.gitignore

@@ -10,3 +10,5 @@ kubernetes/test-postgres-deployment.yaml
 kubernetes/secrets*
 clarin-dev_eurac_edu.key
 clarin_eurac_edu.key
+**/.release
+backup/

CHANGELOG.md

@@ -6,11 +6,76 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+### Added
+### Changed
+- Bump DSPACE_APP_VERSION
+
+### Removed
+### Fixed
+- [nginx] `easy_install supervisor` fails
+
+
+## [1.4.0] - 2021-01
 
 ### Added
+- Use dspace-app image from gitlab.inf.unibz.it:4567/commul/docker/clarin-dspace/dspace-app/
+- Test set-up for #59
+- Debug output for cron-hack in `entrypoint.sh`
+- CephFS backend for clarin-dspace:{dspace,tomcat,shibboleth}:log
+
 ### Changed
+- DEPLOYMENT.md
+- set `lr.reserve.pid.on.start = true` to show users the handle of the finished submission
+- Use dsapce-app image 2020.02.1:1.1
+- Rm apt cache after apt-get update+install
+- Rebuild Postgres image with latest 9.6
+- Avoid tomcat start/kill/restart-cycle at startup
+
 ### Removed
+- Use of https://github.com/ufal/lindat-aai-discovery
+
 ### Fixed
+- #60
+- Changed branch names during git clone/checkout
+- [Open redirect vulnerability](https://wiki.shibboleth.net/confluence/display/SP3/Sessions)
+
+
+## [1.3.5] - 2020-01-22
+
+### Added
+- org.label-schema LABELs for version, build-date, vcs-url in docker images
+- explicit CATALINA_PID path
+- build and install Apache Tomcat Native Library
+
+### Changed
+- bump tomcat to latest 8.0 (=8.0.53) version
+- increase java memory settings for tomcat (just-in-case)
+- use regular catalina.sh start/stop/run commands (which in turn considers setenv.sh)
+- ContacPerson(s) in SP definition
+
+### Removed
+- own catalina.sh (use dist versions)
+- tomcat8 init.d script (wasn't used)
+
+### Fixed
+- (automatic redirects to) https://clarin.eurac.edu:8443/... not working
+    
+
+## [1.3.4] - 2019-10-14
+
+### Changed
+
+- use kube-lego for TLS certs for clarin(-dev).eurac.edu
+- disable k8s-internal secure TLS communication: getting rid of the necessity
+  to (re-)create valid/self-signed certs
+  Note: using HTTP over port 443 for internal communication (Shibboleth mishap)
+- add IdP metadata from CLARIN server later in docker build build
+- Some changes to the liveness probe / "cronjobs" (see #60)
+
+### Fixed
+
+- #62
+
 
 ## [1.3.3] - 2019-07-23
 
@@ -18,6 +83,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - adapted healthcheck "cronjob" to force exit in case it hangs for some reason (#60)
 
+
 ## [1.3.2] - 2019-06-27
 
 ### Added
@@ -38,6 +104,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - fixed get URL for xerces
 - IdP metadata from CLARIN are now downloaded during Docker build and not only once the container is running
 
+
 ## [1.3] - 2018-09-05
 
 ### Added
@@ -54,12 +121,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Made sure that tomcat is stopped with `-force` in entrypoint script to ensure that only one instance is running
 
+
 ## [1.2.2] - 2018-08-31
 
 ### Fixed
 
 - Changed the DSpace config to use the production handle prefix and not the staging one
 
+
 ## [1.2] - 2018-08-27
 
 ### Added
@@ -84,6 +153,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Shibboleth build script now uses fixed version numbers instead of latest
 - Super short session timeout will no longer happen (#44)
 
+
 ## [1.1] - 2018-06-15
 
 ### Added
@@ -105,7 +175,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 This is the first release. It all starts here.
 
-[Unreleased]:https://gitlab.inf.unibz.it/commul/docker/clarin-dspace/compare/v1.3.3...HEAD
+[Unreleased]:https://gitlab.inf.unibz.it/commul/docker/clarin-dspace/compare/v1.4.0...HEAD
+[1.4.0]: https://gitlab.inf.unibz.it/commul/docker/clarin-dspace/compare/v1.3.5...v1.4.0
+[1.3.5]: https://gitlab.inf.unibz.it/commul/docker/clarin-dspace/compare/v1.3.4...v1.3.5
+[1.3.4]: https://gitlab.inf.unibz.it/commul/docker/clarin-dspace/compare/v1.3.3...v1.3.4 
 [1.3.3]: https://gitlab.inf.unibz.it/commul/docker/clarin-dspace/compare/v1.3.2...v1.3.3 
 [1.3.2]: https://gitlab.inf.unibz.it/commul/docker/clarin-dspace/compare/v1.3.1...v1.3.2 
 [1.3.1]: https://gitlab.inf.unibz.it/commul/docker/clarin-dspace/compare/v1.3...v1.3.1

