Calls are held every Thursday at 1 pm eastern time (GMT-5) – convert to your time at http://www.thetimezoneconverter.com – and note that the U.S. is already on daylight savings time

These calls now use WebEx and have no limit on the number of attendees – see the "Call-in Information" at the bottom of this page.

Updates

  • Brown (Ted) – cleaning up mostly humanities data (e.g., how to capture philosophy tv) and working on improved list views
  • Colorado (Alex) – Stephen is continuing his work to replace their current Selenium-based approach with a Harvester approach including improved handling of CSV; had an odd problem with connecting to the right Solr on the production server, where have 4 instances of VIVO and have been running 4 Solr instances (with a different Solr URL in deploy.properties for each VIVO) – looking at Solr thread dumps from the Solr admin user interface. Can the same Solr process serve multiple Solr homes? (Ted) – Solr has a multi-core setup, where can have different cores with separate Solr indexes running under one instance of the Solr software (Richard) Duke did use multiple cores for the VIVO Widget projects – is good documentation out there on multiple cores).
  • Cornell  (Jim/Tim) – Brian Caruso and Jim are focusing on rev. B of the vivosearch.org multi-site search; (Jon) we've had a request from a faculty member to differentiate co-authors and co-investigators from inside home institution in the co-author and co-investigator visualizations; Tim is looking at improving the queries across all list views via small tweaks that might collectively improve performance on profile pages
  • Duke (Richard and Patrick) – a question about Solr – have two load-balanced VIVO instances, one of which kicks off a nightly rebuild of the solr index, but some counts are not getting correctly refreshed – may try to restart the 2nd server to work around the problem.(Jon) - may relate to the swapping of Solr cores that happens when a reindex concludes on the first server, although since the connection is over an HTTP service – if post to the dev list, we can ask Brian Caruso what might be going on. (Alex) thinks he's seen a behavior where the search functionality in VIVO works but displays seem to reflect an out-of-date Solr instance.
  • Florida – 
  • Indiana (team) – Tried to reproduce the problem of the Map of Science on the University of Florida – took 3 to 4 hours, and once it had been cached the visualization was rendered almost instantly.  They checked the total publication count reported on the visualization with the real total and are finding a very close number (within a few hundred on a set of ~100,000).  Could generate the visualization at first, but when tried to regenerate the cache, ran into problems in that are now investigating by looking at memory leaks and tracking the time taken in individual steps in the process – using JProfiler with Ant to have tomcat write out its state.
  • Johns Hopkins (Josh) – looking to move their VIVO from a shared VM and are finding that VIVO and the Harvester together use more memory than the VM – looking to spec out new servers and wants input from other universities on typical setups – memory, processors, disk space. (Alex) – when separated ingest from production at Colorado, were seeing that the ingest versions of Tomcat JVMs were going over the 6 Gb allocated but production was hardly ever going over 2 Gb
  • Memorial University – 
  • NYU – 
  • Scripps (Michaeleen) – working on list view for publications (see discussion list traffic entry below)
  • Stony Brook --
  • UCLA – 
  • UCSF – 
  • WashU –
  • Weill Cornell (Paul) – Have found that can only send small batches of DOIs to PubMed service; Have moved to a new, better performing server; working with Brian Caruso to tweak garbage collection services. Are trying to resume re-computing inferences after running Harvester – now are running it and figures out the correct publication types.  Takes quite a while to run – 24 to 30 hours. Brian Caruso has suggested keeping track of individuals that have changed so that only that set could be re-calculated. (Ted) Is there anything built into the admin interface to just re-compute a set of individuals? (Brian) Not currently; with a full-fledged reasoner, inferences could be generated from tiny bits of data all over the place, but with our simple reasoner that might be do-able for the next release. (Eliza) Issues with special characters have been resolved in MySQL settings – may have to recompile the Harvester to be sure it's generating properly encoded special characters.

Upcoming events

2013 Implementation Fest update – April 25-26 at CU Boulder

  • Looking for some estimates of numbers – would be helpful to make sure we have sessions in the right rooms
  • It would also be helpful to have feedback from people who can't attend but would join by video link –  we don't want to try to support video if people would be too busy to stick with sessions remotely live (or watch recorded video).
    • Scripps would be interested in video being available
    • Johns Hopkins would be interested in video – have people on two campuses – webex or video would work
    • Jon will look to see whether the sched.org site allows people to register for sessions as remote attendees
  • A community hands-on development day is planned as an optional additional activity on Saturday the 27th, e.g. working on internationalization
    • We have interest from Costa Rica, Mexico, and France in principle – there's one room choice option that has H.323 videoconferencing
  • Alex has been looking into options for videoconferencing certain events where interest is strong from people who can't attend
    • Stony Brook is generously offering use of their multi-point H.323 bridge to support better-than-desktop quality video
  • Read the vivoweb.org blog entry, and the 2013 VIVO Implementation Fest page has information on transportation and hotels
  • A registration page is now live – note that there is no registration fee for the workshop
  • A DRAFT schedule is available for preview on sched.org (including for mobile view) and as a Google Doc

2013 VIVO Conference – Workshops Proposals due March 29

  • The 4th annual VIVO Conference will be held on August 14-16 in St. Louis
  • The Call for Workshop Proposals is now out with a deadline to submit workshop proposals by March 29
  • The Call for Papers should be out soon – stay tuned – the goal is to give paper and poster presenters early feedback on what has been accepted to help people make their travel plans
  • topics you'd like to attend if somebody else organizes?
    • Solr functionality in VIVO and how it supports not only search but display functionalities – and relates to caching

Notable implementation and development list traffic

  • Migration to VIVO 1.5 with Windows Server 2012 (64bit), MySQL 5.6, Java 1.6, and Tomcat 7 (Chinese Academy of Sciences) – apparent changes when restart Tomcat.  Is anybody else on the list using Windows?
  • Adding Unicode-related JDBC parameters to deploy.properties – works for Duke, but wants to document on the wiki – have data loads coming in via Jena, not the Harvester.  If run a test load onto a MySQL instance before VIVO has been connected, and then connect VIVO, the data loading process is no longer able to load special characters
  • Removing previous harvests and clarifying TDB and SDB in using the Harvester (Johns Hopkins)
  • Creating a custom list view to include author names in publication citations (Scripps) – but not when there's hundreds
    • Mark reports Griffith is "working on generating citation style language (csl) this would let us generate citations using citeproc-js and any of the hundreds of styles from zotero:

From last week:
  • Conditional validation (Tom)
    • I was wondering if there was a way to change which validation is run based on the submitting button on an EditConfigurationGenerator form?
      I basically have the situation where I've used a custom BaseEditSubmissionPreprocessorVTwo to allow the user to submit the edit and go forward to the created/linked object or backward to the subject. This is working fine, but the cancel link on the form calls the PostEditCleanupController directly, which doesn't call the preprocessor to set the correct entity URI to redirect to. One solution to this is to move the cancel link to a cancel button, but this, predictably, causes the FieldVTwo validation to fail.
      The other solution is to work out how to forcibly invoke the preprocessor, but this seems as though it would be a much bigger issue, so conditional validation seems the easier way to achieve the same effect.

Any topics for special development calls?

  • E.g., Solr – overview of how VIVO uses Solr and walkthrough of how to modify the indexing
  • American Psychological Association has been working on RDF extraction from VIVO to JSON to support submission to ORCID via the ORCID api

Call-in Information

Topic: VIVO weekly call

Date: Every Thursday, no end date

Time: 1:00 pm, Eastern Daylight Time (New York, GMT-04:00)

Meeting Number: 641 825 891

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