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Dates

October 14 - November 1

Participants

  1. Andrew Woods
  2. William Welling
  3. Jim Wood
  4. Ralph O'Flinn
  5. Kristina Heinricy
  6. Robert Nelson
  7. Don Elsborg

Post-Sprint Summary

The sprint started off with six top-level objectives. Based on a reduced team size due to unexpected local priorities, we trimmed the objectives down to the following:

  1. Create/Augment developer-facing documentation for the VIVO Scholars application
  2. Externalize the currently embedded Triple Pattern Fragment server
  3. Add a messaging feature to Vitro

VIVO Scholars

The in-development VIVO Scholars application consists of three primary modules. There is a core module, scholars-discovery, that queries the VIVO triplestore in order to populate a separate Solr index. This module then exposes the content of the Solr index via a REST-API, as well as through a GraphQL endpoint. On top of the REST-API or GraphQL, it is possible for developers to create user interfaces based on JSON data versus RDF triples. There are two additional UI modules that do exactly that. One UI is written with Angular (scholars-angular), and another is written with Go and React (scholars-react).

In an effort to increase engagement from more of the community, documentation was added/updated for these three modules with the objective of simplifying the installation and start-up process. Along with being able to deploy the VIVO Scholars components from the source code, each module also has been Dockerized.

Additional work was put towards making the configuration and customization of VIVO Scholars easier for installations that will want to add their own colors, styles, etc.

Triple Pattern Fragment

In the ongoing effort to make the VIVO codebase more extensible, scalable, and modular, this sprint demonstrated and documented how to install an external Triple Pattern Fragment (TPF) server that serves VIVO content. The upstream project from which VIVO's embedded TPF server was sourced was updated in this sprint to be able to connect to an underlying triplestore via SPARQL-Query, as well updated to be able to deploy in a servlet container, such as Apache Tomcat.

This externalized TPF server was also Dockerized and added to the vivo-docker2 project.

Vitro Messaging

A common pattern for scaling and loosely integrating applications is to use asynchronous messaging. This sprint added a new feature to Vitro that emits messages whenever content is changed in VIVO's triplestore (currently works with TDB store). The messages emitted contain a body in the RDF Patch format. Now it is possible to have decoupled listeners of VIVO/Vitro messages perform any number of tasks based on activity in VIVO.


See the tickets below for more details on what was completed this sprint.



Meetings

Objectives

  1. Orientation to VIVO Scholar for community developers (Don Elsborg , Andrew Woods)
    1. Setting up the environment
    2. Introducing existing documentation
    3. Loading test data
  2. VIVO Scholars community defaults (Don Elsborg , Ralph O'Flinn , Jim Wood)
    1. Defaults should approximate OpenVIVO
    2. Document how to customize branding, look and feel
    3. Document how to extend the ontology
  3. Externalizing the triplestore (Ralph O'Flinn)
    1. Potentially followed by externalizing TPF server
  4. Orcid integration (Kristina HeinricyRalph O'Flinn)
    1. pulling and pushing publications
  5. Vitro messaging service (William Welling)
    1. Documentation for RDF Delta Log Server connection configuration
    2. Documentation for spinning up RDF Delta Log Server
    3. Dockerfile for RDF Delta Log Server
    4. Documentation for Message Broker connection configuration
    5. Documentation for spinning up Message Broker
    6. Dockerfile for Message Broker
  6. NEMO Freemarker templates (Ralph O'Flinn)

Other

  1. Release 1.11.0
    1. Update Solr documentation
    2. VIVO-1706 - Getting issue details... STATUS
  2. Extract ontology from codebase
  3. Extract languages from codebase

Tickets

Scrum Board

  1. Orientation to VIVO Scholars
    1. VIVO-1719 - Getting issue details... STATUS
    2. VIVO-1708 - Getting issue details... STATUS
    3. VIVO-1709 - Getting issue details... STATUS
    4. VIVO-1720 - Getting issue details... STATUS
  2. VIVO Scholars community defaults
    1. VIVO-1710 - Getting issue details... STATUS
    2. VIVO-1712 - Getting issue details... STATUS
    3. VIVO-1713 - Getting issue details... STATUS
    4. VIVO-1714 - Getting issue details... STATUS
    5. VIVO-1715 - Getting issue details... STATUS
    6. VIVO-1716 - Getting issue details... STATUS
    7. VIVO-1717 - Getting issue details... STATUS
    8. VIVO-1721 - Getting issue details... STATUS
  3. Externalizing triplestore
    1. VIVO-1615 - Getting issue details... STATUS
    2. VIVO-983 - Getting issue details... STATUS
    3. VIVO-1707 - Getting issue details... STATUS
    4. VIVO-1723 - Getting issue details... STATUS
    5. VIVO-1728 - Getting issue details... STATUS
    6. VIVO-1730 - Getting issue details... STATUS
  4. Orcid integration
    1. VIVO-210 - Getting issue details... STATUS
    2. VIVO-1530 - Getting issue details... STATUS
    3. VIVO-765 - Getting issue details... STATUS
    4. VIVO-1722 - Getting issue details... STATUS
    5. VIVO-1724 - Getting issue details... STATUS
  5. Vitro messaging
    1. VIVO-1718 - Getting issue details... STATUS
  6. NEMO
    1. VIVO-114 - Getting issue details... STATUS