DEPLOYMENT.md

 # Step by Step deployment guide
 
-- [ ] Edit CHANGELOG.md and add a new section for the upcoming release
-- [ ] Commit to master to make sure that the master branch is clean and all commits are pushed to origin
-- [ ] `git checkout stable`
-- [ ] `git merge --no-ff master`
-- [ ] (Optional) You can now deploy stable to dspace-dev (`./release.sh $VERSION_NUMBER-RC-$RCNUMBER`)
-- [ ] Make sure that the stable branch is clean and all commits are pushed to origin
-- [ ] `git checkout production`
-- [ ] `git checkout -b v$VERSION_NUMBER $HASHID -- .`
-      The $HASHID being the commit were the last merge from stable happened (before clarindev2clarin.sh changes were committed)
-- [ ] `git merge --no-ff stable`
-- [ ] resolve conflicts (though there shouldn't be any) and commit
-- [ ] Change the version number and the registry branch of the images in all deployment yaml files
-- [ ] Run the clarindev2clarin.sh script
-- [ ] `git commit -a `
-- [ ] `git checkout production`
-- [ ] `git merge v1.3-$VERSION_NUMBER`
-- [ ] resolve conflicts and commit
-- [ ] `git tag -a $VERSION_NUMBER -s (-u $GPG_ID_HASH)` defaults to your default GPG key
-- [ ] `git branch -d $VERSION_NUMBER`
-- [ ] `git push --all`
-- [ ] `git push --tags`
-- [ ] `cd dockerfiles`
-- [ ] `./release.sh $VERSION_NUMBER production`
-- [ ] `cd ../kubernetes`
-- [ ] `./stop_kube.sh`
-- [ ] `./start_kube.sh`
-- [ ] `git checkout master`
+- Development
+  - Edit CHANGELOG.md
+    - [ ] Rename [Unreleased] to [$VERSION]
+    - [ ] Reintroduce [Unreleased]
+    - [ ] Fix [Unreleased] and add [$VERSION] named link at the end of CHANGELOG.md
+
+  - [ ] (Optional) Bump versions of
+        - clarin-dspace-app: `DSPACE_APP_VERSION` in docker/clarin-dspace/dockerfiles/Earthfile
+        - lindat-common: settings in docker/clarin-dspace/dockerfiles/commul-customization/variable.makefile
+
+  - Commit to master to make sure that the master branch is clean and all
+    commits are pushed to origin
+    - [ ] `git commit -m"Bump version to $VERSION"`
+    - [ ] `git tag X.Y.Z-rcR`
+    - [ ] `./release.sh`
+    - [ ] # Use the `sed` command at the end to adapt the k8s files
+          # ./start- ... ./stop- or kubectl edit 
+
+- Prepare a release
+  - Make a copy of DEPLOYMENT.md
+    - [ ] cp DEPLOYMENT.md DEPLOYMENT-$VERSION.md
+  
+  - [ ] Check versions are non-rc candidates:
+        - clarin-dspace-app: `DSPACE_APP_VERSION` in docker/clarin-dspace/dockerfiles/Earthfile
+        - lindat-common: settings in docker/clarin-dspace/dockerfiles/commul-customization/variable.makefile
+
+  - [ ] Check CHANGELOG.md has up-to-date edits
+
+  - Check that the master branch is clean and all commits are pushed to origin
+    - [ ] git status
+    - [ ] git push
+ 
+  - Merge changes into stable
+    - [ ] git checkout stable
+    - [ ] git merge --no-ff master
+
+  - [ ] (Optional) You can now deploy stable to dspace-dev
+        This depends on your workflow, for example, you man have already tested
+        from master. In any case, `./release.sh` picks up the tag from `git tag`,
+        i.e. *before* every `./release.sh` there should be a `git tag`. 
+        During testing this `tag` should always be of type `X.Y.Z.-rcR`.
+
+        ```
+        ./release.sh
+        # Use the `sed` command at the end to adapt the k8s files
+        # ./start- ... ./stop- or kubectl edit 
+        ```
+
+  - Check that the stable branch is clean and all commits are pushed to origin
+    - [ ] git status
+    - [ ] git push
+
+  - Create a new version branch for this release
+    - [ ] git checkout -b ver-$VERSION
+
+  - Adapt clarin-dev and dspace-dev & commit changes, tag version, make a
+    release, and push changes
+    - [ ] ./clarindev2clarin.sh
+    - [ ] git commit -m"Add clarindev2clarin.sh changes"
+    - [ ] git tag -a $VERSION -s (-u $GPG_ID_HASH)
+          "
+          Tag version $VERSION 
+
+          Copy&Paste relevant CHANGELOG.md
+          " 
+      - [ ] Make sure to remove '#' for 'TITLE lines' from commit message
+          (otherwise, they will be ignored)
+    - [ ] ./release.sh
+    - [ ] # Use the `sed` command at the end to adapt the k8s files
+    - [ ] git commit -m"Bump version to $VERSION" 
+    - [ ] git push origin ver-$VERSION
+ 
+  - Merge ver-$VERSION into production 
+    - [ ] git checkout production
+    - [ ] git merge --strategy-option=theirs --squash ver-$VERSION
+          "
+          Squashing commits of branch 'v$VERSION' into production
+
+          Commits
+          ...
+          "
+    - [ ] git push origin production
+    - [ ] git push --tags
+
+  - Deploy production to --namespace=dspace and go back to master
+    - [ ] cd ../kubernetes
+    - [ ] ./stop_kube.sh
+    - [ ] ./start_kube.sh
+    - [ ] git checkout master

clarin-dev2clarin.sh

 #!/bin/bash
 
-# outside the docker
-perl -pi -e 's/clarin-dev/clarin/g' dockerfiles/commul-customization/shibboleth2.xml
+# config files
+perl -pi -e 's/clarin-dev/clarin/g' dockerfiles/nginx/shibboleth2.xml
 perl -pi -e 's/clarin-dev/clarin/g' dockerfiles/commul-customization/local.properties
-perl -pi -e 's/clarin-dev/clarin/g' dockerfiles/commul-customization/default-ssl
+perl -pi -e 's/clarin-dev/clarin/g' dockerfiles/nginx/nginx.default.conf
+perl -pi -e 's/clarin-dev/clarin/g' dockerfiles/nginx/Dockerfile
 
-perl -pi -e 's/clarin-dev/clarin/g' dockerfiles/commul-customization/aai.js
-perl -pi -e 's/clarin-dev/clarin/g' dockerfiles/commul-customization/aai_config.js
-perl -pi -e 's/clarin-dev/clarin/g' dockerfiles/commul-customization/aa-statistics.php
-perl -pi -e 's/clarin-dev/clarin/g' dockerfiles/commul-customization/clarin.eurac.edu.template.metadata.xml
-perl -pi -e 's/clarin-dev/clarin/g' dockerfiles/commul-customization/webpage/index.html
-perl -pi -e 's/clarin-dev/clarin/g' dockerfiles/Dockerfile.nginx
+perl -pi -e 's/clarin-dev/clarin/g' dockerfiles/nginx/aa-statistics.php
+perl -pi -e 's/clarin-dev/clarin/g' dockerfiles/nginx/clarin.eurac.edu.template.metadata.xml
+perl -pi -e 's/clarin-dev/clarin/g' dockerfiles/nginx/html/index.html
 
-# adapt URL and prefix for handle server
+# healthcheck id
+sed -i 's/24a81cdc-2906-4faa-89b3-0d57541abef6/0e116e4c-39b4-46e8-a0f1-20bf952b4c7b/' dockerfiles/commul-customization/entrypoint.sh
+
+# URL and prefix for handle server
 perl -pi -e 's/20.500.12084/20.500.12124/g' dockerfiles/commul-customization/config.dct
 perl -pi -e 's/20.500.12084/20.500.12124/g' dockerfiles/commul-customization/local.properties
 
-# adapt shib SP ID
-perl -pi -e 's/_5d15d5a81bc952da1d34986ebc7713c0d5c9ea61/_5d15d5a81bc952da1d34986ebc7713c0d5c9ea91/g' dockerfiles/commul-customization/clarin.eurac.edu.template.metadata.xml
-
-# adapt hostname in docker-compose
+# hostname in docker-compose
 perl -pi -e 's/clarin-dev/clarin/g' dockerfiles/docker-compose.yml
 echo "Modified all files to point to clarin.eurac.edu instead of clarin-dev.eurac.edu."
 
