https://github.com/lren-chuv/mip-meta-db-setup-seed
Seed for metadata projects based on MIP CDE variables
https://github.com/lren-chuv/mip-meta-db-setup-seed
atomist reference-data
Last synced: 3 months ago
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Seed for metadata projects based on MIP CDE variables
- Host: GitHub
- URL: https://github.com/lren-chuv/mip-meta-db-setup-seed
- Owner: LREN-CHUV
- License: other
- Created: 2018-09-03T12:53:27.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2019-05-17T09:06:23.000Z (about 6 years ago)
- Last Synced: 2025-01-19T15:34:29.916Z (5 months ago)
- Topics: atomist, reference-data
- Language: Shell
- Size: 18.6 KB
- Stars: 0
- Watchers: 5
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://www.unil.ch/lren/en/home.html) [](https://github.com/LREN-CHUV/DATASET-data-db-setup/blob/master/LICENSE)
[](https://gitlab.com/hbpmip/DATASET-meta-db-setup/commits/master)
# 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:
```console
$ 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:
```console
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:
```console
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](https://boxfuse.com)
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](https://boxfuse.com).
# 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).