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Close issue 

Create JIRA issue to update CTS2 service to use Apache Commons Collections Version 3.2.1 (security issue)

Set up an ARC meeting for LexEVS 6.4 (no meeting needed)

Sprint Status

Current Sprint -  Sprint 33 34 (June 23July 7, 2016 – July 620, 2016)

LexEVS 6.4 S13-500 Agile Development - Sprint Status

We finished sprint 33.

The HL7 loader issue for namespace is complete

There were three OWL2 loader issues that were resolved

Lucene code has been merged into the master branch

We are also planning for sprint 34 and for the next LexEVS release.

Dev - RC.1

• Status of Deployment and Verification

Deployment to DEV:

• Toky deployed using the Jenkins server
• Once LexEVS is installed via AHP, Tin will test.

ARC Process

• Updates

Deployment to DEV:

• Sara is using our original PTE request to have LexEVS installed on DEV. This ticket has been assigned to Jacob.
• The Systems team will do the install on DEV using AHP.
  • Remote API - This will be a new container (there will be 6.3 and 6.4 instance available)
  • CTS2 - 6.4 This will be used in place of 6.3. CTS2 6.4 will reuse the 6.3 container.
  • URI resolver will not change. We will point to the existing one.
• We don't want to require clients to have to update their client builds for 6.4

OWL2 Loaders discussion

• Feedback regarding cardinality

Quantified Object Of Restrictions -

• Cardinality restriction is covered in this fix.
• What do we do with the other cardinality restrictions?
• Should these be traversable?
  • relationships
  • qualifiers (if they are at the end).

Larry suggested the following:

• Base semantics could be used in the LexEVS
• Full semantics should be in another tool besides LexEVS (possibly a triple store). The LexEVS model doesn't support this.

Scott suggested that we think about the restrictions issue and we will continue our discussion at the meeting set up for this Friday.

Status#SprintStatus-Sprint34

Cory is working on LexEVS 6.4 documentation

Scott is working on an OWL2 loader issue

We are investigating lexevs-1999 - TreeServer API fails on RadLex, Version 3_13_1.

We added lexevs-2078 to this sprint.

RC.2 Deployment and Verification

• Tin to provide testing feedback
• Jacob AHP install feedback

Lexevs API 6.4.0.RC.2 is deployed on DEV. This was done manually by Rob. Jacob is still working on the AHP deploy process and expects to have it completed today.

Testing (Tin):

• Automation script tests are half way complete.
• There is a single character issue. Kim is adjusting his code to fix this issue.
• There is also a single bracket search issue: {Provider}
  • Scott suggested that the Lucene search algorithm is slightly different in 6.4.
  • We have a different approach to cleansing our characters in the search. We are using a standard analyzer in Lucene for this.
  • Scott will investigate further why the query with the brackets is failing for the test use case.

Kim will create a new JIRA issue for the {Provider} issue.

Overview of QA Process (Test Plan)

• Integration tests between LexEVS and the latest browser?

• Are there tests specifically for LexEVS API?  Distributed API?  CTS2?

• JIRA issues verified for LexEVS 6.4

For LexEVS 6.5, we would like to see QA testing done earlier during the development process.

Automated tests go through the term browser and through Selenium automated scripts.

CTS2 and URI Resolver - Tin has a set of manual scripts to test these services. Tin will run these tests on QA.

JIRA issue testing - Tin will run Junits associated to the JIRA issues. Tin will run these tests on QA.

getIsPreffered() 6.4 Investigation

• Cory to discuss investigation findings

• Jira
  server NCI Tracker columns key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution serverId 7954a81f-12da-3366-a0ef-97c806660e7c key LEXEVS-2016

• Gilberto's feedback

Current fix is to call everything an "HL7" namespace object.

Do we need to expand this to multiple namespaces?

Gilberto mentioned the following:

• In the case of the OBI vocabulary, we are using coding scheme to denote the vocabulary, which is in turn composed of several namespaces, GO, ChEBI, IAO, as well as the OBI namespace itself.  
• In the case of HL7, we'd be using "namespace" for the container, while each individual HL7 vocabulary is a "coding scheme" (per the HL7 nomenclature).  

Gilberto asked if this fixes Kim's issue? Yes, there is now a namespace called "HL7".

We agreed to go with this approach for now and have it tested by Kim.

LexEVS External Users

• 2020

This is not needed for LexEVS 6.4 as Rob does has a workaround.

We are assuming this is a loader issue. We agreed to explicitly provide a true/false value for preferred in the loader code.

TODO: Cory will update LEXEVS-2020 with the proposed resolution and exit criteria.

Addition of 2078 to this sprint

getIsPreffered() - Prioritize JIRA Issue

TODO: verify if this was fixed in 6.4.

HTTPs as a requirement for CTS2, Remote API and URI resolver

• Discuss the timeline for this requirement

Larry mentioned that there is an HHS mandate that all services need to move to HTTPS by the end of the year.

Any new services created after this year will need to be HTTPS.

Question: When do existing services need to be updated?

TODO: Create a JIRA issue for this and place it into 6.5 for now.

6.5 Review and Planning

• Planning activities:
  • Prioritization of 6.5 issues from face to face. (30)
    • https://tracker.nci.nih.gov/issues/?jql=(affectedVersion%20%20%3D%206.5%20OR%20fixVersion%20%3D%206.5)%20AND%20labels%3D%202015.12.Face2Face%20and%20project%20%3D%20LEXEVS
  • Prioritization of 6.5 tagged backlog issues (not 2F2). (25)
    • https://tracker.nci.nih.gov/issues/?jql=(affectedVersion%20%20%3D%206.5%20OR%20fixVersion%20%3D%206.5)%20%20and%20labels%20is%20EMPTY%20and%20project%20%3D%20LEXEVS
  • Deliverables by end of Sept?
  • Other timeline?

We should discuss when MySQL should be upgraded to 5.7 or Maria DB 10.x. We are currently on MySQL 5.5.

We also discussed the possibility of node.js being included in the tech stack.

Docker and a Docker repository would also be a good addition.

TODO: Mayo team will send Gilberto a summary note for this discussion.

LexEVS External Users

• HL7 Loader - content from Meta

  • https://github.com/lexevs/lexevs/issues/42

• RF2 Content

  • https://github.com/lexevs/lexevs/issues/7#issuecomment-231646538

HL7 loader - This may be a source issue. Allameda is the author of this content.

Rob mentioned that the MIF loader worked for him.

Scott will follow up with the user to see if they can use the HL7 MIF loader.

It is also possible that the user is not subsetting the HL7 version correctly.

RF2 Content - Our loaders don't support RF2 (Australian content).

We will need to discuss how to proceed with Larry.

This will not be in LexEVS 6.4.

Larry would like us to come up with a plan and try to fit it into the LexEVS 6.5 schedule.

Mayo Team

• Scott - July 15th - 20th