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Merge tag 'rel-1.12.1-RC' into main

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Ralph O'Flinn 2021-12-16 05:07:13 -06:00
commit b1f66ea933
21 changed files with 84 additions and 22 deletions
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2
.github/PULL_REQUEST_TEMPLATE.md vendored
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@ -1,7 +1,7 @@
**Thank you for submitting a pull request! Title this pull request with a brief description of what the pull request fixes/improves/changes. Please describe the pull request in detail using the template below.**
* * *
**[JIRA Issue](https://jira.duraspace.org/projects/VIVO)**: (please link to issue)
**[JIRA Issue](https://jira.lyrasis.org/projects/VIVO)**: (please link to issue)
* Other Relevant Links (Mailing list discussion, related pull requests, etc.)

3
.gitignore vendored
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@ -24,3 +24,6 @@ utilities/sdb_to_tdb/.work
**/.classpath
**/.project
**/bin/
.fake
.ionide

4
README.md
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@ -16,7 +16,7 @@ With Vitro, you can:
* Search your data with Apache Solr
Vitro was originally developed at Cornell University, and is used as the core of the popular
research and scholarship portal, [VIVO](https://duraspace.org/vivo/).
research and scholarship portal, [VIVO](https://lyrasis.org/vivo/).
For more information, contact the [VIVO community](https://duraspace.org/vivo/resources/contact/).
For more information, contact the [VIVO community](https://lyrasis.org/vivo/resources/contact/).

7
api/pom.xml
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@ -21,6 +21,13 @@
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<runOrder>alphabetical</runOrder>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>

10
api/src/test/java/edu/cornell/mannlib/vitro/webapp/dao/jena/JenaBaseDaoTest.java
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@ -22,6 +22,7 @@ import org.apache.jena.vocabulary.RDF;
import org.apache.jena.vocabulary.RDFS;
import org.apache.jena.vocabulary.XSD;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
@ -36,6 +37,9 @@ import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatementImpl;
import edu.cornell.mannlib.vitro.webapp.beans.VClass;
import edu.cornell.mannlib.vitro.webapp.dao.InsertException;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import stubs.edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryStub;
import stubs.edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccessFactoryStub;
import stubs.javax.servlet.ServletContextStub;
public class JenaBaseDaoTest extends AbstractTestClass {
@ -54,6 +58,12 @@ public class JenaBaseDaoTest extends AbstractTestClass {
"@prefix owl: <" + OWL.getURI() + "> . \n" +
"@prefix ex: <http://example.com/> . \n" ;
@Before
public void setup() {
WebappDaoFactoryStub wdf = new WebappDaoFactoryStub();
ServletContextStub ctx = new ServletContextStub();
new ModelAccessFactoryStub().get(ctx).setWebappDaoFactory(wdf);
}
@Test
public void smartRemoveTestForIndivdiualDelete(){

11
api/src/test/java/edu/cornell/mannlib/vitro/webapp/dao/jena/OntModelSegementationTest.java
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@ -4,7 +4,7 @@ package edu.cornell.mannlib.vitro.webapp.dao.jena;
import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
@ -23,6 +23,8 @@ import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
import edu.cornell.mannlib.vitro.webapp.dao.UserAccountsDao;
import edu.cornell.mannlib.vitro.webapp.dao.VClassDao;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import stubs.edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccessFactoryStub;
import stubs.javax.servlet.ServletContextStub;
/**
* Test that the Jena DAOs write different types of data to the appropriate models.
@ -31,11 +33,14 @@ import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
*/
public class OntModelSegementationTest extends AbstractTestClass {
private WebappDaoFactoryJena wadf;
@org.junit.Before
private WebappDaoFactoryJena wadf;
@Before
public void setUpWebappDaoFactoryJena() {
super.setUp();
wadf = new WebappDaoFactoryJena(new SimpleOntModelSelector());
ServletContextStub ctx = new ServletContextStub();
new ModelAccessFactoryStub().get(ctx).setWebappDaoFactory(wadf);
}
@Test

