Merge branch 'master' of gitlab.scientificnet.org:commul/dspace

This is meant to re-integrate the sfn repository and the github
repository into being the same

README.md

@@ -66,3 +66,192 @@ su  -s /bin/sh tomcat8
 cd /opt/repository/sources/dspace/utilities/project_helpers/scripts
 /etc/init.d/tomcat8 start
 ```
+
+# DSpace directory structure
+
+This is the directory structure 
+
+```
+├── clarin-dspace-docker
+│   └── commul-customization
+└── kubernetes
+    ├── helm
+    │   └── dspace
+    │       ├── charts
+    │       │   └── postgresql
+    │       │       └── templates
+    │       └── templates
+    └── yaml
+```
+
+
+* `/clarin-dspace-docker` - Docker files, copied from https://github.com/commul/clarin-dspace-docker @ 74d06d3 . **With this directory, you can build images**
+* `/kubernetes/helm` - Chart Directory. Refer to https://github.com/kubernetes/helm/blob/master/docs/charts.md#the-chart-file-structure :exclamation: **not working yet** :exclamation:
+* `/kubernetes/yaml` - Useful for tests, but helm is a more flexible approach **With this directory, you can deploy images in kubernetes cluster**
+# Introduction
+# Prerequisites
+
+* Kubernetes cluster
+
+## To interact with cluster
+
+* Kubernetes credentials
+* a working [kubectl] (https://kubernetes.io/docs/tasks/tools/install-kubectl/)
+
+## To interact with Helm server (tiller) -- Coming soon
+
+* Kubernetes credentials
+* a working [kubectl] (https://kubernetes.io/docs/tasks/tools/install-kubectl/)
+* a working [helm client] (https://docs.helm.sh/using_helm/#quickstart-guide)
+
+# How to use it
+## Workflow
+First of all, check if a docker image already exists.
+If it exist, pull, otherwise, you need to build one.
+If necessary create a [personal token](https://gitlab.scientificnet.org/profile/personal_access_tokens) and login into GitLab Registry.
+
+```console
+docker login gitlab.scientificnet.org:4567
+```
+ 
+### Use existing Docker image
+```console
+docker image ls -a gitlab.scientificnet.org:4567/commul/dspace/*
+docker pull gitlab.scientificnet.org:4567/commul/dspace/<my_image>:<my tag>
+```
+
+### Build images
+* build your docker image from `/clarin-dspace-docker` directory
+* push to `https://gitlab.scientificnet.org/commul/dspace/container_registry` 
+
+```console
+docker build -t gitlab.scientificnet.org:4567/commul/dspace/<my_image>:<my tag> -f Dockerfile.XX .
+docker push gitlab.scientificnet.org:4567/commul/dspace/<my_image>:<my tag>
+```
+
+# Installation
+This step in a "workspace preparation" and is not directly related with dspace.
+
+Provide gitlab & RBD credentials
+
+```console
+$ kubectl -n dspace-dev create -f gitlab-scientificnet-org-registry.yaml
+```
+```console
+$ kubectl -n dspace-dev create -f rbd-secret.yaml
+```
+## PostgreSQL
+To install PostgreSQL, we need some passwords, so we need Kubernetes secrets
+
+```console
+$ kubectl -n dspace-dev create -f postgresql-secret.yaml 
+secret "dspace-postgresql" created
+```
+
+```console
+$ kubectl -n dspace-dev create -f dspace-secrets.yaml 
+secret "dspace-secrets" created
+```
+
+```console
+$ kubectl -n dspace-dev get secrets
+NAME                                TYPE                                  DATA      AGE
+ceph-rbd-secret                     kubernetes.io/rbd                     1         14m
+default-token-c1pd4                 kubernetes.io/service-account-token   3         4d
+dspace-postgresql                   Opaque                                1         1h
+dspace-secrets                      Opaque                                1         1m
+gitlab-scientificnet-org-registry   kubernetes.io/dockerconfigjson        1         46m
+```
+
+
+
+Next, create a RBD Claim
+```console
+$ kubectl -n dspace-dev create -f postgresql-pvc.yaml 
+persistentvolumeclaim "dspace-postgresql" created
+
+$ kubectl -n dspace-dev get pvc
+NAME                STATUS    VOLUME                                     CAPACITY   ACCESSMODES   STORAGECLASS   AGE
+dspace-postgresql   Bound     pvc-610c358d-a518-11e7-b21c-b60483de6a40   8Gi        RWO           auto           2s
+```
+
+Ok, now we are ready to deploy our PostgreSQL!
