Date

23 Jul 2024

Call-in Information

Time: 10:00 am, Eastern Daylight Time (New York), 4pm Central European Summer Time

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Calendar invitation - ICS file

Slack

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

Attendees

 Indicating note-taker

1. Dragan Ivanovic  
2. Brian Lowe 
3. Ivan Mrsulja 
4. Miloš Popović 
5. Bridget Almas
6. Tom Misilo
7. Ian Slater

Agenda

• • VIVO 1.15.0 Release Announcement
  • VIVO documentation update
  • VIVO ORCID grant
  • VIVO authentication issue - https://github.com/vivo-project/VIVO/issues/3996
  • VIVO - ElasticSearch integration - https://github.com/vivo-project/Vitro/pull/469
  • Installation at Debian 12
    • package javax.xml.soap does not exist
  • Solr docker upgrade - Ian Slater
  • Summer mode
    • 2nd, 9th, 23rd of July, 6th, 20th, 27th of August

Notes 

VIVO 1.15.0 

Dragan discussed the feedback from the test phase, highlighting an issue with the UMLS vocabulary and the need for additional configuration. He also shared that he had prepared a release after resolving the issue (VIVO 1.15.0 Release Announcement) and that there were no known bugs at the time. 

VIVO documentation update

Dragan worked on updating wiki documentation and adding new wiki pages for new features introduced in VIVO 1.15.0 

https://wiki.lyrasis.org/display/VIVODOC115x/Using+Search

https://wiki.lyrasis.org/display/VIVODOC115x/Authorization

https://wiki.lyrasis.org/display/VIVODOC115x/Editing+Your+Account

https://wiki.lyrasis.org/display/VIVODOC115x/The+VIVO+audit+module

https://wiki.lyrasis.org/display/VIVODOC115x/Private+individual+pages

VIVO ORCID grant

Dragan informed the team about the results of the review process for the VIVO-ORCID integration proposal. Unfortunately, the project has been rejected to be funded, although it got quite a high score (55 out of 56). It is not so clear at the moment what should be improved in the next call for funding. Leadership group should discuss whether we should apply again or not. 

VIVO authentication issue 

A GitHub ticket has been opened - https://github.com/vivo-project/VIVO/issues/3996

Brian tried to help, but the issue has not yet been resolved. Dragan can try to invite Elvis (the issue reporter) to join the next call. 

VIVO - ElasticSearch integration 

The pull request has been created, but the review process has not been started  - https://github.com/vivo-project/Vitro/pull/469

Probably, the more progress might be after the summer break.

Installation at Debian 12

Dragan is in communication with Jinu (the reporter) and will try to help in the installation. 

VIVO and Solr docker upgrade 

Ian Slater reported the issue. He is trying to migrate VIVO 1.14 to VIVO 1.15. He tried to migrate data and Solr index. Dragan thinks it is not needed to migrate Solr index, it is enough to migrate data which not require any additional action if the same VIVO_HOME is used in which TDB subdirectories contain data, and after running the new VIVO to log in as system administrator and run reindex (Site admin in the main menu). 

Summer mode

We will continue organizing meetings biweekly till August 20th. Plan for meetings:

• 2nd, 9th, 23rd of July, 6th, 20th, 27th of August

Draft notes in Google Docs

Task List

• Dragan Ivanovic to contact Elvis regarding the issue with authentication
• Dragan Ivanovic to try to help Jinu with the installation issue
• Ian Slater will try to upgrade VIVO 1.14.0 to VIVO 1.15.0 and inform the team back in the case there is still some issue

Previous Tasks 

• Dragan Ivanovic  to investigate the UMLS issue and provide an update on Thursday committers' meeting.
• Bridget Almas to follow up with the Lyrasis hosting team regarding the Vivo demo site and report back. Dragan Ivanovic to investigate data which should be used in demo instance and to check how it might be part of docker. 
• Victor Gabriel Pereira to explore using Elastic Search instead of Solr for VIVO's search functionality. 
• Dragan Ivanovic to coordinate the VIVO 1.15.0 documentation update
• Ivan Mrsulja to test the Elasticsearch integration with Vivo 1.15.0 using ElasticSearch version 7.0 and provide an update on the testing process in the PR description