13
api/src/test/java/edu/cornell/mannlib/vitro/webapp/dao/jena/PropertyInstanceDaoJenaTest.java
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@ -9,7 +9,7 @@ import java.util.Map;
import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
import org.junit.Assert;
import org.junit.Before;
import org.apache.jena.ontology.OntModel;
import org.apache.jena.ontology.OntModelSpec;
import org.apache.jena.rdf.model.Model;
@ -19,6 +19,8 @@ import org.apache.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.beans.PropertyInstance;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import stubs.edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccessFactoryStub;
import stubs.javax.servlet.ServletContextStub;
public class PropertyInstanceDaoJenaTest extends AbstractTestClass {
@ -37,7 +39,16 @@ public class PropertyInstanceDaoJenaTest extends AbstractTestClass {
"@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . \n"+
"@prefix owl: <http://www.w3.org/2002/07/owl#> . \n";
private WebappDaoFactoryJena wadf;
@Before
public void setUpWebappDaoFactoryJena() {
super.setUp();
wadf = new WebappDaoFactoryJena(new SimpleOntModelSelector());
ServletContextStub ctx = new ServletContextStub();
new ModelAccessFactoryStub().get(ctx).setWebappDaoFactory(wadf);
}
void printModels(Model expected, Model result){
System.out.println("Expected:");
expected.write(System.out);

16
api/src/test/java/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassDaoTest.java
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@ -19,11 +19,16 @@ import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.rdf.model.ResourceFactory;
import org.apache.jena.vocabulary.OWL;
import org.junit.Before;
import org.junit.Test;
import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
import edu.cornell.mannlib.vitro.webapp.beans.VClass;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import stubs.edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryStub;
import stubs.edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccessFactoryStub;
import stubs.javax.servlet.ServletContextStub;
/**
*
@ -31,7 +36,14 @@ import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
*/
public class VClassDaoTest extends AbstractTestClass {
@Before
public void setup() {
WebappDaoFactoryStub wdf = new WebappDaoFactoryStub();
ServletContextStub ctx = new ServletContextStub();
new ModelAccessFactoryStub().get(ctx).setWebappDaoFactory(wdf);
}
@Test
// Test that the VClassDaoJena::updateVClass method will only update the jena model for
// those properties in VClass that have a different value from what is already in the
@ -45,7 +57,9 @@ public class VClassDaoTest extends AbstractTestClass {
// it will migrate to the super-model) because of the way jena handles additions and
// deletions with respect to super and sub models. This migration of statements may cause
// undesirable behavior in the vivo/vitro application.
public void modelIsolation(){
// 1. create two models and attach one as a sub-model of the other

15
api/src/test/java/edu/cornell/mannlib/vitro/webapp/dao/jena/VClassJenaTest.java
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@ -7,8 +7,8 @@ import java.net.URLEncoder;
import java.util.Iterator;
import java.util.List;
import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.apache.jena.ontology.AllValuesFromRestriction;
@ -38,11 +38,15 @@ import org.apache.jena.shared.Lock;
import org.apache.jena.util.iterator.ClosableIterator;
import org.apache.jena.vocabulary.RDFS;
import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
import edu.cornell.mannlib.vitro.webapp.beans.BaseResourceBean;
import edu.cornell.mannlib.vitro.webapp.beans.Ontology;
import edu.cornell.mannlib.vitro.webapp.beans.VClass;
import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
import stubs.edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactoryStub;
import stubs.edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccessFactoryStub;
import stubs.javax.servlet.ServletContextStub;
/**
*
@ -51,7 +55,14 @@ import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
*/
public class VClassJenaTest extends AbstractTestClass {
@Before
public void setup() {
WebappDaoFactoryStub wdf = new WebappDaoFactoryStub();
ServletContextStub ctx = new ServletContextStub();
new ModelAccessFactoryStub().get(ctx).setWebappDaoFactory(wdf);
}
@Test
// NIHVIVO-1157 introduced VClassJena.java, a lazy-loading version of VClass.java.
// Per instructions from Brian L., this test tests that for one randomly selected Class,

3
api/src/test/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/validators/AntiXssValidationTest.java
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@ -9,6 +9,7 @@ import java.util.Map;
import org.junit.Assert;
import org.junit.Test;
import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.MultiValueEditSubmission;
@ -16,7 +17,7 @@ import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.fields.FieldVTwo;
import stubs.javax.servlet.http.HttpServletRequestStub;
public class AntiXssValidationTest {
public class AntiXssValidationTest extends AbstractTestClass{
@Test
public void testLiteral( ){

