Greg Von Kuster
a610d0d458
Enhance the Tool Shed and Galaxy APIs to support resetting metadata on repositories in the Tool Shed or installed into Galaxy respectively. When resetting repository metadata in the Tool Shed, if the API key is associated with an admin user, then setting the my_writable param value to True will restrict resetting metadata to only repositories that are writable by the user in addition to those repositories of type tool_dependency_definition. This param is ignored if the current user is not an admin user, in which case this same restriction is automatic. Also, when resetting metadata in the Tool Shed, repositories of type tool_dependency_definition are reset before repositories of type unrestricted. When setting metadata for installed repositories in Galaxy, neither repository types nor order are considered since these concepts are irrelevant in that environment.
2013-10-16 14:19:26 -04:00
John Chilton
683a561521
Improved handling of tools producing unicode in stardard error/output.
...
Without this modification paste cannot render the stderr and/or stdout of such tools. This is a modification on an idea from Simon Guest, utilizing some code (now available as galaxy.util.smart_str) from an older version of Django to solve this problem.
2013-10-16 13:01:15 -05:00
John Chilton
b464456c0b
Improved handling of tools producing unicode in standard error/output.
...
Without this change (modification on idea by Bjoern), sqlite reports errors as follows for such tools:
ProgrammingError: (ProgrammingError) You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings. u'UPDATE job SET update_time=?, stdout=?, stderr=? WHERE job.id = ?' ('2013-10-10 05:00:05.789309', '', '/dev/fd/2 unicode \xc3\xaa\xe0\xaf\xb3\xe0\xbe\x85\xe1\x9d\xb1\xe3\x8e\xb0\n', 11).
2013-10-16 13:01:15 -05:00
John Chilton
60488bf064
Merged in nsoranzo/galaxy-central-tools2 (pull request #234 )
...
Bug fixes for 3 tools (rebased #222 )
2013-10-16 12:49:34 -05:00
John Chilton
cec3bf3fca
Merge pull request #235 .
...
Fix for tools with trailing semi-colons.
2013-10-16 12:48:50 -05:00
John Chilton
7b82a3c990
Restore improvements to job output checking code.
2013-10-16 12:46:59 -05:00
Jeremy Goecks
b944209ced
Remove tipsy because it has been replaced by bootstrap tooltips.
2013-10-16 13:03:47 -04:00
Martin Cech
9ce9231a3a
honeypot trap for bot registering accounts
2013-10-16 11:40:02 -04:00
Aysam Guerler
d9b284bf5e
Modify bowtie error handler
2013-10-16 11:03:51 -04:00
Aysam Guerler
c32b16e12f
Fix textarea background color in new upload front end
2013-10-16 05:16:55 -04:00
Aysam Guerler
2462ae0008
Fix for Firefox
2013-10-16 04:53:59 -04:00
Aysam Guerler
0df6045ded
Show file size for manually created files
2013-10-16 04:05:53 -04:00
Aysam Guerler
d9573ebb96
Add url, text input field to upload form
2013-10-16 03:36:17 -04:00
Aysam Guerler
20db76ddc0
Sort genomes in genome selector
2013-10-15 23:40:46 -04:00
Aysam Guerler
6a48a732ad
Add genome selector to file upload
2013-10-15 21:04:47 -04:00
Dave Bouvier
d7eccdb0f2
Merged in BjoernGruening/galaxy-central-bgruening/action_tpye_autoconf (pull request #218 )
...
Implementation of the ./configure && make && make install as autoconf action type.
2013-10-15 15:21:52 -04:00
Bjoern Gruening
f04f9400a3
merge
2013-10-15 21:03:05 +02:00
Bjoern Gruening
448e25b8d4
merge
2013-10-15 20:49:11 +02:00
Dave Bouvier
ca85f093e0
Tool dependencies with errors are now individually uninstalled.
2013-10-15 13:47:19 -04:00
Greg Von Kuster
89bbc937ec
Code cleanup in the tool shed's install_util.
2013-10-15 12:09:33 -04:00
Nate Coraor
8b9940d3a9
Include job_runner_external_id in the dataset error email.
2013-10-15 11:48:27 -04:00
Dave Bouvier
b00a3f9046
Merged in BjoernGruening/galaxy-central-bgruening/action_tpye_make_install (pull request #217 )
2013-10-15 11:30:55 -04:00
Dave Bouvier
9cb9c06ff7
Merged in BjoernGruening/galaxy-central-bgruening/R_environment (pull request #219 )
...
