DataLinker in MaMoDaR - Management Molekularer Daten im Research Data Life Cycle

For more information check our official website

How to build

Here we describe how to build this project on Microsoft Windows using Visual Studio Code. Similar requirements have to be meet to build this project in Linux or when using any other IDE.

Requirements

• Git
• PostgreSQL
• JDK >= 11
• Gradle
• Node.js
• Visual Studio Code
• A RDMO server and token

Create a PostgreSQL database

1. Start a shell (cmd.exe)
2. Navigate to your PostgreSQL installation path $postgres (i.e. C:\[USERPATH]\bin\pgsql)
3. Go into the \bin subdirectory (cd bin)
4. Create a data directory (mkdir data)
5. Start PostgreSQL pg_ctl.exe start -D "C:\[USERPATH]\bin\pgsql\data"
6. Create the datalinker database createdb.exe datalinker
7. Create the user datalinker
8. Use misc/generate_database.sql to generate all tables and views in the datalinker database (psql -U postgres -d datalinker -a -f misc/generate_database.sql)

Set-Up

1. Start Visual Studio Code
2. Install two Extensions (fifth icon on the left bar):
   2.1 Gradle Tasks (richardwillis.vscode-gradle)
   2.1 npm (eg2.vscode-npm-script)
3. Update server\application.properties
   3.1. Fill in spring.datasource.username and spring.datasource.password using the PostgreSQL data
   3.2. Update rdmo.token and rdmo.url to point to a previous setup RDMO server
4. In Source Control (third icon on the left bar)
   4.1. Clone repository: https://github.com/mamodar/datalinker
   4.2. Select a local folder to clone code to (no server!)
   4.3. Open folder in Visual Studio Code
5. Go to Terminal, Run task: npm: build -web

Run project

1. Start database (if not started already)
   1.1. Start a shell (cmd.exe)
   1.2. Navigate to your PostgreSQL installation path (i.e. C:\[USERPATH]\bin\pgsql)
   1.3. Start PostgreSQL pg_ctl.exe start -D "C:\[USERPATH]\bin\pgsql\data"
2. Start backend
   2.1. In Visual Studio Code: Got to Terminal in the Taskbar at the top
   2.2. Run task: gradle:server:bootRun
3. Start frontend
   3.1. In Visual Studio Code: Got to Terminal in the Taskbar at the top
   3.2. Run task: npm: start -web
4. Open a browser at http://localhost:4200/

How to run

Here we describe how to run the DataLinker on an Ubuntu 18.04 LTS server.

Prerequisites

For the DataLinker we need an apache server, a JRE, and a postgreSQL database.
To install these packages on Debian/Ubuntu use: sudo apt install apache2 postgresql openjdk-11-jre For the required packages of RDMO see the RDMO documentation. We suggest that to create a RDMO instance first before starting the DataLinker instance.

Configure PostgreSQL database

Connect to your server and login into postgres sudo -u postgres psql postgres, in postgres:

1. create the datalinker database CREATE DATABASE datalinker;
2. connect to the datalinker database \connect datalinker
3. create a datalinker postgres user CREATE ROLE datalinker;
4. set a password for the datalinker user \password datalinker
5. create all tables, views, and functions by calling the content of the file misc\generate_database.sql.
6. quit postgres \q

Build and start DataLinker frontend

1. in web\src\environments\environment.prod.ts set appUrl: to the URL of your server.
2. build the frontend npm buildprod or ng build --prod
3. copy the files in web\dist\web to the apache web folder on your server (usually /var/www/html/)

Build and start DataLinker backend

1. create a non-sudo user datalinker on the server sudo adduser datalinker --home /srv/datalinker
2. build the backend gradle datalinker:server bootJar
3. copy the jar from server/build/libs to the home directory of the datalinker user
4. copy server/application.properties to the home directory of the datalinker user
5. open the copied application.properties in a text editor
   5.1. set spring.datasource.username and spring.datasource.password to the datalinker user created in psql
   5.2. set rdmo.url and rdmo.token to the URL of your RDMO instance and add the correct token
   5.3. set dspace.url, dspace.collection, dspace.user and dspace.password to the correct values of your dspace/edoc instance. 5.3. set zenodo.url and zenodo.access_token to the correct values of zenodo.
6. start the backend as nohup java -jar server-0.0.3-SNAPSHOT.jar -Dspring.config.location=/application.properties -Xms512m -Xmx2g -d64 > log 2> err &
   6.1. make sure the user datalinker is running the process

RDMO

To install and configure RDMO please refer to the RDMO documentation.

Documentation

ReadTheDocs
JavaDoc
Compodoc