Docker updates

.env

@@ -1,4 +1,7 @@
+LOCAL_SOLR_DATA=./vivo-solr
+RESET_CORE=false
+
 LOCAL_VIVO_HOME=./vivo-home
 RESET_HOME=false
-RESET_CORE=false
+
 VERBOSE=no

.github/workflows/build.yml

@@ -30,4 +30,4 @@ jobs:
       - name: Maven Build
         run: |
           cd ../VIVO
-          mvn clean package -s installer/example-settings.xml
+          mvn clean install

.github/workflows/deploy.yml

@@ -37,7 +37,7 @@ jobs:
       - name: Maven Deploy
         run: |
           cd ../VIVO
-          mvn --batch-mode deploy -Pskip
+          mvn --batch-mode deploy
         env:
           MAVEN_USERNAME: ${{ secrets.OSSRH_USERNAME }}
           MAVEN_PASSWORD: ${{ secrets.OSSRH_TOKEN }}

.github/workflows/docker.yml

@@ -34,7 +34,7 @@ jobs:
       - name: Maven Build
         run: |
           cd ../VIVO
-          mvn clean package -s installer/example-settings.xml
+          mvn clean install
 
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v1
@@ -47,7 +47,7 @@ jobs:
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
-      
+
       - name: Build and push
         id: docker_build
         uses: docker/build-push-action@v2

.gitignore

@@ -22,6 +22,7 @@ utilities/rdbmigration/.work
 **/bin/
 
 vivo-home/
+vivo-solr/
 
 .fake
 .ionide

Dockerfile

@@ -1,20 +1,42 @@
 FROM tomcat:9-jdk11-openjdk
+ARG USER_ID=3001
+ARG USER_NAME=vivo
+ARG USER_HOME_DIR=/home/$USER_NAME
 
-ARG SOLR_URL=http://localhost:8983/solr/vivocore
-ARG VIVO_DIR=/usr/local/vivo/home
-ARG TDB_FILE_MODE=direct
+ENV TOMCAT_CONTEXT_PATH=ROOT
+ENV VIVO_HOME_DIR=/usr/local/vivo/home
+ENV TDB_FILE_MODE=direct
+ENV ROOT_USER_ADDRESS=vivo_root@mydomain.edu
+ENV DEFAULT_NAMESPACE=http://vivo.mydomain.edu/individual/
 
-ENV SOLR_URL=${SOLR_URL}
-ENV JAVA_OPTS="${JAVA_OPTS} -Dtdb:fileMode=$TDB_FILE_MODE"
+ENV SOLR_URL=http://localhost:8983/solr/vivocore
+ENV SELF_ID_MATCHING_PROPERTY=http://vivo.mydomain.edu/ns
 
-RUN mkdir /usr/local/vivo
-RUN mkdir /usr/local/vivo/home
+ENV LOAD_SAMPLE_DATA=false
+ENV SAMPLE_DATA_REPO_URL=https://github.com/vivo-project/sample-data.git
+ENV SAMPLE_DATA_BRANCH=main
+ENV SAMPLE_DATA_DIRECTORY=openvivo
 
-COPY ./installer/home/target/vivo /vivo-home
-COPY ./installer/webapp/target/vivo.war /usr/local/tomcat/webapps/ROOT.war
+ENV RECONFIGURE=false
 
-COPY start.sh /start.sh
+RUN \
+  apt-get update -y && \
+  apt-get upgrade -y && \
+  apt install git -y
+
+RUN \
+  addgroup --disabled-password --gid $USER_ID $USER_NAME && \
+  adduser --disabled-password --home $USER_HOME_DIR --uid $USER_ID --gid $USER_ID $USER_NAME
+
+RUN mkdir -p $VIVO_HOME_DIR
+
+COPY ./installer/webapp/target/vivo.war /tmp/vivo.war
+
+COPY ./home/src/main/resources/config/default.applicationSetup.n3 /tmp/applicationSetup.n3
+COPY ./home/src/main/resources/config/default.runtime.properties /tmp/runtime.properties
+
+COPY start.sh /usr/local/vivo/start.sh
 
 EXPOSE 8080
 
-CMD ["/bin/bash", "/start.sh"]
+CMD ["/bin/bash", "/usr/local/vivo/start.sh"]