+```console
+$ kubectl -n dspace-dev create -f postgresql.yaml 
+
+$ kubectl -n dspace-dev get po
+NAME                                 READY     STATUS              RESTARTS   AGE
+dspace-postgresql-1806947503-cj077   0/1       ContainerCreating   0          2s
+
+$ kubectl -n dspace-dev get po
+NAME                                 READY     STATUS    RESTARTS   AGE
+dspace-postgresql-1806947503-qw8q4   0/1       Running   0          9s
+
+$ kubectl -n dspace-dev get po
+NAME                                 READY     STATUS    RESTARTS   AGE
+dspace-postgresql-1806947503-qw8q4   1/1       Running   0          46s
+```
+
+We have now launched the pod but we have to wait until the pod is up before accessing it
+```console
+$ kubectl -n dspace-dev exec -it dspace-postgresql-1806947503-qw8q4 bash
+root@dspace-postgresql-1806947503-qw8q4:/#
+```
+
+Also, we can also test our PostgreSQL installation with a port forward
+```console
+$ kubectl -n dspace-dev port-forward dspace-postgresql-1806947503-qw8q4 5432:5432
+```
+now we are able to connect to localhost:5432
+![pgAdmin_connect](pgadmin_1.png)
+![pgAdmin_showTables](pgadmin_2.png)
+
+```console
+$ kubectl -n dspace-dev create -f postgresql-service.yaml
+service "dspace-postgresql" created
+```
+```console
+$ kubectl -n dspace-dev exec -it servlet env | grep POSTGRESQL
+DSPACE_POSTGRESQL_SERVICE_PORT_POSTGRESQL=5432
+DSPACE_POSTGRESQL_PORT_5432_TCP_ADDR=10.13.0.173
+DSPACE_POSTGRESQL_SERVICE_HOST=10.13.0.173
+DSPACE_POSTGRESQL_PORT_5432_TCP_PROTO=tcp
+DSPACE_POSTGRESQL_PORT_5432_TCP_PORT=5432
+DSPACE_POSTGRESQL_SERVICE_PORT=5432
+DSPACE_POSTGRESQL_PORT=tcp://10.13.0.173:5432
+DSPACE_POSTGRESQL_PORT_5432_TCP=tcp://10.13.0.173:5432
+```
+
+## DSpace
+```console
+$ kubectl -n dspace-dev create -f servlet.yaml 
+pod "servlet" created
+```
+```console
+$ kubectl -n dspace-dev get po
+NAME                                 READY     STATUS    RESTARTS   AGE
+dspace-postgresql-1806947503-qw8q4   1/1       Running   0          4d
+servlet                              1/1       Running   0          34s
+```
+```console
+$ kubectl -n dspace-dev logs servlet
+[Wed Oct  4 12:24:25 UTC 2017] Starting 
+[Wed Oct  4 12:24:25 UTC 2017] Cloning lindat-dspace repository...skip! /opt/repository/sources/dspace already exists 
+[Wed Oct  4 12:24:25 UTC 2017] Creating workspace...skip! /opt/repository/workspace already exists 
+[Wed Oct  4 12:24:25 UTC 2017] Copy makefile...skip! /opt/repository/workspace/config/variable.makefile already exists
+[Wed Oct  4 12:24:25 UTC 2017] Copy local.properties...skip! /opt/repository/workspace/sources/local.properties already exists
+[Wed Oct  4 12:24:25 UTC 2017] Compilation and Deployment of DSpace...already done 
+already done 
+already done 
+[Wed Oct  4 12:24:25 UTC 2017] Copy aai_config.js...skip! /opt/lindat-dspace/installation/webapps/xmlui/themes/UFAL/lib/js/aai_config.js already exists
+[Wed Oct  4 12:24:25 UTC 2017] Create dspace admin...already done 
+[Wed Oct  4 12:24:25 UTC 2017] Starting Tomcat...Starting Tomcat 8...
