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Author SHA1 Message Date
John Chilton dd7bddcaa6 Optimize initial queueing of jobs. 
- Don't refresh job when this is the only thread fetching it.
 - Avoid a bunch of unnecessary flushes, just flush once essentially during process.

Brings this process from taking over 1 second per job on average on sqlite for cat1 on my laptop to around 400 ms on average.
 2015-12-03 10:15:11 +00:00
John Chilton 67c98f54ca Merge pull request #1200 from nsoranzo/tool_shed_fixes 
Tool shed fixes.
 2015-12-01 23:51:47 -05:00
Nicola Soranzo 194d871e38 Fix Tool Shed export capsule for Mercurial >= 3.4 . 
Fix the following error:
tool_shed.capsule.capsule_manager ERROR 2015-12-01 12:24:37,542 unable to find mercurial command "archive"
Traceback (most recent call last):
  File "/opt/galaxy/lib/tool_shed/capsule/capsule_manager.py", line 88, in export_repository
    work_dir )
  File "/opt/galaxy/lib/tool_shed/capsule/capsule_manager.py", line 148, in generate_repository_archive
    changeset_revision )
  File "/opt/galaxy/lib/tool_shed/util/hg_util.py", line 28, in archive_repository_revision
    options_dict = get_mercurial_default_options_dict( 'archive' )
  File "/opt/galaxy/lib/tool_shed/util/hg_util.py", line 200, in get_mercurial_default_options_dict
    raise Exception('unable to find mercurial command "%s"' % command)
Exception: unable to find mercurial command "archive"
 2015-12-01 16:45:25 +00:00
Nicola Soranzo 657afa89d3 Small fixes. 2015-12-01 16:45:25 +00:00
Nicola Soranzo ff619df394 Downgrade Mercurial wheel to 3.4.2 to restore hg push of Tool Shed repositories. Fix #1183. 2015-12-01 16:45:19 +00:00
Dannon Baker 84464288b1 Merge pull request #1184 from guerler/fix_download_links_002 
Filter download links, avoid warning dialog
 2015-12-01 10:19:22 -05:00
Nicola Soranzo 3524476bc6 Merge branch 'master' into dev 2015-12-01 11:42:16 +00:00
Eric Rasche da2cc588e5 Merge pull request #1194 from martenson/release_15.10 
[15.10] docs - deprecate TS direct hg api
 2015-11-30 13:39:17 -06:00
Martin Cech 5bd898118f deprecate TS direct hg api 2015-11-30 14:35:45 -05:00
Nate Coraor 9e28f2e786 Merge branch 'release_15.10' into dev 2015-11-30 14:13:26 -05:00
John Chilton a03404c04d Merge pull request #1162 from martenson/fix-datalibs 
[15.10] Fix two bugs in datalibs
v15.10 		2015-11-30 13:57:15 -05:00
Martin Cech c532f6808e Merge pull request #1186 from gregvonkuster/release_15.10 
[15.10] Add support for Strand-specific Coordinate Count datatype
 2015-11-30 13:56:24 -05:00
Martin Cech 492fcdab9f Merge pull request #1193 from mvdbeek/gvk_ts_fixes 
Add enhancements to the Galaxy repository install process
 2015-11-30 13:16:06 -05:00
Dannon Baker f35bd9ae02 Merge pull request #1181 from souravsingh/rename_file 
Renames reports_wsgi.ini
 2015-11-30 11:49:41 -05:00
Greg Von Kuster 2829cab105 Add enhancements to the Galaxy repository install process 
to cleanly handle the case described here:
https://github.com/galaxyproject/galaxy/issues/667.  Specifically, the
following scenario is now cleanly handled:

Example use case: In a toolshed I have a repository of a tool, say

package_new_gene_db_1_2_3, and in revision 1 it depends on
package_sqlite_1_0_0:

package_new_gene_db_1_2_3
package_sqlite_1_0_0

At some point in time I discover that postgres is a better solution for
my gene database, and I upload revision 2:

package_new_gene_db_1_2_3
package_postgres__2_0_0

And I remove the dependecy of sqlite.  If I go to my galaxy instance and
I remove revision 1 and install revision 2, the installation is cleanly
handled with theis PR.

