get_protocol_steps

Retrieve detailed steps for scientific protocols by providing the protocol ID, enabling access to structured methodology information from protocols.io.

Instructions

Retrieve the steps for a specific protocol by its protocol ID.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`protocol_id`	Yes	Unique identifier for the protocol

Implementation Reference

src/protocols_io_mcp/tools/protocol.py:203-214 (handler)

The handler function for the 'get_protocol_steps' tool. It takes a protocol_id, calls the protocols.io API to fetch steps, parses them into ProtocolStep objects, or returns an error.

@mcp.tool()
async def get_protocol_steps(
    protocol_id: Annotated[int, Field(description="Unique identifier for the protocol")]
) -> list[ProtocolStep] | ErrorMessage:
    """
    Retrieve the steps for a specific protocol by its protocol ID.
    """
    response = await helpers.access_protocols_io_resource("GET", f"/v4/protocols/{protocol_id}/steps?content_format=markdown")
    if response["status_code"] != 0:
        return ErrorMessage.from_string(response["status_text"])
    steps = [ProtocolStep.from_api_response(step) for step in response.get("payload", [])]
    return steps

src/protocols_io_mcp/tools/protocol.py:55-110 (schema)

Pydantic model for ProtocolStep, defining the output structure for protocol steps, including parsing logic from API response.

class ProtocolStep(BaseModel):
    id: Annotated[str, Field(description="Unique identifier for the step")]
    description: Annotated[str, Field(description="Description of the step")]
    materials: Annotated[list[Material], Field(description="Materials required for this step. Empty if no materials are needed or if source data could not be parsed")] = Field(default_factory=list)
    reference_protocol_ids: Annotated[list[int], Field(description="Protocol IDs referenced by this step. Empty if no references exist or if source data could not be parsed")] = Field(default_factory=list)

    @staticmethod
    def parse(step: str) -> dict:
        description = []
        materials = []
        reference_protocol_ids = []
        material_flag = False
        reference_flag = False
        for line in step.splitlines():
            if material_flag is False and reference_flag is False:
                if line == "[Materials]":
                    material_flag = True
                    reference_flag = False
                elif line == "[Protocol References]":
                    reference_flag = True
                    material_flag = False
                elif len(line) > 0:
                    description.append(line)
            elif material_flag:
                if len(line) == 0 or line[0] != '-':
                    material_flag = False
                    continue
                data = line.split()
                materials.append(Material(
                    name=data[1],
                    quantity=float(data[2]),
                    unit=data[3]
                ))
            elif reference_flag:
                if len(line) == 0 or line[0] != '-':
                    reference_flag = False
                    continue
                data = line.split("[")[1].split("]")[0]
                reference_protocol_ids.append(int(data))
        description = "\n".join(description)
        return {
            "description": description,
            "materials": materials,
            "reference_protocol_ids": reference_protocol_ids
        }

    @classmethod
    def from_api_response(cls, data: dict) -> "ProtocolStep":
        parsed_step = ProtocolStep.parse(data["step"])
        return cls(
            id=data["guid"],
            description=parsed_step["description"],
            materials=parsed_step["materials"],
            reference_protocol_ids=parsed_step["reference_protocol_ids"]
        )

src/protocols_io_mcp/server.py:10-10 (registration)
Registration of tools by importing the tools module, which executes the @mcp.tool() decorators in protocol.py to register 'get_protocol_steps' and other tools.
```
importlib.import_module('protocols_io_mcp.tools')
```

src/protocols_io_mcp/utils/helpers.py:10-17 (helper)

Helper function used by the tool to make authenticated HTTP requests to the protocols.io API.

async def access_protocols_io_resource(method: Literal["GET", "POST", "PUT", "DELETE"], path: str, data: dict = None) -> dict[str, Any]:
    """Access protocols.io API with specified method and path."""
    headers = {
        "Authorization": f"Bearer {PROTOCOLS_IO_CLIENT_ACCESS_TOKEN}"
    }
    async with httpx.AsyncClient(timeout=30.0) as client:
        response = await client.request(method, f"{PROTOCOLS_IO_API_URL}{path}", json=data, headers=headers)
        return response.json()

protocols-io-mcp-server