Reference

Stand-up Reports

 2019-10-25 (Fri)

Jim

[VIVO Sprint Standup]
Finished yesterday:
- Validated colorscheme for VIVO-1713 - Getting issue details... STATUS
Working on today:
- None
Blockers:
- None

Rob

[VIVO Sprint Standup]
Finished yesterday:
- None
Working on today:
- Getting Duke data into scholars-discovery SOLR index (using harvester interface)
Blocker:
- None

Andrew

[VIVO Sprint Standup]
Finished yesterday:
- Progress on "Dockerize External TPF Server"
- https://jira.duraspace.org/browse/VIVO-1730
Working on today:
- "Dockerize External TPF Server"
- https://jira.duraspace.org/browse/VIVO-1730
- Review other's completed tickets
Blockers:
- None

William

[VIVO Sprint Standup]
Finished yesterday:
- TDB RDF Delta Patch Messaging
Working on today:
- finalizing PR, documentation, and vagrant
- Artemis ActiveMQ dockerization
- RDF Delta Server dockerization
Blocker:
- None


 2019-10-24 (Thurs)

Andrew

[VIVO Sprint Standup]
Finished yesterday:
- Documented how to install/configure externalized TPF
- https://jira.duraspace.org/browse/VIVO-1728
- Reviewed: "Document customization of styling for scholars-react"
- https://jira.duraspace.org/browse/VIVO-1715
Working on today:
- Dockerize External TPF Server
- https://jira.duraspace.org/browse/VIVO-1730
Blockers:
- None

Jim

[VIVO Sprint Standup]
Finished yesterday:
- Update Custom Page documentation based on feedback for: https://jira.duraspace.org/browse/VIVO-1715
- Update native Go startup steps based on feedback for: https://jira.duraspace.org/browse/VIVO-1715
Working on today:
- Validating colorscheme for https://jira.duraspace.org/browse/VIVO-1713
Blockers:
- None

Rob

[VIVO Sprint Standup]
Finished yesterday:
- None
Working on today:
- Getting Duke data into scholars-discovery SOLR index (using harvester interface)
Blocker:
- None

William

[VIVO Sprint Standup]
Finished yesterday:
- None
Working on today:
- TDB RDF Delta Patch Messaging
- https://jira.duraspace.org/browse/VIVO-1718
- https://github.com/vivo-project/Vitro/pull/128
- resolve jena dependency conflicts with Vitro and RDF Delta Client
- publishing design document
- Artemis ActiveMQ docker deployment
- RDF Delta Server docker deployment
Blocker:
- None


 2019-10-23 (Wed)

Andrew

[VIVO Sprint Standup]
Finished yesterday:
 - None
Working on today:
 - Document how to install/configure externalized TPF
   - https://jira.duraspace.org/browse/VIVO-1728
Blockers:
 - None

William

[VIVO Sprint Standup]
Finished yesterday:
- None
Working on today:
- TDB RDF Delta Patch Messaging
- https://jira.duraspace.org/browse/VIVO-1718
- https://github.com/vivo-project/Vitro/pull/128
- resolving issues discovered during testing
- publishing design document
- Artemis ActiveMQ docker deployment
- RDF Delta Server docker deployment
Blocker:
- None

Rob

[VIVO Sprint Standup]
Finished yesterday:
- None
Working on today:
- Getting Duke data into scholars-discovery SOLR index (using harvester interface)
Blocker:
- None

Jim

[VIVO Sprint Standup]
Finished yesterday:
- None
Working on today:
- Update documentation based on feedback for: https://jira.duraspace.org/browse/VIVO-1715
- Validating colorscheme for https://jira.duraspace.org/browse/VIVO-1713
Blockers:
- None


 2019-10-22 (Tues)

Rob

[VIVO Sprint Standup]
Finished yesterday:
- None
Working on today:
- Getting Duke data into scholars-discovery SOLR index (using harvester interface)
Blocker:
- None