README.md

@@ -23,30 +23,93 @@ https://wiki.lyrasis.org/display/VIVODOC112x/Installing+VIVO
 
 ### Docker
 
-VIVO docker container is available at [vivoweb/vivo](https://hub.docker.com/repository/docker/vivoweb/vivo) with accompanying [vivoweb/vivo-solr](https://hub.docker.com/repository/docker/vivoweb/vivo-solr). These can be used independently or with docker-compose.
+VIVO docker container is available at [vivoweb/vivo](https://hub.docker.com/r/vivoweb/vivo) with accompanying [vivoweb/vivo-solr](https://hub.docker.com/r/vivoweb/vivo-solr). These can be used independently or with docker-compose.
+
+#### Build Args
+
+Build args are used at time of building the Docker image.
+
+| Variable                      | Description                  | Default                              |
+| ----------------------------- | -----------------------------| ------------------------------------ |
+| USER_ID                       | User id                      | 3001                                 |
+| USER_NAME                     | User name                    | vivo                                 |
+| USER_HOME_DIR                 | User home directory          | /home/vivo                           |
+
+#### Environment
+
+| Variable                      | Description                                                      | Default                                         |
+| ----------------------------- | ---------------------------------------------------------------- | ----------------------------------------------- |
+| TOMCAT_CONTEXT_PATH           | Tomcat webapp context path                                       | ROOT                                            |
+| VIVO_HOME_DIR                 | VIVO home directory in container                                 | /usr/local/vivo/home                            |
+| TDB_FILE_MODE                 | TDB file mode                                                    | direct                                          |
+| ROOT_USER_ADDRESS             | Root user email address                                          | vivo_root@mydomain.edu                          |
+| DEFAULT_NAMESPACE             | Default namespace                                                | http://vivo.mydomain.edu/individual/            |
+| SOLR_URL                      | VIVO Solr URL                                                    | http://localhost:8983/solr/vivocore             |
+| SELF_ID_MATCHING_PROPERTY     | Individual property associated with user account                 | http://vivo.mydomain.edu/ns#networkId           |
+| EMAIL_SMTP_HOST               | Email SMTP host                                                  | not defined                                     |
+| EMAIL_PORT                    | Email server port                                                | not defined                                     |
+| EMAIL_USERNAME                | Email server username                                            | not defined                                     |
+| EMAIL_PASSWORD                | Email server password                                            | not defined                                     |
+| EMAIL_REPLY_TO                | Reply to email address                                           | not defined                                     |
+| LANGUAGE_FILTER_ENABLED       | Enable language filter to respect browser Accept-Language header | not defined                                     |
+| FORCE_LOCALE                  | Ignore browser Accept-Language header                            | not defined                                     |
+| SELECTABLE_LOCALES            | Selectable locales                                               | not defined                                     |
+| RESET_CORE                    | Reset VIVO Solr core                                             | false                                           |
+| RESET_HOME                    | Reset VIVO home directory                                        | false                                           |
+| LOAD_SAMPLE_DATA              | Load sample data                                                 | false                                           |
+| SAMPLE_DATA_REPO_URL          | Sample data GitHub repository                                    | https://github.com/vivo-project/sample-data.git |
+| SAMPLE_DATA_BRANCH            | Sample data GitHub repository branch                             | main                                            |
+| SAMPLE_DATA_DIRECTORY         | Sample data directory                                            | openvivo                                        |
+| RECONFIGURE                   | Whether to update runtime properties and application setup       | false                                           |
+
+> Both RESET_HOME and LOAD_SAMPLE_DATA must be true in order to load sample data.
+
+#### Running VIVO from published Docker images.
+
+Create a docker [network](https://docs.docker.com/engine/reference/commandline/network_create/).
+```
+docker network create vivo_net
+```
+
+Run vivo-solr [detached](https://docs.docker.com/engine/reference/run/#detached-vs-foreground) with [port forwarding](https://docs.docker.com/engine/reference/run/#expose-incoming-ports) and on a above [network](https://docs.docker.com/engine/reference/run/#network-settings).
+```
+docker run -d -p 8983:8983 --hostname solr --network vivo_net vivoweb/vivo-solr
+```
+
+Run vivo with [port forwarding](https://docs.docker.com/engine/reference/run/#expose-incoming-ports), on a above [network](https://docs.docker.com/engine/reference/run/#network-settings), defining Solr URL [environment variable](https://docs.docker.com/engine/reference/run/#env-environment-variables), and local [volume](https://docs.docker.com/engine/reference/run/#volume-shared-filesystems) mounted to VIVO home directory.
+```
+docker run -p 8080:8080 --network vivo_net -e "SOLR_URL=http://solr:8983/solr/vivocore" -v "./vivo-home:/opt/vivo/home" vivoweb/vivo
+```
 
 ### Docker Compose
 
 Docker Compose environment variables:
 
 .env defaults
 ```
+LOCAL_SOLR_DATA=./vivo-solr
+RESET_CORE=false
+
 LOCAL_VIVO_HOME=./vivo-home
 RESET_HOME=false
-RESET_CORE=false
+
+VERBOSE=no
 ```
 
