Nicola Soranzo
f4203ca051
Fix errors reported by flake8 3.6.0
...
Ignore W504.
2018-10-24 23:22:19 +01:00
Nicola Soranzo
949dcfdbc3
Do not log exceptions twice
...
`logging.exception()` already adds the the exception information after
the supplied message.
Also: the `message` attribute of `Exception` class has been dropped in
Python 3, always use `str(e)`.
xref. https://github.com/galaxyproject/galaxy/issues/1715
2018-10-24 12:57:05 +01:00
Nate Coraor
44c291bc66
Merge remote-tracking branch 'origin/dev' into ini_to_yaml_config
2018-01-18 12:30:05 -05:00
Nicola Soranzo
14259b11d9
Python3: finish first pass on whole codebase
2017-12-14 12:01:01 +00:00
John Chilton
7bae23e105
yaml_config - update code base for converting galaxy.ini.sample to YAML.
2017-12-06 20:28:20 -05:00
Nicola Soranzo
9b4de72ca6
Fix all E722 errors and ignore E741
...
Introduced in flake8 3.5.0
Fix import order.
2017-10-24 11:29:09 +01:00
Nicola Soranzo
b956406c4d
Fix Python3 compatibility and import order for 21 files
2017-10-16 19:43:01 +01:00
Nicola Soranzo
d1bc98dfcb
Python3: fix remaining print statements
...
Remove some debugging prints.
Fix import order.
Consolidate exception logging in ToolShed database migrations.
2017-10-12 18:34:29 +01:00
Nicola Soranzo
9b1832abb1
Fix import order for cron/, scripts/ and test/
2017-09-25 23:44:39 +01:00
E Rasche
290971ca7a
more review comments
2017-09-25 11:39:15 +02:00
E Rasche
9b8e76f9d9
Convert urllib to requests
...
Which has built-in protection against urls like "file:///tmp/a"
2017-09-25 11:39:13 +02:00
Martin Cech
095c1045b6
add logging to ts index building
2017-09-06 14:05:05 -04:00
Nicola Soranzo
a8d7b2df8b
Fix more indentation errors
2017-08-17 11:35:39 +01:00
Nicola Soranzo
a353b2e88f
Fix E127 errors introduced by previous commit
...
using:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E127 .
```
2017-08-17 11:35:39 +01:00
Nicola Soranzo
21b44bf348
Fix all E201 and E202 style errors
...
using the following command:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 .
```
2017-08-17 11:35:39 +01:00
Nicola Soranzo
1d17a29c79
Fixes for pycodestyle 2.2.0
2016-11-15 16:56:50 +00:00
Nicola Soranzo
7a604c67d9
Merge branch 'release_16.07' into dev
2016-09-23 17:59:52 +01:00
Dave Bouvier
2c8a5d9d58
Correct import order.
2016-09-23 12:13:10 -04:00
Dave Bouvier
b83f0a1024
Fix whoosh indexing.
2016-09-21 14:40:12 -04:00
Nicola Soranzo
de3c50a5ef
Python3 support and import order fixes for lib/tool_shed/
2016-08-04 13:41:36 +01:00
Nicola Soranzo
6ba6f798ec
Fix more E203 flake8 errors
2016-05-17 23:53:16 +01:00
Nicola Soranzo
8a43b2b492
Python 3: use "as" instead of comma in except clause
2016-05-17 23:53:16 +01:00
Nicola Soranzo
ed4132d9c0
Python3: Use open() instead of file()
2016-05-17 23:53:16 +01:00
Nicola Soranzo
a9d675f5e8
Fix sys.path.insert() after #2093 .
2016-04-11 20:27:25 +01:00
Nicola Soranzo
27f418c52d
Remove scripts which depend on install_and_test_tool_shed_repositories.
2016-04-11 20:27:25 +01:00
Dave Bouvier
fbf8cfce2a
Remove unused import.
2016-04-05 14:23:56 -04:00
Dave Bouvier
9f1490cc60
Fix sys.path.insert some more.
2016-04-05 13:55:21 -04:00
Dave Bouvier
9bf3976e8a
Fix sys.path.insert
2016-04-05 13:50:51 -04:00
Dave Bouvier
77353902ee
Move scripts out of lib/tool_shed.
2016-04-05 13:04:44 -04:00
Nicola Soranzo
d85db9daa6
Use __file__ when adding paths to sys.path instead of os.getcwd() .
...
Also insert additional paths in position 1 unless strictly necessary.
2016-02-18 15:45:15 +00:00
Nicola Soranzo
93348e7199
Fix the remaining 1334 flake8 errors in scripts/ . Close #391 .
2016-02-18 15:45:15 +00:00
Nate Coraor
0469ed29e0
Remove egg cruft from scripts/
2015-09-21 15:55:07 -04:00
Martin Cech
4d697b7b50
fix overriding the name variable
2015-08-06 10:38:12 -04:00
Martin Cech
d583c376a5
flake8 spotted by @nsoranzo
2015-08-05 14:27:25 -04:00
Martin Cech
0ad5c8a1a8
fix TS search index building script to properly visit subdirectories
2015-08-05 13:55:01 -04:00
Martin Cech
eb54b1d854
expose searching full TS toolset over a separate index
...
the index is created by the same script (build_ts_whoosh_index.py)
2015-06-19 16:24:27 -04:00
Martin Cech
e0c7e02e40
do not require option that is actualy in the config
2015-05-07 16:50:27 -04:00
Martin Cech
16ee7fa74c
add default config for TS search; rename to match TS playbook
2015-04-21 11:59:01 -04:00
Martin Cech
dc736c73f2
remove another abspath; use optparse;
2015-04-14 11:31:44 -04:00
Martin Cech
66e61271b1
add comments and example; add consistency checks; remove bash script
2015-04-14 10:55:34 -04:00
Martin Cech
c12b8063e3
remove abspath
2015-04-13 14:39:31 -04:00
Martin Cech
a9bc7dc5ca
generate separate index for tools in repositories
2015-04-13 13:45:32 -04:00
Martin Cech
9f454b404f
found a known Whoosh bug, trying to avoid it
...
https://bitbucket.org/mchaput/whoosh/issue/386/keyerror-1l
2015-01-29 11:43:29 -05:00
Martin Cech
f10ed7d184
way better search; dont query DB; repair final scoring functions
2015-01-28 15:24:10 -05:00
Martin Cech
fd8a7da910
adjust schema, start dynamic scoring
2015-01-27 17:15:18 -05:00
Martin Cech
05e9ea637e
initial version of TS search API and Index builder script
...
beware: always returns jsonp for now
2015-01-26 13:08:16 -05:00
Daniel Blankenberg
0c945b7c3b
Add a script to check toolshed dependency files for broken/invalid download URLs.
2014-02-17 12:51:34 -05:00
Greg Von Kuster
ae39ab8f2b
Rename community_wsgi.ini.sample to be tool_shed_wsgi.ini.sample, run_community.sh to run_tool_shed.sh, and fix references to these files in the code.
2013-03-18 10:24:03 -04:00
Greg Von Kuster
f539d3071b
Change the name and path of the community webapp to be tool_shed.
2013-02-27 16:23:19 -05:00
Greg Von Kuster
cbd7fd8caa
Commit versions of tools from the last_gen tool shed in order of oldest -> newest in the next-gen tool shed. Fixes issue # 578.
2011-06-07 11:32:11 -04:00
Nicola Soranzo