not an artificial pancreas system, tools for exploring DIY openaps
Python Shell Makefile
Latest commit 953347a Dec 26, 2016 @scottleibrand scottleibrand committed on GitHub Merge pull request #99 from openaps/dev
prep for 0.2.0 release

README.md

openaps utility belt

These are the core utilities needed to develop an open source artificial pancreas.

This is part of a series of tools to support a self-driven DIY implementation based on the OpenAPS reference design. The tools may be categorized as monitor (collecting data about environment, and operational status of devices and/or aggregating as much data as is relevant into one place), predict (make predictions about what should happen next), or control (enacting changes, and feeding more data back into the monitor).

By proceeding using these tools or any piece within, you agree to the copyright (see LICENSE.txt for more information) and release any contributors from liability.

Check out the openaps docs to help get you started.

Note: This is intended to be a set of tools to support a self-driven DIY implementation and any person choosing to use these tools is solely responsible for testing and implement these tools independently or together as a system. The DIY part of OpenAPS is important. While formal training or experience as an engineer or a developer is not required, what is required is a growth mindset to learn what are essentially "building blocks" to implement an OpenAPS instance. This is not a "set and forget" system; it requires diligent and consistent testing and monitoring to ensure each piece of the system is monitoring, predicting, and performing as desired. The performance and quality of your system lies solely with you.

Additionally, this community of contributors believes in "paying it forward", and individuals who are implementing these tools are asked to contribute by asking questions, helping improve documentation, and contribute in other ways.

openaps loop hardware

This is not an artificial pancreas, but rather tools which independently allow:

  • monitor - Collect data about environment, and operational status of devices. Aggregate as much data relevant to therapy as possible into one place. We propose a tool, openaps-use as a proof of concept.

  • predict - Can make predictions about what should happen next.

  • control - Can enact changes in the world: emails, placing phone calls, SMS, issuing commands to pumps.

Install

There are two ways to install openaps, from source, and as a python package via setuptools.

The following apt-get dependencies are required (they can be installed through variety of means, in debian/ubuntu and apt based systems the following packages are recommended/required:

sudo apt-get install python python-dev python-setuptools python-software-properties python-numpy

From source

See GettingStarted for more important information about versions of software dependencies, but to install from source clone this repo, and issue:

sudo python setup.py develop

From pypi

To install from pypi:

sudo pip install -U openaps

This installs openaps system wide. Do not use openaps commands in the the openaps repo. Only use the openaps directory for hacking on the core library, or for managing upgrades through git. Running openaps inside of the openaps source directory will error in the best case, and mess up your openaps install in the worst case.

Updating
sudo easy_install -ZU openaps

Usage

usage: openaps [-h] [-c C C] [-C CONFIG] [--version] [command] ...

openaps - openaps: a toolkit for DIY artificial pancreas system

positional arguments:
  • command
  • args

optional arguments:

-h, --help            show this help message and exit
-c C C
-C CONFIG, --config CONFIG
--version             show program's version number and exit

Utilities for developing an artificial pancreas system. openaps helps you manage and structure reports for various devices.

All of the device and report add and show commands modify openaps.ini in the current working directory, which is assumed to be a git repo explicitily dedicated to helping develop and configure a DIY artificial pancreas system. This means openaps is an SDK for an artificial pancreas system, not an artificial pancreas system.

See openaps init for setting up a brand new instance of your own openaps, or see the notes below for details on how to convert an existing git repo into an instance of openaps.

Common workflows:

openaps init
openaps device <cmd>

  Device commands allow you to match a device driver, with a name
  and a configuration.

  add     - add device config to `openaps.ini`
  remove  - remove device from `openaps.ini`
  show    - print device uri, list all by default

openaps use [--format <json,stdout,text>]
            [--output <filename>]
        <device>
        <use>
        [use-args...]

  For each device registered, the vendor implementation provides a
  number of uses.  This allows users to experiment with reports.

openaps report <cmd>

  Reports match a device use to a format and filename.

  add     - add report config to `openaps.ini`
  remove  - remove report from `openaps.ini`
  show    - print report uri, list all by default
  invoke  - run and save report in file

Init new openaps environment

Do not use openaps commands in the the openaps repo. Only use the openaps directory for hacking on the core library, or for managing upgrades through git. Instead change to a new directory, not managed by git: cd ~/Documents.

Setup of new instance:

openaps init myopenaps    - this creates an instance of openaps in a new
                            directory, called myopenaps


cd myopenaps - change directory to root of new repo

A valid instance of openaps is a git repo with a file called openaps.ini present.

openaps will track configuration and some status information inside of openaps.ini.

Init existing git repo as openaps-environment

If you already have a git repo which you would like to become a valid openaps environent, in the root of your repo, run:

touch openaps.ini
git add openaps.ini
git commit -avm 'init openaps'

Now, wth a valid openaps environment, you can register devices for use. A device is implemented by a vendor. openaps provides a modular, language and process independent environment for creating vendors and devices.