-# adapt namespace in kubernetes yaml files
+# namespace in kubernetes yaml files
 sed -i 's/dspace-dev/dspace/' kubernetes/*.yaml
 perl -pi -e 's/clarin-dev/clarin/g' kubernetes/{dspace-ingress,dspace-deployment,nginx-deployment}.yaml
+echo "Modified kubernetes/ to point to --ns=dsapce instead of --ns=dsapce-dev and clarin.eurac.edu instead of clarin-dev.eurac.edu."

difference-between-clarin-dev-and-clarin.txt

-
-Lindat Production workflow
-
-nach Schritt './password_mod.sh'
-
-./clarin-dev2clarin.sh
-
-nach Schritt 'make new_deploy'
-grep -rl clarin-dev /opt/lindat-common/public/ | xargs -i perl -pi -e 's/clarin-dev/clarin/g' {}
-
-
-

dockerfiles/.dockerignore

+Dockerfile.*
+release.sh

dockerfiles/Dockerfile.dspace → dockerfiles/Dockerfile

-############################################################
+##############################################################################
 # Dockerfile to build LINDAT Dspace container images
 # Based on Ubuntu
-############################################################
+##############################################################################
+ARG DSPACE_APP_VERSION
+ARG UBUNTU_VERSION=16.04
 
-FROM ubuntu:16.04
-LABEL maintainer="Alexander König <Alexander.Koenig@eurac.edu>"
+FROM gitlab.inf.unibz.it:4567/commul/docker/clarin-dspace/dspace-app/2020.02.1:$DSPACE_APP_VERSION as dspace-app
 
-# install cpanm and dependencies
-RUN apt-get update \
-&&  apt-get -y upgrade \
-&&  apt-get -y install make gcc wget cpanminus
+FROM ubuntu:$UBUNTU_VERSION
+ARG UBUNTU_VERSION
+
+LABEL author="Alexander König <Alexander.Koenig@eurac.edu>, \
+Egon W. Stemle <egon.stemle@eurac.edu>"
+LABEL maintainer="Egon W. Stemle <egon.stemle@eurac.edu>"
 
-RUN cpanm -n File::Spec::Functions
-RUN cpanm Term::ReadLine
+ENV TOMCAT_VERSION="8.0.53"
+ENV TOMCAT_SHA512="cd8a4e48a629a2f2bb4ce6b101ebcce41da52b506064396ec1b2915c0b0d8d82123091242f2929a649bcd8b65ecf6cd1ab9c7d90ac0e261821097ab6fbe22df9 *apache-tomcat-8.0.53.tar.gz"
+# https://archive.apache.org/dist/tomcat/tomcat-8/v8.0.53/bin/apache-tomcat-8.0.53.tar.gz.sha512
 
+ENV TERM linux
+# APT(-GET) tweaks
+# Set some sane defaults for apt inside docker
+ENV DEBIAN_FRONTEND=noninteractive
+COPY apt.local.conf /etc/apt/apt.conf.d/99local.conf
+RUN apt-get update && \
+    apt-get upgrade && \
+    rm -rf /var/lib/apt/lists/*
+
+# install cpanm and dependencies
 # install jdk, ant, psql, mvn, make, libxml, xsltproc, zip, wget
-RUN apt-get update && apt-get -y install openjdk-8-jdk ant maven libxml2-utils xsltproc unzip curl git
+RUN apt-get update && apt-get install \
+    unzip curl wget git \
+    make gcc \
+    cpanminus \
+    openjdk-8-jdk ant maven libxml2-utils xsltproc \
+    libapr1-dev && \
+    rm -rf /var/lib/apt/lists/*
 
-# install convenience apps for debug purposes (vim and jsbeautifier)
-RUN apt-get update && apt-get -y install vim less python-pip
-RUN pip install --upgrade pip
-RUN pip install jsbeautifier
-COPY commul-customization/__init__.py /usr/local/lib/python2.7/dist-packages/jsbeautifier/
+RUN cpanm -n File::Spec::Functions && \
+    cpanm Term::ReadLine
 
 # set up a proper locale
-RUN apt-get -y install locales
+RUN apt-get update && apt-get install locales && rm -rf /var/lib/apt/lists/*
 RUN locale-gen en_US.UTF-8
-COPY commul-customization/default_locale /etc/default/locale
+COPY default_locale /etc/default/locale
 RUN chmod 0755 /etc/default/locale
 
