Add docker-compose build system

.dockerignore

@@ -0,0 +1,7 @@
+/.git/
+/.github/
+/conf/docker-compose/postgres-bind/
+/conf/docker-compose/solr-bind/
+/conf/docker-compose/seaweedfs-bind/
+/conf/docker-compose/dataverse-docroot-bind/
+/conf/docker-compose/dataverse-logos-bind/

.env

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+# timezone
+# https://en.wikipedia.org/wiki/List_of_tz_database_time_zones
+TZ="America/Denver"
+
+# dataverse service
+HOST_DNS_ADDRESS=dataverse
+GLASSFISH_USER=dataverse
+GLASSFISH_PASSWORD=secret
+GLASSFISH_ADMIN_USER=admin
+GLASSFISH_ADMIN_PASSWORD=secret
+ADMIN_EMAIL=noreply@mydomain.com
+MAIL_SERVER=localhost
+POSTGRES_ADMIN_PASSWORD=secret
+POSTGRES_SERVER=postgres
+POSTGRES_PORT=5432
+POSTGRES_DATABASE=dataverse
+POSTGRES_PASSWORD=secret
+POSTGRES_USER=dataverse
+SOLR_LOCATION=solr:8983
+RSERVE_HOST=rserve
+RSERVE_PORT=6311
+# the rserve credentials are hardcoded in the Dockerfile, edit both if you want to change them
+RSERVE_USER=rserve
+RSERVE_PASSWORD=rserve
+
+# disable DOI validation checks, true or false, set this to true for your development environment
+DISABLE_DOI=true
+
+# exclude emails from exports
+# https://guides.dataverse.org/en/latest/installation/config.html#excludeemailfromexport
+EXCLUDE_EMAIL_EXPORTS=true
+
+# s3 keys
+S3_ACCESS_KEY=secret
+S3_SECRET_KEY=secret
+
+# fully qualified domain name (FQDN) and site URL
+# recommend keeping this as dataverse because it's used internally for routing within Docker
+# if you change this, s3 storage will break
+DATAVERSE_FQDN=dataverse
+# make sure to escape characters like :
+DATAVERSE_SITE_URL=http\://localhost

Dockerfile

@@ -1 +1,88 @@
-# See http://guides.dataverse.org/en/latest/developers/containers.html
+# https://hub.docker.com/_/ubuntu
+FROM ubuntu:22.04
+
+ENV DEBIAN_FRONTEND noninteractive
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+    gcc python3-dev tzdata nano dos2unix curl wget openjdk-11-jdk maven unzip jq imagemagick python3 python3-pip python3-psycopg2 wait-for-it ca-certificates && \
+    apt-get -y upgrade && \
+    rm -rf /var/lib/apt/lists/*
+
+WORKDIR /
+
+RUN useradd --create-home --shell /bin/bash dataverse
+
+# https://guides.dataverse.org/en/5.8/installation/prerequisites.html
+RUN wget https://s3-eu-west-1.amazonaws.com/payara.fish/Payara+Downloads/5.2022.3/payara-5.2022.3.zip
+
+RUN unzip payara-5.2022.3.zip && \
+  mv payara5 /usr/local && \
+  rm payara-5.2022.3.zip
+
+RUN chown -R root:root /usr/local/payara5 && \
+  chown dataverse /usr/local/payara5/glassfish/lib && \
+  chown -R dataverse:dataverse /usr/local/payara5/glassfish/domains/domain1
+
+# ENV JAVA_HOME "/usr/lib/jvm/java-11-openjdk-${ARCHITECTURE}"
+# RUN export JAVA_HOME="$(dirname $(dirname $(readlink -f $(which java))))"
+
+# install Counter Processor
+# https://guides.dataverse.org/en/latest/installation/prerequisites.html#counter-processor
+RUN cd /usr/local && \
+  wget https://github.com/CDLUC3/counter-processor/archive/refs/tags/v0.1.04.tar.gz && \
+  tar xvfz v0.1.04.tar.gz && \
+  rm v0.1.04.tar.gz && \
+  cd counter-processor-0.1.04 && \
+  pip3 install -r requirements.txt
+
+RUN useradd --create-home --shell /bin/bash counter && \
+  chown -R counter:counter /usr/local/counter-processor-0.1.04
+
+# install awscli
+RUN pip3 install --no-cache-dir awscli
+
+# switch to non-root user as this is more secure
+USER dataverse
+WORKDIR /
+
+RUN mkdir -p /home/dataverse/.aws/
+COPY --chown=dataverse:dataverse ./conf/docker-compose/dataverse/config /home/dataverse/.aws/config
+COPY --chown=dataverse:dataverse ./conf/docker-compose/dataverse/credentials /home/dataverse/.aws/credentials
+
+RUN cp -R /home/dataverse/.aws/ /usr/local/payara5/glassfish/domains/domain1/
+
+# if you want to speed up the Maven build you can copy over
+# cached packages here
+# COPY --chown=dataverse:dataverse ./conf/docker-compose/dataverse/.m2/ /home/dataverse/.m2/
+
+# copy over sourcecode and build files needed to compile the .war
+# as well as installer files
+COPY --chown=dataverse:dataverse pom.xml /dataverse/
+COPY --chown=dataverse:dataverse src /dataverse/src/
+COPY --chown=dataverse:dataverse modules /dataverse/modules/
+COPY --chown=dataverse:dataverse scripts /dataverse/scripts/
+COPY --chown=dataverse:dataverse conf/jhove/ /dataverse/conf/jhove/
+COPY --chown=dataverse:dataverse local_lib /dataverse/local_lib/
+
+# this likely isn't needed on Linux but was needed on a Windows build
+RUN find /dataverse -type f -print0 | xargs -0 -n 1 -P 4 dos2unix
+
+# this can take some time to download all the dependencies
+RUN cd /dataverse/ && \
+  export dpkgArch="$(dpkg --print-architecture)" && \
+  export JAVA_HOME="/usr/lib/jvm/java-11-openjdk-${dpkgArch}" && \
+  mvn package -DskipTests --no-transfer-progress
+
+# delete the cached dependencies so we don't get any inaccurate "false flags" on container scanning for security issues
+RUN rm -rf ~/.m2/
+
+USER root
+COPY --chown=dataverse:dataverse ./conf/docker-compose/dataverse/startup.sh /startup.sh
+RUN chmod +x /startup.sh && dos2unix /startup.sh
+
+USER dataverse
+CMD ["wait-for-it", "postgres:5432", "--", "/startup.sh"]
+
+# helpful for debugging purposes to just start up the container
+# CMD ["tail", "-f", "/dev/null"]

