Page History

Updates

• Brown (Ted) -- Meeting with faculty departments to get feedback, e.g. faculty might want to upload a full CV and link to that from VIVO profile

• • the pairtree-derived file system set to store arbitrary files -- we happen to use it only for images so far

  • in the ontology is related to the person’s URI via a mainImage property and has a MIME type

  • but have never tried to store anything but

  • could also explore uploading to Fedora Commons (the repository, not the Linux OS)

  • Faculty are also interested in linking to full text of their publications.    

• Colorado (Alex and LIz) -- starting publications work. Stephen has been working on replacing a Selenium-based ingest with a Harvester-based approach; this week the results matched up when run in parallel so are ready to start the switchover. The Harvester-based approach is much faster because it does not work through the UI.  Starting to work on visualizations showing collaboration around research interests, not just co-authors and co-investigators. This should be valuable for institutions not ready to undertake collecting publications data.

• • Using D3.js -- iDevice friendly visualizations

  • Example is a new college being created around media, technology, and art -- trying to find where those connections already exist on campus

• Cornell (Jon and Jim)

• • working on 1.6 ontology changes, trying to keep migration patterns for context nodes like Positions and Advising Relationships

  • Jon and Jim at Implementation Fest

  • Jim looking into caching issue with help from Arve at Griffith and Ted from Brown

  • IFest internationalization work is being shared by JohnF at a UN meeting on collab of international agriculture researchers

• Duke (Patrick and Sherri)

• • May 13 School of Medicine go live -- finalizing / curating data as needed, majority of faculty so a big group

• Johns Hopkins

• Indiana -- should we schedule a code review?

• • Jim has been iterating with Rohan et. al. based on their pull request

• Memorial (Lisa)

• • back from the I-Fest safely and looking forward to the conference

• NYU (Yin)

• tried to join IFest code sprint, would still like to connect with some VIVO devs interactively to review his approach, use of VIVO GitHub, etc

• Maybe see https://wiki.duraspace.org/display/VIVO/VIVO+Developer+Setup+101 

• Alex: is there a use case for submitting changes back to VIVO even if they are options that not all sites may want? A community branch? but that may get forked, and someone will need to integrate the changes back into the branch they originated from

• Stony Brook (Erich and Tammy)

• • new university wide VIVO instance work starting

  • question about generating distinct URIs in a way consistent with VIVO’s approach (Brian Lowe: IndividualDaoJena code calls URI generation code)

• UCSF (Eric)

• • next release of Profiles on their plate

  • ORNG gadgets (http://www.orng.info) for adding multimedia to Profile pages, considering Cornell’s VIVO and ontology they see “media contributions” meta data but they can’t see the media itself, ex. a video clip of a faculty interview on Channel 7 or a press release

  • ORNG understanding RDF on page?

• Weill Cornell (Paul)

• • Eliza more productive when Paul’s in Boulder :)
  • working on automating publication ingest process to free up devs
  • met with Grad School Office interested in tracking pubs by current students, question about alumni pubs
  • Jon discussed use case of monitoring compliance with NIH public access mandate on a grant with 1,000+ co-investigators – PI could receive 115 notices from NIH system for investigators who have not uploaded copies of their NIH-funded publications to PubMed. NIH tracks by grant and Weill can track by publication to notify the correct authors

 I-Fest outcomes and feedback

Apologies to those who tried to remote in --

New – Google Doc for notes during the call

• http://goo.gl/cTLlC is open for editing
• add your own updates, questions, or notes and see what others are typing

Updates

add more bullets as necessary

• Brown 
• Colorado
• Cornell
• Duke
• Indiana – should we schedule a code review?
• Memorial
• NYU
• Penn
• PSU
• Stony Brook
• UCLA
• UCSF
• Weill Cornell

Implementation Fest outcomes and feedback

For those who attended, what did you find most useful? What did you learn? What impressed you about other VIVO implementations?

Report on Saturday coding activities

• Ted, Stephen and Jim working on internationalization -- documented on the wiki (search “multiple language support”)
• Stephen ran into an issue after upgrading to Java 1.7 with Tomcat 6 -- resolved by upgrading to Tomcat 7
• Jon and Alex working on setting up Jon’s Mac and start of wiki page (https://wiki.duraspace.org/display/VIVO/VIVO+Developer+Setup+101)
• Pedro from USC working with Michael and Bill from PennState on using Karma to get data in
• will be trying Google Hangouts for small group coding and/or implementation support activities

If you haven't yet, please provide feedback (anonymously if desired) at at http://goo.gl/z9lUr 

Twitter stream:   https://twitter.com/search?q=%23vivoifest13&src=hash 

Slides and other materials are shared on SourceForge file repository -- also there were some notes captured as Google Docs (how do we collect these)

2013 VIVO Conference Call for

...

Papers and Posters due May 10

...

• Call for

  Apps

   entries are

  due July 31

• Additional details on the VIVOWeb.org blog

Upcoming Webinars

Upcoming VIVO Webinars (all Tuesdays at 11)

• May 14 -- Overview of VIVO

• June 4 -- Case Studies: VIVO

• DuraSpace will be organizing and publicizing a series of 3 webinars in May and June focusing on VIVO
• The first (May 14) will be a general introduction
• The second (June 4) will include 3 case study presentations on VIVO implementations

  at Colorado, Brown, Duke and Weill Cornell Medical College

• The final webinar will be a "technical deep dive" on

  June 11 -- VIVO Technical Deep Dive

 
 Notable implementation and development list

...

issues

• Harvester transfer dying unexpectedly (Giuseppe)

• on a 64-bit

...

• machine I experience this strange issue of the harvester-transfer reporting

• "killed". Here's the extract of the log.

• • • 2013-04-26 18:08:51.747 TRACE [o.v.h.u.r.JenaConnect] loading record:

...

• • • publication/75007

    • 2013-04-26 18:08:53.570 TRACE [o.v.h.u.r.JenaConnect] loading record:

...

• • • publication/75008

    • /root/vivo/harvester/bin/harvester-transfer: line 29:  1328

    • Killed java $OPTS -Dprocess-task=Transfer

...

• • • org.vivoweb.harvester.transfer.Transfer "$@"

• • Note that this happens after hundreds of publications have been loaded.

• Search in

...

• Chinese (Jianwei)

...

• – a local fix that will be added to VIVO 1.6

• • Locate the file vitro-core/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/UrlBuilder.java

  • In this file, search for the two occurrences of "ISO-8859-1" and replace them with "UTF-8"

  • Rerun "ant all" to rebuild VIVO

  • After restarting Tomcat, the links on the right side of the search results should work properly with Chinese characters

• SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object (Tom T.)

• • related to MySQL max_connections configuration? – seems unlikely

  • checking vivo e 'show processlist' while performing a reindex if possible

  • may relate to the shift in connection pool libraries between VIVO 1.4 and VIVO 1.5

  • Alex will follow up with Tom to see if someone from Symplectic is in the loop

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