 ENV LC_ALL=en_US.UTF-8
 ENV LANG=en_US.UTF-8
 ENV LANGUAGE=en_US.UTF-8
 
-# build tomcat 8.0.35, version recommended by LINDAT
-RUN wget -O /tmp/apache-tomcat-8.0.52.tar.gz https://archive.apache.org/dist/tomcat/tomcat-8/v8.0.52/bin/apache-tomcat-8.0.52.tar.gz
-RUN mkdir /opt/tomcat8
-RUN tar xvzf /tmp/apache-tomcat-8.0.52.tar.gz -C /opt/tomcat8/ --strip-components=1
-RUN groupadd tomcat8
-RUN useradd -s /bin/false -g tomcat8 -d /opt/tomcat8/ tomcat8
-
-# change permissions
-RUN chown -R tomcat8:tomcat8 /opt/tomcat8
-# copy config files etc. (init script,catalina.sh,setenv.sh,server.xml
-COPY commul-customization/tomcat8 /etc/init.d/
-RUN chmod a+x /etc/init.d/tomcat8
-COPY commul-customization/catalina.sh /opt/tomcat8/bin/
-COPY commul-customization/setenv.sh /opt/tomcat8/bin/
+### Install Tomcat
+#
+# build tomcat $TOMCAT_VERSION (> 8.0.35), version recommended by LINDAT
+RUN wget -O /tmp/apache-tomcat-$TOMCAT_VERSION.tar.gz \
+        https://archive.apache.org/dist/tomcat/tomcat-8/v$TOMCAT_VERSION/bin/apache-tomcat-$TOMCAT_VERSION.tar.gz
+WORKDIR /tmp
+
+# checksum check the download
+RUN echo "$TOMCAT_SHA512" > /tmp/apache-tomcat.sha512 && \
+    sha512sum --check apache-tomcat.sha512
+
+RUN mkdir /opt/tomcat8 && \
+    tar xzf /tmp/apache-tomcat-$TOMCAT_VERSION.tar.gz \
+        -C /opt/tomcat8/ \
+        --strip-components=1 && \
+    groupadd tomcat8 && \
+    useradd -s /bin/false -g tomcat8 -d /opt/tomcat8/ tomcat8 && \
+    chown -R tomcat8:tomcat8 /opt/tomcat8
+
+# Install Apache Tomcat Native
+# prerequisites: libopenssl, libapr1, jdk
+RUN mkdir /opt/tomcat8/bin/tomcat-native && \
+    tar xzf /opt/tomcat8/bin/tomcat-native.tar.gz \
+        -C /opt/tomcat8/bin/tomcat-native \
+        --strip-components=1 && \
+    cd /opt/tomcat8/bin/tomcat-native/native && \
+    ./configure \
+        --with-java-home=/usr/lib/jvm/java-8-openjdk-amd64/ \
+        --prefix=/usr/local/ && \
+    make && make install
+
+# copy config files etc. (setenv.sh,server.xml)
+COPY commul-customization/tomcat-setenv.sh /opt/tomcat8/bin/setenv.sh
 COPY commul-customization/tomcat-server.xml /opt/tomcat8/conf/server.xml
 
 
-# install Dspace
-# pre-fetch maven dependencies
-RUN git clone https://github.com/commul/clarin-dspace.git -b commul-custom /opt/repository/sources/dspace
-WORKDIR /opt/repository/sources/dspace
-RUN mvn compile
-#COPY commul-customization/dspace-pom.xml /tmp/pom.xml
-#WORKDIR /tmp/
-## RUN mvn dependency:resolve
-#RUN mvn -B -T 4 dependency:copy-dependencies dependency:resolve-plugins dependency:go-offline  clean
-# all files could be copied into a /tmp folder within the container first (maybe that could be mounted?); see also dspace-entrypoint.sh
-# this checks if there was a new commit since the last build
-ADD https://api.github.com/repos/commul/clarin-dspace/git/refs/heads/commul-custom /tmp/version.json
-RUN git pull
+### Install Dspace
+COPY --from=dspace-app /app /opt/repository/sources/dspace
+
 WORKDIR /opt/repository/sources/dspace/utilities/project_helpers
 RUN ./setup.sh /opt/repository/workspace
 COPY commul-customization/variable.makefile /opt/repository/workspace/config/variable.makefile
-# COPY commul-customization/dspace.cfg /opt/repository/sources/dspace/dspace/config/dspace.cfg
 
 # install python modules: magic dateutil, lxml
-RUN apt-get update && apt-get install -y python-magic python-dateutil python-lxml
+# install poppler-utils for dspace.cfg: filter.plugins = PDF Text Extractor
+RUN apt-get update && apt-get install \
+    python-magic python-dateutil python-lxml poppler-utils && \
+    rm -rf /var/lib/apt/lists/*
 
 # copy over configs and startup scripts
 COPY commul-customization/start_stack.sh /opt/repository/workspace/scripts/
@@ -86,9 +114,6 @@ RUN make new_deploy
 
 # DEBUG: to be able to access tomcat manager through browser
 # COPY commul-customization/tomcat-users.xml /opt/tomcat8/conf/
-# adapt some config files
-RUN perl -pi -e 's/#useProxies = true/useProxies = true/' /opt/lindat-dspace/installation/config/dspace.cfg
-RUN perl -pi -e 's#    (?s).*org.apache.catalina.connector.ClientAbortException: java.io.IOException: Broken pipe.*#    (?s).*org.apache.catalina.connector.ClientAbortException: java.io.IOException: Broken pipe.*,\\\n    (?s).*user-agent=.kube-probe.*#' /opt/lindat-dspace/installation/config/modules/lr.cfg
 
 # set up handle server
 COPY commul-customization/hdl-setup.tmp /tmp/
@@ -99,6 +124,12 @@ RUN cp /opt/repository/workspace/config/etc/init.d/handle-server /etc/init.d/
 RUN chmod +x /etc/init.d/handle-server
 RUN perl -pi -e 's#DSPACE_INSTALLATION_DIRECTORY=#DSPACE_INSTALLATION_DIRECTORY=/opt/lindat-dspace/installation#' /etc/default/handle-server
 
+# Install ping for livenessProbe
+RUN apt-get update && apt-get install iputils-ping && rm -rf /var/lib/apt/lists/*
+
+# Make directory to share shibboleth log files for analytics
+RUN mkdir -p /opt/shibboleth-sp-fastcgi/var/log/shibboleth
+
 # copy entrypoint script and start
 COPY commul-customization/entrypoint.sh /usr/bin/entrypoint.sh
 RUN chmod u+x /usr/bin/entrypoint.sh