conf/docker-compose/.gitignore

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+/solr/*.xml
+/dataverse/.m2/
+/postgres-bind/
+/solr-bind/
+/seaweedfs-bind/
+/dataverse-docroot-bind/
+/dataverse-logos-bind/
+/traefik/traefik.key
+/traefik/traefik.crt

conf/docker-compose/README.md

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+# docker-compose version of Dataverse
+
+## Requirements
+
+* [docker-compose](https://docs.docker.com/compose/)
+* [Docker](https://docker.com) (or some other supported container engine)
+* [Maven](https://maven.apache.org/)
+
+## Setup
+
+Edit the `.env` file as needed.  Make sure to properly secure it in terms of file permissions.
+
+Edit `./seaweedfs/config.json` and enter your [credential keys](https://github.com/chrislusf/seaweedfs/wiki/Amazon-S3-API#static-configuration) for s3 storage.
+
+If you're running locally and don't have a key, you'll
+need to generate it yourself with something like Git Bash.  Make sure
+[Posix to Windows path conversion](https://github.com/git-for-windows/git/issues/577#issuecomment-166118846) doesn't
+take place with the forward slashes using `MSYS_NO_PATHCONV=1` if you're on Windows.
+
+```shell
+MSYS_NO_PATHCONV=1 openssl req -x509 -nodes -days 4096 -newkey rsa:4096 -out traefik.crt -keyout traefik.key -subj "/C=US/ST=New Mexico/L=ABQ/O=Local/CN=127.0.0.1" -addext "subjectAltName = IP:127.0.0.1"
+```
+
+Or grab your public/private keys from your sysadmin or provider and rename them to `traefik.key` and `traefik.crt`.
+
+Then copy the `traefik.key` and `traefik.crt` files into the `traefik` folder.
+
+## Building
+
+Run `build-containers.sh`.  This will copy a few files and setup the build environment before
+running maven builds for each of the container services.
+
+Pull and build the Docker containers
+
+```shell
+# this uses Compose v2, if you're on an older version you may
+# need to change this call to docker-compose
+docker compose pull
+docker compose build
+```
+
+## Deploying
+
+```shell
+docker-compose up -d
+```
+
+Note that this can take a couple minutes to start up.  Wait until it shows `healthy` as the status.
+
+For the bind mounts (see `docker-compose.yml`) you may need to set the permissions
+on those folders `*-bind` so they can be written from within the containers.  Alternatively,
+you can create local users or do UID/GID mappings.
+
+```shell
+docker ps
+```
+
+Then go to the following URL in your browser:
+
+[https://localhost](https://localhost)
+
+Default credentials for login are:
+
+* username: `dataverseAdmin`
+* password: `admin`
+
+Make sure to change this password right away.
+
+## How It Works
+
+* Builds a copy of the `.war` deployable code from source
+* Stands up various services and pieces needed:
+  * seaweedfs - for s3 storage
+  * traefik - reverse proxy, HTTP is re-routed automatically to HTTPS
+  * postgres - database backend
+  * solr - text indexing database
+  * rserve - R server for running R commands
+  * dataverse - the main Dataverse web application
+* sets up two storage options, one is the default `<id>=files` for local storage
+and the other is `<id>=s3`for s3 storage
+
+## Uninstall / Teardown
+
+```shell
+docker-compose down -v
+```
+
+## Development References
+
+There are many community led efforts to utilize containers, Kubernetes, and more to help automate
+and setup Dataverse.
+
+* [https://github.com/fzappa/rocky-dataverse/blob/main/rocky-dataverse.sh](https://github.com/fzappa/rocky-dataverse/blob/main/rocky-dataverse.sh)
+* [https://github.com/IQSS/dataverse/tree/develop/conf/docker-aio](https://github.com/IQSS/dataverse/tree/develop/conf/docker-aio)
+* [https://github.com/gdcc/dataverse-kubernetes/blob/develop/docker-compose.yaml](https://github.com/gdcc/dataverse-kubernetes/blob/develop/docker-compose.yaml)
+* [https://github.com/gdcc/dataverse-kubernetes](https://github.com/gdcc/dataverse-kubernetes)
+* [https://github.com/EOSC-synergy/dataverse-kubernetes](https://github.com/EOSC-synergy/dataverse-kubernetes)
+* [https://github.com/IQSS/dataverse-docker](https://github.com/IQSS/dataverse-docker)