+Tomcat started.
+```
+```console
+$ kubectl -n dspace-dev port-forward servlet 8080:8080
+Forwarding from 127.0.0.1:8080 -> 8080
+Forwarding from [::1]:8080 -> 8080
+```
+
+connect to http://localhost:8080/repository/xmlui/#

clarin-dspace-docker/.gitignore

+commul-customization/certs/*
+password_mod.sh

clarin-dspace-docker/Dockerfile.dspace

+############################################################
+# Dockerfile to build LINDAT Dspace container images
+# Based on Ubuntu
+############################################################
+
+FROM ubuntu
+LABEL maintainer="Alexander König <Alexander.Koenig@eurac.edu>"
+
+# install cpanm and dependencies
+RUN apt-get update &&\
+        apt-get -y upgrade &&\
+        apt-get -y install make gcc wget cpanminus
+
+RUN cpanm File::Spec::Functions
+RUN cpanm Term::ReadLine
+
+# install jdk, ant, psql, mvn, make, libxml, xsltproc, zip, wget
+RUN apt-get -y install openjdk-8-jdk ant maven libxml2-utils xsltproc unzip curl git
+
+# install convenience apps for debug purposes (vim and jsbeautifier)
+RUN 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/
+
+# set up a proper locale
+RUN apt-get -y install locales
+RUN locale-gen en_US.UTF-8
+COPY commul-customization/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-8.0.35.tar.gz https://archive.apache.org/dist/tomcat/tomcat-8/v8.0.35/bin/apache-tomcat-8.0.35.tar.gz
+RUN mkdir /opt/tomcat8
+RUN tar xvzf /tmp/apache-tomcat-8.0.35.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/
+COPY commul-customization/tomcat-server.xml /opt/tomcat8/conf/server.xml
+
+
+# install Dspace
+RUN mkdir /tmp/commul-customization
+COPY commul-customization/variable.makefile /tmp/commul-customization/
+
+# copy over configs and startup scripts
+COPY commul-customization/start_stack.sh /tmp/commul-customization/
+COPY commul-customization/stop_stack.sh /tmp/commul-customization/
+COPY commul-customization/local.properties /tmp/commul-customization/
+
+# copy over config files
+COPY commul-customization/aai_config.js /tmp/commul-customization/
+#CMD tail -f /opt/repository/sources/dspace/dspace-api/src/test/data/dspaceFolder/log/dspace.log
+
+COPY dspace-entrypoint.sh /
+RUN chmod +x dspace-entrypoint.sh
+
+ENTRYPOINT ["/dspace-entrypoint.sh"]
+
+

clarin-dspace-docker/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"]

clarin-dspace-docker/Dockerfile.nginx

+#######################################################################
+# Dockerfile to build nginx and shibboleth for LINDAT Dspace container
+# Based on Ubuntu
+#######################################################################
+
+FROM ubuntu
+LABEL maintainer="Alexander König <Alexander.Koenig@eurac.edu>"
+
+# install cpanm and dependencies
+RUN apt-get update &&\
+        apt-get -y upgrade &&\
+        apt-get -y install make gcc wget cpanminus
+
+RUN cpanm File::Spec::Functions
+RUN cpanm Term::ReadLine
+
+# install jdk, ant, psql, mvn, make, libxml, xsltproc, zip, wget
+RUN apt-get -y install openjdk-8-jdk ant maven libxml2-utils xsltproc unzip curl
+
+# install convenience apps for debug purposes (vim and jsbeautifier)
+RUN 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/
+
+# set up a proper locale
+RUN apt-get -y install locales
+RUN locale-gen en_US.UTF-8
+COPY commul-customization/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 nginx
+RUN apt-get install -y zlib1g zlib1g-dev libpcre3 libpcre3-dev curl
+RUN cpanm File::Spec::Functions
