Debugging

By Docker

  1. Download Docker Desktop
  2. Clone and go to the file path
  3. build the image
    1. docker build -t "image_name:latest" .
  4. run the image
    1. docker run -d -p 5000:5000 image_name

By local virtual machine

  • start a virtual environment
source venv/bin/activate
python3 -m venv venv
  • activate the virtual environment
source venv/bin/activate
source venv/bin/activate
  • use pip to install pkgs
source venv/bin/activate
pip install -r requirements.txt
  • run the program
source venv/bin/activate
flask run --debug

By Visual Studio Code


Servers

The test server can be accessed from MongoDB Atlas, please follow the MongoDB Atlas section in this guide.

The prod server is on BioHPC and we can access it through Postman, etc. Be careful when sending requests to the prod server.

Postman

Postman is useful for sending HTTP requests to the back-end APIs. 

  1. Install Postman
  2. Checkout Mobile APIs  for Backend Online APIs

Notes (mobile)

Samples are identified by their barcode ids. If submit two surveys with the same barcode, then the latest submitted survey will replace the old one. Even if different users use the same barcode, the sample will get replaced. So when testing, if you do not scan a barcode, the sample will always be stored as no barcode, and the database will always only store the latest survey.

Sample Model

Class PropertiesNote

_id = db.StringField(required=True)

_id is the same with barcode_id

survey_data = db.DictField(required=False)


email = db.StringField(required=True)


image = db.ImageField()

image type can be either png or jpeg

date_time = db.DateTimeField(required=True)

the server time when backend upload data to the DB

milk_barcode_id = db.StringField(required=False)


sample_data = db.DictField(required=False)

the json file in SampleData including readable survey data

barcode_id = db.StringField(required=True)



User Model

Class PropertiesNote
_id = db.StringField(required=True)_id is the same with email
email = db.StringField(required=True)
password = db.StringField()
first_name = db.StringField(max_length=50)
last_name = db.StringField(max_length=50)


is_real_customer = db.BooleanField(required=True)

whether the customer is a real customer

created_at = db.DateTimeField(required=True,default=datetime.utcnow()
Class PropertiesNote
_id = db.StringField(required=True)_id is the same with email
sign_up_survey_data = db.DictField(required=True)store whatever survey asked and customer filled

Survey Model

Class PropertiesNote
survey_name = db.StringField(required=True)Name of the survey that is being retrieved

questions = db.ListField(db.DictField(), required=False)

These are the questions that are associated with the survey. Each survey has a list of dictionaries with each dictionary representing a question

Upload Model

To fully understand these fields, especially the sample_species_read, please contact Min-Ting Li and ask for merged data set to see data columns.

Class PropertiesNote

_id = db.StringField(required = True)

id is the barcode id. example: "BS70002STOOL"

email = db.StringField(required=True)

uploader
date_time = db.DateTimeField(default=datetime.datetime.now,required=True)
sample_id=StringField(required=True)sample id, example: BS7_01
sample_species_read = db.DictField(required=False)

ALL data columns followed by barcode id, example:

"sample_species_read": {
      "Actinotignum_timeonense": "24286",
      "Aeriscardovia_aeriphila": "0"
}












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