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
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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
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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
Nicola Soranzo