Merge branch 'develop' into 4139-curator-edits-in-review #4139

Dockerfile

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+# See `conf/docker` for Docker images

conf/docker/build.sh

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+#!/bin/sh
+# Creates images and pushes them to Docker Hub.
+# The "kick-the-tires" tag should be relatively stable. No breaking changes.
+# Push to custom tags or tags based on branch names to iterate on the images.
+if [ -z "$1" ]; then
+  echo "No argument supplied. Please specify \"branch\" or \"custom my-custom-tag\" for experiments or \"stable\" if your change won't break anything."
+  exit 1
+fi
+
+if [ "$1" == 'branch' ]; then
+  echo "We'll push a tag to the branch you're on."
+  GIT_BRANCH=$(git rev-parse --abbrev-ref HEAD)
+  TAG=$GIT_BRANCH
+elif [ "$1" == 'stable' ]; then
+  echo "We'll push a tag to the most stable tag (which isn't saying much!)."
+  TAG=kick-the-tires
+elif [ "$1" == 'custom' ]; then
+  if [ -z "$1" ]; then
+    echo "You must provide a custom tag as the second argument."
+    exit 1
+  else
+    echo "We'll push a custom tag."
+    TAG=$2
+  fi
+else
+  echo "Unexpected argument: $1. Exiting. Run with no arguments for help."
+  exit 1
+fi
+echo Images will be pushed to Docker Hub with the tag \"$TAG\".
+# Use "conf" directory as context so we can copy schema.xml into Solr image.
+docker build -t iqss/dataverse-solr:$TAG -f solr/Dockerfile ../../conf
+docker push iqss/dataverse-solr:$TAG
+# TODO: Think about if we really need dataverse.war because it's in dvinstall.zip.
+# FIXME: Automate the building of dataverse.war and dvinstall.zip. Think about https://github.com/IQSS/dataverse/issues/3974 and https://github.com/IQSS/dataverse/pull/3975
+cp ../../target/dataverse*.war dataverse-glassfish/dataverse.war
+cp ../../scripts/installer/dvinstall.zip dataverse-glassfish
+cp ../../doc/sphinx-guides/source/_static/util/default.config dataverse-glassfish
+cp ../../downloads/glassfish-4.1.zip dataverse-glassfish
+cp ../../downloads/weld-osgi-bundle-2.2.10.Final-glassfish4.jar dataverse-glassfish
+docker build -t iqss/dataverse-glassfish:$TAG dataverse-glassfish
+# FIXME: Check the output of `docker build` and only push on success.
+docker push iqss/dataverse-glassfish:$TAG

conf/docker/dataverse-glassfish/.gitignore

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+glassfish-4.1.zip
+weld-osgi-bundle-2.2.10.Final-glassfish4.jar
+dvinstall.zip
+dataverse.war
+default.config

conf/docker/dataverse-glassfish/Dockerfile

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+FROM centos:7.2.1511
+MAINTAINER Dataverse (support@dataverse.org)
+
+COPY glassfish-4.1.zip /tmp
+COPY weld-osgi-bundle-2.2.10.Final-glassfish4.jar /tmp
+COPY default.config /tmp
+COPY dvinstall.zip /tmp
+
+# Install dependencies
+#RUN yum install -y unzip
+RUN yum install -y \
+    cronie \
+    git \
+    java-1.8.0-openjdk-devel \
+    nc \
+    perl \
+    postgresql \
+    sha1sum \
+    unzip \
+    wget
+
+ENV GLASSFISH_DOWNLOAD_SHA1 d1a103d06682eb08722fbc9a93089211befaa080
+ENV GLASSFISH_DIRECTORY "/usr/local/glassfish4"
+ENV HOST_DNS_ADDRESS "localhost"
+ENV POSTGRES_DB "dvndb"
+ENV POSTGRES_USER "dvnapp"
+ENV RSERVE_USER "rserve"
+ENV RSERVE_PASSWORD "rserve"
+
+#RUN ls /tmp
+#
+RUN find /tmp
+#
+#RUN exitEarly
+
+# Install Glassfish 4.1
+
+RUN cd /tmp \ 
+    && unzip glassfish-4.1.zip \
+    && mv glassfish4 /usr/local \
+    && cd /usr/local/glassfish4/glassfish/modules \
+    && rm weld-osgi-bundle.jar \
+    && cp /tmp/weld-osgi-bundle-2.2.10.Final-glassfish4.jar . \
+    #FIXME: Patch Grizzly too!
+    && echo "Done installing and patching Glassfish"
+
+RUN chmod g=u /etc/passwd
+
+RUN mkdir -p /home/glassfish
+RUN chgrp -R 0 /home/glassfish && \
+    chmod -R g=u /home/glassfish
+
+RUN mkdir -p /usr/local/glassfish4
+RUN chgrp -R 0 /usr/local/glassfish4 && \
+    chmod -R g=u /usr/local/glassfish4
+
+
+#RUN exitEarlyBeforeJq
+RUN yum -y install epel-release
+RUN yum install -y jq 
+
+# Install jq
+#RUN cd /tmp \  
+#    && wget https://github.com/stedolan/jq/releases/download/jq-1.5/jq-linux64 \
+#    && mv jq-linux64 /usr/local/bin \
+#    && chmod +x /usr/local/bin/jq-linux64 \
+#    && ln -s /usr/local/bin/jq-linux64 /usr/local/bin/jq
+
+# Customized persistence xml to avoid database recreation
+#RUN mkdir -p /tmp/WEB-INF/classes/META-INF/ 
+#COPY WEB-INF/classes/META-INF/persistence.xml /tmp/WEB-INF/classes/META-INF/
+
+# Install iRods iCommands
+#RUN  cd /tmp \
+#   && yum -y install epel-release \
+#   && yum -y install ftp://ftp.renci.org/pub/irods/releases/4.1.6/centos7/irods-icommands-4.1.6-centos7-x86_64.rpm 
+
+#COPY config-glassfish /root/dvinstall
+#COPY restart-glassfish /root/dvinstall
+#COPY config-dataverse /root/dvinstall
+
+#RUN cd /root/dvinstall && ./config-dataverse
+
+COPY ./entrypoint.sh /
+#COPY ./ddl /root/dvinstall
+#COPY ./init-postgres /root/dvinstall
+#COPY ./init-glassfish /root/dvinstall
+#COPY ./init-dataverse /root/dvinstall
+#COPY ./setup-all.sh /root/dvinstall
+#COPY ./setup-irods.sh /root/dvinstall
+COPY ./Dockerfile /
+
+VOLUME /usr/local/glassfish4/glassfish/domains/domain1/files
+
+EXPOSE      8080 
+
+ENTRYPOINT ["/entrypoint.sh"]
+CMD ["dataverse"]

