LexEVS Meeting Minutes - 2023.11.15

Agenda

EVS Discussion

Open System Tickets

Ticket	Description	Actions, Update
	Issues deploying prod software to DataQA	Will be moved once all configurations working on Stage/Prod. On Stage now
NCI-INC0778085	MEME ticket	DNS
	Report Exporter deployment ticket	Stage
	CTS2 / CTS2Docs deployment tickets	Stage

SYSTEMS

EVS transition to virtual machines

STATUS: As decided from last week, we will wait to switch STAGE from on prem to VM once PROD VM is ready; so we can switch both PROD and STAGE at same time .

Check on status

Systems

BACKGROUND:

On Friday Sept 29th, we were asked to deploy a banner on public-facing websites if the government was shutdown. There was confusion about who was responsible for which pages - and how to do it quickly (especially if systems groups goes to bare-bones support level. While the government was not shut down, we still want the ability to handle it better in the future.

OBJECTIVE:

to be able to update public-facing pages with banners quickly and efficiently, with Consistent styling desired for all sites - in case the need ever arises again (in case of another shutdown/emergency/etc)

ACTION:

Build responsibility list for public facing pages (Jason Lucas compiled the list)

Application	URL	Developer/POC	Status
Term Browser	https://nciterms.nci.nih.gov/	Guidehouse/Kim Ong	On Stage
Metathesaurus Browser	https://ncim.nci.nih.gov/	Guidehouse/Kim Ong	On Stage
Term Suggestion Application	https://ncitermform.nci.nih.gov/	Guidehouse/Kim Ong	On Stage - deployment issue
EVS Explore	https://evsexplore.semantics.cancer.gov	WCI/Brian Carlsen	On Stage - being tested
EVSRESTAPI (Swagger Page)	https://api-evsrest.nci.nih.gov/swagger-ui/index.html	WCI/Brian Carlsen	On Stage
~~EVS website~~	https://evs.nci.nih.gov/	Clint Malone?	On Prod
Report Exporter	https://evs.cancer.gov/report-exporter	Mayo/Andrew Moore	Ticket for Stage
LexEVS CTS2 docs	https://lexevscts2docs.nci.nih.gov	Mayo/Tracy Safran	Ticket for Stage
LexEVS CTS2 Landing Page	https://lexevscts2.nci.nih.gov/lexevscts2/	Mayo/Tracy Safran	Ticket for Stage
EVS Semantic Integration Platform	https://sip.evs.cancer.gov/evssip/	ESI/Ye Wu	On Stage

ACTION:

LEXEVS UPDATES

Monthly Planning and Focus

Completed Sprint - Sprint 213 (Oct 2 - Oct 27) – LINK TO Jira Sprint 213

Current Sprint - Sprint 214 (Oct 28 - Nov24) LINK TO Jira Sprint 214

For the month of November 2023, the Mayo group is planning to:

Complete Report Exporter refactoring and dependency updates
- (see EVSREPEXP-475 -> 483)
RMI Retirement - in progress
- Unfortunately, I do not have a detailed update at this time, other than there are efforts to update the test script. I believe that the the RMI is turned off on STAGE, and the test script would test other components to verity that there are no unseen side-effects.
Improvements, Refactoring Code Debt, Feature development:
- LEXEVS-5341 Update Spring to Spring 6
- LEXEVSCTS2-453 Update CTS2 welcome with digital sytle requirements (header, footer, etc)
Examine feasibility of Java 17
- BACKGROUND: a small number of LexEVS components (aka dependencies) are being phased off of java 8 (or are no longer being supported on java 8). We ideally want to use a current version of those components (dependencies). IF the current version of that component is only supported on Java 14 or later (just as an example), then we would have to migrate the ENTIRE LexEVS stack to Java 14 or later. (Note that the current Java version is Java 21 LTS, and the most popular non-LTS version is Java 14). So there is a risk that a vulnerability is found in the older version of the component/dependency and we would have to either migrate everything quickly to a new version, or not use that component (which might not be possible), or shutdown LexEVS entirely. Note that there are certain versions of Java which are "long-term support" versions - meaning that they will be supported for several years beyond non-LTS versions. LTS versions are Java 8, Java 11, Java 17, and Java 21.
- OBJECTIVE: find out what would it be like to upgrade from Java 8 LTS to Java 17 LTS. How hard would it be? How long might it take?
- LEXEVS-5361- Investigate Java 17
Miscellaneous bug fixes (several small bugs that have been identified over time and need to be addressed)
- EVSREPEXP-491 resolve branch-download list not being displayed on chrome browser (now FIXED)
- EVSREPEXP-433 Security issue: set-value vulnerability (in progress)
- LEXEVSCTS2-452 test_associations_subject_of call revealed hierarchy bug
- EVSREPEXP-478 Feedback form is not coming up
- LEXEVS-5252 Read an Entity by URI throwing a 302 error
- LEXEVSCTS2-431 Service resource does not populate Service name/version
- Investigate ERROR messages (both reported by Jason Lucas, and in catalina.out )

