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Author SHA1 Message Date
Marius van den Beek 062371585a Merge pull request #18289 from davelopez/24.0_fix_copy_modal_login_link 
[24.0] Use correct link for log in or register in Copy Modal
 2024-05-31 19:06:42 +02:00
Marius van den Beek 268aa814e2 Merge pull request #18294 from jdavcs/240_ts_db_revision_tags 
[24.0] Add TS db revision tags for 24.0
 2024-05-31 18:42:30 +02:00
John Davis 6c998adeac Add TS db revision tags for 24.0 2024-05-31 12:39:40 -04:00
John Davis 29cd573d93 Merge release_23.2 into release_24.0 2024-05-31 12:35:02 -04:00
Marius van den Beek 192fbde15f Merge pull request #18293 from jdavcs/232_ts_db_revision_tags 
[23.2] Add toolshed database revision tags for 23.2
 2024-05-31 18:33:32 +02:00
John Davis 579884db75 Add TS db revision tags for 23.2 2024-05-31 12:25:40 -04:00
John Davis 7a9148bf02 Merge release_23.1 into release_23.2 2024-05-31 12:19:52 -04:00
davelopez 234933b6a9 Use correct link for log in or register in Copy Modal 2024-05-31 15:58:05 +02:00
Marius van den Beek d5e44b654a Merge pull request #18284 from mvdbeek/fix_up_first_dataset_element_type_hint 
[24.0] Fix first_dataset_element type hint
 2024-05-31 15:25:23 +02:00
mvdbeek 99aeadec06 Fix first_dataset_element type hint 2024-05-31 15:09:31 +02:00
Marius van den Beek 8dd7a9e570 Merge pull request #18263 from mvdbeek/page_summary_fix 
[24.0] Set page importable to false when serializing
 2024-05-31 12:37:30 +02:00
Marius van den Beek 93a07857c2 Merge pull request #18278 from mvdbeek/collection_download 
Don't attempt to download purged datasets
 2024-05-31 12:37:06 +02:00
Nicola Soranzo 761a8d9f04 Merge pull request #18236 from mvdbeek/none_delete_error 
[24.0] Only log error if deleting directory really failed
 2024-05-31 10:42:54 +01:00
Marius van den Beek 48231391a8 Drop key argument 
Did not want to do that actually
 2024-05-31 10:18:23 +02:00
Marius van den Beek aeaafc0cdc Merge pull request #18271 from jdavcs/231_ts_revision_tags 
[23.1] Add revision tags for TS migration in 23.1
 2024-05-31 10:02:29 +02:00
Marius van den Beek 942ddea389 Merge pull request #18255 from davelopez/24.0_fix_invenio_credentials_handling 
[24.0] Fix Invenio credentials handling
 2024-05-31 10:01:42 +02:00
John Chilton 4c8b4bf2a7 Merge pull request #18249 from mvdbeek/fix_no_elements_exception_extract_dataset 
[24.0] Raise exception when extracting dataset from collection without datasets
 2024-05-30 17:54:24 -04:00
John Chilton 1dd31f08f6 Merge pull request #18248 from mvdbeek/enable_transparent_use_of_compressed_datasets_in_DatasetDataProvider 
[24.0] Transparently open compressed files in DatasetDataProvider
 2024-05-30 17:53:20 -04:00
Martin Cech 0daf36d5d6 Merge pull request #18273 from nsoranzo/release_24.0_black 
[24.0] Format with black
 2024-05-30 23:03:56 +02:00
Nicola Soranzo 53bf8ce1de Format with black 2024-05-30 17:58:42 +01:00
Nicola Soranzo 3ea8de4ce5 Merge branch 'release_23.2' into release_24.0 2024-05-30 16:45:28 +01:00
Nicola Soranzo 94ebebf4ac Merge pull request #18268 from nsoranzo/release_23.2_fix_TestToolShedConfig 
[23.2] Add ``hgweb_repo_prefix`` attribute to ``TestToolShedConfig``
 2024-05-30 16:43:35 +01:00
John Davis 05eecfc219 Add revision tags for TS migration in 23.1 2024-05-30 11:36:57 -04:00
John Davis 15a8e6cc9a Merge branch 'release_23.2' into release_24.0 2024-05-30 11:11:12 -04:00
John Davis dbd063e00d Merge release_23.1 into release_23.2 2024-05-30 10:57:20 -04:00
Nicola Soranzo 6d068ca5f9 Add `hgweb_repo_prefix attribute to TestToolShedConfig` 
Fix the following error in unit tests:

```
AttributeError: 'TestToolShedConfig' object has no attribute 'hgweb_repo_prefix'
```

caused by merging commit b00beec3d2
forward.