conf/docker/dataverse-glassfish/entrypoint.sh

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+#!/bin/bash -x
+
+# Entrypoint script for Dataverse web application. This script waits
+# for dependent services (Rserve, Postgres, Solr) to start before
+# initializing Glassfish.
+
+echo "whoami before..."
+whoami
+if ! whoami &> /dev/null; then
+  if [ -w /etc/passwd ]; then
+    # Make `whoami` return the glassfish user.  # See https://docs.openshift.org/3.6/creating_images/guidelines.html#openshift-origin-specific-guidelines
+    # Fancy bash magic from https://github.com/RHsyseng/container-rhel-examples/blob/1208dcd7d4f431fc6598184dba6341b9465f4197/starter-arbitrary-uid/bin/uid_entrypoint#L4
+    echo "${USER_NAME:-glassfish}:x:$(id -u):0:${USER_NAME:-glassfish} user:/home/glassfish:/bin/bash" >> /etc/passwd
+  fi
+fi
+echo "whoami after"
+whoami
+
+set -e
+
+if [ "$1" = 'dataverse' ]; then
+
+    export GLASSFISH_DIRECTORY=/usr/local/glassfish4
+    export HOST_DNS_ADDRESS=localhost
+
+    TIMEOUT=30
+
+    if [ -n "$RSERVE_SERVICE_HOST" ]; then
+        RSERVE_HOST=$RSERVE_SERVICE_HOST
+    elif [ -n "$RSERVE_PORT_6311_TCP_ADDR" ]; then
+        RSERVE_HOST=$RSERVE_PORT_6311_TCP_ADDR
+    elif [ -z "$RSERVE_HOST" ]; then
+        RSERVE_HOST="localhost"
+    fi
+    export RSERVE_HOST
+
+    if [ -n "$RSERVE_SERVICE_PORT" ]; then
+        RSERVE_PORT=$RSERVE_SERVICE_PORT
+    elif [ -n "$RSERVE_PORT_6311_TCP_PORT" ]; then
+        RSERVE_PORT=$RSERVE_PORT_6311_TCP_PORT
+    elif [ -z "$RSERVE_PORT" ]; then
+        RSERVE_PORT="6311"
+    fi
+    export RSERVE_PORT
+
+    echo "Using Rserve at $RSERVE_HOST:$RSERVE_PORT"
+
+    if ncat $RSERVE_HOST $RSERVE_PORT -w $TIMEOUT --send-only < /dev/null > /dev/null 2>&1 ; then 
+        echo Rserve running; 
+    else
+        echo Optional service Rserve not running. 
+    fi
+
+
+    # postgres
+    if [ -n "$POSTGRES_SERVICE_HOST" ]; then
+        POSTGRES_HOST=$POSTGRES_SERVICE_HOST
+    elif [ -n "$POSTGRES_PORT_5432_TCP_ADDR" ]; then
+        POSTGRES_HOST=$POSTGRES_PORT_5432_TCP_ADDR
+    elif [ -z "$POSTGRES_HOST" ]; then
+        POSTGRES_HOST="localhost"
+    fi
+    export POSTGRES_HOST
+
+    if [ -n "$POSTGRES_SERVICE_PORT" ]; then
+        POSTGRES_PORT=$POSTGRES_SERVICE_PORT
+    elif [ -n "$POSTGRES_PORT_5432_TCP_PORT" ]; then
+        POSTGRES_PORT=$POSTGRES_PORT_5432_TCP_PORT
+    else
+        POSTGRES_PORT=5432
+    fi 
+    export POSTGRES_PORT
+
+    echo "Using Postgres at $POSTGRES_HOST:$POSTGRES_PORT"
+
+    if ncat $POSTGRES_HOST $POSTGRES_PORT -w $TIMEOUT --send-only < /dev/null > /dev/null 2>&1 ; then 
+        echo Postgres running; 
+    else
+        echo Required service Postgres not running. Have you started the required services?
+        exit 1 
+    fi
+
+    # solr
+    if [ -n "$SOLR_SERVICE_HOST" ]; then
+        SOLR_HOST=$SOLR_SERVICE_HOST
