world-reference-mcp 0.3.2__tar.gz → 0.3.4__tar.gz

{world_reference_mcp-0.3.2/world_reference_mcp.egg-info → world_reference_mcp-0.3.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: world-reference-mcp
-Version: 0.3.2
+Version: 0.3.4
 Summary: World-reference data (taxonomy, OBO terms, nutrition, observations, Wikidata alignment) MCP server and agent-connector-sdk source adapters
 Author-email: Project Maintainers <maintainers@users.noreply.github.com>
 License: MIT
@@ -12,7 +12,7 @@ Classifier: Programming Language :: Python :: 3
 Requires-Python: <3.15,>=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: agent-connector-sdk[mcp]<1.0.0,>=0.3.18
+Requires-Dist: agent-connector-sdk[mcp]<1.0.0,>=0.4.1
 Requires-Dist: httpx>=0.28.1
 Provides-Extra: test
 Requires-Dist: pytest-xdist>=3.8.0; extra == "test"
@@ -23,7 +23,7 @@ Dynamic: license-file
 
 # world-reference-mcp
 
-*Version: 0.3.2*
+*Version: 0.3.4*
 
 World-reference data — organism taxonomy, OBO reference terms, food/nutrition
 composition, organism and weather observations, and Wikidata alignment — as an

{world_reference_mcp-0.3.2 → world_reference_mcp-0.3.4}/README.md

@@ -1,6 +1,6 @@
 # world-reference-mcp
 
-*Version: 0.3.2*
+*Version: 0.3.4*
 
 World-reference data — organism taxonomy, OBO reference terms, food/nutrition
 composition, organism and weather observations, and Wikidata alignment — as an

{world_reference_mcp-0.3.2 → world_reference_mcp-0.3.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "world-reference-mcp"
-version = "0.3.2"
+version = "0.3.4"
 description = "World-reference data (taxonomy, OBO terms, nutrition, observations, Wikidata alignment) MCP server and agent-connector-sdk source adapters"
 readme = "README.md"
 classifiers = [
@@ -16,7 +16,7 @@ classifiers = [
 ]
 requires-python = ">=3.12, <3.15"
 dependencies = [
-    "agent-connector-sdk[mcp]>=0.3.18,<1.0.0",
+    "agent-connector-sdk[mcp]>=0.4.1,<1.0.0",
     "httpx>=0.28.1",
 ]
 
@@ -42,8 +42,9 @@ world-reference-mcp = "world_reference_mcp.ontology"
 [project.entry-points."agent_connector_sdk.prompt_providers"]
 world-reference-mcp = "world_reference_mcp.prompts"
 
-[project.entry-points."agent_connector_sdk.source_connector_providers"]
-world-reference-mcp = "world_reference_mcp.connectors"
+# The one declared connector identity: the fleet name (SDK-CONNECTOR-CONTROL-R071).
+[project.entry-points."agent_connector_sdk.connector"]
+world-reference-mcp = "world_reference_mcp"
 
 [tool.uv.workspace]
 members = ["."]

{world_reference_mcp-0.3.2 → world_reference_mcp-0.3.4}/tests/test_adapter_conformance.py

@@ -103,7 +103,7 @@ async def _verified_adapter(sessions: SessionFactory) -> McpToolSourceAdapter:
         preset,
         connector="world-reference-mcp",
         tool_schema_sha256=live.compatibility_sha256,
-        mapping_reference="manifest:world-reference-mcp#schema_mappings/taxon_ncbi_small",
+        mapping_reference="connector:world-reference-mcp#mappings/taxon_ncbi_small",
         schema_mappings={"taxon_ncbi_small": SchemaMapping(ontology_class="Taxon")},
     )
 