• Dragan Ivanovic to prepare 1.14.3 release
• Ivan Mrsulja to continue working on integration of VIVO with the ElasticSearch engine

• Georgy Litvinov to fix https://github.com/vivo-project/VIVO/issues/3987
•  Dragan Ivanovic to discuss with Georgy about upload of images issue
• Bridget Almas to review Wilma responsive PR
• Dragan Ivanovic to investigate GitHub - Zenodo integration (already in place - https://zenodo.org/account/settings/github/repository/vivo-project/VIVO
• Dragan Ivanovic to discuss with Don Elsborg about VIVO - ElasticSearch integration
• Dragan Ivanovic will prepared slides for presenting VIVO at the CRIS 2024 conference
• Dragan Ivanovic will monitor call for ORCID project
• Dragan Ivanovic will try to reproduce the issue by using VIVO 1.14.x release, to cherry pick the commit which is resolving the issue https://github.com/vivo-project/VIVO/issues/3934 and check whether it is resolving the issue reported by Diego
• Diego Rivas will confirm whether it resolves the issue
• Dragan Ivanovic will prepare VIVO 1.14.2 release candidate
• Ivan Mrsulja will add screenshots of email notifications for the password reset
• Dragan Ivanovic to contact native speakers to help in the validation of messages in https://github.com/vivo-project/Vitro/pull/421
• Dragan Ivanovic to update pull request template
• Dragan Ivanovic to draft contributing.md
• Dragan Ivanovic to update Readme.md file
• Dragan Ivanovic to review https://github.com/vivo-project/Vitro/pull/443, https://github.com/vivo-project/Vitro/pull/444, https://github.com/vivo-project/Vitro/pull/445
• Ivan Mrsulja to complete I forgot my password PR by adding draft translations of email notifications messages into all VIVO supported languages
• Dragan Ivanovic to invite Ian Sleter to join VIVO team and to review PR for docker improvements
• Dragan Ivanovic to respond on Humberto email - https://groups.google.com/g/vivo-community/c/6K651KthQAk/m/WjSjP0ZXAQAJ?utm_medium=email&utm_source=footer
• William Welling will create a PR for addressing docker issue https://github.com/vivo-project/VIVO/issues/3939
• Dragan Ivanovic will coordinate writing extended abstract for CRIS 2024 conference
• Dragan Ivanovic will review https://github.com/vivo-project/Vitro/pull/440
• Georgy Litvinov to investigate further the reported issue about sorting. If the issue exist it will be probably a new ticket and new PR for fixing that, Miloš Popović will open a ticket if that is needed.
• Georgy Litvinov to review I forgot my password PR
• Dragan Ivanovic and Ivan Mrsulja to complete review for Hiding (organization) profile pages
• Brian Lowe will respond on the Manuel Hidalgo email
• Dragan Ivanovic  will contact Benjamin or Matthias for German validation, Michel for French validation, and Anna for Spanish validation - https://github.com/vivo-project/Vitro/pull/431/files 
• Ivan Mrsulja  will implement the suggestion to set the difficulty to easy by default - https://github.com/vivo-project/VIVO/issues/3918
• William Welling to review https://github.com/vivo-project/Vitro/pull/434
• Miloš Popović to improve Wilma theme to resolve issues reported by Georgy - https://github.com/vivo-project/VIVO/pull/3932
• Benjamin Kampe to help in validation of German labels - https://github.com/vivo-project/Vitro/pull/431/files#diff-bb423927e0836a896cfcf4a59808797d6f8cae5e3404d98d1572ed80d270d28e and https://github.com/vivo-project/Vitro/pull/431/files#diff-6cc406bfdad29755775006f31ce273b41dcbe69026af82c4e002fc919a6ee125 and https://github.com/vivo-project/VIVO/pull/3928/files#diff-0183b2b90ba7554c506b18de36fc3229985ddd1b12ad06198c546f0cb5992a54
• Dragan Ivanovic to organize writing wiki documentation for new features
• Georgy Litvinov to continue working on https://github.com/vivo-project/Vitro/pull/433
• Ivan Mrsulja to improve I forgot my password PR in accordance with discussion (sending notification to system administrator).
• Miloš Popović to review the audit tool PR (https://github.com/vivo-project/Vitro/pull/390, https://github.com/vivo-project/VIVO/pull/3879)
• Georgy Litvinov to review the CAPTCHA PR (https://github.com/vivo-project/Vitro/pull/427, https://github.com/vivo-project/VIVO/pull/3920)
• Kshitij Sinha to test VIVO on his mac machine
• Dragan Ivanovic to remind community about language validation in some PR
• Miloš Popović will work on fixing the issue with Nemo theme

