Dave Bouvier
d206339d2b
Fix resetting all metadata based on issue found by Nicola Soranzo.
2014-06-04 15:04:33 -04:00
Daniel Blankenberg
42d9136147
Fix for installing from toolshed that uses 307 redirects that are not being handled nicely by urllib2.urlopen when the urllib2.Request has data provided.
2014-06-04 11:05:36 -04:00
Daniel Blankenberg
a391491747
Fix for Safari Caching External View application 302 redirect links. See https://trello.com/c/optldnPm
2014-06-03 17:03:17 -04:00
Dave Bouvier
dd95c9303a
Add change that was lost when resolving a merge conflict.
2014-06-03 16:52:18 -04:00
Greg Von Kuster
96f28b6e17
Fix for installing tool dependencies with type set_environment.
2014-06-03 15:34:53 -04:00
Dannon Baker
5f3c681ac4
Cleanly terminate the control worker. Resolves a buildbot issue.
2014-06-02 11:14:18 -04:00
Dannon Baker
8f0990e6b2
Improve assertion logging for upload_store mismatch
2014-05-29 17:23:51 -04:00
Carl Eberhard
2c9637f42b
Silence log warnings when class names are not found in the visualizations registry applicability tests
2014-05-29 16:25:44 -04:00
Dannon Baker
72d1da540b
Fix dep_value being undefined at use. Someone needs to look at the logic here, this is purely an operational fix preventing a crash -- there's logic that still needs to happen somewhere in the chain here.
2014-05-27 17:11:01 -04:00
John Chilton
3e7b1b511a
Bugfix: Hadn't implemented clean way to iterate of collection element names in tools.
...
Perhaps stretching the definition of bugfix here to get this in next-stable.
2014-05-27 12:52:41 -05:00
Greg Von Kuster
82334f9ae7
Improve exception handling for generated Tool Shed URLs.
2014-05-27 13:32:49 -04:00
John Chilton
ebd48be297
English fix: Spelling error in a5f0972.
2014-05-27 09:06:44 -05:00
John Chilton
d6ff59ee0e
Bugfix: Don't show deleted HDCAs when displaying tool selection options.
2014-05-27 09:06:44 -05:00
John Chilton
fc8ee54ce2
Bugfix: Explicitly enforce implicit collection unique element identifier constraint.
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Think this is responsible for bug when collections API does not create as many collections as requested.
2014-05-27 08:20:39 -05:00
John Chilton
d636f62a77
Add some more colllection creation logging.
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Bug report from takadonet of collection request with 280 items only creating 60 - want to know if request got chopped off by proxy or paste, there was some logic error in my code, or if it hit some sort of db/transaction limit. This logging should help dianose that (hopefully). If I find the bug, I will remove this extra logging.
2014-05-23 17:20:55 -05:00
Dannon Baker
8e1a67284b
pep8 api/users controller.
2014-05-23 12:00:21 -04:00
Dannon Baker
4dc23122c3
Force user api to validate creation of new users, raising RequestParameterInvalid on failure to do so.
2014-05-23 11:49:39 -04:00
Dave Bouvier
66d68d661e
Fix server error when registering a new account.
2014-05-23 10:00:33 -04:00
Dannon Baker
94ef41e180
Pep8/spacing
2014-05-22 19:31:34 -04:00
Dannon Baker
035de6882f
Don't validate empty publicnames. This is required.
2014-05-22 19:30:59 -04:00
Dannon Baker
049064ac0f
Combine validation issues so as not to play whack-le-mole at registration time.
2014-05-22 19:29:24 -04:00
Dannon Baker
d333298b3f
Remove cruft from user controller.
2014-05-22 19:26:44 -04:00
Dannon Baker
41c92830bf
Correct comparisons in user controller.
2014-05-22 19:25:57 -04:00
Dannon Baker
a4d91a65e9
Clean up/pep8 user controller.
2014-05-22 19:25:31 -04:00
Dave Bouvier
7725f12598
Enable running the create_users and create_categories scripts via run_tool_shed.sh
2014-05-22 10:59:18 -04:00
John Chilton
9dbbc0fb80
Fix for running workflows with collection inptus.
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takadonet reported running such workflows were not behaving correctly when copying inputs to new history is enabled.
2014-05-21 15:09:52 -05:00
John Chilton
b0c250d791
Fix provenance controller for non-admins.
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Cannot pass check_accessible=True to get_object with HistoryDatasetAssociations (because item.user is undefined.).