world_reference_mcp-0.3.4/tests/test_default_content_surfaces.py

@@ -0,0 +1,43 @@
+"""CONN-WORLD-REFERENCE-MCP-CONNECTOR-CONTENT-R001: the server lists its packaged skills, ontology and prompts by default."""
+
+from __future__ import annotations
+
+import asyncio
+import importlib
+from pathlib import Path
+
+import pytest
+from fastmcp import Client
+
+PACKAGE = "world_reference_mcp"
+ROOT = Path(list(importlib.import_module(PACKAGE).__path__)[0])
+
+pytestmark = pytest.mark.spec("CONN-WORLD-REFERENCE-MCP-CONNECTOR-CONTENT-R001")
+
+
+def _server():
+    namespace = {"__name__": PACKAGE + ".mcp_server"}
+    exec(
+        "from agent_connector_sdk.mcp.server import create_mcp_server\n"
+        "result = create_mcp_server('world-reference-mcp', version='0', command_args=[])",
+        namespace,
+    )
+    return namespace["result"][1]
+
+
+async def _listings():
+    async with Client(_server()) as client:
+        resources = {str(r.uri) for r in await client.list_resources()}
+        prompts = {p.name for p in await client.list_prompts()}
+    return resources, prompts
+
+
+def test_default_content_surfaces() -> None:
+    resources, prompts = asyncio.run(_listings())
+    if list(ROOT.glob("skills/*/SKILL.md")):
+        assert any(u.startswith("skill://") for u in resources)
+    if list(ROOT.glob("ontology/*.ttl")):
+        assert any(u.startswith("ontology://world-reference-mcp/") for u in resources)
+    for path in ROOT.glob("prompts/*.json"):
+        if not path.name.startswith("_"):
+            assert path.stem in prompts

world_reference_mcp-0.3.4/tests/test_startup.py

@@ -0,0 +1,13 @@
+"""Import-time smoke test and a bare server-build smoke test."""
+
+from __future__ import annotations
+
+
+def test_build_server_with_no_auth_configured() -> None:
+    from world_reference_mcp.mcp.server import build_server
+
+    mcp, args, middlewares, clients = build_server(command_args=[])
+    assert mcp.name == "world-reference-mcp"
+    assert args.transport == "stdio"
+    assert isinstance(middlewares, list)
+    assert clients.ncbi.config.base_url.endswith("eutils")

{world_reference_mcp-0.3.2 → world_reference_mcp-0.3.4}/world_reference_mcp/_version.py

@@ -2,4 +2,4 @@
 
 from __future__ import annotations
 
-__version__ = "0.3.2"
+__version__ = "0.3.4"

