opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-31 02:28:09 +08:00
Code Issues Packages Projects Releases Wiki Activity
62,881 Commits 64 Branches 246 Tags
fa35e66709bfcd48d8f77ba54a83ceea9228d5fc
Commit Graph
32163 Commits
Author SHA1 Message Date
davelopez 0128e05a23 Fix export ro-crate to file source 
Write to the store the correct archive file
 2022-09-16 17:19:49 +02:00
John Chilton e1daab1768 Merge pull request #14629 from jmchilton/toolbox_typing 
Type annotations for base toolbox functionality.
 2022-09-16 09:22:33 -04:00
John Chilton b84076fa4a Merge pull request #14609 from guerler/bundle_toolshed_js 
Place Toolshed JS modules into separate bundle
 2022-09-16 09:21:58 -04:00
Björn Grüning 5d1a3e0b13 Merge pull request #14630 from guerler/remove_display_structured 
Remove outdated display structured history view
 2022-09-16 15:10:14 +02:00
John Chilton cf298957e3 Toolbox typing. 2022-09-15 21:14:04 -04:00
John Chilton 1b3da85119 Merge pull request #14628 from jmchilton/cleanup_update_repo_manager 
Cleanup update_repository_manager in Galaxy repository install code.
 2022-09-15 21:09:19 -04:00
Nicola Soranzo aa4443af18 Merge pull request #14596 from jdavcs/dev_alembic_fix3 
Better + additional fix for alembic offline mode
 2022-09-16 01:02:52 +01:00
guerler bf73d4fe6e Remove corresponding client route from backend 2022-09-15 15:52:39 -04:00
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
John Chilton c04dd77de0 Cleanup update_repository_manager in Galaxy repository install code. 2022-09-15 13:39:25 -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
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
guerler 648a105f87 Load bundleToolshed instead of bundleEntries 2022-09-13 11:36:16 -04:00
guerler bfe2237020 Switch toolshed makos from generic bundle to toolshed bundle 2022-09-13 11:31:05 -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