Fix the following error in unit tests:
```
AttributeError: 'TestToolShedConfig' object has no attribute 'hgweb_repo_prefix'
```
caused by merging commit b00beec3d2
forward.
Fixes https://github.com/galaxyproject/galaxy/issues/17959:
```
NotNullViolation: null value in column "workflow_step_id" of relation "workflow_output" violates not-null constraint
DETAIL: Failing row contains (3843428, null, multiqc_fastqc_html, multiqc_fastqc_html, 1d8a0c348b6f446eb4d84770365f570f).
File "sqlalchemy/engine/base.py", line 1890, in _execute_context
self.dialect.do_executemany(
File "sqlalchemy/dialects/postgresql/psycopg2.py", line 982, in do_executemany
context._psycopg2_fetched_rows = xtras.execute_values(
File "psycopg2/extras.py", line 1299, in execute_values
cur.execute(b''.join(parts))
IntegrityError: (psycopg2.errors.NotNullViolation) null value in column "workflow_step_id" of relation "workflow_output" violates not-null constraint
DETAIL: Failing row contains (3843428, null, multiqc_fastqc_html, multiqc_fastqc_html, 1d8a0c348b6f446eb4d84770365f570f).
[SQL: INSERT INTO workflow_output (workflow_step_id, output_name, label, uuid) VALUES (%(workflow_step_id)s, %(output_name)s, %(label)s, %(uuid)s) RETURNING workflow_output.id]
[parameters: ({'workflow_step_id': None, 'output_name': 'multiqc_fastqc_html', 'label': 'multiqc_fastqc_html', 'uuid': '1d8a0c348b6f446eb4d84770365f570f'}, {'workflow_step_id': None, 'output_name': 'multiqc_cutadapt_html', 'label': 'multiqc_cutadapt_html', 'uuid': '11fef12f5cf24904b31dac7a277f5fda'}, {'workflow_step_id': None, 'output_name': 'multiqc_star_html', 'label': 'multiqc_star_html', 'uuid': '383da02d5a4b4af7ac2933b9cfad316f'}, {'workflow_step_id': None, 'output_name': 'STAR_BAM', 'label': 'STAR_BAM', 'uuid': '6aed76c8a4a5491bacd2f995f16df86b'}, {'workflow_step_id': None,...
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 108, 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/workflows.py", line 987, in refactor
return self.service.refactor(trans, workflow_id, payload, instance or False)
File "galaxy/webapps/galaxy/services/workflows.py", line 218, in refactor
return self._workflow_contents_manager.refactor(trans, stored_workflow, payload)
File "galaxy/managers/workflows.py", line 1963, in refactor
refactored_workflow, action_executions = self.do_refactor(trans, stored_workflow, refactor_request)
File "galaxy/managers/workflows.py", line 1948, in do_refactor
refactored_workflow, errors = self.update_workflow_from_raw_description(
File "galaxy/managers/workflows.py", line 728, in update_workflow_from_raw_description
trans.tag_handler.set_tags_from_list(
File "galaxy/model/tags.py", line 94, in set_tags_from_list
self.apply_item_tags(user, item, unicodify(new_tags_str, "utf-8"), flush=flush)
File "galaxy/model/tags.py", line 265, in apply_item_tags
self.apply_item_tag(user, item, name, value, flush=flush)
File "galaxy/model/tags.py", line 249, in apply_item_tag
self.sa_session.commit()
File "<string>", line 2, in commit
File "sqlalchemy/orm/session.py", line 1454, in commit
self._transaction.commit(_to_root=self.future)
File "sqlalchemy/orm/session.py", line 832, in commit
self._prepare_impl()
File "sqlalchemy/orm/session.py", line 811, in _prepare_impl
self.session.flush()
File "sqlalchemy/orm/session.py", line 3449, in flush
self._flush(objects)
File "sqlalchemy/orm/session.py", line 3588, in _flush
with util.safe_reraise():
File "sqlalchemy/util/langhelpers.py", line 70, in __exit__
compat.raise_(
File "sqlalchemy/util/compat.py", line 211, in raise_
raise exception
File "sqlalchemy/orm/session.py", line 3549, in _flush
flush_context.execute()
File "sqlalchemy/orm/unitofwork.py", line 456, in execute
rec.execute(self)
File "sqlalchemy/orm/unitofwork.py", line 630, in execute
util.preloaded.orm_persistence.save_obj(
File "sqlalchemy/orm/persistence.py", line 245, in save_obj
_emit_insert_statements(
File "sqlalchemy/orm/persistence.py", line 1156, in _emit_insert_statements
c = connection._execute_20(
File "sqlalchemy/engine/base.py", line 1710, in _execute_20
return meth(self, args_10style, kwargs_10style, execution_options)
File "sqlalchemy/sql/elements.py", line 334, in _execute_on_connection
return connection._execute_clauseelement(
File "sqlalchemy/engine/base.py", line 1577, in _execute_clauseelement
ret = self._execute_context(
File "sqlalchemy/engine/base.py", line 1953, in _execute_context
self._handle_dbapi_exception(
File "sqlalchemy/engine/base.py", line 2134, in _handle_dbapi_exception
util.raise_(
File "sqlalchemy/util/compat.py", line 211, in raise_
raise exception
File "sqlalchemy/engine/base.py", line 1890, in _execute_context
self.dialect.do_executemany(
File "sqlalchemy/dialects/postgresql/psycopg2.py", line 982, in do_executemany
context._psycopg2_fetched_rows = xtras.execute_values(
File "psycopg2/extras.py", line 1299, in execute_values
cur.execute(b''.join(parts))
```
broken in https://github.com/galaxyproject/galaxy/commit/b00a94c1f7972dcd1060069fe83fece7b8943165
This test fails because cut fails on the compressed input with
`cut: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpu8gqd71c/tmpmae9egoz/tmpz8sonmgx/database/objects/6/9/8/dataset_69847aef-7b3f-4915-a8ae-394921dbe388.dat: Illegal byte sequence`
with the ``CONVERTER_gz_to_uncompressed`` tool.
Previously, if a user forced an incorrect datatype to a compressed input
dataset (e.g. `fastqsanger` instead of `fastqsanger.gz`), then the output
datatype assigned by this tool would be an invalid one (`fastqsan`).
Fix#17938.
John Davis