Create README.md

Author: jrlegrand

README.md

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+# ParseRx
+Medication sig parser.
+
+
+## Getting started
+
+python3 -m venv venv
+source venv/bin/activate
+pip install django
+pip install djangorestframework
+pip install "djangorestframework-api-key==2.*"
+pip install django-cors-headers
+pip install djoser
+sudo apt-get install python3-dev default-libmysqlclient-dev build-essential
+pip install mysqlclient
+
+
+## Initialize the database
+
+How to initially setup MySQL: https://www.digitalocean.com/community/tutorials/how-to-install-mysql-on-ubuntu-20-04
+Info on MySQLClient: https://pypi.org/project/mysqlclient/
+Gunicorn/Nginx: https://realpython.com/django-nginx-gunicorn/#replacing-wsgiserver-with-gunicorn
+
+sudo mysql
+ALTER USER 'root'@'localhost' IDENTIFIED WITH mysql_native_password by 'mynewpassword';
+GRANT ALL PRIVILEGES ON parserx.* TO 'parserx'@'localhost' WITH GRANT OPTION;
+
+Terminal
+
+mysql -u parserx -p
+<enter password>
+drop database parserx;
+create database parserx;
+quit
+source venv/bin/activate
+python manage.py makemigrations
+python manage.py makemigrations sig
+python manage.py migrate
+python manage.py createsuperuser
+<follow createsuperuser prompts>
+python manage.py runserver 0.0.0.0:8000
+
+Postman
+
+1.) Authenticate with superuser
+POST localhost:8000/auth/token/login/
+Headers
+Content-Type application/json
+Body
+{
+	"username": "jrlegrand",
+	"password": "<password>"
+}
+Response
+{
+    "auth_token": "<auth token>"
+}
+
+2.) Run ParseRx on csv file via API
+POST localhost:8000/csv_sig/
+Headers
+Content-Type application/json
+Authorization Token <auth token>
+
+NOTE: to change the csv file that the API runs:
+    - Go to parserx/sig/views
+    - Edit filepath in the create method of CsvSigCreateViewSet
+    - The csv file is stored in parserx/parsers/csv
+
+
+## Authenticate and parse a sig via the API
+
+1.) Authenticate with user
+POST localhost:8000/auth/token/login/
+Headers
+Content-Type application/json
+Body
+{
+	"username": "<username>",
+	"password": "<password>"
+}
+Response
+{
+    "auth_token": "<auth token>"
+}
+
+2.) Run query via API
+POST localhost:8000/sig/
+Headers
+Content-Type    application/json
+Authorization   Token <auth token>
+
+
+## Parsing / reparsing an entire CSV of sigs
+
+Edit the name of the csv file in parserx.io/sig/views.py to be the csv you want to parse.
+***NOTE: ensure you have converted it to just one column full of sigs with no header.
+
+Postman
+
+1.) Authenticate with superuser
+POST localhost:8000/auth/token/login/
+Headers
+Content-Type application/json
+Body
+{
+	"username": "<username>",
+	"password": "<password>"
+}
+Response
+{
+    "auth_token": "<auth token>"
+}
+
+2.) Run ParseRx on csv file via API
+POST localhost:8000/csv_sig/
+Headers
+Content-Type	application/json
+Authorization	Token <auth token>
+
+
+## Submiting batch sig reviews to ParseRx via API (feedback loop)
+
+1.) Get auth token from ParseRx
+POST api.parserx.io/auth/token/login/
+Headers
+Content-Type application/json
+Body
+{
+	"username": "<username>",
+	"password": "<password>"
+}
+Response
+{
+    "auth_token": "<auth token>"
+}
+
+2.) Sumbit batch reviews to ParseRx
+POST api.parserx.io/sig_reviewed/
+Headers
+Content-Type application/json
+Authorization Token <auth token>
+Body
+[
+    {
+        "owner": <user_id>,
+        "sig_parsed": <sig_parsed_id>,
+        "sig_correct": "<true|false>",
+        "sig_corrected": "<sig_corrected>"        
+    }
+]