SEAB-7740 Add slimmed TRS MCP tools

.env.example

@@ -14,3 +14,7 @@ DOCKSTORE_MCP_LOG_LEVEL=INFO
 
 # The Dockstore instance whose APIs this server exposes.
 DOCKSTORE_MCP_DOCKSTORE_URL=https://dockstore.org
+
+# Git tag or ref reported in the User-Agent sent to Dockstore. Normally set at
+# build time; left unset, the package version is used.
+# DOCKSTORE_MCP_GIT_REF=

.github/workflows/ci.yml

@@ -8,7 +8,7 @@ on:
 jobs:
   test:
     name: Test (Python ${{ matrix.python-version }})
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     strategy:
       fail-fast: false
       matrix:
@@ -34,7 +34,7 @@ jobs:
 
   git-secrets:
     name: git-secrets scan
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     steps:
       - uses: actions/checkout@v7
       - name: Install git-secrets
@@ -51,7 +51,7 @@ jobs:
 
   docker:
     name: Build image
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
     steps:
       - uses: actions/checkout@v7
       - name: Build

.github/workflows/deploy_tagged.yml

@@ -19,7 +19,7 @@ jobs:
 
   build:
     needs: ci
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-26.04
 
     permissions:
       id-token: write
@@ -55,6 +55,7 @@ jobs:
           context: .
           load: true
           tags: quay.io/dockstore/dockstore-mcp:${{ steps.ref.outputs.sanitized }}
+          build-args: GIT_REF=${{ steps.ref.outputs.sanitized }}
 
       # Test the exact image about to be published, not just the one CI built
       - name: Smoke test

CLAUDE.md

@@ -9,7 +9,7 @@ An MCP (Model Context Protocol) server, built on FastMCP 4, that exposes Docksto
 assistants. It is a standalone process deployed alongside the Dockstore webservice,
 talking to Dockstore's GA4GH Tool Registry Service (TRS) API and its own proprietary API.
 
-**Status: scaffold.** Only the `hello` tool has a working body. The four Dockstore
+**Status: prototype without search.** The GA4GH TRS tools in `trs.py` have working bodies. The four Dockstore
 tools (`search_entries`, `get_entry`, `get_version`, `get_file`) are fully declared
 (names, arguments, response models, docstrings) but each raises `NotImplementedError`
 until wired up to the real Dockstore API.
@@ -31,7 +31,7 @@ Run a single test with pytest directly (no Makefile target for this):
 
 ```bash
 .venv/bin/pytest tests/test_tools.py::test_search_takes_every_facet
-.venv/bin/pytest -k "hello"
+.venv/bin/pytest -k "trs_info"
 ```
 
 Tests use FastMCP's in-memory `Client`/`FastMCP` pairing (see `tests/conftest.py`), so
@@ -94,7 +94,8 @@ back from the installed package's metadata at runtime (`importlib.metadata.versi
 - `src/dockstore_mcp/tools/` — one module per cohesive tool group, each exposing
   `register(mcp: FastMCP, settings: Settings) -> None`. `tools/__init__.py`'s
   `register_all` calls each in turn; new tool modules must be added there.
-  - `hello.py` — smoke-test tool, implemented.
+  - `trs.py` — the GA4GH TRS tools, implemented. `get_trs_info(local_only=True)` doubles as a
+    smoke test that never contacts Dockstore.
   - `search.py` — `search_entries`, the Dockstore Search page equivalent.
   - `entries.py` — `get_entry` → `get_version` → `get_file`, a lookup chain: an
     entry's `version_ids` feed `get_version`, whose `file_paths` feed `get_file`.

Dockerfile

@@ -33,6 +33,10 @@ RUN pip install . \
 # ---- runtime --------------------------------------------------------------
 FROM python:3.13-alpine3.24
 
+# Git tag or ref the image is built from, reported in the User-Agent sent to
+# Dockstore. Left empty, the server falls back to the package version.
+ARG GIT_REF=""
+
 LABEL org.opencontainers.image.title="dockstore-mcp" \
       org.opencontainers.image.description="Model Context Protocol server for Dockstore" \
       org.opencontainers.image.url="https://dockstore.org" \
@@ -56,7 +60,8 @@ ENV PATH="/opt/venv/bin:${PATH}" \
     DOCKSTORE_MCP_HOST=0.0.0.0 \
     DOCKSTORE_MCP_PORT=8000 \
     DOCKSTORE_MCP_PATH=/mcp \
-    DOCKSTORE_MCP_DOCKSTORE_URL=https://dockstore.org
+    DOCKSTORE_MCP_DOCKSTORE_URL=https://dockstore.org \
+    DOCKSTORE_MCP_GIT_REF=${GIT_REF}
 
