Merge pull request #19 from TIK-NFL/update_v5.9

Update v5.9

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,53 @@
+---
+name: Bug report
+about: Did you encounter something unexpected or incorrect in the Dataverse software? We'd like to hear about it!
+title: ''
+labels: ''
+assignees: ''
+
+---
+<!--
+Thank you for contributing to the Dataverse Project through the creation of a bug report!
+
+WARNING: If this is a security issue it should be reported privately to [email protected]
+
+More information on bug issues and contributions can be found in the "Contributing to Dataverse" page:
+https://github.com/IQSS/dataverse/blob/develop/CONTRIBUTING.md#bug-reportsissues
+
+Please fill out as much of the template as you can.
+Start below this comment section.
+-->
+**What steps does it take to reproduce the issue?**
+
+* When does this issue occur?
+
+
+* Which page(s) does it occurs on?
+
+
+* What happens?
+
+
+* To whom does it occur (all users, curators, superusers)?
+
+
+* What did you expect to happen?
+
+
+
+**Which version of Dataverse are you using?**
+
+
+
+**Any related open or closed issues to this bug report?**
+
+
+
+**Screenshots:**
+
+No matter the issue, screenshots are always welcome.
+
+To add a screenshot, please use one of the following formats and/or methods described here:
+
+* https://help.github.com/en/articles/file-attachments-on-issues-and-pull-requests
+*

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,35 @@
+---
+name: Feature request
+about: Suggest an idea or new feature for the Dataverse software!
+title: 'Feature Request/Idea:'
+labels: ''
+assignees: ''
+
+---
+<!--
+Thank you for contributing to the Dataverse Project through the creation of a feature request!
+
+More information on ideas/feature requests and contributions can be found in the "Contributing to Dataverse" page:
+https://github.com/IQSS/dataverse/blob/develop/CONTRIBUTING.md#ideasfeature-requests
+
+Please fill out as much of the template as you can.
+Start below this comment section.
+-->
+
+**Overview of the Feature Request**
+
+
+**What kind of user is the feature intended for?**
+(Example users roles: API User, Curator, Depositor, Guest, Superuser, Sysadmin)
+
+
+**What inspired the request?**
+
+
+**What existing behavior do you want changed?**
+
+
+**Any brand new behavior do you want to add to Dataverse?**
+
+
+**Any related open or closed issues to this feature request?**

.travis.yml.future → .github/workflows/cypress_ui.yml.future

@@ -1,16 +1,17 @@
+###############################################################################
+#
+#   THIS IS AN OLD TRAVIS-CI.ORG JOB FILE
+#   To be used with Github Actions, it would be necessary to refactor it.
+#   Keeping it as the future example it has been before.
+#   See also #5846
+#
+###############################################################################
+
 services:
   - docker
 
 jobs:
   include:
-    # Execute java unit- and integration tests
-    - stage: test
-      language: java
-      jdk:
-        - oraclejdk8
-      script: mvn -DcompilerArgument=-Xlint:unchecked test -P all-unit-tests
-      after_success: mvn jacoco:report coveralls:report
-
     # Execute Cypress for UI testing
     # see https://docs.cypress.io/guides/guides/continuous-integration.html
     - stage: test

.github/workflows/guides_build_sphinx.yml

@@ -9,6 +9,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2
-    - uses: ammaraskar/sphinx-action@master
+    - uses: OdumInstitute/sphinx-action@master
       with:
         docs-folder: "doc/sphinx-guides/"