ACTIONS

Benson, Mark (NIH/NCI) [C] to add JIRA ticket to debug error messages found during outage to Sprint 213

Technical Debt remediation

LexEVS Code Debt Refactoring

Coding complete on lexevs services - except for isolated dependencies
- The isolated dependencies largely depend on using an updated version of Java (e.g. they are using more current Java versions. Java 21 LTS is the current version. The more popular non-LTS Java version is Java 14)
- Scott is investigating costs and feasibility of Java 17 (see LEXEVS-5361 above)
- LEXEVSCTS2-447 javax-servlet - on hold, until we update Java 17
- LEXEVSCTS2-446 spring-boot - on hold, until we update Java 17
Work on NCIt Browser - ehcache beta on stage. Already set at 12g for memory
CTS2 - JQuery and commons-text

Report Exporter

Banner changes being implemented for potential govt shutdown

Moved to Dev but needs Apache configuration change
Workaround - hardcoded banner

Feedback form

Need to research approval procedure, Mark was asked to reach out to OCPL
Andrew supplied copy of survey form from RE

Next work item is adding templates

ACTIONS

Security

see JQuery issue under Systems

Working on commons-lang3/commons-text
Possibly move CTS2 behind firewall

Statistics Dashboard

OBJECTIVE
Complete Migration of Statistics Dashboard from SumoLogic to DataDog by March 2024

STATUS

The queries used in the Statistics Dashboard have been shared with < someone on migration team > (as of Sept 2023).

They are working on migrating from "SumoLogic" format to DataDog format

SumoLogic Query:
Data Dog Query

<note: removed images of DataDog vs SumoLogic queries, as they didn't add much to the discussion anyway >

ACTIONS

Safran, Tracy (NIH/NCI) [C] ask how migration is going (show # of queries, # migrated, etc)

Comparison/Mapping Tool

On Hold

AWS Cloud to be in Separate Account

Waiting on AWS team

Team Absences

Mayo Team - Andrew off Nov15 & 24, Tracy off 22-24th

MSC - Kim off Tue-Fri

Leidos -

QA -

Gov -

EVS SERVICE AND ARCHITECTURE GROUP UPDATES

EVS Service and Architecture Group

Github repository - NCIEVS impacted. Need to look at user admin responsibility.

Check with Larry Brem to find out procedure for user admin - add new local admin?
Other privileges allowing creation of repositories

DATA UPDATES

Data

DECIDED:

NCIt on Stage - delayed due to high priority banner testing

BROWSER UPDATES

Browser

NCITERM-925 - Missing 'maps' link on NCIT on stage. Possibly clash of extension jars on upper tiers.
- Considered vital - need to debug before deploying on upper tiers
Term-form not working on Stage after deployment. Worked on QA and Dev

QA UPDATES

QA

Report Exporter - working on the sanity completion, should be completed today
- note that this is a manual test/push

TERMINOLOGIES LIFECYCLE REPORT

Terminology Updates and Schedule

Mark Benson TPM Update

LexEVS Technical Debt Progress

Technical Debt Related Update	Estimated Effort	Status
Report Exporter vulnerabilities - design	4 days
Report Exporter vulnerabilities - implementation	5 days
Unit testing	2 days
QA	2 days
Deployment	5 days (elapsed)

