LREN-CHUV / mip-meta-db-setup-seed

Seed for metadata projects based on MIP CDE variables

DATASET_LABEL meta database setup

This Docker image manages the database migration scripts for the DATASET_LABEL dataset.

DATASET_LABEL dataset is split into table mip_cde_features for the CDE features and DATASET_features for the DATASET_LABEL specific features.

The view mip_local_features contains the variables from both MIP CDE and DATASET_LABEL.

Introduction

This project uses Flyway to manage the database migration scripts for the 'meta-db' database used by MIP.

This database contains the metadata used for reference, including:

• the list of variables and groups for the Common Data Elements (CDE) defined by MIP.
• the list of variables and groups for DATASET_LABEL

Usage

Run:

$ docker run -i -t --rm -e FLYWAY_HOST=`hostname` registry.gitlab.com/hbpmip_private/DATASET-meta-db-setup:0.0.1 migrate

where the environment variables are:

• FLYWAY_HOST: database host, default to 'db'.
• FLYWAY_PORT: database port, default to 5432.
• FLYWAY_DATABASE_NAME: name of the database or schema, default to 'meta'
• FLYWAY_URL: JDBC url to the database, constructed by default from FLYWAY_DBMS, FLYWAY_HOST, FLYWAY_PORT and FLYWAY_DATABASE_NAME
• FLYWAY_DRIVER: Fully qualified classname of the jdbc driver (autodetected by default based on flyway.url)
• FLYWAY_USER: database user, default to 'meta'.
• FLYWAY_PASSWORD: database password, default to 'meta'.
• FLYWAY_SCHEMAS: Optional, comma-separated list of schemas managed by Flyway
• FLYWAY_TABLE: Optional, name of Flyway's metadata table (default: schema_version)

Development

Regenerate the Json patch using the command:

  rm mip.patch.json
  ../meta-db-setup/create-patch.amm variables.json mip.patch.json
  pre-commit run --all-files

Regenerate the variables hierarchy json using the command:

  rm variables.json
  ../meta-db-setup/apply-patch.amm variables.json mip.patch.json
  pre-commit run --all-files

Build the Docker image

Run: ./build.sh

Publish on Docker Hub

Run: ./publish.sh

License

DATASET-meta-db-setup

(this project)

Copyright (C) 2018 IRCCS DATASET_LABEL and LREN CHUV

Contains proprietary data.

DO NOT REDISTRIBUTE.

Flyway

Copyright (C) 2016-2017 Boxfuse GmbH

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Trademark

Flyway is a registered trademark of Boxfuse GmbH.

Acknowledgements

This work has been funded by the European Union Seventh Framework Program (FP7/2007­2013) under grant agreement no. 604102 (HBP)

This work is part of SP8 of the Human Brain Project (SGA2).