Nicola Soranzo
b09b7d53ce
Write unicode strings to files opened with io.open(path, w, encoding=utf-8)
...
Otherwise under Python2 the following exception is raised:
```
$ python2
Python 2.7.17 (default, Nov 7 2019, 10:07:09)
[GCC 7.4.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import io
>>> with io.open('foo.txt', 'w', encoding='utf-8') as fh:
... fh.write('foo')
...
Traceback (most recent call last):
File "<stdin>", line 2, in <module>
TypeError: write() argument 1 must be unicode, not str
```
2020-01-09 17:51:24 +00:00
mvdbeek
d5fc7d426e
Fix interactivetool python 3 support and tests
...
- enables docker destination for interactivetool tests
- fixes a wrong argument in entrypoint management
- fixes the test setup that targeted a previous iteration (which was
still called realtimetools)
- prevents deleting the working directory before python has a chance to
start the container monitor (that's the sleep command)
- fixes some odd interactive tool test assertions
- uses unicode arguments in key_type_token_mapping.py.
uwsgi arguments are always passed as bytestrings.
2020-01-09 14:40:48 +01:00
M Bernt
aec4a88634
umask: switch back to 027 instead 0o027
2019-12-17 17:20:59 +01:00
M Bernt
e03a3b5c80
umask to string
2019-12-17 17:20:59 +01:00
M Bernt
8c809725af
uWSGI umask change to 027
...
- add `scripts/get_uwsgi_args.py`
- add docs
2019-12-17 17:20:59 +01:00
Nicola Soranzo
2fcbe0afa3
changectx() method was dropped in mercurial 4.6
...
in favour of `__getitem__()`.
2019-12-05 18:31:26 +00:00
John Chilton
d3c62e3d41
Merge pull request #9029 from dannon/hmr-client-dev
...
Hot module reloading using webpack-dev-server for client dev
2019-11-25 17:05:04 -05:00
Martin Cech
5a18a486bd
when building ts index log parse errors as debug level
2019-11-22 17:27:07 -05:00
Dannon Baker
fe6313ce8d
If we're running webpack dev server, skip the client build on startup.
2019-11-21 17:19:54 -05:00
Dannon Baker
682e8ae764
Rename targets and env var to be more clear
2019-11-21 16:57:23 -05:00
Dannon Baker
b4a5d7afc8
Add env var to allow runtime configuration of hmr server route
2019-11-21 15:47:28 -05:00
Nicola Soranzo
72186b40a1
Merge branch 'release_19.09' into dev
2019-11-19 23:30:02 +01:00
Martin Cech and Marius van den Beek
fc8b832888
Apply suggestions from code review @mvdbeek
...
Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com >
2019-11-19 09:32:15 -05:00
Martin Cech
0d82973ffe
fix path to ts uwsgi app
2019-11-18 21:18:33 -05:00
Martin Cech
0c075f73b4
set logging level according to the argument
...
also report the run summary as 'info' level
2019-11-18 12:05:02 -05:00
Martin Cech
8668441c9f
use configured config file when using uwsgi directly
2019-11-18 12:01:26 -05:00
Martin Cech
5c495d6514
refactor logging
2019-11-18 11:25:47 -05:00
Martin Cech
19c56c725b
add exec timer
2019-11-18 09:56:15 -05:00
Martin Cech
4725903b0f
switch from every minute to every hour
2019-11-14 18:17:32 -05:00
Martin Cech
dfc20759a7
use built-in uwsgi CRON-like feature to build shed search idnexes every hour
2019-11-14 18:07:48 -05:00
Martin Cech
c9d9009299
refactor and modernize toolshed search indexes build script
...
mainly so it can read yml config
2019-11-14 18:07:06 -05:00
John Chilton
72bae33923
Migrate selenium tests into lib/galaxy_test for packaging.
2019-11-12 09:05:08 -05:00
John Chilton
45019c3fbd
Move galaxy testing utilities into more sane package structure.
...
Split test/base into lib/galaxy_test/base and lib/galaxy_test/driver. Dividing things on whether they import galaxy-app code or not - with the goal of a galaxy-test-base package that doesn't depend on galaxy-app and a galaxy-test-driver package that does.
I've been refactoring around this division for a long time. Certain tests (namely the integration tests) always need to bootstrap Galaxy - but the API tests and the Selenium tests should be installable and runnable without Galaxy in the Python environment. So future galaxy-test-api and galaxy-test-selenium packages should have only an optional dependency on galaxy-test-driver.
Properly sturcturing these namespaces is a precursor for real packages on PyPI, clean separation of the tool shed testing code, and cleans up all the flake8 noqa hacks in test/.
