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Always install `fastmcp`
in preparation for pydantic-ai 2.0.0, which replaced the
dependency on `fastmcp` with `fastmcp-slim[client]`.
Otherwise Galaxy fails to start with:
```
Traceback (most recent call last):
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/fastmcp/server/__init__.py", line 6, in <module>
from .context import Context
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/fastmcp/server/context.py", line 28, in <module>
from uncalled_for import SharedContext
ModuleNotFoundError: No module named 'uncalled_for'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/fastmcp/__init__.py", line 57, in __getattr__
from fastmcp.server.context import Context
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/fastmcp/server/__init__.py", line 9, in <module>
raise ImportError(_install_hints.SERVER_SUPPORT) from exc
ImportError: FastMCP server support is not installed. Install `fastmcp` or `fastmcp-slim[server]`.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/bin/gunicorn", line 10, in <module>
sys.exit(run())
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/gunicorn/app/wsgiapp.py", line 66, in run
WSGIApplication("%(prog)s [OPTIONS] [APP_MODULE]", prog=prog).run()
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/gunicorn/app/base.py", line 235, in run
super().run()
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/gunicorn/app/base.py", line 71, in run
Arbiter(self).run()
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/gunicorn/arbiter.py", line 63, in __init__
self.setup(app)
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/gunicorn/arbiter.py", line 139, in setup
self.app.wsgi()
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/gunicorn/app/base.py", line 66, in wsgi
self.callable = self.load()
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/gunicorn/app/wsgiapp.py", line 57, in load
return self.load_wsgiapp()
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/gunicorn/app/wsgiapp.py", line 47, in load_wsgiapp
return util.import_app(self.app_uri)
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/gunicorn/util.py", line 464, in import_app
app = app(*args, **kwargs)
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/webapps/galaxy/fast_factory.py", line 63, in factory
gx_wsgi_webapp, gx_app = app_pair(
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 178, in app_pair
populate_api_routes(webapp, app)
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 362, in populate_api_routes
webapp.add_api_controllers("galaxy.webapps.galaxy.api", app)
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/webapps/base/webapp.py", line 252, in add_api_controllers
for name, module in base.walk_controller_modules(package_name):
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/web/framework/base.py", line 624, in walk_controller_modules
module = import_module(module_name)
File "/usr/lib/python3.10/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1050, in _gcd_import
File "<frozen importlib._bootstrap>", line 1027, in _find_and_load
File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 688, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 883, in exec_module
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/webapps/galaxy/api/mcp.py", line 15, in <module>
from fastmcp import (
File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/fastmcp/__init__.py", line 59, in __getattr__
raise ImportError(_install_hints.SERVER_SUPPORT) from exc
ImportError: FastMCP server support is not installed. Install `fastmcp` or `fastmcp-slim[server]`.
```
This commit is contained in:
Nicola Soranzo
@@ -318,9 +318,6 @@ class ConditionalDependencies:
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self.config.get("ai_api_key", None) is not None or self.config.get("inference_services", None) is not None
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)
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def check_fastmcp(self):
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return asbool(self.config.get("enable_mcp_server", False))
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def check_weasyprint(self):
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# See notes in ./conditional-requirements.txt for more information.
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return os.environ.get("GALAXY_DEPENDENCIES_INSTALL_WEASYPRINT") == "1"
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@@ -16,7 +16,6 @@ galaxycloudrunner
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pkce
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total-perspective-vortex>=3.2.1,<4
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openai
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fastmcp>=2.13.0
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# upper version constraint because of https://github.com/galaxyproject/galaxy/issues/20600
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redis>=5.3.0,<6
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@@ -36,6 +36,7 @@ from galaxy.webapps.base.webapp import (
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_is_embed_request,
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config_allows_origin,
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)
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from galaxy.webapps.galaxy.api.mcp import get_mcp_app
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from galaxy.webapps.openapi._compat.v2 import GenerateJsonSchema
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from galaxy.webapps.openapi.utils import get_openapi
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@@ -267,13 +268,8 @@ def get_mcp_lifespan(gx_app):
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return None, None
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try:
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from galaxy.webapps.galaxy.api.mcp import get_mcp_app
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mcp_app = get_mcp_app(gx_app)
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return mcp_app, mcp_app.lifespan
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except ImportError:
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log.info("MCP server dependencies not installed (fastmcp), skipping")
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return None, None
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except Exception:
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log.exception("Failed to initialize MCP server")
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return None, None
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@@ -28,6 +28,7 @@ dependencies = [
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"Babel",
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"CT3>=3.3.3",
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"fastapi>=0.133.0",
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"fastmcp>=2.13.0",
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"gunicorn!=25.1.0",
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"httpx",
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"gxformat2>=0.27.0",
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@@ -38,6 +38,7 @@ dependencies = [
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"dparse",
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"edam-ontology",
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"fastapi>=0.133.0", # First version compatible with starlette>=1.0.0
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"fastmcp>=2.13.0",
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"fissix",
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"fs",
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"future>=1.0.0", # Python 3.12 support
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