From badfc2433fe2a5c532760cddb92ff1ea0608fa23 Mon Sep 17 00:00:00 2001 From: Rajeev Jain Date: Fri, 23 Oct 2026 14:13:39 -0500 Subject: [PATCH 1/3] Take toolregistry 0.19 and toolregistry-server 0.7 Both released today. 0.19 carries the union fix we have been waiting on (Oaklight/ToolRegistry#269, our #165), and the pair changes three things that reach clients. The union fix is real: a heterogeneous union now renders as `anyOf` instead of silently dropping branches. The floor moves to 0.19.0 so an older registry cannot be resolved, because the schema repair that used to cover for it is no longer shaped the same way. What we serve for `lat_spec` still is not upstream's rendering, though. The annotation is `tuple | float | list[Any] | None`, and `tuple` and `list` both render as `array`, so 0.19 emits the array branch twice with untyped items: anyOf: [ {array, items:{}}, {number}, {array, items:{}} ] A duplicated branch is noise in a payload we measure, and untyped items say less than we know. `_type_untyped_unions` now replaces that rendering rather than only filling an absence, and serves the canonical form: anyOf: [ {number}, {array, items:{number}} ] The core tool specification goes 36271 -> 36143 bytes as a result, so no budget moves. Two behaviour changes in toolregistry-server 0.7: - An unknown tool name is now a JSON-RPC -32602 rather than a `CallToolResult` with `isError`. That is the correct reading -- `isError` is for a tool that ran and failed, and an unknown name means nothing ran -- so the test asserts the new contract instead of pinning the old one. - 0.7 infers annotations of its own, and marked `manage_session` and `resume_workflow` `readOnlyHint=True`. Neither is read-only: `manage_session` resets session state and clears artifacts, `resume_workflow` runs pending steps. Nine tools we had deliberately left unrated came back carrying hints, and a client reading `readOnlyHint` may auto-approve on the strength of it. Our shim deferred to any annotation already present, which handed the decision to whoever guessed first. It now asserts our rating where we have one and clears the field where we have not. Absence is the honest answer for a tool nobody rated; an inferred hint is a claim no one checked, and a wrong safe-to-run claim is the one failure direction that costs a user something. `TestUpstreamInferenceDoesNotOverruleUs` pins both halves, and names `manage_session` and `resume_workflow` specifically so a future release making the same guess fails here rather than in a client. 1540 passed, 1 skipped, 44 deselected, 1 xfailed. Does not close #165: the checklist there also asks to drop the workaround entirely, and the duplicate-branch rendering above means it still earns its place. Updated there with what 0.19 did and did not fix. --- pyproject.toml | 15 ++++++---- src/uxarray_mcp/annotations.py | 18 ++++++++++-- src/uxarray_mcp/registry.py | 42 ++++++++++++++++++++-------- tests/test_mcp_protocol.py | 16 +++++++++-- tests/test_tool_annotations.py | 51 ++++++++++++++++++++++++++++++++++ uv.lock | 18 ++++++------ 6 files changed, 130 insertions(+), 30 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index d652d83..4e2d667 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -39,15 +39,20 @@ license = { file = "LICENSE" } # declare >=3.10, so 3.11 is a conservative floor. requires-python = ">=3.11" dependencies = [ - # 0.6.0 is the floor: its v2 tools/list handler reads the calling session - # off the request context, and it pairs with toolregistry 0.17+ below. - "toolregistry-server[mcp]>=0.6.0", + # 0.7.0 is the floor: it pairs with toolregistry 0.19 below, whose + # schema change alters what every served tool advertises. + "toolregistry-server[mcp]>=0.7.0", # Imported directly (ToolRegistry, ToolTag), so it is declared directly # rather than leaned on transitively. 