2014-05-21 14:33:24 -05:00
John Chilton
c46be5c0dc
Fix admin check in security_check for userless admin keys.
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... by removing duplicated check of trans.user, this check is done in trans.user_is_admin if needed.
2014-05-21 14:33:24 -05:00
Greg Von Kuster
633d3d5a2f
Enhance the Tool Shed API to be able to retrieve an API key for an authenticated user.
2014-05-21 15:06:41 -04:00
Daniel Blankenberg
06c3e549d4
Provide a visual clue that those odd len files as dbkeys are from the history.
2014-05-21 14:24:05 -04:00
Daniel Blankenberg
628d16ad6a
Fix for when a dbkey should be displayed multiple times, but with possibly different names.
2014-05-21 14:08:04 -04:00
Dannon Baker
034a1be99f
When using AMQP, if the AMQP server goes down this will now more nicely catch the Connection refused error in send_control_task
2014-05-20 11:55:24 -04:00
Daniel Blankenberg
b616072582
Fix for reports app's default database/sqlite settings. Most of the reports app will still not work with sqlite however.
2014-05-20 10:32:13 -04:00
Daniel Blankenberg
ca7c93c729
To maintain previous behavior, list custom genome build names first.
2014-05-20 10:18:28 -04:00
Daniel Blankenberg
49e1e48a59
Cleanup for dbkey handling.
2014-05-20 10:01:28 -04:00
Dannon Baker
33e132bf03
Additional anyjson requires (appeared to cause Toolshed issues for Greg)
2014-05-19 19:54:05 -04:00
Dannon Baker
fceadaf1f2
Kombu also requires ordereddict backport to support python2.6, more eggs.
2014-05-19 18:58:13 -04:00
Dannon Baker
c05bef0908
Add conditional requirement of importlib for python 2.6/kombu.
2014-05-19 18:11:52 -04:00
Dannon Baker
e878d8ac5d
Fix get_chrom_info to take (and use) the tool in question.
2014-05-19 17:47:20 -04:00
Dannon Baker
3e66202c08
Fix (kind of a guess as to the intended functionality) input_dbkey error.
2014-05-19 17:42:05 -04:00
John Chilton
a0471e8705
HACK: Fix circular dependency non-sense related to tools and dataset collections.
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https://gist.github.com/jmchilton/6e19d248002b1080e8ba .
2014-05-19 16:18:02 -05:00
Dannon Baker
8c4a0f096e
Initial internal control message queue for IPC implementation. Needs significant refactoring, as noted in some TODOs, but this is a minimally functional version so it makes the next-stable cutoff. Currently only handles reloading tools and data tables, but adding additional tasks is simple and should be straightforward.
2014-05-19 16:56:08 -04:00
Daniel Blankenberg
0c1efa4831
Fix for tool shed handling new GenomeBuilds manager.
2014-05-19 15:35:58 -04:00
Daniel Blankenberg
75aa0a2a9b
First pass at allowing dbkeys / genome builds to be loaded from Tool Data Tables.
2014-05-19 15:08:26 -04:00
Dave Bouvier
a3018feb02
Migrate 22 tools from the distribution to the tool shed.
2014-05-19 13:01:46 -04:00
John Chilton
650626db4e
More performant database interaction during collection creation.
2014-05-19 12:15:48 -05:00
John Chilton
3cd33a70f2
Rework, improve validation of dataset creation requests.
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Being more thorough fixes some potential security problems and will allow some performance optimizations I'm planning.
2014-05-19 11:51:07 -05:00
Dannon Baker
ea906a5a6f
Followup from commentary on PR394, cleaned up incorrect log.exception usage in base controller.
2014-05-19 12:47:10 -04:00
Dannon Baker
5b77b623ad
Merge PR394 from stable.
2014-05-19 12:39:59 -04:00
Nicola Soranzo
b04eb27990
Fix for "'HistoryTagsController' object has no attribute 'security_check'".
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Trying to access /api/histories/$history_id/tags gives this error:
Execption in get_object check for History 1723db999e478a37: 'HistoryTagsController' object has no attribute 'security_check'
Traceback (most recent call last):
File "/opt/galaxy/lib/galaxy/web/base/controller.py", line 233, in get_object
check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted )
File "/opt/galaxy/lib/galaxy/web/base/controller.py", line 131, in get_object
self.security_check( trans, item, check_ownership, check_accessible )
AttributeError: 'HistoryTagsController' object has no attribute 'security_check'
The same happens for workflow tags.
2014-05-19 18:03:21 +02:00
Dave Bouvier