Martin Cech
0001e596fa
Merge pull request #25 from blankenberg/release_15.03
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[Stable] Fix for reloading tools. Previously, when a tool was reloaded (of the sa...
2015-03-18 16:09:04 -04:00
John Chilton
546385da62
Merge pull request #27 from dannon/dataset_calculation
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[STABLE] Fix purge quota adjustment via manager functionality.
2015-03-17 14:20:06 -05:00
Dannon Baker
55a774bd7d
Fix purge quota adjustment via manager functionality.
2015-03-17 14:08:07 -04:00
Daniel Blankenberg
ea426438cf
Fix for reloading tools. Previously, when a tool was reloaded (of the same version), you would get the new/correct tool when clicking in Tool Panel, but the rerun button would return the old/pre-reload tool; this is due to the reload not replacing the entries in _tool_versions_by_id.
2015-03-17 13:40:35 -04:00
Nate Coraor
4d0efe583f
Bump version to 15.03.1
2015-03-16 22:24:47 -04:00
dannon
e2118e5bfc
Add information about making history accessible to initial export archive message.
2015-03-16 17:21:08 -04:00
dannon
0989106391
Don't log exception to errormsg on workflow import failure.
2015-03-16 15:28:20 -04:00
Nate Coraor
e6090de6f5
Because __call_method was private, DistributedObjectStore's
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__call_method was never being called, only HierarchicalObjectStore's. .
Make it pseudo-protected by renaming to _call_method.
2015-03-16 14:18:53 -04:00
Nate Coraor
710dfcf9f9
In the metadata tool action, ensure job_working_directory exists before
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trying to get its path. Otherwise, hierarchical/distributed object
stores will be broken.
2015-03-16 10:05:37 -04:00
Nate Coraor
ad9686d136
galaxy.metadata symlink so running jobs do not fail.
2015-03-13 15:56:10 -04:00
Nate Coraor
1172b13a04
Ensure that set_metadata always loads the galaxy module from the same
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version of Galaxy it is in.
2015-03-13 13:32:54 -04:00
Nate Coraor
f481e9d58c
Move set_metadata (once again), to galaxy_ext so that the galaxy
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namespace does not conflict with others (e.g. the galaxy-ops package in
the toolshed).
2015-03-13 13:31:58 -04:00
Nate Coraor
567a952bb1
Use the correct path to the set_metadata temp script on remote compute
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resources.
2015-03-13 12:20:51 -04:00
Nate Coraor
6cfa12123c
Use job working directory for MetadataFiles created with auto-detect.
2015-03-13 11:30:57 -04:00
Nate Coraor
2b6c2a6793
One more change missed in my rebase.
2015-03-12 23:36:25 -04:00
Nate Coraor
c0ccff7dda
DELETED_NEW is part of the Job.finished property...
2015-03-12 22:56:21 -04:00
Nate Coraor
827218a43b
Another change missed in the rebase/commit.
2015-03-12 22:45:05 -04:00
Nate Coraor
54b8ca7958
Fix things that I somehow missed in the rebase for PR #22 .
2015-03-12 21:31:30 -04:00
Nate Coraor
70a443f608
Add minor and combined major+minor version to version.py.
2015-03-12 21:11:39 -04:00
John Chilton
a0783d4371
Merge pull request #22 from natefoo/release_15.03
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Fix command line generation with setting metadata and history export
2015-03-12 14:11:19 -04:00
Nate Coraor
da229c8c2a
Run history export jobs in the same manner as metadata auto-detection
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(so the absolute path of the web galaxy dir is not part of the command
line and can be computed at runtime).
(cherry picked from commit de5d6d1150
2015-03-12 13:18:33 -04:00
Nate Coraor
ee1a2b8972
Relocate the external set_metadata script to the galaxy_utils package.
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A temporary script in the job working directory will be created to
import and call it (trusting that `$PYTHONPATH` in a job script is
always set to `galaxy/lib`). This is so the auto-detect button can defer
command line generation until job preparation time for the case that
handlers and web processes run from different paths.
Related Trello card: https://trello.com/c/v2eCOYZi
(cherry picked from commit b043d43a35e093f58d634443b64eaed2422861878116d2c917
2015-03-12 13:17:41 -04:00
Dannon Baker
85f236ceb5
Process *all* replacements in Rename PJA, instead of just the first one
2015-03-12 12:36:43 -04:00
Dannon Baker
f250ec4ce6
Merge pull request #21 from natefoo/release_15.03
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Also delete/stop jobs when purging from the history grid
2015-03-12 11:46:16 -04:00
Nate Coraor
cac730987f
Make history purge behavior consistent across all UI paths (always
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attempt to stop jobs if the creating job is in the purged history),
previously this was not implemented in the grid history view.
