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Author SHA1 Message Date
Martin Cech d4e2f6d59e Merge pull request #6875 from nsoranzo/release_18.09_fix_commit_changeset 
[18.09] Do not traceback when uploading a TS repo with no changes
 2018-10-15 16:30:18 -04:00
Nicola Soranzo b9a01761b0 Do not traceback when uploading a TS repo with no changes 
Fix the following traceback when executing `planemo shed_update`:

```
galaxy.web.framework.decorators ERROR 2018-10-15 18:07:38,736 [p:30249,w:1,m:0] [uWSGIWorker1Core1] Uncaught exception in exposed API method:
Traceback (most recent call last):
  File "lib/galaxy/web/framework/decorators.py", line 154, in decorator
    rval = func(self, trans, *args, **kwargs)
  File "lib/galaxy/webapps/tool_shed/api/repositories.py", line 1116, in create_changeset_revision
    new_repo_alert
  File "lib/tool_shed/util/repository_content_util.py", line 64, in upload_tar
    undesirable_files_removed)
  File "lib/tool_shed/util/commit_util.py", line 225, in handle_directory_changes
    message=commit_message)
  File "lib/tool_shed/util/hg_util.py", line 65, in commit_changeset
    raise Exception(error_message)
Exception: Error committing '/opt/galaxy/database/community_files/000/repo_1' to repository: Command '['hg', 'commit', '-u', u'earlhaminst', '-m', u'planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 22231ebc4e5e990c61243a3609b3347cf63fa024', '/opt/galaxy/database/community_files/000/repo_1']' returned non-zero exit status 1
Output was:
nothing changed

127.0.0.1 - - [15/Oct/2018:18:07:38 +0100] "POST /api/repositories/adb5f5c93f827949/changeset_revision HTTP/1.1" 500 - "-" "python-requests/2.18.4"
```
 2018-10-15 20:35:04 +01:00
Martin Cech 03073ed124 Merge pull request #6867 from mvdbeek/fix_xlsx_unpacking 
[18.09] Keep xlsx files compressed
 2018-10-15 11:26:35 -04:00
mvdbeek 0c7cc50e73 Only warn about multi-file zips if we don't keep the compressed archive 2018-10-13 17:49:19 +02:00
mvdbeek 8edb7499c8 Keep xlsx files compressed 
Fixes https://github.com/galaxyproject/galaxy/issues/6849
 2018-10-13 17:37:41 +02:00
Marius van den Beek 01f1f1b95f Merge pull request #6858 from jmchilton/fix_metadata_revert 
[18.09] Revert selective metadata flushing - breaks multiple uploads/outputs.
 2018-10-12 15:44:01 +02:00
John Chilton f3da0864b4 Test case for regression #6856. 2018-10-12 09:03:12 -04:00
Marius van den Beek 4805304e0b Merge pull request #6863 from nsoranzo/release_18.09_fix_LocalShell_doctest 
[18.09] Fix ``LocalShell`` doctest
 2018-10-12 14:33:42 +02:00
Nicola Soranzo 19f716de91 Fix `LocalShell` doctest 
Broken in commit 57a1f19b06 .
 2018-10-12 11:48:17 +01:00
Nicola Soranzo d22f652f91 Merge branch 'release_18.05' into release_18.09 2018-10-12 09:44:18 +01:00
Nicola Soranzo a8fa5a1d4a Merge branch 'release_18.01' into release_18.05 2018-10-12 09:43:01 +01:00
Nicola Soranzo 2c14c2afc4 Merge pull request #6859 from martenson/paramiko-update 
[18.09] update paramiko dep
 2018-10-12 01:23:54 +01:00
Martin Cech 20f60a5a44 update paramiko dep 2018-10-11 16:15:00 -04:00
John Chilton d791a2c80f Revert selective metadata flushing - seems to break upload changes. 2018-10-11 16:01:45 -04:00
Nicola Soranzo 9251484e72 Merge pull request #6731 from galaxyproject/18.09_release_notes 
[18.09] 18.09 release notes
 2018-10-11 17:56:33 +01:00
Nicola Soranzo d42b899b78 Embellish 18.09 release notes 2018-10-11 17:51:07 +01:00
Dannon Baker d33006cf33 Final docs update 2018-10-11 12:28:32 -04:00
Nate Coraor baa992d217 Merge pull request #6836 from mvdbeek/fix_job_monitor_thread 
[18.01] Register job monitor thread as postfork function
 2018-10-11 11:45:32 -04:00
Dannon Baker 7cb2eb57ac Merge branch '18.09_release_notes' of github.com:galaxyproject/galaxy into 18.09_release_notes 2018-10-11 10:38:15 -04:00
Dannon Baker c6193ca440 Update DEVTEAM, rebuild, include a few new PRs. 2018-10-11 10:37:54 -04:00
Nicola Soranzo c1383bc2d5 Small fixes 2018-10-11 15:22:23 +01:00
Dannon fd0b24ecd2 Merge pull request #6845 from mvdbeek/fix_slurm_cli_on_secure_shell 
[18.05] Fix slurm cli on secure shell
 2018-10-11 10:16:18 -04:00
Dannon fe6c1738c0 Merge pull request #6851 from martenson/backport-gie-kwds 
[18.05] Updated volume kwds for GIEs
 2018-10-11 08:38:23 -04:00
thobalose a1f7634fd7 Updated volume kwds. 2018-10-10 18:28:39 -04:00
Martin Cech cd62461e84 Merge pull request #6839 from dannon/unified-panel-style-tweaks 
[18.09] Unified panel style bottom padding fix
 2018-10-10 13:22:57 -04:00
Nicola Soranzo ac3e1ca1d0 Use Crypto to generate SSH keys 
Also remove key files in `stop_ssh_docker()`.
