Felicity Web Based Instrument Interface

This package provides a command line interface for:

1. RS-232 device connection.
2. MLLP client and Server

Setup

Make sure you have MariaDb installed

create databse create database db_name;

grant all privileges on databse_name.* TO 'username'@'%' identified by '<password>';

flush privileges;

Download Miniconda and fix python to 3.11

$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-s390x.sh
$ bash Miniconda3-latest-Linux-s390x.sh
$ conda install python=3.11

Check python version

$ python3 --version or python --version
Python 3.x.x

git clone https://github.com/beak-insights/felicity-lablink.git
cd felicity-lablink && git checkput hl7tcp
pip3 install -r requirements.txt

Install the package as a simlink in order to local changes tracking:

$ pip install -e .

Update configs

cd felicity-lablink/src/flablink/
nano config.py  # and update as necessary

Make sure you have a working database before proceeding to this step

# Run alembic migrations to generate our database tables
cd felicity-lablink/src/flablink/
bash ./al_upgrade.sh

Seed the Db with starter config data

    $ flablink seed

Check for the latest device connected to your computer by:

$ s -lh /dev/

add user to dialout

You might get a permission denied to accedd usb and serial ports: Add and reboot

$ sudo gpasswd -a $USER dialout or sudo usermod -a -G dialout $USER

Simulation Tests

Simulation test with socat:

$ sudo apt-get install socat
$ socat -d -d pty,raw,echo=0 pty,raw,echo=0
2019/05/27 09:49:54 socat[19584] N PTY is /dev/pts/5
2019/05/27 09:49:54 socat[19584] N PTY is /dev/pts/6
2019/05/27 09:49:54 socat[19584] N starting data transfer loop with FDs [5,5] and [7,7]

Start the receiver (serial):

$ serial -s -p /dev/pts/6

Simulate the receiver (instrument):

$ echo -n -e '\x05' > /dev/pts/5
Opening session
-> <ENQ>
Initiating Establishment Phase ...
Ready for Transfer Phase ...
<- <ACK>
   
$ echo -n -e '\x021This is my first and last frame\x03F0\x0D\x0A' > /dev/pts/5
-> <STX>1This is my first and last frame<ETX>F0<CR><LF>
 Frame accepted
Transfer phase completed:
--------------------------------------------------------------------------------
This is my first and last frame
--------------------------------------------------------------------------------
Closing session: neutral state
<- <ACK>

$ echo -n -e '\x05' > /dev/pts/5
$ echo -n -e '\x021This is my first frame\x17F0\x0D\x0A' > /dev/pts/5
$ echo -n -e '\x022This is my second frame\x17F0\x0D\x0A' > /dev/pts/5
$ echo -n -e '\x023This is my third frame\x17F0\x0D\x0A' > /dev/pts/5
$ echo -n -e '\x024This is my fourth and last frame\x03F0\x0D\x0A' > /dev/pts/5
Opening session
-> <ENQ>
Initiating Establishment Phase ...
Ready for Transfer Phase ...
<- <ACK>
-> <STX>1This is my first frame<ETB>F0<CR><LF>
 Frame accepted
 Waiting for a new frame ...
<- <ACK>
-> <STX>2This is my second frame<ETB>F0<CR><LF>
 Frame accepted
 Waiting for a new frame ...
<- <ACK>
-> <STX>3This is my third frame<ETB>F0<CR><LF>
 Frame accepted
 Waiting for a new frame ...
<- <ACK>
-> <STX>4This is my fourth and last frame<ETX>F0<CR><LF>
 Frame accepted
Transfer phase completed:
--------------------------------------------------------------------------------
This is my first frame
This is my second frame
This is my third frame
This is my fourth and last frame
--------------------------------------------------------------------------------
Closing session: neutral state
<- <ACK>

Real Insrtument Setup

Serial ports are mostly set with a baudrate of 9600 by default, but you can modify these settings with stty command, if needed. Eg:

$ sudo stty -F /dev/ttyUSB0 9600

The same command, but without specifying the baudrate will give you the actual configuration

$ sudo stty -F /dev/ttyUSB0
speed 9600 baud; line = 0;
-brkint -imaxbel

All should be up by now: Test your serial or tcptip conections (Nb: use Web interface for production)

flablink serial --uid 0 --name AbbottM2000SP --code AbM200SP --path /dev/tty/USB0 --baud 9600 --protocol astm
flablink tcpip  --uid 1 --name AbbotAlinityM --code AlinityM --address 192.167.24.33 --port 3120 --socket server --protocol hl7

Serial Management with supervisor

Setup supervisor for easier script management manager

installation:

$ sudo apt update && sudo apt install supervisor

check status:

$ sudo systemctl status supervisor

open supervisor config file:

$ sudo nano /etc/supervisor/conf.d/felicity_lablink.conf

Copy and Paste any of the following programs based on available serial devices

[program:felicity_lablink]
command=/home/<user>/miniconda3/bin/python /home/<user>/miniconda3/bin/flablink serve --host 0.0.0.0 --port 8080
autostart=true
autorestart=true
stderr_logfile=/var/log/felicity_lablink.err.log
stdout_logfile=/var/log/felicity_lablink.out.log

inform supervisor of our new programs:

$ sudo supervisorctl reread

tell superviror enact any changes:

$ sudo supervisorctl update

Supervisor management commands

check program status:

$ sudo supervisorctl status

reload all services

$ sudo supervisorctl reload

reload or retart a single program:

$ sudo supervisorctl restart felicity_lablink

tail error logs:

$ sudo supervisorctl tail -f felicity_lablink stderr
or tail -f /var/log/felicity_lablink.err.log

tail output logs:

$ sudo supervisorctl tail -f felicity_lablink stdout
or tail -f /var/log/felicity_lablink.out.log

Done!