Vocabularies Slated for Production

Terminology Updates and Schedule

Vocabulary Name	Local Name	Version	Arrival Date	Loaded to data-qa DB	Date to Stage	Date to Production
Vocabulary Name in LexBIG	Short Name	Version identifier	Date the vocabulary arrived for processing	Has the vocabulary been loaded to the data-qa database?	Approximate date the vocabulary version is scheduled to move to staging	Approximate date the vocabulary version is scheduled to move to production
NCI Thesaurus	NCIt	23.08d	08/28/2023	yes	09/11/23	09/13/23
NCIt-ChEBI	NCIt-ChEBI	AUg2023	08/28/2023	yes	09/11/23	09/13/23
NCIt-HGNC	NCIt-HGNC	Aug2023	08/28/2023	yes	09/11/23	09/13/23
SwissProt	SwissProt	Aug2023	08/28/2023	yes	09/11/23	09/13/23
ChEBI	ChEBI	v225	09/05/23	yes	09/15/23	09/18/23
HGNC	HGNC	Sept2023	09/05/23	yes	09/15/23	09/18/23

QA Schedule and Status

see QA Scheduling and Status

SECTION FOR FUNCTIONAL SYSTEM TESTING STATUS ::

Application and Version	Percentage Complete	Estimated Completion Date per Iteration	Priority Level	Type Of Testing	Current Tier for Release (DEV, QA, Stage, Prod)	Expected Production Date
EVS REST API (v1.6)	100%	5/27/2022	High	Progression + Regression	QA	6/6/2022
EVS Explore (v1.6)	100%	5/27/2022	High	Progression + Regression	QA	6/6/2022
EVS REST API(v1.6)	100%	6/1/2022	High	Regression	Stage	6/6/2022
EVS Explore(v1.6)	100%	6/2/2022	High	Regression	Stage	6/7/2022
EVS REST API(22.05e) - Monthly Data Deployment	100%	6/1/2022	High	Regression	Stage	6/3/2022
EVS REST API(22.05e) - Monthly Data Deployment	100%	6/3/2022	High	Regression	Production	6/3/2022
EVS REST API(v1.6)	100%	6/6/2022	High	Regression	Production	6/6/2022
EVS Explore(v1.6)	100%	6/7/2022	High	Regression	Production	6/7/2022
NCIt,NCIm,TermForm(22.05e + GO & HGNC Jun 2022 Deployment)	100%	6/3/2022	High	Regression	Stage	6/6/2022
NCIt,NCIm,TermForm(22.05e + GO & HGNC Jun 2022 Deployment)	100%	6/6/2022	High	Regression	Production	6/8/2022
EVS REST API(22.06d) - Monthly Data Deployment	100%	6/30/2022	High	Regression	Stage , Production	6/30/2022
NCIt,NCIm,TermForm(22.06d) - Monthly Data Deployment	100%	7/8/2022	High	Smoke	Stage,Production	7/8/2022
NCIt,NCIm,TermForm(22.05e + GO & HGNC Jun 2022 Deployment)	100%	6/3/2022	High	Regression	Stage	6/6/2022
NCIt,NCIm,TermForm(22.06d) - Monthly Data Deployment	100%	7/8/2022	High	Smoke	Stage,Production	7/8/2022
NCIt,NCIm,TermForm(ChEBI, GO & HGNC July 2022 Deployment)	100%	7/12/2022	High	Smoke	Stage	7/12/2022
NCIt,NCIm,TermForm(ChEBI, GO & HGNC July 2022 Deployment)	100%	7/13/2022	High	Smoke	Production	7/13/2022
EVS REST API(22.07d) - Monthly Data Deployment	100%	7/27/2022	High	Regression	Stage , Production	7/27/2022
NCIt,NCIm,TermForm(22.07d) - Monthly Data Deployment	100%	8/1/2022	High	Smoke	Stage,Production	8/1/2022
NCIt,NCIm,TermForm(CanMED, GO & HGNC AUG 2022 Deployment)	100%	8/3/2022	High	Smoke	Stage,Production	8/3/2022
EVS REST API - 1.6.1 (Hot Fix Deployment)	100 %	8/3/2022	Highest	Progression + Regression	Stage,Production	8/4/2022

Attendees

Name	Role	Present
Remennik, Lyubov	NIH/NCI
Safran, Tracy	NIH/NCI [C]
Ong, Kim L	NIH/NCI [C]
Lucas, Jason R	NIH/NCI [C]
Bauer, Scott	NIH/NCI [C]
Alkis, Barry	NIH/NCI [C]	<checked in>
Solie, Chuck	NIH/NCI [C]
Kondareddy, Swathi	NIH/NCI [C]
Singh, Itendra	NIH/NCI [C]
Zhang, Chao	NIH/NCI [C]
Johnson, Connie	NIH/NCI [C]
Whiteman, Lori	NIH/NCI [C]
Benson, Mark	NIH/NCI [C]
Andrew Moore	NIH/NCI [C]

