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Author SHA1 Message Date
John Chilton 8cd1503860 Correct data fetch API in the client. 
More defensive backend to prevent these errors.
 2022-04-04 15:58:44 -04:00
Marius van den Beek d4e0d3dc4c Merge pull request #13668 from dannon/toolshed-style-loading-fix 
[22.01] Fix toolshed style loading
 2022-04-04 20:09:59 +02:00
Nicola Soranzo 88f3d6d509 Merge branch 'release_21.09' into release_22.01 2022-04-04 18:02:42 +01:00
Nicola Soranzo 7275b2f8e1 Merge pull request #13667 from nsoranzo/release_21.09_add_rich_requirement 2022-04-04 17:58:51 +01:00
Dannon Baker de71354678 Drop debugging commentary from base mako 2022-04-04 12:44:53 -04:00
Dannon Baker cd5128b7bd Fix toolshed style loading 2022-04-04 12:42:29 -04:00
Nicola Soranzo 48a01454e4 Add missing pin for rich, dependency of refgenconf 0.12.0 
Pinning to the version that was current when
https://github.com/galaxyproject/galaxy/pull/12435
was merged to fix the following traceback with rich 12.1.0:

```
2022-04-04T14:16:19.5073158Z   File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/tools/data/__init__.py", line 21, in <module>
2022-04-04T14:16:19.5073535Z     import refgenconf
2022-04-04T14:16:19.5074393Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/refgenconf/__init__.py", line 6, in <module>
2022-04-04T14:16:19.5074853Z     from .populator import looper_refgenie_populate
2022-04-04T14:16:19.5075535Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/refgenconf/populator.py", line 9, in <module>
2022-04-04T14:16:19.5075970Z     from . import refgenconf
2022-04-04T14:16:19.5076607Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/refgenconf/refgenconf.py", line 27, in <module>
2022-04-04T14:16:19.5077091Z     from rich.progress import BarColumn, Progress, TextColumn
2022-04-04T14:16:19.5077768Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/progress.py", line 43, in <module>
2022-04-04T14:16:19.5078272Z     from .console import Console, JustifyMethod, RenderableType, Group
2022-04-04T14:16:19.5078956Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/console.py", line 46, in <module>
2022-04-04T14:16:19.5079437Z     from ._log_render import FormatTimeCallable, LogRender
2022-04-04T14:16:19.5080105Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/_log_render.py", line 5, in <module>
2022-04-04T14:16:19.5124479Z     from .text import Text, TextType
2022-04-04T14:16:19.5130069Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/text.py", line 5, in <module>
2022-04-04T14:16:19.5134858Z     from rich.emoji import EmojiVariant
2022-04-04T14:16:19.5139847Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/emoji.py", line 4, in <module>
2022-04-04T14:16:19.5144648Z     from .jupyter import JupyterMixin
2022-04-04T14:16:19.5147478Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/jupyter.py", line 4, in <module>
2022-04-04T14:16:19.5150060Z     from .segment import Segment
2022-04-04T14:16:19.5152862Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/segment.py", line 19, in <module>
2022-04-04T14:16:19.5155442Z     from .cells import (
2022-04-04T14:16:19.5158112Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/cells.py", line 6, in <module>
2022-04-04T14:16:19.5159612Z     from ._lru_cache import LRUCache
2022-04-04T14:16:19.5161691Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/_lru_cache.py", line 8, in <module>
2022-04-04T14:16:19.5163233Z     from typing_extensions import OrderedDict
2022-04-04T14:16:19.5165289Z ImportError: cannot import name 'OrderedDict' from 'typing_extensions' (/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/typing_extensions.py)
```
 2022-04-04 15:43:43 +01:00
Nicola Soranzo c7ce60a351 Merge branch 'release_21.05' into release_21.09 2022-04-04 15:11:17 +01:00
Marius van den Beek 06d37d99f0 Merge pull request #13664 from nsoranzo/release_21.05_backport_dbf7ac364a20835acf16ccdffea3018a58023e2d 
[21.05] Partially backport #13532 to fix `test_github_search` mulled unit test
 2022-04-04 15:52:53 +02:00
Nicola Soranzo 2cbbf1ea50 Check GitHub API rate limit in GitHubSearch. Deprecate get_json() search 
Follow-up on https://github.com/galaxyproject/galaxy/pull/13509 .
