Nate Coraor
7210e5d46e
Move, rather than copy files staged back to Galaxy via the job files
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api. Moving is a rename when the source and destination are on the same
filesystem, which is nearly instantaneous and greatly reduces the
possibility for failure due to mid-copy restarts.
2015-04-10 15:30:31 -04:00
Nate Coraor
1167c7d724
Enable use of nginx_upload_module for the job files api.
2015-04-10 15:29:18 -04:00
Dannon Baker
3ac516291c
Another pool disposal fix, for reports.
2015-04-08 14:21:39 -04:00
Dannon Baker
d403c43123
Similar fix as the previous -- Galaxy wasn't disposing of pooled connections prior to returning webapp and (potential) forking.
2015-04-08 14:21:34 -04:00
Dannon Baker
d6bf6fc2b2
Potential fix for recent uwsgi toolshed database issues. In any event, this current pool disposal is definitely broken (and hidden from view due to blanket passing except) in the current implementation.
2015-04-08 14:21:27 -04:00
John Chilton
2b2064179a
Merge pull request #79 from guerler/pr_dataset_mapping
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[STABLE] Revise re-run mapping of datasets and collections for imported ...
2015-04-07 11:35:35 -05:00
Dannon Baker
7e075a6ffd
Merge pull request #88 from carlfeberhard/fix.dataset-purge
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[STABLE] Fix: datasets.purge_async/_purge to allow purging hdas within non-curren...
2015-04-06 16:24:47 -04:00
Carl Eberhard
fb3d622041
Fix: datasets.purge_async/_purge to allow purging hdas within non-current histories
2015-04-06 13:44:21 -04:00
Daniel Blankenberg
3d92202402
Fixes for displaying certain valid tool interfaces in the ToolShed.
2015-04-03 14:39:40 -04:00
guerler
3bca8799b5
[STABLE] Revise re-run mapping of datasets and collections for imported and copied history items. The previous method (from tool_runner.py) had difficulties with consistently hashing history items which caused issues for imported datasets. We fixed that, however now datasets copied back to the same history are shown instead of the original dataset.
2015-04-03 11:46:17 -04:00
Dannon Baker
fcb35e023a
More fixes for removal of trans from various manager functions.
2015-04-02 15:42:38 -04:00
Dannon Baker
93bd09d228
Merge pull request #71 from carlfeberhard/release_15.03
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[STABLE] Fix: hda manager trans param in visualizations controller and tools api ...
2015-04-02 11:49:41 -04:00
Carl Eberhard
f5e5812473
Fix: hda manager trans param in visualizations controller and tools api _rerun_tool
2015-04-02 11:38:30 -04:00
John Chilton
fb2c7bcd5a
Merge pull request #68 from dannon/fix_for_marten
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[STABLE] fix metadata string formatting error @martenson reported yesterday
2015-04-02 10:09:27 -05:00
Dannon Baker
b307de98b7
Fix spacing to follow our guidelines.
2015-04-02 08:26:30 -04:00
Dannon Baker
5914524b9e
Fix error in toolshed metadata generator reported by @martenson
2015-04-02 08:26:17 -04:00
Dannon Baker
8bbd24007c
Fix get_options_from_code to correctly use an expresioncontext as well, this would have prevented it working in repeats/etc
2015-04-02 08:19:37 -04:00
Dannon Baker
6e5cd74a31
Fix dynamic options not filling properly
2015-04-02 08:19:31 -04:00
John Chilton
b109a0459c
Merge pull request #58 from natefoo/stable_resubmitted
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[STABLE] Fix the "resubmitted" job state
2015-03-31 12:48:24 -05:00
Dannon Baker
a6256b5471
Merge pull request #52 from jmchilton/job_flush
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[STABLE] Fix database deadlocks when running large workflows.
2015-03-30 18:33:09 -04:00
Nate Coraor
4658fb4a18
Get rid of the "resubmitted" dataset state and provide a slightly useful
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message on job/job_state_history.info explaining the resubmit reason.