2015-03-12 11:40:25 -04:00
Dannon Baker
58925b3b2e
Merge pull request #20 from natefoo/release_15.03
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Fix copied outputs being discarded when deleting/purging histories in the view all histories interface
2015-03-12 11:24:37 -04:00
Nate Coraor
f4aa8e59cd
Restore job deletion when purging a history and tracking jobs in the
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database.
2015-03-12 11:22:59 -04:00
Nate Coraor
c8596d4c2a
Prevent the deletion of jobs that are already terminal, and prevent
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their outputs from being discarded.
2015-03-12 11:16:35 -04:00
Dannon Baker
dfd08b3aee
Sanely size the workflow parameter input boxes (at runtime), tweak formatting a bit.
2015-03-12 10:34:01 -04:00
guerler
25df2412f6
Merge branch 'release_15.03' of https://github.com/galaxyproject/galaxy into release_15.03
2015-03-11 16:58:22 -04:00
guerler
5ace1a1964
Map imported datasets and collections to current history without hash_util
2015-03-11 16:53:22 -04:00
Carl Eberhard
2ec40287f7
UI, history: (in the client) when calling purge on the history model, mark the history as deleted as well
2015-03-11 12:51:54 -04:00
Dannon Baker
f86a0c5d13
Cherry-pick over non-terminal-only job stop fix.
2015-03-11 10:16:18 -04:00
Dannon Baker
d0667de0cf
No longer mark job as deleted when purging hdas. I can't find a reason we would want to do this anyway, and doing so cascades deletion of copied hdas, which is bad.
2015-03-11 10:12:41 -04:00
Dannon Baker
0dd7590176
Allow admin to create users via API when config.allow_user_creation is False
2015-03-10 16:14:30 -04:00
guerler
c78b7b67f6
Merge branch 'release_15.03' of https://github.com/galaxyproject/galaxy into release_15.03
2015-03-09 13:55:47 -04:00
guerler
4d347dcfe1
Fix select2 field arrow style
2015-03-09 13:55:18 -04:00
Dannon Baker
dd5b7659e8
Cherry-pick e01310e3f8 over to release_15.03
2015-03-09 11:56:29 -04:00
Dannon Baker
d0c97944ed
Ensure path was well constructed (has value) before trying to determine whether or not it exists.
2015-03-06 16:04:43 -05:00
Dannon Baker
eb9d3a9640
Minor wording tweaks.
2015-03-06 15:49:14 -05:00
guerler
f515e29504
Enable remap condition
2015-03-06 15:28:22 -05:00
guerler
949b785fac
Merge branch 'release_15.03' of https://github.com/galaxyproject/galaxy into release_15.03
2015-03-06 15:26:24 -05:00
guerler
d079ad8f8c
Add resume option for job dependencies
2015-03-06 15:24:31 -05:00
Daniel Blankenberg
18d77b008f
Make api/config /version usable as sessionless in addition to anonymous.
2015-03-06 14:18:48 -05:00
guerler
f0bebc997f
Merge branch 'release_15.03' of https://github.com/galaxyproject/galaxy into release_15.03
2015-03-05 22:16:54 -05:00
guerler
1a1f5a33c9
Fix dataset and collection mapping for re-run in imported histories
2015-03-05 22:15:21 -05:00
Daniel Blankenberg
9316cccbb5
Fix for displaying Tools in ToolShed that use Dynamically Generated multiple selects as checkboxes and for displaying select lists using old-style dynamic options.
2015-03-05 17:02:45 -05:00
Dannon Baker
6db6b7e93b
Tweaks to the password reset email template to help email clients not mangle it, and when they do, to suggest copying and pasting.
2015-03-05 13:27:22 -05:00
Dannon Baker
826f69fb62
Python 2.6 has a bug in deepcopy that causes an error when attempting to copy datasets between users (which uses deepcopy). Py2.7 worked fine. Now they both should.
2015-03-04 18:04:00 -05:00
John Chilton
9364b9d3c5
API fixes for tools and datatypes.
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By replacing _future_expose_api_anonymous with _future_expose_api_anonymous_and_sessionless.
2015-03-04 14:51:43 -05:00
Martin Cech