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 --
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 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
Apps due July 31
Upcoming VIVO Webinars (all Tuesdays at 11)
May 14 -- Overview of VIVO
June 4 -- Case Studies: VIVO at Colorado, Brown, Duke and Weill Cornell Medical College
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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