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Project Description

Overview

This repository provides several python scripts that can be used as either standalone executables or as modules in python code. The common theme of this respository is process (and file) management. The following scripts/modules are provided:

  • pman: a process manager;
  • pfioh: a file IO manager;
  • purl: a tool to transfer data using HTTP (similar to curl);
  • crunner: a low-level encapsulator that runs commands (and is used by pman).

pman

Most simply, pman manages processes, i.e. programs or applications that are run by an underlying system. Typically, these processes are command line applications (i.e. have no GUI) and usually do not interact really with a user at all. The primary purpose of pman is to provide other software agents the ability to execute processes via http. In addition, pman keeps a record of the current and historical state of processes that it has executed and is thus able to respond to queries about the processes. Some of the queries that pman can address are

  • state: Is job <XYZ> still running?
  • result: What is the stdout (or stderr) from job <XYZ>?
  • control: Kill job <XYZ>

pman also maintains a persistent human-readable/friendly database-in-the-filesystem of jobs and states of jobs.

pfioh

While pman is a service that runs other programs (and provides information about them), pfioh is a service that pushes/pulls files and directories between different locations.

purl

Since both pman and pfioh are services that listen for messages transported via http , a companion client application called purl is provided that can be used to speak to both pman and pfioh.

crunner

crunner is the actual “shim” or “wrapper” around an underlying system process. Most users will not need nor want necessarily to use crunner directly, although in many respects pman is a thin layer above crunner.

Installation

Installation is relatively straightforward, and we recommend using either python virtual environments or docker.

Python Virtual Environment

On Ubuntu, install the Python virtual environment creator

sudo apt install virtualenv

Then, create a directory for your virtual environments e.g.:

mkdir ~/python-envs

You might want to add to your .bashrc file these two lines:

export WORKON_HOME=~/python-envs
source /usr/local/bin/virtualenvwrapper.sh

Then you can source your .bashrc and create a new Python3 virtual environment:

source .bashrc
mkvirtualenv --python=python3 python_env

To activate or “enter” the virtual env:

workon python_env

To deactivate virtual env:

deactivate

Using the fnndsc/ubuntu-python3 dock

We provide a slim docker image with python3 based off Ubuntu. If you want to play inside this dock and install pman manually, do

docker pull fnndsc/ubuntu-python3

This docker has an entry point python3. To enter the dock at a different entry and install your own stuff:

docker run -ti --entrypoint /bin/bash fnndsc/ubuntu-python3

Now, install pman and friends using pip

apt update && \
apt install -y libssl-dev libcurl4-openssl-dev librtmp-dev && \
pip install pman

If you do the above, remember to commit your changes to the docker image otherwise they’ll be lost when you remove the dock instance!

 docker commit <container-ID> local/ubuntu-python3-pman

where ``<container-ID>`` is the ID of the above container.

Using the fnndsc/pman dock

The easiest option however, is to just use the fnndsc/pman dock.

docker pull fnndsc/pman

and then run

docker run --name pman fnndsc/pman

Usage

For usage of the individual components, pman, pfioh, and purl, consult the relevant wiki pages.

pman usage

For pman detailed information, see the pman wiki page.

pfioh usage

For pfioh detailed information, see the pfioh wiki page.

purl usage

For purl detailed information, see the purl wiki page.

Release History

Release History

0.12.7

This version

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0.12.6

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0.12.5

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0.12.4

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0.12.3

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0.12.2

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0.12.1

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0.12.0

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0.11.4

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0.11.3

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0.11.2

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0.11.1

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0.11.0

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0.10.4

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0.10.3

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0.10.2

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0.10.1

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0.10

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0.9.1

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0.9

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0.8

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0.7.1

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0.7

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0.6

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0.5.1

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0.5

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0.4

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0.3

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0.2

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0.1

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Download Files

Download Files

TODO: Brief introduction on what you do with files - including link to relevant help section.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
pman-0.12.7.tar.gz (67.5 kB) Copy SHA256 Checksum SHA256 Source Mar 21, 2017

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