 2018-10-10 16:22:05 +01:00
mvdbeek b08c6219c3 Simplify ssh key handling in integration test 2018-10-10 14:56:05 +02:00
mvdbeek 5e12e509bf Fix selection of job plugin and image 
Thanks @nsoranzo.
 2018-10-10 14:56:05 +02:00
mvdbeek fc28e0bd83 Use long-form options 2018-10-10 14:56:05 +02:00
mvdbeek 57a1f19b06 Fix slurm cli plugin by avoiding shell=True in subprocess 
Fixes the remaining issue in https://github.com/galaxyproject/galaxy/issues/6831#issuecomment-428097520
 2018-10-10 10:12:18 +02:00
mvdbeek 5844bdc7aa Add integration test for remote shell CLI runners 
This tests both the SecureShell and Paramiko shell plugins and the
Slurm and Torque CLI runner.
 2018-10-10 10:10:51 +02:00
Dannon a43a60656a Merge pull request #6830 from nsoranzo/release_18.09_channel_priority_update 
[18.09] Update conda channel priority: conda-forge > bioconda
 2018-10-09 09:13:51 -04:00
Dannon Baker 6b62a57047 Should fix bug Jen saw with history panel being masked at bottom 2018-10-08 16:32:43 -04:00
mvdbeek 02410b270d Register job monitor as postfork function 
This should fix https://github.com/galaxyproject/galaxy/issues/6831,
and might fix https://github.com/galaxyproject/galaxy/issues/6261.
 2018-10-08 21:33:20 +02:00
Dannon Baker 381d6ad831 Add two recently merged PRs. 2018-10-08 15:25:57 -04:00
John Chilton 5205ed7eeb Merge pull request #6828 from dannon/null_exit_bug_fix 
[18.09] Upgrade concurrently for 'null' return fix
 2018-10-08 07:36:58 -04:00
Nicola Soranzo 9b6833b5a0 make config-rebuild 2018-10-08 11:03:46 +01:00
Nicola Soranzo c83c5cb784 Change conda channel priority: conda-forge > bioconda 
xref. https://github.com/bioconda/bioconda-utils/issues/330
 2018-10-08 11:02:23 +01:00
Nicola Soranzo b99fedefa8 Update to latest galaxy-lib 
Includes:
- change channel priority ( https://github.com/galaxyproject/galaxy-lib/pull/132 )
- channel cleanup ( https://github.com/galaxyproject/galaxy-lib/pull/136 )
 2018-10-08 10:08:02 +01:00
Martin Cech 58ea67eb45 Merge pull request #6823 from jmchilton/tag_input_tests 
[18.09] Allow testing tags in input collections.
 2018-10-07 22:03:38 -04:00
Dannon Baker 9044e614f0 Upgrade concurrently; this fixes a 'null' return from webpack run vi aconcurrently, which can fail the build in some situations. 2018-10-07 20:30:59 -04:00
John Chilton 98a9c86bad Allow testing tags in input collections. 2018-10-06 09:36:41 -04:00
Dannon Baker fdaf9ac864 Link up workflow PRs 2018-10-04 15:27:56 -04:00
Dannon Baker 386229d1ce Re-add removed PRs (bad merge I think) 2018-10-04 15:20:33 -04:00
John Chilton 4d165a5671 Merge branch '18.09_release_notes' of github.com:jmchilton/galaxy into 18.09_release_notes 2018-10-04 14:11:53 -04:00
John Chilton eacec03d10 Update.... 2018-10-04 14:11:08 -04:00
Dannon Baker afffd9bdaa Add final PR. 2018-10-04 13:11:59 -04:00
Marius van den Beek 8ea455303a Merge pull request #6810 from martenson/fix-nonUS-keyboards 
[18.09] do not rule out numbers that are accessed with shift modifier
 2018-10-04 18:53:43 +02:00
Dannon Baker 9071884309 Add deprecation notice for username being null 2018-10-04 12:31:33 -04:00
John Chilton 1c4a4ed8cb Merge remote-tracking branch 'galaxyproject/release_18.05' into release_18.09 2018-10-04 11:43:05 -04:00