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Author SHA1 Message Date
Dannon Baker 9b24afc592 Update version to 18.09 show 2018-10-25 14:57:25 -04:00
Martin Cech 43d9787295 Merge pull request #6923 from dannon/18.09_final_notes 
[18.09] Final release notes updates
 2018-10-25 12:36:12 -04:00
Nate Coraor 3263aba44a Add a warning to the 18.09 release notes informing admins that job 
handling will block until old `new` state jobs have been migrated to a
terminal state.
 2018-10-25 12:08:37 -04:00
Dannon Baker 17f4f7955f s/sources/artifacts 2018-10-25 11:58:53 -04:00
Dannon Baker b6e716b289 Correct javascript caps 2018-10-25 10:37:45 -04:00
Dannon Baker 5a71a744ed Add client artifact note 2018-10-25 10:36:38 -04:00
Dannon Baker 6a072ab29d Four more RN PRs. 2018-10-25 10:14:44 -04:00
Nicola Soranzo 843474e5e3 Merge pull request #6915 from mvdbeek/6904_followup 
[18.09] Small followup to #6904
 2018-10-24 10:37:37 +01:00
mvdbeek 91a9dbaf5c Revert unncessary double logging of exception 2018-10-24 09:50:56 +02:00
mvdbeek c862d55ec8 Use with statement when handling NamedTemporaryFile 2018-10-24 09:50:33 +02:00
John Chilton 328c410fdc Merge pull request #6904 from mvdbeek/fix_weird_xml 
[18.09] Fix pretty printing of shed_tool_conf.xml file
 2018-10-23 18:51:15 -04:00
John Chilton 3638378569 Merge pull request #6912 from natefoo/fix-drmaa-job-stop 
[18.09] Fix stopping DRMAA jobs
 2018-10-23 18:43:21 -04:00
Nate Coraor 3f172cc988 Fix job stopping from DRMAA jobs broken in 
a1c58a7088 and improve logging around it.
 2018-10-23 14:32:26 -04:00
Nicola Soranzo ecb56d80a1 Merge branch 'release_18.05' into release_18.09 2018-10-23 14:28:54 +01:00
mvdbeek 57a4e50d8c Fix capsule export in docker testing 
Found this by removing the blank try/except in the previous commit.
This only affects testing when python can't determine the correct
locale and falls back to ASCII.
 2018-10-23 15:23:54 +02:00
mvdbeek a465543260 Drop threading lock and global try/except 
The Lock wasn't actually preventing anything, and I don't think
anything would need ot be protected here. mkdtemp should be thread-safe.

We also remove the try/except Statement. I think it'd be better to
expose any exceptions here instead of producing broken capsules and
logging an exception.
 2018-10-23 15:19:09 +02:00
mvdbeek 8a39f27b3c Fix toolshed tests 2018-10-23 14:51:14 +02:00
John Chilton 1943587034 Merge pull request #6908 from nsoranzo/release_18.09_config_validate 
[18.09] Fix ``make config-validate``
 2018-10-23 08:51:02 -04:00
Nicola Soranzo 4dd2ecb13f Fix `make config-validate` 2018-10-23 12:28:47 +01:00
John Chilton 88b840d2c6 Merge pull request #6893 from martenson/backport-6884 
[18.09] check presence of attribute in addition to value
 2018-10-22 14:58:58 -04:00
mvdbeek 794d1e03be Fix messed up printing of shed_tool_conf.xml file 
This drops xml_to_string from lib/tool_shed/util/xml_util.py
and uses xml_to_string form lib/galaxy/utils/__init__.py.
Also reduces plain string manipulation of xml structures.
Uses xml.dom.minidom to make xml pretty if necessary.
 2018-10-22 20:37:30 +02:00
John Chilton 3411852fed Merge pull request #6885 from mvdbeek/create_in_new_file_path 
[18.05] Create composite file archives in new_file_path instead of TMP
 2018-10-21 15:51:37 -04:00
guerler 46e56417dd Use hasattr instead of relying on value 2018-10-17 15:08:47 -04:00
Dannon 0aca12ce96 Merge pull request #6892 from martenson/security-notes 
[18.09] add discovered tool vulnerabilities to RN
 2018-10-17 13:21:22 -04:00
Martin Cech fa212c3c31 specify which gemini tools were fixed 2018-10-17 11:45:25 -04:00
Martin Cech 9735146f28 add discovered tool vulnerabilities to RN 2018-10-17 10:53:09 -04:00
Nicola Soranzo 89fbe9c934 Merge pull request #6890 from dannon/18.09_release_notes_updates 
[18.09] One last batch of PRs added to RN
 2018-10-17 14:11:02 +01:00
Dannon Baker d19effdf3c One last batch of PRs. 2018-10-17 08:36:33 -04:00
mvdbeek 126ee5fe2b Create composite file archives in new_file_path instead of TMP 2018-10-17 11:06:55 +02:00
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