SchemaTools

Overview

This Java tool will configure a Fair Data Point to use the Health-ri metamodel version 2.

Features

• Reads SHACL files from a specified directory or github
• Use of excel template to create SHACL files.
• Uploads the combined data to a Fair Data Point
• Configurable via a YAML properties file

Requirements

• Java (JDK 17 or higher)
• Maven (mot needed if you use the prebuild jar file)

Installation

if you want to use the prebuild jar file:

Clone the repository

    git clone https://github.com/Health-RI/FairDataPointSchemaTool.git
    cd FairDataPointSchemaTool/jar/

if you want to build the tool yourself using maven:

Clone the repository and build

    git clone https://github.com/Health-RI/FairDataPointSchemaTool.git
    cd FairDataPointSchemaTool/
    mvn install:install-file -Dfile=./xls2rdf-lib-3.2.1.jar -DgroupId=fr.sparna.rdf.xls2rdf -DartifactId=xls2rdf-pom -Dversion=3.2.1 -Dpackaging=jar 
    mvn install

Usage

Run the tool with the required configuration file:

    java -jar FairDataPointSchemaTool-1.0.jar -i /path/to/Properties.yaml -h address_of_fdp -p yourpassword -u username -c command

-i path to Properties.yaml, you can use relative location (default is ./Properties.yaml) works if the property file is located at the some location as the jar file.

-u fdp admin user (default: albert.einstein@example.com)

-p password (default: password)

-c Determine what the tool will do: we have 4 options:

• both -> Schema and resource will be updated. (default option)
• schema -> The schema will be updated
• resource -> Resource descriptions will be updated.
• template -> will create Shacl files, from Excel templates (this option is for internal use only.)

Docker

First, copy the example .env file and modify the values to your FDP deployment.

cp .env.example .env

Second, run the container:

docker compose up

Configuration File (YAML Format)

The tool requires a properties file in YAML format to specify input schemas and resource information. Below is an example: In most cases the property file doesn't need to be updated.

---
---
schemas:
  #The FDP shape files are constructed using the files in the PiecesShape folder.
  Catalog:
    - "Catalog.ttl"
    - "Agent.ttl"
    - "Kind.ttl"
    - "PeriodOfTime.ttl"
  Dataset:
    - "Dataset.ttl"
    - "Agent.ttl"
    - "Kind.ttl"
    - "PeriodOfTime.ttl"
  Dataset Series:
    - "DatasetSeries.ttl"
    - "Agent.ttl"
    - "Kind.ttl"
  Resource:
    - "Resource.ttl"
  Distribution:
    - "Distribution.ttl"
    - "PeriodOfTime.ttl"
    - "Checksum.ttl"
  Data Service:
    - "DataService.ttl"
    - "Agent.ttl"
    - "Kind.ttl"
# Some schemas are extending the Resource schema.
parentChild:
  Resource:
    - "Dataset"
    - "Catalog"
    - "Data Service"
#the resources for the FDP, note we are using Parent relation instead of Childeren (as the FDP does)
resources:
  Sample Distribution:
    parentResource: "Dataset"
    parentRelationIri: "http://www.w3.org/ns/adms#sample"
    schema: "Distribution"
  Dataset Series:
    parentResource: "Dataset"
    parentRelationIri: "http://www.w3.org/ns/dcat#inSeries"
    schema: "Dataset Series"
  Analytics Distribution:
    parentResource: "Dataset"
    parentRelationIri: "http://healthdataportal.eu/ns/health#analytics"
    schema: "Distribution"
schemasToPublish:
  - "Resource"
  - "Catalog"
  - "Dataset"
  - "Dataset Series"
  - "Distribution"
  - "Data Service"
schemaVersion: "2.0.0"
#Location of the shapes files used for uploading to FDP.
inputDir: "https://raw.githubusercontent.com/Health-RI/health-ri-metadata/v2.0.0/Formalisation(shacl)/Core/PiecesShape/"
#for use with the template option, uses Excel template to generate shapes files (Health-ri use only!)
templateDir: "C:\\Users\\PatrickDekker(Health\\templates\\"
outputRoot: "C:\\Users\\PatrickDekker(Health\\IdeaProjects\\health-ri-metadata\\Formalisation(shacl)\\\
  Core\\"
piecesDir: "PiecesShape"
fairDataPointDir: "FairDataPointShape"
validationDir: "ValidationShape"

Note schema names can have spaces, but the turtle filename will be without spaces.

License

This project is licensed under the MIT License. See the LICENSE file for details. This tool uses https://github.com/sparna-git/xls2rdf for conversion of excel templates to shacl.

Contributing

Contributions are welcome! Please submit a pull request or open an issue for discussion.