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A sample and measurement metadata database

Project description

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 --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 \
    -e SAMPLEDB_FILE_STORAGE_PATH=/home/sampledb/files/ \
    -v `pwd`/files:/home/sampledb/files:rw \
    --restart=always \
    --name sampledb \
    -p 8000:8000 \
    sciapp/sampledb:0.18.0

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 have any questions about SampleDB or run into any issues setting up or running SampleDB, please open an issue on GitHub.

Project details


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