Commit Graph
58553 Commits
Author SHA1 Message Date
mvdbeek 31dd8e4b46 Fix tool_shed entrypoint and default port 2022-02-22 17:58:28 +01:00
mvdbeek 11af89cd8c Wrap reports and tool_shed app in static
That broke in https://github.com/galaxyproject/galaxy/pull/13103,
but we only noticed it when we started the apps with gunicorn
instead of uwsgi, since uwsgi has its own static mapping.
2022-02-22 17:58:28 +01:00
Nicola Soranzo 9357138c43 Merge branch 'release_21.09' into release_22.01 2022-02-22 14:03:24 +00:00
Marius van den Beek 44633db751 Merge pull request #13425 from mvdbeek/fix_remove_file_in_repo_option
[21.09] Fix repository uploads with remove_repo_files_not_in_tar
2022-02-22 11:31:18 +01:00
mvdbeek 907130d772 Fix repository uploads with remove_repo_files_not_in_tar
This fixes erroneously deleting the just uploaded files, which otherwise
happens in
```
                    if full_name not in filenames_in_archive:
                        files_to_remove.append(full_name)
```
2022-02-21 10:28:41 +01:00
Nicola Soranzo d2981d369c Merge pull request #13403 from blankenberg/22.01-refgenie
[22.01] Always display digest in name for refgenie assets.
2022-02-20 23:56:25 +00:00
Marius van den Beek 8643b8e2da Merge pull request #13417 from nuwang/vault_doumentation_typo_fix
[22.01] Fix typo in vault docs
2022-02-19 17:07:37 +01:00
Nuwan Goonasekera ab0de0b423 Fix typo in vault docs 2022-02-19 20:33:24 +05:30
John Chilton a0d555a6e6 Merge pull request #13396 from mvdbeek/a2wsgi
[22.01] Use a2wsgi to serve WSGI app
2022-02-18 11:02:56 -05:00
Marius van den Beek 3d0a8d3c70 Merge pull request #13407 from simonbray/wf-exec-tool-versions-2201
[22.01] Block workflow invocation if wrong tool versions installed
2022-02-18 14:36:03 +01:00
Simon Bray cc79e028ed remove test_run_workflow_with_missing_tool() from API tests 2022-02-18 10:07:39 +01:00
Simon Bray 50636056f4 add integration test for invoking workflows with nonexistent tool_ids or tool_versions 2022-02-18 10:06:54 +01:00
Simon Bray 7f8a198af3 revert change to toolbox's get_tool() 2022-02-18 10:06:39 +01:00
Simon Bray 8078dab412 fix small bug in toolbox's get_tool() so non-shed tool can be used for missing tool workflow invocation test 2022-02-18 10:06:28 +01:00
Simon Bray bbe90dd3f7 block workflow invocation if wrong tool versions installed 2022-02-18 10:06:04 +01:00
Daniel Blankenberg e92410cbcf Always display digest in name for refgenie assets. 2022-02-17 15:40:36 -05:00
Marius van den Beek 55e067f3b9 Merge pull request #13385 from jmchilton/unit_test_more_of_dict_parser
Try to unit test more of DictParser in Viz component.
2022-02-17 16:11:11 +01:00
mvdbeek 9732f8c7c9 Fix up unit tests that attempt to set url_for 2022-02-17 16:07:18 +01:00
mvdbeek 1aaf9c02c1 Fix path lookup for metdata_file
And use trans.url_builder in model serializers if possible.
