Commit Graph
63034 Commits
Author SHA1 Message Date
Alireza Heidari 00a9471559 setDraggingHistoryItem on drag start and end events 2022-09-23 03:18:31 +02:00
Alireza Heidari fe53edcaaa add draggingHistoryItem to history store 2022-09-23 03:15:05 +02:00
Alireza Heidari 2743e04975 refactor dataset services 2022-09-23 03:15:04 +02:00
Alireza Heidari 00d832040e disable collection items drag 2022-09-23 03:15:04 +02:00
Alireza Heidari 4ca49de5e0 add drag and drop to copy datasets and collections between histories 2022-09-23 03:08:41 +02:00
Aysam Guerler 35ba809db6 Merge pull request #14660 from guerler/strip_history_from_makos
Remove legacy history from code base
2022-09-22 19:51:20 -04:00
John Chilton 1d4801fdbf Merge pull request #14681 from jmchilton/tool_shed_cleanup_4
Tool Shed and Tool Utility Cleanup
2022-09-22 17:37:47 -04:00
John Chilton 079b5189dc Remove unused code from basic_util. 2022-09-22 11:29:19 -04:00
John Chilton 7606b81e13 Typing for toolbox parser... 2022-09-22 11:29:19 -04:00
John Chilton e27ff0e507 Move tool shed utility only used by tool shed into tool shed repository_util.
Doesn't belong in Galaxy utilities.
2022-09-22 11:29:19 -04:00
John Chilton ba9df94510 Merge pull request #14674 from nsoranzo/replace_self.assert_methods
Replace ``self.assert*()`` method calls with plain asserts
2022-09-22 11:20:29 -04:00
guerler 27efdd7c6b Fix failing selenium test 2022-09-22 10:59:29 -04:00
Marius van den Beek c682a49aef Merge pull request #14675 from mvdbeek/somewhat_valid_dynamic_class_names
Generate somewhat valid SafeStringWrapper-wrapped class names
2022-09-22 16:27:38 +02:00
John Chilton 227614ae3d Merge pull request #14668 from jmchilton/tool_util_cleanup
Cleanup tool_util.py
2022-09-22 10:23:15 -04:00
John Davis 06c9475683 Merge pull request #14537 from jdavcs/dev_managedb_cli
A replacement for manage_db.sh + rewrite of migration system documentation
2022-09-22 10:06:45 -04:00
Marius van den BeekandNicola Soranzo 71ec24ec87 Drop unnecessary list comprehension
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
2022-09-22 13:13:13 +02:00
guerler 990dc1eb2c Add history store client test case 2022-09-22 05:39:53 -04:00
mvdbeek ac27540c57 Generate somewhat valid SafeStringWrapper-wrapped class names
I don't think there's any downside, and the upside is that we can use
https://github.com/kensho-technologies/pytest-annotate to kickstart type
annotations. Applying collected annotations (e.g. `pyannotate --py3
--type-info ./annotations.json lib/galaxy/workflow/run.py` currently fails with:
```
Traceback (most recent call last):
  File "/Users/mvandenb/src/galaxy/.venv/bin/pyannotate", line 8, in <module>
    sys.exit(main())
  File "/Users/mvandenb/src/galaxy/.venv/lib/python3.9/site-packages/pyannotate_tools/annotations/__main__.py", line 122, in main
    data = generate_annotations_json_string(
  File "/Users/mvandenb/src/galaxy/.venv/lib/python3.9/site-packages/pyannotate_tools/annotations/main.py", line 60, in generate_annotations_json_string
    signature = unify_type_comments(item.type_comments)
  File "/Users/mvandenb/src/galaxy/.venv/lib/python3.9/site-packages/pyannotate_tools/annotations/main.py", line 27, in unify_type_comments
    arg_types, return_type = infer_annotation(type_comments)
  File "/Users/mvandenb/src/galaxy/.venv/lib/python3.9/site-packages/pyannotate_tools/annotations/infer.py", line 45, in infer_annotation
    arg_types, return_type = parse_type_comment(comment)
  File "/Users/mvandenb/src/galaxy/.venv/lib/python3.9/site-packages/pyannotate_tools/annotations/parse.py", line 216, in parse_type_comment
    return Parser(comment).parse()
  File "/Users/mvandenb/src/galaxy/.venv/lib/python3.9/site-packages/pyannotate_tools/annotations/parse.py", line 225, in __init__
    self.tokens = tokenize(comment)
  File "/Users/mvandenb/src/galaxy/.venv/lib/python3.9/site-packages/pyannotate_tools/annotations/parse.py", line 193, in tokenize
    raise ParseError(original)
pyannotate_tools.annotations.parse.ParseError: Invalid type comment: (galaxy.app.UniverseApplication, Dict, Dict[str, galaxy.model.HistoryDatasetAssociation], Dict[Union[galaxy.security.object_wrapper:SafeStringWrapper(str:<class 'NoneType'>,<class 'NotImplementedType'>,<class 'bool'>,<class 'bytearray'>,<class 'ellipsis'>,<class 'galaxy.security.object_wrapper.SafeStringWrapper'>,<class 'galaxy.tools.wrappers.ToolParameterValueWrapper'>,<class 'numbers.Number'>), str], Union[galaxy.security.object_wrapper.CallableSafeStringWrapper, galaxy.security.object_wrapper:SafeStringWrapper(str:<class 'NoneType'>,<class 'NotImplementedType'>,<class 'bool'>,<class 'bytearray'>,<class 'ellipsis'>,<class 'galaxy.security.object_wrapper.SafeStringWrapper'>,<class 'galaxy.tools.wrappers.ToolParameterValueWrapper'>,<class 'numbers.Number'>), str]]) -> None
```
This fixes that.
