Nate Coraor 395d98857b Fix config file finding for the manage_db script

2019-08-07 16:33:40 -04:00

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api

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

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

auth

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cleanup_datasets

cleanup: use logging instead of print

2019-08-01 09:25:13 +02:00

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

loc_files

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

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

metagenomics

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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

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tool_shed

Update import paths for loader_directory

2019-07-06 00:52:45 +02:00

tools

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__init__.py

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apply_tags.py

Change all remaining old-style classes to new style

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

bootstrap_history.py

Fixes and enhancements for release note generation.

2019-05-24 16:59:32 -04:00

build_toolbox.py

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check_eggs.py

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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 activation of `_galaxy_` conda env

2018-12-14 00:22:12 +00:00

common_startup.sh

Fix issues reported by shellcheck

2019-07-17 12:46:46 +01:00

config_sample_to_kwalify.py

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create_db.py

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db_shell.py

Fix traceback in `printquery()`

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

docker_swarm_manager.py

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drmaa_external_killer.py

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drmaa_external_runner.py

external_runner: load json template first

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

dump_library_paths.py

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edam_mapping.py

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external_chown_script.py

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extract_dataset_part.py

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extract_toolbox_sections.py

Fix deprecated `getchildren()`

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

fetch_eggs.py

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functional_tests.py

Rework and simplify data manager testing

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

galaxy

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galaxy-main

Fix galaxy-main running from source now that setup,py is no longer in the root

2019-07-07 18:23:49 +02:00

get_platforms.py

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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

Fix config file finding for the manage_db script

2019-08-07 16:33:40 -04:00

manage_tool_dependencies.py

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

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

nosetests.py

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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

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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

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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

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set_user_disk_usage.py

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summarize_timings.py

Fix errors reported by flake8 3.6.0

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

sync_reports_config.py

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transfer.py

Fix errors reported by flake8 3.6.0

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

update_shed_config_path.py

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validate_tools.sh

Fix issues reported by ShellCheck

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