+RUN cpanm Term::ReadLine
+COPY commul-customization/nginx_build.sh /tmp/nginx_build.sh
+RUN chmod a+x /tmp/nginx_build.sh
+WORKDIR /tmp/
+RUN ./nginx_build.sh
+# copy the init script
+COPY commul-customization/nginx /etc/init.d/
+RUN chmod a+x /etc/init.d/nginx
+# add a symlink
+RUN ln -s /opt/nginx/sbin/nginx /usr/sbin/nginx
+# copy over static html
+RUN mkdir /opt/nginx/html/img
+COPY commul-customization/index.html /opt/nginx/html/
+COPY commul-customization/eurac.png /opt/nginx/html/img/
+# create the test secure folder
+RUN mkdir /opt/nginx/html/secure
+COPY commul-customization/shib_test.pl /opt/nginx/html/secure/
+
+# get aai project
+RUN apt-get install -y git
+RUN git clone https://github.com/ufal/lindat-aai-discovery.git /opt/repository/sources/lindat-aai-discovery
+
+# install shibboleth
+COPY commul-customization/shibboleth_sp_with_fastcgi.sh /tmp/
+WORKDIR /tmp
+RUN chmod u+x /tmp/shibboleth_sp_with_fastcgi.sh
+RUN /tmp/shibboleth_sp_with_fastcgi.sh
+# copy the init script
+RUN cp /opt/shibboleth-sp-fastcgi/etc/shibboleth/shibd-debian /etc/init.d/shibd
+RUN chmod a+x /etc/init.d/shibd
+
+
+# install supervisor
+RUN apt-get install -y python-setuptools
+RUN easy_install supervisor
+COPY commul-customization/supervisord.conf /etc/
+RUN mkdir -p /var/log/supervisor
+
+# copy over config files
+COPY commul-customization/default-ssl /opt/nginx/conf/
+COPY commul-customization/nginx.conf /opt/nginx/conf/
+COPY commul-customization/repository_auth /opt/nginx/conf/
+COPY commul-customization/shibboleth2.xml /opt/shibboleth-sp-fastcgi/etc/shibboleth/
+COPY commul-customization/clarin.eurac.edu.template.metadata.xml /opt/shibboleth-sp-fastcgi/etc/shibboleth/
+COPY commul-customization/shib_clear_headers /opt/nginx/conf/
+
+# copy over config files
+COPY commul-customization/aai.js /opt/repository/sources/lindat-aai-discovery/
+WORKDIR /opt/repository/sources/lindat-aai-discovery/
+RUN touch /opt/repository/sources/lindat-aai-discovery/aai.js
+RUN make aai.min.js
+
+# copy certificate for clarin-dev
+COPY commul-customization/certs/lindat-dev.key /etc/ssl/private/
+COPY commul-customization/certs/lindat-dev_eurac_edu.pem /etc/ssl/certs/
+
+# if deployed on clarin instead of clarin-dev comment the two lines above and uncomment the following lines
+
+## copy certificate for clarin
+# COPY commul-customization/certs/lindat_eurac_edu.key /etc/ssl/private/
+# COPY commul-customization/certs/lindat_eurac_edu.crt /etc/ssl/certs/
+
+
+ENTRYPOINT ["/usr/local/bin/supervisord", "-c", "/etc/supervisord.conf"]
+

clarin-dspace-docker/Dockerfile.psql

+FROM postgres:9.6.3
+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/
+
+# copy utilities generating script
+RUN mkdir /tmp/sql/
+COPY adapt_utilities_sql.sh /tmp/sql/
+RUN /tmp/sql/adapt_utilities_sql.sh

clarin-dspace-docker/README.md

+# dockerized CLARIN DSpace
+
+This is meant to provide an easy way to install [CLARIN DSpace](https://github.com/ufal/clarin-dspace) by providing a Docker Compose setup that automatizes the installation as far as possible. Additionally all files that need to be customized or added are also part of this repository.
+
+# How to use it
+
+You need a Linux server (we tested on Ubuntu 16.04 and CentOS 7.3) with a recent install of Docker (we tested with 17.05.0-ce). Clone this git repository onto the server. Then you need to look through all the files in commul-customization and adapt the configuration to your server (domain name, user names, etc). 