.github/workflows/maven_unit_test.yml

@@ -0,0 +1,42 @@
+name: Maven Unit Tests
+
+on:
+    push:
+        paths:
+            - "**.java"
+    pull_request:
+        paths:
+            - "**.java"
+
+jobs:
+    unittest:
+        name: (JDK ${{ matrix.jdk }} / ${{ matrix.os }}) Unit Tests
+        strategy:
+            fail-fast: false
+            matrix:
+                os: [ ubuntu-latest ]
+                jdk: [ '11' ]
+                #include:
+                #    -   os: ubuntu-latest
+                #        jdk: '16'
+        runs-on: ${{ matrix.os }}
+        steps:
+          - uses: actions/checkout@v2
+          - name: Set up JDK ${{ matrix.jdk }}
+            uses: actions/setup-java@v2
+            with:
+                java-version: ${{ matrix.jdk }}
+                distribution: 'adopt'
+          - name: Cache Maven packages
+            uses: actions/cache@v2
+            with:
+                path: ~/.m2
+                key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}
+                restore-keys: ${{ runner.os }}-m2
+          - name: Build with Maven
+            run: mvn -DcompilerArgument=-Xlint:unchecked -P all-unit-tests clean test
+          - name: Maven Code Coverage
+            env:
+                CI_NAME: github
+                COVERALLS_SECRET: ${{ secrets.GITHUB_TOKEN }}
+            run: mvn -V -B jacoco:report coveralls:report -DrepoToken=${COVERALLS_SECRET} -DpullRequest=${{ github.event.number }}

.github/workflows/reviewdog_checkstyle.yml

@@ -0,0 +1,21 @@
+name: Maven CheckStyle Task
+on:
+   pull_request:
+       paths:
+           - "**.java"
+
+jobs:
+    checkstyle_job:
+        runs-on: ubuntu-latest
+        name: Checkstyle job
+        steps:
+            - name: Checkout
+              uses: actions/checkout@v2
+            - name: Run check style
+              uses: nikitasavinov/checkstyle-action@master
+              with:
+                  fail_on_error: true
+                  reporter: github-pr-review
+                  checkstyle_config: checkstyle.xml
+                  github_token: ${{ secrets.GITHUB_TOKEN }}
+

.github/workflows/shellspec.yml

@@ -0,0 +1,83 @@
+name: "Shellspec"
+on:
+    push:
+        paths:
+            - tests/shell/**
+            - conf/solr/**
+            # add more when more specs are written relying on data
+    pull_request:
+        paths:
+            - tests/shell/**
+            - conf/solr/**
+            # add more when more specs are written relying on data
+env:
+    SHELLSPEC_VERSION: 0.28.1
+jobs:
+    shellcheck:
+        name: Shellcheck
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v2
+            - name: shellcheck
+              uses: reviewdog/action-shellcheck@v1
+              with:
+                  github_token: ${{ secrets.github_token }}
+                  reporter: github-pr-review # Change reporter.
+                  fail_on_error: true
+                  exclude: "./tests/shell/*"
+    shellspec-ubuntu:
+        name: "Ubuntu"
+        runs-on: ubuntu-latest
+        steps:
+            - name: Install shellspec
+              run: curl -fsSL https://git.io/shellspec | sh -s ${{ env.SHELLSPEC_VERSION }} --yes
+            - uses: actions/checkout@v2
+            - name: Run Shellspec
+              run: |
+                  cd tests/shell
+                  shellspec
+    shellspec-centos7:
+        name: "CentOS 7"
+        runs-on: ubuntu-latest
+        container:
+            image: centos:7
+        steps:
+            - uses: actions/checkout@v2
+            - name: Install shellspec
+              run: |
+                  curl -fsSL https://github.com/shellspec/shellspec/releases/download/${{ env.SHELLSPEC_VERSION }}/shellspec-dist.tar.gz | tar -xz -C /usr/share
+                  ln -s /usr/share/shellspec/shellspec /usr/bin/shellspec
+            - name: Install dependencies
+              run: yum install -y ed
+            - name: Run shellspec
+              run: |
+                  cd tests/shell
+                  shellspec
+    shellspec-rocky8:
+        name: "RockyLinux 8"
+        runs-on: ubuntu-latest
+        container:
+            image: rockylinux/rockylinux:8
+        steps:
+            - uses: actions/checkout@v2
+            - name: Install shellspec
+              run: |
+                  curl -fsSL https://github.com/shellspec/shellspec/releases/download/${{ env.SHELLSPEC_VERSION }}/shellspec-dist.tar.gz | tar -xz -C /usr/share
+                  ln -s /usr/share/shellspec/shellspec /usr/bin/shellspec
+            - name: Install dependencies
+              run: dnf install -y ed bc diffutils
+            - name: Run shellspec
+              run: |
+                  cd tests/shell
+                  shellspec
+    shellspec-macos:
+        name: "MacOS"
+        runs-on: macos-10.15
+        steps:
+            - name: Install shellspec
+              run: curl -fsSL https://git.io/shellspec | sh -s 0.28.1 --yes
+            - uses: actions/checkout@v2
+            - name: Run Shellspec
+              run: |
+                  cd tests/shell
+                  /Users/runner/.local/bin/shellspec

