John Chilton d69962e7f4 Implement model abstraction for `ImplicitCollectionJobs`. ...

These aggregate all the jobs contributing to an implicitly created HistoryDatasetCollectionAssociation.

- Model enhancements that allow this.
- API endpoint for jobs summary of history content (somewhat uniform across HDAs and HDCAs just for consistency).
- Test cases.
- Rework history contents API a bit to eliminate more costly state summary checks by default.

2017-11-30 10:02:02 -05:00

..

api

Python3: fix remaining print statements

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

auth

Fixes for pycodestyle 2.2.0

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

cleanup_datasets

Fix all E722 errors and ignore E741

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

communication

Fix import order and Python3 compatibility

2017-08-18 12:35:04 +01:00

data_libraries

Backport of hardening fixes to 17.09

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

grt

Backport of hardening fixes to 17.09

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

loc_files

Fix all E722 errors and ignore E741

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

metagenomics

Python3: fix remaining print statements

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

microbes

Fix all E722 errors and ignore E741

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

migrate_tools

Python3: fix remaining print statements

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

others

Fix all E722 errors and ignore E741

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

slideshow

Python3: fix remaining print statements

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

taxonomy

Tweaks to taxonomy tools

2010-11-15 15:04:59 -05:00

tool_shed

Fix all E722 errors and ignore E741

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

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

bootstrap_history.py

Absolute pins on linting dependencies.

2017-10-26 15:53:25 -04:00

build_toolbox.py

Fix all E722 errors and ignore E741

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

build_universe_config.py

Fixes for pycodestyle 2.2.0

2016-11-15 16:56:50 +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_galaxy.py

Fix all E722 errors and ignore E741

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

check_python.py

Fix all E201 and E202 style errors

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

common_startup_functions.sh

Small tweaks to fixup #2866.

2017-09-22 14:47:15 -04:00

common_startup.sh

If installing dev dependencies, do so along side regular dependencies.

2017-11-02 09:49:08 -04:00

config_sample_to_kwalify.py

Scripts to manage configuration infrastructure.

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

create_db.py

Fixes for pycodestyle 2.2.0

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

db_shell.py

Implement model abstraction for `ImplicitCollectionJobs`.

2017-11-30 10:02:02 -05:00

drmaa_external_killer.py

Fix all E201 and E202 style errors

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

drmaa_external_runner.py

Fix all E722 errors and ignore E741

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

dump_tour.py

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

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

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

Python3: fix remaining print statements

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

fetch_eggs.py

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

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

functional_tests.py

Fix import order everywhere

2017-11-14 19:42:39 +00:00

galaxy-main

Add multi-farm support to the main script

2017-11-17 17:09:36 -05:00

get_platforms.py

Python3: fix remaining print statements

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

get_uwsgi_args.py

Do not autostart uWSGI mules

2017-11-17 17:05:43 -05:00

helper.py

Fix all E722 errors and ignore E741

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

manage_db.py

Fix all E201 and E202 style errors

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

manage_tool_dependencies.py

To avoid duplication, move common utilities used by external scripts to

2017-11-13 12:18:09 -05:00

nosetests.py

Fix all E201 and E202 style errors

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

paster.py

Fix all E722 errors and ignore E741

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

patch.sh

Add the script I used to create security patches

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

rst2html.py

Fix all E722 errors and ignore E741

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

runtime_stats.py

Fix all E722 errors and ignore E741

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

secret_decoder_ring.py

Fix import order and Python3 compatibility

2017-08-18 12:35:04 +01:00

set_dataset_sizes.py

Python3: fix remaining print statements

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

set_user_disk_usage.py

Python3: fix remaining print statements

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

summarize_timings.py

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

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

sync_reports_config.py

Fixes for pycodestyle 2.2.0

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

transfer.py

Backport of hardening fixes to 17.09

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

update_shed_config_path.py

Python3: fix remaining print statements

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

validate_tools.sh

Refactor most of tool validation for CI into a standalone script.

2016-09-16 15:07:42 -04:00