Andrew

[VIVO Sprint Standup]
Finished yesterday:
- Implemented TPF server that connects via SPARQL
- "Externalize TPF Server": https://jira.duraspace.org/browse/VIVO-1723
- Was merged into upstream project: https://github.com/LinkedDataFragments/Server.Java/pull/58
Working on today:
- Document how to install/configure externalized TPF
- https://jira.duraspace.org/browse/VIVO-1728
Blockers:
- None

William

[VIVO Sprint Standup]
Finished yesterday:
- finally have functional vagrant for testing VIVO-1718
Working on today:
- TDB RDF Delta Patch Messaging
- https://jira.duraspace.org/browse/VIVO-1718
- https://github.com/vivo-project/Vitro/pull/128
- publishing design document
- Artemis ActiveMQ docker deployment
- RDF Delta Server docker deployment
Blocker:
- permissions to publish wiki page under https://wiki.duraspace.org/display/VIVODOC111x/Architecture

Jim

[VIVO Sprint Standup]
Finished yesterday:
- Added ticket for shared test VIVO instance - https://jira.duraspace.org/browse/VIVO-1725
Working on today:
- Update documentation based on feedback for: https://jira.duraspace.org/browse/VIVO-1715
- Validating colorscheme for https://jira.duraspace.org/browse/VIVO-1713
Blockers:
- None


 2019-10-21 (Mon)

Rob

[VIVO Sprint Standup]
Finished yesterday (Friday):
- Getting rid of bootstrap css in scholars-react
Working on today:
- Getting Duke data into scholars-discovery SOLR index (using harvester interface)
- Make publications web component expand/collapse author list (scholars-react)
Blocker:
- None

Jim

[VIVO Sprint Standup]
Finished yesterday:
- None
Working on today:
- Update documentation based on feedback for: https://jira.duraspace.org/browse/VIVO-1715
- Validating colorscheme for https://jira.duraspace.org/browse/VIVO-1713
- Add JIRA ticket for shared VIVO instance to gather test data
Blockers:
- None

Andrew

[VIVO Sprint Standup]
Finished yesterday:
- Implemented initial proof-of-concept of TPF server that connect via SPARQL
- "Externalize TPF Server": https://jira.duraspace.org/browse/VIVO-1723
Working on today:
- Finalize TPF server that connect via SPARQL
- "Externalize TPF Server": https://jira.duraspace.org/browse/VIVO-1723
Blockers:
- None


 2019-10-18 (Fri)

Andrew

[VIVO Sprint Standup]
Finished yesterday:
- Reviewed https://jira.duraspace.org/browse/VIVO-1715
- Reviewed https://github.com/vivo-project/Vitro/pull/128
Working on today:
- Continuing with "Externalize TPF Server", by exploring TPF server options that connect via SPARQL
- https://jira.duraspace.org/browse/VIVO-1723
Blockers:
- None

William

[VIVO Sprint Standup]
Finished yesterday:
- None
Working on today:
- TDB RDF Delta Patch Messaging
- https://jira.duraspace.org/browse/VIVO-1718
- Resolving change requests to PR
- https://github.com/vivo-project/Vitro/pull/128
- Debugging vagrant deployment and testing
- Wrapping up design document
Blocker:
- vivo-vagrant tomcat not working
- resolved tar download
- resolved tomcat.service JAVA_HOME
- still failing, see error below
- https://github.com/vivo-community/vivo-vagrant

Rob

[VIVO Sprint Standup]
Finished yesterday:
- None
Working on today:
- Getting Duke data into scholars-discovery SOLR index (using harvester interface)
- Getting rid of bootstrap css in scholars-react
Blocker:
- None

Jim

[VIVO Sprint Standup]
Finished yesterday:
 - None
Working on today:
 - Update documentation based on feedback for: https://jira.duraspace.org/browse/VIVO-1715
 - Validate colorscheme for https://jira.duraspace.org/browse/VIVO-1713
Blockers:
 - None


 2019-10-17 (Thurs)

William

[VIVO Sprint Standup]
Finished yesterday:
- None
Working on today:
- TDB RDF Delta Patch Messaging
- https://jira.duraspace.org/browse/VIVO-1718
- Soliciting code quality review and review of approch
- https://github.com/vivo-project/Vitro/pull/128
- Wrapping up vagrant deployment and testing
- Wrapping up design document
Blocker:
- None