• Miloš Popović will complete PR for making wilma theme responsive
• Ivan Mrsulja will improve messages in the CAPTCHA PR and add refresh button
• Ivan Mrsulja to improve I forgot my password PR in accordance with discussion
• Internationalization  of  I forgot  my  password  PR
  • Georgy Litvinov Russian - https://github.com/vivo-project/Vitro/pull/421/files#diff-3ffc5887a2994488b1d34ea8315f7999011503d1c61d347781177d4a7853c4dd
  • Ivan Mrsulja Serbian - https://github.com/vivo-project/Vitro/pull/421/files#diff-888fdf7c9524715ee088725a3c6d60c1758ffac8503898de632616f234bfefb1
  • Brian Lowe or William Welling English - https://github.com/vivo-project/Vitro/pull/421/files#diff-29efe10b5804f4b7ab1c2b2beb52900c856753a493766a898e2a00910f83563b, and Canadian English - https://github.com/vivo-project/Vitro/pull/421/files#diff-38f8bc0f9c1b89de85f0b073f7ca0b720b543f50373eb53bf58b235285f8cb85
  • Benjamin Kampe or Matthias Lühr German - https://github.com/vivo-project/Vitro/pull/421/files#diff-587a60dcfe07fa0925445a18726ec1d40d4d359c65b531b959b652442b6a4fb1
  • Michel Héon French - https://github.com/vivo-project/Vitro/pull/421/files#diff-5c318e62acc2d1d3b968c1e0c40caa6684d899f8d89ddf77feeb6d94e0b80729
  • Anna Guillaumet Spain - https://github.com/vivo-project/Vitro/pull/421/files#diff-29efe10b5804f4b7ab1c2b2beb52900c856753a493766a898e2a00910f83563b
  • Jose Francisco Salm Jr Portuguese - https://github.com/vivo-project/Vitro/pull/421/files#diff-c5d45c0d26fd4b72bfb00b96aa238fc7c6f8b05e37f504f41de8b0e6cf6459aa

• Georgy Litvinov to review https://github.com/vivo-project/Vitro/pull/421
• Miloš Popović to further investigate M1 mac issue (argon update approach)
• Miloš Popović to align Responsive Wilma theme PR with new contributions on main branch (after merging Extended search PR)
• Ivan Mrsulja to document I forgot my password at Editing Your Profile and a flag to toggle this option at Configuration Reference
• Georgy Litvinov to document the Extended search at Using Search 

• Ivan Mrsulja to align implementation of "I forgot my password" PR in accordance with discussion - create a neutral message, return back link to contact form, investigate whether CAPTCHA can be used
• Dragan Ivanovic to discuss with Georgy Litvinov and Miloš Popović whether bootstrap.min.js is needed or not in the new responsive wilma theme
• Garrett Armstrong to share his solution about using Docker to overcome issue with Mac M1 chip and VIVO
•  Dragan Ivanovic to respond to the email https://groups.google.com/g/vivo-tech/c/3rSwC3ywXlI and request more details about environment (VIVO version) and maybe some logs. 
• Dragan Ivanovic to announce next week presentation of BrCRIS
• Ivan Mrsulja and Miloš Popović to complete implementation of "I forgot my password" feature
• All - to review PR assigned to them
• Dragan Ivanovic to create a PR fixing the issue with CodeQL GitHub action - https://github.com/vivo-project/VIVO/issues/3902
  • https://github.com/vivo-project/VIVO/pull/3903
• Don Elsborg will continue testing new VIVO with different versions of Solr and report back about the result. 

