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Commit Graph
32146 Commits
Author SHA1 Message Date
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
davelopezandMarius 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
Dannon bb2d22327f Merge pull request #14391 from ahmedhamidawan/Impr_tool_search 
Feature: Advanced Tool Search Menu
 2022-09-08 21:31:41 -04:00
Nicola Soranzo dc0ac34fc4 Merge pull request #14588 from mvdbeek/fix_noisy_exception_logging_when_unicode_null_in_session_key 
[22.05] Ensure guid is hexadecimal value
 2022-09-08 19:05:54 +01:00
John Chilton 67b06a54a7 Remove unused datatype/model code. 2022-09-08 12:01:05 -04:00
John Chilton 5af55e251a API endpoint for launching tasks to compute hashes of datasets. 2022-09-08 12:01:05 -04:00