+
+None of the files contain passwords, but all files which need passwords in them are in the repository as .dist files. To insert the passwords you need to remove the dist ending and then run password_mod.sh (after you've modified it with your passwords).
+
+# Exemplary workflow
+
+## get Dockerfiles
+```
+git clone https://github.com/commul/clarin-dspace-docker
+cd clarin-dspace-docker
+```
+
+## get my versions of dist files
+```
+cp password_mod.sh.dist password_mod.sh
+cp commul-customization/init-dspace-dbs.sh.dist commul-customization/init-dspace-dbs.sh
+cp commul-customization/local.properties.dist commul-customization/local.properties
+```
+
+## change passwords
+```
+vi password_mod.sh
+chmod +x password_mod.sh
+./password_mod.sh
+```
+
+## make sure the certificate and key are there
+```
+cp -r /tmp/certs ./commul-customization/
+```
+
+## build the images
+```
+docker-compose up -d --build
+```
+
+## enter the DSpace container
+```
+docker exec -ti clarindspacedocker_dspace_1 bash
+```
+
+## deploy DSpace
+```
+make new_deploy
+```
+
+## copy over modified aai_config.js
+```
+cp /tmp/aai_config.js /opt/lindat-dspace/installation/webapps/xmlui/themes/UFAL/lib/js/
+```
+
+## create dspace admin as tomcat8, so that the log files have the right owner
+```
+su  -s /bin/sh tomcat8
+/opt/lindat-dspace/installation/bin/dspace create-administrator
+```
+
+## start the dspace webapp
+```
+cd /opt/repository/sources/dspace/utilities/project_helpers/scripts
+/etc/init.d/tomcat8 start
+```

clarin-dspace-docker/adapt_utilities_sql.sh

+#!/bin/bash
+
+git clone https://github.com/commul/clarin-dspace.git -b clarin /tmp/dspace
+cp /tmp/dspace/utilities/utilities.sql /tmp/sql/
+cp /tmp/dspace/utilities/license_definition.txt /tmp/sql/
+perl -pi -e "s#afile :utildir '/license_definition.txt'#afile '/tmp/sql/license_definition.txt'#;" /tmp/sql/utilities.sql
+rm -rf /tmp/dspace

clarin-dspace-docker/changelog.txt

+Releases
+========
+
+gitlab.scientificnet.org:4567/commul/dspace/dspace
+
+0.3
+added dspace-entrypoint.sh v0.2
+
+0.2
+Removed DSpace's installation from the Dockerfile.
+Moved commul-customization into /tmp , so is possible to mount external volumes into /opt/repository/ and then  copying files again from /tmp
+
+0.1
+Original build from https://github.com/commul/clarin-dspace-docker @ e5ad160
+
+
+gitlab.scientificnet.org:4567/commul/dspace/postgres
+
+0.3
+added env variables
+
+0.2
+
+0.1
+Original build from https://github.com/commul/clarin-dspace-docker @ e5ad160

clarin-dspace-docker/clarin-dev2clarin.sh

+#!/bin/bash
+
+# outside the docker
+perl -pi -e 's/clarin-dev/clarin/g' commul-customization/shibboleth2.xml
+perl -pi -e 's/clarin-dev/clarin/g' commul-customization/local.properties
+perl -pi -e 's/lindat-dev_eurac_edu.pem/lindat_eurac_edu.crt/;' commul-customization/default-ssl
+perl -pi -e 's/lindat-dev.key/lindat_eurac_edu.key/;' commul-customization/default-ssl
+perl -pi -e 's/clarin-dev/clarin/g' commul-customization/default-ssl
+
+perl -pi -e 's/clarin-dev/clarin/g' commul-customization/aai.js
+perl -pi -e 's/clarin-dev/clarin/g' commul-customization/aai_config.js 
+perl -pi -e 's/clarin-dev/clarin/g' commul-customization/lindat.eurac.edu.template.metadata.xml
+
+echo "Modified all files to point to clarin.eurac.edu instead of clarin-dev.eurac.edu. Do not forget to also edit docker-compose.yml and Dockerfile.nginx."

