Expedition 378T Application Developer Technical Report

Contributors

Tim Blaisdell, James Brattin, Paul Foster, Algie Morgan, James Zhao

Summary

This document highlights changes to the JOIDES Resolution laboratory data management environment during Expedition 378T.

Five application developers were on-board for this abbreviated expedition / transit operations in order to upgrade our infrastructure to Java 11 and Tomcat 9. These upgrades necessitated upgrading all of our Java desktop applications to run under Java 11 and many of our other applications that call web services since Tomcat 9 is much stricter about enforcing HTTP encoding standards. The developers also took this opportunity to create and deploy IODPLauncher, a new application and framework for deploying our software. Application Developers also worked with Expedition 378T techs to fully implement the software issues reporting system deployed on Confluence ( see: All Reported Software Issues).

Selected issues are highlighted, but not reviewed in exhaustive detail. In general, see the ship activity log and product pages on the developer site for additional detail: Application Developer - Ship Activity Log
At the end of this expedition the activity log specific to this expedition will be archived here: JR Activity Log Archive

Special Projects

During Expedition 378T the developers worked on the following projects:

Worked with MCS's to upgrade web servers from Tomcat 8 to Tomcat 9.
Worked with MCS's to upgrade all Java applications from Java 8 to Java 11. Purged all instances of Java JRE from all workstations on the ship; installed open source Java 11 JRE on limited number of host computers that require it to run L2E and Thin Section Report Writer applications.
Upgrade all web services to Java 11 and modified to run under Tomcat 9.
Upgraded all Java desktop applications to run under Java 11.
Upgraded all desk top applications (SampleMaster, DESClogik, etc.) to make web services calls adhere to stricter URL encoding requirements under Tomcat 9.
Deployed new IODPLauncher application that allows developers to deploy all of our applications using a single deployment method.
GEODESC project support: participated in twice-weekly meetings with ship and shore team members to design a suite of applications that will replace DESClogik in collecting descriptive data. Revised several mockups and specification documents for the various component software tools of the project.
Data Publishing project support: Development and testing of applications to support the data publishing process as recently redefined by scope change.
Fixed several bugs in applications that were discovered as a result of testing of the new Java and Tomcat environment.

General Duties Performed

During Expedition 378T the developers participated in:

Routine expedition support.
Maintenance of software applications (as detailed in the sections below).
Assist with data management in cases where LIME and other software tools do not suffice.
Perform database export and clean up operations at begin and end of expedition.
Other duties as assigned.

Change Summary -

(this does not include prior work done on shore for Java 11 and Tomcat 9 migration that was deployed on ship during this transit.)

Produce	Current Version	Release Notes
Chem Work List		Modified to adhere to new deployment and launch protocol.
Cahn Balance		Modified to adhere to new deployment and launch protocol.
CorrDownloader		Modified to adhere to new deployment and launch protocol; Java application, upgraded to Java 11.
DESClogik		Modified to adhere to new deployment and launch protocol; fixed a bug that caused errors when importing new templates.
ImageCapture		Modified to adhere to new deployment and launch protocol.
ImageGrabber		Modified to adhere to new deployment and launch protocol; Java application, upgraded to Java 11.
MADMax		Modified to adhere to new deployment and launch protocol; minor bug fixes to display proper cell number in pycnometer display window.
MegaUploadaTron		Modified to adhere to new deployment and launch protocol.
Mettler Toledo		Modified to adhere to new deployment and launch protocol.
SampleMaster		Modified to adhere to new deployment and launch protocol.
SEMUploader		Modified to adhere to new deployment and launch protocol; Java application, upgraded to Java 11
SpreadsheetUploader		Modified to adhere to new deployment and launch protocol.
GasMonitorUploader		Removed per request from chem techs.
RequestCodeManager		Modified to adhere to new deployment and launch protocol.
ThermCon		Modified to adhere to new deployment and launch protocol.
ThermconFileConverter		Modified to adhere to new deployment and launch protocol.
Thin Section Report Writer		Modified to adhere to new deployment and launch protocol; Java application, upgraded to Java 11.
TPFit (Downhole Temperature Uploader)		Modified to adhere to new deployment and launch protocol.
Value List Manager		Modified to adhere to new requirements for Tomcat 9.
VirtualPhotoTable		Modified to adhere to new deployment and launch protocol.
IMS-10		WRMSL: PWAVE setup page has a display for liner-delay-time, but the application does not display the current value; modified the I_PI_PWAVE plug-in module to correct this issue. Scanning a label for an expedition with a non-numeric character (e.g. 378T) causes the application to display a non-descriptive error. Work to correct this error is in progress.
Velocity		The Caliper motion system does not initialize properly on application start-up; application behaves normally after launch. Reloaded the motion parameters into the Exlar actuator's onboard memory, this corrected the issue.

Outstanding Issues

Outstanding Issues are logged on the ship Confluence site: All Reported Software Issues

Special Projects / Issues

Velocity [Carried over from previous expedition.]

Technician on previous expedition demonstrated that user does not have a chance to review data, in particular the offset value, before the data is saved and uploaded. They would like a small change to Velocity to add a "pause and review" feature after they pick the first arrival (or it is auto-picked by the application) to allow them to review all of the information to make sure it correct before the data is saved and uploaded. This issue remains outstanding.

CahnBalance / Coulometer Applications

[Carried over from previous expedition.]

Home Screen Module

Chemistry technicians requested a small change to the login module. When a user clicks "Change Login" on home screen it immediately logs the current user out and so the user must login again before they can continue using the application. They would like this changed so they have an opportunity to cancel out of the login screen and keep the current user credentials so they can continue measuring samples. This issue remains outstanding.

History Module

Chemistry techs reported that the history display screen sorts all columns in character order. They would like the numeric fields (standard-deviation, mass, ,etc.) and date fields (timestamp, etc.) to sort in proper numeric and date order respectively. This represents a significant modification to the history module; including initializing it with data-type information when it is started by the main application. This issue remains outstanding.

Development Tooling and Infrastructure Changes

Worked with MCS to acquire a Mac Mini for the Developer station in the logging office; this is necessitated by the need to package Java applications in platform-specific builds. Since we have several applications that must run on Macs we need a machine that supports requirement.

Hardware and Server

Deployment of applications and testing of both internal and third party applications was conducted on multiple computers upgraded from Windows 7 to Windows 10. Custom deployment for the SEM uploader as a 32 bit solution was required as the SEM instrument requires a 32 bit environment. A copy of the 32 bit Java 11 JDK is available on dml and on the developer's computer at their station.