2019-11-12 09:03:06 -05:00
John Chilton
559b664b07
Refactor tool_shed webapp out of Galaxy.
2019-11-11 12:32:19 -05:00
Martin Cech
a48c7420d7
Merge pull request #8956 from jmchilton/remove_ts_api
...
Remove tool shed API examples.
2019-11-11 10:41:22 -05:00
Nicola Soranzo
6b1bacc2b8
Merge pull request #8957 from jmchilton/remove_legacy_shed
...
Remove script for migrating tools to the tool shed...
2019-11-11 10:54:27 +00:00
John Chilton
d4196b61a4
Remove tool shed API examples.
...
These aren't tested, bioblend likely has better documentation (https://bioblend.readthedocs.io/en/latest/api_docs/toolshed/all.html ), and we should be encouraging TS interactions to be done through Planemo and not raw API calls.
Excluding scripts used by bootstrap.
2019-11-11 02:55:26 -05:00
John Chilton
a27beb0fd8
Remove script for migrating tools to the tool shed...
...
from an older tool shed? I completely forgot there even was an older tool shed.
2019-11-11 02:50:12 -05:00
John Chilton
fbe21f94bf
Remove tool dependency scripts.
2019-11-11 02:35:31 -05:00
Nicola Soranzo
303f9ec871
Merge pull request #8908 from bernt-matthias/topic/pgcleanup-also-delete
...
make pgcleanup also delete HDAs
2019-11-04 10:21:04 +00:00
Nicola Soranzo
3e64bbb460
Merge branch 'release_19.09' into dev
2019-11-04 09:50:29 +00:00
Sergey Golitsynskiy
a855e2ca64
Fix TypeError in logging commands
...
Fix the following exception:
```
TypeError: not all arguments converted during string formatting
```
Also, make other log format strings more consistent: %d for numeric object IDs.
2019-11-03 21:35:07 +00:00
M Bernt
6f010bd49c
make pgcleanup also delete HDAs
...
follow up to https://github.com/galaxyproject/galaxy/pull/3572
2019-10-30 13:42:31 +01:00
Nicola Soranzo
85f7f91206
Fix script shebangs
...
Improve tools.
2019-10-26 20:20:01 +01:00
Martin Cech
fd6142f6ce
Merge branch 'release_19.09' into merge-1909
2019-10-07 10:24:12 -04:00
John Chilton
7620880a9b
Release notes for 19.09.
2019-10-01 13:42:46 -04:00
Nicola Soranzo
f659c2f86c
Merge pull request #8712 from erasche/grt-fixes-n
...
GRT: Ensure correct encoding, no partial lines
2019-09-27 12:19:39 +01:00
Helena Rasche and Nicola Soranzo
584dbb28df
Apply suggestions from code review
...
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com >
2019-09-26 14:36:43 +02:00
Helena Rasche
f56cc13699
two spaces
2019-09-26 14:35:49 +02:00
Helena Rasche
e75a9f67b0
swap to io.open
2019-09-26 13:42:41 +02:00
Helena Rasche
f200835445
Ensure correct encoding, no partial lines
2019-09-26 12:12:22 +02:00
will
009611cf04
add .gitattributes file and normalize line endings to use LF instead of CLRF
2019-09-18 22:03:37 -04:00
John Chilton
4287bb787f
Merge pull request #8621 from martenson/ux-ts-installer
...
[19.09] allow the TS search API to bypass wildcard search
2019-09-12 13:35:01 -04:00
Martin Cech
99ec4ecf75
adjust indexing and searching of special keywords to be case-insensitive
2019-09-11 16:39:14 -04:00
Martin Cech
02a3342bd6
regenerate ts search indexes in tmp directory
2019-09-10 16:06:21 -04:00
Dannon Baker
9d1e784868
Alternate approach to plugin building; this should be useful as a stepping stone towards moving these out of the repo completely, and it'll work *right now*.
2019-09-06 14:56:10 -04:00
Daniel Blankenberg and Nicola Soranzo
a2199ee575
Update scripts/interactivetools/key_type_token_mapping.py
...
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com >
2019-08-23 11:29:36 -04:00
Daniel Blankenberg
995fce6b9b
Little more RealTimeTools cleanup.
2019-08-23 09:24:55 -04:00
mvdbeek
a820e52f2a
Fix missed control_worker->queue_worker rename
...
Missed that one in 6b52f62fe4
2019-08-22 10:58:01 +02:00
Daniel Blankenberg
55c929768c
more realtime to interactivetools name changes
2019-08-20 16:58:55 -04:00
Nicola Soranzo