README.md

Swagger Enabled Flask Server

Local Development

Initial Setup

Applies when there are changes made to the database and a new models.py file needs to be generated, otherwise skip to Local Environment.

The models.py file is generated using sqlacodegen

Need to add import statement to sqlacodegen/codegen.pyin order to account for geoalchemy2. The codegen.py file is part of the sqlacodegen package installed by pip.

From the top level of the repository:

$ cd server/
$ virtualenv -p /PATH_TO/python3 venv
$ source venv/bin/activate
$ pip3 install -r requirements.txt

Assuming venv is the name of the virtualenv directory the codegen.py files will be at: /nih-exposures-api/server/venv/lib/python3.6/site-packages/sqlacodegen/codegen.py.

Update it as follows:

from sqlalchemy.types import Boolean, String
import sqlalchemy
from geoalchemy2 import Geometry, Geography # <-- this line

From the terminal generate the models.py file.

$ sqlacodegen --outfile models.py postgres://datatrans:datatrans@POSTGRES_DB_IP:5432/exposures

Where POSTGRES_DB_IP is the actual IP of the database.

Update the generated models.py file with appropriate imports.

from sqlalchemy.dialects.postgresql import TEXT, DOUBLE_PRECISION

Local Environment

From the top level of the repository:

$ cd server/
$ virtualenv -p /PATH_TO/python3 venv
$ source venv/bin/activate
$ pip3 install -r requirements.txt

ini/connexion.ini

Set up the ini/connexion.ini file to match your environment. An example file named ini/connexion.ini.example has been provided as a template.

$ cp ini/connexion.ini.example ini/connexion.ini

• Change /PATH_TO/ to be the actual path to the code.

• If using the docker based database update the FQDN_OR_IP to be that of the platform docker is being run from.

   [connexion]
   server =
   debug = True
   port = 5000
   keyfile =
   certfile =
   
   [sys-path]
   exposures = /PATH_TO/nih-exposures-api/server/exposures
   controllers = /PATH_TO/nih-exposures-api/server/controllers
   
   [postgres]
   host = FQDN_OR_IP
   port = 5432
   database = exposures
   username = datatrans
   password = datatrans
  

Ensure the database is running

• Docker implemented database described in database/README.md

To run the server, please execute the following:

python3 app.py

and open your browser to here:

http://localhost:5000/v1/ui/

Your Swagger definition lives here:

http://localhost:5000/v1/swagger.json

Docker Development

TODO

Production Deployment

TODO