Nicola Soranzo
31e78461bd
Merge branch 'release_18.05' into dev
2018-06-23 00:05:40 +01:00
Martin Cech
572f38d1fb
move the sanitization to the try/except block
...
as it may fail (and it did, on Main)
2018-06-21 15:44:05 -04:00
Dannon Baker
f9ba72f0ae
Merge remote-tracking branch 'upstream/release_18.05' into dev
2018-06-20 10:15:29 -04:00
Martin Cech
f21c8caf83
unname the exception
2018-06-18 16:47:19 -04:00
Martin Cech
2b8b4e198d
grt - wrap every write in try-except
...
and just fail the row if the data is crap
(like {NULL, SOH, STX, ETX} and friends)
2018-06-18 16:16:05 -04:00
Nicola Soranzo
6e02c9aff7
Merge branch 'release_18.05' into dev
2018-06-17 13:11:47 +01:00
Dannon Baker
4cdd210bb2
Use os.pardir instead of ../. Thanks @nsoranzo
2018-06-15 14:49:46 -04:00
Dannon Baker
8364ebebcd
Add static-safe mapping for uwsgi for plugin static dirs, which are accessible via symlink
2018-06-15 14:11:19 -04:00
Dannon Baker
370ea25d2c
Minor refactoring, comments.
2018-06-15 12:48:02 -04:00
Dannon Baker
e110489cc5
Call plugin static dir regeneration in the event client isn't being built (which also does this, albeit slightly differently)
2018-06-15 11:46:08 -04:00
Dannon Baker
fc47618f67
Initial python-based plugin staging. to be used from common startup.
2018-06-15 11:41:06 -04:00
mvdbeek
6120183182
Allow Python 3 if in a virtualenv
2018-06-13 03:12:45 +01:00
Nicola Soranzo
d66a63012a
Replace unmaintained pycrypto dependency with pycryptodome
...
Minimum secret key length for Blowfish was increased from 4 to 5 bytes.
First argument to Blowfish.new() must be a bytestring, and the `mode`
argument is no more optional.
Remove unused `encode_id` function from `scripts/api/common.py` .
Documentation updated, then rebuilt with `make config-rebuild` .
2018-06-13 03:07:04 +01:00
Nicola Soranzo
99c1da2f62
Merge branch 'release_18.05' into dev
2018-06-11 14:14:20 +01:00
Martin Cech
36fcb5c1b7
Merge pull request #6301 from martenson/grt-config
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[18.05] add the canonical url to grt config
2018-06-07 15:01:03 -05:00
Martin Cech
ed56454ca0
add the canonical url to grt config
2018-06-07 09:15:47 -04:00
Martin Cech
d95dcecbea
Merge branch 'release_18.05' into dev
2018-06-06 11:46:19 -04:00
Helena Rasche
acb4cdf584
Merge pull request #6285 from martenson/grt-defensive
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[18.05] telescope export: change to a more defensive approach
2018-06-06 15:15:27 +00:00
Nicola Soranzo
d330a79c8d
Merge branch 'release_18.05' into dev
2018-06-06 16:08:20 +01:00
Nicola Soranzo
2b8beb69c4
Merge branch 'release_18.01' into release_18.05
2018-06-06 15:58:08 +01:00
Martin Cech
e767438afc
add spaces before inline comment
2018-06-05 16:38:56 -04:00
Martin Cech
b62099f418
change to a more defensive approach, clarify varnames
2018-06-05 16:19:04 -04:00
Martin Cech
7a7560ad73
Merge branch 'release_18.05' into dev
2018-06-05 13:03:35 -04:00
Anastasia Tyryshkina
c37e384454
style fix
2018-06-05 12:47:19 -04:00
Anastasia Tyryshkina
dd4de3f3b2
catch dataset_id=None
2018-06-05 12:23:02 -04:00
Anastasia Tyryshkina
6db9fd3d51
style fix
2018-06-04 16:01:32 -04:00
Anastasia Tyryshkina
191a134bbc
got rid of things that are no longer necessary
2018-06-04 15:57:22 -04:00
Anastasia Tyryshkina
948d0767eb
more style fixes
2018-06-04 14:34:09 -04:00
Anastasia Tyryshkina
ba45c15fff
tried to fix some of stylization fails
2018-06-04 14:27:24 -04:00
Anastasia Tyryshkina
4630994fd0
get output datasets as well
2018-06-04 13:33:59 -04:00
Anastasia Tyryshkina
5b7055fc6f
respect blacklisted tools
2018-06-04 12:56:47 -04:00
Anastasia Tyryshkina
0c852257bb
delete comment thats no longer necessary
2018-06-04 12:39:55 -04:00
Anastasia Tyryshkina
aa062f8546
fixed the issues with the last pull
2018-06-04 11:53:14 -04:00
Nicola Soranzo
aaff474142
Use consistent preference order for config files
...
