guerler
0372dfc1ea
Remove structure display selenium tests
2022-09-15 15:50:31 -04:00
guerler
8806869356
Remove unused legacy history controller template helpers
2022-09-15 14:24:33 -04:00
guerler
fa5d24b017
Remove unused import
2022-09-15 14:21:54 -04:00
guerler
bb10689ffe
Remove display structured controller endpoint
2022-09-15 14:04:52 -04:00
Björn Grüning
01fffdf175
Merge pull request #14617 from jmchilton/remove_propertiary_datatypes
...
Remove legacy tool shed datatype handling
2022-09-15 18:21:43 +02:00
Björn Grüning
89803553db
Merge pull request #14624 from davelopez/fix_invocation_export_with_celery
...
Fix `toolbox` access in invocation export
2022-09-15 18:20:12 +02:00
John Chilton
a887fc894d
Merge pull request #14616 from jmchilton/ts_tests_1
...
More tool shed API tests (+fixes)
2022-09-15 09:08:31 -04:00
John Chilton
1c6c697d55
Merge pull request #14615 from jmchilton/ts_cleanup_3
...
More Tool Shed Cleanup
2022-09-15 09:04:39 -04:00
davelopez and Marius van den Beek
07b38ba429
Fix toolbox access in invocation export
...
When exporting an invocation using Celery we don't have access to the ToolBox and also don't need it so we make it optional.
Thanks Marius for the solution.
In addition:
- Fix mypy by raising a tool missing exception in the `augment` method
- Also remove unused `inputs` parameter
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2022-09-15 14:42:50 +02:00
David López
2741b20841
Merge pull request #14595 from jmchilton/ro_crate
...
Implement RO Crate export of Galaxy histories and invocations.
2022-09-15 08:55:19 +02:00
John Chilton
0f9dbb4045
Remove more datatype legacy handling code.
2022-09-14 11:51:39 -04:00
John Chilton
3b1331de51
Remove code and config option related to loading shed datatypes.
2022-09-14 11:51:38 -04:00
John Chilton
f8c1c11016
API tests for tool shed search APIs.
2022-09-14 09:31:27 -04:00
John Chilton
e5bbad2f36
Flush out pydantic models for tool shed metadata.
2022-09-14 09:31:25 -04:00
John Chilton
b2a4cdeb82
Remove now unused function.
2022-09-14 09:24:25 -04:00
John Chilton
0869bfd17f
Rename method to indicate an internal method.
2022-09-14 09:23:55 -04:00
John Chilton
9351be5c96
Refactor method name to make clear it is private.
2022-09-14 09:07:43 -04:00
John Chilton
d26cade072
Remove more unused tool shed code.
2022-09-14 09:07:43 -04:00
John Chilton
90858d3137
Move create_element into the only place it is used.
2022-09-14 09:07:43 -04:00
Nicola Soranzo
b4a3735999
Change HTTP status code for `DeprecatedMethod` exception to 410
...
Replaced the 404 (Not Found) HTTP response status code with 410 (Gone),
which is more correct, see details at:
https://developer.mozilla.org/en-US/docs/Web/HTTP/Status#client_error_responses
2022-09-14 13:24:24 +01:00
Marius van den Beek
2ee253cbbd
Merge pull request #14612 from jmchilton/ts_unused_1
...
Remove unused tool shed functions.
2022-09-14 10:32:28 +02:00
John Chilton
3dbe2891e7
Implement RO Crate export of Galaxy histories and invocations.
2022-09-13 19:20:48 -04:00
John Chilton
3fe2674aa1
Remove unused function in shed common_util - get_tool_dependencies.
2022-09-13 17:31:33 -04:00
John Chilton
6d1e86ea48
Remove unused function in shed common_util - get_non_shed_tool_panel_configs.
2022-09-13 17:31:33 -04:00
John Chilton
7caef14a23
Remove unused function from tool shed common_util.
2022-09-13 17:31:23 -04:00
Dannon Baker
d18504fb83
Unused import
2022-09-13 13:33:33 -04:00
Dannon Baker
3849850739
Drop old history multi-panel
2022-09-13 11:19:40 -04:00
John Chilton
42364892ac
Merge pull request #14604 from bernt-matthias/topic/lint-duplicate-inputs
...
linter: check for inputs with duplicated names
2022-09-12 15:24:01 -04:00
Dannon
d7fdf0ddc2
Merge pull request #14576 from jmchilton/compute_dataset_hash
...
Implement API endpoint for calculating dataset hashes asynchronously
2022-09-12 11:55:46 -04:00
John Chilton
e60280230e
Merge pull request #14582 from jmchilton/tool_data_table_tests
...
Unit tests and type fixes for tool data tables code.
2022-09-12 10:37:42 -04:00
John Chilton
3a643433c5
Merge pull request #14598 from jmchilton/path_typing
...
Some additional typing for galaxy.util.path.
2022-09-12 10:35:35 -04:00
Matthias Bernt
3ff56e1276
fix typing issue
2022-09-12 16:25:58 +02:00
Matthias Bernt
ec04666cc1
linter: check for inputs with duplicated names
...
and outputs
2022-09-12 15:23:50 +02:00
Bjoern Gruening
32fdbfa8d7
fix linting
2022-09-11 13:05:50 +02:00
Bjoern Gruening
84a21b29f2
fix bad merge
2022-09-11 12:22:00 +02:00
Björn Grüning
764ac42e5f
fix spelling of testcase
2022-09-11 02:16:35 +02:00
Björn Grüning
2db5af6890
Merge pull request #14535 from dannon/panel-cleanup
...
Panel init template cleanup
2022-09-10 20:53:18 +02:00
Björn Grüning
2168933d7c
fix PathLike annotation
2022-09-10 20:12:54 +02:00
Björn Grüning
78960c6fc6
Merge pull request #14553 from jmchilton/more_ts_api_tests
...
More API tests for the tool shed.
2022-09-10 20:01:15 +02:00
Björn Grüning
6fb1e24898
Merge pull request #13985 from itisAliRH/new-history-multiple-view
...
New history multiple view
2022-09-10 19:20:19 +02:00
galaxybot
1c4dfd85d4
Update Python dependencies
2022-09-10 03:57:44 +00:00
John Chilton
d31c9ac5dd
Some typing for galaxy.util.path...
2022-09-09 18:52:14 -04:00
Nicola Soranzo
e08deef224
Merge pull request #14592 from nsoranzo/misc_fixes_202209
...
Misc fixes 202209
2022-09-09 21:34:38 +01:00
Dannon Baker
1438658d2c
Drop broken panel_init from toolshed/base_panels
2022-09-09 13:44:47 -04:00
John Chilton
09b6b59ee9
Merge pull request #14564 from jdavcs/dev_alembic_fix1
...
Don't query the database when running migrations in offline mode
2022-09-09 13:19:06 -04:00
John Chilton
1e664c3206
More tool data table typing and testing.
2022-09-09 13:12:30 -04:00
John Chilton
019db37411
Unit tests for tool_data...
2022-09-09 13:11:39 -04:00
John Chilton
98f367344e
Type fixes for galaxy.tools.data
2022-09-09 13:11:39 -04:00
Nicola Soranzo
ac6ffb28d1
Fix typos
2022-09-09 17:20:23 +01:00
Nicola Soranzo
cb012c7fb2
Merge branch 'release_22.05' into dev
2022-09-09 17:14:20 +01:00
guerler