Python Tool

Note

Available in v0.9.0 and later

A PythonTool is a Janis mechanism for running arbitrary Python code inside a container.

class janis.PythonTool(**connections)

static code_block(**kwargs) → Dict[str, Any]

This code block must be 100% self contained. All libraries and functions must be imported and declared from within this block. :param kwargs: :return:

How to build my own Tool

• Create a class that inherits from PythonTool,
• The PythonTool uses the code signature for code_block to determine the inputs. This means you must use Python type annotations.
• The default image is python:3.8.1, this is overridable by overriding the container method.

Extra notes about the code_block:

• It must be totally self contained (including ALL imports and functions)
• The only information you have available is those that you specify within your method.

• Annotation notes:

  • You can annotate with regular Python types, like: str or int
  • You can annotate optionality with typings, like: Optional[str] or List[Optional[str]]
  • Do NOT use Array(String), use List[String] instead.
  • Annotating with Janis types (like String, File, BamBai, etc) might cause issues with your type hints in an IDE.

• A File type will be presented to your function as a string. You will need to open the file within your function.
• You must return a dictionary with keys corresponding to the outputs of your tool. - File outputs should be presented as a string, and will be coerced to a File / Directory later.
• Do NOT use j.$TYPE annotations (prefixed with j., eg: j.File or j.String) as annotations as this will fail at runtime.

from janis_core import PythonTool, TOutput, File
from typing import Dict, Optional, List, Any

class MyPythonTool(PythonTool):
    @staticmethod
    def code_block(in_string: str, in_file: File, in_integer: int) -> Dict[str, Any]:
        from shutil import copyfile

        copyfile(in_file, "./out.file")

        return {
            "myout": in_string + "-appended!",
            "myfileout": "out.file",
            "myinteger": in_integer + 1
        }

    def outputs(self) -> List[TOutput]:
        return [
            TOutput("myout", str),
            TOutput("myfileout", File),
            TOutput("myinteger", int)
        ]

    def id(self) -> str:
        return "MyPythonTool"

    def version(self):
        return "v0.1.0"

How to include a File inside your container

Use the type annotation File, and open it yourself, for example:

from janis_core import PythonTool, TOutput, File
from typing import Dict, Optional, List, Any

class CatPythonTool(PythonTool):
    @staticmethod
    def code_block(my_file: File) -> Dict[str, Any]:

        with open(my_file, "r") as f:
            return {
                "out": f.read()
            }

    def outputs(self) -> List[TOutput]:
        return [
            TOutput("out", str)
        ]

How to include an Array of strings inside my container

from janis_core import PythonTool, TOutput, File
from typing import Dict, Optional, List, Any

class JoinStrings(PythonTool):
    @staticmethod
    def code_block(my_strings: List[str], separator: str=",") -> Dict[str, Any]:

        return {"out": separator.join(my_strings)}

    def outputs(self) -> List[TOutput]:
        return [
            TOutput("out", str)
        ]