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
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
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 |
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.
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 |
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 in
cde-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.