• Michel Héon to share presentation slides with VIVO community via slack channel
• Dragan Ivanovic to document publication claiming feature - Editing Your Profile#PositionsandPublications
• Kshitij Sinha will inform Michael Bentz and other UF members about progress in resolving issue related to the long delay in logging in 
• Dragan Ivanovic will communicate further will Ceci and Rodrigo about csv import into the VIVO graph
• Brian Lowe will complete https://github.com/vivo-project/Vitro/pull/397, Dragan Ivanovic and Georgy Litvinov will review
• Brian Lowe will review https://github.com/vivo-project/Vitro/pull/395
• Dragan Ivanovic will prepare RC once when all blocking issues are resolved
• Dragan Ivanovic to discuss with VIVO committers whether we can improve VIVO WCAG  compliance
• Brian Lowe will work on implementation of https://github.com/vivo-project/VIVO/issues/3770
• Dragan Ivanovic will increase priority of https://github.com/vivo-project/VIVO/issues/3858, and https://github.com/vivo-project/VIVO/issues/3859 
• Dragan Ivanovic will continue communication with Joseph about the issue with mass removing data via slack
• Dragan Ivanovic to share results of discussion about using Docker images with Rodrigo via https://groups.google.com/g/vivo-tech/c/yAOHcsJg8ro (the problem might be that VIVO docker container is not seeing vivo-solr container, meaning it is a network mode issue)
• Dragan Ivanovic to reorganize VIVO upgrade wiki pages - Upgrading VIVO
• Maxim Prokopenko to open a ticket (bug) for Solr index directory mount with docker compose (https://github.com/vivo-project/VIVO/issues/3857)
• All to think about priorities for further development of VIVO   
• Dragan Ivanovic to check whether PDFDocument class is needed at all (and itext dependency)
• Dragan Ivanovic to open a ticket (github issue) for ingesting sample data memory problem
• all
  • to provide feedback on https://docs.google.com/document/d/1jIIr90vTpI4l5KZeM30f_gOc-TpmlgKol-2oOEaU2Is/edit?usp=sharing,
  • consider participating in https://forms.gle/16QbRU62CmJCaeJp8
  • check personal calendars for the next sprint (May 22nd - June 9th, 2023)
• Dragan Ivanovic to announce publishing VIVO 1.14.0 RC2
• someone to test RC2
  • Ivan Mrsulja tested RC2
• Dragan Ivanovic to create survey for collecting standard practice in VIVO deployment process 

• Dragan Ivanovic to add columns in the project board for Priority and Difficulty.
• Sprint participants to read description of issues and think about their preferences. 

• Dragan Ivanovic will contact Lyrasis admins to get an account for https://vivo.lyrasis.org/
• Dragan Ivanovic will fix issues with layout and French sample data and publication graph - https://github.com/vivo-project/VIVO/pull/3810
• Georgy Litvinov will fix the issue with faux data properties with xml literal range - https://github.com/vivo-project/Vitro/pull/363
• William Welling will review previously described issues
• Dragan Ivanovic will work on specification of tasks for the next sprint - https://github.com/orgs/vivo-project/projects/5 and https://github.com/orgs/vivo-project/projects/6
• Dragan Ivanovic to send a test email through contact form - https://vivo.lyrasis.org/contact/
• William Welling to complete review/testing of  https://github.com/vivo-project/VIVO/pull/3805 and to summarize results in the PRs comments
•  Dragan Ivanovic to review William's comments and check what should be fixed/resolved before merging of the the branch
  • Georgy Litvinov to fix issues with Russian email templates
  • Georgy Litvinov to fix issues with faux data properties
• All to think about organization/improvements of sample data, Dragan Ivanovic to add an item in the next week agenda for discussion
• Dragan Ivanovic in communication with Georgy Litvinov to write/update documentation for faux (data) properties
• Dragan Ivanovic to review and merge 
  • https://github.com/vivo-project/Vitro/pull/360
  • https://github.com/vivo-project/Vitro/pull/361

