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Are you interested in contributing effort to one or more of the items below? Please contact Graham Triggs or Mike Conlon. VIVO is able to move forward with items for which there is effort.

Upgrading to VIVO

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1.

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10.0 requires Java 8 and a triple store reload

As a result of the upgrade to Jena 3, upgrading to VIVO 21.010.0 requires Java 8 and a triple store reload – your triple store most be unloaded using a provided utilityutility  (jena2tools), your system upgraded, and then the triple store reloaded using a second provided utility .  These processes are currently in test mode.  See VIVO 2.0(jena3tools). See VIVO 1.10.0 Release Testing.  Please participate in testing and report findings to vivo-tech@googlegroups.com

Issues included in beta Release 2.0.0

Issues without Jiras, or without resolved Jiras may be included.

Bug Fixes

  • [VIVO-855] - RDF export not working correctly
  • [VIVO-1060] - Add DumpRestoreController to Vitro web.xml
  • [VIVO-1310] - pom.xml implies that VIVO develop branch can still run under Java 1.7
  • [VIVO-1311] - Remove or replace the UMLS concept source
  • [VIVO-1324] - Security vulnerabilties in 1.9.x release
  • [VIVO-1342] - Ampersands (and possibly other characters?) not escaped in GraphML export of collaborator network graph
  • [VIVO-1394] - AboxRecomputer does not generate correct mostSpecificType for equivalent classes
  • [VIVO-1404] - Some SPARQL queries trigger Chrome XSS Auditor
  • [VIVO-1435] - Compliance with ORCID style guidelines

New Feature

  • [VIVO-1252] - Incorporate Cornell's DataDistributor API into core Vitro.
  • [VIVO-1312] - Implement Linked Data Fragments
  • [VIVO-1335] - Create Bootstrap Theme

Task

  • [VIVO-812] - Automate the process of adjusting documentation to the release
  • [VIVO-1316] - Place external lookup base architecture in Vitro layer

Improvement

  • [VIVO-1063] - Update included jQuery library
  • [VIVO-1246] - Improve the ConfigurationBeanLoader
  • [VIVO-1247] - Remove duplicate code, based on improvements in ConfigurationBeanLoader
  • [VIVO-1248] - Add functionality to the edu.cornell.mannlib.vitro.webapp.utils.sparql package
  • [VIVO-1260] - Make http.createCacheHeaders true by default
  • [VIVO-1270] - Update Jena to latest release
  • [VIVO-1272] - Inject JSP content to Freemarker, instead of having secondary layout
  • [VIVO-1273] - Update DOI URL Schema to follow recomendations from Crossref
  • [VIVO-1290] - Improve Multi-Lingual Support
  • [VIVO-1294] - Language values (all.properties) should not be part of theme
  • [VIVO-1307] - Remove dom4j from the project
  • [VIVO-1309] - Update DWR to more recent version
  • [VIVO-1317] - Reduce the number of JSON libraries in the dependencies
  • [VIVO-1318] - In the ORCID client code, use Jackson library to handle JSON data
  • [VIVO-1319] - Remove dependency on sourceforge.net JSON parser.
  • [VIVO-1367] - AGROVOC external service not working
  • [VIVO-1375] - Upgrade to Servlet 3.0 spec and annotations
  • [VIVO-1376] - Add smoke test to ensure that there are no XSD:Strings in SDB
  • [VIVO-1381] - Upgrade Solr to 4.10.4
  • [VIVO-1382] - Update JFact dependency
  • [VIVO-1383] - Update pooling libraries
  • [VIVO-1384] - Use commons-lang3 throughout
  • [VIVO-1385] - Replace unmaintained CSV parser with commons-csv
  • [VIVO-1386] - Make consistent use of HttpClient 4.5, remove conflicting dependencies
  • [VIVO-1387] - Update all dependencies with known vulnerabilities to latest versions
  • [VIVO-1393] - Replace isotope jQuery plugin
  • [VIVO-1397] - Improve performance and reliability of search indexing
  • [VIVO-1400] - Have optional "precise subquery" elements in list views for triple stores that perform better with more selective queries
  • [VIVO-1403] - Improve update performance
  • [VIVO-1405] - Defeat browser cacheing for new versions of JavaScript and CSS files.
  • [VIVO-1406] - Visualisations in a multi-lingual release
  • [VIVO-1410] - Release the next version of VIVO and Vitro
  • [VIVO-1438] - Some text on Forms are made of different strings associated following english syntax
  • [VIVO-1458] - Update to Jena 3.6
  • [VIVO-1463] - Update ontologies.owl
  • [VIVO-1464] - Identify and separate candidate ontologies for removal
  • [VIVO-1470] - Improve cross-platform support in build

