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1281 Commits
Author SHA1 Message Date
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
Nate Coraor 09feaf6f4d - Do all logging configuration other than paste fileConfig logging from 
dictConfig. Default log message format varies by stack.
- Refactor a lot of file extension handling in to galaxy.util.path.
- Simplify and improve config file finding.
- Simplify and improve native app creation.
- Integrate uWSGI argument generation with @jmchilton's improvements to
  the startup scripts.
- Fix starting without a config file under uWSGI
 2017-09-01 01:08:16 -04:00
Nate Coraor bcfa874158 Fix for job_handler_count = 0 2017-08-28 16:52:06 -04:00
Nate Coraor 4d962d4ad2 Only include --paste-logger in uWSGI args if logging is configured in 
the PasteDeploy config
 2017-08-28 16:34:02 -04:00
Nate Coraor 1326a4d671 Cleaning, lint and test fixes. 2017-08-28 16:22:11 -04:00
Nate Coraor 17ea3d671f Improve automatic uWSGI startup options interaction with [uwsgi] section 
in config file
 2017-08-28 15:18:09 -04:00
Nate Coraor aff0a7460e Finish dictConfig logging feature 2017-08-28 14:13:31 -04:00
Nate Coraor 14e9dddade WIP: support log configuration from yaml/json app config with 
logging.config.dictConfig. Still working on yaml/json config loading in
the webless app.
 2017-08-28 09:54:21 -04:00
Nate Coraor 68542b615c Remove unneeded server_name manipulation from galaxy-main script 2017-08-21 21:57:56 -04:00
Nate Coraor d7dd9b2b65 WIP: drop stack configurability, this will come later. Cleanup for WIP 
PR
 2017-08-21 21:50:46 -04:00
Nate Coraor 27a0b1ba40 WIP: attempted to support workers shared between pools, but locking 
won't allow for this, since you can't wait on messages from a specific
farm.
 2017-08-21 21:48:01 -04:00
Nate Coraor ece3f242fb Abandoning unprogrammed mules (for now), fixes for programmed mules 2017-08-21 21:46:39 -04:00
Nate Coraor 092a6b4923 WIP uWSGI mule job handlers - it works! 2017-08-21 21:39:30 -04:00
Nate Coraor e2e3e5f7d1 WIP job handlers as uWSGI mules from GCC 2017 Hackathon. 2017-08-21 21:39:00 -04:00
Nate Coraor 85ea2d2728 Script reusage and generate uWSGI mule args 2017-08-21 21:36:48 -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