clarin-dspace-docker/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);

clarin-dspace-docker/commul-customization/aai_config.js

+"use strict";jQuery(document).ready(function(){var a=(function(){var b={};b.port=(window.location.port===""?"":":"+window.location.port);b.host=window.location.protocol+"//"+window.location.hostname;b.repoPath=jQuery("a#repository_path").attr("href");if(b.repoPath.charAt(b.repoPath.length-1)!=="/"){b.repoPath=b.repoPath+"/"}b.target=b.host+b.port+b.repoPath;b.responseUrl=(window.location.hostname.search("clarin-dev.eurac.edu")>=0)?"":b.host+b.port+b.repoPath+"themes/UFAL/lib/html/disco-juice.html?";b.metadataFeed=b.target+"discojuice/feeds";b.serviceName="Eurac Research CLARIN Centre";b.localauth='<form method="post" action="'+b.target+'password-login"> <p>Sign in using your local account obtained from the Eurac Research CLARIN Centre 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="'+b.target+'forgot">Forgot your password?</a></p><p  style="" ><input type="submit" style="margin: 20px 2px" name="submit" value="Sign in" /></p></form>';b.target=b.target+"shibboleth-login";return b})();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(a)});

clarin-dspace-docker/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="_5d15d5a81bc952da1d34986ebc7713c0d5c9ea60" entityID="https://dspace-clarin-it.ilc.cnr.it/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>
+        </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/img/eurac.png</mdui:Logo>                    
+                <mdui:PrivacyStatementURL xml:lang="en">https://clarin-dev.eurac.edu/repository/xmlui/page/privacypolicy</mdui:PrivacyStatementURL>
+                <mdui:PrivacyStatementURL xml:lang="de">https://clarin-dev.eurac.edu/repository/xmlui/page/privacypolicy</mdui:PrivacyStatementURL>
+                <mdui:PrivacyStatementURL xml:lang="it">https://clarin-dev.eurac.edu/repository/xmlui/page/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="true"/>
+        </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>

clarin-dspace-docker/commul-customization/default-ssl

+upstream tomcats {
+                    server dspace:8009;
+                    keepalive 10;
+            }
+
+server {
+    listen 80;
+    listen [::]:80;
+    server_name clarin-dev.eurac.edu;
+    return 301 https://$server_name$request_uri;
+}
+
+server {
+  listen 443;
+  server_name clarin-dev.eurac.edu localhost;
+
+  root  /opt/nginx/html;
+  index index.html index.htm;
+
+  ssl on;
+  ssl_certificate /etc/ssl/certs/lindat-dev_eurac_edu.pem;
+  ssl_certificate_key /etc/ssl/private/lindat-dev.key;
+
+  ssl_protocols        TLSv1 TLSv1.1 TLSv1.2;
+  ssl_ciphers RC4:HIGH:!aNULL:!MD5;
+  ssl_prefer_server_ciphers on;
+  keepalive_timeout    70;
+  ssl_session_cache    shared:SSL:10m;
+  ssl_session_timeout  10m;
+
+  add_header 'Access-Control-Allow-Origin' "*";
+  add_header 'Access-Control-Allow-Credentials' 'true';
+
+  # redirect different legacy forms to repository/xmlui
+  rewrite ^/xmlui(.*)$ /repository/xmlui$1 redirect;
+  rewrite ^/repository.?$ /repository/xmlui/ redirect;
+  rewrite ^/solr(.*)$ /repository/solr$1 redirect;
