LIMS Sample Status Reporter

A command line tool to report LIMS changes to the sample-tracking service.

System Integration

As updating sample statuses in more then one place can lead to errors and frustration, automation of this process is deemed important. The sample-status-reporter automates the migration of updated sample statuses from an openBis LIMS to the sample-tracking-service.

Interaction with the sample-tracking-service

To propagate information to the sample-tracking service, the app queries the following endpoints:

• PUT /v2/samples/{sampleCode}/status/

Please see the sample-tracking-service SwaggerHub entry for further detail.

Integration with the openBIS LIMS

The sample information is retrieved automatically from an openBIS instance acting as LIMS. The configuration of the openBIS needs to make sure each sample provides a QBiC barcode (containing Q) and a sample status. Furthermore, the names of the properties providing this information needs to be provided (see Environment Variables).

• The sample status may contain values from ["Sample received", "QC passed", "QC failed", "Library completed"].

Besides that you can configure LIMS statuses this tools will ignore. For this pass a comma-separated list in the LIMS_IGNORED_STATUSES environment variable. This tool acts in the role of a user configured by you. Please make sure, that the configured user only sees projects where you want to propagate the status to the sample-tracking system.

How to run

To run the application, first make sure you provide a correct configuration.

Checkout the latest code from main and run the maven goal spring-boot:run:

mvn spring-boot:run [-Dspring-boot.run.arguments=[-hV],[-t=<timePoint>]]
  -h, --help      Show this help message and exit.
  -t, --time-point=<timePoint>
                  Point in time from where to search for updates e.g. '2022-01-01T00:00:00Z'.
                  Defaults to the last successful run. 
                  If never run successfully defaults to the same time yesterday.
  -V, --version   Print version information and exit.

Alternatively you can package the application and run it as .jar. First compile the project and build an executable java archive:

mvn clean package

The JAR file will be created in the /target folder:

|-target
|---sample-status-reporter-1.0.0.jar
|---...

Now change into the folder and run the REST service app with:

java -jar sample-status-reporter-1.0.0.jar [-hV] [-t=<timePoint>]
  -h, --help      Show this help message and exit.
  -t, --time-point=<timePoint>
                  Point in time from where to search for updates e.g. '2022-01-01T00:00:00Z'.
                  Defaults to the last successful run. 
                  If never run successfully defaults to the same time yesterday.
  -V, --version   Print version information and exit.

Configuration

Please note that this project requires java 17.

Environment Variables

For this application to be run the following environment variables need to be set:

Environment Variable	Description	Default Value
LAST_UPDATE_FILE	A path to a persistent file. The last successful run is stored here.	last-updated.txt
LIMS_PASSWORD	The password to access the OpenBiS LIMS
LIMS_SERVER_URL	The URL to the OpenBiS LIMS API
LIMS_USER	The user to access the OpenBiS LIMS
LIMS_BARCODE_PROPERTY	The name of the property in the OpenBiS LIMS from which to read the QBiC barcode
LIMS_STATUS_PROPERTY	The name of the property in the OpenBis LIMS from which to read the sample status information
LIMS_IGNORED_STATUSES	A comma-separated list of LIMS sample statuses to be ignored by the reporter
LOG_PATH	A path in which the log file generated by this application is stored	log/path/
SAMPLE_TRACKING_AUTH_PASSWORD	The password for the sample tracking user	astrongpassphrase!
SAMPLE_TRACKING_AUTH_USER	The username for the sample tracking service	qbic
SAMPLE_TRACKING_LOCATION_ENDPOINT	The endpoint to list all locations. This does not contain the base url	/locations
SAMPLE_TRACKING_LOCATION_USER	The sample tracking user currently using the application	[email protected]
SAMPLE_TRACKING_URL	The base URL for the sample tracking service	http://localhost.de
USER_DB_DIALECT	The database dialect of the user database	org.hibernate.dialect.MariaDBDialect
USER_DB_DRIVER	The database driver for the user database	com.mysql.cj.jdbc.Driver
USER_DB_HOST	The URL to the host of the user database containing the database name	localhost
USER_DB_USER_NAME	The database user name	myusername
USER_DB_USER_PW	The database user password	astrongpassphrase!