SEEK API

Example ipython notebook to use the SEEK writeAPI (SEEK version 1.8.1+, https://github.com/seek4science/seek).

Creates a Project --> Investigation --> Study --> Assay(s) --> Assets, all based on each other, which result in the following ISA structure:

The Event and the Publication are not included in the code (Event is possible to add, Publication is not yet in the writeAPI code).

In addition, contains examples on how to POST assets both based on uploads, or remote URLs, and an Assay with links to pre-existing assets.

'token' should contain a base64 encrypted "username:password" string to your SEEK instance.

Installation

Setup python virtual environment

mkvirtualenv seek --python==python3.8
(seek) pip install -r requirements.txt --upgrade
(seek) pip install jupyterlab --upgrade
(seek) python -m ipykernel install --user --name seek --display-name "seek"
(seek) jupyter lab

API token

For the connection with the database an API token is required. Make sure this token is not tracked in the repository.

echo -n 'user:password' | base64 > token

Local SEEK instance

Setup for local testing and development.

Docker compose

cd ~/Download
sudo curl -L "https://github.com/docker/compose/releases/download/1.22.0/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose
sudo chmod +x /usr/local/bin/docker-compose
docker-compose --version

Build seek

git clone https://github.com/seek4science/seek
cd seek

docker volume create --name=seek-filestore
docker volume create --name=seek-mysql-db
docker volume create --name=seek-solr-data
docker volume create --name=seek-cache

docker-compose up

Instance

Seek is running on port 3000

http://localhost:3000

SEEK API

Swagger documentation is avaiblable here:
https://app.swaggerhub.com/apis/FAIRDOM/SEEK/0.1