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Call-in Information

Time: 11:00 am, Eastern Daylight Time (New York, GMT-04:00)

To join the online meeting:



(star)  Indicating note-taker

  1. Brian Lowe (star)
  2. Ralph O'Flinn
  3. Andrew Woods
  4. Maria Florez
  5. Rafa
  6. Alex Viggio
  7. Benjamin Gross
  8. Don Elsborg   


  1. Sprint update (June 17th - 28th) - see slack channel #vivo-scholar
    1. External Search

      1. Merge 'sprint-search' (vivo, vitro) into 'develop'?
    2. Enable connection of decoupled, read-only "profiles" user interface to VIVO

    3. Define "shapes" of VIVO entities

    4. Dockerize appropriate components

  2. Tickets in-review
    1. Needing one more review
      1. VIVO-1687 - Getting issue details... STATUS
    2.  Click here to expand...

      T Key Summary Assignee Reporter P Status Resolution Created Updated Due

  3. Working towards the VIVO 1.11.0 release
    1. Landing Design - External Search
    2. Other tickets we want to include?
      1. Docker work:
        1. VIVO-1679 - Getting issue details... STATUS  - Don Elsborg to review?  Ralph O'Flinn Reviewing
        2. VIVO-1680 - Getting issue details... STATUS  - Don Elsborg to review? Ralph O'Flinn Reviewing
        3. VIVO-1682 - Getting issue details... STATUS  - Ralph O'Flinn to review - Now in
      2. VIVO-1670 - Getting issue details... STATUS  - mis-rebased
      3. VIVO-1415 - Getting issue details... STATUS  - appears to have an unrelated commit in pull-request
      4. VIVO-1692 - Getting issue details... STATUS
    3. Release manager?


  1. Status of In-Review tickets

     Click here to expand...

    T Key Summary Assignee Reporter P Status Resolution Created Updated Due

  2. Received

     Click here to expand...
     Click here to expand...

    T Key Summary Assignee Reporter P Status Resolution Created Updated Due

    1. VIVO-1666 - Getting issue details... STATUS

      1. (re-)Raises interest in reconsidering first-time, every-time, tdbconfig design

    2. VIVO-1665 - Getting issue details... STATUS
      1. Should be low-hanging
    3. VIVO-1663 - Getting issue details... STATUS

      1. Where does this stand? What is needed to add more person identifiers to VIVO?

    4. VIVO-1644 - Getting issue details... STATUS
      1. Mike Conlon : thoughts on where this stands?
  3. Bugs (1.11)

     Click here to expand...

    T Key Summary Assignee Reporter P Status Resolution Created Updated Due


Draft notes in Google-Doc  


  • Andrew Woods
  • Ralph O’Flinn
  • Brian Lowe
  • María Amalia
  • Benjamin Gross
  • Alex Viggio
  • Don Elsborg
  • Rafa


Sprint Updates

1a. External Search

  • Ralph:  ‘Sprint-search’ branch seems to be working really well
    • 1a: ready to merge back down into develop now
  • Andrew:  Welcome María Amalia to the call
  • Ralph:  Merged develop into ‘dev-search’ branch to confirm that everything is working before merging back into develop; no problems have jumped out.  MariaDB and latest version of Tomcat 9 and Java 11 LTS. Tested in Redhat Linux as well as Windows. Will use for Dockerization in 3.b.i. 1, 2, 3.
    • Resolved merge conflicts with Graham’s changes.
  • Andrew:  Would be valuable to have at least two other people give this a spin before we put it in.
    • Don expects to get to this Wednesday or Thursday.
    • Don was expecting to test it; may need a reminder.
  • Andrew:  This is the primary blocker for the 1.11 release.
  • Benjamin:  I’m very interested in seeing this roll in.  My only complaint in testing was the problem of getting the externalized SOLR populated with the right schema.  Have to POST to it? Needs clear documentation on how to do this because it’s not going to happen automatically.
  • Action: Andrew will move a Github repository from his personal Github ( into vivo-community.
  • Ralph:  shouldn’t need to manually add the schema file to SOLR if you use the ‘core’.  All the little config files you need are included.
    • Confirmed:  the vivo core contains schema.xml (point of repository above).
  • Andrew:  If Don is able to review this, we can get it merged.

1b. Enable connection of decoupled, read-only profiles

  • Populate separate SOLR index with SPARQL queries, serve UI from this index.
  • Moving along with Texas A&M, Duke, Ralph, Andrew and others.
  • Working on using OpenVIVO as source data in order to generalize and not have data with institutional assumptions.

1c. Shapes

  • Using OpenVIVO and generalizing the read-only UI is adding clarity to the shapes, but we are unlikely to have actual shapes in this sprint.
    • Don:  Was there already a working group working on making shapes?
    • Ralph is part of a group that is doing data modeling.  
    • Don: it would be nice if shapes were not part of code but were in something like XML that could be used to transform into JSON. It would be good for any language to be able to process that shape definition.
    • Andrew:  User-configurable shape definition and an automatic way of putting data into those shapes.

1d. Dockerizing appropriate components

  • Andrew:  Docker seems like a constructive trend.  Easy to spin up particular environments for testing (e.g. Java 11)
  • Don:  Would be beneficial to have Tomcat, MariaDB and Java on CentOS.
    • Ralph is building a Docker Compose for Redhat.
  • Ralph believes he has the Blazegraph changes merged in, but will check.

2. VIVO-1687 needs another review to be merged; low-hanging fruit. One-liner.

Action:  Andrew will check with Mike to see if we can close ontology issues VIVO-1652 and VIVO-1287.

3. Working towards the release

  • VIVO-1670 needs cleanup from some sort of Git problem.
  • Claiming from PubMed and CrossRef
    • Maria interested in using these features
    • Benjamin has used them in the past, but not in production.  Seem to work.
    • VIVO-1415 has this functionality.  Has a pull request.
    • If Rafa or Maria have comments about functionality, they should add comments to ticket VIVO-14155.
    • Very helpful to add a comment indicating approval if everything works.



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