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Author SHA1 Message Date
Dannon Baker 6804ce681b Merge dev, resolve conflicts from console re-enablement. 2015-09-23 10:39:46 -04:00
Dannon Baker 8b404205c0 Resolve client merge conflict, repack. 2015-09-23 09:47:35 -04:00
John Chilton 91da5f8068 Merge pull request #775 from erasche/462-followup 
Quote value to fix configparser error in GIEs
 2015-09-23 14:34:03 +01:00
Eric Rasche c96f0e3585 Quote value to fix configparser error 2015-09-22 19:16:17 -05:00
Dannon Baker fe642fe7fa Tweak tool execution to automatically pull detail ids for new hdas on execution success model update so rerun can be immediate. 2015-09-22 19:48:59 -04:00
Dannon Baker 21f777d608 Merge pull request #771 from blankenberg/error-report 
Add encoded IDs to job error reports and also include a link to show_params
 2015-09-22 14:51:52 -04:00
Daniel Blankenberg eac449ed1e white space fix 2015-09-22 14:37:26 -04:00
Daniel Blankenberg b2433f077d Add encoded IDs to job error reports and also include a direct link to dataset's show_params. 2015-09-22 14:26:13 -04:00
Dannon Baker 3d697937c7 Rerun improvement -- instead of allowing someone to try to rerun the upload tool and showing an error message, just don't provide the option for it in the first place. 2015-09-22 10:33:25 -04:00
Martin Cech 419d94e8b0 Merge pull request #769 from blankenberg/ui-fixes 
Add "Galaxy" title to templates/webapps/galaxy/root/index.mako
 2015-09-22 10:16:31 -04:00
Daniel Blankenberg aeda77c600 Add "Galaxy" title to templates/webapps/galaxy/root/index.mako 2015-09-22 10:07:12 -04:00
Nicola Soranzo 248ce3075b Merge pull request #765 from jmchilton/multi_min_max 
Implement min/max for multiple data input parameters.
 2015-09-22 14:52:47 +01:00
Dannon Baker acfd8673b6 Merge from dev." 2015-09-21 17:28:39 -04:00
Björn Grüning fb54be7767 Merge pull request #766 from blankenberg/toolform-rerun 
Tool form error messages and rerun fixes
 2015-09-21 22:14:16 +02:00
Daniel Blankenberg aed76f3744 Do not attempt to rerun non-rerunable tools. 2015-09-21 16:10:13 -04:00
Daniel Blankenberg 7ca661bb01 Fix for displaying tool form errors caused by http exceptions and when tool form doesn't exist. 2015-09-21 16:09:51 -04:00
Nicola Soranzo 5e419197d1 Merge pull request #764 from jmchilton/format_discover 
Allow discover_datasets tag to use format attribute (instead of ext).
 2015-09-21 19:44:07 +01:00
John Chilton 4525b4b911 Merge pull request #763 from martenson/fix-bare-exceptions 
make except catch just Exceptions, not everything
 2015-09-21 18:54:00 +01:00
Martin Cech 56f10c9a1d make except catch just Exceptions, not everything 
I am not sure when these are hapenning (error initialized with encoded
id & tool without id) but this should be safe fix
 2015-09-21 13:51:41 -04:00
Martin Cech c7394bd0b3 Merge pull request #761 from blankenberg/error-tool-id 
When submitting tool error reports, include 'old' tool id as part of subject line.
 2015-09-21 13:01:17 -04:00
Daniel Blankenberg b89c6e56a5 When submitting tool error reports, include 'old' tool id as part of subject line. Makes sifting through bug report emails easier, old id is used for brevity, but full guid is still included in text of report. 2015-09-21 12:50:18 -04:00
Dannon Baker 83bd9dd541 repack without --develop 2015-09-21 12:01:44 -04:00
Dannon Baker b9913d2931 Swap tool form to use Galaxy.modal 2015-09-21 11:53:29 -04:00
John Chilton 87d5063a0d Implement min/max for multiple data input parameters. 2015-09-21 15:51:58 +01:00
Nicola Soranzo 2bfc12d666 Merge pull request #760 from jmchilton/test_error 
Bugfix in test error reporting handling code.
 2015-09-21 15:23:14 +01:00
John Chilton 07dd69edd5 Allow discover_datasets tag to use format attribute (instead of ext). 
https://github.com/TGAC/tgac-galaxytools/commit/93514438cb50fab48d0e211f1e1869b0f591ed66#commitcomment-13349396.
 2015-09-21 14:24:24 +01:00
John Chilton 311100ff9e Bugfix in test error reporting handling code. 
