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Commit Graph
1002 Commits
Author SHA1 Message Date
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
E Rasche 5ed50dba1c Allow sending subsets 2017-08-04 16:03:54 +02:00
E Rasche 70f4bc957e update documentation and fix blacklisting bug 2017-08-04 13:45:01 +02:00
E Rasche 16f17efe49 remove remenants of __any__ 2017-08-04 13:07:19 +02:00
E Rasche 058c4a74b8 remove text metrics 2017-08-04 13:05:48 +02:00
E Rasche 08aeea3e92 add headers 2017-08-04 13:05:43 +02:00
E Rasche 5e6d1cba40 Some simplification which should significantly speed up parsing 2017-08-02 18:12:39 +02:00
E Rasche 6caded2125 unused function 2017-08-01 15:40:34 +02:00
E Rasche cefa47c698 remove keys from testing 2017-08-01 15:38:48 +02:00
E Rasche cf4dc28c5f Disable sanitization by default 2017-08-01 15:16:25 +02:00
E Rasche 94a8a9a841 default to sharing toolbox 2017-08-01 15:10:36 +02:00
E Rasche 07faeaa5ce Batched sql queries, sanitization 2017-08-01 14:35:50 +02:00
E Rasche df33d4f708 Super optimised GRT 2017-08-01 13:50:21 +02:00
E Rasche 50156d8e7b import from grt 2017-08-01 12:03:18 +02:00
E Rasche 93eac6dfcf remove redundant code 2017-08-01 11:50:38 +02:00
E Rasche a0292a46c7 Revert submission of instance metadata 2017-08-01 10:56:03 +02:00
E Rasche d453231226 Various optimisations 2017-07-31 16:30:31 +02:00
E Rasche 11ac796f2d Include hash for transport 2017-07-21 19:27:44 +00:00
E Rasche 2cd2c3967a document GRT a bit more 2017-07-21 19:06:43 +00:00
E Rasche 163127b4b2 Also dump toolbox 2017-07-21 15:59:25 +00:00
E Rasche c14d37fbd6 timings 2017-07-21 15:39:34 +00:00
E Rasche b0428352e0 Split out the submission portion 2017-07-21 15:21:44 +00:00
E Rasche 5abbf1102e at loop time 2017-07-21 15:14:11 +00:00
E Rasche 9803dc600c More updates to GRT 2017-07-21 15:10:41 +00:00
Enis Afgan 6a77a186a8 Script doc correction 2017-07-14 11:21:56 -04:00
Matthias Bernt 698075c3d7 Merge remote-tracking branch 'upstream/dev' into dev 2017-06-19 10:40:55 +02:00