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
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
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
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
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
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
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
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
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
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
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
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
John Chilton
3dbcc7c83c
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).
2018-04-24 16:57:43 -04:00
Nicola Soranzo
284795b94f
Merge branch 'release_18.01' into dev
2018-04-23 15:21:12 +01:00
Matthias Bernt
0c321cb86e
removed config.ini parameter from cleanup scripts
...
fixes https://github.com/galaxyproject/galaxy/issues/5941
2018-04-23 14:58:48 +02:00
John Chilton
2829a1f164
Merge pull request #5854 from natefoo/run-scripts-conda
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Improve startup interoperability with Conda
2018-04-18 16:08:13 -04:00
Nate Coraor
564f7ecafe
Make the swarm manager recover on uncaught exceptions. It should do a
...
better job of catching them in the application, but this is good enough
for the moment.
2018-04-13 12:34:55 -04:00
Nate Coraor
e651b34156
Remove swarm manager from lib
2018-04-12 16:52:10 -04:00
Nate Coraor
c5262e8971
Look for both base and root conda envs
2018-04-04 23:18:57 -04:00
Nate Coraor
b3eff87a1b
Clean up and useability enhancements
2018-04-04 21:03:08 -04:00
Nate Coraor
a88e19064a
Don't set uWSGI's virtualenv option when running from Conda
2018-04-04 16:47:36 -04:00
Dannon Baker