BPS2 - Blood Parameters Storage System

BPS2 is a simple command line interface written in bash to store previous measured blood parameters such as pressure (diastolic, systolic and pulse) and sugar level. By default, data is stored in sqlite file named blood.db in local directory. There is possibility to synchronize blood.db with postgresql server.

Installation

Prerequisites

sqlite3
postgresql ( :hand: optional)
bash

Install BPS2

Download and configure

Clone GitHub repository:

$ git clone git@github.com:pa810p/bps2.git

Copy blood_template.properties to blood.properties:

$ cp blood_template.properties blood.properties

Edit blood.properties according to your needs (database access :arrow_down:).

Initialize database:

sqlite (:bulb: note that sqlite3 database is default one so there is no need to use option -e sqlite)

./blood.sh -i createdb.sqlite

Then you can test if it works by inserting your first measurement:

$ ./blood.sh -p 123/80/90/
Using: blood.properties
measurement: 123/80/90/
Systolic: "123"
Diastolic: "80"
Pulse: "90"
Comment: ""

And check if it is persisted in database by using query:

$ ./blood.sh -q 'SELECT * FROM blood;'
Using: blood.properties
Executing query: SELECT * FROM blood;
2023-10-29 14:50:13|123|80|90|

postgresql ( :hand: optional) Create role and database on your postgresql system or ask administrator to create it:

postgres=# CREATE USER blood WITH ENCRYPTED PASSWORD 'password';
CREATE ROLE
postgres=# CREATE DATABASE blood;
CREATE DATABASE
postgres=# ALTER DATABASE blood OWNER TO blood; 
ALTER DATABASE

Initialize database:

$ ./blood.sh -i createdb.sql -e pgsql
Using: blood.properties
psql postgresql://blood:password@:5433/blood < createdb.sql
NOTICE:  table "blood" does not exist, skipping
DROP TABLE
NOTICE:  sequence "blood_id_seq" does not exist, skipping
DROP SEQUENCE
CREATE SEQUENCE
CREATE TABLE
NOTICE:  table "sugar" does not exist, skipping
DROP TABLE
NOTICE:  sequence "sugar_id_seq" does not exist, skipping
DROP SEQUENCE
CREATE SEQUENCE
CREATE TABLE

Then you can test if it works by inserting your first measurement:

$ ./blood.sh -e pgsql -p 123/12/12
Using: blood.properties
measurement: 123/12/12
Systolic: "123"
Diastolic: "12"
Pulse: "12"
Comment: ""
INSERT 0 1

And check if it is persisted in database by using query:

$ ./blood.sh -e pgsql -q 'SELECT * FROM blood;'
Using: blood.properties
Executing query: SELECT * FROM blood;
id |         datetime          | systolic | diastolic | pulse | comment 
----+---------------------------+----------+-----------+-------+---------
1 | 2023-10-29 14:33:52.10622 |      123 |        12 |    12 | 
(1 row)