Documentation

  • [VIVO-31] - Improve documentation of Google Analytics
  • [VIVO-34] - Make it easy to do "next", "previous" and "up" links in a Confluence page
  • [VIVO-242] - Establish Wiki versioning process
  • [VIVO-813] - Improve document details
  • [VIVO-917] - Create a confluence macro to show sections numbers for multi-page documents
  • [VIVO-1274] - Improve documentation process for next release
  • [VIVO-1334] - Create a recommendation for the use of string and langString
  • [VIVO-1351] - Write "TPF Endpoint" for Tech doc
  • Interface
    • Jira
      serverDuraSpace JIRA
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-1335
    • Jira
      serverDuraSpace JIRA
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-1290
    • Jira
      serverDuraSpace JIRA
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-1272
    • Jira
      serverDuraSpace JIRA
      columnskey,summary,type,created,updated,due,assignee,reporter,priority,status,resolution
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-1272
  • Data Services
    • Jira
      serverDuraSpace JIRA
      columnskey,summary,type,created,updated,due,assignee,reporter,priority,status,resolution
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-1312
  • Architecture
    • Vitro clean-up and improvements based on the work of Cornell
    • Jira
      serverDuraSpace JIRA
      columnskey,summary,type,created,updated,due,assignee,reporter,priority,status,resolution
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-1248
    • Jira
      serverDuraSpace JIRA
      columnskey,summary,type,created,updated,due,assignee,reporter,priority,status,resolution
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-1270
       
  • Ontology
    • Domain definition and processes.  See Ontology Improvement Task Force
    • Domain modularization and selectable loading of domain modules
    • Jira
      serverDuraSpace JIRA
      columnskey,summary,type,created,updated,due,assignee,reporter,priority,status,resolution
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-1277
    • Jira
      serverDuraSpace JIRA
      columnskey,summary,type,created,updated,due,assignee,reporter,priority,status,resolution
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-1278
    • Jira
      serverDuraSpace JIRA
      columnskey,summary,type,created,updated,due,assignee,reporter,priority,status,resolution
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-1279
    • Ontology editing enhancements based on work of Cornell
    • Jira
      serverDuraSpace JIRA
      columnskey,summary,type,created,updated,due,assignee,reporter,priority,status,resolution
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-1103
    • Jira
      serverDuraSpace JIRA
      columnskey,summary,type,created,updated,due,assignee,reporter,priority,status,resolution
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-1284
  • Data Management
    • Jira
      serverDuraSpace JIRA
      columnskey,summary,type,created,updated,due,assignee,reporter,priority,status,resolution
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-1280
       See Data Loader Task Force
    • Jira
      serverDuraSpace JIRA
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-1275
    • Jira
      serverDuraSpace JIRA
      columnskey,summary,type,created,updated,due,assignee,reporter,priority,status,resolution
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-1084
    • Upgrade VIVO Harvester to use Jena 3.1
  • Documentation
    • Jira
      serverDuraSpace JIRA
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-242
    • Jira
      serverDuraSpace JIRA
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-1274
    • Jira
      serverDuraSpace JIRA
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-53
    • Jira
      serverDuraSpace JIRA
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-226
    • Jira
      serverDuraSpace JIRA
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-813
    • Jira
      serverDuraSpace JIRA
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-842
    • Jira
      serverDuraSpace JIRA
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-259
    • Jira
      serverDuraSpace JIRA
      columnskey,summary,type,created,updated,due,assignee,reporter,priority,status,resolution
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-684
    • Jira
      serverDuraSpace JIRA
      columnskey,summary,type,created,updated,due,assignee,reporter,priority,status,resolution
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-1339
  • System Administration and Development
    • Jira
      serverDuraSpace JIRA
      columnskey,summary,type,created,updated,due,assignee,reporter,priority,status,resolution
      serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
      keyVIVO-1220
  • Other improvements and bug fixes
  • Jira
    serverDuraSpace JIRA
    columnskey,summary,type,created,updated,due,assignee,reporter,priority,status,resolution
    serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
    keyVIVO-1273
  • Jira
    serverDuraSpace JIRA
    columnskey,summary,type,created,updated,due,assignee,reporter,priority,status,resolution
    serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
    keyVIVO-365
  • Jira
    serverDuraSpace JIRA
    columnskey,summary,type,created,updated,due,assignee,reporter,priority,status,resolution
    serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
    keyVIVO-1250
  • Jira
    serverDuraSpace JIRA
    columnskey,summary,type,created,updated,due,assignee,reporter,priority,status,resolution
    serverIdc815ca92-fd23-34c2-8fe3-956808caf8c5
    keyVIVO-1247
    • JiraserverDuraSpace JIRAcolumnskey,summary,type,created,updated,due,assignee,reporter,priority,status,resolutionserverIdc815ca92-fd23-34c2-8fe3-956808caf8c5keyVIVO-1246