0.16.0 taught is_content_block_list # about audio/resource_link/resource; 0.17 froze ToolMetadata, so the # policy-tag merge has to mutate the tag sets in place rather than # rebind them, and 0.18 registers call_deferred beside discover_tools. - "toolregistry>=0.18.0", + # 0.19 is the floor because it emits `anyOf` for a heterogeneous union + # instead of dropping branches (Oaklight/ToolRegistry#269). Below it, + # `lat_spec` reached clients as an untyped blob and we repaired the + # schema on the way out; that repair is gone, so an older registry + # would silently under-advertise the parameter. See #165. + "toolregistry>=0.19.0", # Both SDK generations are in range and register handlers differently: # 1.27.2 has the per-method decorators and no `add_request_handler`, 2.1.1 # has `add_request_handler` and no decorators. `resources.py` registers @@ -76,7 +81,7 @@ dependencies = [ [project.optional-dependencies] openapi = [ - "toolregistry-server[openapi]>=0.6.0", + "toolregistry-server[openapi]>=0.7.0", ] hpc = [ "academy-py>=0.3.1", diff --git a/src/uxarray_mcp/annotations.py b/src/uxarray_mcp/annotations.py index 0cd50c3..22b4ad2 100644 --- a/src/uxarray_mcp/annotations.py +++ b/src/uxarray_mcp/annotations.py @@ -186,11 +186,25 @@ async def on_list_tools(*args: Any, **kwargs: Any) -> Any: # nothing on the floor and silently annotated no tool at all. payload = getattr(result, "root", result) for tool in getattr(payload, "tools", []): - if getattr(tool, "annotations", None) is not None: - continue hints = annotations_for(tool.name) if hints: + # Ours wins. toolregistry-server 0.7.0 began inferring + # annotations of its own, and deferring to what was already + # there would let an inference overrule a rating we made + # deliberately. tool.annotations = ToolAnnotations(**hints) + elif getattr(tool, "annotations", None) is not None: + # Unclassified here, annotated by upstream. 0.7.0 marks + # `manage_session` and `resume_workflow` readOnlyHint=True; + # the first can reset state and clear artifacts, the second + # runs pending workflow steps. Neither is read-only, and a + # client reading that hint may auto-approve them. + # + # Absence is the honest answer for anything we have not + # rated: an inferred hint is a claim nobody checked, and a + # wrong safe-to-run claim is the one failure direction that + # costs a user something. + tool.annotations = None return result if hasattr(entry, "handler"): diff --git a/src/uxarray_mcp/registry.py b/src/uxarray_mcp/registry.py index 727b9ae..b838ff2 100644 --- a/src/uxarray_mcp/registry.py +++ b/src/uxarray_mcp/registry.py @@ -673,15 +673,27 @@ def _trim_wire_schema(tool: Any) -> None: _type_untyped_unions(params) -#: JSON Schema for parameters whose Python annotation toolregistry cannot -#: express. ``tuple | float | list[Any] | None`` comes out as ``{"default": -#: null}`` -- no ``type`` at all -- and ``float | list[float] | None`` as -#: ``{"type": "number"}``, which drops the list. A client reading the first -#: has nothing to go on and sends the literal text ``"[-60, 60]"``, which -#: the server's own validator then refuses as neither number nor list. The -#: parameter was unusable from every MCP client, while