Sergey Golitsynskiy 3cd1c7f1c7 Handle DedupedColumnCollection in db_indexes ...

This should fix the `scripts/check_model.py` script and the database
indexes github workflow.

Accessing index columns has changed: index.columns gives access to a
DedupedColumnCollection instead of a ColumnCollection.
Columns can be accessed by key; keys are accessed via keys() attr.

Ref:
https://docs.sqlalchemy.org/en/14/changelog/migration_14.html#select-objects-and-derived-from-clauses-allow-for-duplicate-columns-and-column-labels
https://docs.sqlalchemy.org/en/14/core/sqlelement.html?highlight=dedupecolumncollection#sqlalchemy.sql.expression.ColumnCollection

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

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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

Fix cleanup_datasets.py script

2021-05-11 18:34:30 +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

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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

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

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

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

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

Upgrade syntax using pyupgrade --py36-plus

2020-11-18 16:16:46 +00:00

release.sh

Fix usage of sed -i on macOS in release script

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

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