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

..

api

Use `yaml.safe_load() instead of load()`

2019-04-23 16:50:55 +01:00

auth

Fixes for pycodestyle 2.2.0

2016-11-15 16:56:50 +00:00

cleanup_datasets

Fix TypeError in logging commands

2019-11-03 21:35:07 +00:00

communication

Refactor galaxy.web.security into galaxy.security.idencoding.

2019-03-19 14:28:31 -04:00

grt

swap to exception

2019-04-26 13:29:12 +02:00

interactivetools

Update scripts/interactivetools/key_type_token_mapping.py

2019-08-23 11:29:36 -04:00

loc_files

Replace deprecated xml.etree.ElementTree.Element.getiterator() with iter()

2018-09-18 10:06:13 +01:00

metagenomics

Python3: fix remaining print statements

2017-10-12 18:34:29 +01:00

microbes

Change all remaining old-style classes to new style

2018-09-17 12:26:07 +01:00

slideshow

Fix many links

2018-09-03 14:34:13 +01:00

taxonomy

…

tool_shed

Merge pull request #8621 from martenson/ux-ts-installer

2019-09-12 13:35:01 -04:00

tools

Python3: fix remaining print statements

2017-10-12 18:34:29 +01:00

__init__.py

Adding db_shell.py that can be used to simplify writing command line

2012-03-05 12:11:53 -06:00

apply_tags.py

Change all remaining old-style classes to new style

2018-09-17 12:26:07 +01:00

bootstrap_history.py

Release notes for 19.09.

2019-10-01 13:42:46 -04:00

build_toolbox.py

Fix all E722 errors and ignore E741

2017-10-24 11:29:09 +01:00

check_eggs.py

Add stub fetch_eggs.py/check_eggs.py for people whose build/test/run

2015-11-06 11:06:11 -05:00

check_python.py

Drop support for Python 3.4. Officially support Python >=3.5

2019-01-31 23:31:44 +00:00

common_startup_functions.sh

Fix startup checks when using a Conda env

2019-08-19 01:28:35 +01:00

common_startup.sh

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

config_sample_to_kwalify.py

Scripts to manage configuration infrastructure.

2017-08-10 13:14:55 -04:00

create_db.py

Enable on-screen logging for create_db.py and manage_db.py

2019-08-18 11:17:34 +01:00

db_shell.py

Fix traceback in `printquery()`

2019-06-11 11:31:40 +01:00

docker_swarm_manager.py

Make the swarm manager recover on uncaught exceptions. It should do a

2018-04-13 12:34:55 -04:00

drmaa_external_killer.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

drmaa_external_runner.py

external_runner: load json template first

2018-11-09 17:48:36 +01:00

dump_library_paths.py

Add a script for dumping library file paths for backup

2018-02-01 13:05:16 -05:00

edam_mapping.py

Backport of hardening fixes to 17.09

2017-10-18 13:03:49 -04:00

external_chown_script.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

extract_dataset_part.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

extract_toolbox_sections.py

Fix deprecated `getchildren()`

2019-04-23 12:51:13 +01:00

fetch_eggs.py

Fix import order for cron/, scripts/ and test/

2017-09-25 23:44:39 +01:00

functional_tests.py

Rework and simplify data manager testing

2018-08-13 17:19:25 +02:00

galaxy

Make Galaxy installable the Pythonic way via setup.py. Incomplete, but

2016-07-07 13:49:27 -04:00

galaxy-main

Fix missed control_worker->queue_worker rename

2019-08-22 10:58:01 +02:00

get_platforms.py

Python3: fix remaining print statements

2017-10-12 18:34:29 +01:00

get_uwsgi_args.py

Drop static-safe navigation to plugin dirs. These are no longer symlinks, they are staged files.

2019-03-14 13:23:45 -04:00

helper.py

Refactor galaxy.web.security into galaxy.security.idencoding.

2019-03-19 14:28:31 -04:00

maintenance.sh

Fix issues reported by ShellCheck

2019-06-13 12:53:26 +01:00

manage_db.py

Enable on-screen logging for create_db.py and manage_db.py

2019-08-18 11:17:34 +01:00

manage_tool_dependencies.py

Rework config locating logic (it was reading the sample again).

2019-07-08 11:28:31 +02:00

nosetests.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

pages_identifier_conversion.py

clean-fix-page-api - move page revision creation to manager.

2019-05-29 13:43:49 -04:00

paster.py

Remove log_tempfile.

2019-07-08 14:52:13 +02:00

patch.sh

Add the script I used to create security patches

2016-02-24 16:54:30 -05:00

plugin_staging.py

Update plugin_staging to actually stage instead of symlink, since it no longer needs to be quite as fast (on startup). This will allow us to drop unnecessary trust rules from uwsgi static.

2019-03-14 13:18:43 -04:00

rst2html.py

Fix all E722 errors and ignore E741

2017-10-24 11:29:09 +01:00

runtime_stats.py

Fix errors reported by flake8 3.6.0

2018-10-24 23:22:19 +01:00

secret_decoder_ring.py

Refactor galaxy.web.security into galaxy.security.idencoding.

2019-03-19 14:28:31 -04:00

set_dataset_sizes.py

Unification of Galaxy configuration parsing for scripts/*

2018-03-23 16:14:49 -04:00

set_user_disk_usage.py

Refactor into model

2019-08-14 16:15:49 +02:00

summarize_timings.py

Fix errors reported by flake8 3.6.0

2018-10-24 23:22:19 +01:00

update_shed_config_path.py

Python3: finish first pass on whole codebase

2017-12-14 12:01:01 +00:00

validate_tools.sh

Fix issues reported by ShellCheck

2019-06-13 12:53:26 +01:00