Nicola Soranzo
df8abbe3ef
Prefer unicodify() for binary-to-text conversion
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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
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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
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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
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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
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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
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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
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- 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
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
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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
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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
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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
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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()
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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
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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
Nicola Soranzo