 2022-04-04 12:56:07 +01:00
Nicola Soranzo 58d7e3cd96 Raise exception if GET request returned an unsuccessful status code 2022-04-04 12:40:16 +01:00
Nicola Soranzo 5b85b6595b Merge pull request #13557 from mvdbeek/fix_job_message_override 2022-03-28 22:28:26 +01:00
mvdbeek 0ebe2af5ea Drop redundant statement 2022-03-28 18:58:37 +02:00
David López cee063511d Merge pull request #13621 from mvdbeek/doc_backport 
[22.01] Point to GTN tutorial in visualizations readme
 2022-03-25 12:57:32 +01:00
Beatriz Serrano-Solano 21e3ba013d Point to GTN tutorial in visualizations readme 2022-03-25 12:06:57 +01:00
Marius van den Beek 3231165d7c Merge pull request #13564 from bernt-matthias/datatype/mzqc 
[22.01] add mzqc datatype
 2022-03-21 17:29:00 +01:00
John Chilton b06bdc077e Merge pull request #13560 from mvdbeek/enable_model_store_sources 
[22.01] Attach dataset source in model store imports
 2022-03-21 10:15:19 -04:00
mvdbeek 6bfa842314 Replace container kill trap if present 2022-03-19 14:54:00 +01:00
mvdbeek cd2716f259 Fix stdout/stderr capture for container commands 
By pulling `capture_stdout_stderr` to the outer scope the capture
runs on the "host" instead of the container.
 2022-03-19 14:54:00 +01:00
mvdbeek 2e61fccb1c Extend kubernetes logs to check that job logs are properly recorded 2022-03-19 12:11:41 +01:00
Marius van den Beek 38509cac8e Merge pull request #13576 from nsoranzo/release_22.01_fix_broken_model_discovery_tests 
[22.01] Fix model discovery unit tests
 2022-03-18 22:55:39 +01:00
Nicola Soranzo 0075ecb275 Fix model discovery unit tests 
that I broke when merging
https://github.com/galaxyproject/galaxy/pull/13552 forward.

Fix:

```
app = <galaxy.model.unittest_utils.data_app.GalaxyDataTestApp object at 0x7f0e00dd3640>, target = '/tmp/tmpyj5d8268', work_directory = '/tmp/tmp_a7e191v'

    def _import_directory_to_history(app, target, work_directory):
        sa_session = app.model.context

        u = model.User(email="collection@example.com", password="password")
        import_history = model.History(name="Test History for Import", user=u)

        sa_session = app.model.context
        sa_session.add_all([u, import_history])
        sa_session.flush()

        assert len(import_history.datasets) == 0

        import_options = store.ImportOptions(allow_dataset_object_edit=True)
>       import_model_store = store.get_import_model_store_for_directory(target, app=app, user=u, import_options=import_options, tag_handler=app.tag_handler.create_tag_handler_session())
E       AttributeError: 'GalaxyDataTestApp' object has no attribute 'tag_handler'

test/unit/data/model/test_model_discovery.py:235: AttributeError
```
 2022-03-18 19:12:20 +00:00
Nicola Soranzo 5114b67902 Merge branch 'release_21.09' into release_22.01 2022-03-18 18:28:15 +00:00
Nicola Soranzo 8e4bdb58e4 Merge branch 'release_21.05' into release_21.09 2022-03-18 18:08:10 +00:00
mvdbeek dab6237bbc Fix tee pattern for stdout/stderr streaming 2022-03-18 17:26:10 +01:00
mvdbeek f8c39d5289 Unit test for named pipe capture 2022-03-18 16:50:40 +01:00
Marius van den Beek 74a51d990a Merge pull request #13552 from mvdbeek/fix_tag_creation_metadata_strategy_extended 
[21.09] Fix creating tags within sessionless context
 2022-03-18 15:42:43 +01:00
John Chilton 316998dea1 Merge pull request #13573 from mvdbeek/fix_tool_shed_bootstrapping 
[22.01] Fix tool shed bootstrapping
 2022-03-18 09:11:53 -04:00
mvdbeek 434991101f One more f-string 2022-03-18 13:03:05 +01:00
mvdbeek 747efeb640 Move stdout/stderr capture 2022-03-18 13:02:28 +01:00
mvdbeek 43e4e895d0 Only yield captured retun code when we're capturing the return code 2022-03-18 12:42:41 +01:00
mvdbeek 7aae40d1af Include unit test for sessionless export/import with tags 
Seems like the only way you could previously include tags
was if you included them in the data fetch tool.
