placeholder -- LIS1 protocol listening server

version: 20201030a

A flask based project that collects and retransmits Quidel instrument data. The Sofia2 is a Fluorescent Immunoassay Analyzer and has been used to communicate testing results via the LIS1/ASTM protocol to this service.

Install/Setup

Install packages needed to compile python libraries

sudo apt install git git-flow build-essential autoconf  zlib1g-dev libncursesw5-dev \
libreadline-gplv2-dev libssl-dev libgdbm-dev libc6-dev libsqlite3-dev libbz2-dev \
libffi-dev liblzma-dev postgresql postgresql-contrib \
postgresql-server-dev-all libacl1-dev libpango1.0-0 libcairo2 libpq-dev \
libtiff-dev keychain  uuid-dev libcap-dev libpcre3 libpcre3-dev libjpeg-dev \
automake autotools-dev dh-make debhelper devscripts fakeroot xutils lintian pbuilder

Setup Pyenv : [https://github.com/pyenv/pyenv]

git clone https://github.com/pyenv/pyenv.git ~/.pyenv
git clone https://github.com/pyenv/pyenv-virtualenv.git ~/.pyenv/plugins/pyenv-virtualenv
## update shell
# - bash only -
echo 'export PYENV_ROOT="$HOME/.pyenv"' >> ~/.bash_profile
echo 'export PATH="$PYENV_ROOT/bin:$PATH"' >> ~/.bash_profile
echo 'eval "$(pyenv virtualenv-init -)"' >> ~/.bash_profile
# - zsh only -
echo 'export PYENV_ROOT="$HOME/.pyenv"' >> ~/.zshrc
echo 'export PATH="$PYENV_ROOT/bin:$PATH"' >> ~/.zshrc
echo 'eval "$(pyenv virtualenv-init -)"' >> ~/.zshrc
# reload shell
git clone https://github.com/pyenv/pyenv-update.git $(pyenv root)/plugins/pyenv-update
git clone https://github.com/pyenv/pyenv-doctor.git $(pyenv root)/plugins/pyenv-doctor
git clone https://github.com/doloopwhile/pyenv-register.git $(pyenv root)/plugins/pyenv-register
git clone https://github.com/pyenv/pyenv-which-ext.git $(pyenv root)/plugins/pyenv-which-ext
# Reload shell again

Install python under pyenv

pyenv install 3.7.9
pyenv virtualenv 3.7.9 lis-env
# Clone "project"
mkdir -p $HOME/projects/placeholder-dev
cd $HOME/projects/placeholder-dev
git clone [email protected]:ua-data7/placeholder.git placeholder
pyenv local lis-env
cd ./placeholder
pip install -r requirements.txt

Setup Config

cp example.env .env

Now edit the .env file and change:

• SQLALCHEMY_DATABASE_URI
• SECRET_KEY
• DEFAULT_LIS_NIC
• DEFAULT_LIS_PORT
• SARS_UPLINK_API_URL
• SARS_UPLINK_API_KEY

Note the value for SQLALCHEMY_DATABASE_URI is set as:

SQLALCHEMY_DATABASE_URI='postgresql://databaseuser:databasepass@localhost:5432/databasename'

Which might look like:

SQLALCHEMY_DATABASE_URI='postgresql://agentpi:somesecretpassword@localhost:5432/agentpidb'

Setup database

Become postgres admin

sudo su - postgres

Create a user for our app (define password)

createuser agentpi -P

Create a database for our app

createdb --template=template1 --encoding=UTF8 --owner=agentpi agentpidb

Test service is working

In three separate terminals, launch the following commands:

1. Terminal #1 LIS service flask start_lis_server
2. Terminal #2 Webserver flask run
3. Terminal #3 Test command flask send_lis_test

This should result in a message on flask webserver like so:

{
   'resultTime': '20200727154712',
   'results': 'negative',
   'serialNo': '29000021',
   'testType': 'SARS',
   'vialId': 'TST1-0000001'
}

Usage

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Contributing

1. Fork it!
2. Create your feature branch: git checkout -b my-new-feature
3. Commit your changes: git commit -am 'Add some feature'
4. Push to the branch: git push origin my-new-feature
5. Submit a pull request :D

History

None yet

Credits

Hagan Franks / Jim Davis / Nirav Merchant / ....

License

see license documentation here