[25.0] Run landing request state through validator

[mvdbeek]

Should resolve the inconsistency in #21084

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

[ahmedhamidawan]

Trying to test this locally, and this seems to produce an error for me:

INFO:     127.0.0.1:60184 - "POST /api/workflow_landings HTTP/1.1" 500 Internal Server Error
ERROR:    Exception in ASGI application
Traceback (most recent call last):
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/engine/base.py", line 1815, in _execute_context
    context = constructor(
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/engine/default.py", line 1525, in _init_compiled
    d_param = {
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/engine/default.py", line 1527, in <dictcomp>
    flattened_processors[key](compiled_params[key])
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/sql/type_api.py", line 2103, in process
    fixed_process_param(value, dialect)
  File "/home/ahmedhamidawan/repos/galaxy2/lib/galaxy/model/custom_types.py", line 98, in process_bind_param
    value = json_encoder.encode(value).encode()
  File "/usr/lib/python3.10/json/encoder.py", line 199, in encode
    chunks = self.iterencode(o, _one_shot=True)
  File "/usr/lib/python3.10/json/encoder.py", line 257, in iterencode
    return _iterencode(o, 0)
  File "/home/ahmedhamidawan/repos/galaxy2/lib/galaxy/model/custom_types.py", line 40, in default
    return json.JSONEncoder.default(self, obj)
  File "/usr/lib/python3.10/json/encoder.py", line 179, in default
    raise TypeError(f'Object of type {o.__class__.__name__} '
TypeError: Object of type FileRequestUri is not JSON serializable

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/uvicorn/protocols/http/h11_impl.py", line 403, in run_asgi
    result = await app(  # type: ignore[func-returns-value]
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/uvicorn/middleware/proxy_headers.py", line 60, in __call__
    return await self.app(scope, receive, send)
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/fastapi/applications.py", line 1082, in __call__
    await super().__call__(scope, receive, send)
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/starlette/applications.py", line 113, in __call__
    await self.middleware_stack(scope, receive, send)
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/starlette/middleware/errors.py", line 186, in __call__
    raise exc
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/starlette/middleware/errors.py", line 164, in __call__
    await self.app(scope, receive, _send)
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/starlette_context/middleware/raw_middleware.py", line 94, in __call__
    await self.app(scope, receive, send_wrapper)
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/starlette/middleware/base.py", line 182, in __call__
    with recv_stream, send_stream, collapse_excgroups():
  File "/usr/lib/python3.10/contextlib.py", line 153, in __exit__
    self.gen.throw(typ, value, traceback)
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/starlette/_utils.py", line 85, in collapse_excgroups
    raise exc
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/starlette/middleware/base.py", line 184, in __call__
    response = await self.dispatch_func(request, call_next)
  File "/home/ahmedhamidawan/repos/galaxy2/lib/galaxy/webapps/galaxy/fast_app.py", line 108, in add_x_frame_options
    response = await call_next(request)
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/starlette/middleware/base.py", line 159, in call_next
    raise app_exc
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/starlette/middleware/base.py", line 144, in coro
    await self.app(scope, receive_or_disconnect, send_no_error)
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/starlette/middleware/exceptions.py", line 63, in __call__
    await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send)
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
    raise exc
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/starlette/_exception_handler.py", line 42, in wrapped_app
    await app(scope, receive, sender)
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/starlette/routing.py", line 716, in __call__
    await self.middleware_stack(scope, receive, send)
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/starlette/routing.py", line 736, in app
    await route.handle(scope, receive, send)
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/starlette/routing.py", line 290, in handle
    await self.app(scope, receive, send)
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/starlette/routing.py", line 78, in app
    await wrap_app_handling_exceptions(app, request)(scope, receive, send)
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
    raise exc
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/starlette/_exception_handler.py", line 42, in wrapped_app
    await app(scope, receive, sender)
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/starlette/routing.py", line 75, in app
    response = await f(request)
  File "/home/ahmedhamidawan/repos/galaxy2/lib/galaxy/webapps/galaxy/api/__init__.py", line 553, in custom_route_handler
    response: Response = await original_route_handler(request)
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/fastapi/routing.py", line 308, in app
    raw_response = await run_endpoint_function(
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/fastapi/routing.py", line 221, in run_endpoint_function
    return await run_in_threadpool(dependant.call, **values)
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/starlette/concurrency.py", line 38, in run_in_threadpool
    return await anyio.to_thread.run_sync(func)
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/anyio/to_thread.py", line 56, in run_sync
    return await get_async_backend().run_sync_in_worker_thread(
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/anyio/_backends/_asyncio.py", line 2485, in run_sync_in_worker_thread
    return await future
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/anyio/_backends/_asyncio.py", line 976, in run
    result = context.run(func, *args)
  File "/home/ahmedhamidawan/repos/galaxy2/lib/galaxy/webapps/galaxy/api/workflows.py", line 1171, in create_landing
    return self.landing_manager.create_workflow_landing_request(workflow_landing_request)
  File "/home/ahmedhamidawan/repos/galaxy2/lib/galaxy/managers/landing.py", line 79, in create_workflow_landing_request
    self._save(model)
  File "/home/ahmedhamidawan/repos/galaxy2/lib/galaxy/managers/landing.py", line 213, in _save
    sa_session.commit()
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/orm/scoping.py", line 599, in commit
    return self._proxied.commit()
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/orm/session.py", line 2032, in commit
    trans.commit(_to_root=True)
  File "<string>", line 2, in commit
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/orm/state_changes.py", line 137, in _go
    ret_value = fn(self, *arg, **kw)
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/orm/session.py", line 1313, in commit
    self._prepare_impl()
  File "<string>", line 2, in _prepare_impl
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/orm/state_changes.py", line 137, in _go
    ret_value = fn(self, *arg, **kw)
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/orm/session.py", line 1288, in _prepare_impl
    self.session.flush()
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/orm/session.py", line 4345, in flush
    self._flush(objects)
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/orm/session.py", line 4480, in _flush
    with util.safe_reraise():
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/util/langhelpers.py", line 224, in __exit__
    raise exc_value.with_traceback(exc_tb)
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/orm/session.py", line 4441, in _flush
    flush_context.execute()
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/orm/unitofwork.py", line 466, in execute
    rec.execute(self)
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/orm/unitofwork.py", line 642, in execute
    util.preloaded.orm_persistence.save_obj(
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/orm/persistence.py", line 93, in save_obj
    _emit_insert_statements(
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/orm/persistence.py", line 1233, in _emit_insert_statements
    result = connection.execute(
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/engine/base.py", line 1419, in execute
    return meth(
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/sql/elements.py", line 526, in _execute_on_connection
    return connection._execute_clauseelement(
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/engine/base.py", line 1641, in _execute_clauseelement
    ret = self._execute_context(
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/engine/base.py", line 1821, in _execute_context
    self._handle_dbapi_exception(
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/engine/base.py", line 2355, in _handle_dbapi_exception
    raise sqlalchemy_exception.with_traceback(exc_info[2]) from e
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/engine/base.py", line 1815, in _execute_context
    context = constructor(
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/engine/default.py", line 1525, in _init_compiled
    d_param = {
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/engine/default.py", line 1527, in <dictcomp>
    flattened_processors[key](compiled_params[key])
  File "/home/ahmedhamidawan/repos/galaxy2/.venv/lib/python3.10/site-packages/sqlalchemy/sql/type_api.py", line 2103, in process
    fixed_process_param(value, dialect)
  File "/home/ahmedhamidawan/repos/galaxy2/lib/galaxy/model/custom_types.py", line 98, in process_bind_param
    value = json_encoder.encode(value).encode()
  File "/usr/lib/python3.10/json/encoder.py", line 199, in encode
    chunks = self.iterencode(o, _one_shot=True)
  File "/usr/lib/python3.10/json/encoder.py", line 257, in iterencode
    return _iterencode(o, 0)
  File "/home/ahmedhamidawan/repos/galaxy2/lib/galaxy/model/custom_types.py", line 40, in default
    return json.JSONEncoder.default(self, obj)
  File "/usr/lib/python3.10/json/encoder.py", line 179, in default
    raise TypeError(f'Object of type {o.__class__.__name__} '
sqlalchemy.exc.StatementError: (builtins.TypeError) Object of type FileRequestUri is not JSON serializable
[SQL: INSERT INTO workflow_landing_request (user_id, workflow_id, stored_workflow_id, create_time, update_time, uuid, request_state, client_secret, workflow_source, workflow_source_type, public) VALUES (%(user_id)s, %(workflow_id)s, %(stored_workflow_id)s, %(create_time)s, %(update_time)s, %(uuid)s, %(request_state)s, %(client_secret)s, %(workflow_source)s, %(workflow_source_type)s, %(public)s) RETURNING workflow_landing_request.id]
[parameters: [{'stored_workflow_id': 497, 'public': False, 'request_state': {'The Input Dataset': FileRequestUri(url='https://raw.githubusercontent.com/galaxyprojec ... (220 characters truncated) ... 19b-62f8-4d9d-a280-b12ffff0628b'), 'client_secret': None, 'user_id': None, 'workflow_source_type': None, 'workflow_source': None, 'workflow_id': None}]]

