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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 – 
  • Colorado (Stephen) – did a test of new data release yesterday that went well; an intermediate step between original Selenium scripts and a fully automated Harvester-based ingest process.  Also getting ready for the Implementation Fest in 3 weeks.
  • Cornell – (Tim) still working on changes we're making to the home page – map changes are complete with a global, U.S., and a New York State view.  Now working on changes to statistics shown about counts in VIVO and some randomized selections of faculty, research facilities, etc.  Other sites would be able to swap in other states or regions on the maps.
  • Duke – (Patrick) Jim is working on getting a SPARQL endpoint up with Fuseki and running into memory problems running certain kinds of queries.  Looking at running multiple instances; not immediately going to have sites consuming data from the endpoint(s) but want to encourage migration of data feeds from SDB to the SPARQL endpoint.
  • Florida – 
  • Indiana – (Chin Hua and Ronan) – Did a couple of experiments to see whether the problem generating Map of Science visualizations are due to simultaneous requests; observed that each request completed on its own, but if put in 20-25 requests simultaneously, no visualizations were generated.  A question: 
  • Johns Hopkins – We're unable to hop on the call today (we have Epic EMR going live at many campuses) but could use a little guidance. 
    • We keep bumping into issues with harvesting PubMed data through Harvester. We've broken up the data into smaller chunks and have successfully(ish) completed an update. The problem is that we now have duplicate articles, authors, etc. (see screenshot)
      • What are we missing?
    • What recommendations do you have for the frequency of updates? Should we consider less frequent updates (semi-annual? annual?) for older publications?
    • Why does it take nearly twice as long to run an update through Harvester? Our first pass through took about 16 hours. The second, over 20. 
  • Memorial University – 
  • NYU – 
  • Scripps – 
  • Stony Brook – 
  • UCLA – 
  • UCSF – 
  • WashU – 
  • Weill Cornell – 

Upcoming events

2013 Implementation Fest – April 25-26 at CU Boulder

  • 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
  • 2013 VIVO Implementation Fest page has information on transportation and hotels
  • Registration page – 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

Security issue 

Arve Solland of Griffith University points out a security issue via an email to VIVO developers at Cornell. The issue affects release 1.5.1. The fix will be easy to develop, but how should we distribute it? What level of publicity/documentation is appropriate?

Notable implementation and development list traffic


New
  • (Alex) Question about licensing of linked data – http://vivo.cornell.edu/termsOfUse, http://creativecommons.org/licenses/by/3.0/, 
    http://creativecommons.org/publicdomain/zero/1.0/
  • (Michael) Restrictions that return two types of classes – 
    • (Brian) – What you're supposed to be able to do (and has worked in the past) is to create a restriction with a union of multiple classes in another editor, such as Protege, and upload it to VIVO.  Unfortunately, it looks like there may have been a regression somewhere in version 1.5 because I can't seem to get the form for adding properties to an individual to offer the right values now when I use a union.  (The ontology editor properly displays the union class, so I know it's in there.) I'll have to look into this further, and at the very least I'll create a JIRA issue to make sure the latter piece gets unbroken for 1.6.
  • (Stephen) Found the source code for the DV-Docs to generate CVs from VIVO
  • (Kelly) Harvester duplicates and speed issues for pulling from PubMed
  • (Mark) I stopped and started tomcat when VIVO 1.5.1 got slow when editing. Now we get: There is currently no Graduate Student content in the system, There is currently no Undergraduate Student content in the system, There is currently no Person content in the system – I've rebuilt the index and it rebuilds with no change in results. I don't have any explicit documentation on backup/recovery, but i have recent mysql dumps and a copy of /usr/local/vivo. Not sure where to go from here. Sure don't want to re-start from bare metal.
Still open:
  • Adding a field to the Solr Index (Gawri)
    • I need some help regarding solr index build. I added a new field called "APPROVED_RECORD" into schema.xml . Also I added following code lines into addObjectPropertyText() function in IndividualToSolrDocument.java file.
  • 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.

Readings

Under the hood -- indexing and ranking in Facebook's graph search

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

To join the online meeting

Go to https://cornell.webex.com/cornell/e.php?AT=WMI&EventID=167096322&RT=MiM2

If requested, enter your name and email address.

Click "Join".

To view in other time zones or languages, please click the link: https://cornell.webex.com/cornell/globalcallin.php?serviceType=MC&ED=167096322&tollFree=1

If those links don't work, please visit the Cornell meeting page and look for a VIVO meeting.

To join the audio conference only

To receive a call back, provide your phone number when you join the meeting, or call the number below and enter the access code.

Call-in toll-free number (US/Canada): 1-855-244-8681

Call-in toll number (US/Canada): 1-650-479-3207

Global call-in numbers: https://cornell.webex.com/cornelluniversity/globalcallin.php?serviceType=MC&ED=161711167&tollFree=1

Toll-free dialing restrictions: http://www.webex.com/pdf/tollfree_restrictions.pdf

Access code:645 873 290

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