direct Python calls +#: JSON Schema for parameters whose Python annotation toolregistry renders +#: badly. +#: +#: Originally this filled in a union that arrived with no ``type`` at all: +#: ``tuple | float | list[Any] | None`` came out as ``{"default": null}``, +#: so a client had nothing to follow and sent the literal text +#: ``"[-60, 60]"``, which the server's own validator then refused. The +#: parameter was unusable from every MCP client while direct Python calls #: and every test passed. Found on the first remote zonal mean through a #: real client. +#: +#: toolregistry 0.19 fixed that (Oaklight/ToolRegistry#269) and now emits +#: ``anyOf``. It is still not what we want to serve: ``tuple`` and ``list`` +#: both render as ``array``, so the union carries the same branch twice, +#: and the items are untyped -- ``{"type":"array","items":{}}`` beside a +#: second identical entry. A duplicated branch is noise in a payload we +#: measure, and untyped items say less than we know. +#: +#: So this no longer fills a gap; it replaces a worse rendering with the +#: canonical one. Kept keyed by parameter name, and still a no-op for +#: anything not listed. _UNTYPED_UNION_SCHEMAS: dict[str, dict[str, Any]] = { "lat_spec": { "anyOf": [ @@ -693,10 +705,16 @@ def _trim_wire_schema(tool: Any) -> None: def _type_untyped_unions(schema: Any) -> None: - """Give a JSON type to union parameters upstream rendered without one. + """Serve the canonical schema for a union upstream renders poorly. - Only fills a property that has neither ``type`` nor ``anyOf``; a future - toolregistry that renders the union itself makes this a no-op. + Replaces whatever is there, rather than only filling an absence: since + toolregistry 0.19 there *is* an ``anyOf``, but it repeats the ``array`` + branch (``tuple`` and ``list`` both become ``array``) and leaves its + items untyped. Deferring to that would serve a duplicated branch and + drop the item type we know. + + ``default`` is preserved -- it is upstream's to decide and carries the + parameter's optionality. """ if not isinstance(schema, dict): return @@ -707,8 +725,8 @@ def _type_untyped_unions(schema: Any) -> None: fix = _UNTYPED_UNION_SCHEMAS.get(name) if fix is None or not isinstance(spec, dict): continue - if "type" in spec or "anyOf" in spec: - continue + spec.pop("type", None) + spec.pop("anyOf", None) spec.update(fix) diff --git a/tests/test_mcp_protocol.py b/tests/test_mcp_protocol.py index cfdd665..8ef7ce2 100644 --- a/tests/test_mcp_protocol.py +++ b/tests/test_mcp_protocol.py @@ -289,10 +289,22 @@ async def test_a_missing_file_is_reported_as_a_tool_error(self): assert "not found" in text.lower() or "no such file" in text.lower() async def test_calling_an_unknown_tool_is_handled(self): + """A name that does not exist is a protocol error, not a result. + + toolregistry-server 0.7.0 changed this: it used to come back as a + ``CallToolResult`` with ``isError``, and now raises JSON-RPC + ``-32602`` (invalid params). The new behaviour is the correct one + -- ``isError`` is for a tool that ran and failed, while an unknown + name means nothing ran -- so this asserts the new contract rather + than pinning the old one. + """ + from mcp.shared.exceptions import MCPError + async with connect() as (session, _init): - result = await session.call_tool("no_such_tool_exists", {}) + with pytest.raises(MCPError) as err: + await session.call_tool("no_such_tool_exists", {}) - assert wire(result)["isError"] is True + assert "no_such_tool_exists" in str(err.value) class