JIRA Issues

Recent EVS Stats Dashboard Related Bugs and Features

Key	Summary	T	Created	Reporter	P	Status

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Recent Report Exporter Related Bugs and Features

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Key	Summary	T	Created	Reporter	P	Status

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Recent LexEVS Related Bugs and Features

Key	Summary	T	Created	Reporter	P	Status

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Recent CTS2 Service Related Issues

Key	Summary	T	Created	Updated	Due	Assignee	Reporter	P	Status	Resolution

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ASSIGNED ACTION ITEMS

Description	Due date	Assignee	Task appears on
Benson, Mark (NIH/NCI) [C] to follow-up with Systems if no meeting is scheduled by 09 Oct 2023 - on this ticket; also note	09 Oct 2023	Benson, Mark (NIH/NCI) [C]	LexEVS Meeting Minutes - 2023.10.25
Benson, Mark (NIH/NCI) [C] to schedule a mtg/ discuss a possible CSS file/ENV variable for banner message and report on 11 Oct 2023	11 Oct 2023	Benson, Mark (NIH/NCI) [C]	LexEVS Meeting Minutes - 2023.10.25
Benson, Mark (NIH/NCI) [C] to report on info found out from OCPL on 11 Oct 2023	11 Oct 2023	Benson, Mark (NIH/NCI) [C]	LexEVS Meeting Minutes - 2023.10.25
Benson, Mark (NIH/NCI) [C] to schedule a mtg/ discuss a possible CSS file/ENV variable for banner message and report on 11 Oct 2023	11 Oct 2023	Benson, Mark (NIH/NCI) [C]	LexEVS Meeting Minutes - 2023.10.18
Benson, Mark (NIH/NCI) [C] to report on info found out from OCPL on 11 Oct 2023	11 Oct 2023	Benson, Mark (NIH/NCI) [C]	LexEVS Meeting Minutes - 2023.10.18
Benson, Mark (NIH/NCI) [C] to schedule a mtg/ discuss a possible CSS file/ENV variable for banner message and report on 11 Oct 2023	11 Oct 2023	Benson, Mark (NIH/NCI) [C]	LexEVS Meeting Minutes - 2023.10.11
Benson, Mark (NIH/NCI) [C] to schedule a mtg/ discuss a possible CSS file/ENV variable for banner message and report on 11 Oct 2023	11 Oct 2023	Benson, Mark (NIH/NCI) [C]	LexEVS Meeting Minutes - 2023.10.04
Benson, Mark (NIH/NCI) [C] to reach out to Clint about https://www.cancer.gov/research/resources/resource/235		Benson, Mark (NIH/NCI) [C]	LexEVS Meeting Minutes - 2024.09.11
Get the Report ready and submitted this week			LexEVS Meeting Minutes - 2024.09.04
Mark to follow up on ticket status/ subproject structure			LexEVS Meeting Minutes - 2024.09.04
Mark to follow up on ticket status/ subproject structure			LexEVS Meeting Minutes - 2024.08.28
Mark to follow up on ticket status/ subproject structure			LexEVS Meeting Minutes - 2024.08.21
Mark to follow up on ticket status/ subproject structure			LexEVS Meeting Minutes - 2024.08.14
Tracy to ping for status			LexEVS Meeting Minutes - 2024.08.14
Tracy to send invite to systems to discuss migration in this meeting			LexEVS Meeting Minutes - 2024.07.17
Temporarily block Singapore traffic			LexEVS Meeting Minutes - 2024.06.05
Tracy to request shut down of instance to save resources			LexEVS Meeting Minutes - 2024.06.05
Temporarily block Singapore traffic			LexEVS Meeting Minutes - 2024.05.29
Tracy to request shut down			LexEVS Meeting Minutes - 2024.05.29
Check status of termform and Tomcat9			LexEVS Meeting Minutes - 2024.05.15

Content

Space Tools

Agenda

EVS Discussion

LexEVS Technical Debt Progress

Vocabularies Slated for Production

QA Schedule and Status

Attendees

JIRA Issues

Recent EVS Stats Dashboard Related Bugs and Features

Recent Report Exporter Related Bugs and Features

Recent LexEVS Related Bugs and Features

Recent CTS2 Service Related Issues