CONTRIBUTING.md

@@ -6,12 +6,11 @@ We aren't just looking for developers. There are many ways to contribute to Data
 
 ## Ideas/Feature Requests
 
-Your idea or feature request might already be captured in the Dataverse [issue tracker] on GitHub but if not, the best way to bring it to the community's attention is by posting on the [dataverse-community Google Group][] or bringing it up on a [Community Call][]. You're also welcome make some noise in the [#dataverse IRC channel][] (which is [logged][]) or cram your idea into 280 characters and mention [@dataverseorg][] on Twitter. To discuss your idea privately, please email it to [email protected]
+Your idea or feature request might already be captured in the Dataverse [issue tracker] on GitHub but if not, the best way to bring it to the community's attention is by posting on the [dataverse-community Google Group][] or bringing it up on a [Community Call][]. You're also welcome to make some noise in [chat.dataverse.org][] or cram your idea into 280 characters and mention [@dataverseorg][] on Twitter. To discuss your idea privately, please email it to [email protected]
 
 There's a chance your idea is already on our roadmap, which is available at https://www.iq.harvard.edu/roadmap-dataverse-project
 
-[#dataverse IRC channel]: http://chat.dataverse.org
-[logged]: http://irclog.iq.harvard.edu/dataverse/today
+[chat.dataverse.org]: http://chat.dataverse.org
 [issue tracker]: https://github.com/IQSS/dataverse/issues
 [@dataverseorg]: https://twitter.com/dataverseorg
 
@@ -29,8 +28,6 @@ If there is no pre-existing issue or it has been closed, please click on the "Ne
 
 If you do not receive a reply to your new issue or comment in a timely manner, please email [email protected] with a link to the issue.
 
-We are aware of the new issue templates described at https://help.github.com/articles/about-issue-and-pull-request-templates but haven't converted over yet.
-
 ### Writing an Issue
 
 For the subject of an issue, please start it by writing the feature or functionality it relates to, i.e. "Create Account:..." or "Dataset Page:...". In the body of the issue, please outline the issue you are reporting with as much detail as possible. In order for the Dataverse development team to best respond to the issue, we need as much information about the issue as you can provide. Include steps to reproduce bugs. Indicate which version you're using, which is shown at the bottom of the page. We love screenshots!
@@ -55,7 +52,7 @@ We love code contributions. Developers are not limited to the main Dataverse cod
 [API Guide]: http://guides.dataverse.org/en/latest/api
 [Installation Guide]: http://guides.dataverse.org/en/latest/installation
 
-If you are interested in working on the main Dataverse code, great! Before you start coding, please reach out to us either on the [dataverse-community Google Group][], the [dataverse-dev Google Group][], [IRC][] (#dataverse on freenode), or via [email protected] to make sure the effort is well coordinated and we avoid merge conflicts. We maintain a list of [community contributors][] and [dev efforts][] the community is working on so please let us know if you'd like to be added or removed from either list.
+If you are interested in working on the main Dataverse code, great! Before you start coding, please reach out to us either on the [dataverse-community Google Group][], the [dataverse-dev Google Group][], [chat.dataverse.org][], or via [email protected] to make sure the effort is well coordinated and we avoid merge conflicts. We maintain a list of [community contributors][] and [dev efforts][] the community is working on so please let us know if you'd like to be added or removed from either list.
 
 Please read http://guides.dataverse.org/en/latest/developers/version-control.html to understand how we use the "git flow" model of development and how we will encourage you to create a GitHub issue (if it doesn't exist already) to associate with your pull request. That page also includes tips on making a pull request.
 