 2024-05-30 15:16:38 +01:00
Marius van den Beek 90c9d4756f Merge pull request #18267 from jdavcs/231_ts_migration 
[23.1] Add missing TS migration
 2024-05-30 15:46:20 +02:00
John Davis d0d16ebf49 Make column non-nullable 2024-05-30 09:34:38 -04:00
Nicola Soranzo 713556029d Merge branch 'release_23.2' into release_24.0 2024-05-30 12:51:06 +01:00
Nicola Soranzo bd9a16988e Merge branch 'release_23.1' into release_23.2 2024-05-30 12:41:23 +01:00
mvdbeek 063d985650 Also set model to nullable=False 2024-05-30 11:50:43 +02:00
mvdbeek 4099fcc15a Set all old keys to deleted 2024-05-30 11:45:12 +02:00
Marius van den Beek 0db89059ef Merge pull request #18250 from mvdbeek/test_robustness 
[24.0] Skip tests if toolshed, dx.doi not responding
 2024-05-30 09:48:26 +02:00
John Davis a774c9234c Add ts db migration: deleted column to api_keys tbl 2024-05-29 22:49:30 -04:00
mvdbeek 0b6d925b8a Set page importable to false when serializing 
Fixes https://github.com/galaxyproject/galaxy/issues/18258
 2024-05-29 18:46:44 +02:00
Nate Coraor b121db548c Merge pull request #18256 from mvdbeek/server_external_hgweb 
[23.1] Minor fix to enable external hgweb process
 2024-05-29 11:58:14 -04:00
mvdbeek 410ccb9ab2 Fix up lock handling in hgweb_config_manager 2024-05-29 17:50:49 +02:00
mvdbeek b00beec3d2 Allow configuring hgweb repo prefix 2024-05-29 17:44:55 +02:00
davelopez 7cfba26fe1 Fix Invenio credentials handling 
Only ask for token when is really required
 2024-05-29 16:51:00 +02:00
mvdbeek 2ea3d342cc Import tool shed url 2024-05-29 15:29:39 +02:00
mvdbeek b0ea69e418 Fix import order 2024-05-29 13:58:09 +02:00
mvdbeek ce1582f46a Move assertions out request error handling 2024-05-29 13:50:29 +02:00
Marius van den BeekandNicola Soranzo 5d2ccdfbe7 Use variable 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2024-05-29 13:49:10 +02:00
mvdbeek d8379a79a1 Also skip unit test 2024-05-29 13:39:26 +02:00
Marius van den BeekandNicola Soranzo 74e8d3257b Make it an f-string 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2024-05-29 13:35:52 +02:00
mvdbeek 5f1ec2b06f Skip tests that require toolshed to be up if toolshed down 2024-05-29 13:30:22 +02:00
mvdbeek 229b1c5bcb Skip doi unit test if request fails 2024-05-29 13:30:22 +02:00
mvdbeek 455a851eef Raise exception when extracting dataset from collection without datasets 
Fixes https://github.com/galaxyproject/galaxy/issues/18240.
