Team:NYU Abu Dhabi/reformat

Software

H A R D W A R E

MIT License

Copyright (c) 2019 - NYUAD IGEM 2019

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.

WHAT IS AN API?

An API (Application Programming Interface) simply put is a way for applications to communicate with each other. It is a system used to store data that can be easily accessed by the intended individuals from some type of database system.

INSPIRATION

The need for an API for the Volatect device came about as we needed a method to get the data collected from airports to be securely accessible to researchers without risking the loss of personal passenger information. The paper, “An extensible framework and database of infectious disease for biosurveillance” authored by Ashlynn R. Daughton in 2017 expresses the importance of biosurveillance, and details a system that allows the creation of organized data system to aid the detection of outbreaks.

USE

The Volatect API is intended to be used by medical researchers. We believe that the data that comes out of air travel disease reports from our device could help immensely in the analysis and prediction of outbreaks around the world as we provide disease diagnosis in relation to the nationality and the flight path of the passengers.

SECURE?

The Volatect API is built according to the REST API standards. Firstly, the API requests take place through a secure SSL channel as we use the recognized https standards. In order to secure the personal passenger information we were inspired by the Google Cloud HealthCare API which uses, “De-identification” to protect sensitive data. Therefore, we use 256bit AES Encryption on any sensitive data we have on the server such as passport numbers so only the Airport control has access to the encrypted data.

HOW TO CALL THE API?

The most simplest way to get all the data that the Volatect Device has collected would be to go to https://igem-nyuad-api.herokuapp.com/request. Once opened, it will request for all the information collected on the device and display it in a JSON format which can be used either programmatically or using software for visualization and analysis.

GETTING MORE SPECIFIC DATA

To get more specific data, you can play with the url path, we allow:

request/by/disease/Malaria
request/by/nationality/Omani
request/by/airportCode/JFK
request/order/by/time/desc
request/order/by/time/asc

Where the text in yellow can be swapped with the information you need. For example, opening https://igem-nyuad-api.herokuapp.com/request/by/disease/Malaria will request and display the data of passengers who at least have Malaria.

Data response is always in JSON format. Data can be programmatically retrieved using the terminal / command line interface using the curl command.

For example: curl -X GET https://igem-nyuad-api.herokuapp.com/request/

Running this command would retrieve all the data in the terminal itself giving you the

JSON response.

Data can also be retrieved more simply as mentioned in the non-technical

documentation by using a browser that has a graphical user interface.

1.1 Request all data

Permissions Required	None
Pathway	/request
HTTP TYPE	GET
Usage	Will return all the data in the database
Example url path:	https://igem-nyuad-api.herokuapp.com/request/

1.2 Request all data ordered by time recorded

Permissions Required	None
Pathway	/request/order/by/time/{ORDER TYPE}
HTTP TYPE	GET
{ORDER TYPE} Parameter options	desc,asc Where desc is for the records with the latest first, asc with the oldest records first.
Usage	Will return all the data in the database in a specified order.
Example url path:	https://igem-nyuad-api.herokuapp.com/request/order/by/time/desc

1.3 Request all data for a specific disease

Permissions Required	None
Pathway	/request/by/disease/{Disease Name}
HTTP TYPE	GET
{Disease Name} Parameter options	malaria,hepatitisB,whoopingCough, tuberculosis, plague
Usage	Will return all the data in the database where passengers have the disease {Disease Name}
Example url path:	https://igem-nyuad-api.herokuapp.com/request/by/disease/malaria

1.4 Request all data from passengers of a specific nationality

Permissions Required	None
Pathway	/request/by/nationality/{Nationality}
HTTP TYPE	GET
{Nationality} Parameter options	2 Letter Abbreviation Code for countries. For a list of them all please visit: https://datahub.io/core/country-list
Usage	Will return all the data in the database where passengers have the disease {Disease Name}
Example url path:	https://igem-nyuad-api.herokuapp.com/request/by/disease/malaria

1.5 Request all data from passengers by airportCode

Permissions Required	None
Pathway	/request/by/airportCode/{Airport Code}
HTTP TYPE	GET
{Airport Code} Parameter options	3 Letter IATA Code for Airports. For a list of them all please visit: https://en.wikipedia.org/wiki/List_of_airports_by_IATA_code:_A
Usage	Will return all the data in the database where passengers have been recorded at the airport with the code: {Airport Code}
Example url path:	https://igem-nyuad-api.herokuapp.com/request/by/airportCode/MCT

1.6 Add record into database

Permissions Required

Super Access. Requires API KEY

Pathway

/request

HTTP TYPE

POST

Parameter options

Parameter Name	Required	Type
apikey	Yes	Secret key string only available to the Airport Control.
identifier	Yes	Passport number string which will be AES 256 BIT Encrypted after sent.
nationality	Yes	2 Letter Abbreviation Code for countries. For a list of them all please visit: https://datahub.io/core/country-list
airportCode	Yes	3 Letter IATA Code for Airports. For a list of them all please visit: https://en.wikipedia.org/wiki/List_of_airports_by_IATA_code:_A
fromAirportCode	Yes
toAirportCode	Yes
malaria	Yes	Number from 0 to 100 inclusive to represent a percentage. 0 would be when the diagnosis is negative and anything above 0 is positive and the magnitude above 0 represents the extent of the disease diagnosed.
tuberculosis	Yes
hepatitisB	Yes
plague	Yes
whoopingCough	Yes

Usage

Will add the data that was sent through the request parameters to the database. This request would happen directly from the Volatect device in the airport.

Example url path:

https://igem-nyuad-api.herokuapp.com/request/

System Specifications

We use Heroku as a hosting server of our API and database. The database system used is Heroku Postgres SQL.

Database Schema

Column Name	Column Type	Nullable	Primary Key
Identifier	text	Not null	Primary Key
Time	timestamp	Not null
AirportCode	text	Not null
Malaria	int	Not null
HepatitisB	int	Not null
WhoopingCough	int	Not null
Tuberculosis	int	Not null
Plague	int	Not null
Nationality	int	Not null
FromAirportCode	text	Not null
ToAirportCode	text	Not null
"diseasedatabase_pkey" PRIMARY KEY, btree (identifier)