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CHUV License Codacy Badge CircleCI

Setup for database 'meta-db' with the selection of variables for mip-cde

Introduction

This Docker image 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, under alias mip-cde.

Usage

Run:

$ docker run -i -t --rm -e FLYWAY_HOST=`hostname` hbpmip/mip-cde-meta-db-setup:1.3.5 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)

Build

Run: ./build.sh

Publish on Docker Hub

Run: ./publish.sh

License

mip-cde-meta-db-setup

(this project)

Copyright (C) 2017 LREN CHUV

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

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 (SGA1).