Date

05 Mar 2019

Call-in Information

Time: 11:00 am, Eastern Time (New York, GMT-05:00)

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Slack

• https://vivo-project.slack.com
  • Self-register at:   https://goo.gl/forms/JxQFkut4TYj4Ehww1 
    

Attendees

 Indicating note-taker

1.  Don Elsborg
2. Ralph O'Flinn 
3. Huda Khan
4. Andrew Woods  
5. Benjamin Gross 
6. Brian Lowe 
7. Mike Conlon
8. @Harry Thakkar
9. Jim Blake
10. Steven McCauley
11. Richard Outten

Agenda

1. Review from last week's dev meeting
2. VIVO Conference proposals

3. March (18-29) sprint planning

   1. Finish work on externalizing Solr and Elasticsearch
   2. Decoupling - Dockerize: Solr, Elasticsearch, MySQL, rest-of-VIVO
      1. Reference: Docker 101 and 102

4. Mailing list messages

   1. Some triples not getting deleted in VIVO?
      
   2. How can I backup the custom Pages that have been created?

5. Status of In-Review tickets

   
   

   1. Soft balls

      1. 

         1. Low-hanging - need one more reviewer - Brian Loweis reviewing

      2. 
         1. Low-hanging, documentation - Mike Conlon, can you give this one a review?
   2. Regular balls
      

      1. 

         1. New

      2. 

         1. Kitio Fofack ? Orcid and i18n

      3. 
         1. Is this feature of broader interest?
      4. 
         1. Andrew Woods to look into
      5. 
         1. Mostly trivial, with conversation around Tomcat version support
      6. 
         1. Relatively straight-forward bug fix
      7. 
         1. An important step for i18n... resolves many other open issues
      8. 
         1. Kitio Fofack to review?

6. Received

   (re-)Raises interest in reconsidering first-time, every-time, tdbconfig design   Should be low-hanging   Where does this stand? What is needed to add more person identifiers to VIVO?   Mike Conlon : thoughts on where this stands?

   
   

7. Bugs (1.11)

   
   

   
   

Notes 

Draft notes in Google-Doc

• Review of last week’s call:  any follow-in actions?

• Ralph feels last week went very well; answered all questions.

• Have not gotten additional follow-up questions

• Ralph received questions in advance

• Seemed very constructive

• Directed new people to Slack and the groups

• Mike: Things to take to heart:  They were not aware of APIs for data loading. They’ve been active for more than a year.  Whatever they searched for they didn’t find it, so that was a pretty big concern.

• Ralph: problems with searching the wiki were raised.  Had to implement workarounds because they didn’t find the better answer.

• Andrew: did the SPARQL update API seem like it would suit their needs?

• Not clear yet; they have to look into it.

• Should follow up to see how things are going.

• Should encourage people to come and ask questions on future calls.

• Welcome to Harry Thakkar at Duke.

• Doing DevOps and containerizing

• Mike has been on the road lately.  Things to share?

• The ontology interest group is talking through what it would take to improve the ontology.  The ontology community is looking forward to that. Want an ontology of scholarship that can be used more broadly.

• Very good meeting; personal connections with important people in the ontology community.

• When/if/how the next-generation VIVO ontology is adopted by any particular software is a separate question.  No immediate change to the software.

• National Forum on Expert Finder Systems.  Hosted by Elsevier; lack of VIVO perspective in the event organization.  Dominated by people who facilitate connections between commercial entities and universities.  Also people from government working in this space.

• Good-sized meeting.  Smaller; able to talk to people about what they needed.  Both keynotes were affiliated with the VIVO project: Robert McDonald, Noshir Contractor.

• Possible interest in a joint conference with VIVO in the future.

• VIVO conference: if people are going, brainstorming ideas for proposals

• Mike says alternative presentation formats are to be considered.

• Andrew: product evolution effort should have some presence there.

• Richard: hasn’t been discussed on the product evolution calls yet.

• Andrew planning to put in a proposal about the architecture and road forward coming out of the face-to-face meeting in Orlando. Happy to do that jointly.  Ralph happy to help if he has funding to attend.

• Andrew: would be nice to have a developers’ session where we dive into some concrete actions around what needs to happen.

• Huda is interested in helping craft some things.  Curious what people think about the conference tracks.  Prefers one-track conferences, but means you have fewer presentations total.

• Sprint

• Sprint is coming up in 13 days.

• Would be ideal to have some names in the participants list in advance so we can scope the tasks appropriately.

• Docker container for the search index, the backing database to the triple store, and for the rest of VIVO.

• Details to work out about how they will be configured.

• Andrew and Ralph:  the three efforts need to be coordinated and use a common approach.

• Richard: might use Docker Compose.  May also be able to use official images from Docker Hub.  Question of how to configure and inject environment variables.

• Andrew: I assume we will want to publish our results to Docker Hub?

• Yes, eventually.  Might be an overreach for the sprint.

• Harry: First goal is to define light components that can be composed in Docker Compose.  A light image does just one thing. Application as one image; web server as another. Every process runs in a different image.

• Don:  looking at issue of a Tomcat container.  There are nuances with glibc compatibility/argon.  Is that a place where we create our own OpenJDK Tomcat image?  Assume build is outside the container?

• Richard: can do the build in the container.  You can specify what stage of the build process you want to run.  

• Harry: don’t have to have OpenJDK locally to build this way.  Container with Maven where you build stuff; then use same docker file in another container.

• Andrew: also question of the third tier and how to manage the flexibility of customization with Docker.  Would be good if this came out of the sprint as well.

• Don:  I think it would look like what Harry and Richard were describing.  Do a three-tier Maven build in one container and deploy the war to another container.

• Andrew:  implies that people would have their own institutional images rather than standard VIVO images.

• Would be valuable to have an out-of-the-box installation, but also have some clear documentation for what to do if you do have your own custom third tier.

• Don:  not sure if third tier is in scope for Docker.

• Andrew: one of the goals of the sprint should be clear approach and documentation for how to support a customized installation.

• Don: TDB versus SDB issue.  Are we going to build Docker with SDB?

• Ralph brought up a fly-in but too detailed for that discussion.

• Should probably have a separate meeting to discuss just this issue.

• Jim:  before we change the default that VIVO ships with, we need to be sure that what we’re recommending is performant.

• Andrew:  performance metrics would inform that conversation.

• Jim wishes we could get away from SDB, but right now that doesn’t seem wise.

• Andrew:  add your name to sprint planning page.  Two mailing list questions to answer; outstanding issues.

• Outstanding mailing list topics

• Issues

Actions

•  - Brian Loweis reviewing
•  - Mike Conlon, can you give this one a review?

Previous Actions