+    elif [ -n "$SOLR_PORT_8983_TCP_ADDR" ]; then
+        SOLR_HOST=$SOLR_PORT_8983_TCP_ADDR
+    elif [ -z "$SOLR_HOST" ]; then
+        SOLR_HOST="localhost"
+    fi
+    export SOLR_HOST
+
+    if [ -n "$SOLR_SERVICE_PORT" ]; then
+        SOLR_PORT=$SOLR_SERVICE_PORT
+    elif [ -n "$SOLR_PORT_8983_TCP_PORT" ]; then
+        SOLR_PORT=$SOLR_PORT_8983_TCP_PORT
+    else
+        SOLR_PORT=8983
+    fi 
+    export SOLR_PORT
+
+    echo "Using Solr at $SOLR_HOST:$SOLR_PORT"
+
+    if ncat $SOLR_HOST $SOLR_PORT -w $TIMEOUT --send-only < /dev/null > /dev/null 2>&1 ; then 
+        echo Solr running; 
+    else
+        echo Required service Solr not running. Have you started the required services?
+        exit 1 
+    fi
+
+    GLASSFISH_INSTALL_DIR="/usr/local/glassfish4"
+    cd $GLASSFISH_INSTALL_DIR
+    cp /tmp/dvinstall.zip $GLASSFISH_INSTALL_DIR
+    unzip dvinstall.zip
+    cd dvinstall
+    echo Copying the non-interactive file into place
+    cp /tmp/default.config .
+    echo Looking at first few lines of default.config
+    head default.config
+    # non-interactive install
+    echo Running non-interactive install
+    #./install -y -f > install.out 2> install.err
+    ./install -y -f
+
+#    if [ -n "$DVICAT_PORT_1247_TCP_PORT" ]; then
+#        ./setup-irods.sh
+#    fi
+
+    echo -e "\n\nDataverse started"
+
+    sleep infinity
+else
+    exec "$@"
+fi
+

conf/docker/postgresql/Dockerfile

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+# PostgreSQL for Dataverse (but consider switching to the image from CentOS)
+#
+# See also conf/docker/dataverse-glassfish/Dockerfile

conf/docker/solr/Dockerfile

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+FROM centos:7.2.1511
+MAINTAINER Dataverse (support@dataverse.org)
+
+RUN yum install -y wget unzip perl git java-1.8.0-openjdk-devel postgresql.x86_64
+
+# Install Solr 4.6.0
+# The context of the build is the "conf" directory.
+COPY solr/4.6.0/schema.xml /tmp
+
+RUN cd /tmp && wget https://archive.apache.org/dist/lucene/solr/4.6.0/solr-4.6.0.tgz  && \
+	tar xvzf solr-4.6.0.tgz  && \
+	mv solr-4.6.0 /usr/local/  && \
+	cd /usr/local/solr-4.6.0/example/solr/collection1/conf/  && \
+	mv schema.xml schema.xml.backup  && \
+	cp /tmp/schema.xml . && \
+	rm /tmp/solr-4.6.0.tgz
+
+RUN ln -s /usr/local/solr-4.6.0/example/logs /var/log/solr
+
+VOLUME  /usr/local/solr-4.6.0/example/solr/collection1/data
+
+EXPOSE 8983
+
+COPY docker/solr/Dockerfile /Dockerfile
+COPY docker/solr/entrypoint.sh /
+
+ENTRYPOINT ["/entrypoint.sh"]
+CMD ["solr"]

conf/docker/solr/entrypoint.sh

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+#!/bin/bash
+
+if [ "$1" = 'solr' ]; then
+    cd /usr/local/solr-4.6.0/example/
+    java -jar start.jar 
+elif [ "$1" = 'usage' ]; then
+    echo  'docker run -d iqss/dataverse-solr solr'
+else
+    exec "$@"
+fi