Usage

$ ./blood.sh
Version: 1.2.6
Usage: ./blood.sh [OPTIONS]
OPTIONS include:
-a --urine-acid URINE_ACID           urine acid in blood in µmol/l using format of: 370/'comment'
-b --database-port DATABASE_PORT     database port
-A --import-urine-acid FILENAME      import urine acid from csv FILENAME
-c --cholesterol CHOLESTEROL         cholesterol in blood in µmol/l using format of: 370/'comment'
-C --import-cholesterol FILENAME     import cholesterol from csv FILENME
-D --dbname DATABASE_NAME            database name
-e --engine DATABASE_ENGINE          database engine can be either sqlite or pgsql
-f --format                          format display (column names, formatting, colors)
-h --help                            help screen
-H --host DATABASE_HOST              database host
-i --initialize INIT_FILENAME        initialize filename
-l [LIST_ENTRIES]                    list last LIST_ENTRIES (default from properties) entries of both pressure and sugar
   --list-cholesterol [LIST_ENTRIES] list last LIST_ENTRIES (default from properties) entries of cholesterol
   --list-pressure [LIST_ENTRIES]    list last LIST ENTRIES (default from properties) entries of pressure
   --list-sugar [LIST_ENTRIES]       list last LIST_ENTRIES (default from properties) entries of sugar
   --list-urine-acid [LIST_ENTRIES]  list last LIST_ENTRIES (default from properties) entries of urine acid
   --log-level [LEVEL]               logging level where LEVEL may be (0=critical, 1=error, 2=warning, 3=info
                                     4=debug)
-p --pressure MEASUREMENT            blood pressure measurement in format of: 120/80/90/'comment'
-P --import_pressure FILENAME        import pressure from csv FILENAME
                                     (systolic/diastolic/pulse/'comment') where comment is optional
-q --query QUERY                     SQL query provided to sqlite database (query should correspond with engine -e option)
-s --sugar SUGAR_LEVEL               sugar level in blood in mg/dL using format of: 123/'comment'
                                     where 'comment' is optional
   --empty                           measurement on empty stomach
   --full                            measurement on full stomach
-S --import-sugar FILENAME           import sugar from csv FILENAME
                                     where 'comment' is optional
-t --time TIME                       sets time in format 'yyyy-MM-dd HH:mm' or 'HH:mm'
                                     if 'HH:mm' format is used date is set to today
-U --user USERNAME                   database user name
-v --version                         displays version information and exits
-X --sync SOURCE:DESTINATION         synchronize databases (copy data from SOURCE to DESTINATION database
                                     either SOURCE or DESTINATION may be: sqlite, pgsql

Example: 
./blood.sh -e pgsql -i createdb.sql
./blood.sh -p 123/80/90/'my fancy comment'
./blood.sh -p 123/80/90/'my fancy comment' -t '2024-05-30 06:26'
./blood.sh -p 123/80/90/'my fancy comment' -t '06:31'

Example usage

Store blood pressure to sqlite database:

$ ./blood.sh -p 120/80/80/'after jogging'
$ ./blood.sh -p 120/80/80/

Store sugar level to sqlite database:

$ ./blood.sh -s 95/'2 hours after lunch'
$ ./blood.sh -s 95/

Synchronize local sqlite database with postgresql

$ ./blood.sh -X sqlite:pgsql

Web interface

Not implemented yet, see TODO section

Visualization

Grafana

Testing

Prerequisites

Tests are launched in dockerized environment Make sure you have installed:

docker

Install bats wherever you want, then copy directories : bats and test_helper into tests folder:

$ git init
$ git submodule add https://github.com/bats-core/bats-core.git test/bats
$ git submodule add https://github.com/bats-core/bats-support.git test/test_helper/bats-support
$ git submodule add https://github.com/bats-core/bats-assert.git test/test_helper/bats-assert
$ git submodule add https://github.com/bats-core/bats-assert.git test/test_helper/bats-files

:warning: Probably you'll need to rename ./tests/test_helper/bats_files to ./tests/test_helper/bats_file

$ mv ./tests/test_helper/bats_files ./tests/test_helper/bats_files
$ ls ./tests
bats  blood.bats  test_helper

Run tests

$ ./run_blood_tests.sh

TODO

add units option to _bloodtemplate.properties so user can specify unit of value he provide to system
add web interface with features like:
- GUI interface to :
- input data manually
- visualise data with various graphs
- REST interface
- support for multiple users, accounts, login page
import data from various number of file format:
- json
- xml
publish code from grafana that generates fancy graphs
dockerize postgresql with volume on local storage

pa810p / bps2

readme

BPS2 - Blood Parameters Storage System

Installation

Prerequisites

Install BPS2

Download and configure

Initialize database:

Usage

Example usage

Store blood pressure to sqlite database:

Store sugar level to sqlite database:

Synchronize local sqlite database with postgresql

Web interface

Visualization

Grafana

Testing

Prerequisites

Run tests

TODO