FNNDSC / pfmongo

A class-based module (and script) to interact with a docker-compose managed MongoDB.

pfmongo

Table of Contents

Quick Overview

pfmongo is a python client/module (CLI and API) for simplifying the interaction with a MongoDB. The module provides some idiosyncratic abstractions that are nonetheless hoped to be logically straightforward. The repository includes a docker-compose.yml that allows for easy instantiation of the MongoDB infrastructure.

Warning, Will Robinson!

If you wish to use pfmongo on your own computer, you do need to note these prerequisites:

docker and docker-compose

Since pfmongo interacts with a MongoDB, the easiest mechanism to deploy this database is via docker-compose and hence docker. Installation of these is beyond the scope of this document, but should be straightforward enough. Google is your friend in that quest.

Overview

pfmongo provides a somewhat opinionated abstraction for interacting with a MongoDB.

Installation

Using PyPI

The best method of installing this script and all of its dependencies is by fetching it from PyPI using a python virtual environment.

pip3 install pfmongo

Using CLI

Alternatively, from a cloned version of the repository:

pip3 install -r requirements.txt -U ./

or for development purposes

pip3 install -r requirements.txt -e ./

Running

Ecosystem

Assuming you have docker and docker-compose on your system, do

docker-compose up -d

Environment

Several environment variables need to be set prior to using pfmongo:

Linux

export MD_URI=mongodb://localhost:27017 && export MD_USERNAME=admin && export MD_PASSWORD=admin && export MD_SESSIONUSER=rudolph

Windows

$env:MD_USERNAME=admin
$env:MD_PASSWORD=admin
$env:MD_URI=mongodb://localhost:27017
$env:MD_SESSIONUER=rudolph

Command line arguments

pfmongo --help

Examples

alias mdb='pfmongo'
mdb database connect PACSDCM
mdb collection connect MRN
mdb document add --file examples/lld.json --id lld.json

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