openaps 0.1.5

DIY Open Source Artificial Pancreas System.

# openaps utility belt

These are the [core utilities][proposal] 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][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]
(http://bit.ly/1NBbZtO). 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.

[GettingStarted]: https://github.com/openaps/openaps/wiki/GettingStarted
[wiki]: https://github.com/openaps/openaps/wiki
[proposal]: https://gist.github.com/bewest/a690eaf35c69be898711
[the openaps docs]: https://github.com/openaps/docs


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][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](https://pypi.python.org/pypi/openaps):

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 **device**s 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.