 2024-05-29 10:20:56 +02:00
mvdbeek dea0d523c6 Transparently open compressed files in DatasetDataProvider 
Fixes https://sentry.galaxyproject.org/share/issue/026b0ea1f8aa478daea1cdb0b18df78a/:
```
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
  File "starlette/applications.py", line 123, in __call__
    await self.middleware_stack(scope, receive, send)
  File "starlette/middleware/errors.py", line 186, in __call__
    raise exc
  File "starlette/middleware/errors.py", line 164, in __call__
    await self.app(scope, receive, _send)
  File "starlette_context/middleware/raw_middleware.py", line 92, in __call__
    await self.app(scope, receive, send_wrapper)
  File "starlette/middleware/base.py", line 189, in __call__
    with collapse_excgroups():
  File "contextlib.py", line 155, in __exit__
    self.gen.throw(typ, value, traceback)
  File "starlette/_utils.py", line 93, in collapse_excgroups
    raise exc
  File "starlette/middleware/base.py", line 191, in __call__
    response = await self.dispatch_func(request, call_next)
  File "galaxy/webapps/galaxy/fast_app.py", line 109, in add_x_frame_options
    response = await call_next(request)
  File "starlette/middleware/base.py", line 165, in call_next
    raise app_exc
  File "starlette/middleware/base.py", line 151, in coro
    await self.app(scope, receive_or_disconnect, send_no_error)
  File "starlette/middleware/exceptions.py", line 62, in __call__
    await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send)
  File "starlette/_exception_handler.py", line 64, in wrapped_app
    raise exc
  File "starlette/_exception_handler.py", line 53, in wrapped_app
    await app(scope, receive, sender)
  File "starlette/routing.py", line 758, in __call__
    await self.middleware_stack(scope, receive, send)
  File "starlette/routing.py", line 778, in app
    await route.handle(scope, receive, send)
  File "starlette/routing.py", line 299, in handle
    await self.app(scope, receive, send)
  File "starlette/routing.py", line 79, in app
    await wrap_app_handling_exceptions(app, request)(scope, receive, send)
  File "starlette/_exception_handler.py", line 64, in wrapped_app
    raise exc
  File "starlette/_exception_handler.py", line 53, in wrapped_app
    await app(scope, receive, sender)
  File "starlette/routing.py", line 74, in app
    response = await func(request)
  File "fastapi/routing.py", line 278, in app
    raw_response = await run_endpoint_function(
  File "fastapi/routing.py", line 193, in run_endpoint_function
    return await run_in_threadpool(dependant.call, **values)
  File "starlette/concurrency.py", line 42, in run_in_threadpool
    return await anyio.to_thread.run_sync(func, *args)
  File "anyio/to_thread.py", line 56, in run_sync
    return await get_async_backend().run_sync_in_worker_thread(
  File "anyio/_backends/_asyncio.py", line 2144, in run_sync_in_worker_thread
    return await future
  File "anyio/_backends/_asyncio.py", line 851, in run
    result = context.run(func, *args)
  File "galaxy/webapps/galaxy/api/datasets.py", line 446, in show
    return self.service.show(trans, dataset_id, hda_ldda, serialization_params, data_type, **extra_params)
  File "galaxy/webapps/galaxy/services/datasets.py", line 395, in show
    rval = self._raw_data(trans, dataset, **extra_params)
  File "galaxy/webapps/galaxy/services/datasets.py", line 1009, in _raw_data
    return DataResult(data=list(dataset.datatype.dataprovider(dataset, provider, **kwargs)))
  File "galaxy/datatypes/dataproviders/base.py", line 262, in __iter__
    for datum in parent_gen:
  File "galaxy/datatypes/dataproviders/base.py", line 199, in __iter__
    for datum in parent_gen:
  File "galaxy/datatypes/dataproviders/base.py", line 137, in __iter__
    yield from self.source
  File "galaxy/datatypes/dataproviders/base.py", line 137, in __iter__
    yield from self.source
  File "<frozen codecs>", line 322, in decode
```
 2024-05-29 10:09:29 +02:00
Ahmed Hamid Awan c2438b2f06 Merge pull request #18243 from davelopez/24.0_fix_userOwnsHistory_conditions 
[24.0] Fix userOwnsHistory conditions
 2024-05-28 12:12:06 -05:00