Commit 72402bc3 authored by Yakubov, Sergey's avatar Yakubov, Sergey
Browse files

Merge branch '32-add-tool-runner-class' into 'main' 

Add tool runner class

Closes #32

See merge request ndip/public-packages/nova-galaxy!24
parents 586fe193 4867159f

.pre-commit-config.yaml

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@@ -20,7 +20,7 @@ repos: 
  hooks:

    - id: mypy

      name: mypy

      entry: poetry run mypy src

      entry: poetry run mypy .

      language: system

      types: [python]

      verbose: true

docs/api_reference.rst

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@@ -20,3 +20,6 @@ API Reference 


.. automodule:: nova.galaxy.tool

   :members:



.. automodule:: nova.galaxy.tool_runner

   :members:

docs/core_concepts/index.rst

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@@ -14,3 +14,4 @@ nova-galaxy revolves around several key concepts that facilitate interaction wit 
   interactive_tools

   outputs

   parameters

   tool_runner

docs/core_concepts/tool_runner.rst

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.. _tool_runner:



Tool Runner

--------------



The `ToolRunner` is a helper class to run Galaxy tools using Blinker signals. This allows connect to connect

Galaxy with GUI in a decoupled way.



.. code-block:: python



   import blinker

   from nova.galaxy import ToolRunner

   from nova.common.signals import Signal, ToolCommand, get_signal_id





   # create tool runner

   ToolRunner("runner_id", SomeTool(), lambda: "store_name", GALAXY_URL, GALAXY_API_KEY)



   # from somewhere else, e.g. reacting to a button click:

   async def start_tool():

       execution_signal = blinker.signal(get_signal_id("runner_id", Signal.TOOL_COMMAND))

       await execution_signal.send_async("sender_id", command=ToolCommand.START)



The ToolRunner needs a Tool class which it will manage. This class should inherit from the `BasicTool` and define

functions specific to the tool. For example:



.. code-block:: python



    from nova.galaxy import BasicTool

    from nova.galaxy import Connection, Parameters, Tool



    class RemoteCommandTool(BasicTool):

        """Class that prepares RemoteCommandTool tool."""



        def __init__(self) -> None:

            super().__init__()



        def prepare_tool(self) -> Tool:

            tool_params = Parameters()

            tool = Tool(id="neutrons_remote_command")

            return tool, tool_params



        def get_results(self, tool: Tool) -> bytes:

            outputs = tool.get_results()

            data = outputs.get_dataset("output1")

            return data.get_content()

poetry.lock

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