+  rewrite ^/handle/(.*)$ /repository/xmlui/handle/$1 redirect;
+
+  set $oai_index /repository/oai/request?verb=Identify;
+  rewrite ^/oai$ $oai_index redirect;
+  location /oai {
+    return 301 https://$http_host/repository$request_uri;
+  }
+  rewrite ^/repository/oai$ $oai_index redirect;
+
+  if ($http_accept ~ "(.*xml.cmdi.*)"){
+    rewrite ^/(.*)/xmlui/handle/(.*)$ https://$http_host/repository/oai/cite?metadataPrefix=cmdi&handle=$2? redirect;
+  }
+
+  if ($query_string ~* "format=cmdi"){
+    rewrite ^/(.*)/xmlui/handle/(.*)$ https://$http_host/repository/oai/cite?metadataPrefix=cmdi&handle=$2? redirect;
+  }
+
+  if ($query_string ~* "format=cite_(cmdi|bibtex|html)"){
+    rewrite ^/(.*)/xmlui/handle/(.*)$ https://$http_host/repository/oai/cite?metadataPrefix=%1&handle=$2? redirect;
+  }
+
+#  location = / {
+#    return 301 /repository;
+#  }
+
+  location / {
+    index index.php index.html index.htm;
+
+#    try_files $uri $uri/ /index.php?$args;
+
+#    location ~ \.php$ {
+#      include process_php;
+#    }
+  }
+
+  location /repository {
+
+    client_body_buffer_size 32K;
+
+    client_max_body_size 4G;
+
+    sendfile on;
+    send_timeout 300s;
+
+    ajp_keep_conn on;
+    ajp_pass tomcats;
+
+    location /repository/solr {
+      satisfy any;
+
+      auth_basic           "Restricted App";
+      auth_basic_user_file /etc/apache2/passwd/passwords;
+
+      allow 127.0.0.1;
+      deny all;
+
+      ajp_keep_conn on;
+      ajp_pass tomcats;
+    }
+
+    location /repository/JSON/solr/ {
+      rewrite /repository/JSON/solr/(.*) /repository/solr/search/select/?q=*:*&rows=0&facet=on&wt=json&indent=true&facet.field=$1 break;
+
+      proxy_pass http://localhost:8080;
+    }
+
+  }
+
+  # define aai location
+  location /aai {
+    alias /opt/repository/sources/lindat-aai-discovery; }
+
+  # add path your repository path that will be protected by shibboleth
+  location /repository/xmlui/shibboleth-login { 
+	include repository_auth; 
+    ajp_keep_conn on;
+    ajp_pass tomcats;
+	}
+
+  location /xmlui/shibboleth-login            { 
+	include repository_auth; 
+	ajp_keep_conn on;
+    ajp_pass tomcats;
+	}
+
+  # remove the robots and favicon from the logs
+  location ~ /robots.txt$  { access_log off; log_not_found off; }
+  location ~ ^/favicon.ico$ { access_log off; log_not_found off; }
+
+  # this prevents hidden files (beginning with a period) from being served
+  location ~ /\.           { access_log off; log_not_found off; deny all; }
+
+  # FastCGI authorizer for Auth Request module
+  location = /shibauthorizer {
+    internal;
+    include fastcgi_params;
+    fastcgi_pass unix:/opt/shibboleth-sp-fastcgi/shibauthorizer.sock;
+  }
+
+  # FastCGI responder
+  location /Shibboleth.sso {
+    include fastcgi_params;
+    fastcgi_pass unix:/opt/shibboleth-sp-fastcgi/shibresponder.sock;
+  }
+
+  # Resources for the Shibboleth error pages
+  location /shibboleth-sp {
+    alias /opt/shibboleth-sp-fastcgi/share/shibboleth/;
+  }
+ 
+  location /secure {
+    alias /opt/repository/sources/secure;
+    include shib_clear_headers;
+         #Add your attributes here. They get introduced as headers
+         #by the FastCGI authorizer so we must prevent spoofing.
