almahmoud
ab8bfe4b10
Change default prefix
2021-05-13 12:04:51 -04:00
almahmoud
b0a7c770c8
Merge branch 'release_21.05' of https://github.com/galaxyproject/galaxy into alex_branch
2021-05-12 17:41:37 -04:00
almahmoud
e1f517cf4b
Remove separate conf files
2021-05-12 13:37:21 -04:00
mvdbeek
e80e1a80d6
Convert timezone aware datetime to naive datetime
...
sqlalchemy DateTime columns are not timezone aware, so parse `since`
into timezone-aware datetime and then convert to naive datetime object
representing UTC, assuming history.update_time represents UTC time.
2021-05-12 11:57:45 +02:00
almahmoud
be2967b24d
Fix for subdomain ITs
2021-05-11 20:20:05 -04:00
almahmoud
d0971cc1b5
Move configs to schema
2021-05-11 16:43:46 -04:00
mvdbeek
0a088624a6
Use dateutil for python 3.6 compatibility
...
datetime.fromisoformat was added in python 3.6
2021-05-11 21:46:41 +02:00
almahmoud
3fcceedaa0
Merge branch 'release_21.05' of https://github.com/galaxyproject/galaxy into alex_branch
2021-05-11 13:46:15 -04:00
mvdbeek
191a4b848e
Merge branch 'release_21.01' into release_21.05
2021-05-11 18:28:04 +02:00
mvdbeek
2552ab47f1
Use f-strings in forward-merged code
2021-05-11 18:09:53 +02:00
mvdbeek
41aca51d2b
Merge branch 'release_20.09' into release_21.01
2021-05-11 18:01:46 +02:00
Marius van den Beek
f963b67a6e
Merge pull request #11955 from mvdbeek/fix_ipv6_port_parsing
...
[20.09] Fix container port parsing if IPv6 hostname is ``::``
2021-05-11 17:59:47 +02:00
mvdbeek
01cdbd3ebd
Fix port_parse rsplit usage
2021-05-11 16:40:57 +02:00
Marius van den Beek and Nicola Soranzo
4db3af8e5d
Open container_monitor_exception.txt in write mode
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2021-05-11 14:54:56 +02:00
Marius van den Beek and Nicola Soranzo
7b9d2dbeb9
Skip :: hostname only
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2021-05-11 14:54:28 +02:00
mvdbeek
75f5877951
Log exceptions IT port monitor fails and stop job
...
That should make it significantly easier to debug issues when the
container monitor dies unexpectedly (which I sort of expect in the
future given that we parse output from the docker CLI).
2021-05-10 17:43:46 +02:00
mvdbeek
a1ececdcf8
Fix contianer port parsing if ::: in port line
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:: is an unspecified ipv6 address and just recently appeared in the
docker port output.
2021-05-10 17:37:29 +02:00
mvdbeek
c19a98b8e3
Include tool_id, exit_code and stderr in Exception
...
That'll be useful to figure out what's going on when data staging fails.
2021-05-07 21:44:25 +02:00
mvdbeek
bdc366c64f
Fix pause message when over walltime
2021-05-07 13:20:59 +02:00
Maiken Pedersen
958e52642b
Fix job query filter in walltime check
2021-05-07 13:19:29 +02:00
almahmoud
18a9dd42b9
Linting
2021-05-06 13:35:11 -04:00
almahmoud
84e563cfce
SSL support for ITs
2021-05-06 13:17:14 -04:00
almahmoud
6254961cfd
Consolidate IT cleanup
2021-05-06 11:50:52 -04:00
mvdbeek
e1eef06243
Make guest_ports more reliable
2021-05-06 11:34:49 -04:00
almahmoud
7f87571824
Merge branch 'release_21.05' of https://github.com/galaxyproject/galaxy into release_21.05
2021-05-06 11:33:40 -04:00
John Chilton
75e93a5d43
Fix package CI.
2021-05-06 12:20:53 +01:00
Nicola Soranzo
65ea55bb02
Merge branch 'release_21.01' into release_21.05
2021-05-06 11:45:26 +01:00
Nicola Soranzo
fa58f37f28
Merge branch 'release_20.09' into release_21.01
2021-05-06 11:39:48 +01:00
almahmoud
f7a4ac94e2
Accept user/group IDs as ints
2021-05-05 17:31:52 -04:00
almahmoud
67432c63c2
Add shorten url
2021-05-05 17:31:21 -04:00
mvdbeek
40795140d9
Update version to 21.05.rc1
2021-05-05 21:30:54 +02:00
mvdbeek
b4e24ea69b
Merge branch 'k8s_runner_its' of https://github.com/almahmoud/galaxy into k8s_runner_its
2021-05-05 20:47:08 +02:00
mvdbeek
b7f1b7d81c
Fix package tests
2021-05-05 20:44:09 +02:00
almahmoud
5448124118
Back to old apiversion
2021-05-05 14:23:12 -04:00
Alexandru Mahmoud and Marius van den Beek
1e8a8d1337
Apply suggestions from code review
...
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2021-05-05 13:09:50 -04:00
almahmoud
ed362c48b9
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into alex_branch
2021-05-05 12:47:09 -04:00
John Chilton
51243f185c
Merge pull request #11934 from nsoranzo/fix_test_history_contents
...
Don't move the `update_time` goalpost
2021-05-05 11:31:45 -04:00
Nicola Soranzo
ffb41c2013
Don't move the update_time goalpost
...
In the previous implementation, the tests will raise an Exception if
the dataset collection were updated between `self._get_content()` and
`datetime.utcnow()` .
2021-05-05 14:27:36 +01:00
Nicola Soranzo and Dannon
8e6d56bf3a
Fix indentation
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Co-authored-by: Dannon <dannon.baker@gmail.com >
2021-05-05 13:56:07 +01:00
Nicola Soranzo
6430408fa0
Fix GET /api/datasets/ docs
2021-05-05 13:13:01 +01:00
Marius van den Beek
632d734b18
Merge pull request #11928 from jmchilton/filter_types_fixup
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Fix up package structure for recent filter linting changes.
2021-05-05 10:48:10 +02:00
almahmoud
2d9a7e28b9
Using guest_ports
2021-05-04 20:14:56 -04:00
almahmoud
63510bea23
Container monitor in destination
2021-05-04 17:09:23 -04:00
John Chilton
112a55ede5
Fixup filter type linting imports.
2021-05-04 15:38:18 -04:00
mvdbeek
89e5994219
Merge branch 'release_21.01' into dev
2021-05-04 20:03:58 +02:00
Alexandru Mahmoud and Marius van den Beek
10b5bfb572
Removing debug comment
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2021-05-04 13:57:06 -04:00
almahmoud
caa482115e
More cleanup
2021-05-04 13:56:05 -04:00
almahmoud
d4660e6f38
linting
2021-05-04 13:51:20 -04:00
Alexandru Mahmoud and Marius van den Beek
33461fd5e4
Change error message
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2021-05-04 13:49:51 -04:00
almahmoud
ec026579a5
Ingress spec
2021-05-04 13:48:00 -04:00
almahmoud