This happens for any request_state i try, but i was specifically trying something like:

simple_workflow:
  # Encoded ID for a workflow to target - if workflow_target_type is stored_workflow this
  # will always be the latest version of that workflow and stored workflow ID should be provided.
  # If instead workflow_target_type is workflow - this is a particular version of a workflow and
  # the workflow ID should be provided.
  workflow_id: e96c6ce43a3d239a
  workflow_target_type: stored_workflow
  # request state provides prepopulated parameters for this workflow or stored workflow when the
  # user navigates to the landing URL.
  request_state:
    The Input Dataset:
      class: File
      location: https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/1.bed
      ext: txt
simple_workflow_1:
  # Encoded ID for a workflow to target - if workflow_target_type is stored_workflow this
  # will always be the latest version of that workflow and stored workflow ID should be provided.
  # If instead workflow_target_type is workflow - this is a particular version of a workflow and
  # the workflow ID should be provided.
  workflow_id: e96c6ce43a3d239a
  workflow_target_type: stored_workflow
  # request state provides prepopulated parameters for this workflow or stored workflow when the
  # user navigates to the landing URL.
  request_state:
    The Input Dataset:
      class: File
      location: https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/1.bed
      filetype: txt

Both fail.

I also confirmed that specifically removing your change here was fixing it, and a landing was being generated

[ahmedhamidawan]

However, though this does produce a nice detailed response, the new keys will still not match what the client expects in client/src/components/Form/Elements/FormData/types.ts

The request state I tried here was:

request_state:
    The Input Dataset:
      class: File
      location: https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/1.bed
      filetype: txt

Before	After

Though yes, we are nicely ensuring it is always ext and not filetype, however, notice how Class has become Class_, and location has become url.

[mvdbeek]

That should be fixed by persisting via by_alias=True. I've added a test case that makes sure url is turned into location, but if you can run a sanity check that'd be appreciated.

[ahmedhamidawan]

Thank you! I will test this out again locally and let you know!

[ahmedhamidawan]

Bingo!

Works perfectly, tried all sorts of structures/keys!