Nicola Soranzo
9d74bba7fb
Drop support for retired Python 3.5
...
Upgrade syntax using `pyupgrade --py36-plus` .
Manually drop several `six` imports.
Also:
- Remove broken pr_cache in scripts/bootstrap_history.py
- Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
2020-10-07 11:52:13 +01:00
Nicola Soranzo
b09b7d53ce
Write unicode strings to files opened with io.open(path, w, encoding=utf-8)
...
Otherwise under Python2 the following exception is raised:
```
$ python2
Python 2.7.17 (default, Nov 7 2019, 10:07:09)
[GCC 7.4.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import io
>>> with io.open('foo.txt', 'w', encoding='utf-8') as fh:
... fh.write('foo')
...
Traceback (most recent call last):
File "<stdin>", line 2, in <module>
TypeError: write() argument 1 must be unicode, not str
```
2020-01-09 17:51:24 +00:00
Helena Rasche and Nicola Soranzo
584dbb28df
Apply suggestions from code review
...
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com >
2019-09-26 14:36:43 +02:00
Helena Rasche
f56cc13699
two spaces
2019-09-26 14:35:49 +02:00
Helena Rasche
e75a9f67b0
swap to io.open
2019-09-26 13:42:41 +02:00
Helena Rasche
f200835445
Ensure correct encoding, no partial lines
2019-09-26 12:12:22 +02:00
Helena Rasche
1b6b52ce10
swap to exception
2019-04-26 13:29:12 +02:00
Helena Rasche
c54bddd3f3
it is pointless to load sample config
2019-04-26 13:27:59 +02:00
Helena Rasche
cb7b26e25e
Remove now-deprecated params + more defensive
2019-04-26 13:20:37 +02:00
Helena Rasche
dcfff4d5de
ensure a string is returned
...
Very old values in EU db were missing this.
2019-04-26 13:20:26 +02:00
Helena Rasche
855ccb1279
GRT: Rip out all parameters, round file sizes
2018-11-23 12:10:14 +01:00
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
...
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
Martin Cech
ab760f5d27
revert the datasource tool sanitation, set default # for export
2018-07-10 12:39:14 -04:00
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
...
- 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
...
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
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
...
[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
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
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
Helena Rasche
94ae2e6a95
permit actual numbers in conf file
2018-05-23 16:31:40 +02:00
Martin Cech
8255d1ccc8
Merge pull request #5613 from erasche/fix-fraking-grt
...
[18.01] File sizes not being annotated in GRT
2018-05-07 11:55:55 -04:00
John Chilton
bb90ae93d8
More grt fixes - spotted by @nsoranzo.
2018-03-23 16:14:50 -04:00
John Chilton
5f3f792f6f
Unification of Galaxy configuration parsing for scripts/*
2018-03-23 16:14:49 -04:00
John Chilton
8fa8660b25
Small improvements to scripts/grt/export.py for testing.
...
- Don't rely on external sha256sum, use Python hashing (add utility to hash_util to enable this).
- Drop unused galaxy_config from grt.yml.sample - it isn't used anywhere as far as I can tell.
2018-03-23 16:14:49 -04:00
E Rasche
6a20984c57
try harder to handle unexpected values
2018-02-27 18:06:52 +01:00
E Rasche
71c79fda32
File sizes were not being added
2018-02-27 17:56:31 +01:00
Nicola Soranzo
9b1832abb1
Fix import order for cron/, scripts/ and test/
2017-09-25 23:44:39 +01:00
E Rasche
32b85ecb59
Only permit yaml.safe_loading of data
...
Event trusted data, belt + suspenders method.
2017-09-25 11:39:12 +02:00
E Rasche
a177ccd026
not needed
2017-08-10 14:02:18 +02:00
Nicola Soranzo