conf/docker-compose/build-containers.sh

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+#!/bin/bash
+
+# Solr XML schema files
+cp ../solr/8.11.1/*.xml ../../modules/container-solr/src/main/docker/
+
+# go back to git root directory
+cd ../../
+
+# prep Solr beforehand so it has the appropriate permissions
+# 8983 is the UID hard-coded in the stock Solr Dockerfile
+mkdir -p ./conf/docker-compose/solr-bind/
+sudo chown 8983:8983 ./conf/docker-compose/solr-bind/
+
+# copy sourcecode and installer files over
+cp pom.xml modules/container-dataverse/src/main/docker/
+cp -R ./src/ modules/container-dataverse/src/main/docker/src/
+cp -R ./modules/dataverse-parent/ modules/container-dataverse/src/main/docker/modules/dataverse-parent/
+cp -R ./scripts/ modules/container-dataverse/src/main/docker/scripts/
+cp -R ./conf/ modules/container-dataverse/src/main/docker/conf/
+cp -R ./local_lib/ modules/container-dataverse/src/main/docker/local_lib/
+
+# build out each of the images
+mvn -Pct -f modules/container-base clean install -Dmaven.test.skip -Ddocker.verbose=true
+mvn -Pct -f modules/container-postgresql clean install -Dmaven.test.skip -Ddocker.verbose=true
+mvn -Pct -f modules/container-rserve clean install -Dmaven.test.skip -Ddocker.verbose=true
+mvn -Pct -f modules/container-seaweedfs clean install -Dmaven.test.skip -Ddocker.verbose=true
+mvn -Pct -f modules/container-solr clean install -Dmaven.test.skip -Ddocker.verbose=true
+mvn -Pct -f modules/container-traefik clean install -Dmaven.test.skip -Ddocker.verbose=true
+mvn -Pct -f modules/container-dataverse clean install -Dmaven.test.skip -Ddocker.verbose=true

conf/docker-compose/dataverse/config

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+[default]
+region = us-east-1
+s3 =
+  signature_version = s3v4

conf/docker-compose/dataverse/credentials

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+[default]
+aws_access_key_id = secret
+aws_secret_access_key = secret

