Date

09 Oct 2018

Call-in Information

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

To join the online meeting:

• Go to: https://duraspace.zoom.us/j/823948749
• Or iPhone one-tap :
  • US: +14086380968,,823948749#  or +16468769923,,823948749#
• Or Telephone:
  • Dial(for higher quality, dial a number based on your current location):
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  • Meeting ID: 823 948 749
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Slack

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

Development Process

• See https://github.com/vivo-project/VIVO/wiki/Development-Processes

Attendees

 Indicating note-taker

1. Huda Khan
   

2. Ralph O'Flinn 

3. Benjamin Gross 

4. Jim Blake 

5. Muhammad Javed 

6. Don Elsborg
   
   

Agenda

1. Advanced Role Management 3-day fiesta!

   1. Oct 24th - 26th, come join the fun
   2. 

2. New pull requests

   1. [VIVO-1605] Update to latest Error Prone plugin and configuration to support JDK 11: https://github.com/vivo-project/VIVO/pull/89 / https://github.com/vivo-project/Vitro/pull/88

   2. has collaborator is reflexive: https://github.com/vivo-project/VIVO/pull/90

3. 1.10 

   1. bugs (1.10.1?)

      
      

   2. Plans for a 1.10.1 patch release

4. Recent mailing list topics:
   1. Change in Home page
   2. Change user password
   3. Adding External Vocabularies

Notes 

Draft notes in Google-Doc

Changing Solr smoke tests

• Necessary because cores have changed in Solr 5

• New Solr has nested and restful capabilities

Ralph: wants to better document technical requirements. E.g. we discovered that VIVO 1.10 doesn’t work with older versions of Linux

• We need to explore compatibility with new versions of Java, especially moving away from Oracle

New pull request: https://github.com/vivo-project/Vitro/pull/88

[VIVO-1605] Update to latest Error Prone plugin and configuration to support JDK 11

• Addresses problem during compilation

• Jim left a comment, perhaps it could be updated to use a non-SNAPSHOT version of the dependency

• Latest version of google error prone is v2.3.1 which came out April 20.

• We can hopefully just use 2.3.2 https://github.com/google/error-prone/issues/1127

• Also not building w/ Travis for Vitro: [WARNING] Failure to transfer com.google.errorprone:error_prone_check_api:2.3.2-SNAPSHOT/maven-metadata.xml from https://repository.apache.org/snapshots/ was cached in the local repository, resolution will not be reattempted until the update interval of apache-snapshots has elapsed or updates are forced. Original error: Could not transfer metadata com.google.errorprone:error_prone_check_api:2.3.2-SNAPSHOT/maven-metadata.xml from/to apache-snapshots (https://repository.apache.org/snapshots/): Connect to repository.apache.org:443 [repository.apache.org/207.244.88.140] failed: Connection timed out (Connection timed out)

• Don: We will continue to support Java 8?

Compiling VIVO against various OS?

• Can this be done with Travis CI?

• If so, does it come with undue burden? Would we be required to pay extra?

• New wiki table: https://wiki.duraspace.org/display/VIVODOC110x/System+Requirements

• Should Solaris be included? We are building with this for a client.

Don - Should we create a link to this in the requirements doc? https://wiki.duraspace.org/display/VIVODOC18x/Running+VIVO+behind+an+Apache+server

• As written, VIVO starts twice

• Ralph- we are using something similar

• Don - we have to use Apache, but doing this is a pain

• Ralph - serving VIVO as top level - created a symlink from Tomcat ROOT directory to the VIVO directory

• Should be updated!

New Jira issues

https://jira.duraspace.org/browse/VIVO-1608

• Another new error: 2018-10-08 13:32:35,113 WARN  [beans] Overriding freemarker.ext.beans.BeansWrapper.finetuneMethodAppearance is deprecated and will be banned sometimes in the future. Use setMethodAppearanceFineTuner instead.

• 2018-10-08 13:32:21,944 WARN  [SAXParsers] http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit not supported by parser type org.apache.xerces.jaxp.SAXParserImpl, error message: Property 'http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit' is not recognized.

• 2018-10-08 13:32:21,945 WARN  [SAXParsers] entityExpansionLimit not supported by parser type org.apache.xerces.jaxp.SAXParserImpl, error

message: Property 'entityExpansionLimit' is not recognized.

• 2018-10-08 13:32:22,349 ERROR [OWLRDFConsumer] Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error1 for type Class

• https://jira.duraspace.org/browse/VIVO-1607

Don - Ralph’s symlink worked

Action items - Don to create new page for 1.10 for running VIVO behind Apache

Benjamin - new Jira issue for additional errors thrown startup.

Actions

•  Don Elsborg to create new page for 1.10 for running VIVO behind Apache
• Benjamin Gross to create new Jira issue for additional errors thrown startup.
  

Previous Actions

• Don Elsborg - Create ticket to update 1.10 requirements to show glibc 2.14 dependencies and centos 6 incompatibility
• Don Elsborg - add jira tickets for abox/tbox use cases - one ticket for each use case
• Andrew Woods - find out from Mike where the abox/tbox documentation should be in the wiki
• Brian Lowe  - check with ontology group on handles
• Alex Viggio will bring news of Elasticsearch instead of Solr up with Product Evolution.  Might there be consequences for the September sprint.