dockerfiles/Dockerfile.handle

-############################################################
-# Dockerfile to build a handle server
-# Based on Ubuntu
-############################################################
-
-FROM ubuntu
-LABEL maintainer="Alexander König <Alexander.Koenig@eurac.edu>"
-
-ENV TERM linux
-
-RUN apt-get update &&\
-	apt-get -y upgrade &&\
-	apt-get -y install openjdk-8-jdk unzip wget make cpanminus gcc
-
-# convenience packages
-RUN apt-get -y install less vim
-
-RUN cpanm Term::ReadLine
-RUN cpanm File::Spec::Functions
-
-RUN mkdir -p /hs/svr_1
-WORKDIR /hs
-RUN wget http://www.handle.net/hnr-source/hsj-8.1.1.tar.gz
-RUN tar -xzf /hs/hsj-8.1.1.tar.gz
-RUN mv hsj-8.1.1 hsj-8
-COPY commul-customization/hdl-setup.tmp /tmp/
-WORKDIR /hs/hsj-8
-RUN cat /tmp/hdl-setup.tmp | bin/hdl-setup-server /hs/svr_1/
-RUN perl -pi -e 's/YOUR_PREFIX/20.500.12084/' /hs/svr_1/config.dct
-RUN perl -pi -e 's/case_sensitive" = "no/case_sensitive" = "yes/' /hs/svr_1/config.dct
-RUN perl -i -plne 'print "    \"storage_type\" = \"CUSTOM\"\n\    \"storage_class\" = \"org.dspace.handle.HandlePlugin\"" if(/max_session/);' /hs/svr_1/config.dct
-# ENTRYPOINT ["/bin/bash"]
-CMD tail -f /hs/svr_1/config.dct

dockerfiles/Dockerfile.postgres

-FROM postgres:9.6
-LABEL maintainer="Alexander König <Alexander.Koenig@eurac.edu>"
-
-# install git
-RUN apt-get update && apt-get -y install git
-
-# copy int db script
-RUN mkdir -p /docker-entrypoint-initdb.d
-COPY commul-customization/init-dspace-dbs.sh /docker-entrypoint-initdb.d/
-RUN chmod +x /docker-entrypoint-initdb.d/*
-
-# copy over modified config file
-#COPY commul-customization/postgresql.conf /tmp/
-#COPY commul-customization/updateConfig.sh /docker-entrypoint-initdb.d/_updateConfig.sh
-
-# copy script generating utilities db
-RUN mkdir /tmp/sql/
-COPY adapt_utilities_sql.sh /tmp/sql/
-RUN /tmp/sql/adapt_utilities_sql.sh
-
-

dockerfiles/Earthfile

+# Usage: earthly --push [--no-cache] +docker
+ARG DSPACE_APP_VERSION=1.2-rc3
+
+docker-from-docker:
+    FROM DOCKERFILE --build-arg DSPACE_APP_VERSION=$DSPACE_APP_VERSION .
+
+    ARG DOCKER_BASE_URL="gitlab.inf.unibz.it:4567"
+    ARG EARTHLY_GIT_PROJECT_NAME  # https://docs.earthly.dev/earthfile/builtin-args
+    ARG GIT_PROJECT_NAME="commul/docker/clarin-dspace"
+    ARG COMMUL_REGISTRY_URL="https://gitlab.inf.unibz.it/commul/docker/clarin-dspace/container_registry/"
+    ARG LABEL_VCS_URL="https://gitlab.inf.unibz.it/commul/docker/clarin-dspace"
+
+    ARG AUTHOR="Egon W. Stemle <egon.stemle@eurac.edu>"
+    ARG MAINTAINER="Egon W. Stemle <egon.stemle@eurac.edu>"
+    LABEL author="$AUTHOR"
+    LABEL maintainer="$MAINTAINER"
+
+    # An updated VERSION ARG triggers an update of the texlive installation
+    ARG EARTHLY_TARGET_TAG
+    ARG VERSION=$EARTHLY_TARGET_TAG
+
+    ARG EARTHLY_GIT_HASH
+    ARG GIT_HASH=$EARTHLY_GIT_HASH
+    ARG EARTHLY_TARGET_TAG_DOCKER
+    ARG TARGET_TAG_DOCKER=$EARTHLY_TARGET_TAG_DOCKER
+    ARG DOCKER_URL="$DOCKER_BASE_URL/$GIT_PROJECT_NAME/dspace-bundle/dspace"
+
+    LABEL org.label-schema.schema-version="1.0" \  # http://label-schema.org/rc1/
+          org.label-schema.version="$VERSION" \
+          org.label-schema.vcs-url="$LABEL_VCS_URL" \
+          org.commul.git-hash="$GIT_HASH" \
+          org.commul.registry-url="$COMMUL_REGISTRY_URL" \
+          org.commul.docker-url="$DOCKER_URL"
+
+    RUN echo $VERSION > /tmp/release
+    SAVE ARTIFACT --keep-ts /tmp/release AS LOCAL ./.release
+
+    SAVE IMAGE dspace:latest
+    SAVE IMAGE --push "$DOCKER_URL:latest"
+    SAVE IMAGE --push "$DOCKER_URL:$VERSION"
+
+docker:
+    BUILD ./nginx/+docker
+    BUILD --build-arg DSPACE_APP_VERSION=$DSPACE_APP_VERSION ./postgres/+docker
+    BUILD --build-arg DSPACE_APP_VERSION=$DSPACE_APP_VERSION +docker-from-docker

dockerfiles/adapt_utilities_sql.sh

-#!/bin/bash
-
-git clone https://github.com/commul/clarin-dspace.git -b commul-custom /tmp/dspace
-cp /tmp/dspace/utilities/utilities.sql /tmp/sql/
-cp /tmp/dspace/utilities/license_definition.txt /tmp/sql/
-chmod -R a+w /tmp/sql/
-perl -pi -e "s#afile :utildir '/license_definition.txt'#afile '/tmp/sql/license_definition.txt'#;" /tmp/sql/utilities.sql
-#perl -pi -e 's/\$DSPACE_USER/$ENV{DSPACE_USER}/g;' /tmp/sql/utilities.sql
-rm -rf /tmp/dspace

dockerfiles/apt.local.conf

+# Set some sane defaults for docker
+APT { GET { Assume-Yes "true"; }; };
+APT { GET { Fix-Broken "true"; }; };

