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https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
mvdbeek
ec576b8eac
This fixes handling of `ToolInputsNotOK` exceptions, which would fail
with
```
Message
Uncaught exception in exposed API method:
Stack Trace
Newest
TypeError: Object of type ToolInputsNotOKException is not JSON serializable
File "galaxy/util/json.py", line 74, in safe_dumps
dumped = json.dumps(obj, allow_nan=False, **kwargs)
File "__init__.py", line 238, in dumps
**kw).encode(obj)
File "json/encoder.py", line 200, in encode
chunks = self.iterencode(o, _one_shot=True)
File "json/encoder.py", line 258, in iterencode
return _iterencode(o, 0)
File "json/encoder.py", line 180, in default
raise TypeError(f'Object of type {o.__class__.__name__} '
TypeError: Object of type ToolInputsNotOKException is not JSON serializable
File "galaxy/web/framework/decorators.py", line 350, in decorator
rval = format_return_as_json(rval, jsonp_callback, pretty=trans.debug)
File "galaxy/web/framework/decorators.py", line 387, in format_return_as_json
json = safe_dumps(rval, **dumps_kwargs)
File "galaxy/util/json.py", line 77, in safe_dumps
dumped = json.dumps(obj, allow_nan=False, **kwargs)
File "__init__.py", line 238, in dumps
**kw).encode(obj)
File "json/encoder.py", line 200, in encode
chunks = self.iterencode(o, _one_shot=True)
File "json/encoder.py", line 258, in iterencode
return _iterencode(o, 0)
File "json/encoder.py", line 180, in default
raise TypeError(f'Object of type {o.__class__.__name__} '
```
This also required making the tool form error modal dependent on the
returned errors, instead of only popping up on non-200 status codes
or if all jobs failed.
Fixes https://github.com/galaxyproject/galaxy/issues/19482
57 lines
2.3 KiB
Python
57 lines
2.3 KiB
Python
from sqlalchemy import select
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from galaxy.model import HistoryDatasetAssociation
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from galaxy_test.base.populators import (
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DatasetCollectionPopulator,
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DatasetPopulator,
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)
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from galaxy_test.driver import integration_util
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class TestFailJobWhenToolUnavailable(integration_util.IntegrationTestCase):
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dataset_populator: DatasetPopulator
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dataset_collection_populator: DatasetCollectionPopulator
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require_admin_user = True
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def setUp(self):
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super().setUp()
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self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
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self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)
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@property
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def sa_session(self):
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return self._app.model.session
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def test_partial_job_success_error_handling(self):
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with self.dataset_populator.test_history() as history_id:
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create_response = self.dataset_collection_populator.create_list_in_history(
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history_id, contents=["xxx\n", "yyy\n"], wait=True
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).json()
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hdca_id = create_response["output_collections"][0]["id"]
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first_hda_id = self.dataset_populator.get_history_collection_details(history_id, content_id=hdca_id)[
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"elements"
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][0]["object"]["id"]
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database_id = self._get(f"configuration/decode/{first_hda_id}").json()["decoded_id"]
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hda = self.sa_session.scalar(
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select(HistoryDatasetAssociation).where(HistoryDatasetAssociation.id == database_id)
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)
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assert hda
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hda.state = HistoryDatasetAssociation.states.FAILED_METADATA
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self.sa_session.add(hda)
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self.sa_session.commit()
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response = self.dataset_populator.run_tool_raw(
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tool_id="__FILTER_NULL__",
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inputs={"input": {"src": "hdca", "id": hdca_id}},
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history_id=history_id,
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).json()
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assert response["errors"] == [
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{
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"err_code": 0,
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"err_msg": "Tool requires inputs to be in valid state, but "
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"dataset with hid 2 is in state 'failed_metadata'",
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"id": "eb142648ac45b77086610f67617bec2ad3808fd4409d175f",
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"input_name": "input1",
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"src": "hda",
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}
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]
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