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De Coronado, Sherri    

Safran, Tracy

Kuntipuram, Kumar

Sprint Status

Current Sprint -  Sprint 50 51 (February 16March 2, 2017 – March 115, 2017)

16X237 Agile Development - Sprint Status#16X237AgileDevelopment-SprintStatus-Sprint50Sprint51

Triple store discussion

• Gilberto

Discussion Points:

• Gilberto gave an overview of the current status of the triple stores.
• Gilberto is waiting for quotes to come back.
• Stardog has another version coming out that may improve performance.
  

Decision Points:

• The team decided to go with Stardog if we can get several developer licenses for a discount.  (They charge $8600/developer license).  Otherwise we will go with Virtuoso.

DEV Server Configurations

• DEV Blade
  • 6.4.1.3.FINAL
  Mayo DEV VM
  • 6.5.0 SNAPSHOTSeparate DB

Discussion Points:

• LexEVS Jacob anticipates the DEV blade VM will be installed with the 6.4.1.3 .FINAL is loaded on Mayo DEV VM
• LexEVS 6.5.0 SNAPSHOT will be loaded on DEV Blade with CentOS 7.
  • Jacob has a ticket for this work.
• FINAL by early next week.
   
• Cory created a ticket for Jacob to create separate We will want a separate DB ( MySQL 5.6 ) DBs for the Blade DEV blade and the VM Dev instances.

Decision Points:

Value Set Loading Enhancements

• Load Update

Discussion Points:

• Scott and team have identified the current issues with the value set failures.
• Tracy has not had an opportunity to test the mass load script yet.
  
• Mayo team will meet with Jason and Kim to discuss value sets architecture tomorrow.
  

Decision Points:

• LexEVS Meeting Minutes - Value Set Architecture Planning Session - 2017.03.02
• We discussed how we could automate testing of loaded value set definitions and resolved value sets (in the meeting link above).
• Tracy suggested starting from scratch to fix this error-prone approach.
• Rob asked if we could we use the content of Thesaurus for populating the value set?
• We could look into using an OWL based approach
  
  • Concept in subset.
• Tracy suggested that this could be a prototype for outside groups to use too.
• We will continue this discussion at our value set meeting next Tuesday, 3/14.
  

Decision Points:

• Scott to test the value set load on the NCI DEV system.
• Mayo dev team will look into a new architecture/design for generating the value sets.
  

Discussion Points:

• The Mayo dev team will look looked at the new 6 CTS2 JIRA issues created by Tracy.
• We will determine if our current implementation can accommodate the request.
• If it can't, can we implement it in CTS2.
• If that can't be done, we can look at implementing it in a different service.
  
• Larry suggested that there should be a simpler REST interface than CTS2.
  • Larry mentioned that they (customers) are coming up with some criteria and examples of what they would like. 
  • They will have some examples/criteria in the next couple of weeks.
  • This may be something like convenience methods or CTS2 extensions.
    

Decision Points:

• The dev team will hold off looking at the existing JIRA issues and see if CTS2 can accommodate this in the next sprint.
• The dev team will work on the tree extensions instead in this sprint.
  

LexEVS Logical Role Relationship

• Discussion with Kim

• issues and determined what was possible for each.
  
  
• LEXEVSCTS2-138: This fits within the realm of the CTS2 spec and could be implemented as a part of that specification
• LEXEVSCTS2-139, 140: These are LexEVS coding scheme metadata and don’t really have a good counterpart or fit in CTS2.  We’d likely want to provide a separate resource or service for these. 
• LEXEVSCTS2-142: Return only the specified information on an entity
  
  • This would be a new call that returned a new partial resource
• LEXEVSCTS2-143: Return a property type for an entity 
  • This would be a new call that returned a new partial resource
  • Example Call
    
    • https://lexevscts2.nci.nih.gov/lexevscts2/codesystem/NCI_Thesaurus/version/16.12d/entity/C422?format=json
  • Would need to filter the properties to return this specific property type 
• LEXEVSCTS2-144:  Retrieve a concept based on the presence of a restriction
  • Workflow - series of calls to get from CTS2
  • A new wrapper/extension REST call would need to be created to do this in one call.

• Priorities (suggested by Tracy)
• • Ability to retrieve the FULL_SYN information (Larry)
  • Search on property for a given criteria
    • Give me all the concepts that have a specific property
  • Limit the result set coming back.
   

Decision Points:

Discussion Points:

•  

  Jira
  server NCI Tracker columns key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution serverId 7954a81f-12da-3366-a0ef-97c806660e7c key LEXEVS-2764

• We will leave this issue open until Kim can verify.

• Set up meeting to look at examples and discuss.
• Start to add to sprints - convenience methods for
  
  • LEXEVSCTS2-142, LEXEVSCTS2-143

Discussion Points:

• There is an example in the OBI OWL2 source.
• The AnyURI is declared as data type in the annotation property.
  
• This doesn't fit into LexEVS model (an association on an association).  The LexEVS API wouldn't handle this well either.
  

Decision Points:

• Scott mentioned that our load will ignore this case
• Scott will sent a snippet source example to Gilberto.
  

• Gilberto - from the snippet that Scott provided: an annotation property that doesn't have a range.
• There have been JIRA issues that were created for the points that Gilberto discussed.
   

Decision Points:

• Gilberto to send an OBO example code snippet for the issues he discussed

Discussion Points:

• Docker Contacts: Mike Stockwell & Sue Pan

Decision Points:

Resolving all relationships for a given association

Discussion Points:

• Our loads are now making a lot of calls into the ontology class.
• This is increasing our Thesaurus OWL2 loads from 1hr to 3-6hrs.
  

Decision Points:

Remote API timeout issue

• Discussion with Kim

Discussion Points:

• What is the use case for resolving all relationships for a given association. 
  
• Is there a requirement for Enumerations
  
• There is a workaround that can retrieve these relationships, but we should discuss implementing a more efficient API call
•  Intermittent socket timeouts from the Remote API.
• Scott is able to reproduce this issue locally.

Decision Points:

Discussion Points:

Decision Points:

Mayo Team

• Cory -
• Scott -
• Craig - March 6-13

NCI

• Tracy
  • March 9-17
• Rob
  

  • March 20-24