world_reference_mcp-0.3.4/world_reference_mcp/connector_sources.py

@@ -0,0 +1,251 @@
+"""Data sources of this connector, declared by tool name (generated by connector-ontology-map migrate).
+
+Served live as ``connector://resources``. Regenerate by editing the declarations, not the tools.
+"""
+
+# ruff: noqa: E501
+from __future__ import annotations
+
+from typing import Any
+
+from agent_connector_sdk.ingest.live_declaration import source_meta
+from agent_connector_sdk.ingest.sources import IngestSourceDeclaration, IngestSourceSpec
+
+CONNECTOR: str = "world-reference-mcp"
+
+SOURCES: tuple[Any, ...] = (
+    source_meta(
+        tool="fdc_food_search",
+        source_id="food_fdc",
+        record_type="food",
+        id_field="fdc_id",
+        page_param="page_number",
+        page_size_param="page_size",
+        pagination="page",
+        preset={
+            "arguments": {
+                "query": "*",
+            },
+            "doc_type": "food",
+            "ontology_class": "FoodCompositionRecord",
+            "page_kind": "number",
+            "page_size": 50,
+            "params_style": "args",
+            "start_page": 1,
+        },
+        records_path="items",
+        server="world-reference-mcp",
+        title_field="description",
+    ),
+    source_meta(
+        tool="gbif_occurrence_search",
+        source_id="organism_observation_gbif",
+        record_type="organism_observation",
+        id_field="occurrence_id",
+        cursor_field="last_parsed",
+        preset={
+            "arguments": {
+                "scientific_name": "Vulpes vulpes",
+            },
+            "doc_type": "organism_observation",
+            "ontology_class": "OrganismObservation",
+            "page_param": "offset",
+            "page_size": 100,
+            "page_size_param": "limit",
+            "pagination": "offset",
+            "params_style": "args",
+        },
+        records_path="items",
+        server="world-reference-mcp",
+    ),
+    source_meta(
+        tool="inaturalist_observation_search",
+        source_id="organism_observation_inaturalist",
+        record_type="organism_observation",
+        id_field="observation_id",
+        cursor_field="time_observed_at",
+        page_param="page",
+        page_size_param="per_page",
+        pagination="page",
+        preset={
+            "arguments": {
+                "taxon_name": "Vulpes vulpes",
+            },
+            "doc_type": "organism_observation",
+            "ontology_class": "OrganismObservation",
+            "page_kind": "number",
+            "page_size": 50,
+            "params_style": "args",
+            "start_page": 1,
+        },
+        records_path="items",
+        server="world-reference-mcp",
+    ),
+    source_meta(
+        tool="reference_term_list",
+        source_id="reference_term_uberon",
+        record_type="reference_term",
+        id_field="iri",
+        page_param="page",
+        page_size_param="size",
+        pagination="page",
+        preset={
+            "arguments": {
+                "ontology": "uberon",
+            },
+            "doc_type": "reference_term",
+            "ontology_class": "AnatomyTerm",
+            "page_kind": "number",
+            "page_size": 100,
+            "params_style": "args",
+            "start_page": 0,
+        },
+        records_path="items",
+        server="world-reference-mcp",
+        title_field="label",
+    ),
+    source_meta(
+        tool="taxonomy_gbif_search",
+        source_id="taxon_gbif",
+        record_type="taxon",
+        id_field="gbif_taxon_key",
+        preset={
+            "arguments": {
+                "query": "Mammalia",
+                "rank": "SPECIES",
+            },
+            "doc_type": "taxon",
+            "ontology_class": "Taxon",
+            "page_param": "offset",
+            "page_size": 100,
+            "page_size_param": "limit",
+            "pagination": "offset",
+            "params_style": "args",
+        },
+        records_path="items",
+        server="world-reference-mcp",
+        title_field="scientific_name",
+    ),
+    source_meta(
+        tool="taxonomy_ncbi_search",
+        source_id="taxon_ncbi",
+        record_type="taxon",
+        id_field="ncbi_taxon_id",
+        cursor_field="modification_date",
+        preset={
+            "arguments": {
+                "term": "Mammalia[Subtree]",
+            },
+            "doc_type": "taxon",
+            "ontology_class": "Taxon",
+            "page_param": "retstart",
+            "page_size": 50,
+            "page_size_param": "retmax",
+            "pagination": "offset",
+            "params_style": "args",
+            "updated_since_param": "modified_since",
+        },
+        records_path="items",
+        server="world-reference-mcp",
+        title_field="scientific_name",
+    ),
+    source_meta(
+        tool="noaa_ghcnd_daily",
+        source_id="weather_observation_noaa",
+        record_type="weather_observation",
+        id_field="observation_id",
+        preset={
+            "arguments": {
+                "end_date": "2026-01-31",
+                "start_date": "2026-01-01",
+                "station_id": "GHCND:USW00023174",
+            },
+            "doc_type": "weather_observation",
+            "ontology_class": "WeatherObservation",
+            "page_param": "offset",
+            "page_size": 200,
+            "page_size_param": "limit",
+            "pagination": "offset",
+            "params_style": "args",
+        },
+        records_path="items",
+        server="world-reference-mcp",
+    ),
+    source_meta(
+        tool="open_meteo_weather_observation",
+        source_id="weather_observation_open_meteo",
+        record_type="weather_observation",
+        id_field="observation_date",
+        preset={
+            "arguments": {
+                "latitude": 52.52,
+                "longitude": 13.405,
+                "window_days": 30,
+            },
+            "cursor_param": "start_date",
+            "cursor_path": "next_cursor",
+            "doc_type": "weather_observation",
+            "ontology_class": "WeatherObservation",
+            "pagination": "cursor",
+            "params_style": "args",
+        },
+        records_path="items",
+        server="world-reference-mcp",
+    ),
+    source_meta(
+        tool="wikidata_alignment_search",
+        source_id="wikidata_alignment_taxon_ncbi",
+        record_type="wikidata_alignment",
+        id_field="wikidata_id",
+        preset={
+            "arguments": {
+                "entity_type": "taxon_ncbi",
+            },
+            "doc_type": "wikidata_alignment",
+            "ontology_class": "Taxon",
+            "page_param": "offset",
+            "page_size": 100,
+            "page_size_param": "limit",
+            "pagination": "offset",
+            "params_style": "args",
+        },
+        records_path="items",
+        server="world-reference-mcp",
+        title_field="label",
+    ),
+)
+
+SCHEMA_MAPPINGS: dict[str, Any] = {
+    "ReferenceSyncRun": {
+        "fields": {},
+        "ontology_class": None,
+    },
+}
+
+RESOURCES: tuple[dict[str, str], ...] = (
+    {
+        "id_prefix": "referencesyncrun",
+        "label": "Reference Sync Run",
+        "name": "ReferenceSyncRun",
+    },
+)
+
+
+def declaration() -> IngestSourceDeclaration:
+    """The declaration the server assembles from this module."""
+    specs: list[IngestSourceSpec] = []
+    for item in SOURCES:
+        for entry in item["connector_sources"]:
+            body: dict[str, Any] = {
+                k: v for k, v in entry.items() if k not in ("tool", "mapping")
+            }
+            spec = {**body, "tools": (entry["tool"],)}
+            specs.append(IngestSourceSpec.model_validate(spec))
+    return IngestSourceDeclaration.model_validate(
+        {
+            "connector": CONNECTOR,
+            "sources": specs,
+            "schema_mappings": SCHEMA_MAPPINGS,
+            "resources": RESOURCES,
+        }
+    )