1) galaxy.yml
2) galaxy.ini
3) universe_wsgi.ini
Also:
- properly quote variables which may contain spaces
- no need to pass the config file to `./scripts/manage_tool_dependencies.py`
- simplify `scripts/maintenance.sh` by moving the `cd` up and reusing
functions from `scripts/common_startup_functions.sh`
2018-06-02 03:28:54 +01:00
Nicola Soranzo
c9daa60e91
Look for config file inside galaxy.dependencies.optional()
...
Also don't fail if no config file is found, just print a message on
stderr.
This allows the removal of the code to set `GALAXY_CONFIG_FILE` from
`scripts/common_startup.sh` .
2018-06-02 03:14:38 +01:00
Nicola Soranzo
0ea8107191
Use separate pid_log_paster_args variable
...
to store --pid-file and --log-file options of `./scripts/paster.py` .
https://github.com/galaxyproject/galaxy/pull/6239 fixed 3 bugs:
- `GALAXY_RUN_ALL=1 ./run.sh` was reusing the same pid and log files for
all Galaxy processes;
- `./run.sh restart` was always using `paster.pid` and `paster.log` instead
of the configured files
- `./run.sh status` was always using `paster.pid`
but also introduced a regression, i.e. the plain `./run.sh` started
writing to the log file instead of the standard output (console).
This fixes the regression by using a separate variable for these options
instead of conflating them in `paster_args` or `server_args`.
2018-06-02 01:09:10 +01:00
Anastasia Tyryshkina
11575132dc
exports a dataset tsv
2018-06-01 16:47:57 -04:00
Anastasia Tyryshkina
6dee708ae8
export another tsv file named datasets.tsv
2018-06-01 16:43:45 -04:00
Martin Cech
53d2664b0b
Merge pull request #6200 from erasche/grt-asdf
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Permit numeric values of GRT instance ID in config
2018-05-31 15:31:59 -05:00
Dannon Baker
06d0fcc0de
Merge remote-tracking branch 'upstream/release_18.05' into dev
2018-05-31 16:09:26 -04:00
Dannon Baker
44b42e7e7e
Merge remote-tracking branch 'upstream/release_18.01' into release_18.05
2018-05-31 16:08:55 -04:00
Lance Parsons
88c94fc49b
Set pid and log file for paster in server_args
...
This avoids setting log and pid file in paster_args so that with
GALAXY_RUN_ALL they can be set individually, but ensures they are set
when running paster otherwise.
2018-05-31 12:07:02 -04:00
Lance Parsons
ce9b671bd4
Hack paster args to not duplicate pid file stuff for RUN_ALL.
2018-05-29 11:57:30 -04:00
Helena Rasche
94ae2e6a95
permit actual numbers in conf file
2018-05-23 16:31:40 +02:00
Martin Cech
c67c4b4b82
Merge branch 'release_18.05' into dev
2018-05-07 12:34:46 -04:00
Martin Cech
0cfac515b5
Merge branch 'release_18.01' into release_18.05
2018-05-07 12:34:08 -04:00
Martin Cech
8255d1ccc8
Merge pull request #5613 from erasche/fix-fraking-grt
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[18.01] File sizes not being annotated in GRT
2018-05-07 11:55:55 -04:00
Nicola Soranzo
479e76ff13
Add closing old milestone to release issue
2018-04-30 16:13:08 +01:00
John Chilton
74939a3f11
Update release process - do not require merge PRs to have milestones.
2018-04-27 11:17:36 -04:00
John Chilton
a29770ca55
Pin the version of node we use in CI, etc....
...
Our dependencies won't resolve under node 10 currently (because of upath at least https://github.com/anodynos/upath/blob/master/package.json#L43 but maybe other packages as well).
2018-04-27 08:09:51 -04:00
Nicola Soranzo