+- `LOCAL_VIVO_HOME`: VIVO Solr data directory on your host machine which will mount to volume in Solr docker container. Set this environment variable to persist your VIVO Solr data on your host machine.
+- `RESET_CORE`: Convenience to reset VIVO Solr core when starting container. **Caution**, will require complete reindex.
+
 - `LOCAL_VIVO_HOME`: VIVO home directory on your host machine which will mount to volume in docker container. Set this environment variable to persist your VIVO data on your host machine.
 - `RESET_HOME`: Convenience to reset VIVO home when starting container. **Caution**, will delete local configuration, content, and configuration model.
-- `RESET_CORE`: Convenience to reset VIVO Solr core when starting container. **Caution**, will require complete reindex.
 
-Before building VIVO, you will also need to clone (and switch to the same branch, if other than main) of [Vitro](https://github.com/vivo-project/Vitro). The Vitro project must be cloned to a sibling directory next to VIVO so that it can be found during the build. 
+Build and start VIVO using Docker Compose.
+
+Before building VIVO, you will also need to clone (and switch to the same branch, if other than main) of [Vitro](https://github.com/vivo-project/Vitro). The Vitro project must be cloned to a sibling directory next to VIVO so that it can be found during the build.
 
 Build and start VIVO.
 
-1. In VIVO (with Vitro cloned alongside it), run:
 ```
-mvn clean package -s installer/example-settings.xml
+mvn clean package
 docker-compose up
 ```
 

docker-compose.yml

@@ -1,36 +1,51 @@
 version: '3.2'
 
+networks:
+  net:
+
 services:
 
   solr:
     image: vivoweb/vivo-solr:latest
+    hostname: solr
     environment:
-      - RESET_CORE=${RESET_CORE}
       - VERBOSE=${VERBOSE}
+      - RESET_CORE=true
     ports:
       - 8983:8983
+    volumes:
+      - ${LOCAL_SOLR_DATA}:/opt/solr/server/solr/mycores
     networks:
-      - vivo
+      - net
 
   tomcat:
     container_name: vivo
     hostname: vivo
     build:
       context: ./
       dockerfile: Dockerfile
-      args:
-        - VIVO_DIR=/usr/local/vivo/home
-        - TDB_FILE_MODE=direct
-        - SOLR_URL=http://solr:8983/solr/vivocore
     environment:
-      - RESET_HOME=${RESET_HOME}
       - VERBOSE=${VERBOSE}
+      - RESET_HOME=true
+      - SOLR_URL=http://solr:8983/solr/vivocore
+      - LANGUAGE_FILTER_ENABLED=true
+      - SELECTABLE_LOCALES=en_US,de_DE,sr_Latn_RS,ru_RU,fr_CA,en_CA,es,pt_BR
+      - LOAD_SAMPLE_DATA=true
+      - SAMPLE_DATA_REPO_URL=https://github.com/chenejac/sample-data.git
+      - SAMPLE_DATA_BRANCH=reorganization
+      - SAMPLE_DATA_DIRECTORY=i18n
     ports:
       - 8080:8080
     volumes:
       - ${LOCAL_VIVO_HOME}:/usr/local/vivo/home
+    depends_on:
+      - solr
     networks:
-      - vivo
-
-networks:
-  vivo:
+      - net
+    entrypoint:
+      - /bin/bash
+      - '-c'
+      - |
+        while (!</dev/tcp/solr/8983) > /dev/null 2>&1; do sleep 1; done;
+        sleep 5
+        /usr/local/vivo/start.sh

home/pom.xml

@@ -69,4 +69,4 @@
             <type>tar.gz</type>
         </dependency>
     </dependencies>
-</project>
+</project>

home/src/main/resources/config/example.runtime.properties → home/src/main/resources/config/default.runtime.properties

@@ -19,26 +19,6 @@
 # BASIC PROPERTIES
 # -----------------------------------------------------------------------------
 
-  #
-  # This namespace will be used when generating URIs for objects created in the
-  # editor. In order to serve linked data, the default namespace must be composed
-  # as follows (optional elements in parentheses):
-  #
-  # scheme + server_name (+ port) (+ servlet_context) + "/individual/"
-  #
-  # For example, Cornell's default namespace is:
-  #
-  # http://vivo.cornell.edu/individual/
-  #
-Vitro.defaultNamespace = http://vivo.mydomain.edu/individual/
-
-  #
-  # The email address of the root user for the VIVO application. The password
-  # for this user is initially set to "rootPassword", but you will be asked to
-  # change the password the first time you log in.
-  #
-rootUser.emailAddress = vivo_root@mydomain.edu
-
 #
 # Argon2 password hashing parameters for time, memory and parallelism required to
 # compute a hash.