2
api/src/test/resources/testontologies/SolrQueryTestRDF/vivo15.2.n3
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@ -33,7 +33,7 @@
@prefix vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#>.
<http://vivo.cornell.edu/individual/individualIssueVivo15> vivo:overview "There is a form feed in the following text. Hex 0c, that sometimes displays as ^L. Star Award for excellence in scientic publication and for productive collaborations with other Center scientists, U.S. Department of the Interior, 2009. Publications Award for scientist at Florida Integrated Science Center with highest annual scien-tic productivity as measured by number, quality, and impact of publications., U.S. Department of the Interior, 2009.";
vivo:webpage <https://jira.duraspace.org/browse/VIVO-15>;
vivo:webpage <https://jira.lyrasis.org/browse/VIVO-15>;
a mann:CornellNonAcademicStaff,
local:InternalThing,
vivoc:CornellAffiliatedPerson,

2
api/src/test/resources/testontologies/SolrQueryTestRDF/vivo15.n3
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@ -33,7 +33,7 @@
@prefix vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#>.
<http://vivo.cornell.edu/individual/individualIssueVivo15> vivo:overview "There is a form feed in the following text. Hex 0c, that sometimes displays as ^L. Star Award for excellence in scienti c publication and for productive collaborations with other Center scientists, U.S. Department of the Interior, 2009. Publications Award for scientist at Florida Integrated Science Center with highest annual scien-ti c productivity as measured by number, quality, and impact of publications., U.S. Department of the Interior, 2009.";
vivo:webpage <https://jira.duraspace.org/browse/VIVO-15>;
vivo:webpage <https://jira.lyrasis.org/browse/VIVO-15>;
a mann:CornellNonAcademicStaff,
local:InternalThing,
vivoc:CornellAffiliatedPerson,

2
home/src/main/resources/config/example.developer.properties
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@ -14,7 +14,7 @@
# not be enabled in a production instance of VIVO.
#
# For more information go to
# https://wiki.duraspace.org/display/VIVO/The+Developer+Panel
# https://wiki.lyrasis.org/display/VDOC16/The+Developer+Panel
#
# -----------------------------------------------------------------------------
#

2
home/src/main/resources/config/example.runtime.properties
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@ -145,7 +145,7 @@ proxy.eligibleTypeList = http://www.w3.org/2002/07/owl#Thing
# profile pages that it creates.
#
# For more information, see
# https://wiki.duraspace.org/display/VIVO/Use+HTTP+caching+to+improve+performance
# https://wiki.lyrasis.org/display/VIVODOC112x/Use+HTTP+caching+to+improve+performance
#
# Developers will likely want to leave caching disabled, since a change to a
# Freemarker template or to a Java class would not cause the page to be

2
rc_script.sh
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@ -1,7 +1,7 @@
#!/bin/bash
# RC Script
RC_VERSION=1.11.1
RC_VERSION=1.12.0
RC_NUM=1
git checkout master

2
update-versions.sh
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@ -2,7 +2,7 @@
if [ -z "$1" ]
then
echo 'New version number required eg. 1.9.0-rc1'
echo 'New version number required eg. 1.12.0-RC1'
exit 1
fi

2
webapp/src/main/webapp/WEB-INF/resources/shortview_config.n3
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@ -9,5 +9,5 @@
# Ontology is complete.
#
# Find out how to use this file at
# https://wiki.duraspace.org/display/VIVO/Using+Short+Views+in+Release+1.5
# https://wiki.lyrasis.org/display/VIVODOC112x/Creating+short+views+of+individuals
#

2
webapp/src/main/webapp/WEB-INF/resources/startup_listeners.txt
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@ -2,7 +2,7 @@
# ServletContextListeners for Vitro, to be instantiated and run by the StartupManager.
#
# For more information,
# https://wiki.duraspace.org/display/VIVO/The+StartupManager
# https://wiki.lyrasis.org/display/VIVODOC112x/The+StartupManager
#
edu.cornell.mannlib.vitro.webapp.servlet.setup.JvmSmokeTests

2
webapp/src/main/webapp/config/listViewConfig-dataDefault.xml
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@ -3,7 +3,7 @@
<!-- VIVO-specific default list view config file for object properties
See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
<list-view-config>
<query-select>

2
webapp/src/main/webapp/config/listViewConfig-default.xml
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@ -3,7 +3,7 @@
<!-- Default list view config file for object properties
See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
<list-view-config>
<query-select>

2
webapp/src/main/webapp/config/listViewConfig-hasElement.xml
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@ -3,7 +3,7 @@
<!-- Custom list view config file for display:hasElement property (used for menu system)
See guidelines at https://wiki.duraspace.org/x/eYXVAw -->
See guidelines at https://wiki.lyrasis.org/display/VIVODOC112x/Custom+List+View+Configurations -->
<list-view-config>
<query-select>