dockerfiles/commul-customization/aai.js

-'use strict';
-(function(window){
-  function AAI() {
-    var host = 'https://' + window.location.hostname,
-        ourEntityID = host.match("clarin-dev.eurac.edu") ? "https://clarin-dev.eurac.edu" : host;
-    this.defaults = {
-      //host : 'https://ufal-point.mff.cuni.cz',
-      host : host, //better default (useful when testing on ufal-point-dev)
-      // do not add protocol because an error will appear in the DJ dialog
-      // if you see the error, your SP is not listed among djc trusted (edugain is enough to be trusted)
-      responseUrl: window.location.protocol + '//clarin-dev.eurac.edu/aai/discojuiceDiscoveryResponse.html',
-      ourEntityID: ourEntityID + '/Shibboleth.sso/Metadata',
-      serviceName: '',
-      metadataFeed: host + '/xmlui/discojuice/feeds',
-      selector: 'a.signon', // selector for login button
-      autoInitialize: true, // auto attach DiscoJuice to DOM
-      textHelpMore: "First check you are searching under the right country.\nIf your provider is not listed, please read <a href='https://clarin-dev.eurac.edu/how-do-i-sign-up' style='text-decoration: underline; font-weight: bold;'>these instructions</a> to obtain an account."
-    };
-    this.setup = function(options) {
-      var opts = jQuery.extend({}, this.defaults, options),
-          defaultCallback = function(e) {
-            window.location = opts.host + '/Shibboleth.sso/Login?SAMLDS=1&target=' + opts.target + '&entityID=' + window.encodeURIComponent(e.entityID);
-          };
-      //console.log(opts);
-      if(!opts.target){
-        throw 'You need to set the \'target\' parameter.';
-      }
-      // call disco juice setup
-      if (!opts.autoInitialize || $(opts.selector).length > 0) {
-        if(! window.DiscoJuice ){
-          throw 'Failed to find DiscoJuice. Did you include all that is necessary?';
-        }
-        var djc = DiscoJuice.Hosted.getConfig(
-          opts.serviceName,
-          opts.ourEntityID,
-          opts.responseUrl,
-          [ ],
-          opts.host + '/Shibboleth.sso/Login?SAMLDS=1&target='+opts.target+'&entityID=');
-        djc.metadata = [opts.metadataFeed];
-        djc.subtitle = "Login via Your home institution (e.g. university)";
-        djc.textHelp = opts.textHelp;
-        djc.textHelpMore = opts.textHelpMore;
-
-        djc.inlinemetadata = typeof opts.inlinemetadata === 'object' ? opts.inlinemetadata : [];
-        djc.inlinemetadata.push({
-          'country': '_all_',
-          'entityID': 'https://idm.clarin.eu',
-          'geo': {'lat': '51.833298', 'lon': '5.866699'},
-          'title': 'Clarin.eu website account',
-          'weight': -801
-        });
-        djc.inlinemetadata.push({
-          'country': 'IT',
-          'entityID': 'https://idp.eurac.edu/idp/shibboleth',
-          'geo': {'lat': '46.494281', 'lon': '11.346842'},
-          'title': 'Eurac Research',
-          'weight': -1000
-        });
-
-        if(opts.localauth) {
-          djc.inlinemetadata.push(
-            {
-              'entityID': 'local://',
-              'auth': 'local',
-              'title': 'Local authentication',
-              'country': '_all_',
-              'geo': null,
-              'weight': 1000
-            });
-          djc.callback = function(e){
-            var auth = e.auth || null;
-            switch(auth) {
-              case 'local':
-                DiscoJuice.UI.setScreen(opts.localauth);
-                jQuery('input#login').focus();
-                break;
-              //case 'saml':
-              default:
-                defaultCallback(e);
-                break;
-            }
-          };
-        }
-
-        if (opts.callback && typeof opts.callback === 'function') {
-          djc.callback = function(e) {
-            opts.callback(e, opts, defaultCallback);
-          };
-        }
-
-        if (opts.autoInitialize) {
-          jQuery(opts.selector).DiscoJuice( djc );
-        }
-
-        return djc;
-      } //if jQuery(selector)
-    };
-  }
-
-  if (!window.aai) {
-    window.aai = new AAI();
-  }
-})(window);

dockerfiles/commul-customization/aai_config.js

-/*global jQuery */
-/*jshint globalstrict: true*/
-'use strict';
-
-jQuery(document).ready(
-    function () {
-        var opts = (function () {
-            var instance = {};
-	    instance.autoInitialize = false;
-            //if ever port is needed (eg. testing other tomcat) it should be in responseUrl and target
-            instance.port = (window.location.port === "" ? "" : ":" + window.location.port);
-            instance.host = window.location.protocol + '//' +
-                window.location.hostname;
-            instance.repoPath = jQuery("a#repository_path").attr("href");
-            if (instance.repoPath.charAt(instance.repoPath.length - 1) !== '/') {
-                instance.repoPath = instance.repoPath + '/';
-        }
-            instance.target = instance.host + instance.port + instance.repoPath;
-            //In order to use the discojuice store (improve score of used IDPs)
-            //Works only with "verified" SPs - ie. ufal-point, displays error on ufal-point-dev
-            instance.responseUrl =
-                (window.location.hostname.search("clarin-dev") >= 0) ?
-                        "" :
-                        instance.host + instance.port + instance.repoPath +
-                            "themes/UFAL/lib/html/disco-juice.html?";
-            instance.metadataFeed = instance.target + "discojuice/feeds";
-            instance.serviceName = "Eurac Research CLARIN Centre";
-            instance.localauth =
-                '<form method="post" action="' + instance.target + 'password-login"> ' +
-                    '<p>Sign in using your local account obtained from the ERCC administrator.</p>' +
-                    '<p style="margin: 5px; color: #888" ><input type="text" name="login_email" style="font-size: 160%; width: 100%" id="login" /> <label for="login">E-Mail Address</label></p>' +
-                    '<p style="margin: 5px; color: #888" ><input type="password" name="login_password" style="font-size: 160%; width: 100%" id="pass" /> <label for="pass">Password</label></p>' +
-                    '<p style="margin: 5px; color: #607890; text-decoration: underline;"><a href="' + instance.target + 'forgot">Forgot your password?</a></p>' +
-                    '<p  style="" ><input type="submit" style="margin: 20px 2px" name="submit" value="Sign in" /></p>' +
-                    '</form>';
-            instance.target = instance.target + "shibboleth-login";
-            return instance;
-    })();
-    if (!("aai" in window)) {
-            throw "Failed to find UFAL AAI object. See https://redmine.ms.mff.cuni.cz/projects/lindat-aai for more details!";
-    }
-        window.aai.setup(opts);
-    }
-); // ready