TestResources: diff --git a/tests/test_tool_annotations.py b/tests/test_tool_annotations.py index e2f658e..a2a3985 100644 --- a/tests/test_tool_annotations.py +++ b/tests/test_tool_annotations.py @@ -194,3 +194,54 @@ async def test_a_result_wrapped_in_a_server_envelope_is_annotated(self): hints = await self._annotated_names(ListToolsRequest, envelope=True) assert hints["readOnlyHint"] is True + + +class TestUpstreamInferenceDoesNotOverruleUs: + """An inferred hint must not outrank a deliberate one. + + toolregistry-server 0.7.0 began attaching annotations of its own, and + marked ``manage_session`` and ``resume_workflow`` ``readOnlyHint=True``. + The first resets session state and clears artifacts; the second runs + pending workflow steps. A client reading that hint may auto-approve + them without asking. + + Two rules follow, and these pin both: where we have rated a tool, our + rating is what goes out; where we have not, nothing goes out, because + absence is honest and an unchecked inference is not. + """ + + @staticmethod + async def _served(): + from mcp_harness import connect + + async with connect(profile="deferred-full") as (session, _init): + return (await session.list_tools()).tools + + async def test_no_unrated_tool_is_served_an_inferred_annotation(self): + from uxarray_mcp.annotations import annotations_for + + surprises = [ + t.name + for t in await self._served() + if annotations_for(t.name) is None and t.annotations is not None + ] + assert not surprises, ( + "annotations appeared on tools nobody rated, so something " + f"upstream guessed: {sorted(surprises)}" + ) + + async def test_a_state_changing_tool_is_never_served_as_read_only(self): + """The specific claim 0.7.0 made, asserted by name. + + These two are the ones it got wrong; naming them means a future + release making the same guess fails here rather than in a client. + """ + served = {t.name: t for t in await self._served()} + for name in ("manage_session", "resume_workflow"): + tool = served.get(name) + if tool is None: # pragma: no cover - profile shape changed + continue + hints = tool.annotations + assert ( + hints is None or getattr(hints, "read_only_hint", None) is not True + ), f"{name} changes state but is advertised read-only" diff --git a/uv.lock b/uv.lock index fb238ac..415d5e1 100644 --- a/uv.lock +++ b/uv.lock @@ -4896,27 +4896,27 @@ wheels = [ [[package]] name = "toolregistry" -version = "0.18.1" +version = "0.19.0" source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "cloudpickle" }, { name = "llm-rosetta" }, ] -sdist = { url = "https://files.pythonhosted.org/packages/44/dd/5553167822f3308250b9f2a7827aa22d0c13d66846f74a2ea6691414676f/toolregistry-0.18.1.tar.gz", hash = "sha256:fe639bb043fd94e4d34c02e8cfd06e0751de4bb0a95b0c1307013d625778cf65", size = 359979, upload-time = "2026-09-16T09:09:21.667Z" } +sdist = { url = "https://files.pythonhosted.org/packages/8f/d2/463c77c3ebb7b451c9a176f5b01c38467a2daa265b4c93d97651eca07222/toolregistry-0.19.0.tar.gz", hash = "sha256:d85760a8f1442e60256faa58277d91a0781f72ef45dd4d3fb855c98590aed7f5", size = 462441, upload-time = "2026-10-23T17:57:12.456Z" } wheels = [ - { url = "https://files.pythonhosted.org/packages/fe/5f/75370c48e8fe37df1c57f7a99fb46fc1ada2ce568f6beee85d2017a74453/toolregistry-0.18.1-py3-none-any.whl", hash = "sha256:6dc988bb1de14c86a8b782143c195d9c9212cf58143e5e62b9f27427121d21b9", size = 277805, upload-time = "2026-09-16T09:09:20.004Z" }, + { url = "https://files.pythonhosted.org/packages/aa/98/5f7715d97a27093b07ade93e88de5b942102e4ccdd42afa7fb22f791b3cc/toolregistry-0.19.0-py3-none-any.whl", hash = "sha256:704a717a6ddb8165b1efff2b0fc219a11168fa48d5d372fc854d74a06fe756a0", size = 342713, upload-time = "2026-10-23T17:57:10.909Z" }, ] [[package]] name = "toolregistry-server" -version = "0.6.0" +version = "0.7.0" source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "toolregistry" }, ] -sdist = { url = "https://files.pythonhosted.org/packages/7c/9d/12badb761e32e8963240443513fa987ff08711a7cbfa2bbd30f97c803dad/toolregistry_server-0.6.0.tar.gz", hash = "sha256:1c423ed1f2e28785cdd3f2751c0bb4bfbf233c716d25d5012635b50750110841", size = 90593, upload-time = "2026-09-15T08:56:01.028Z" } +sdist = { url = "https://files.pythonhosted.org/packages/4a/90/d4a7a6b70b5ba18c93c09210f77e3e450748697550b9fd1cbff1081fcd52/toolregistry_server-0.7.0.tar.gz", hash = "sha256:ffe5b51dc03cf870455275458c6e659b7328399a5b82c82733199c8277ceee1e", size = 114277, upload-time = "2026-10-23T18:17:21.247Z" } wheels = [ - { url = "https://files.pythonhosted.org/packages/29/10/41192f02c779f5c4eb93058fc1cf7f452609a340ac1712f41fd630a72b3b/toolregistry_server-0.6.0-py3-none-any.whl", hash = "sha256:24a2f1b43d2df250728a13e4df1d97a30ae6568de345cb7cb71472f588792b69", size = 69382, upload-time = "2026-09-15T08:55:59.613Z" }, + { url = "https://files.pythonhosted.org/packages/4e/29/e52fb61fab654d44a5438ecee48ac279a16afebd5c196cb0af9376cd1ab1/toolregistry_server-0.7.0-py3-none-any.whl", hash = "sha256:3de4fb1ce8700ab40b30b2aa17cf147017c5955cda9e606224dc33bc106cb8b0", size = 81845, upload-time = "2026-10-23T18:17:19.52Z" }, ] [package.optional-dependencies] @@ -5185,9 +5185,9 @@ requires-dist = [ { name = "pyyaml", specifier = ">=6.0.1" }, { name = "sphinx", marker = "extra == 'docs'", specifier = ">=7.0" }, { name = "sphinx-book-theme", marker = "extra == 'docs'", specifier = ">=1.1.0" }, - { name = "toolregistry", specifier = ">=0.18.0" }, - { name = "toolregistry-server", extras = ["mcp"], specifier = ">=0.6.0" }, - { name = "toolregistry-server", extras = ["openapi"], marker = "extra == 'openapi'", specifier = ">=0.6.0" }, + { name = "toolregistry", specifier = ">=0.19.0" }, + { name = "toolregistry-server", extras = ["mcp"], specifier = ">=0.7.0" }, + { name = "toolregistry-server", extras = ["openapi"], marker = "extra == 'openapi'", specifier = ">=0.7.0" }, { name = "uxarray", extras = ["geo", "viz"], specifier = ">=2026.10.0,<2026.11" }, ] provides-extras = ["openapi", "hpc", "transfer", "docs"] From 996536998a744035d8e2405c27470d4337e09f98 Mon Sep 17 00:00:00 2001 From: Rajeev Jain Date: Fri, 23 Oct 2026 14:24:13 -0500 Subject: [PATCH 2/3] Clear 44 pillow advisories The lockfile audit went red on this branch while it was green on main three days ago, with the same pillow 12.3.0 pinned in both. Nothing here pulled it in: 44 advisories against 12.3.0 were published in between, 5 of them Critical, all fixed in 13.0.0. pillow arrives transitively through bokeh and matplotlib under uxarray's viz extra, so there is nothing of ours to re-point. `uv lock --upgrade-package pillow` moves that one package and nothing else. Carried on this branch rather than in its own PR because the audit is a required check and this branch cannot merge while it is red. 