protocols-io-mcp-server

Instructions

Implementation Reference

• src/protocols_io_mcp/tools/protocol.py:349-364 (handler)

  The main handler function for the 'delete_protocol_step' tool. It is decorated with @mcp.tool(), which registers it as an MCP tool. The function deletes a specific step from a protocol using the Protocols.io API and returns the updated list of steps.

  @mcp.tool()
  async def delete_protocol_step(
      protocol_id: Annotated[int, Field(description="Unique identifier for the protocol")],
      step_id: Annotated[str, Field(description="Unique identifier for the step to be deleted")]
  ) -> list[ProtocolStep] | ErrorMessage:
      """
      Delete a specific step from a protocol by providing both the protocol ID and step ID.
      """
      response_delete_protocol_step = await helpers.access_protocols_io_resource("DELETE", f"/v4/protocols/{protocol_id}/steps", {"steps": [step_id]})
      if response_delete_protocol_step["status_code"] != 0:
          return ErrorMessage.from_string(response_delete_protocol_step["status_text"])
      response_get_protocol_steps = await helpers.access_protocols_io_resource("GET", f"/v4/protocols/{protocol_id}/steps?content_format=markdown")
      if response_get_protocol_steps["status_code"] != 0:
          return ErrorMessage.from_string(response_get_protocol_steps["status_text"])
      steps = [ProtocolStep.from_api_response(step) for step in response_get_protocol_steps.get("payload", [])]
      return steps

• src/protocols_io_mcp/tools/protocol.py:349-349 (registration)

  The @mcp.tool() decorator registers the delete_protocol_step function as an MCP tool.

  @mcp.tool()

• src/protocols_io_mcp/tools/protocol.py:350-364 (schema)

  Input schema defined via Annotated types in the function signature: protocol_id (int), step_id (str). Output is list[ProtocolStep] or ErrorMessage.

  async def delete_protocol_step(
      protocol_id: Annotated[int, Field(description="Unique identifier for the protocol")],
      step_id: Annotated[str, Field(description="Unique identifier for the step to be deleted")]
  ) -> list[ProtocolStep] | ErrorMessage:
      """
      Delete a specific step from a protocol by providing both the protocol ID and step ID.
      """
      response_delete_protocol_step = await helpers.access_protocols_io_resource("DELETE", f"/v4/protocols/{protocol_id}/steps", {"steps": [step_id]})
      if response_delete_protocol_step["status_code"] != 0:
          return ErrorMessage.from_string(response_delete_protocol_step["status_text"])
      response_get_protocol_steps = await helpers.access_protocols_io_resource("GET", f"/v4/protocols/{protocol_id}/steps?content_format=markdown")
      if response_get_protocol_steps["status_code"] != 0:
          return ErrorMessage.from_string(response_get_protocol_steps["status_text"])
      steps = [ProtocolStep.from_api_response(step) for step in response_get_protocol_steps.get("payload", [])]
      return steps

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

  ProtocolStep model used for parsing and returning steps in the tool's output.

  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/tools/protocol.py:148-154 (helper)

  ErrorMessage model used for error responses in the tool.

  class ErrorMessage(BaseModel):
      error_message: Annotated[str, Field(description="Error message describing the issue encountered")]
  
      @classmethod
      def from_string(cls, message: str) -> "ErrorMessage":
          return cls(error_message=message)