Merge branch 'develop' into 6819-jdbc-driver-war IQSS#6819

Conflicts:
pom.xml (payara version .2 vs .6)

conf/docker-aio/0prep_deps.sh

@@ -4,10 +4,10 @@ if [ ! -d dv/deps ]; then
 fi
 wdir=`pwd`
 
-if [ ! -e dv/deps/payara-5.2020.2.zip ]; then
+if [ ! -e dv/deps/payara-5.2020.6.zip ]; then
 	echo "payara dependency prep"
 	# no more fiddly patching :)
-	wget https://github.com/payara/Payara/releases/download/payara-server-5.2020.2/payara-5.2020.2.zip  -O dv/deps/payara-5.2020.2.zip
+	wget https://s3-eu-west-1.amazonaws.com/payara.fish/Payara+Downloads/5.2020.6/payara-5.2020.6.zip  -O dv/deps/payara-5.2020.6.zip
 fi
 
 if [ ! -e dv/deps/solr-7.7.2dv.tgz ]; then

conf/docker-aio/c8.dockerfile

@@ -18,7 +18,7 @@ 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-7.7.2dv.tgz 
-RUN cd /opt ; unzip /tmp/dv/deps/payara-5.2020.2.zip ; ln -s /opt/payara5 /opt/glassfish4
+RUN cd /opt ; unzip /tmp/dv/deps/payara-5.2020.6.zip ; ln -s /opt/payara5 /opt/glassfish4
 
 # 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`
 COPY domain-restmonitor.xml /opt/payara5/glassfish/domains/domain1/config/domain.xml

doc/release-notes/7417-payara-5.2020.6.md

@@ -0,0 +1,12 @@
+## Update to Payara Platform 5.2020.6
+
+In contrast to good old Glassfish 4, the Payara application server
+is a maintained product, receiving both feature and - more important -
+security and dependent technology updates. You should update the
+application server platform on a regular basis, as it is a key component
+of a running Dataverse deployment.
+
+<!-- REQUIREMENT MARKER FOR LATER USE WITH #6819 AS HTML COMMENT. MAY BE OMMITED. -->
+
+Instructions how to update can be found in the
+[Payara documentation](https://docs.payara.fish/community/docs/5.2020.6/documentation/user-guides/upgrade-payara.html)

doc/sphinx-guides/source/developers/dev-environment.rst

@@ -85,9 +85,9 @@ To install Payara, run the following commands:
 
 ``cd /usr/local``
 
-``sudo curl -O -L https://github.com/payara/Payara/releases/download/payara-server-5.2020.2/payara-5.2020.2.zip``
+``sudo curl -O -L https://s3-eu-west-1.amazonaws.com/payara.fish/Payara+Downloads/5.2020.6/payara-5.2020.6.zip``
 
-``sudo unzip payara-5.2020.2.zip``
+``sudo unzip payara-5.2020.6.zip``
 
 ``sudo chown -R $USER /usr/local/payara5``
 

doc/sphinx-guides/source/developers/testing.rst

@@ -41,7 +41,7 @@ We use a variety of tools to write, execute, and measure the code coverage of un
 
 As you prepare to make a pull request, as described in the :doc:`version-control` section, you will be working on a new branch you create from the "develop" branch. Let's say your branch is called ``1012-private-url``. As you work, you are constantly invoking Maven to build the war file. When you do a "clean and build" in Netbeans, Maven runs all the unit tests (anything ending with ``Test.java``) and the runs the results through a tool called Jacoco that calculates code coverage. When you push your branch to GitHub and make a pull request, a web service called Travis CI runs Maven and Jacoco on your branch and pushes the results to Coveralls, which is a web service that tracks changes to code coverage over time.
 
-To make this more concrete, observe that https://github.com/IQSS/dataverse/pull/3111 has comments from a GitHub user called ``coveralls`` saying things like "Coverage increased (+0.5%) to 5.547% when pulling dd6ceb1 on 1012-private-url into be5b26e on develop." Clicking on the comment should lead you to a URL such as https://coveralls.io/builds/7013870 which shows how code coverage has gone up or down. That page links to a page such as https://travis-ci.org/IQSS/dataverse/builds/144840165 which shows the build on the Travis side that pushed the results ton Coveralls.
+To make this more concrete, observe that https://github.com/IQSS/dataverse/pull/3111 has comments from a GitHub user called ``coveralls`` saying things like "Coverage increased (+0.5%) to 5.547% when pulling dd6ceb1 on 1012-private-url into be5b26e on develop." Clicking on the comment should lead you to a URL such as https://coveralls.io/builds/7013870 which shows how code coverage has gone up or down. That page links to a page such as https://travis-ci.org/IQSS/dataverse/builds/144840165 which shows the build on the Travis side that pushed the results to Coveralls. Note that we have configured Coveralls to not mark small decreases in code coverage as a failure.
 
 The main takeaway should be that we care about unit testing enough to measure the changes to code coverage over time using automation. Now let's talk about how you can help keep our code coverage up by writing unit tests with JUnit.
 

doc/sphinx-guides/source/installation/prerequisites.rst

@@ -47,7 +47,7 @@ If you don't want to be prompted, here is an example of the non-interactive invo
 Payara
 ------
 
-Payara 5.2020.2 is recommended. Newer versions might work fine.
+Payara 5.2020.6 is recommended. Newer versions might work fine, regular updates are recommended.
 
