v4.20

CODE_OF_CONDUCT.md

@@ -0,0 +1,76 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+ advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+ address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at support at dataverse dot org. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

README.md

@@ -18,6 +18,7 @@ Dataverse is a trademark of President and Fellows of Harvard College and is regi
 [![Dataverse Project logo](src/main/webapp/resources/images/dataverseproject_logo.jpg?raw=true "Dataverse Project")](http://dataverse.org)
 
 [![API Test Status](https://jenkins.dataverse.org/buildStatus/icon?job=IQSS-dataverse-develop&subject=API%20Test%20Status)](https://jenkins.dataverse.org/job/IQSS-dataverse-develop/)
+[![API Test Coverage](https://img.shields.io/jenkins/coverage/jacoco?jobUrl=https%3A%2F%2Fjenkins.dataverse.org%2Fjob%2FIQSS-dataverse-develop&label=API%20Test%20Coverage)](https://jenkins.dataverse.org/job/IQSS-dataverse-develop/)
 [![Unit Test Status](https://img.shields.io/travis/IQSS/dataverse?label=Unit%20Test%20Status)](https://travis-ci.org/IQSS/dataverse)
 [![Unit Test Coverage](https://img.shields.io/coveralls/github/IQSS/dataverse?label=Unit%20Test%20Coverage)](https://coveralls.io/github/IQSS/dataverse?branch=develop)
 

conf/docker-aio/0prep_deps.sh

@@ -17,12 +17,12 @@ if [ ! -e dv/deps/glassfish4dv.tgz ]; then
 	# assuming that folks usually have /tmp auto-clean as needed
 fi
 
-if [ ! -e dv/deps/solr-7.3.1dv.tgz ]; then
+if [ ! -e dv/deps/solr-7.7.2dv.tgz ]; then
 	echo "solr dependency prep"
 	# schema changes *should* be the only ones...
 	cd dv/deps/
 	#wget https://archive.apache.org/dist/lucene/solr/7.3.0/solr-7.3.0.tgz -O solr-7.3.0dv.tgz
-	wget https://archive.apache.org/dist/lucene/solr/7.3.1/solr-7.3.1.tgz -O solr-7.3.1dv.tgz
+	wget https://archive.apache.org/dist/lucene/solr/7.7.2/solr-7.7.2.tgz -O solr-7.7.2dv.tgz
 	cd ../../
 fi
 

conf/docker-aio/1prep.sh

@@ -4,9 +4,9 @@
 # this was based off the phoenix deployment; and is likely uglier and bulkier than necessary in a perfect world
 
 mkdir -p testdata/doc/sphinx-guides/source/_static/util/
-cp ../solr/7.3.1/schema*.xml testdata/
-cp ../solr/7.3.1/solrconfig.xml testdata/
-cp ../solr/7.3.1/updateSchemaMDB.sh testdata/
+cp ../solr/7.7.2/schema*.xml testdata/
+cp ../solr/7.7.2/solrconfig.xml testdata/
+cp ../solr/7.7.2/updateSchemaMDB.sh testdata/
 cp ../jhove/jhove.conf testdata/
 cp ../jhove/jhoveConfig.xsd testdata/
 cd ../../

conf/docker-aio/c7.dockerfile

@@ -17,7 +17,7 @@ COPY testdata/sushi_sample_logs.json /tmp/
 COPY disableipv6.conf /etc/sysctl.d/
 RUN rm /etc/httpd/conf/*
 COPY httpd.conf /etc/httpd/conf 
-RUN cd /opt ; tar zxf /tmp/dv/deps/solr-7.3.1dv.tgz 
+RUN cd /opt ; tar zxf /tmp/dv/deps/solr-7.7.2dv.tgz 
 RUN cd /opt ; tar zxf /tmp/dv/deps/glassfish4dv.tgz
 
 # this copy of domain.xml is the result of running `asadmin set server.monitoring-service.module-monitoring-levels.jvm=LOW` on a default glassfish installation (aka - enable the glassfish REST monitir endpoint for the jvm`
@@ -28,9 +28,9 @@ RUN sudo -u postgres /usr/pgsql-9.6/bin/initdb -D /var/lib/pgsql/data
 
 # copy configuration related files
 RUN cp /tmp/dv/pg_hba.conf /var/lib/pgsql/data/
-RUN cp -r /opt/solr-7.3.1/server/solr/configsets/_default /opt/solr-7.3.1/server/solr/collection1
-RUN cp /tmp/dv/schema*.xml /opt/solr-7.3.1/server/solr/collection1/conf/
-RUN cp /tmp/dv/solrconfig.xml /opt/solr-7.3.1/server/solr/collection1/conf/solrconfig.xml
+RUN cp -r /opt/solr-7.7.2/server/solr/configsets/_default /opt/solr-7.7.2/server/solr/collection1
+RUN cp /tmp/dv/schema*.xml /opt/solr-7.7.2/server/solr/collection1/conf/
+RUN cp /tmp/dv/solrconfig.xml /opt/solr-7.7.2/server/solr/collection1/conf/solrconfig.xml
 
