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Create a ROMI database to host, receive & serve plant scansLink

To follow this guide you should have a conda environment, see here. For the sake of clarity it will be called plantscans_db.

Note

Since this is still under development, the packages are installed in "editable mode" with the -e option.

Note

If you do not want the hassle of having to create environment & install python libraries, there is a pre-built docker image, with usage instructions here.

Install plantdb sourcesLink

Activate your plantscans_db environment!

conda activate plantscans_db

To create an active ROMI database, you have to install the plantdb package:

git clone https://github.com/romi/plantdb.git && \
cd plantdb && \
git checkout dev && \
python3.7 -m pip install setuptools setuptools-scm && \
python3.7 -m pip install luigi pillow && \
python3.7 -m pip install flask flask-restful flask-cors && \
python3.7 -m pip install .

Initialize a ROMI databaseLink

The FSDB class from the plantdb module is used to manage a local file system for data storage. A database is any folder which contains a file named plantdb.

To create an empty database, just create a new folder, and an empty file named plantdb in it. For example:

mkdir /data/romi_db
touch /data/romi_db/plantdb

Then define its location in an environment variable DB_LOCATION:

export DB_LOCATION='/data/ROMI/DB'

Note

To permanently set this directory as the location of the DB, add it to your ~/.bashrc file. 

echo 'export DB_LOCATION=/data/ROMI/DB' >> ~/.bashrc

Serve the REST APILink

Then you can start the REST API with romi_scanner_rest_api:

romi_scanner_rest_api

You should see something like:

n scans = 2
 * Serving Flask app "romi_scanner_rest_api" (lazy loading)
 * Environment: production
   WARNING: This is a development server. Do not use it in a production deployment.
   Use a production WSGI server instead.
 * Debug mode: off
 * Running on http://0.0.0.0:5000/ (Press CTRL+C to quit)

To access the REST API, open your favorite browser and use URLs to access:

You should see JSON formatted text.

Troubleshooting: When starting the REST API with romi_scanner_rest_api, if you get an error message about this executable not being found, it may be missing from the $PATH environment variable. Add it with:

export PATH=$PATH:"/home/$USER/.local/bin"

Note

To permanently set this in your bash terminal, add it to your ~/.bashrc file. 

echo 'export PATH=$PATH:/home/$USER/.local/bin' >> ~/.bashrc