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)
```
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
```
so far imported macro element were inserted into the macros element
of the tool xml .. just to be removed again in the end (except for
template macros)
so it seems cleaner (and maybe a bit faster) to store the macros
in lists (kept in a dict separating xml, token, and template macros)
if no nativespec is given for a univa destination the runner
does not know how much run time / memory was given to a job
which led to a comparison with `None`.
Now we default to infinite runtime and memory.
This fixes
```
ERROR galaxy.tools.actions:__init__.py:683 Cannot remap rerun dependencies.
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/actions/__init__.py", line 664, in _remap_job_on_rerun
self.__remap_parameters(job_to_remap, jtid, jtod, out_data)
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/actions/__init__.py", line 694, in __remap_parameters
input_values = {p.name: json.loads(p.value) for p in job_to_remap.parameters}
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/actions/__init__.py", line 694, in <dictcomp>
input_values = {p.name: json.loads(p.value) for p in job_to_remap.parameters}
File "/usr/local/Cellar/python@3.9/3.9.10/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py", line 339, in loads
raise TypeError(f'the JSON object must be str, bytes or bytearray, '
TypeError: the JSON object must be str, bytes or bytearray, not
NoneType
```
Optional data inputs or optional selects are stored as `None` (super
inconsistent, since most other parameters are stored as JOSN. We should
create "basic_2.py" using pydantic at one point not too far into the
future ...). This means we can't call `json.loads` on these. Fortunately
this is the only place we do it, and we don't need to consider optional
parameters here anyway.
mvdbeek