Andrew

[VIVO Sprint Standup]
Finished yesterday:
- Resolved: "Verify installation documentation for Scholars angular"
- https://jira.duraspace.org/browse/VIVO-1708
- Resolved: "Admin documentation for externalized Solr"
- https://jira.duraspace.org/browse/VIVO-1706
- Explored: "Externalize TPF Server"
- https://jira.duraspace.org/browse/VIVO-1723
- Success with connecting standalone TPF server with VIVO's TDB (see PR in ticket above)
Working on today:
- Continuing with "Externalize TPF Server", by exploring TPF server options that connect via SPARQL
- https://jira.duraspace.org/browse/VIVO-1723
Blockers:
- None

Rob

[VIVO Sprint Standup]
Finished yesterday:
- Made simplistic sidebar web-component for scholars-react
Working on today:
- Getting Duke data into scholars-discovery SOLR index (using harvester interface)
- getting rid of bootstrap css in scholars-react
Blocker:
- None

Jim

[VIVO Sprint Standup]
Finished yesterday:
- Custom Page documentation for https://jira.duraspace.org/browse/VIVO-1715
- Ready for Review
Working on today:
- Validating colorscheme for https://jira.duraspace.org/browse/VIVO-1713
Blockers:
- Question: I'm not entirely clear on the development workflow. Is there a document? I moved a ticket to Review but haven't merged - is that right?


 2019-10-16 (Wed)

Rob

[VIVO Sprint Standup]
Finished yesterday:
- None
Working on today:
- Getting Duke data into scholars-discovery SOLR index (using harvester interface)
- Making sidebar web-component for scholars-react
Blocker:
- None

William

[VIVO Sprint Standup]
Finished yesterday:
- None
Working on today:
- TDB RDF Delta Patch Messaging
- VIVO-1718 - Getting issue details... STATUS
- Continuing vagrant deployment and testing
- Continuing design document
Blocker:
- None

Andrew

[VIVO Sprint Standup]
Finished yesterday:
- Initial testing of scholars-angular setup
- https://jira.duraspace.org/browse/VIVO-1708
- Works, but more documentation would be helpful
Working on today:
- Add more description to scholars-angular README
- https://jira.duraspace.org/browse/VIVO-1708
- Add to Benjamin Gross documentation for VIVO 1.11.0 Solr installation
- https://jira.duraspace.org/browse/VIVO-1706
Blockers:
- None

Don

[VIVO Sprint Standup]
Finished yesterday:
- Setup space on a RHEL7 system to do this work
- Installed and compiled VIVO harvester ( develop branch )
- updated our CU Faculty Test data
- Attempted to do an intial harvest on some faculty data to rdf output, but it failed
Working on today:
- Install VIVO 1.11 into a docker image on our RHEL7 server. This will use a TDB datastore
- Attempt to harvest faculty test data into new image
- if above works - download scholars discovery, compile, and attempt to extract VIVO data to create SOLR model
Blockers:
- Don't have tomcat running natively on our RHEL7 server, so need to run in docker. Will have to point the harvester to a shared volumne that holds the VIVO TDB datastore. This will be "interesting"

Jim

[VIVO Sprint Standup]
Finished yesterday:
- scholars-react README updates for VIVO-1715 - Getting issue details... STATUS
Working on today:
- Working example of a custom page and query pair for same
Blockers:
- None


 2019-10-15 (Tues)

Andrew

[VIVO Sprint Standup]
Finished yesterday:
- Updated sprint tickets (all, please review)
- https://wiki.duraspace.org/display/VIVO/2019-10+Sprint#id-2019-10Sprint-Tickets
- Resolved: "Verify installation documentation for Scholars discovery"
- https://jira.duraspace.org/browse/VIVO-1719
- Need reviewer(s)!
Working on today:
- "Verify installation documentation for Scholars angular"
- https://jira.duraspace.org/browse/VIVO-1708
- Time permitting, begin investigation of "Externalize Triplestore"
- https://jira.duraspace.org/browse/VIVO-1707
Blockers:
- None
Note:
- Please assignee yourself to any tickets that you are working on, and click the "Start Work" button if you have started work.


Rob

[VIVO Sprint Standup]
Working on today:
- Getting Duke data into scholars-discovery SOLR index (using harvester interface)
- Making sidebar web-component for scholars-react
Blocker:
- None


William

[VIVO Sprint Standup]
Finished yesterday:
- None
Working on today:
- TDB RDF Delta Patch Messaging
- VIVO-1718 - Getting issue details... STATUS
- working on vagrant to deploy and test
- working on design document
Blockers:
- None


Jim

[VIVO Sprint Standup]
Finished yesterday:
- Tab Component for Vivo Scholars Sprint 9
- https://github.com/vivo-community/scholars-react/issues/5
Working on today:
- Document theme and customization methods for scholars react
- https://jira.duraspace.org/browse/VIVO-1715
Blockers:
- None



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