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50 Commits
Author SHA1 Message Date
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
Greg Von Kuster 5dde45d61b Eliminate all suport for tool / tool suite archives from the tool shed. Yikes! 2011-06-02 15:18:35 -04:00
Greg Von Kuster 212433fe2c First pass of the next-gen Galaxy tool shed. See it demonsrated and discussed at the 2011 Gallaxy Community Conference in Lunteren on May 24,25,26. 2011-05-20 16:04:30 -04:00