flowsaber 0.1.3.7.0

A dataflow based workflow framework

A dataflow based workflow framework.

work in progress

Features

• Dataflow-like flow/task composing syntax inspired from nextflow 's DSL2.
• Pure python: No DSL, Import/Compose/Modify Task/Flow python objects at will.
  • Extensible and interactive due to dynamic nature of Python.
    • Task Cache.
    • ...
• Distributable: Use Dask distributed as Task executor, can deploy in local, cluster, cloud.
• Hybrid model.
  • Build Flow in Local python or web UI.
  • Schedule/Monitor flow execution in remote server through python or web UI.

Web UI

sabermap

Install

pip install flowsaber

Example

• A minimal working example consists most features and usages of flowsaber.

from flowsaber.api import *

@task
def add(self, num):  # self is optional
    return num + 1

@task
def multiply(num1, num2):
    return num1 * num2

@shell
def write(num):
    """echo {num} > {num}.txt"""
    return '*.txt'

@task
def read(f: File):
    return open(str(f)).readlines()

@flow
def sub_flow(num):
    return add(num) | map_(lambda x: x ** 2) | add

@flow
def my_flow(num):
    [sub_flow(num), sub_flow(num)] | multiply \
    | write | read | flatten \
    | map_(lambda x: int(x.strip())) \
    | view

num_ch = Channel.values(1, 2, 3, 4, 5, 6, 7, 8)
# resolve dependencies
workflow = my_flow(num=num_ch)
run(workflow)

Example to run in remote

Both server and agent need to be run in background before submitting flowruns.

Start server(API endpoint)

In bash shell.

flowsaber server

Start agent(Flow dispatcher)

In bash shell.

flowsaber agent --server "http://127.0.0.1:8000" --id test

Create flow and schedule for running

In python script or IPython console.

from flowsaber.api import *
@task
def add(num):
    print("This is meesage send by print to stdout in task")
    print("This is meesage send by print to stderr in task", file= sys.stderr)
    a = 1
    for i in range(10000000):
        a += 1
    return num + 1

@flow
def myflow(num):
    return num | add | add | view | add | view

num_ch = Channel.values(*list(range(10)))
f = myflow(num_ch)

run(f, server_address="http://127.0.0.1:8000", agent_id="test")

Test

python -m pytest tests -s -o log_cli=True -vvvv

TODO

• Pbs/Torque executor
• More cache mode.
• Supportrun in Cloud platform.
• Run CWL script, Convert between CWL and flowsaber flow.

Reference

• nextflow
• prefect