world_reference_mcp-0.3.4/world_reference_mcp/connectors/__init__.py

@@ -0,0 +1 @@
+"""Connector package; the data sources are declared in ``world_reference_mcp.connector_sources``."""

{world_reference_mcp-0.3.2 → world_reference_mcp-0.3.4}/world_reference_mcp/ontology/certification.json

@@ -1,9 +1,6 @@
 {
   "api_version": "arbora.io/v1",
   "artifacts": {
-    "connector_manifest.yml": "55d3adcd6e44770c9e88c10d799cd3467139d38c1d57004e7c45ab30e4eea697",
-    "world_reference_mcp/connectors/mcp_source_presets.json": "8bda3239bc749241467d9986d7cd684c3af55e297c312b4cb6dee1c176762fd8",
-    "world_reference_mcp/connectors/tool_schema_fingerprints.json": "c4701082264f0b47f47322ad2fe20137b1832f95a0ec09e7aa19dea13bacf82d",
     "world_reference_mcp/ontology/fixtures/records.json": "3b7253452b8991f268716eb6e0e161089ef1bcb79dd283c0cff5ec905fc82da6",
     "world_reference_mcp/ontology/mappings/source.yaml": "d7361816d2bbac3bbd7bc2ebbcab6985b30afa6d61b67d3e12d051319268b5a0",
     "world_reference_mcp/ontology/migrations/manifest.json": "d0de575ae95abdf603f03178e734527e0d82cbd48b6d0a92ad1dca9b56d49efa",

{world_reference_mcp-0.3.2 → world_reference_mcp-0.3.4}/world_reference_mcp/ontology/world_reference.ttl

@@ -14,7 +14,7 @@
 # (crates/eg-core/ontology/{life,environment,nutrition}-v1.ttl) on EG branch
 # `feat/world-model-ontology`. This connector maps each of its 17 declared
 # streams onto one of those existing classes through
-# `connectors/mcp_source_presets.json`'s `ontology_class` hint, resolved at
+# `connectors/world_reference_mcp.connector_sources`'s `ontology_class` hint, resolved at
 # runtime by `world_reference_mcp.connectors.adapters.build_schema_mappings`
 # — never by duplicating the class here. See AGENTS.md "Ontology mapping".
 
@@ -38,5 +38,4 @@
     federated into the agent-utilities knowledge-graph hub. The world-model
     domain classes each stream lands on are epistemic-graph-owned; this
     ontology models only this connector's own admin state, not a second copy
-    of that domain.""" ;
-    owl:imports <http://knuckles.team/kg> .
+    of that domain.""" .

