SampleDB

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.

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contributors

Cite this software

What SampleDB can do for you

SampleDB

MIT license DOI DOI

SampleDB is a web-based sample and measurement metadata database.

Documentation

You can find the documentation for the current release at https://scientific-it-systems.iffgit.fz-juelich.de/SampleDB/.

Getting Started

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.

Using docker-compose

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

Using docker commands

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_EMAIL=sampledb@example.com \
    -e SAMPLEDB_MAIL_SERVER=mail.example.com \
    -e SAMPLEDB_MAIL_SENDER=sampledb@example.com \
    -e SAMPLEDB_ADMIN_PASSWORD=password \
    -e SAMPLEDB_SQLALCHEMY_DATABASE_URI=postgresql+psycopg2://postgres:password@sampledb-postgres:5432/postgres \
    --restart=always \
    --name sampledb \
    -p 8000:8000 \
    sciapp/sampledb:0.27.0

Once it's started

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.

Contributing

If you want to improve SampleDB, please read the contribution guide for a few notes on how to report issues or submit changes.

Support

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.

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Keywords
Programming languages
  • Python 70%
  • HTML 16%
  • JavaScript 13%
  • CSS 1%
License
  • MIT
</>Source code

Contributors

FR
Florian Rhiem
Lead Developer
Forschungszentrum Jülich
MD
Malte Deckers
DK
Daniel Kaiser
JS
Jannik Streitberg
DN
Du Kim Nguyen
MH
Maximilian Heuwes