Managing devices

To register devices for use, see openaps device commands:

openaps device -h
openaps device add <name> <vendor> [opts...]
eg:
# register a medtronic device named pump
openaps device add pump medtronic 665455
# register a dexcom device named cgm
openaps device add cgm dexcom

Using devices

Now that devices are known, and we have a variety of commands available. We can explore how to produce reports by using devices with the openaps use command:

openaps use <device-name> <use-name> [opts]

openaps use commands can only be used after devices have been added to the openaps.ini config using openaps device add. Eg:

openaps use pump -h        - show available commands for the
                             device known as "pump"
openaps use pump iter_pump 100 - get last 100 pump history records
                             from the device called pump
openaps use cgm -h         - show available commands for the
                             device known as "cgm"
openaps use cgm glucose

Save reports

After experimenting with openaps use commands, users can save reports using the openaps report commands. openaps report commands map openaps use commands to filenames:

openaps report add

Adding a report means configuring a use command with a format and a output, most commonly, a filename is used as the output.

openaps report add <report-name> <report-formatter> <device> <use> [opts]

# add a report, saved in a file called pump-history.json, which is
# JSON format, from device pump using use iter_pump.
openaps report add pump-history.json JSON pump iter_pump 100

# add a report, saved in a file called glucose.json, which is
# JSON format, from device cgm using use glucose.
openaps report add glucose.json JSON cgm glucose

invoke reports to run and save the results of the use

openaps report invoke

Invoking a report means running a use command according to it's configuration.

# invoke the report to create glucose.json
openaps report invoke glucose.json

# invoke the report to create pump-history.json
openaps report invoke pump-history.json

All commands support tab completion, and -h help options to help explore the live help system.

Sample use commands

medtronic

Assuming device is named pump:

usage: openaps-use pump [-h]
                        {Session, bolus, iter_glucose, iter_pump,
                        model, mytest, read_basal_profile_A,
                        read_basal_profile_B,
                        read_basal_profile_std, read_carb_ratios,
                        read_clock, read_current_glucose_pages,
                        read_current_history_pages,
                        read_glucose_data, read_history_data,
                        read_selected_basal_profile,
                        read_settings, read_status,
                        read_temp_basal, reservoir, resume_pump,
                        scan, set_temp_basal, settings, status,
                        suspend_pump}
                        ...

positional arguments:
  {Session, bolus, iter_glucose, iter_pump, model, mytest,
  read_basal_profile_A, read_basal_profile_B,
  read_basal_profile_std, read_carb_ratios, read_clock,
  read_current_glucose_pages, read_current_history_pages,
  read_glucose_data, read_history_data,
  read_selected_basal_profile, read_settings, read_status,
  read_temp_basal, reservoir, resume_pump, scan, set_temp_basal,
  settings, status, suspend_pump}
                        Operation
    Session             session for pump
    bolus               Send bolus.
    iter_glucose        Read latest 100 glucose records
    iter_pump           Read latest 100 pump records
    model               Get model number
    mytest              Testing read_settings
    read_basal_profile_A
                        Read basal profile A.
    read_basal_profile_B
                        Read basal profile B.
    read_basal_profile_std
                        Read default basal profile.
    read_carb_ratios    Read carb_ratios.
    read_clock          Read date/time of pump
    read_current_glucose_pages
                        Read current glucose pages.
    read_current_history_pages
                        Read current history pages.
    read_glucose_data   Read pump glucose page
    read_history_data   Read pump history page
    read_selected_basal_profile
                        Fetch the currently selected basal profile.
    read_settings       Read settings.
    read_status         Get pump status
    read_temp_basal     Read temporary basal rates.
    reservoir           Get pump remaining insulin
    resume_pump         resume pumping.
    scan                scan for usb stick
    set_temp_basal      Set temporary basal rates.
    settings            Get pump settings
    status              Get pump status (alias for read_status)
    suspend_pump        Suspend pumping.

optional arguments:
  -h, --help            show this help message and exit

Some commands like read_glucose_data, read_history_data take a page parameter, describing which page to fetch.

Some commands like bolus, set_temp_basal, take an input parameter which may be - for stdin or a filename containing a json data structure which represents the request.

All commands support -h and --help output.

dexcom

usage: openaps-use cgm [-h] {glucose,iter_glucose,scan} ...

positional arguments:
  {glucose,iter_glucose,scan}
                        Operation
    glucose             glucose (will pull all records)
    iter_glucose <n>       glucose ('n' for the number of records you want)
    scan                scan for usb stick

optional arguments:
  -h, --help            show this help message and exit

License

MIT License

Copyright (c) 2016 Ben West Copyright (c) 2015 Ben West

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.