It should be noted that this enhancement could adversely impact
reproducibility if best practices are not followed with regard to
defining package dependencies.  Since it is now cleanly possible to
eliminate dependencies over time, best practices must be followed to
ensure that elimination of a dependency does not affect the output of a
tool that uses the underlying hierarchy of packages.
 2015-11-30 17:49:11 +01:00
Dannon Baker c2f9331611 Merge pull request #1174 from jmchilton/workflow_runtime_fix 
Fix interface and usage of WorkflowModule.get_runtime_inputs.
 2015-11-30 10:29:48 -05:00
Dannon Baker dc41856812 Merge pull request #1173 from jmchilton/wfcfix 
Fixes for WorkflowContentsManager requiring app during init.
 2015-11-30 10:28:25 -05:00
Sourav Singh 9e353028d5 Updated run_reports.sh 
Updated run_reports.sh to mark the latest changes.
 2015-11-30 20:05:15 +05:30
Sourav Singh 8971badb10 Updated gitignore 2015-11-30 19:53:36 +05:30
Dannon Baker 1b06e8d674 Merge pull request #1126 from jgoecks/farbtastic-fix 
Readd jquery.migrate to galaxy.panels template because it is needed f…
 2015-11-30 09:05:33 -05:00
Greg Von Kuster 21fad8ac88 Set the column names and edit the comments section 2015-11-30 07:48:08 -05:00
Greg Von Kuster 6fdff2d2f8 Add Strand-specific Coordinate Count datatype entry to the datatypes config. 2015-11-28 14:32:12 -05:00
Greg Von Kuster 87b9d1a5f4 Add support for Strand-specific COordinate Count datatype 2015-11-28 14:28:38 -05:00
Sourav Singh 7b85684683 Updated run_reports.sh 
Updated run_reports.sh to reflect new changes.
 2015-11-29 00:35:32 +05:30
guerler 2e97553194 Filter download links 2015-11-28 04:35:58 -05:00
Sourav Singh ca3e3760cc Changed reports_wsgi.ini to reports.ini 2015-11-27 23:53:42 +05:30
Sourav Singh 9fceddf8a2 Changed reports_wsgi.ini to reports.ini 2015-11-27 23:50:46 +05:30
Sourav Singh a366835596 Changed reports_wsgi.ini to reports.ini 2015-11-27 23:47:52 +05:30
Sourav Singh 2568e85e7b Renames reports_wsgi.ini 2015-11-27 23:29:48 +05:30
Eric Rasche f4dab5523b Merge pull request #1178 from bgruening/obbeforechange_ie 
Prevent GIEs from being closed without user confirmation
 2015-11-26 07:29:44 -06:00
Nicola Soranzo 2a54ff0829 Merge pull request #1176 from jmchilton/auto_migrate 
Do not check for tool migrations when running tests.
 2015-11-26 10:57:34 +00:00
Bjoern Gruening 62474100f8 add onbeforeunload to IE 2015-11-26 00:48:05 +01:00
Eric Rasche 0c75af7192 Merge pull request #1157 from guerler/revise_iframe_unload_001 
Call onbeforeunload before hiding iframe through display()
 2015-11-25 14:27:46 -06:00
Nicola Soranzo 6fda0e0aac Merge branch 'master' into dev 
Conflicts:
	run_tests.sh
 2015-11-25 17:35:18 +00:00
Nicola Soranzo a5200a4d5f Merge pull request #1172 from martenson/fix-dockerimage-version 
[15.10] run 15.10 tests on older docker image
 2015-11-25 17:33:44 +00:00
Nicola Soranzo 4f6aad473d Merge branch 'master' into dev 2015-11-25 16:18:37 +00:00
Martin Cech be7b003c77 try running 15.10 on older docker image 2015-11-25 11:14:50 -05:00
Nicola Soranzo d89670e939 Merge pull request #1170 from martenson/fix-password-reset 
[15.10] fix missing configuration which broke TS password reset
 2015-11-25 16:06:00 +00:00
Martin Cech aa52b6cff1 add pretty_datetime_format to TS config sample 2015-11-25 10:56:04 -05:00
John Chilton c408b0ec65 Do not check for tool migrations when running tests. 
This is an inappropriate time for the check and causes slow down when running tests.
 2015-11-25 15:19:30 +00:00
Martin Cech 7a4be88693 fix missing configuration; broke TS password reset 2015-11-25 09:53:11 -05:00
John Chilton 6752fcc100 Fix interface and usage of WorkflowModule.get_runtime_inputs. 
Run workflow workflow form was broken for workflows with pause steps.

Fixes #1015 (thanks @afgane).
 2015-11-25 13:36:34 +00:00
John Chilton 4261403fad Fixes for WorkflowContentsManager requiring app during init. 2015-11-25 13:24:17 +00:00
Daniel Blankenberg 11edf3559d Merge pull request #1166 from jmchilton/tool_opts_2 
Another set of tool execution optimizations
 2015-11-24 16:49:24 -05:00
Daniel Blankenberg 853efcea14 Merge pull request #1163 from jmchilton/tool_opts_1 
Small optimizations to running tools.
 2015-11-24 10:28:24 -05:00
John Chilton 01c57908ea Another tool execution optimization... 
Prefetch all groups, roles, and associations when using User.all_users(). This reduces three queries down to one if the user has no groups or group roles and only belongs to the private user role, obviously the number of queries saved would increase more and more if the user belonged to multiple roles or groups.
 2015-11-24 15:10:43 +00:00
John Chilton 42d006162c Another tool dataset creation optimization... 
Rather than using three transactions to create an HDA, a dataset, and its roles - do this all in one transaction.
 2015-11-24 15:09:09 +00:00
John Chilton 1ea68f9384 Save a query per output during tool execution. 2015-11-24 10:18:04 +00:00
John Chilton 32728e2392 Small optimizations to running tools. 2015-11-24 09:56:37 +00:00
Martin Cech e19b7f656f fix the extra slash in URL when creating folder 2015-11-23 15:14:15 -05:00