mvdbeek 600f59b0ee Use client-logic to run upload tool ...

It is pretty cool to use hooks and an alternative tool submission
endpoint, but this is less invasive. We'd have to do this anyway for
cases where the upload is already on the server and the pre-finish hook
doesn't fire.

2021-10-12 13:43:45 +02:00

..

api

Fix printing non-dict output

2021-02-02 16:04:44 -05:00

auth

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

cleanup_datasets

Merge branch 'release_21.05' into dev

2021-08-09 18:45:05 +02:00

grt

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

interactivetools

Fix remaining issues reported by bugbear; add it to flake8 reqs

2021-01-16 05:58:15 +00:00

loc_files

Fix remaining issues reported by bugbear; add it to flake8 reqs

2021-01-16 05:58:15 +00:00

metagenomics

Fix remaining issues reported by bugbear; add it to flake8 reqs

2021-01-16 05:58:15 +00:00

microbes

Fix remaining issues reported by bugbear; add it to flake8 reqs

2021-01-16 05:58:15 +00:00

objectstore

Fix all E203, E741 and W504 flake8 errors

2021-01-18 10:35:41 +00:00

slideshow

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

taxonomy

…

tool_shed

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

tools

Drop support for retired Python 3.5

2020-10-07 11:52:13 +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

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

bootstrap_history.py

Release process overhaul

2021-03-30 12:11:48 -04:00

build_toolbox.py

Fix remaining issues reported by bugbear; add it to flake8 reqs

2021-01-16 05:58:15 +00:00

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_model.py

Handle DedupedColumnCollection in db_indexes

2021-05-18 19:00:55 -04:00

check_python.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

common_startup_functions.sh

Restore pastescript, make new stack depend on APP_WEBSERVER=dev

2021-04-07 14:39:06 +02:00

common_startup.sh

Run client-y tests with --frozen-lockfile

2021-06-30 13:06:24 +02:00

config_sample_to_kwalify.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

create_db.py

Create install database with create_db.sh

2021-03-30 13:44:36 +02:00

db_shell.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

docker_swarm_manager.py

Fix all E203, E741 and W504 flake8 errors

2021-01-18 10:35:41 +00:00

drmaa_external_killer.py

Fix all E201 and E202 style errors

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

drmaa_external_runner.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +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

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

external_chown_script.py

Fix all E201 and E202 style errors

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

extract_dataset_part.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

extract_toolbox_sections.py

Fix all E203, E741 and W504 flake8 errors

2021-01-18 10:35:41 +00:00

fetch_eggs.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

fix_dm_versions.py

add script for fixing shed_data_manager_conf.xml

2021-07-14 17:13:26 +02:00

functional_tests.py

Cleanup galaxy_test.base.api_util.

2021-01-16 20:11:39 -05:00

galaxy

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

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

galaxy_main.py

First pass fstring conversion

2021-05-11 13:47:00 -04:00

galaxy_schemadisp.py

Lint fixes, prompt for sqlalchemy_schemadisplay install

2021-01-12 08:23:10 -05:00

galaxy-main

Adjust galaxy-main script so we can import from it for easy app setup

2020-12-22 11:18:00 +01:00

get_platforms.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

get_uwsgi_args.py

Drop CLIENT_DEV_SERVER from webserver internals completely (we just proxy instead)

2021-03-05 09:52:02 -05:00

helper.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

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

Restore pastescript, make new stack depend on APP_WEBSERVER=dev

2021-04-07 14:39:06 +02:00

patch.sh

Add the script I used to create security patches

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

plugin_staging.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

release-diff.py

Lint fix

2021-06-10 19:41:24 +02:00

release.sh

Fix usage of sed -i on macOS in release script

2021-05-06 11:27:48 -04:00

resumable_upload.py

Use client-logic to run upload tool

2021-10-12 13:43:45 +02:00

rst2html.py

Fix all E722 errors and ignore E741

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

runtime_stats.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +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

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

set_user_disk_usage.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

summarize_timings.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

tests_markdown_compare.tpl

Performance metrics for tests.

2021-02-12 20:44:05 -05:00

tests_markdown.py

Performance metrics for tests.

2021-02-12 20:44:05 -05:00

tests_markdown.tpl

Performance metrics for tests.

2021-02-12 20:44:05 -05:00

update_shed_config_path.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

validate_tools.sh

Switch to lxml for xml parsing

2020-05-12 15:00:27 +02:00