• Brian Lowe to review https://github.com/vivo-project/VIVO/pull/3788 and https://github.com/vivo-project/Vitro/pull/341 preferably by end of the week (11/25/2022)
• Brian Lowe to review https://github.com/vivo-project/Vitro/pull/347
• Michel Héon to validate https://github.com/vivo-project/Vitro/pull/347 and test performance with remote Fuseki 
• Anyone to validate https://github.com/vivo-project/Vitro/pull/348 and https://github.com/vivo-project/VIVO/pull/3797 preferably by end of the week (11/25/2022)  - description how it should be validated provided in the PR description
• Benjamin Kampe to review https://github.com/vivo-project/Vitro/pull/349 and https://github.com/vivo-project/VIVO/pull/3795 preferably by end of the week (11/25/2022)
• Dragan Ivanovic to create PR in cooperation with Michel Héon for merging ttl files (labels' translations) into Vitro/VIVO repositories
• Dragan Ivanovic to ask Arif for more info on the reported issue - https://groups.google.com/g/vivo-tech/c/gmyQIMWbm_Y
• Dragan Ivanovic to open a ticket for https://groups.google.com/g/vivo-tech/c/wDblxLmeTjs. Done, ticket available at https://github.com/vivo-project/VIVO/issues/3772
• Dragan Ivanovic will redirect reporter of this issue https://github.com/vivo-community/vivo-docker2/issues/22 to https://github.com/vivo-project/VIVO#docker
• All to analyze the issue reported in the slack (https://vivo-project.slack.com/archives/C8RL9L98A/p1663253504895989) and check whether we should open a GitHub issue and add to the i18n redesign project board - https://github.com/orgs/vivo-project/projects/4 
• Brian Lowe will respond on the email https://groups.google.com/g/vivo-tech/c/5AY9h15h4vc/m/OjqekVxlBgAJ?utm_medium=email&utm_source=footer&pli=1
• All to consider participation in the sprint and register via https://forms.gle/qLi1PhRrrpvUrrYRA
• Dragan Ivanovic to work on specification of tasks for the sprint - GitHub project board
• Michel Héon to work on the translation messages ontology
• Dragan Ivanovic will bring up with leadership group that we would like to set up task force for dynamic API
• Dragan Ivanovic will create infrastructure for the next sprint (slack channel, GitHub project board, wiki page, GitHub branch, GitHub issues, etc.)
• Michel Héon to work on the ontology for UI labels (in multiple languages)
• All to think about dates for the next sprint
• Dragan Ivanovic to resolve conflicts for https://github.com/vivo-project/Vitro/pull/311 and https://github.com/vivo-project/Vitro/pull/297
• Dragan Ivanovic to write script for preparing a release candidate - started at https://github.com/chenejac/VIVO-release-publisher
• All to test the release candidate - Release Testing - 1.13.0
• Dragan Ivanovic to publish VIVO 1.13.0 release (if there is no reported issue till 1st of September)
• Dragan Ivanovic to prepare presentation for demo meeting - 2022-07-07 - Dynamic API demo meeting
• Dragan Ivanovic to send reminder for the demo meeting - 2022-07-07 - Dynamic API demo meeting
• Dragan Ivanovic to open an issue for a reverse proxy (redirecting) - https://vivo-project.slack.com/archives/C8RL9L98A/p1651739159126489
  • https://github.com/vivo-project/VIVO/issues/3698
• Dragan Ivanovic to contact Andrew Wood for resolving the issue with registration for the Slack channel
• All to consider participation in the sprint and if decide  to participate to register for the sprint - link
• Dragan Ivanovic to send a require to add in the Leadership group agenda a topic for discussing Copyright owner in License
• All please help in filling this document - spreadsheet
•  Dragan Ivanovic to create a draft version of a Google Spreadsheet document with labeled columns representing requirements and to share with committers
• Committers to review the structure of the document and to fill it with data for JS and CSS frameworks