2022-02-17 16:07:18 +01:00
mvdbeek 2eb56c2bd0 Make history tests rerunnable by generating unique history names 2022-02-17 11:54:11 +01:00
mvdbeek 61dab21990 Use a2wsgi to serve WSGI app
instead of the deprecated starlette WSGIMiddleware that was vendored by
fastAPI. I'm also hoping this fixes the weird exceptions a la:
```
uvicorn.error ERROR 2022-02-14 11:59:42,141 [pN:main,p:4823,tN:Thread-216] Exception in ASGI application
Traceback (most recent call last):
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/uvicorn/protocols/http/h11_impl.py", line 364, in run_asgi
    result = await app(self.scope, self.receive, self.send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/uvicorn/middleware/proxy_headers.py", line 75, in __call__
    return await self.app(scope, receive, send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/fastapi/applications.py", line 212, in __call__
    await super().__call__(scope, receive, send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/applications.py", line 112, in __call__
    await self.middleware_stack(scope, receive, send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/middleware/errors.py", line 159, in __call__
    await self.app(scope, receive, _send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/exceptions.py", line 71, in __call__
    await self.app(scope, receive, sender)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/routing.py", line 656, in __call__
    await route.handle(scope, receive, send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/routing.py", line 408, in handle
    await self.app(scope, receive, send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/fastapi/applications.py", line 212, in __call__
    await super().__call__(scope, receive, send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/applications.py", line 112, in __call__
    await self.middleware_stack(scope, receive, send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/middleware/errors.py", line 159, in __call__
    await self.app(scope, receive, _send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette_context/middleware/raw_middleware.py", line 96, in __call__
    await self.app(scope, receive, send_wrapper)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/middleware/base.py", line 65, in __call__
    task_group.cancel_scope.cancel()
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/_backends/_asyncio.py", line 574, in __aexit__
    raise exceptions[0]
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/_backends/_asyncio.py", line 611, in _run_wrapped_task
    await coro
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/middleware/base.py", line 34, in coro
    await self.app(scope, request.receive, send_stream.send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/exceptions.py", line 71, in __call__
    await self.app(scope, receive, sender)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/routing.py", line 656, in __call__
    await route.handle(scope, receive, send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/routing.py", line 408, in handle
    await self.app(scope, receive, send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/middleware/wsgi.py", line 64, in __call__
    await responder(receive, send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/middleware/wsgi.py", line 91, in __call__
    await anyio.to_thread.run_sync(self.wsgi, environ, self.start_response)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/_backends/_asyncio.py", line 572, in __aexit__
    raise ExceptionGroup(exceptions)
anyio._backends._asyncio.ExceptionGroup: 2 exceptions were raised in the task group:
----------------------------
Traceback (most recent call last):
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/_backends/_asyncio.py", line 611, in _run_wrapped_task
    await coro
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/middleware/wsgi.py", line 98, in sender
    await send(message)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/exceptions.py", line 68, in sender
    await send(message)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/streams/memory.py", line 193, in send
    self.send_nowait(item)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/streams/memory.py", line 177, in send_nowait
    raise BrokenResourceError
anyio.BrokenResourceError
----------------------------
Traceback (most recent call last):
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/middleware/wsgi.py", line 91, in __call__
    await anyio.to_thread.run_sync(self.wsgi, environ, self.start_response)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/to_thread.py", line 29, in run_sync
    limiter=limiter)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/_backends/_asyncio.py", line 818, in run_sync_in_worker_thread
    return await future
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/_backends/_asyncio.py", line 754, in run
    result = context.run(func, *args)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/middleware/wsgi.py", line 132, in wsgi
    self.stream_send.send, {"type": "http.response.body", "body": b""}
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/from_thread.py", line 35, in run
    return asynclib.run_async_from_thread(func, *args)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/_backends/_asyncio.py", line 847, in run_async_from_thread
    return f.result()
  File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/concurrent/futures/_base.py", line 435, in result
    return self.__get_result()
  File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
    raise self._exception
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/streams/memory.py", line 193, in send
    self.send_nowait(item)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/streams/memory.py", line 177, in send_nowait
    raise BrokenResourceError
anyio.BrokenResourceError
```
2022-02-17 09:36:26 +01:00
Marius van den Beek c14eca9649 Merge pull request #13373 from bernt-matthias/fix/macro_parsing
[22.01] Fix macro parsing
2022-02-16 20:11:13 +01:00
Dannon Baker 2914a7161a Merge remote-tracking branch 'upstream/release_21.09' into release_22.01 2022-02-16 13:53:03 -05:00
Dannon Baker f40274f6b9 Merge remote-tracking branch 'upstream/release_21.05' into release_21.09 2022-02-16 13:52:36 -05:00
Dannon Baker 5b629534ed Merge remote-tracking branch 'upstream/release_21.01' into release_21.05 2022-02-16 13:51:59 -05:00
Dannon Baker 3f59f5933a Merge remote-tracking branch 'upstream/release_20.09' into release_21.01 2022-02-16 13:51:28 -05:00
Dannon Baker 9e4463e043 Merge remote-tracking branch 'upstream/release_20.05' into release_20.09 2022-02-16 13:50:51 -05:00
Dannon 10a6b6fc10 Merge pull request #13390 from davelopez/fix_close_popover
[22.01] Fix history search help popover not closing on click outside
2022-02-16 13:45:15 -05:00
Dannon d4384baa45 Merge pull request #13387 from mvdbeek/fix_history_export_include_hidden_handling
[20.05] Fix history export include hidden handling
2022-02-16 13:12:07 -05:00
Nicola Soranzo 9cc9c62890 Merge branch 'release_21.09' into release_22.01 2022-02-16 17:47:08 +00:00
Nicola Soranzo 23f7ff18a8 Merge pull request #13392 from natefoo/gravity-state-dir-2 2022-02-16 17:39:07 +00:00
Nate Coraor 0297eb1bc8 Ensure $GRAVITY_STATE_DIR is present in venv activate script any time
run.sh/common_startup.sh is called normally (without --skip-venv or
--no-create-venv).