{world_reference_mcp-0.3.2 → world_reference_mcp-0.3.4}/world_reference_mcp/prompts/main_agent.json

@@ -4,8 +4,6 @@
   "type": "prompt",
   "source": "world-reference-mcp",
   "description": "World-reference data (taxonomy, OBO terms, nutrition, observations, Wikidata alignment) MCP Server",
-  "extends": "agent-utilities:base",
-  "compose": "append",
   "identity": {
     "role": "World Reference Agent",
     "goal": "World-reference data (taxonomy, OBO terms, nutrition, observations, Wikidata alignment) MCP Server"

{world_reference_mcp-0.3.2 → world_reference_mcp-0.3.4}/world_reference_mcp/prompts/world_reference_specialist.json

@@ -4,8 +4,6 @@
   "schema_version": "1.0",
   "prompt_version": "0.2.0",
   "source": "world-reference-mcp",
-  "extends": "agent-utilities:base",
-  "compose": "append",
   "description": "World-reference specialist: organism taxonomy, OBO reference terms, food composition, organism/weather observations, and Wikidata cross-source alignment over the world-reference-mcp MCP server.",
   "metadata": {
     "topic": "World-reference data (taxonomy, ontology terms, nutrition, observations, alignment)",

{world_reference_mcp-0.3.2 → world_reference_mcp-0.3.4/world_reference_mcp.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: world-reference-mcp
-Version: 0.3.2
+Version: 0.3.4
 Summary: World-reference data (taxonomy, OBO terms, nutrition, observations, Wikidata alignment) MCP server and agent-connector-sdk source adapters
 Author-email: Project Maintainers <maintainers@users.noreply.github.com>
 License: MIT
@@ -12,7 +12,7 @@ Classifier: Programming Language :: Python :: 3
 Requires-Python: <3.15,>=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: agent-connector-sdk[mcp]<1.0.0,>=0.3.18
+Requires-Dist: agent-connector-sdk[mcp]<1.0.0,>=0.4.1
 Requires-Dist: httpx>=0.28.1
 Provides-Extra: test
 Requires-Dist: pytest-xdist>=3.8.0; extra == "test"
@@ -23,7 +23,7 @@ Dynamic: license-file
 
 # world-reference-mcp
 
-*Version: 0.3.2*
+*Version: 0.3.4*
 
 World-reference data — organism taxonomy, OBO reference terms, food/nutrition
 composition, organism and weather observations, and Wikidata alignment — as an

{world_reference_mcp-0.3.2 → world_reference_mcp-0.3.4}/world_reference_mcp.egg-info/SOURCES.txt

@@ -1,7 +1,6 @@
 LICENSE
 README.md
 pyproject.toml
-scripts/compute_tool_fingerprints.py
 scripts/security_sanitizer.py
 tests/conftest.py
 tests/test_adapter_conformance.py
@@ -14,14 +13,15 @@ tests/test_api_ols4.py
 tests/test_api_open_meteo.py
 tests/test_api_wikidata.py
 tests/test_concept_parity.py
+tests/test_default_content_surfaces.py
 tests/test_init_dynamics.py
-tests/test_presets_and_adapters.py
 tests/test_sdk_rate_limiter.py
 tests/test_startup.py
 world_reference_mcp/__init__.py
 world_reference_mcp/__main__.py
 world_reference_mcp/_version.py
 world_reference_mcp/config.py
+world_reference_mcp/connector_sources.py
 world_reference_mcp/credentials.py
 world_reference_mcp/errors.py
 world_reference_mcp/http_clients.py
@@ -43,9 +43,6 @@ world_reference_mcp/api/ols4.py
 world_reference_mcp/api/open_meteo.py
 world_reference_mcp/api/wikidata.py
 world_reference_mcp/connectors/__init__.py
-world_reference_mcp/connectors/adapters.py
-world_reference_mcp/connectors/mcp_source_presets.json
-world_reference_mcp/connectors/tool_schema_fingerprints.json
 world_reference_mcp/mcp/__init__.py
 world_reference_mcp/mcp/clients.py
 world_reference_mcp/mcp/server.py

{world_reference_mcp-0.3.2 → world_reference_mcp-0.3.4}/world_reference_mcp.egg-info/entry_points.txt

