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10686 Commits
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
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
Nate Coraor 9e28f2e786 Merge branch 'release_15.10' into dev 2015-11-30 14:13:26 -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
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
Greg Von Kuster 21fad8ac88 Set the column names and edit the comments section 2015-11-30 07:48:08 -05:00
Greg Von Kuster 87b9d1a5f4 Add support for Strand-specific COordinate Count datatype 2015-11-28 14:28:38 -05:00
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
Nicola Soranzo 4f6aad473d Merge branch 'master' into dev 2015-11-25 16:18:37 +00:00
John Chilton 4261403fad Fixes for WorkflowContentsManager requiring app during init. 2015-11-25 13:24:17 +00:00
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
Nicola Soranzo b6451d0be6 Fix bugs in test and code introduced in PR #1113. 2015-11-23 15:18:57 +00:00
Greg Von Kuster 82ce624465 Fix for re-installing an uninstalled TS repository with a dependency 
where both the repository and the dependency were updated in the TS
after the repository was uninstalled.
 2015-11-23 09:52:40 -05:00
Greg Von Kuster a16cb06705 Fix for re-installing an uninstalled TS repository with a dependency 
where both the repository and the dependency were updated in the TS
after the repository was uninstalled.
 2015-11-22 16:50:39 -05:00
Martin Cech 2e510bd5e1 Merge pull request #1113 from jmchilton/format_source_collection 
Allow accessing collection elements in format_source.
 2015-11-21 23:38:39 -05:00
Martin Cech 286f714287 Merge pull request #1085 from guerler/fix_grids_000 
[15.10] Fix dataset grid history change
 2015-11-20 13:08:26 -05:00
Martin Cech 7bb88b3f44 Merge pull request #1097 from jmchilton/cwl_refactoring 
Small Tool and Workflow Cleanups from CWL Work.
 2015-11-20 12:57:43 -05:00
Dannon Baker 05ed245353 Fix the bad merge :( 2015-11-19 20:48:16 -05:00
Dannon Baker f61ec1c3c0 Merge and rebuild client 2015-11-19 20:34:32 -05:00
Dannon Baker 0fdca7d40a A large assortment of escaping fixes to primarily grids and javascript templating, and one bad-data-ingress fix (copy history name). 2015-11-19 20:27:25 -05:00
Dannon Baker 96b17bd856 Merge pull request #1117 from jmchilton/input_hang 
Don't let $input hang cheetah evaluation...
 2015-11-19 17:18:57 -05:00
Eric Rasche 81f842743d Merge pull request #1131 from bgruening/IE_iobio 
Add BAM iobio visualisation as Interactive Environment
 2015-11-19 15:02:37 -06:00
Bjoern Gruening 5188b41790 make travis happy 2015-11-19 20:53:30 +01:00
Bjoern Gruening af36ca6d94 add BAM iobio visualisation as Interactive Environment 2015-11-19 18:58:43 +01:00
Nicola Soranzo d2bab13fa9 Merge pull request #1119 from jmchilton/maxseconds 
Revise and fix waiting for tool tests.
 2015-11-19 10:54:10 +00:00
John Chilton f770128915 Merge pull request #991 from erasche/fix-932 
Fixes #932
 2015-11-18 13:48:34 -05:00
John Chilton e4e44be27b Merge pull request #1004 from jj-umn/uniprotxml_datatype 
UniProtXML datatype
 2015-11-18 13:47:27 -05:00
John Chilton 7fef50f45f Merge pull request #881 from scholtalbers/role-page-fix 
Fix the issue where too many datasets are linked to a certain role
 2015-11-18 13:46:29 -05:00
John Chilton ee2b34c387 Merge pull request #950 from fescudie/dev 
Add BIOM v1 in default datatypes.
 2015-11-18 13:41:02 -05:00
John Chilton 05f3da308d Fix macro bug with empty CDATA being None instead of ''. 
Fixes galaxyproject/planemo#362 thanks for the report @erasche.

Test using the following command:

```
nosetests test/unit/tools/test_tool_loader.py
```
 2015-11-18 12:25:38 +00:00
John Chilton b25b8c3f24 Revise and fix waiting for tool tests. 
- maxseconds on test tag stopped being respected at some point, fix that.
- maxseconds on test tag stopped being parsed at some later point, fix that.
- Revise default behavior so it can be overridden with yet another testing environment variable GALAXY_TEST_DEFAULT_WAIT.
- Add test case to ensure there is no future regression of these behaviors.
 2015-11-18 11:22:40 +00:00
John Chilton 0ff8a21891 Add example tools demonstrating cheetah problem (unbound variable). 
Refine default override of input to raise an exception instead of just throwing in a dummy string.
 2015-11-18 10:40:57 +00:00
John Chilton 704144c169 Don't let $input hang cheetah evaluation... 
If $input is undefined. The Python input command was being used and causing Galaxy to hang during evaluation.
 2015-11-18 10:20:23 +00:00
Nicola Soranzo c252987b4c Merge branch 'master' into dev 2015-11-18 10:15:22 +00:00
Nicola Soranzo 73f46f4e08 Merge branch 'release_15.07' into release_15.10 2015-11-18 10:06:53 +00:00
Martin Cech 729ed463aa Merge pull request #1108 from yhoogstrate/cram_datatype 
CRAM datatype definiton
 2015-11-17 16:27:22 -05:00
Dannon Baker 1063c175be Merge pull request #1114 from jmchilton/sync_more 
Give writing job script more time to flush and sync during verification.
 2015-11-17 15:36:52 -05:00
Dannon Baker e6d651be32 Merge pull request #1091 from natefoo/webob-string-to-none 
Fix bug with referer attribute type change in WebOb
 2015-11-17 15:17:29 -05:00
Nate Coraor d5fe49ec6f Incorporate @nsoranzo's suggestions 2015-11-17 12:50:20 -05:00
Nate Coraor d8152f3336 Merge branch 'release_15.10' into dev 2015-11-17 11:37:05 -05:00
John Chilton 7018753bc9 Give writing job script more time to flush and sync during verification. 
Still having occasional failures - https://jenkins.galaxyproject.org/job/docker-api/1172/testReport/junit/api.test_tools/ToolsTestCase/test_multirun_non_data_parameter/.
 2015-11-17 15:18:50 +00:00
John Chilton 0030f4c549 API test fix from @nsoranzo. 2015-11-17 15:13:49 +00:00
John Chilton 312746d169 Allow accessing collection elements in format_source. 
Can do it by numeric index or element name, e.g. input[0] or input["forward"]. Only works for 1-D collections.

Implements #699.

Run new and most relevant existing tests with the following commands:

```
nosetests test/unit/tools/test_actions.py
./run_tests.sh -framework -id output_format_collection
./run_tests.sh -framework -id output_format
```
 2015-11-17 14:13:14 +00:00