mirror of
https://github.com/galaxyproject/galaxy.git
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mvdbeek
61dab21990
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
```
124 lines
2.8 KiB
TOML
124 lines
2.8 KiB
TOML
[tool.poetry]
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name = "galaxy"
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version = "22.01.dev0"
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description = "Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational research."
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authors = ["Galaxy Contributors"]
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license = "AFL-3.0"
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readme = "README.rst"
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homepage = "https://galaxyproject.org/"
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repository = "https://github.com/galaxyproject/galaxy/"
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documentation = "https://docs.galaxyproject.org/"
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[[tool.poetry.source]]
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name = "galaxyproject"
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url = "https://wheels.galaxyproject.org/simple"
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[tool.poetry.dependencies]
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a2wsgi = "*"
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aiofiles = "*"
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Babel = "*"
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bdbag = "*"
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Beaker = "1.11.0"
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bioblend = "*"
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bleach = "*"
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boltons = "*"
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boto = "*"
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bx-python = "*"
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celery = "*"
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Cheetah3 = "!=3.2.6.post2" # yanked release, https://github.com/python-poetry/poetry/issues/2453
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cloudauthz = "==0.6.0"
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cloudbridge = "*"
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circus = "*"
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cwltool = "==3.1.20211107152837"
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dictobj = "*"
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docutils = "!=0.17, !=0.17.1"
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edam-ontology = "*"
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Fabric3 = "*"
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fastapi = ">=0.68.2, !=0.69.0, !=0.70.0, !=0.70.1" # https://github.com/tiangolo/fastapi/issues/4041
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fastapi-utils = "*"
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fs = "*"
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future = "*"
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galaxy_sequence_utils = "*"
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gravity = {git = "https://github.com/galaxyproject/gravity.git", branch = "main"}
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gunicorn = "*"
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gxformat2 = "*"
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h5py = "*"
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importlib_resources = "*"
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isa-rwval = "*"
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kombu = "*"
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lagom = "*"
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Mako = "*"
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Markdown = "*"
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MarkupSafe = "*"
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Mercurial = "*"
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mrcfile = "*"
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nodeenv = "*"
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nose = "*"
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numpy = "*"
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paramiko = "!=2.9.0, !=2.9.1" # https://github.com/paramiko/paramiko/issues/1961
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Parsley = "*"
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Paste = "*"
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psutil = "*"
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pulsar-galaxy-lib = ">=0.14.13"
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pycryptodome = "*"
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pydantic = "*"
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pykwalify = "*"
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pyparsing = "*"
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pysam = "*"
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python = ">=3.7,<4"
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python-multipart = "*" # required to support form parsing in FastAPI/Starlette
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pyuwsgi = "*"
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PyYAML = "*"
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refgenconf = ">=0.12.0"
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requests = "*"
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Routes = "*"
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social-auth-core = {version = "==4.0.3", extras = ["openidconnect"]}
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sortedcontainers = "*"
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SQLAlchemy = ">=1.4.25,<2"
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sqlalchemy-migrate = "*"
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sqlitedict = "*"
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sqlparse = "*"
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starlette = "*"
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starlette-context = "*"
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svgwrite = "*"
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tifffile = "*"
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tuswsgi = "*"
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typing-extensions = "*"
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uvicorn = "*"
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uvloop = "*"
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WebOb = "*"
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Whoosh = "*"
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zipstream-new = "*"
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[tool.poetry.dev-dependencies]
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cwltest = "2.2.20210901154959"
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darker = "*"
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fluent-logger = "*"
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httpx = "*"
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lxml = "!=4.2.2"
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markdown-it-reporter = "*"
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NoseHTML = "*"
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PyGithub = "*"
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pytest = "*"
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pytest-asyncio = "*"
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pytest-celery = "*"
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pytest-cov = "*"
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pytest-html = "*"
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python-irodsclient = "*"
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pytest-json-report = "*"
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pytest-mock = "*"
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pytest-pythonpath = "*"
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pytest-postgresql = "!=3.0.0" # https://github.com/ClearcodeHQ/pytest-postgresql/issues/426
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pytest-shard = "*"
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recommonmark = "*"
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responses = "*"
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selenium = "*"
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Sphinx = ">=4.0" # support docutils 0.17
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sphinx_markdown_tables = "*"
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sphinx_rtd_theme = "*"
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statsd = "*"
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testfixtures = "*"
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tuspy = "*"
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twill = "*"
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watchdog = "*"
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