PMB ELN Bridge

Description

A polling service for printing labels from the IDBS electronic lab notebook (ELN) via Print My Barcode (PMB) and SPrint.

Usage

• Property folders contain config information for the ELN PMB Bridge, Printers and Mailing, and various setup directories.
• The ELN drops a file whose name ends in _TEMP into the poll folder.
• The ELN adds the print request to this file, then renames it, removing the _TEMP suffix.
• The Watch Service pulls the newly named file, and create a print job request.
• This request is sent to a print service, which prints the labels.
• The file is moved to an archive or an error directory.

Running

Execute the jar in the console:

java -jar target/eln_pmb_bridge-jar-with-dependencies.jar

Pass in a command line argument into Main such as env=devel

Or when running it from IntelliJ: ctrl + alt + r > Edit Configurations > Program Arguments

Deployment

• The test version is deployed at web-idbs-dev02:/sccp/eln_pmb_bridge (used by ELN for test)
• The prod version is deployed at web-idbs-live02:/sccp/eln_pmb_bridge (used by ELN for prod)

Build the jar using the jar-with-dependencies in pom.xml:

Maven > Lifecycle > clean
Maven > Lifecycle > package

###Make sure you use JDK 1.8 to compile Even with the target version set to 1.8, compiling with a later JDK has been seen to cause runtime errors when the application is deployed and running on JRE 1.8.

Secure copy the jar from local to the server:

scp target/eln_pmb_bridge-jar-with-dependencies.jar [host]:.

Secure copy the jre (if it doesn't exist) from one server to another scp -r /sccp/jre/ [host]:/sccp

Ssh onto the host.

Change user to sccp

sudo -su sccp

Run the application (this will only create the folders, then error out):

/sccp/jre/jre1.8.0_131/bin/java -jar eln_pmb_bridge-jar-with-dependencies.jar

Change permission on folders to 777 (poll/prop/error/archive)

chmod 777 archive_folder/ error_folder/ properties_folder/ poll_folder/

Copy over the property files

scp -r properties_folder/devel [host]:/sccp/eln_pmb_bridge/properties_folder/devel

(or prod in place of devel when deploying to production)

Copy over the java control file

scp -r java_control.sh [host]:/sccp/eln_pmb_bridge/.

Make sure all files are owned by the sccp user.
chown is not available to normal users, so the way to get the files under the correct ownership is:

• become sccp: sudo -u sccp bash
• create a copy (owned by sccp): cp ~username/eln_pmb_bridge-jar-with-dependencies.jar /sccp/eln_pmb_bridge/.
• delete the old file: rm ~username/eln_pmb_bridge-jar-with-dependencies.jar

You can do this on a whole directory at once, if you use the -r flag for cp and rm. (Be careful with rm.)

Change permission on java control file to 755 (only executable by the owner)

chmod 755 java_control.sh

Start the application using java_control.

The java_control.sh script allows you to start, stop and restart the java process:

./java_control.sh stop env=abc
./java_control.sh start env=abc
./java_control.sh restart env=abc

The env=abc part can be omitted if the java_control.sh script includes:

ENV=${2:-env=abc}

using the appropriate environment for that server in place of abc.

Another option is:

./java_control.sh start --nostartemail

Different environments are:

• test
• devel
• wip
• uat
• prod

Test

Secure copy to drop a file into the polling folder on the server with the _TEMP extension:

scp file.txt web-idbs-dev02:/sccp/eln_pmb_bridge/poll_folder/file.txt_TEMP

On the server, rename the file to remove the _TEMP extension:

mv poll_folder/file.txt_TEMP poll_folder/file.txt

Example File

An example IDBS-ELN file

Request

Format of the request built in PMBClient buildJson():

{
    "data":{
        "attributes":{
            "printer_name":"",
            "label_template_id":,
            "labels":{
                "body":[
                    { "label_1":
                        {
                            "date":"",
                            "media_type":"",
                            "cell_line":"",
                            "passage_number":"",
                            "user":""
                        }
                    }
                ]
            }
        }
    }
}