Tenderfoot is a new, responsive theme for VIVO. Based on the work by Symplectic, it uses Bootstrap 3 to provide a view that scales better to different sizes of devices.

Argon 2i Password Hashing

VIVO now hashes passwords using Argon-2i replacing MD5. See Configuration Reference.

Branding and Theming Improvements

...

Note that the configuration options have been changed, and you will need to update your runtime.properties.

The only options that are required now properties are:

Code Block

orcid.clientId = 0000-0000-0000-000X
orcid.clientPassword = 00000000-0000-0000-0000-000000000000
orcid.webappBaseUrl = http://localhost:8080/vivo
orcid.externalIdCommonName = VIVO Cornell Identifier
orcid.apiVersion = 2.0
orcid.api = sandbox

...

For any sites wishing to participate in the Direct2Experts federated site - http://direct2experts.org/ - VIVO now includes the necessary endpoints. Please see the See Direct2Experts websites for more information on how to participate.

RDF 1.1 support

API for a description of the VIVO implementation in 1.10, and information regarding participation in this federated search site.

RDF 1.1 support

VIVO has now been updated to use Jena 3, which brings full RDF 1.1 support. As a result, internally all literals are treated as having a datatype - those with a language tag are rdf:langString, and any other are xsd:string, and the triple stores need to be reloaded to ensure that they have consistent internal representations. Only applications that directly open the triple stores using Jena libraries, or have SPARQL that explicitly references datatypes will be affected. Please see the upgrade notes for how to perform the migration and evaluate any impact.

...

Full handling of TDB type conversions, preventing isomorphic test failures that result resulted in reloading filegraph on restart.

...

Note that Selenium IDE no longer works with the current versions of Firefox. Whilst we can currently run the test suite using a Java project and WebDriver, we will need to consider how these tests can be maintained in the future.

Contributors

Qazi Azim Ijaz Ahmed, TIB Hannover

Sabih Ali, Digital Science

Matthew Barber, TIB Hannover

Jim Blake, Cornell

Mike Conlon, University of Florida

Don Elsborg, University of Colorda

Kitio Fofack, Université du Québec à Montréal

Ken Geis, UC Berkeley

Benjamin Gross, UNAVCO / Clarivate Analytics

Huda Khan, Cornell

Ted Lawless, Clarivate Analytics / Brown University

Jacob Levernier, University of Pennsylvania

Jose Luis Martin, UC3M

Christian Hauschke, TIB Hannover

Steve McKay, Plum Analytics

Javed Muhammed, Cornell University

Simon Porter, Digital Science

Graham Triggs, Duraspace / TIB Hannover

Tatiana Walther, TIB Hannover

Marijane White, Oregon Health Science University

Stefan Wolff, TU Dresden

Rebecca Younes, Cornell

Issues Resolved

Sub-task

[VIVO-1476] - Export and provide link of Jena 2 VIVO dataset for testing

Bug

[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
[VIVO-1461] - Assertions are ascribed to Vcard, but terms are not in the Vcard ontology
[VIVO-1465] - Jena2tools NullPointerException on read
[VIVO-1479] - Set version in pom.xml to 1.10.0-SNAPSHOT
[VIVO-1483] - VIVO hangs on startup after upgrading using jena3tools
[VIVO-1497] - Overview can not be manually edited
[VIVO-1517] - Jenatools expects package names instead of namespaces

New Feature

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

Story

[VIVO-1451] - Making Capability Map i18n Compliant

Task

[VIVO-812] - Automate the process of adjusting documentation to the release
[VIVO-1316] - Place external lookup base architecture in Vitro layer
[VIVO-1486] - Update mysql-connector-java dependency in jenatools to 8.0.11

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-1373] - VIVO 1.10 Beta 2 does not support FROM and FROM NAMED queries
[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-1377] - Add output format selection to jenatools
[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-1408] - ConifigurationBeanLoader should recognize RDF namespaces in java: URIs
[VIVO-1438] - Some text on Forms are made of different strings associated following english syntax
[VIVO-1447] - Organize the ontology files. Produce a vivo.owl
[VIVO-1448] - Move password encryption from MD5 to a salted hash
[VIVO-1458] - Update to Jena 3.6
[VIVO-1463] - Update ontologies.owl
[VIVO-1470] - Improve cross-platform support in build
[VIVO-1478] - MySQL driver throws InvalidConnectionAttributeException
[VIVO-1487] - Improve VIVO home page text -- replace scientists with scholars
[VIVO-1488] - Read runtime.properties from {vivo-home}/config
[VIVO-1490] - Missing '.' in aboutMapOfScience_en_US.ftl

Test

[VIVO-1410] - Release the next version of VIVO and Vitro
[VIVO-1496] - Add OpenVIVO and UF data to sample-data

Documentation

...

