cde-in-box

This repository contains software to create and deploy CDEs

To use CDE in box solutions clone this repository to your machine.

git clone https://github.com/ejp-rd-vp/cde-in-box

Instructions

Configuring bootstrap services

GraphDB

The docker-compose.yml file in directory cde-in-box/bootstrap will setup up graphDB triple store and creates fdp and cde repositories in graphDB. These two repositories are used by other services in CDE in box so make sure that bootstrap services are property setup before you proceed further.

To run docker-compose.yml file in cde-in-box/bootstrap you need graphDB triple store free edition. Follow the steps below to get free edition of graphdb.

Step 1: GO to this url and registry to download GraphDB free edition.

Step 2: The download will be sent to your email. From the email follow link to download page and click on "Download as a stand-alone server". This step will download "graphdb-free-{version}-dist.zip" file to your machine.

Step 3: Move "graphdb-free-{version}-dist.zip" file to the following location

mv graphdb-free-{version}-dist.zip cde-in-box/bootstrap/graph-db

Step 4: If your graphdb version is different from 9.7.0 then change the version number of graph DB in the docker-compose file.

graph_db:
    build:
      context: ./graph-db
      dockerfile: Dockerfile        
      args:
        version: 9.7.0

Running bootstrap services

Once you have done above configurations you can run bootstrap services by running docker-compose.yml file in cde-in-box/bootstrap directory.

docker-compose up -d

If the deployment is successful then you can access the graphDB by visiting the following URL.

Service name	Local deployment	Production deployment
GraphDB	http://localhost:7200	http://SERVER-IP:7200

By default GraphDB service is secured so you need credentials to login to the graphDB. Please find the default graphDB's credentials in the table below.

Username	Password
`admin`	`root`

Configuring metadata services

FAIR Data Point

The docker-compose.yml file in directory cde-in-box/metadata will setup up FAIR Data Point and connects FAIR Data Point to triple store created in the bootstrapping step.

Step 1: Before you run metadata services make sure that graphDB triple store is up running. You can check by going to this url http:server_ip:7200

Step 2: Check if fdp repository is available in the graphDB triple store.

Running metadata services

Once you have done above checks you can run metadata services by running docker-compose.yml file in cde-in-box/metadata directory.

docker-compose up -d

If the deployment is successful then you can access the FAIR Data Point by visiting the following URL.

Service name	Local deployment	Production deployment
FAIR Data Point	http://localhost:8080	http://SERVER-IP:8080

In order to add content to the FAIR Data Point you need credentials with write access. Please find the default FAIR Data Point's credentials in the table below.

Username	Password
`albert.einstein@example.com`	`password`

Configuring data transformation services

Configuring configuration and data folders

Step 1: Create the following folder structure, relative to where you plan to keep your pre and post-transformed data:

        .
        ./data/   
        ./data/mydataX.csv  (input csv files, e.g. "height.csv")
        ./data/mydataY.csv...
        ./data/triples/  (output FAIR data ends up here)
        ./config/
        ./config/XXXX_yarrrml_template.yaml (XXXX is a one-word tag of the "type" of data, e.g. "height")

Step 2: Running data transformation services

Once you have done the above configurations you can run data transformation services setup by running ``docker-compose.ymlfile incde-in-box/cde-ready-to-go` directory. IN THE FOLDER THAT CONTAINS THE ./data/triples and ./config and subfolders

docker-compose up -d

Step 3: Executing transformations

Put an appropriately columned XXXX.csv into the ./data folder

Put a matching YARRRML template file called XXXX_yarrrml_template.yaml into the ./config folder

call the url: http://localhost:4567 to trigger the transformation of each CSV file, and auto-load into graphDB (this will over-write what is currrently loaded! We will make this behaviour more flexible later)

There is sample data in the "sample_data" folder that can be used to test your installation.

fdlk / cde-in-box