 # skipping glassfish user and solr user (run both as root)
 

conf/docker-aio/entrypoint.bash

@@ -2,7 +2,7 @@
 export LANG=en_US.UTF-8
 #sudo -u postgres /usr/bin/postgres -D /var/lib/pgsql/data &
 sudo -u postgres /usr/pgsql-9.6/bin/postgres -D /var/lib/pgsql/data &
-cd /opt/solr-7.3.1/
+cd /opt/solr-7.7.2/
 # TODO: Run Solr as non-root and remove "-force".
 bin/solr start -force
 bin/solr create_core -c collection1 -d server/solr/collection1/conf -force

conf/docker-aio/testscripts/install

@@ -15,7 +15,7 @@ export SMTP_SERVER=localhost
 export MEM_HEAP_SIZE=2048
 export GLASSFISH_DOMAIN=domain1
 cd scripts/installer
-cp pgdriver/postgresql-42.2.2.jar $GLASSFISH_ROOT/glassfish/lib
+cp pgdriver/postgresql-42.2.9.jar $GLASSFISH_ROOT/glassfish/lib
 #cp ../../conf/jhove/jhove.conf $GLASSFISH_ROOT/glassfish/domains/$GLASSFISH_DOMAIN/config/jhove.conf
 cp /opt/dv/testdata/jhove.conf $GLASSFISH_ROOT/glassfish/domains/$GLASSFISH_DOMAIN/config/jhove.conf
 cp /opt/dv/testdata/jhoveConfig.xsd $GLASSFISH_ROOT/glassfish/domains/$GLASSFISH_DOMAIN/config/jhoveConfig.xsd

conf/docker/dataverse-glassfish/Dockerfile

@@ -70,7 +70,7 @@ RUN /tmp/dvinstall/glassfish-setup.sh
 ###glassfish-setup will handle everything in Dockerbuild
 
 ##install jdbc driver 
-RUN cp /tmp/dvinstall/pgdriver/postgresql-42.2.2.jar /usr/local/glassfish4/glassfish/domains/domain1/lib
+RUN cp /tmp/dvinstall/pgdriver/postgresql-42.2.9.jar /usr/local/glassfish4/glassfish/domains/domain1/lib
 
 # Customized persistence xml to avoid database recreation
 #RUN mkdir -p /tmp/WEB-INF/classes/META-INF/ 

conf/solr/7.3.1/schema.xml → conf/solr/7.7.2/schema.xml

@@ -171,6 +171,12 @@
     <field name="variableName" type="text_en" stored="true" indexed="true" multiValued="true"/>
     <field name="variableLabel" type="text_en" stored="true" indexed="true" multiValued="true"/>
 
+    <field name="literalQuestion" type="text_en" stored="true" indexed="true" multiValued="true"/>
+    <field name="interviewInstructions" type="text_en" stored="true" indexed="true" multiValued="true"/>
+    <field name="postQuestion" type="text_en" stored="true" indexed="true" multiValued="true"/>
+    <field name="variableUniverse" type="text_en" stored="true" indexed="true" multiValued="true"/>
+    <field name="variableNotes" type="text_en" stored="true" indexed="true" multiValued="true"/>
+
     <field name="fileDescription" type="text_en" stored="true" indexed="true" multiValued="false"/>
 
     <field name="fileTypeGroupFacet" type="string" stored="true" indexed="true" multiValued="false"/>
@@ -229,6 +235,12 @@
     <!-- Added for Dataverse 4.0 Beta: make variable names and labels searchable in basic search https://redmine.hmdc.harvard.edu/issues/3945 -->
     <copyField source="variableName" dest="_text_" maxChars="3000"/>
     <copyField source="variableLabel" dest="_text_" maxChars="3000"/>
+    <!-- Added variable level metadata that can be updated from DCT -->
+    <copyField source="literalQuestion" dest="_text_" maxChars="3000"/>
+    <copyField source="interviewInstructions" dest="_text_" maxChars="3000"/>
+    <copyField source="postQuestion" dest="_text_" maxChars="3000"/>
+    <copyField source="variableUniverse" dest="_text_" maxChars="3000"/>
+    <copyField source="variableNotes" dest="_text_" maxChars="3000"/>
     <!-- Make dataverse subject and affiliation searchable from basic search: https://github.com/IQSS/dataverse/issues/1431 -->
     <copyField source="dvSubject" dest="_text_" maxChars="3000"/>
     <copyField source="dvAlias" dest="_text_" maxChars="3000"/>
@@ -281,7 +293,7 @@
     <!-- Dataverse copyField from http://localhost:8080/api/admin/index/solr/schema -->
     <xi:include href="schema_dv_mdb_copies.xml" xmlns:xi="http://www.w3.org/2001/XInclude" />
 
-<!-- End: Dataverse Specific -->
+<!-- End: Dataverse-specific -->
 
     <!-- This can be enabled, in case the client does not know what fields may be searched. It isn't enabled by default
          because it's very expensive to index everything twice. -->

doc/release-notes/4.16-release-notes.md

@@ -91,6 +91,7 @@ If this is a new installation, please see our <a href=http://guides.dataverse.or
 - &lt;glassfish install path&gt;/glassfish4/bin/asadmin deploy &lt;path&gt;dataverse-4.16.war
 
 4. Restart glassfish  
+
 5. Update Citation Metadata Block    
 
    `curl http://localhost:8080/api/admin/datasetfield/load -X POST --data-binary @citation.tsv -H "Content-type: text/tab-separated-values"`  

doc/release-notes/4.19-release-notes.md

@@ -83,7 +83,7 @@ Additional fields are now available via the Search API, mostly related to inform
 
 ## Complete List of Changes
 
-For the complete list of code changes in this release, see the <a href="https://github.com/IQSS/dataverse/milestone/86?closed=1">4.19 milestone</a> in Github.
+For the complete list of code changes in this release, see the <a href="https://github.com/IQSS/dataverse/milestone/87?closed=1">4.19 milestone</a> in Github.
 
 For help with upgrading, installing, or general questions please post to the <a href="https://groups.google.com/forum/#!forum/dataverse-community">Dataverse Google Group</a> or email support@dataverse.org.