 Installing Payara
 =================
@@ -58,8 +58,8 @@ Installing Payara
 
 - Download and install Payara (installed in ``/usr/local/payara5`` in the example commands below)::
 
-	# wget https://github.com/payara/Payara/releases/download/payara-server-5.2020.2/payara-5.2020.2.zip
-	# unzip payara-5.2020.2.zip
+	# wget https://s3-eu-west-1.amazonaws.com/payara.fish/Payara+Downloads/5.2020.6/payara-5.2020.6.zip
+	# unzip payara-5.2020.6.zip
 	# mv payara5 /usr/local
 
 If you intend to install and run Payara under a service account (and we hope you do), chown -R the Payara hierarchy to root to protect it but give the service account access to the below directories:
@@ -322,7 +322,7 @@ components and libraries. Please consult the instructions in the
 Installing R
 ============
 
-For RHEL/CentOS, the EPEL distribution is strongly recommended::
+For RHEL/CentOS, the EPEL distribution is strongly recommended:
 
 If :fixedwidthplain:`yum` isn't configured to use EPEL repositories ( https://fedoraproject.org/wiki/EPEL ):
 

downloads/download.sh

@@ -1,5 +1,5 @@
 #!/bin/sh
-curl -L -O https://github.com/payara/Payara/releases/download/payara-server-5.2020.2/payara-5.2020.2.zip
+curl -L -O https://s3-eu-west-1.amazonaws.com/payara.fish/Payara+Downloads/5.2020.6/payara-5.2020.6.zip
 curl -L -O https://archive.apache.org/dist/lucene/solr/7.7.2/solr-7.7.2.tgz
 curl -L -O https://search.maven.org/remotecontent?filepath=org/jboss/weld/weld-osgi-bundle/2.2.10.Final/weld-osgi-bundle-2.2.10.Final-glassfish4.jar
 curl -s -L http://sourceforge.net/projects/schemaspy/files/schemaspy/SchemaSpy%205.0.0/schemaSpy_5.0.0.jar/download > schemaSpy_5.0.0.jar

pom.xml

@@ -26,7 +26,7 @@
         <skipUnitTests>false</skipUnitTests>
 
         <jakartaee-api.version>8.0.0</jakartaee-api.version>
-        <payara.version>5.2020.2</payara.version>
+        <payara.version>5.2020.6</payara.version>
         <postgresql.version>42.2.18</postgresql.version>
         <aws.version>1.11.762</aws.version>
         <commons.logging.version>1.2</commons.logging.version>

scripts/vagrant/setup.sh

@@ -43,7 +43,7 @@ SOLR_USER=solr
 echo "Ensuring Unix user '$SOLR_USER' exists"
 useradd $SOLR_USER || :
 DOWNLOAD_DIR='/dataverse/downloads'
-PAYARA_ZIP="$DOWNLOAD_DIR/payara-5.2020.2.zip"
+PAYARA_ZIP="$DOWNLOAD_DIR/payara-5.2020.6.zip"
 SOLR_TGZ="$DOWNLOAD_DIR/solr-7.7.2.tgz"
 if [ ! -f $PAYARA_ZIP ] || [ ! -f $SOLR_TGZ ]; then
     echo "Couldn't find $PAYARA_ZIP or $SOLR_TGZ! Running download script...."

src/main/webapp/dataset.xhtml

@@ -828,15 +828,16 @@
                     </div>
                     <!-- END: Create/Save Dataset Button Panel BTM editMode -->
                     <p:blockUI block="datasetForm" widgetVar="blockDatasetForm"/>
-                    <!-- POPUPS -->                    
-                    <ui:include src="file-edit-popup-fragment.xhtml">
-                        <ui:param name="datasetVersion" value="#{DatasetPage.workingVersion}"/>   
-                        <ui:param name="fileMetadataForAction" value="#{DatasetPage.fileMetadataForAction}"/>                        
-                        <ui:param name="bean" value="#{DatasetPage}"/>                        
-                        <ui:param name="restrictFileAction" value="restrictFiles"/>
-                        <ui:param name="deleteFileAction" value="deleteFiles"/> 
-                    </ui:include>                  
-
+                    <!-- POPUPS -->
+                    <ui:fragment rendered="#{DatasetPage.editMode == 'CREATE' or empty DatasetPage.editMode }">                    
+                        <ui:include src="file-edit-popup-fragment.xhtml">
+                              <ui:param name="datasetVersion" value="#{DatasetPage.workingVersion}"/>   
+                              <ui:param name="fileMetadataForAction" value="#{DatasetPage.fileMetadataForAction}"/>                        
+                              <ui:param name="bean" value="#{DatasetPage}"/>                        
+                              <ui:param name="restrictFileAction" value="restrictFiles"/>
+                              <ui:param name="deleteFileAction" value="deleteFiles"/> 
+                        </ui:include>                  
+                    </ui:fragment>
                     <p:dialog id="shareDialog" header="#{bundle['dataset.share.datasetShare']}" widgetVar="shareDialog" modal="true" rendered="#{!DatasetPage.workingVersion.deaccessioned}">
                         <p class="help-block">#{bundle['dataset.share.datasetShare.tip']}</p>
                         <div id="sharrre-widget" data-url="#{DatasetPage.dataverseSiteUrl}/dataset.xhtml?persistentId=#{dataset.globalId}" data-text="#{bundle['dataset.share.datasetShare.shareText']}"></div>