@@ -1,3 +1,6 @@
+[agent_connector_sdk.connector]
+world-reference-mcp = world_reference_mcp
+
 [agent_connector_sdk.ontology_providers]
 world-reference-mcp = world_reference_mcp.ontology
 
@@ -7,8 +10,5 @@ world-reference-mcp = world_reference_mcp.prompts
 [agent_connector_sdk.skill_providers]
 world-reference-mcp = world_reference_mcp.skills
 
-[agent_connector_sdk.source_connector_providers]
-world-reference-mcp = world_reference_mcp.connectors
-
 [console_scripts]
 world-reference-mcp = world_reference_mcp.mcp_server:mcp_server

{world_reference_mcp-0.3.2 → world_reference_mcp-0.3.4}/world_reference_mcp.egg-info/requires.txt

@@ -1,4 +1,4 @@
-agent-connector-sdk[mcp]<1.0.0,>=0.3.18
+agent-connector-sdk[mcp]<1.0.0,>=0.4.1
 httpx>=0.28.1
 
 [test]

world_reference_mcp-0.3.2/scripts/compute_tool_fingerprints.py

@@ -1,79 +0,0 @@
-#!/usr/bin/env python3
-"""Regenerate ``connectors/tool_schema_fingerprints.json`` from the live tool surface.
-
-Connects an in-process FastMCP client to a plain server carrying this
-package's nine tools (no auth/network/fleet-registration wiring — those are
-concerns of ``agent_connector_sdk.mcp.server.create_mcp_server``, irrelevant
-to a tool's client-visible schema) and fingerprints exactly what a real
-client's ``tools/list`` would see, via
-``agent_connector_sdk.certify.fingerprints.tool_fingerprint`` — the same
-function ``discover()`` verifies against at extraction time.
-
-Run after changing any tool's signature or docstring-derived schema:
-
-    uv run --frozen python scripts/compute_tool_fingerprints.py --apply
-"""
-
-from __future__ import annotations
-
-import argparse
-import asyncio
-import json
-from pathlib import Path
-
-from agent_connector_sdk.certify.fingerprints import tool_fingerprint
-from fastmcp import Client, FastMCP
-
-from world_reference_mcp.mcp.clients import Clients
-from world_reference_mcp.mcp.tools_nutrition import register_nutrition_tools
-from world_reference_mcp.mcp.tools_observations import register_observation_tools
-from world_reference_mcp.mcp.tools_taxonomy import register_taxonomy_tools
-from world_reference_mcp.mcp.tools_terms import register_term_tools
-from world_reference_mcp.mcp.tools_wikidata import register_wikidata_tools
-
-_OUTPUT = Path(__file__).resolve().parent.parent / (
-    "world_reference_mcp/connectors/tool_schema_fingerprints.json"
-)
-
-
-def _bare_server() -> FastMCP:
-    mcp: FastMCP = FastMCP("world-reference-mcp")
-    clients = Clients()
-    register_taxonomy_tools(mcp, clients)
-    register_term_tools(mcp, clients)
-    register_nutrition_tools(mcp, clients)
-    register_observation_tools(mcp, clients)
-    register_wikidata_tools(mcp, clients)
-    return mcp
-
-
-async def _fingerprints() -> dict[str, str]:
-    mcp = _bare_server()
-    async with Client(mcp) as client:
-        tools = await client.list_tools()
-    return {tool.name: tool_fingerprint(tool) for tool in tools}
-
-
-def main() -> int:
-    parser = argparse.ArgumentParser(description=__doc__)
-    parser.add_argument("--apply", action="store_true", help="write the output file")
-    args = parser.parse_args()
-    fingerprints = asyncio.run(_fingerprints())
-    document = {
-        "_comment": (
-            "Generated by scripts/compute_tool_fingerprints.py from the live "
-            "tools/list schema. Never hand-edit."
-        ),
-        "tools": dict(sorted(fingerprints.items())),
-    }
-    text = json.dumps(document, indent=2, sort_keys=False) + "\n"
-    if args.apply:
-        _OUTPUT.write_text(text)
-        print(f"wrote {_OUTPUT}")
-    else:
-        print(text)
-    return 0
-
-
-if __name__ == "__main__":
-    raise SystemExit(main())