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
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Follow-up on commit 39d78c7226https://github.com/galaxyproject/galaxy/pull/2383
2017-09-25 23:37:23 +01:00
John Chilton
0c6dfd7a41
Merge pull request #4604 from erasche/hardening
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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
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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
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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
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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
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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
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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.
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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.
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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.
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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.
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- 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
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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
Nicola Soranzo