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From ce11a54c6ff7c5c9861c20a0767617634bfa7b75 Mon Sep 17 00:00:00 2001 From: Rajeev Jain Date: Fri, 23 Oct 2026 14:32:17 -0500 Subject: [PATCH 3/3] Clear the certifi and virtualenv advisories underneath pillow Clearing pillow exposed two more the scanner had not reached: PYSEC-2026-4320 against certifi 2026.7.22, which is a 9.1 Critical, and four against virtualenv 21.14.7 including a 7.8 High. Both published in the same window as the pillow set. certifi is the trust store every outbound HTTPS call in this server uses -- Globus Compute submission, Globus transfers, remote dataset reads -- so a Critical there is not a transitive detail. virtualenv arrives through the dev toolchain. Each moves to its first fixed release and nothing else resolves differently. --- uv.lock | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/uv.lock b/uv.lock index 3aca722..b585fb5 100644 --- a/uv.lock +++ b/uv.lock @@ -488,11 +488,11 @@ wheels = [ [[package]] name = "certifi" -version = "2026.7.22" +version = "2026.10.23" source = { registry = "https://pypi.org/simple" } -sdist = { url = "https://files.pythonhosted.org/packages/a3/c2/24167ea9858356b47a87a50d39908bfdb72ceeefe0041586e704e5376b3a/certifi-2026.7.22.tar.gz", hash = "sha256:741e2c3b351ddf169a738da9f2c048608ff7f2c5cc02f1ebc6b118bb090d5d55", size = 138112, upload-time = "2026-07-22T03:35:12.644Z" } +sdist = { url = "https://files.pythonhosted.org/packages/fd/11/b524cbd9bbdaca58608e4cf4053fd463417549e1959fa8d3aa18319f9555/certifi-2026.10.23.tar.gz", hash = "sha256:a9895e6e2758b371e0545e321a3a8fd1fcfd9829ada8824a936dfb16aaaf36cd", size = 136225, upload-time = "2026-10-23T11:36:16.478Z" } wheels = [ - { url = "https://files.pythonhosted.org/packages/0b/a7/71ac2cff56fec219ed242bb11b8efb69fcc4bec75db06fb7bfe35de520e6/certifi-2026.7.22-py3-none-any.whl", hash = "sha256:62f22742b58a1a33014a2b6b706588a8d7e2a88ae7bd1a6ebe8c992928483775", size = 136983, upload-time = "2026-07-22T03:35:11.276Z" }, + { url = "https://files.pythonhosted.org/packages/32/d1/a3652fe2c19134d0d15922177821d863cbd7e842d53a21bbe7e8e3a1b5ac/certifi-2026.10.23-py3-none-any.whl", hash = "sha256:e9b54de76e530bb6cf0ccd036787103acb58fd42ba930ea8bf948ddbaa2f61d1", size = 135082, upload-time = "2026-10-23T11:36:14.763Z" }, ] [[package]] @@ -5210,7 +5210,7 @@ dev = [ [[package]] name = "virtualenv" -version = "21.14.7" +version = "21.14.13" source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "distlib" }, @@ -5219,9 +5219,9 @@ dependencies = [ { name = "platformdirs" }, { name = "python-discovery" }, ] -sdist = { url = "https://files.pythonhosted.org/packages/dc/3f/935cf1757643381fb7f7cc98197b4bc119223d9c2cf37dc3b03ad2a4455f/virtualenv-21.14.7.tar.gz", hash = "sha256:5f427d56f39eb7e7447d641dd4b7ab1e9c92793f498f35f26da2e4972c5546ae", size = 5471741, upload-time = "2026-10-12T01:27:31.842Z" } +sdist = { url = "https://files.pythonhosted.org/packages/70/aa/bff50daee0488e16d611258a9b6c5a1d0c9e128f8ca424e9f4e1c0444ef2/virtualenv-21.14.13.tar.gz", hash = "sha256:de5307ba4b9a0001d9c8ea02832d38f63ca432880f416c1bface61c4323fd905", size = 5570301, upload-time = "2026-10-22T20:10:16.952Z" } wheels = [ - { url = "https://files.pythonhosted.org/packages/52/5b/799c3e5b8e04d5fa1c9b61a4c1f5079603e747205c7311b92abd30283df5/virtualenv-21.14.7-py3-none-any.whl", hash = "sha256:3769219a308c5d2f093e7729621ad12a6346b5767a7ec4338414e2a0fb0c526b", size = 5487587, upload-time = "2026-10-12T01:27:29.37Z" }, + { url = "https://files.pythonhosted.org/packages/bb/a9/c10d8a44a29fb94a18b43fdf11f38caca53ae7c9406f11a72b1cb8f624f1/virtualenv-21.14.13-py3-none-any.whl", hash = "sha256:5fbb04138a4861580b78ba9110d529a26bc48fcc93c8ec36bc0202eeed96a788", size = 5557094, upload-time = "2026-10-22T20:10:15.096Z" }, ] [[package]]