Implementation of the a r_environment to easily install R packages in a reproducible way.
2013-10-15 11:24:21 -04:00
Dave Bouvier
dc950c15dd
Merged in BjoernGruening/galaxy-central-bgruening/action_type_misc (pull request #216 )
...
Move the evaluate_template function to the td_common_util file.
2013-10-15 11:15:57 -04:00
Aysam Guerler
73670bd2dc
Make icon number in icon bar a little bit smaller
2013-10-15 11:14:23 -04:00
Aysam Guerler
81610722c2
Add onbeforeunload functions to iconbar item
2013-10-15 00:12:08 -04:00
John Chilton
0f63caaff0
Bug fix in scripts/functional_tests.py.
...
A tempdir is referenced before it is created in certain cases.
2013-10-14 21:50:12 -05:00
John Chilton
ce643e393a
Bug fix in test exception handling code.
2013-10-14 21:50:12 -05:00
Ross Lazarus
273632f31c
branch merge
2013-10-15 09:38:19 +11:00
Dave Bouvier
ff28741642
Explicitly uninstall tool dependencies that are in an error state.
2013-10-14 16:46:41 -04:00
Aysam Guerler
3e8f294ea5
Improvements for the upload box
2013-10-14 16:35:09 -04:00
Aysam Guerler
b30c8e126d
Upload box add user validation
2013-10-14 15:11:49 -04:00
Dave Bouvier
a948eaa352
Fill form by name instead of number.
2013-10-14 13:55:39 -04:00
Aysam Guerler
fbffe7f8e7
Add logging information to upload box
2013-10-14 13:52:41 -04:00
Martin Cech
d81c761fa6
registration form tweaks, preventing the form to be accidentally submitted multiple times (creating duplicate users), includes user-side basic validation
2013-10-14 12:06:34 -04:00
Nate Coraor
ff8366081b
Revert changes from 384240b8cd29 that result in a failure to detect job completion in the drmaa runner on DRMs that do not retain jo
...
b information once a job has exited the queue.
2013-10-14 12:00:57 -04:00
Greg Von Kuster
2a5c2cdf2d
Make communication between Galaxy and the Tool Shed to get status information for installed repositories backward compatible to the 12/20/12 Galaxy release.
2013-10-14 11:12:07 -04:00
Ross Lazarus
c860c25f77
Remove unused test-data/rtestouts
...
Remove references in converters to g2.bx.psu.edu
Note leaving rgenetics converters and datatypes - ped still used in genomic variation tools.
2013-10-14 21:43:32 +11:00
Jeremy Goecks
a62bdf7d2f
Update Trackster reference track config. Pack script.
2013-10-13 17:39:27 -04:00
Jeremy Goecks
cc8bf8d613
Trackster: prevent inadvertent keyboard navigation when configuring track.
2013-10-13 17:09:39 -04:00
Jeremy Goecks
191880fb5c
Trackster: fold name attribute into object preferences.
2013-10-13 17:00:27 -04:00
Jeremy Goecks
b0e4c28a0b
Trackster: fold content_visible flag into config.
2013-10-13 16:28:13 -04:00
Jeremy Goecks
076c2c4b5f
Automated merge.
2013-10-13 15:46:27 -04:00
Jeremy Goecks
1659128179
Trackster: simplify constructor and config logic using object attributes.
2013-10-13 15:39:08 -04:00
Aysam Guerler
b61c2d528b
Fix upload box plugin
2013-10-12 13:07:00 -04:00
Jeremy Goecks
f40d396f4f
Trackster: clean up link attributes.
2013-10-11 21:59:34 -04:00
Jeremy Goecks
c8ec1df754
JSHint-driven Trackster code cleanup.
2013-10-11 17:27:18 -04:00
Jeremy Goecks
be3e3864a8
More trackster cleanup.
2013-10-11 16:34:28 -04:00
Aysam Guerler
03f09b47cc
Fix for removed galaxy.css
2013-10-11 16:09:16 -04:00
Daniel Blankenberg
e9d2043132
Better handling of creating peek for tabular files when metadata is missing.
2013-10-11 15:03:13 -04:00
Greg Von Kuster