+         more_clear_input_headers 'displayName' 'mail' 'persistent-id';
+         shib_request /shibauthorizer;
+         shib_request_use_headers on;
+         proxy_pass http://localhost:8080;
+     }
+
+  include /opt/nginx/conf/proxies-enabled/*;
+}
+

clarin-dspace-docker/commul-customization/default_locale

+#  File generated by update-locale
+LANG="en_US.UTF-8"
+LC_NUMERIC="en_US.UTF-8"
+LC_TIME="en_US.UTF-8"
+LC_MONETARY="en_US.UTF-8"
+LC_PAPER="en_US.UTF-8"
+LC_NAME="en_US.UTF-8"
+LC_ADDRESS="en_US.UTF-8"
+LC_TELEPHONE="en_US.UTF-8"
+LC_MEASUREMENT="en_US.UTF-8"
+LC_IDENTIFICATION="en_US.UTF-8"

clarin-dspace-docker/commul-customization/discojuiceDiscoveryResponse.html

+<!DOCTYPE html>
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+	<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
+	<meta http-equiv="Cache-Control" content="no-cache">
+	<meta http-equiv="Pragma" content="no-cache">
+	<title>IdP Discovery Response Receiver</title>
+
+	<script type="text/javascript">
+
+function parseURL(url) {
+	var a =  document.createElement('a');
+    a.href = url;
+    return a.hostname;
+}
+
+function receive() {
+	var urlParams = {},
+		cid = null,
+		idpentityid,
+		subid,
+		rsearch
+		;
+
+	(function () {
+		var e,
+			a = /\+/g,  // Regex for replacing addition symbol with a space
+			r = /([^&;=]+)=?([^&;]*)/g,
+			d = function (s) { return decodeURIComponent(s.replace(a, " ")); },
+			q = window.location.search.substring(1);
+
+		while (e = r.exec(q))
+		   urlParams[d(e[1])] = d(e[2]);
+	})();
+
+	if (urlParams.cid) cid = urlParams.cid;
+
+	var sender = parseURL(document.referrer);
+
+	// Received a specific entity ID from the storage.
+	if (urlParams.entityID) {
+
+		window.parent.DiscoJuice.Utils.log("Entity id parameter was " + urlParams.entityID);
+
+		rsearch = urlParams.entityID.match(/^(.*)#(.*)$/);
+		if (rsearch) {
+			idpentityid = rsearch[1];
+			subid = rsearch[2];
+		} else {
+			idpentityid = urlParams.entityID;
+			subid = null;
+		}
+		window.parent.DiscoJuice.Utils.log('ResponseLocation: Response from discovery service [' + sender + ']: ' + idpentityid + '   subID: ' + subid);
+		window.parent.DiscoJuice.Control.discoResponse(sender, idpentityid, subid, cid);
+
+	// Received a textual error from the storage, to show in the debug log.
+	} else if (urlParams['error']) {
+		window.parent.DiscoJuice.Control.discoResponseError(cid,
+			"Error from IdP Discovery Service [" + sender + "]:  " + urlParams.error);
+
+	// Did not receive a response parameter. This probably means that the Disco storage did not have a stored preference
+	// for the user. Consequently: no error.
+	} else {
+		window.parent.DiscoJuice.Utils.log('No valid response parameters. cid[' + cid + ']');
+		window.parent.DiscoJuice.Control.discoResponseError(cid);
+	}
+
+}
+
+	</script>
+</head>
+
+<body onload="receive();">
+
+</body>
+</html>

clarin-dspace-docker/commul-customization/fastcgi.conf

+
+fastcgi_param  SCRIPT_FILENAME    $document_root$fastcgi_script_name;
+fastcgi_param  QUERY_STRING       $query_string;
+fastcgi_param  REQUEST_METHOD     $request_method;
+fastcgi_param  CONTENT_TYPE       $content_type;
+fastcgi_param  CONTENT_LENGTH     $content_length;
+
+fastcgi_param  SCRIPT_NAME        $fastcgi_script_name;
+fastcgi_param  REQUEST_URI        $request_uri;
+fastcgi_param  DOCUMENT_URI       $document_uri;
+fastcgi_param  DOCUMENT_ROOT      $document_root;
+fastcgi_param  SERVER_PROTOCOL    $server_protocol;
+fastcgi_param  REQUEST_SCHEME     $scheme;
+fastcgi_param  HTTPS              $https if_not_empty;
+
+fastcgi_param  GATEWAY_INTERFACE  CGI/1.1;
+fastcgi_param  SERVER_SOFTWARE    nginx/$nginx_version;
+
+fastcgi_param  REMOTE_ADDR        $remote_addr;
+fastcgi_param  REMOTE_PORT        $remote_port;
+fastcgi_param  SERVER_ADDR        $server_addr;
+fastcgi_param  SERVER_PORT        $server_port;
+fastcgi_param  SERVER_NAME        $server_name;
+
+# PHP only, required if PHP was built with --enable-force-cgi-redirect
+fastcgi_param  REDIRECT_STATUS    200;