Nicola Soranzo
5e71401a7e
Merge branch 'release_18.09' into dev
2018-10-12 09:47:34 +01:00
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
c6193ca440
Update DEVTEAM, rebuild, include a few new PRs.
2018-10-11 10:37:54 -04:00
Nicola Soranzo
260e37f2bc
Merge branch 'release_18.09' into dev
2018-10-01 17:27:30 +01:00
mvdbeek
b64c82921e
Need quotes around export?
2018-10-01 14:06:12 +02:00
mvdbeek
702870c17c
Allow starting Galaxy under gunicorn when using galaxy.ini
...
and starting Galaxy with `APP_WEBSERVER=gunicorn sh run.sh`.
Additional gunicorn cmdline arguments can be passed using
`GUNICORN_CMD_ARGS`. In a first pass this will allow
running planemo {server, test} under python 3, as Paste
has some problems under python 3:
```
galaxy.web.stack INFO 2018-09-29 22:16:00,216 Galaxy server instance 'main' is running
Traceback (most recent call last):
File "./scripts/paster.py", line 27, in <module>
serve.run()
File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 1055, in run
invoke(command, command_name, options, args[1:])
File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 1061, in invoke
exit_code = runner.run(args)
File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 226, in run
result = self.command()
File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 676, in command
serve()
File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 653, in serve
server(app)
File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/loadwsgi.py", line 232, in server_wrapper
**context.local_conf)
File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/loadwsgi.py", line 90, in fix_call
val = callable(*args, **kw)
File "/home/travis/.planemo/gx_venv_3_release_18.09/lib/python3.6/site-packages/paste/httpserver.py", line 1353, in server_runner
for name, value in kwargs.items():
RuntimeError: dictionary changed size during iteration
```
That said gunicorn is a nice pure-python alternative to paste going
forward.
2018-09-30 13:18:21 +02:00
Nate Coraor
8dbf140cce
Add a pgcleanup action to purge HDAs of purged histories
2018-09-28 16:39:30 -04:00
Dannon Baker
e9e2b6d9e2
Minor reminders that would have been nice (for me, at least) to have on the release scaffold.
2018-09-26 16:07:42 -04:00
Dannon Baker
7787d3ae8e
Merge remote-tracking branch 'upstream/release_18.09' into dev
2018-09-26 10:46:58 -04:00
Dannon Baker
3f8c2beff2
Swap to a production w/ sourcemaps build by default for autobuilder (though, of course, folks can manually do whatever -- seems like the most sensible default though)
2018-09-21 12:24:15 -04:00
Dannon Baker
f3298953d4
Don't skip build on release/master moving forward.
2018-09-21 11:42:51 -04:00
John Chilton
7481d97a33
Merge pull request #6736 from natefoo/pgcleanup
...
pgcleanup.py enhancements
2018-09-20 14:24:46 -04:00
Dannon Baker
101f2009f8
Merge branch 'release_18.09' into dev
2018-09-19 16:41:29 -04:00
Dannon
b64754dee9
Merge pull request #6743 from martenson/fix-favicon-uwsgi
...
[18.09] fix favicon.ico for uwsgi deployments
2018-09-19 13:00:53 -04:00
Nicola Soranzo
4723ad6672
Merge branch 'release_18.09' into dev
2018-09-19 17:12:46 +01:00
Nicola Soranzo
4ce8086c20
Merge branch 'release_18.05' into release_18.09
2018-09-19 16:58:46 +01:00
Martin Cech
420f43645a
map the favicon in uwsgi config
2018-09-19 11:52:35 -04:00
Nicola Soranzo
35754dc49a
Fix symlinking during plugin staging
...
Remove also broken symlinks before creating the new ones.
2018-09-19 11:16:54 +01:00
Nate Coraor
7b8af87091
Add a pgcleanup function for purging error HDAs
2018-09-18 18:24:02 -04:00
Nate Coraor
eae35fab33
Deduplicate pgcleanup.py
2018-09-18 18:23:34 -04:00
Nicola Soranzo
8982212d39
Replace deprecated xml.etree.ElementTree.Element.getiterator() with iter()
2018-09-18 10:06:13 +01:00
Nicola Soranzo
0c931235af
Change all remaining old-style classes to new style
2018-09-17 12:26:07 +01:00
Nicola Soranzo
e950579bf2
Replace deprecated xml.etree.ElementTree.Element.getiterator() with iter()
2018-09-17 11:00:08 +01:00
Dannon Baker
b8fe2fe294
Merge branch 'release_18.05' into dev
2018-09-10 17:31:24 -04:00
Dannon Baker
1ee673306c
Skip the commit attempt, just flush on success
2018-09-07 13:20:34 -04:00
Dannon
6787dbc9ee
Merge pull request #6642 from natefoo/galaxy-main-import
...