 USER dockstore
 WORKDIR /home/dockstore

Makefile

@@ -4,6 +4,8 @@ VENV ?= .venv
 PY   ?= $(VENV)/bin/python
 PIP  ?= $(VENV)/bin/pip
 IMAGE ?= dockstore/dockstore-mcp:local
+# Reported in the User-Agent the server sends to Dockstore.
+GIT_REF ?= $(shell git describe --tags --always 2>/dev/null)
 
 help: ## Show this help
 	@grep -hE '^[a-zA-Z_-]+:.*?## ' $(MAKEFILE_LIST) | awk 'BEGIN {FS = ":.*?## "}; {printf "  \033[36m%-14s\033[0m %s\n", $$1, $$2}'
@@ -35,13 +37,13 @@ typecheck: ## Run the type checker
 check: lint typecheck test ## Everything CI runs
 
 run: ## Run the server over stdio
-	$(VENV)/bin/dockstore-mcp
+	DOCKSTORE_MCP_GIT_REF=$(GIT_REF) $(VENV)/bin/dockstore-mcp
 
 run-http: ## Run the server over HTTP on port 8000
-	$(VENV)/bin/dockstore-mcp --transport http --port 8000
+	DOCKSTORE_MCP_GIT_REF=$(GIT_REF) $(VENV)/bin/dockstore-mcp --transport http --port 8000
 
 docker-build: ## Build the container image
-	docker build -t $(IMAGE) .
+	docker build --build-arg GIT_REF=$(GIT_REF) -t $(IMAGE) .
 
 docker-run: ## Run the container image on port 8000
 	docker run --rm -p 8000:8000 $(IMAGE)

README.md

@@ -13,10 +13,10 @@ MCP, so it is deployed alongside the Dockstore webservice rather than inside it.
 
 It is built on [FastMCP](https://gofastmcp.com) 4 and ships as a container image.
 
-> **Status: scaffold.** `hello`, `get_trs_info`, and `list_tool_classes` have working
-> bodies; the other four Dockstore tools are declared — names, arguments, and response
-> shapes — but each one raises `NotImplementedError` until it is wired up to the
-> Dockstore API.
+> **Status: prototype without search.** The GA4GH TRS tools (`get_trs_info` through
+> `get_tool_descriptor_by_path`) have working bodies; the other four Dockstore tools are
+> declared — names, arguments, and response shapes — but each one raises
+> `NotImplementedError` until it is wired up to the Dockstore API.
 
 ## Requirements
 
@@ -116,29 +116,39 @@ over the environment.
 | `DOCKSTORE_MCP_PATH`          | `--path`          | `/mcp`                  | Path the MCP endpoint is served from             |
 | `DOCKSTORE_MCP_LOG_LEVEL`     | `--log-level`     | `INFO`                  | Logging verbosity                                |
 | `DOCKSTORE_MCP_DOCKSTORE_URL` | `--dockstore-url` | `https://dockstore.org` | Dockstore instance whose APIs are exposed        |
+| `DOCKSTORE_MCP_GIT_REF`       |                   | package version         | Version in the `dockstore-mcp/<ref>` User-Agent  |
 
 The container image overrides the first four so that it listens on `0.0.0.0:8000` out of
-the box. It also sets a few `FASTMCP_*` variables so that a deployed server logs plainly
-and does not check PyPI for updates on startup; see the
-[FastMCP settings](https://gofastmcp.com) for the full list.
+the box, and sets `DOCKSTORE_MCP_GIT_REF` from its `GIT_REF` build argument, which the
+release workflow and `make docker-build` fill in with the git tag or ref being built. It
+also sets a few `FASTMCP_*` variables so that a deployed server logs plainly and does not
+check PyPI for updates on startup; see the [FastMCP settings](https://gofastmcp.com) for
+the full list.
 
