release_15.05' into release_15.07 2015-09-25 18:21:27 +01:00
Nicola Soranzo ac8b5eae02 Fix errors when starting "./run_tests.sh -with_framework_test_tools -api" 2015-09-25 17:51:21 +01:00
Daniel Blankenberg 05f02cf9b4 Fix for not respecting tool errors when trying to execute tools where the error occurs within a repeat. 2015-09-25 12:01:13 -04:00
John Chilton 6d3ea7ee00 Merge pull request #790 from erasche/gie-docker-launch 
Refactor GIE Launching to use -P
 2015-09-25 16:05:35 +01:00