dockerfiles/commul-customization/clarin.eurac.edu.template.metadata.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<md:EntityDescriptor xmlns:md="urn:oasis:names:tc:SAML:2.0:metadata" ID="_5d15d5a81bc952da1d34986ebc7713c0d5c9ea61" entityID="https://clarin-dev.eurac.edu/Shibboleth.sso/Metadata">
-    <md:Extensions>
-        <mdattr:EntityAttributes xmlns:mdattr="urn:oasis:names:tc:SAML:metadata:attribute">
-            <saml:Attribute xmlns:saml="urn:oasis:names:tc:SAML:2.0:assertion" Name="http://macedir.org/entity-category" NameFormat="urn:oasis:names:tc:SAML:2.0:attrname-format:uri">
-                <saml:AttributeValue>http://www.geant.net/uri/dataprotection-code-of-conduct/v1</saml:AttributeValue>
-            </saml:Attribute>
-            <saml:Attribute
-                xmlns:saml="urn:oasis:names:tc:SAML:2.0:assertion"
-                Name="http://macedir.org/entity-category"
-                NameFormat="urn:oasis:names:tc:SAML:2.0:attrname-format:uri">
-                <saml:AttributeValue>http://refeds.org/category/research-and-scholarship</saml:AttributeValue>
-            </saml:Attribute>
-            <saml:Attribute 
-               xmlns:saml="urn:oasis:names:tc:SAML:2.0:assertion" Name="http://macedir.org/entity-category" NameFormat="urn:oasis:names:tc:SAML:2.0:attrname-format:uri">
-                <saml:AttributeValue>http://clarin.eu/category/clarin-member</saml:AttributeValue>
-            </saml:Attribute>
-        </mdattr:EntityAttributes>
-    </md:Extensions>
-    <md:SPSSODescriptor protocolSupportEnumeration="urn:oasis:names:tc:SAML:2.0:protocol urn:oasis:names:tc:SAML:1.1:protocol urn:oasis:names:tc:SAML:1.0:protocol">
-        <md:Extensions xmlns="urn:oasis:names:tc:SAML:2.0:metadata">
-            <mdui:UIInfo xmlns:mdui="urn:oasis:names:tc:SAML:metadata:ui">
-                <mdui:DisplayName xml:lang="en">Eurac Research CLARIN Centre</mdui:DisplayName>
-                <mdui:DisplayName xml:lang="de">Eurac Research CLARIN Centre</mdui:DisplayName>
-                <mdui:DisplayName xml:lang="it">Eurac Research CLARIN Centre</mdui:DisplayName>
-                <mdui:Description xml:lang="en">Eurac Research CLARIN Centre: Digital repository for language data</mdui:Description>
-                <mdui:Description xml:lang="de">Eurac Research CLARIN Centre: Digitales Repository für Sprachdaten</mdui:Description>
-                <mdui:Description xml:lang="it">Eurac Research CLARIN Centre: repository digitale di risorse linguistiche</mdui:Description>
-                <mdui:InformationURL xml:lang="en">https://clarin-dev.eurac.edu/repository/xmlui/page/about</mdui:InformationURL>
-                <mdui:InformationURL xml:lang="de">https://clarin-dev.eurac.edu/repository/xmlui/page/about</mdui:InformationURL>
-                <mdui:InformationURL xml:lang="it">https://clarin-dev.eurac.edu/repository/xmlui/page/about</mdui:InformationURL>
-		<mdui:Logo height="85" width="180">https://clarin-dev.eurac.edu/repository/xmlui/themes/UFAL/lib/lindat/public/img/eurac_research.svg</mdui:Logo>                    
-                <mdui:PrivacyStatementURL xml:lang="en">https://clarin-dev.eurac.edu/repository/xmlui/page/registration-privacypolicy</mdui:PrivacyStatementURL>
-                <mdui:PrivacyStatementURL xml:lang="de">https://clarin-dev.eurac.edu/repository/xmlui/page/registration-privacypolicy</mdui:PrivacyStatementURL>
-                <mdui:PrivacyStatementURL xml:lang="it">https://clarin-dev.eurac.edu/repository/xmlui/page/registration-privacypolicy</mdui:PrivacyStatementURL>
-            </mdui:UIInfo>          
-        </md:Extensions>
-        <md:AttributeConsumingService index="1">
-            <md:ServiceName xml:lang="en">Digital Repository for the CLARIN Research Infrastructure provided by Eurac Research</md:ServiceName>
-            <md:ServiceName xml:lang="de">Digitales Repository für die CLARIN-Forschungs-Infrastruktur bereitgestellt durch Eurac Research</md:ServiceName>
-            <md:ServiceName xml:lang="it">Repository Digitale per la Infrastruttura di Ricerca CLARIN erogato da Eurac Research</md:ServiceName>
-            <md:ServiceDescription xml:lang="en">Digital Repository and services related to the CLARIN-IT consortium under the CLARIN Research Infrastructure; focused in the fields of terminology and multilingualism. The repository is based at Eurac Research in South Tyrol and managed by the Institute for Applied Linguistics.</md:ServiceDescription>
-            <md:ServiceDescription xml:lang="it">Digitales Repository und Services mit Bezug zum CLARIN-IT-Consortium im Rahmen der CLARIN Forschungsinfrastruktur; mit Fokus auf den Gebieten der Terminologie und Mehrsprachigkeit. Das Repository wird von Eurac Research gehostet und dort vom Institut für Angewandte Sprachforschung betreut.</md:ServiceDescription>
-            <md:ServiceDescription xml:lang="it">Repository Digitale e servizi relativi al consorzio CLARIN-IT sotto l'Infrastruttura di Ricerca CLARIN; focalizzato nel campo della teminologia e multilinguismo. Il repository è basato a Eurac Research in Alto Adige e gestito del Istituto di Linguistica Applicata.</md:ServiceDescription>
-            <md:RequestedAttribute FriendlyName="eduPersonPrincipalName" Name="urn:oid:1.3.6.1.4.1.5923.1.1.1.6" NameFormat="urn:oasis:names:tc:SAML:2.0:attrname-format:uri" isRequired="true"/>
-            <md:RequestedAttribute FriendlyName="email" Name="urn:oid:0.9.2342.19200300.100.1.3" NameFormat="urn:oasis:names:tc:SAML:2.0:attrname-format:uri" isRequired="true"/>
-            <md:RequestedAttribute FriendlyName="cn" Name="urn:oid:2.5.4.3" NameFormat="urn:oasis:names:tc:SAML:2.0:attrname-format:uri" isRequired="false"/>
-            <md:RequestedAttribute FriendlyName="schacHomeOrganization" Name="urn:oid:1.3.6.1.4.1.25178.1.2.9" NameFormat="urn:oasis:names:tc:SAML:2.0:attrname-format:uri" isRequired="false"/>
-            <md:RequestedAttribute FriendlyName="organizationName" Name="urn:oid:2.5.4.10" NameFormat="urn:oasis:names:tc:SAML:2.0:attrname-format:uri" isRequired="false"/>
-            <md:RequestedAttribute FriendlyName="displayName" Name="urn:oid:2.16.840.1.113730.3.1.241" NameFormat="urn:oasis:names:tc:SAML:2.0:attrname-format:uri" isRequired="true"/>
-            <md:RequestedAttribute FriendlyName="eduPersonEntitlement" Name="urn:oid:1.3.6.1.4.1.5923.1.1.1.7" NameFormat="urn:oasis:names:tc:SAML:2.0:attrname-format:uri" isRequired="false"/>
-            <md:RequestedAttribute FriendlyName="eduPersonTargetedID" Name="urn:oid:1.3.6.1.4.1.5923.1.1.1.10" NameFormat="urn:oasis:names:tc:SAML:2.0:attrname-format:uri" isRequired="true"/>
-            <md:RequestedAttribute FriendlyName="eduPersonScopedAffiliation" Name="urn:oid:1.3.6.1.4.1.5923.1.1.1.9" NameFormat="urn:oasis:names:tc:SAML:2.0:attrname-format:uri" isRequired="false"/>
-        </md:AttributeConsumingService>
-    </md:SPSSODescriptor>
-    <md:Organization>
-        <md:OrganizationName xml:lang="en">Eurac Research</md:OrganizationName>
-        <md:OrganizationName xml:lang="de">Eurac Research</md:OrganizationName>
-        <md:OrganizationName xml:lang="it">Eurac Research</md:OrganizationName>
-        <md:OrganizationDisplayName xml:lang="en">Eurac Research</md:OrganizationDisplayName>
-        <md:OrganizationDisplayName xml:lang="de">Eurac Research</md:OrganizationDisplayName>
-        <md:OrganizationDisplayName xml:lang="it">Eurac Research</md:OrganizationDisplayName>    	  
-        <md:OrganizationURL xml:lang="en">http://www.eurac.edu/en</md:OrganizationURL>
-        <md:OrganizationURL xml:lang="de">http://www.eurac.edu/de</md:OrganizationURL>
-        <md:OrganizationURL xml:lang="it">http://www.eurac.edu/it</md:OrganizationURL>
-    </md:Organization>
-    <md:ContactPerson contactType="technical">
-        <md:GivenName>Alexander</md:GivenName>
-        <md:SurName>König</md:SurName>
-        <md:EmailAddress>mailto:Alexander.Koenig@eurac.edu</md:EmailAddress>
-    </md:ContactPerson>
-    <md:ContactPerson contactType="support">
-        <md:GivenName>Alexander</md:GivenName>
-        <md:SurName>König</md:SurName>
-        <md:EmailAddress>mailto:Alexander.Koenig@eurac.edu</md:EmailAddress>
-    </md:ContactPerson>
-    <md:ContactPerson contactType="administrative">
-        <md:GivenName>Andrea</md:GivenName>
-        <md:SurName>Abel</md:SurName>
-        <md:EmailAddress>mailto:Andrea.Abel@eurac.edu</md:EmailAddress>
-    </md:ContactPerson>
-</md:EntityDescriptor>