The code for showing status of histories in error would fail if there are collections in the history. This fixes that and skips over collections.
 2015-09-21 09:22:52 +01:00
Eric Rasche 1f1eed0e05 Merge pull request #759 from jmchilton/dockerize_test 
Updates and fixes for dockerized Galaxy testing.
 2015-09-19 17:12:56 -05:00
Martin Cech 2e55eb11e5 Merge pull request #758 from jmchilton/framework_tests 
API Test Fixes
 2015-09-19 15:03:28 -04:00
John Chilton 134c985f90 Updates and fixes for dockerized Galaxy testing. 2015-09-19 16:52:48 +01:00
Martin Cech c7d7736472 Merge pull request #757 from jmchilton/framework_tests 
Fix failing framework tests.
 2015-09-19 10:34:07 -04:00
John Chilton 69f4ace0bc Fix failing workflow to_dict editor test. 
Generating form HTML as part of this request requires a history now (since https://github.com/galaxyproject/galaxy/commit/a00461eaf61bdeeea0c42b8098ae5e6cfbe79694). This is a less than ideal since it should definitely not require a history, but it is also less than idea to be shipping HTML via the API for non-web transactions. So rather than solving the former problem, this solves the latter and just doesn't attach form HTML for API requests.

Fixes #734.
 2015-09-19 12:31:12 +01:00
John Chilton 45d5e29c1d Extend test_map_over_two_collections timeout. 
May be the cause of intermittent test failure on jenkins (https://jenkins.galaxyproject.org/job/G-API/lastCompletedBuild/default/testReport/api.test_tools/ToolsTestCase/test_map_over_two_collections/).
 2015-09-19 11:55:12 +01:00
John Chilton c6be0bc12c Remove compare_bam_as_sam.xml test. 
It never passed, it was originally used by me to test failing tests compared output of bams as sam files. Now that we want all these tests to pass we need to rethink how to test that aspect of the testing framework.
 2015-09-19 10:29:23 +01:00
John Chilton 2b02677e85 Workaround for metadata_bam.xml failure. 2015-09-19 10:27:09 +01:00
Nicola Soranzo 31c2d33ede Merge pull request #756 from dannon/oops 
Fix lack of a return in hda manager
 2015-09-19 00:29:06 +01:00
Dannon Baker cb303a46ef Fix the fix I added to make the unit tests pass. 2015-09-18 18:39:28 -04:00
Björn Grüning ce9fe44b93 Merge pull request #721 from dib-lab/add-oxli-datatypes 
add Oxli datatypes
 2015-09-18 20:28:57 +02:00
nitesh1989 304e569730 Revert "Fixed broken RData sniffer" 
This reverts commit b2e9c8a36f.
 2015-09-18 14:19:22 -04:00
nitesh1989 b2e9c8a36f Fixed broken RData sniffer 2015-09-18 14:16:42 -04:00
Martin Cech ca733d33f9 Merge pull request #752 from nsoranzo/dev 
Fixes for #744.
 2015-09-18 13:01:42 -04:00
Nicola Soranzo d585a4a03d Clearer error message when setting metadata for BCF and SAM/BAM files. 
When the shutil.move() fails.
 2015-09-18 17:56:21 +01:00
Nicola Soranzo 92a152d89c Uniform and slight increase the default timeout of API tests. 2015-09-18 17:48:59 +01:00
Nicola Soranzo 989191d3ce Fix output_format framework test. 2015-09-18 17:48:59 +01:00
Nicola Soranzo 3de7bb6699 Merge pull request #751 from dannon/api_docstrings 
Jobs API docstring {job_id} to {id} convention fix.  Elsewhere we ref…
 2015-09-18 16:41:25 +01:00
Nicola Soranzo 35621ca118 Merge pull request #748 from dannon/sample_cleanup 
Remove deprecated objectstore options from sample; the new way is to …
 2015-09-18 15:34:30 +01:00
Dannon Baker 4fb4873934 Jobs API docstring {job_id} to {id} convention fix. Elsewhere we refer to a member's id as simply 'id' in docs, and this is the parameter name. 2015-09-18 10:20:53 -04:00
Dannon Baker 0ea4ad69a0 Remove deprecated objectstore options from sample; the new way is to set object_store_conf and use it. 2015-09-18 09:29:08 -04:00
Martin Cech fec26b39c2 Merge pull request #742 from carlfeberhard/history.copy-dialog 
History copy dialog & API fix
 2015-09-17 15:35:42 -04:00
Carl Eberhard 3f71220bcf UI, history: clean up copy dialog 2015-09-17 15:09:11 -04:00