2022-09-22 10:55:29 +02:00
Marius van den Beek ed44a94ddf Merge pull request #14671 from dannon/fix-vcf-rendering
VCF/Tabular display fix
2022-09-22 09:43:12 +02:00
guerler d08196a170 Remove unused modules, clear directories 2022-09-22 01:42:40 -04:00
guerler ab2ac4251b Remove legacy entry point view 2022-09-21 23:21:49 -04:00
guerler 9a7b2d5d81 Move poll file to only component which uses it 2022-09-21 23:20:43 -04:00
guerler 1565b87786 Remove base collection handling 2022-09-21 23:17:10 -04:00
guerler 20e9e0b40e Move model file from mvc/library 2022-09-21 23:15:45 -04:00
guerler 7da1c86af9 Remove legacy collection and dataset handling 2022-09-21 23:08:35 -04:00
guerler 04453800d3 Fix inconsistent collection edit routs 2022-09-21 22:49:40 -04:00
guerler 03a2b95b29 Restore masthead redirect without window manager 2022-09-21 21:28:46 -04:00
Nicola Soranzo a5c41adb96 Remove unused `get_suite()` functions 2022-09-22 02:21:12 +01:00
guerler 635eedafe9 Fix state handling 2022-09-21 21:08:08 -04:00
guerler 28911a6bb4 Remove legacy tests from qunit test bundle 2022-09-21 20:46:58 -04:00
guerler 8a3a0602eb Remove loading span from history view 2022-09-21 20:44:32 -04:00
guerler 24b800ec40 Remove legacy qunit tests 2022-09-21 20:27:53 -04:00
guerler 163dfddc8b Remove legacy history from code base 2022-09-21 20:20:04 -04:00
guerler 2f5dd3a2ff Move grid related histroy list to Grids component 2022-09-21 20:19:13 -04:00
guerler ebd4d4ba06 Move job state model out of mvc/history to utils 2022-09-21 20:16:38 -04:00
guerler dd3f3a17c2 Remove all legacy history imports from bundle 2022-09-21 20:02:30 -04:00
guerler 4b6888b70a Replace legacy history with link to view in legacy html pages 2022-09-21 19:54:06 -04:00
guerler 7d38e66598 Remove legacy window manager route handling options 2022-09-21 19:44:36 -04:00
guerler 18308720a6 Remove legacy iframe add helper 2022-09-21 19:40:47 -04:00
guerler 568a3769f8 Handle window manager within route processing, fix invalid datasets edit route 2022-09-21 19:29:26 -04:00
guerler 68751fc3d1 Remove legacy iframe redirect from iframe add helper 2022-09-21 19:14:14 -04:00
guerler 7911fe41aa Use router for data display operation, add router to history view mount 2022-09-21 19:06:27 -04:00
Nicola Soranzo 2ec191e764 Fix typos 2022-09-21 23:50:06 +01:00
Nicola Soranzo 853c8f913a Use `self.assertRaises*()` as a context manager 2022-09-21 23:50:06 +01:00
Nicola Soranzo f3b04b8f26 Remove `unittest.main()` calls 2022-09-21 23:50:05 +01:00
Nicola Soranzo b5c7e2c86a Replace `self.assert* method calls with plain asserts in test/`
using https://github.com/pytest-dev/unittest2pytest with the following command:

```
unittest2pytest -f self_assert -w -n test/
```

(excluding ``self.assertRaises*`` method calls).
2022-09-21 23:50:05 +01:00
Nicola Soranzo a69103dd2c Replace `self.assert* method calls with plain asserts in lib/galaxy_test/`
using https://github.com/pytest-dev/unittest2pytest with the following command:

```
unittest2pytest -f self_assert -w -n lib/galaxy_test/
```
2022-09-21 23:50:04 +01:00
John Chilton 23e78c5425 Import galaxy version of tool shed utils in admin_toolshed. 2022-09-21 16:45:07 -04:00
John Chilton 6dce7be430 Merge pull request #14669 from jmchilton/misc_ts_cleanup
Various unsorted tool shed code cleanup.
2022-09-21 15:53:49 -04:00
John Chilton 5059ec02f0 Merge pull request #14662 from jmchilton/cleanup_ts_tests
Cleanup Tool Shed Tests
2022-09-21 15:49:43 -04:00