dockerfiles/commul-customization/entrypoint.sh

@@ -13,36 +13,35 @@ perl -pi -e 's/\$\{HANDLE_USER\}/$ENV{HANDLE_USER}/; s/\$\{HANDLE_PASSWORD\}/$EN
 /etc/init.d/handle-server start
 
 # initialize statistics & co
-/opt/tomcat8/bin/startup.sh
 cd /opt/repository/workspace/scripts
 make init_statistics
 
-# https://ubuntuforums.org/showthread.php?t=979694
-# Start process in the background and send its output to file descriptor 3
-exec 3< <(while (true); do
-    timeout -k 30 300 make update_oai
-    timeout -k 30 300 make update_statistics
-    timeout -k 30 300 make update_sitemap
-    timeout -k 30 300 make lift_embargos
-    timeout -k 30 300 make update_openaire_cache
-    timeout -k 30 300 make update_discovery
-    timeout -k 30 300 make send_info
-    echo "INIT DONE."
-    sleep 86400
-done)
-
-# Read the output of the process line by line until one line contains Ready
-while read line; do
-   case "$line" in
-   "INIT DONE.")
-      break
-      ;;
-   esac
-done <&3
-
-# Close the file descriptor
-exec <&3 3<&-
-/opt/tomcat8/bin/shutdown.sh -force
+# Start cron job in the background
+cron_hack(){
+    INIT="false"
+    while (true); do
+        # the first time, wait for tomcat to start...
+        [ "$INIT" = "false" ] && sleep 180 && INIT="true"
+
+        set -x
+        LOGID=$(( (LOGID+1) % 5))
+        LOG="/tmp/entrypoint.log.$LOGID"
+        echo "$LOG" > $LOG
+        timeout -k 30 300 make update_oai | tee -a $LOG
+        timeout -k 30 300 make update_statistics | tee -a $LOG
+        timeout -k 30 300 make update_sitemap | tee -a $LOG
+        timeout -k 30 300 make lift_embargos | tee -a $LOG
+        timeout -k 30 300 make update_openaire_cache | tee -a $LOG
+        timeout -k 30 300 make update_discovery | tee -a $LOG
+        timeout -k 30 300 make send_info | tee -a $LOG
+        date >> $LOG
+        echo "INIT DONE."
+        wget --no-check-certificate https://healthchecks.local.iiegn.eu/ping/24a81cdc-2906-4faa-89b3-0d57541abef6 -T 10 -t 5 -O /dev/null
+        set +x
+        sleep 86400
+    done
+}
+cron_hack &
 
 # start tomcat
 /opt/tomcat8/bin/catalina.sh run