conf/docker-compose/dataverse/startup.sh

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+#!/bin/bash
+
+export dpkgArch="$(dpkg --print-architecture)"
+export JAVA_HOME="/usr/lib/jvm/java-11-openjdk-${dpkgArch}"
+
+# create the config file that has all our environment settings
+
+echo -e "
+[glassfish]
+HOST_DNS_ADDRESS=${HOST_DNS_ADDRESS}
+GLASSFISH_USER = ${GLASSFISH_USER}
+GLASSFISH_DIRECTORY = /usr/local/payara5/
+GLASSFISH_ADMIN_USER = ${GLASSFISH_ADMIN_USER}
+GLASSFISH_ADMIN_PASSWORD = ${GLASSFISH_ADMIN_PASSWORD}
+GLASSFISH_HEAP = 2048
+GLASSFISH_REQUEST_TIMEOUT = 1800
+
+[database]
+POSTGRES_ADMIN_PASSWORD=${POSTGRES_ADMIN_PASSWORD}
+POSTGRES_SERVER=${POSTGRES_SERVER}
+POSTGRES_PORT=${POSTGRES_PORT}
+POSTGRES_DATABASE=${POSTGRES_DATABASE}
+POSTGRES_PASSWORD=${POSTGRES_PASSWORD}
+POSTGRES_USER=${POSTGRES_USER}
+
+[system]
+ADMIN_EMAIL=${ADMIN_EMAIL}
+MAIL_SERVER=${MAIL_SERVER}
+SOLR_LOCATION=${SOLR_LOCATION}
+
+[rserve]
+RSERVE_HOST=${RSERVE_HOST}
+RSERVE_PORT=${RSERVE_PORT}
+RSERVE_USER=${RSERVE_USER}
+RSERVE_PASSWORD=${RSERVE_PASSWORD}
+
+[doi]
+DOI_USERNAME = dataciteuser
+DOI_PASSWORD = datacitepassword
+DOI_BASEURL = https://mds.test.datacite.org
+DOI_DATACITERESTAPIURL = https://api.test.datacite.org
+" > /dataverse/scripts/installer/default.config
+
+# https://github.com/poikilotherm/dataverse/blob/ct-mvn-mod/modules/container-base/src/main/docker/Dockerfile
+# https://guides.dataverse.org/en/latest/installation/config.html#amazon-s3-storage-or-compatible
+# set s3 storage settings
+if ! grep -q "Ddataverse.files.s3.type=s3" "/usr/local/payara5/glassfish/domains/domain1/config/domain.xml"; then
+  # use : as delimiter
+  sed -i "s:</java-config>:<jvm-options>-Ddataverse.files.s3.type=s3</jvm-options>\n</java-config>:" /usr/local/payara5/glassfish/domains/domain1/config/domain.xml
+  sed -i "s:</java-config>:<jvm-options>-Ddataverse.files.s3.label=s3</jvm-options>\n</java-config>:" /usr/local/payara5/glassfish/domains/domain1/config/domain.xml
+  sed -i "s:</java-config>:<jvm-options>-Ddataverse.files.s3.access-key=${S3_ACCESS_KEY}</jvm-options>\n</java-config>:" /usr/local/payara5/glassfish/domains/domain1/config/domain.xml
+  sed -i "s:</java-config>:<jvm-options>-Ddataverse.files.s3.secret-key=${S3_SECRET_KEY}</jvm-options>\n</java-config>:" /usr/local/payara5/glassfish/domains/domain1/config/domain.xml
+  sed -i "s:</java-config>:<jvm-options>-Ddataverse.files.s3.custom-endpoint-url=http\:\/\/seaweedfs\:8333</jvm-options>\n</java-config>:" /usr/local/payara5/glassfish/domains/domain1/config/domain.xml
+  # keep this as dataverse as it's hardcoded elsewhere
+  sed -i "s:</java-config>:<jvm-options>-Ddataverse.files.s3.bucket-name=dataverse</jvm-options>\n</java-config>:" /usr/local/payara5/glassfish/domains/domain1/config/domain.xml
+  sed -i "s:</java-config>:<jvm-options>-Ddataverse.files.s3.custom-endpoint-region=us-east-1</jvm-options>\n</java-config>:" /usr/local/payara5/glassfish/domains/domain1/config/domain.xml
+  # # Use path style buckets instead of subdomains
+  sed -i "s:</java-config>:<jvm-options>-Ddataverse.files.s3.path-style-access=true</jvm-options>\n</java-config>:" /usr/local/payara5/glassfish/domains/domain1/config/domain.xml
+fi
+
+cd /dataverse/scripts/installer/
+
+# the installer needs to run from within the directory, it cannot be run from / for example
+# this can take some time to run, be patient
+python3 install.py --noninteractive --force
+
+# check if we should disable DOI validation
+if [[ ! -z "${DISABLE_DOI}" ]] && [[ "true" = "${DISABLE_DOI}" ]]; then
+  echo "Disabling DOI validation"
+  curl -X PUT -d FAKE http://localhost:8080/api/admin/settings/:DoiProvider
+fi
+
+# check if we should exclude emails from exports
+if [[ ! -z "${EXCLUDE_EMAIL_EXPORTS}" ]] && [[ "true" = "${EXCLUDE_EMAIL_EXPORTS}" ]]; then
+  echo "Excluding emails in exports"
+  curl -X PUT -d true http://localhost:8080/api/admin/settings/:ExcludeEmailFromExport
+fi
+
+# create an empty s3 bucket in seaweedfs if it doesn't already exist
+curl -X POST "http://seaweedfs:8888/buckets/"
+curl -X POST "http://seaweedfs:8888/buckets/dataverse/"
+
+wait-for-it localhost:8080 -- tail -f /usr/local/payara5/glassfish/domains/domain1/logs/server.log

conf/docker-compose/postgres/Dockerfile

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+# https://hub.docker.com/_/postgres
+FROM postgres:14
+
+RUN apt-get update && \
+    apt-get -y upgrade && \
+    rm -rf /var/lib/apt/lists/*