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aacdf8d939e554ef9dca9fea3075813f1c0862d3
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1027 Commits
Author SHA1 Message Date
Nicola Soranzo aacdf8d939 Merge branch 'release_17.09' into dev 
Conflicts:
	static/style/blue/base.css
 2017-10-30 19:15:50 +00:00
Nicola Soranzo 45d4fefe63 Merge pull request #4898 from jmchilton/fix_extra_index 
[17.09] Fix extra index URL call in common startup.
 2017-10-30 15:52:41 +00:00
John Chilton 09fdac513d Fix extra index URL call in common startup. 
- Use it for dev requirements also.
- Use more correct API target that supports older versions of dependencies on PyPI.

xref https://gist.github.com/jmchilton/ad8f180f5ac1eb5f689f815b04f603fa
 2017-10-30 10:49:29 -04:00
John Chilton 62826a1160 Merge pull request #4847 from nsoranzo/flake8_3.5.0 
Fix all E722 errors and ignore E741
 2017-10-24 13:04:22 -04:00
Martin Cech f08700b208 rename wiki to hub 2017-10-24 10:48:16 -04:00
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
Nate Coraor b8dfceb72a Merge branch 'release_17.09' into dev 2017-10-23 10:38:14 -04:00
Nate Coraor 646a8d1092 Support a log directory argument for pgcleanup.py 2017-10-20 12:43:09 -04:00
E Rasche 0f311470d9 Backport of hardening fixes to 17.09 2017-10-18 13:03:49 -04:00
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
Nicola Soranzo 8c984c9b3e Remove unused binary_compatibility.py script 
Follow-up on commit 39d78c7226 from
PR https://github.com/galaxyproject/galaxy/pull/2383
 2017-09-25 23:37:23 +01:00
John Chilton 0c6dfd7a41 Merge pull request #4604 from erasche/hardening 
Various bits of hardening
 2017-09-25 15:15:48 -04:00
Nicola Soranzo 0c23d40b22 Merge branch 'release_17.09' into dev 2017-09-25 10:56:37 +01:00
E Rasche 15c73233c5 fix lint 2017-09-25 11:39:15 +02:00
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
E Rasche 32b85ecb59 Only permit yaml.safe_loading of data 
Event trusted data, belt + suspenders method.
 2017-09-25 11:39:12 +02:00
John Chilton 8fa1f9a2fe Small tweaks to fixup #2866. 2017-09-22 14:47:15 -04:00
Nate Coraor 244fc834cd Explicitly include PyPI as an --extra-index-url to pip so we can install 
from PyPI even when a package exists (but the correct version or
architecture does not exist) on wheels.galaxyproject.org. Previously,
PyPI was only checked after wheels.galaxyproject.org because pypiserver
performs an automatic redirect to PyPI for any packages that do not
exist in its index.
 2017-09-21 16:33:40 -04:00
Martin Cech 095c1045b6 add logging to ts index building 2017-09-06 14:05:05 -04:00
Nicola Soranzo bd88524a10 Fix import order and Python3 compatibility 2017-08-18 12:35:04 +01:00
Nicola Soranzo e32ad2864f Remove container config log message from cleanup scripts logs 2017-08-18 12:35:04 +01:00
Nicola Soranzo 4e75635d62 Use log.warning() instead of deprecated warn() 2017-08-18 12:35:04 +01:00
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
Matt Chambers 25bd7178c1 Remove print of non-existent attribute 'content' 2017-08-16 14:44:51 -05:00
Max Schaefer 43ddd47320 Add missing var declarations. 
In all these cases, a variable was not declared to be a local using `var` (and hence was implicitly interpreted as a global variable), but all uses of that variable were preceded by a definition within the same function, suggesting that the variable was, in fact, meant to be local, not global.
 2017-08-16 15:22:42 +01:00
John Chilton 8189a1f1e2 Scripts to manage configuration infrastructure. 
This has been rebased several times and includes a variety of fixes (some thanks to martenson).
 2017-08-10 13:14:55 -04:00
John Chilton 1bdb99bbd7 Update galaxy.util.properties to allow YAML. 2017-08-10 13:14:55 -04:00
John Chilton 72e5a00ba0 Centralize launching server for reports and tool shed. 
Initial outline of allowing launch via uwsgi.
 2017-08-10 13:14:55 -04:00
John Chilton 6a7cc34e1b Bring Galaxy, reports, and shed run scripts in sync. 
- They now uniformly handle server option processing.
- Reports and Tool Shed now respect many new and important options such as --skip_venv.
- Reports and Tool Shed now do extra checking around Python version that Galaxy does.

In addition to improving the reports and tool shed startup scripts and reducing cognative load with respect to option handling, this is an important pre-condition to us being able us to switch on uwsgi by default for all three services simultaneously without a bunch of copy and pasting.
 2017-08-10 13:14:55 -04:00
E Rasche a177ccd026 not needed 2017-08-10 14:02:18 +02:00
E Rasche 4961697194 fix extension 2017-08-10 14:01:32 +02:00
E Rasche 847df13fc0 this should not have been missed 2017-08-10 14:00:43 +02:00
E Rasche c5b3612864 cleanup url in case 2017-08-10 13:51:41 +02:00
E Rasche f4383bd983 Fun things you find in production 2017-08-10 13:48:53 +02:00
E Rasche bdbe360305 fix pardir 2017-08-10 13:44:10 +02:00
John Chilton 68c7b0982b Merge pull request #4376 from erasche/grt-update-2 
Galactic Radio Telescope Update
 2017-08-07 07:41:50 -04:00
E Rasche a6fcb95a15 default false with expl 2017-08-07 10:52:39 +02:00
E Rasche 5b83c6c330 Merge branch 'grt-update-2' of github.com:erasche/galaxy into grt-update-2 2017-08-07 10:50:45 +02:00
E Rasche ddcddecb4a rename scripts 2017-08-07 10:49:56 +02:00
E Rasche 7e94cf20b0 fix todo 2017-08-07 10:48:16 +02:00
E Rasche 0ed3571f0d Fix various logging statements 2017-08-07 10:48:10 +02:00
E Rasche e8b367bde3 move to subdir 2017-08-07 10:44:54 +02:00
Eric Rasche d3b271761f remove a blank line 2017-08-04 17:18:09 +02:00
E Rasche b381a90fcb flake8 2017-08-04 17:00:47 +02:00
E Rasche 7deff20622 move up to fix print statement 2017-08-04 16:17:24 +02:00