Merge pull request #86 from mderuijter/update-embargo-to-5.5

Update embargo to 5.5

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
 
@@ -55,7 +54,7 @@ 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 +65,5 @@ 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

conf/docker-aio/c8.dockerfile

@@ -1,10 +1,11 @@
 FROM centos:8
 # OS dependencies
-# PG 10 is the default in centos8; keep the repo comment for when we bump to 11+
-#RUN yum install -y https://download.postgresql.org/pub/repos/yum/reporpms/EL-8-x86_64/pgdg-redhat-repo-latest.noarch.rpm
+# IQSS now recommends Postgres 13.
+RUN dnf -qy module disable postgresql
+RUN yum install -y https://download.postgresql.org/pub/repos/yum/reporpms/EL-8-x86_64/pgdg-redhat-repo-latest.noarch.rpm
 
 RUN echo "fastestmirror=true" >> /etc/dnf/dnf.conf
-RUN yum install -y java-11-openjdk-devel postgresql-server sudo epel-release unzip curl httpd python2 diffutils
+RUN yum install -y java-11-openjdk-devel postgresql13-server sudo epel-release unzip curl httpd python2 diffutils
 RUN yum install -y jq lsof awscli
 
 # for older search scripts
@@ -29,10 +30,10 @@ RUN cd /opt ; unzip /tmp/dv/deps/payara-5.2020.6.zip ; ln -s /opt/payara5 /opt/g
 # this dies under Java 11, do we keep it?
 #COPY domain-restmonitor.xml /opt/payara5/glassfish/domains/domain1/config/domain.xml
 
-RUN sudo -u postgres /usr/bin/initdb /var/lib/pgsql/data
+RUN sudo -u postgres /usr/pgsql-13/bin/initdb -D /var/lib/pgsql/13/data
 
 # copy configuration related files
-RUN cp /tmp/dv/pg_hba.conf /var/lib/pgsql/data/
+RUN cp /tmp/dv/pg_hba.conf /var/lib/pgsql/13/data/
 RUN cp -r /opt/solr-8.8.1/server/solr/configsets/_default /opt/solr-8.8.1/server/solr/collection1
 RUN cp /tmp/dv/schema*.xml /opt/solr-8.8.1/server/solr/collection1/conf/
 RUN cp /tmp/dv/solrconfig.xml /opt/solr-8.8.1/server/solr/collection1/conf/solrconfig.xml

conf/docker-aio/entrypoint.bash

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 export LANG=en_US.UTF-8
-sudo -u postgres /usr/bin/pg_ctl start -D /var/lib/pgsql/data &
+sudo -u postgres /usr/pgsql-13/bin/pg_ctl start -D /var/lib/pgsql/13/data &
 cd /opt/solr-8.8.1/
 # TODO: Run Solr as non-root and remove "-force".
 bin/solr start -force
@@ -9,8 +9,8 @@ bin/solr create_core -c collection1 -d server/solr/collection1/conf -force
 # start apache, in both foreground and background...
 apachectl -DFOREGROUND &
 
-# TODO: Run Glassfish as non-root.
-cd /opt/glassfish4
+# TODO: Run Payara as non-root.
+cd /opt/payara5
 bin/asadmin start-domain --debug
 sleep infinity
 

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

@@ -19,7 +19,7 @@ To get started, you'll want to set up your :doc:`dev-environment` and make sure
 Getting Help
 ------------
 
-If you have any questions at all, please reach out to other developers via the channels listed in https://github.com/IQSS/dataverse/blob/develop/CONTRIBUTING.md such as http://chat.dataverse.org (#dataverse on freenode), the `dataverse-dev <https://groups.google.com/forum/#!forum/dataverse-dev>`_ mailing list, `community calls <https://dataverse.org/community-calls>`_, or [email protected].
+If you have any questions at all, please reach out to other developers via the channels listed in https://github.com/IQSS/dataverse/blob/develop/CONTRIBUTING.md such as http://chat.dataverse.org, the `dataverse-dev <https://groups.google.com/forum/#!forum/dataverse-dev>`_ mailing list, `community calls <https://dataverse.org/community-calls>`_, or [email protected].
 
 Core Technologies
 -----------------

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

@@ -36,7 +36,7 @@ Getting Help
 To get help installing or configuring a Dataverse installation, please try one or more of:
 
 - posting to the `dataverse-community <https://groups.google.com/forum/#!forum/dataverse-community>`_ Google Group.
-- asking at http://chat.dataverse.org (#dataverse on the freenode IRC network)
+- asking at http://chat.dataverse.org
 - emailing [email protected] to open a private ticket at https://help.hmdc.harvard.edu
 
 Improving this Guide

scripts/vagrant/setup.sh

@@ -35,16 +35,15 @@ echo "export MAVEN_HOME=/opt/maven" >> /etc/profile.d/maven.sh
 echo "export PATH=/opt/maven/bin:${PATH}" >> /etc/profile.d/maven.sh
 chmod 0755 /etc/profile.d/maven.sh
 
-# disable centos8 postgresql module and install postgresql10-server
-# note: postgresql10 because 9.6 isn't backwards compatible with python3-psycopg2
+# disable centos8 postgresql module and install postgresql13-server
 dnf -qy module disable postgresql
 dnf install -qy https://download.postgresql.org/pub/repos/yum/reporpms/EL-8-x86_64/pgdg-redhat-repo-latest.noarch.rpm
-dnf install -qy postgresql10-server
-/usr/pgsql-10/bin/postgresql-10-setup initdb
-/usr/bin/systemctl stop postgresql-10
-cp /dataverse/conf/vagrant/var/lib/pgsql/data/pg_hba.conf /var/lib/pgsql/10/data/pg_hba.conf
-/usr/bin/systemctl start postgresql-10
-/usr/bin/systemctl enable postgresql-10
+dnf install -qy postgresql13-server
+/usr/pgsql-13/bin/postgresql-13-setup initdb
+/usr/bin/systemctl stop postgresql-13
+cp /dataverse/conf/vagrant/var/lib/pgsql/data/pg_hba.conf /var/lib/pgsql/13/data/pg_hba.conf
+/usr/bin/systemctl start postgresql-13
+/usr/bin/systemctl enable postgresql-13
 
 PAYARA_USER=dataverse
 echo "Ensuring Unix user '$PAYARA_USER' exists"