Also PEP-8 while I'm in there.
(cherry picked from commit bce81719eb
2015-03-30 14:14:56 -04:00
Carl Eberhard
3dceec3258
API, HDAs: properly fetch resubmitted flag from the new job state history table
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(cherry picked from commit b4cf49a449
2015-03-30 14:10:42 -04:00
Martin Cech
476eaa2f05
fix missing defaults for get()
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params class override the method and force default to be included
2015-03-30 13:15:29 -04:00
John Chilton
65a42e9bc6
Fix database deadlocks when running large workflows.
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This fix was first tested and initially verfied by Marius van den Beek with subsequent parallel verification from Philip Mabon and Aaron Petkau.
Likely these deadlocks were introduced in 14.10 when I added an update time to workflow invocations so we can re-evaluate them over time - an explanation for why the deadlocks are likely occuring can be found in the code comments.
2015-03-30 12:39:45 -04:00
Nate Coraor
34df74b6d4
Apply @dannon's change from Galaxy to the Tool Shed disabling static
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middleware when uWSGI is in use.
2015-03-30 11:32:30 -04:00
guerler
112296d865
Set (default) default value to None
2015-03-27 14:17:09 -04:00
guerler
1047255b75
Handle failed late validation
2015-03-27 13:56:20 -04:00
guerler
9c47fba04b
Fix default values for conditional multi select fields
2015-03-27 13:02:48 -04:00
John Chilton
a1bb89802f
Fix proxied API tool downloads.
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From IRC:
17:22 < kellrott> Any ideas about how to deal with https://github.com/bgruening/docker-galaxy-stable/issues/50 ?
17:22 < mrscribe> Title: Tool downloads are not working · Issue #50 · bgruening/docker-galaxy-stable · GitHub (at
github.com)
17:24 < kellrott> I think its from how the tool download function unlinks a file while holding the open file handle
( https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/tools.py#L208 )
17:24 < mrscribe> Title: galaxy/tools.py at dev · galaxyproject/galaxy · GitHub (at github.com)
17:27 < jmchilton> Have you tried not unlinking that file?
17:28 < jmchilton> If that fixes it I have no problem just leaving the file in temp - Galaxy leaves a lot of stuff
in temp anyway
17:46 < kellrott> yep, that does the trick
Closes bgruening/docker-galaxy-stable#50 .
2015-03-26 13:48:08 -04:00
Martin Cech
084e479bb6
Merge pull request #42 from jmchilton/metrics_fix
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[STABLE] Re-enable job metrics by default.
2015-03-26 11:33:53 -04:00
John Chilton
ff1430f5e1
Re-enable job metrics by default.
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This has been broken since 14.10.
2015-03-25 22:01:29 -04:00
Carl Eberhard
dcd0a771aa
HDA API: deserializing None in misc_info/info as the empty string
2015-03-25 18:32:19 -04:00
John Chilton
2169087171
Fix logging_connection_proxy for sqlalchemy upgrade.
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The import * is now importing something call inspect which is masking the actual desired inspect import above it.
2015-03-24 10:43:30 -04:00
John Chilton
cbe953cb70
Merge pull request #34 from blankenberg/view_history_fix
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[Stable] Fix displaying an error message when a user cannot view a history. Previ...
2015-03-20 20:57:22 -05:00
Daniel Blankenberg
59b18ef4ff
Fix displaying an error message when a user cannot view a history. Previously, it was throwing a server error when it was attempting to display from an empty history_dict.
2015-03-20 17:18:08 -04:00
John Chilton
447eb06a94
Merge pull request #28 from dannon/workflow_import_fix
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[STABLE] Fix workflow step uuid handling to handle UUID being the string None in ...
2015-03-19 14:45:35 -05:00
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
Dannon Baker
9a628898b1
Fix workflow step uuid handling to handle UUID being the string None in input JSON. This fixes export/import that was broken with release_15.03.
2015-03-17 15:33:44 -04:00
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