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Author SHA1 Message Date
Nate Coraor 7210e5d46e Move, rather than copy files staged back to Galaxy via the job files 
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
John Chilton 47c278ecb1 Merge pull request #96 from dannon/release_15.03 
[STABLE] Connection pool disposal fixes for all 3 apps
 2015-04-08 15:09:21 -05:00
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
Martin Cech 167fb67ec5 Merge pull request #94 from jmchilton/real_user_doc_fix 
[STABLE] Fix documentation for run-as-real-user parameters.
 2015-04-08 11:48:04 -04:00
John Chilton 54ccd3e4a4 Fix documentation for real user parameters. 
I think what was documented was the ideal case - which would be great if these could be set per destination - but they cannot be so they shouldn't be documented that way.

Documentation broken in https://github.com/galaxyproject/galaxy/commit/9b7775be03728f724c025a83bc7ffa9e28c2c932.
 2015-04-08 08:51:20 -04:00
John Chilton 9fd27f68c7 Merge pull request #92 from guerler/release_15.03 
[STABLE] Fix re-run option for data manager tools
 2015-04-07 12:30:26 -05:00
guerler 3207302e04 Fix re-run option for data manager tools 2015-04-07 13:11:39 -04:00
John Chilton 2b2064179a Merge pull request #79 from guerler/pr_dataset_mapping 
[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 
[STABLE] Fix: datasets.purge_async/_purge to allow purging hdas within non-curren...
 2015-04-06 16:24:47 -04:00
Daniel Blankenberg 05f37eccea Merge pull request #85 from jmchilton/workflow_runtime_bugfixes 
[STABLE] Bugfixes for runtime parameter handling in the workflow run form.
 2015-04-06 15:08:57 -04:00
Dannon Baker f4ab1f8220 Merge pull request #81 from blankenberg/ts_tool_display_fix 
[STABLE] Fixes for displaying certain valid tool interfaces in the ToolShed.
 2015-04-06 14:35:36 -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
Dannon Baker 8b56505a0d Merge pull request #83 from blankenberg/igv_local_stable 
[STABLE] Re-enable IGV local external display application by default.
 2015-04-06 13:22:35 -04:00
John Chilton 6fee45fbfd Bugfixes for runtime parameter handling in the workflow run form. 
The behavior of these forms was modified in PR 433 (https://bitbucket.org/galaxy/galaxy-central/pull-request/433/fix-allow-editing-workflows-on-the-fly-for/diff# - not merged by me :| ) - so that the entire workflow would be submitted as runtime parameters on each submission.

In addition to this causing bugs related to unvalidated parameters https://trello.com/c/72WuZ8mu and other problems with select parameters (e.g. http://dev.list.galaxyproject.org/Workflow-bug-when-loc-entries-are-missing-tc4666875.html) - I just discovered it would also cause the modified value to be submitted even if the user opts to undo the selection of a runtime workflow parameter and restore the previous selection (i.e. the form would show the original value but the new value would be submitted).

This PR restores the previous behavior of giving the submitted form elements a unique name so every value in the workflow is not replaced as part of the submission - fixing the former problem. The new technique also fixes the other problem as well.
 2015-04-06 12:29:40 -04:00
Daniel Blankenberg 62c66d3c92 Re-enable IGV local external display application by default. Add hg38 as available genome. We should probably update this view to either allow any genome or to function like the current web_link_main. 2015-04-06 11:41:44 -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
John Chilton acd67001f8 Merge pull request #77 from dannon/workflow_tag_fix 
[STABLE] More fixes for removal of trans from various manager functions.
 2015-04-02 15:07:27 -05:00
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 
[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 
[STABLE] fix metadata string formatting error @martenson reported yesterday
 2015-04-02 10:09:27 -05:00
John Chilton 1a113a3c6e Merge pull request #67 from dannon/expressionfix 
[STABLE] Fixes for using expression contexts in select parameters.
 2015-04-02 07:44:07 -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
Dannon Baker afc807eda2 Merge pull request #61 from carlfeberhard/fix.circster 
[STABLE] Fix to ba44452: properly scope mod_icon_btn in define not require
 2015-03-31 17:24:56 -04:00
Carl Eberhard f7669f3cd6 Fix to ba44452: properly scope mod_icon_btn in define not require 2015-03-31 17:05:50 -04:00
John Chilton b109a0459c Merge pull request #58 from natefoo/stable_resubmitted 
[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 
[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 
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 
(cherry picked from commit b4cf49a449)
 2015-03-30 14:10:42 -04:00
John Chilton a812633a35 Merge pull request #53 from martenson/release_15.03-fix-paramget-default 
[STABLE] [15.03] fix missing defaults for get()
 2015-03-30 13:06:56 -05:00
Martin Cech 476eaa2f05 fix missing defaults for get() 
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. 
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
Dannon Baker 1fcd055655 Merge pull request #49 from natefoo/toolshed_uwsgi_static 
[STABLE] Tool Shed: Do not load static middleware when loaded with uWSGI
 2015-03-30 11:43:21 -04:00
Nate Coraor 34df74b6d4 Apply @dannon's change from Galaxy to the Tool Shed disabling static 
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 fa60579558 Merge pull request #45 from jmchilton/proxy_tool_download 
[STABLE] Fix proxied API tool downloads.
 2015-03-26 15:04:11 -05:00
John Chilton a1bb89802f Fix proxied API tool downloads. 
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 
[STABLE] Re-enable job metrics by default.
 2015-03-26 11:33:53 -04:00
Daniel Blankenberg 0e26cc5f83 Merge pull request #43 from carlfeberhard/fix.info-none 
[STABLE] HDA API: deserializing None in misc_info/info as the empty string
 2015-03-26 09:57:53 -04:00
John Chilton ff1430f5e1 Re-enable job metrics by default. 
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