README.rst

Sample Tracking Status Overview

Gives a visual overview of sample statuses

How to run

First compile the project and build an executable java archive:

mvn clean package

Note that you will need java 8. The JAR file will be created in the /target folder:

|-target
|---sample-tracking-status-overview-1.0.0-SNAPSHOT.war
|---...

The created war file can then be deployed on a portal system.

Configuration

Environment	Description	Default Value
datasource.url	Connection to datasource	https://openbis.domain.de
datasource.api.url	Connection to API datasource	https://openbis.domain.de/api/path
datasource.user	The user name for the datasource	myuser
datasource.password	The password for the datasource	mypassword
mysql.host	Host address for MySQL database	123.4.56.789
mysql.pass	Password for MySQL database	mypassword
mysql.user	MySQL user	mysqluser
mysql.db	MySQL database	my_sql_database_name
mysql.port	Port to MySQL database	3306
portal.user	Username for QBiC portal	qbcjb02

Test environment

You can run the application in a testing mode:

mvn clean jetty:run -Denvironment=testing -Demail=<email> -Dauth_id=<auth provider id> -Dfirst_name=<first name> -Dlast_name=<last name>

The email property is used to generate your portal-user id, the auth-id is the one that is provided by the authentication provider after successful login into the portal. The first and last name as they are stored in the database need to be provided as well. As we run in test mode here, you need to simulate it with the properties.

Furthermore, you need to provide the sample tracking user and password as ENV variables for the sample tracking service:

SERVICE_USER = <username>
SERVICE_USER_PW = <userpassword>

Datastructures

To show the actual sample and project information, following entities need to be provided: 'ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.Sample' (with code, properties and secondary name) and 'ch.ethz.sis.openbis.generic.asapi.v3.dto.project.Project' (with code, space code and description)

To find the status for each sample the table samples_locations is used

To associate to which projects a person is subscribed, the subscriptions table is used

License

This work is licensed under the MIT license.

Note: This work uses the Vaadin Framework, which is licensed under Apache 2.0.