@@ -66,6 +63,5 @@ Thanks for your contribution!
 [dataverse-community Google Group]: https://groups.google.com/group/dataverse-community
 [Community Call]: https://dataverse.org/community-calls
 [dataverse-dev Google Group]: https://groups.google.com/group/dataverse-dev
-[IRC]: http://chat.dataverse.org
 [community contributors]: https://docs.google.com/spreadsheets/d/1o9DD-MQ0WkrYaEFTD5rF_NtyL8aUISgURsAXSL7Budk/edit?usp=sharing
 [dev efforts]: https://github.com/orgs/IQSS/projects/2#column-5298405

README.md

@@ -19,7 +19,7 @@ Dataverse is a trademark of President and Fellows of Harvard College and is regi
 
 [![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/ws/target/coverage-it/index.html)
-[![Unit Test Status](https://img.shields.io/travis/IQSS/dataverse?label=Unit%20Test%20Status)](https://travis-ci.org/IQSS/dataverse)
+[![Unit Test Status](https://github.com/IQSS/dataverse/actions/workflows/maven_unit_test.yml/badge.svg?branch=develop)](https://github.com/IQSS/dataverse/actions/workflows/maven_unit_test.yml)
 [![Unit Test Coverage](https://img.shields.io/coveralls/github/IQSS/dataverse?label=Unit%20Test%20Coverage)](https://coveralls.io/github/IQSS/dataverse?branch=develop)
 [![Guides Build Status](https://github.com/IQSS/dataverse/actions/workflows/guides_build_sphinx.yml/badge.svg)](https://github.com/IQSS/dataverse/actions/workflows/guides_build_sphinx.yml)
 

Vagrantfile

@@ -4,7 +4,7 @@
 VAGRANTFILE_API_VERSION = "2"
 
 Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
-  config.vm.box = "bento/centos-8.2"
+  config.vm.box = "bento/rockylinux-8.4"
 
   config.vm.provider "virtualbox" do |vbox|
     vbox.cpus = 4

checkstyle.xml

@@ -97,7 +97,9 @@
             <property name="excludes" value="lombok,java.util,org.springframework.web.bind.annotation"/>
         </module>
         -->
-        <!-- <module name="IllegalImport"/> --> <!-- defaults to sun.* packages -->
+        <module name="IllegalImport">
+            <property name="illegalPkgs" value="org.apache.commons.lang"/>
+        </module>
         <!-- <module name="RedundantImport"/> -->
         <!-- <module name="UnusedImports">
             <property name="processJavadoc" value="false"/>

conf/docker-aio/0prep_deps.sh

@@ -4,10 +4,9 @@ if [ ! -d dv/deps ]; then
 fi
 wdir=`pwd`
 
-if [ ! -e dv/deps/payara-5.2020.6.zip ]; then
+if [ ! -e dv/deps/payara-5.2021.5.zip ]; then
 	echo "payara dependency prep"
-	# no more fiddly patching :)
-	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
+	wget https://s3-eu-west-1.amazonaws.com/payara.fish/Payara+Downloads/5.2021.5/payara-5.2021.5.zip  -O dv/deps/payara-5.2021.5.zip
 fi
 
 if [ ! -e dv/deps/solr-8.8.1dv.tgz ]; then

conf/docker-aio/1prep.sh

@@ -6,17 +6,16 @@
 mkdir -p testdata/doc/sphinx-guides/source/_static/util/
 cp ../solr/8.8.1/schema*.xml testdata/
 cp ../solr/8.8.1/solrconfig.xml testdata/
-cp ../solr/8.8.1/updateSchemaMDB.sh testdata/
 cp ../jhove/jhove.conf testdata/
 cp ../jhove/jhoveConfig.xsd testdata/
 cd ../../
 cp -r scripts conf/docker-aio/testdata/
 cp doc/sphinx-guides/source/_static/util/createsequence.sql conf/docker-aio/testdata/doc/sphinx-guides/source/_static/util/
 
-wget -q https://downloads.apache.org/maven/maven-3/3.6.3/binaries/apache-maven-3.6.3-bin.tar.gz
-tar xfz apache-maven-3.6.3-bin.tar.gz
+wget -q https://downloads.apache.org/maven/maven-3/3.8.4/binaries/apache-maven-3.8.4-bin.tar.gz
+tar xfz apache-maven-3.8.4-bin.tar.gz
 mkdir maven
-mv apache-maven-3.6.3/* maven/
+mv apache-maven-3.8.4/* maven/
 echo "export JAVA_HOME=/usr/lib/jvm/jre-openjdk" > maven/maven.sh
 echo "export M2_HOME=../maven" >> maven/maven.sh
 echo "export MAVEN_HOME=../maven" >> maven/maven.sh