 2022-03-18 12:16:17 +01:00
mvdbeek 558cad246e Return tag in get_tag_by_name function 2022-03-18 11:12:06 +01:00
mvdbeek 06f4d36e5b Re-use default_exit_code_file 2022-03-18 10:55:11 +01:00
Marius van den BeekandNicola Soranzo a43458e764 One more string formatting 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-03-17 19:58:02 +01:00
Marius van den BeekandNicola Soranzo aa13988023 Use string formatting instead of concatenation 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-03-17 19:57:32 +01:00
Marius van den BeekandNicola Soranzo 75283c6c9f Simplify capture_return_code 
Since we use it from one place only now

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-03-17 19:56:16 +01:00
mvdbeek 4c7bfd1032 Fix tool shed bootstrapping script 2022-03-17 19:34:43 +01:00
mvdbeek e9d2d683d6 Add --capture-output when running gunicorn in daemon mode 2022-03-17 19:34:16 +01:00
mvdbeek 3d7dde0f9b Fix tool shed /api/authenticate/baseauth/ 
Fixes:
```
AttributeError: 'UniverseApplication' object has no attribute 'user_manager'
  File "galaxy/web/framework/decorators.py", line 312, in decorator
    rval = func(self, trans, *args, **kwargs)
  File "galaxy/webapps/galaxy/api/authenticate.py", line 63, in get_api_key
    user = self.app.user_manager.get_user_by_identity(identity)
```
 2022-03-17 19:33:18 +01:00
mvdbeek 7cac71615c Fix path to exit_code file 2022-03-17 10:34:05 +01:00
mvdbeek 79dbfbf671 Drop redundant exit_code_path writing from DEFAULT_JOB_FILE_TEMPLATE.sh 2022-03-17 10:34:04 +01:00
M Bernt 3a010e1f69 Merge branch 'release_22.01' into datatype/mzqc 2022-03-17 10:28:07 +01:00
mvdbeek 96934420e8 Attach dataset source in model store imports 
Fixes
```
FAILED test/integration_selenium/test_dataset_details_source_transforms.py::DatasetSourceTransformSeleniumIntegrationTestCase::test_displaying_source_transformations_grooming
FAILED test/integration_selenium/test_dataset_details_source_transforms.py::DatasetSourceTransformSeleniumIntegrationTestCase::test_displaying_source_transformations_posixlines
FAILED test/integration_selenium/test_dataset_details_source_transforms.py::DatasetSourceTransformSeleniumIntegrationTestCase::test_displaying_source_transformations_spaces_to_tabs
```
 2022-03-17 10:11:13 +01:00
M Bernt 4084c77ae5 Apply suggestions from code review 2022-03-17 08:51:08 +01:00
Marius van den Beek ce7d376416 Merge pull request #13553 from mvdbeek/fix_extended_metadata_jobs_with_dce_inputs 
[22.01] Fix extended_metadata jobs with dce inputs
 2022-03-17 08:45:03 +01:00
Matthias Bernt 09ca48c623 add mzqc datatype 
needed here https://github.com/galaxyproteomics/tools-galaxyp/pull/653
 2022-03-17 08:27:25 +01:00
Nicola Soranzo bad8ecbda2 Merge pull request #13554 from mvdbeek/fix_sff_extractor_tool 2022-03-16 18:00:25 +00:00
mvdbeek 7129a3a34c Write to exit code file before running metadata script 
We need the exit code in the metadata script to figure out the correct
job messages. This would fix
```
FAILED test/functional/test_toolbox_pytest.py::test_tool[detect_errors_test_1]
FAILED test/functional/test_toolbox_pytest.py::test_tool[detect_errors_test_2]
FAILED test/functional/test_toolbox_pytest.py::test_tool[detect_errors_test_3]
FAILED test/functional/test_toolbox_pytest.py::test_tool[detect_errors_test_5]
FAILED test/functional/test_toolbox_pytest.py::test_tool[detect_errors_test_9]
FAILED test/functional/test_toolbox_pytest.py::test_tool[detect_errors_test_10]
```
that are broken when using `metadata_strategy: extended` (https://github.com/galaxyproject/galaxy/issues/13551).
 2022-03-16 18:51:36 +01:00
mvdbeek e2d43806dc Fix `sff_extract` tool, drop type annotation 
I don't think this tool is really used much, but it is loaded in
`tool_conf.xml`.
https://github.com/galaxyproject/galaxy/pull/11877 added type
annotations, and that's a syntax error on 2.7

The alternative would be to fix the rest of the tool for 3.x,
but I think we're just wasting our time there and we shouldn't
touch this again.
 2022-03-16 15:24:55 +01:00