Issues Resolved

Sub-task

[VIVO-1476] - Export and provide link of Jena 2 VIVO dataset for testing

Bug

[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
[VIVO-1461] - Assertions are ascribed to Vcard, but terms are not in the Vcard ontology
[VIVO-1465] - Jena2tools NullPointerException on read
[VIVO-1479] - Set version in pom.xml to 1.10.0-SNAPSHOT
[VIVO-1483] - VIVO hangs on startup after upgrading using jena3tools
[VIVO-1497] - Overview can not be manually edited
[VIVO-1517] - Jenatools expects package names instead of namespaces

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
[VIVO-1486] - Update mysql-connector-java dependency in jenatools to 8.0.11
[VIVO-1520] - Deploy jenatools 1.1.2 to Maven Central and increment version in Vitro pom.xml

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-1373] - VIVO 1.10 Beta 2 does not support FROM and FROM NAMED queries
[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-1377] - Add output format selection to jenatools
[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-1408] - ConifigurationBeanLoader should recognize RDF namespaces in java: URIs
[VIVO-1438] - Some text on Forms are made of different strings associated following english syntax
[VIVO-1447] - Organize the ontology files. Produce a vivo.owl
[VIVO-1448] - Move password encryption from MD5 to a salted hash
[VIVO-1458] - Update to Jena 3.6
[VIVO-1463] - Update ontologies.owl
[VIVO-1470] - Improve cross-platform support in build
[VIVO-1478] - MySQL driver throws InvalidConnectionAttributeException
[VIVO-1487] - Improve VIVO home page text -- replace scientists with scholars
[VIVO-1488] - Read runtime.properties from {vivo-home}/config
[VIVO-1490] - Missing '.' in aboutMapOfScience_en_US.ftl

Test

[VIVO-1410] - Release the next version of VIVO and Vitro
[VIVO-1496] - Add OpenVIVO and UF data to sample-data

Code Task

[VIVO-1523] - Enable retrieval of SNAPSHOT dependencies

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-772] - Write "Preparing for Production"
[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
[VIVO-1352] - Complete "Using VIVO"
[VIVO-1464] - Identify and separate candidate ontologies for removal
[VIVO-1473] - Write "VIVO for Data Analysts"
[VIVO-1485] - Add jenatools documentation to the tech wiki
[VIVO-1498] - Update Deploying Additional Ontologies
[VIVO-1531] - Write Direct2Experts API
[VIVO-1534] - Document steps for using UMLS vocabulary service

Release Managers

Ralph O'Flinn, University of Alabama, Birmingham

Andrew Woods, DuraSpace

Contributors

Qazi Azim Ijaz Ahmad, TIB Hannover

Sabih Ali, Digital Science

Martin Barber, TIB Hannover

Jim Blake, Cornell

Mike Conlon, University of Florida

Don Elsborg, University of Colorda

Kitio Fofack, Université du Québec à Montréal

Benjamin Gross, UNAVCO / Clarivate Analytics

Christian Hauschke, TIB Hannover

Violeta Ilik, Columbia University

Huda Khan, Cornell

Ted Lawless, Clarivate Analytics / Brown University

Jacob Levernier, University of Pennsylvania

Brian Lowe, Ontocale

Jose Luis Martin, UC3M

Steve McKay, Plum Analytics

Javed Muhammed, Cornell University

Ralph O'Flinn, University of Alabama, Birmingham

Simon Porter, Digital Science

Graham Triggs, Duraspace / TIB Hannover

Tatiana Walther, TIB Hannover

Marijane White, Oregon Health Science University

Stefan Wolff, SLUB Dresden

Andrew Woods, Duraspace

Rebecca Younes, Cornell

...

Page tree

Versions Compared

Old Version 15

New Version Current

Key

Argon 2i Password Hashing

Branding and Theming Improvements

RDF 1.1 support

RDF 1.1 support

Contributors

Issues Resolved

Sub-task

Bug

New Feature

Story

Task

Improvement

Test

Documentation

Issues Resolved

Sub-task

Bug

New Feature

Task

Improvement

Test

Code Task

Documentation

Release Managers

Contributors

Page tree

Page History

Versions Compared

Old Version 15

New Version Current

Key

Argon 2i Password Hashing

Branding and Theming Improvements

RDF 1.1 support

RDF 1.1 support

Contributors

Issues Resolved

Sub-task

Bug

New Feature

Story

Task

Improvement

Test

Documentation

Issues Resolved

Sub-task

Bug

New Feature

Task

Improvement

Test

Code Task

Documentation

Release Managers

Contributors