SampleDB is a web-based electronic lab notebook with a focus on sample and measurement metadata. With SampleDB, you can track each step in the sample lifecycle and its schema system allows you to define exactly what metadata should be stored for each process, from a simple check box to time series.
SampleDB is a web-based sample and measurement metadata database.
You can find the documentation for the current release at https://scientific-it-systems.iffgit.fz-juelich.de/SampleDB/.
We recommend using our pre-built Docker images for setting up
SampleDB. You will need two containers, one for a PostgreSQL database and another for SampleDB itself, and a directory to store all files in.
If you would like to set up a development version of SampleDB instead, please see the contribution guide.
If you do not have Docker installed yet, please install Docker.
First, get the docker-compose.yml configuration file. You can git clone this repo or just get the file:
curl https://raw.githubusercontent.com/sciapp/sampledb/develop/docker-compose.yml.dist --output docker-compose.yml
Then simply bring everything up with:
docker-compose up -d
First, start your database container:
docker run \ -d \ -e POSTGRES_PASSWORD=password \ -e PGDATA=/var/lib/postgresql/data/pgdata \ -v `pwd`/pgdata:/var/lib/postgresql/data/pgdata:rw \ --restart=always \ --name sampledb-postgres \ postgres:12
Next, start the SampleDB container:
docker run \ -d \ --link sampledb-postgres \ -e SAMPLEDB_CONTACT_EMAILemail@example.com \ -e SAMPLEDB_MAIL_SERVER=mail.example.com \ -e SAMPLEDB_MAIL_SENDERfirstname.lastname@example.org \ -e SAMPLEDB_ADMIN_PASSWORD=password \ -e SAMPLEDB_SQLALCHEMY_DATABASE_URI=postgresql+psycopg2://postgres:password@sampledb-postgres:5432/postgres \ -e SAMPLEDB_FILE_STORAGE_PATH=/home/sampledb/files/ \ -v `pwd`/files:/home/sampledb/files:rw \ --restart=always \ --name sampledb \ -p 8000:8000 \ sciapp/sampledb:0.21.5
This will start a minimal SampleDB installation at
http://localhost:8000 and allow you to sign in with the username
admin and the password
password (which you should change immediately after signing in).
To learn how to further set up SampleDB, please follow the rest of the Getting Started guide.
If you want to improve SampleDB, please read the contribution guide for a few notes on how to report issues or submit changes.
If you run into any issues setting up or running SampleDB, please open an issue on GitHub.
You can also subscribe to the SampleDB mailing list to learn about new features and to discuss any questions regarding SampleDB.