Allow running scripts/galaxy-main without Galaxy on sys.path
2018-09-06 08:13:06 -04:00
Nicola Soranzo
923ed2ed49
Simplify importing from galaxy lib
2018-09-05 19:47:48 +01:00
Dannon Baker
cf9d7c53f0
Restructure to allow individual successful conversions to commit, only rolling back individual fails instead of the entire transaction. This is going to be necessary for complicated deployments like main, where we have ~95% working fine but the otehr 5% were busted to start with (and won't parse), etc. Also swap dryrun to difflib display.
2018-09-05 14:11:11 -04:00
Nicola Soranzo
ad02c53154
Fix many links
2018-09-03 14:34:13 +01:00
Dannon Baker
eab6dd8581
Add dry run mode for script to test
2018-08-29 16:27:01 -04:00
Dannon Baker
4fa1cc38ea
Rename page 'fixer' script
2018-08-29 13:08:26 -04:00
Dannon Baker
eb8d80b6d2
Handle item name fetching, enforce accessible
2018-08-29 12:18:27 -04:00
Dannon Baker
f9d791c228
Refactoring, drop BS4. It's faster, for sure, but this leaves us with fewer moving parts and this isn't a script anyone's going to run often. Hopefully.
2018-08-28 16:02:07 -04:00
Dannon Baker
c0c587abdf
Add page_to_raw to decode ids in the database.
2018-08-28 13:19:11 -04:00
Nate Coraor
4ed9df9a94
Set config builder attributes before they're referenced in app_kwds()
2018-08-27 14:03:39 -04:00
Nate Coraor
51b4def4ec
Allow running scripts/galaxy-main without Galaxy on $PYTHONPATH
2018-08-27 13:56:13 -04:00
Nicola Soranzo
df8abbe3ef
Prefer unicodify() for binary-to-text conversion
...
which supports non-utf-8 encodings.
2018-08-21 12:35:05 +01:00
John Chilton
ef0a51537e
Merge pull request #6595 from mvdbeek/modernize_data_manager_testing_strip_twill
...
Modernize data manager testing and strip twill
2018-08-15 10:02:57 -04:00
mvdbeek
dc4a4b0eb5
py3: fix secret decoder script
2018-08-14 14:56:07 +02:00
mvdbeek
344f68ea6d
py3: Fix uwsgi mule startup
2018-08-14 14:56:07 +02:00
mvdbeek
3f032f6c38
Rework and simplify data manager testing
...
We don't rely on TwillTestCase anymore, that is now exclusively used by
ShedTwillTestCase. Then I've just re-used the infrastructure of
ToolsTestCase for discovering tests, while making sure that we do use an
admin API key during testing.
2018-08-13 17:19:25 +02:00
mvdbeek
bd92136841
Setup pytest python3 API testing
2018-08-10 22:08:15 +02:00
John Chilton
111b40ac37
Fix linting issue introduced in #6553 .
2018-07-30 11:58:47 -04:00
Helena Rasche
06a4c603d3
Remove the sharing of toolbox in GRT
...
This has been broken for a while and was never super useful data to
obtain.
Fixes #6534
2018-07-30 12:43:08 +02:00
John Chilton
f33770096c
Merge pull request #6481 from nagoue/patch-1
...
Update common_startup_functions.sh
2018-07-11 09:28:20 -04:00
Martin Cech
ab760f5d27
revert the datasource tool sanitation, set default # for export
2018-07-10 12:39:14 -04:00
Nadia Goué
8077d59fd9
Update common_startup_functions.sh
...
Not to override tool_shed config file.
2018-07-10 14:47:54 +02:00
Martin Cech
390aedf8c8
add all sample tool_conf data source tools to GRT sanitization
2018-07-09 16:27:57 -04:00
Martin Cech
fb449b4990
fix the logging init
...
- properly initialiaze the logger
- change level for some of the logs
- add some debug and critical logs
2018-07-09 15:53:49 -04:00
Nicola Soranzo