Date

03 Dec 2019

Call-in Information

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

To join the online meeting:

• Go to: https://lyrasis.zoom.us/my/vivo1

• One tap mobile:

  • US: +16699006833,,9358074182# or +19292056099,,9358074182#

• Or Telephone:

  • US: +1 669 900 6833 or +1 929 205 6099 or 877 853 5257

  • Meeting ID: 935 807 4182

• International numbers available: https://zoom.us/u/aeANHanzED

Slack

• https://vivo-project.slack.com
  • Self-register at: http://bit.ly/vivo-slack
    

Attendees

 Indicating note-taker

1. Ralph O'Flinn
2. Brian Lowe
3. Mike Conlon
4. Huda Khan
5. Steven McCauley
6. Benjamin Gross 

Agenda

1. Community updates
   1. VIVO Scholars
2. Special topics for future dev calls
   1. 2019-12-06 - Special Topic - TDB vs SDB
3.  In-review tickets 

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   2. Unable to locate Jira server for this macro. It may be due to Application Link configuration.
   3. Click here to expand...

      type	key	summary	assignee	reporter	priority	status	resolution	created	updated	due
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4. Updates from 2019-11-27 - VIVO Committers Meeting

Tickets

1. Status of In-Review tickets

   Click here to expand...

   type	key	summary	assignee	reporter	priority	status	resolution	created	updated	due
   Unable to locate Jira server for this macro. It may be due to Application Link configuration.

Notes 

Draft notes in Google-Doc

• Community updates: 
  • Ralph will do visualization part of video next Monday and that part will be added to the recording
  • TAMU and Duke scholars initiatives with UI development work
  • Any others?
    • JavaScript front-end speaking to TPF
    • https://people.metabolomics.info/person.html?iri=https%3A%2F%2Fvivo.metabolomics.info%2Findividual%2Fp197
    • Clicking on dataset takes directly to metabolomics workbench
    • Clicking on pubmed link goes directly to pubmed
    • VIVO used as a metadata management piece with links going directly to resources linked
    • NIH grant for a 0.3 developer FTE/1 hour meeting with developer and project manager
    • GitHub: https://github.com/ctsit/m3c-web 
  • Mike: https://people.metabolomics.info/ 
  • Ralph: Simple is good sometimes
• VIVO Scholars.  Demoed part of the video.  (http://vivo-scholar-scholar.cloud.duke.edu/ ?)
• Also review committers’ meeting notes from last week (11-27)
• Benjamin (from chat): Nice looking VIVO I haven't seen before that was shared at the German VIVO workshop: https://www.forschungskompass.eu/
• Special topics call: SDB vs TDB
• Meeting scheduled for Friday 9 AM ET
• With TDB, still addressing speed issues
•  In-review tickets
  • https://github.com/vivo-project/jenatools/pull/13 
  • https://github.com/vivo-project/VIVO-languages/pull/26 
  • Benjamin: Did take a look. Issue seems to be the pull request is coming in from a fork so there is more code there than 
  • Ralph will take a look at this
  • Track user changes to the content store
  • https://github.com/vivo-project/Vitro/pull/81
  • Refer to committers’ discussion regarding what defines enterprise software.  Proper logging/transaction tracking is one of the areas that need to be addressed.
  • Can continue discussion next time
  • Updating maven dependencies
  • Ralph: Had to redo a bunch of those
    • Also for libraries and scripts
    • Based off 1.11 code base
    • Requires more care
  • New branch with maven dependency updates: https://github.com/vivo-project/VIVO/tree/vivo-1.11.0-lib-updates
  • Benjamin: circular problem - don’t update dependencies because requires work because some are so old, leading to more work because they get even older, meaning they are even harder to update, meaning… 
  • Ralph has brought us part of the way but it requires more testing
  • Huda: Tried to do so but seems to recall ran into errors so may have switched back to 1.10
  • Ralph: There was a bug that had been released after release 1.11 (check style)
    • JAVA JDK Oracle
    • Cannot use newer version of OpenJDK (it shall crash during build for newer versions)
    • Maven requires: oracle java jdk 8
  • Also need to run off real version of build
  • Mike: Usually just take artifact and documentation and follow through
  • Ralph: Plug for Docker
  • Brian: Would this JAVA issue affect VIVO? Ralph: yes
• https://jira.lyrasis.org/browse/VIVO-1732
• https://jira.lyrasis.org/browse/VIVO-1734 
• https://jira.lyrasis.org/browse/VIVO-1545?src=confmacro 
• Benjamin: Languishing ticket: https://jira.lyrasis.org/browse/VIVO-1642?src=confmacro
• Mike: Anyone tried to build Vitro 1.11?
• Benjamin: Brian, tried to use the service for starting/stopping reasoner but couldn’t get it to work so may reach out to you later.  
• https://github.com/RAP-research-output-impact/rap-custom-vivo/blob/master/custom-vivo/webapp/src/main/java/dk/dtu/adm/rap/controller/IndexingInferenceService.java 
• DTU code repo: Ralph found it!

Actions

• Organize a session on Brown's work on editing