 ## Tools
 
-| Tool                | Description                                                                          |
-| ------------------- | ------------------------------------------------------------------------------------- |
-| `hello`             | Greets the caller and reports the Dockstore instance and server version. No I/O.      |
-| `get_trs_info`      | Describes this instance's GA4GH TRS API: identifiers, version, and operator.          |
-| `list_tool_classes` | Lists the tool classes (e.g. `Workflow`) this instance's TRS API sorts entries into.   |
-| `search_entries`    | Searches entries by keyword and facet, the equivalent of the site's Search page.      |
-| `get_entry`         | Retrieves the requested fields of one entry.                                          |
-| `get_version`       | Retrieves the requested fields of one version of an entry.                            |
-| `get_file`          | Retrieves the requested fields of one file belonging to a version.                    |
-
-`get_trs_info` and `list_tool_classes` call Dockstore's GA4GH TRS V2 API directly. The
-last four are scaffolding and are not implemented yet. They are a chain: `search_entries`
-yields entry identifiers, an entry yields version identifiers, and a version yields file
-paths. Each lookup takes a list of fields so that a caller can ask for a name and a date
-without also pulling down a README or a whole descriptor.
+| Tool                          | Implemented | Description                                                                          |
+| ----------------------------- | ----------- | ------------------------------------------------------------------------------------ |
+| `get_trs_info`                | ✅          | Reports instance and version; unless `local_only`, also TRS info and tool classes.   |
+| `list_tools`                  | ✅          | Lists one page of TRS tools, optionally filtered by name, class, language, etc.      |
+| `get_tool`                    | ✅          | Retrieves one TRS tool by id, with all of its versions in full or summarized.        |
+| `get_tool_version`            | ✅          | Retrieves one version of a TRS tool: authors, images, languages, optionally files.   |
+| `get_tool_descriptor_by_path` | ✅          | Fetches a version's primary descriptor, or any file get_tool_version lists, by path. |
+| `search_entries`              | ❌          | Searches entries by keyword and facet, the equivalent of the site's Search page.     |
+| `get_entry`                   | ❌          | Retrieves the requested fields of one entry.                                         |
+| `get_version`                 | ❌          | Retrieves the requested fields of one version of an entry.                           |
+| `get_file`                    | ❌          | Retrieves the requested fields of one file belonging to a version.                   |
+
+The TRS tools, from `get_trs_info` to `get_tool_descriptor_by_path`, call Dockstore's GA4GH
+TRS V2 API directly. They form a chain: `list_tools` yields tool ids, a
+tool yields version names, and `get_tool_version` with `files` yields the paths that
+`get_tool_descriptor_by_path` takes. Pass `summary` to `list_tools` to get
+each tool's id, languages, and version names without its full README and version details.
+
+The last four are scaffolding and are not implemented yet. They are a chain too:
+`search_entries` yields entry identifiers, an entry yields version identifiers, and a
+version yields file paths. Each lookup takes a list of fields so that a caller can ask
+for a name and a date without also pulling down a README or a whole descriptor.
 
 ## Layout
 
@@ -152,9 +162,8 @@ src/dockstore_mcp/
 └── tools/
     ├── __init__.py  registers every tool group
     ├── entries.py   get_entry, get_version, get_file
-    ├── hello.py     the hello tool
     ├── search.py    search_entries
-    └── trs.py       get_trs_info, list_tool_classes
+    └── trs.py       get_trs_info and the other GA4GH TRS tools
 tests/               pytest suite, using FastMCP's in-memory client
 Dockerfile           two-stage build of the deployable image
 ```

src/dockstore_mcp/config.py

@@ -24,6 +24,8 @@
 from pydantic import Field, field_validator
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
+from dockstore_mcp import __version__
+
 Transport = Literal["stdio", "http"]
 LogLevel = Literal["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]
 
@@ -52,6 +54,14 @@ class Settings(BaseSettings):
         description="Base URL of the Dockstore instance whose APIs this server exposes.",
     )
 
+    git_ref: str | None = Field(
+        default=None,
+        description=(
+            "Git tag or ref this server was built from, e.g. '1.21.0'; set at build time. "
+            "Falls back to the package version."
+        ),
+    )
+
     @field_validator("dockstore_url")
     @classmethod
     def _strip_trailing_slash(cls, value: str) -> str:
@@ -74,6 +84,16 @@ def api_url(self) -> str:
         """Base URL of the instance's proprietary Dockstore API."""
         return f"{self.dockstore_url}/api"
 
+    @property
+    def server_version(self) -> str:
+        """Version this server reports: the git ref it was built from, else the package version."""
+        return self.git_ref or __version__
+
+    @property
+    def user_agent(self) -> str:
+        """User-Agent sent with every request to Dockstore, e.g. 'dockstore-mcp/1.21.0'."""
+        return f"dockstore-mcp/{self.server_version}"
+
 
 @lru_cache(maxsize=1)
 def get_settings() -> Settings: