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Author SHA1 Message Date
Nicola Soranzo 949dcfdbc3 Do not log exceptions twice 
`logging.exception()` already adds the the exception information after
the supplied message.

Also: the `message` attribute of `Exception` class has been dropped in
Python 3, always use `str(e)`.

xref. https://github.com/galaxyproject/galaxy/issues/1715
 2018-10-24 12:57:05 +01:00
Nicola Soranzo 51ca8dc0f5 Merge branch 'release_18.09' into dev 2018-10-24 11:15:54 +01:00
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 096fe9b7b9 Merge pull request #6909 from nsoranzo/error_reports 
Update Bug Reports docs to use YAML syntax
 2018-10-23 18:51:33 -04:00
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 ade72dd8b6 Merge pull request #6905 from guerler/viz_frame 
Fixes for built-in Scatterplot plugin
 2018-10-23 18:50:10 -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 02c71e2429 Merge branch 'release_18.09' into dev 2018-10-23 14:37:09 +01:00
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
John Chilton 3759db3297 Merge pull request #6877 from natefoo/pgcleanup-inactive-users 
Refactor pgcleanup.py and add new routines
 2018-10-23 09:17:47 -04:00
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 cbf8a6658d Update Bug Reports docs to use YAML syntax 2018-10-23 12:43:13 +01:00
Nicola Soranzo a38fc541d1 Simplify imports 2018-10-23 12:32:50 +01:00
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
guerler 4e426ce256 Fix scatterplot saving feature 2018-10-22 14:21:46 -04:00
guerler 77f742d7ff Adjust scatterplot interface style 2018-10-22 14:08:11 -04:00
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
Martin Cech 99bc4b33d2 Merge pull request #5787 from phnmnl/feature/isa_data_type 
Feature/isa data type
 2018-10-19 17:26:52 -04:00
Pierrick ROGER a9eb587a3e Various corrections for py34-lint 
Add second blank line.
Remove useless imports.
 2018-10-18 11:37:04 +02:00
Pierrick ROGER 35093e38fc Remove spaces in blank line. 2018-10-18 11:16:29 +02:00
Pierrick ROGER efc7864cab Merge branch 'dev' into feature/isa_data_type 2018-10-18 10:36:49 +02:00
guerler 46e56417dd Use hasattr instead of relying on value 2018-10-17 15:08:47 -04:00
Martin Cech 81f31d1a29 Merge pull request #6884 from guerler/fix_accessible_links 
Improve resilience on handling sharing attributes
 2018-10-17 15:08:11 -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
Martin Cech af05cb480b Merge pull request #6881 from guerler/fix_selenium 
Fix selenium test selectors for alert messages
 2018-10-17 09:41:57 -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
guerler e66da36f60 Use hasattr instead of relying on value 2018-10-16 18:50:57 -04:00
Martin Cech fbe9e97f19 Merge pull request #6876 from VJalili/refactor_cloud_authz_api 
Specify POST and GET actions for cloudauthz API actions
 2018-10-16 18:06:11 -04:00
Martin Cech 73f691e5b5 reword to reflect refactor 2018-10-16 18:05:52 -04:00
vahid aa20778e0f remove /create from cloudauthz create api docstring. 2018-10-16 13:54:50 -07:00
Martin Cech 2310a509b2 Merge pull request #6882 from almahmoud/published_workflow_bug 
Username filtering for published workflows
 2018-10-16 15:13:55 -04:00
guerler e5186a8110 Align legacy history sharing mako 2018-10-16 14:59:46 -04:00
Martin Cech f4088c89a0 Merge pull request #6871 from almahmoud/rename-bug 
History name not escaped
 2018-10-16 14:45:37 -04:00
almahmoud f8c48b83d2 Username filtering for published workflows 2018-10-16 13:57:21 -04:00
guerler d29e3fc3be Align legacy user info template 2018-10-16 12:05:33 -04:00
guerler 47ad50e1d7 Align legacy registration mako 2018-10-16 12:00:17 -04:00
guerler 222225d3b0 Fix selenium test selectors for alert messages 2018-10-16 11:35:36 -04:00
Dannon fb0f792f8d Merge pull request #6848 from ic4f/dev 
Indicate language in client docs to enable syntax highlighting.
 2018-10-16 11:21:22 -04:00