Please note that these are proposed features for VIVO 1.6, not commitments by the VIVO development community
Background
The VIVO 1.6 development time frame is roughly November through June with the goal of having a VIVO 1.6 out before the VIVO Conference, to be held this year in St. Louis, Missouri from August 14-16.
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PerformanceThere are a number of possible routes to performance improvement for VIVO, and we seek input from the community on what the primary pain points are. Some performance issues are related to installation and configuration of VIVO and we are working on improving documentation, notably on MySQL configuration, tuning, and troubleshooting, but page caching has emerged as the primary performance-related improvement for 1.6.
Page cachingAs more data is added to VIVO, some profiles get very large, most commonly when a person accumulates hundreds of publications that much each be included in rendering the person's profile page. While we continue to look at ways to improve query speeds, if you need your VIVO to display all pages with more or less equivalent, sub-second rendering times, some form of page caching at the Apache level using a tool such as Squid is necessary. Apache is very fast at displaying static HTML pages, and Squid saves a copy of every page rendered in a cache from which the page can be rendered by Apache rather than generated once again by VIVO. The good news:
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Griffith University has implemented page caching and Arve Solland gave a talk on this and other aspects of the Griffith Research Hub at the 2012 VIVO conference.
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Other approaches to performance improvementThere are also other ways to address performance that could be argued are more effective in the long run
- As mentioned above, improved server, Apache, Tomcat, and database configuration and tuning
- If we can identify key areas where some form of intermediate results are being repeatedly requested from the database, implementing Memcached could be another strategy. However, it may be more effective to provide MySQL more memory since it can use its own strategies for query caching
- Tim Worrall has been looking at our page templates for instances where we could avoid issuing SPARQL queries for the same data repeatedly in the course of generating a single page, and has also been optimizing SPARQL queries that come to his attention
- There is also some indication that bugs in Jena's SDB implementation that make queries other than to a single graph or the union of all graphs much less efficient, at least for MySQL. This is hard to verify, and we have mostly been approaching this by exploring the use of other triple stores via the RDF API added with the VIVO 1.5x releases.
Installation and Testing- Brian Caruso has proposed adding a unit test for Solr that would build an index from a standard set of VIVO RDF, start Solr, and run standard searches. This would help prevent breaking existing functionality when addressing issues that have come up such as support for diacritics, stop words, and capital letters in the middle of names
- A unit test has been developed for another related project at Cornell and we hope to be able to port this to VIVO, but perhaps not for 1.6
- Developing repeatable tests of loading one or more large datasets into VIVO. The challenge here is that performance is highly installation dependent. The most urgent problem at Cornell has been the intermittent loss of communication between the VIVO web server and the VIVO database server, which results in some threads of activity simply hanging and never returning. As with many errors that are hard to reproduce, we have developed workarounds that divide large jobs into chunks of data that experience has shown can be removed or added without causing hiccups. Stay tuned.
Site and Page Management- Make the About page and Home page HTML content editable through admin interface – this relates to display model changes
- (Largely complete) Offering improved options for content on the home page, including a set of SPARQL queries to highlight research areas, international focus, or most recent publications
- (Complete) Offering additional individual page template options
- (Complete) Offering the ability to embed SPARQL query results in individual pages on a per-class basis – for example, to show all research areas represented in an academic department
- (Complete) Cornell is working on new individual page templates that include screen-captured versions of related websites for people and organizations, so that in addition to the link to the website we show either a small or large version of a thumbnail of the page. This is done through a commercial image capture service that other sites may not want to use, and will have to become configurable. Another service might not provide the same API or resultant image size, however. In any case, the new individual page templates will have to be optional, since sites may have done a lot of customization work.
- Could put the service-specific aspects in a sub-template that gets imported and could be default not attempt to capture and cache images at all
- are free services out there, but they may not be there in 6 months
Support for sameAs statementsWhen 2 URIs are declared to be the same in VIVO, all the statements about both will be displayed for either (e.g., Israel and Israel). Improvements are needed, however:
- there is no way via the current UI to add or remove owl:sameAs assertions – they have to be added as tiny RDF files via the add/remove RDF command
- sameAs in the subject position
- It will adversely affect performance to require VIVO to detect that two or more URIs for an individual have been declared to be sameAs each other and then retrieve and blend all the data for each URI for rendering on a single page
- This becomes more complicated when the 2nd or higher URI is not in the local VIVO
- It may be a first step to simply show a link to the equivalent URI, with some form of "see also" label
- sameAs in the object position
- when another VIVO individual is linked to one or the other of these Israels, the application is not yet smart enough to show only one object property statement to one instance of Israel, and it looks to users like a duplicate of both the country and the relationship
- Colorado has a use case to assert sameAs relationships between people's profiles in their university-wide VIVO and the separate implementation at the Laboratory for Atmospheric and Space Physics, where additional information about research projects, equipment, and facilities will be stored behind a firewall. They would like to pull data from the CU VIVO into the LASP VIVO dynamically, and pull any publicly visible data from LASP VIVO to supplement the CU VIVO content about a person.
- Colorado also has a need to pull data from the Harvard Profiles system used by the University of Colorado Medical School in Denver to the CU VIVO without replicating more than is necessary. This is a similar use case to the connections needed between VIVO on the Cornell Ithaca campus and the Weill Cornell VIVO.
Web service for the RDF API- Implementing a web service interface (with authentication) to the VIVO RDF API, to allow the Harvester and other tools to add/remove data from VIVO and trigger appropriate search indexing and recomputing of inferences.
- This would also enable round-trip editing of VIVO content from Drupal or another tool external to VIVO via the SPARQL update capability of the RDF api
- Put and delete of data via LOD requests – this has been suggested but we're not sure a specification even exists for an LOD "put" request – please add references here if you're aware of discussion or documentation.
Editing- See comments on VIVOIMPL-15 with respect to improving the permissions scheme for editing and make its functions more transparent to users. The best way forward here would be to transfer what's referred to as the editing policies, now hard-wired in code, to a set of RDF statements conforming to an editing policy ontology and editable from the Site Admin menu. This was the approach taken for the user model, and is proposed as an improved way of managing the display model (primarily for managing menu pages) and the application configuration ontology.
- Improve editing of data held in context nodes from the organization, event, or other related entity, principally via relationships like authorships or positions or via roles realized in processes or events – most custom forms support entry and editing only from the person. This requires no new functionality but will involve implementing additional custom forms
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The URI Tool is a separate, simple application designed to facilitate data cleanup in VIVO following ingest, often from multiple sources. The tool can be configured to run one of four or five pre-defined queries to identify journals, people, organizations, or articles with very similar names. A bare-bones editing interface allows a relatively untrained user to step through lists of paired or grouped candidates for merging, identify which existing properties to keep, and confirm that the candidates should be merged. Links to the actual entry in VIVO facilitate verification. When the review process is complete, the URI Tool application writes out both retraction and addition files, which can then be removed from or added to VIVO using commands on the ingest menu.
This tool does not replace the need for author disambiguation and other cleanup work prior to ingest, for which the Google Refine extensions for VIVO and the Harvester tool have been developed. However, it does have the potential to become a considerable time saver for cleaning data once loaded into VIVO.
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