John Chilton
16d821e12e
Mark scripts/* that don't work with YAML configuraiton options as deprecated.
2018-03-23 16:14:49 -04:00
Nicola Soranzo
14259b11d9
Python3: finish first pass on whole codebase
2017-12-14 12:01:01 +00:00
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
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
8a43b2b492
Python 3: use "as" instead of comma in except clause
2016-05-17 23:53:16 +01:00
Nicola Soranzo
501a10c3f1
Do not import dumps and loads from galaxy.util.json .
2016-03-02 19:04:24 +00:00
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
Nate Coraor
150c17b9e8
Do not explicitly require pexpect. If anyone wants to use the old and
...
mostly unused features that depend on it (namely remote sequencer
transfers via scp) they can pip install pexpect.
2015-09-17 13:56:44 -04:00
Nicola Soranzo
34d9388456
Use os.pardir everywhere instead of '..' .
2015-07-14 16:20:29 +01:00
Nate Coraor
8fadc6392b
Rename universe_wsgi.ini -> galaxy.ini everywhere.
2014-09-15 16:43:51 -04:00
Dannon Baker
038f6dc6d5
Switch to_json_string/from_json_string in galaxy/scripts.
2014-09-09 10:04:28 -04:00
Greg Von Kuster
9102fc3472
1. Add support for manual file transfer from external services to a Galaxy data library using scp. This is currently enabled via the enable_beta_job_managers flag. This should not currently be used because it hits the db significantly to determine if dererred jobs are queued for running. The plan is to use messaging for this, but that approach is not yet implemented. Rabbit mq is still being used to enable manual file transfer to Galaxy data libraries when the enable_beta_job_managers flag is not set.
...
2. Clean up the code that renders the jquery file browser plugin - things work much cleaner now. One remaining item is handing the issue where rsh / ssh keys are not set. Also clean up a lot of code related to manual file transfers in the requests_admin controller.
3. In addition to the new ManualDataTransferPlugin, add the Pacific Biosciences SMRTPortalPlugin that automatically transfers files produced by SMRT Portal to a Galaxy data library.
4. Add the external service type config for Pac Bio SMRT Portal version 1.1.0.
2011-04-13 13:52:05 -04:00
Nate Coraor
0f9e7fc26d
Do away with the daemonized transfer manager and have the deferred job runner start off individual daemonized transfer workers. The workers update their own major states and can be queries for in-transfer progress via a socket, and an interface to that socket in app.transfer_manager. All socket communication is now JSON-RPC.
2011-01-19 10:06:44 -05:00
John Chilton