2022-02-16 10:09:50 -05:00
Marius van den BeekandNicola Soranzo c58f44314d Make test assertions more precise
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
2022-02-16 16:00:06 +01:00
Marius van den Beek 821ce8570e Merge pull request #13389 from mvdbeek/clarify_that_history_exports_are_not_kep_forever
[22.01] Clarify that history exports are not kept forever
2022-02-16 15:34:26 +01:00
mvdbeek 71571026f8 Fix up macros type annotation
We only create XmlMacroDef later on.
2022-02-16 12:59:10 +01:00
mvdbeek cd94efaba9 Clarify that history archive links are not meant to be forever 2022-02-16 12:49:44 +01:00
davelopez 3139cbc74b Fix history search popover not closing on click outside
This is only a partial fix, since the closing event will not be fired when clicking on the central panel
2022-02-16 12:41:58 +01:00
mvdbeek baed73d311 Fix history_export include_hidden=False handling
Fixes https://github.com/galaxyproject/galaxy/issues/13386
2022-02-16 11:41:47 +01:00
mvdbeek cea780cbf8 Test that include_hidden is handled correctly 2022-02-16 11:41:44 +01:00
Matthias Bernt 8e80077f31 fix typing 2022-02-16 09:38:15 +01:00
Matthias Bernt c092b2f2dc add import for Dict 2022-02-15 23:18:12 +01:00
M BerntandMarius van den Beek f0100dc9ec Update lib/galaxy/util/xml_macros.py
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
2022-02-15 22:56:36 +01:00
John Chilton 06ecddf6f8 Try to unit test more of DictParser in Viz component.
Changed a little during 22.01 release cycle - making sure did not regress.
2022-02-15 12:47:21 -05:00
Marius van den Beek 55f5a36c15 Merge pull request #13343 from bernt-matthias/topic/univa-wo-nativespec
[21.09] Allow UNIVA destinations without runtime and memory max given in the nativespec
2022-02-15 12:33:01 +01:00
Marius van den Beek ed8fce2f89 Merge pull request #13333 from dannon/fix-toolbox-cache
[22.01] Fix toolbox cache
2022-02-15 12:23:39 +01:00
Dannon Baker f7e6061903 Fall back to localStorage when indexeddb is unavailable 2022-02-14 23:20:56 -05:00
Dannon Baker 9ca28b29bb deepmerge breaks vuex stores that shouldn't even be touched here -- back down to vuex-persist 2.3 until we replace all this with pinia and isolated stores 2022-02-14 22:34:54 -05:00
Dannon Baker 02df329f4c More explicit configuration of indexeddb for use in store 2022-02-14 21:05:13 -05:00
Dannon Baker a9f8ca99aa Swap in localForage for toolbox persistence; much larger capacity here
and it's async.
2022-02-14 21:05:13 -05:00
Dannon Baker 9da5ef6c93 Drop debugging 2022-02-14 21:05:13 -05:00