WopMars is a database-driven workflow manager written in python similar to GNU Makefile or Snakemake. The difference is that the definition file of WopMars takes into account input/output SQLITE table defined as python paths to SQLAlchemy models.

A Wopmars workflow requires the definition of three types of files:

  • The workflow definition file or wopfile
  • The tool wrappers
  • The models

The wopfile defines the rules to convert inputs into outputs based on a tool:

# Rule1 use SparePartsManufacturer to insert pieces informations into the table piece
rule Rule1:
    tool: 'wrapper.SparePartsManufacturer'
            pieces: 'input/pieces.txt'
            piece: 'model.Piece'

The value of the tool field are python paths to classes called wrappers compatible with WopMars. These wrapper classes are able to process inputs and outputs.

from wopmars.models.ToolWrapper import ToolWrapper

class SparePartsManufacturer(ToolWrapper):
    __mapper_args__ = {
        "polymorphic_identity": __module__

    def specify_input_file(self):
        return ["pieces"]

    def specify_output_table(self):
        return ["piece"]

    def specify_params(self):
        return {
            "max_price": int

    def run(self):
        session = self.session
        Piece = self.output_table("piece")

        with open(self.input_file("pieces")) as wr:
            lines = wr.readlines()

        for line in lines:
            splitted_line = line.split(";")
            piece_serial_number = splitted_line[0]
            piece_type = splitted_line[1]
            piece_price = float(splitted_line[2])
            if (self.option("max_price") and self.option("max_price" >= piece_price)) \
                    or self.option("max_price") is None:
                session.add(Piece(serial_number=piece_serial_number, price=piece_price, type=piece_type))


Input or output fields can contain file fields with normal file paths or table fields. The values of table fields are python paths to SQL Alchemy models in the PYTHONPATH:

from wopmars.Base import Base

from sqlalchemy import Column, Integer, String, Float

class Piece(Base):
    __tablename__ = "piece"

    id = Column(Integer, primary_key=True, autoincrement=True)
    serial_number = Column(String, unique=True)
    type = Column(String)
    price = Column(Float)

We recomend to organize wrappers and models for a particular aim in a python package to simplify development and installation of wrappers and classes.

|-- Wopfile.yml
|-- Wopfile2
|-- Wopfile3
|-- __init__.py
|-- bats.sh
|-- input
|   `-- pieces.txt
|-- model
|   |-- DatedPiece.py
|   |-- Piece.py
|   |-- PieceCar.py
|   |-- __init__.py
|-- output
|-- setup.py
`-- wrapper
    |-- AddDateToPiece.py
    |-- CarAssembler.py
    |-- SparePartsManufacturer.py
    |-- __init__.py

As shown in the next section (Quick start) After defining wrappers and modes in a dedicated python package and installing it you can run the workflow using a commands

wopmars -w Wopfile -D "sqlite:///db.sqlite" -v -p

Now that you should understand the basics components of WopMars, I recommend you to go to the quick start section to try a working example.