New DOCKERFILE using new maven and jdk images and without dependencie…

…s on HBPMedical repos.

Removed many unused old files.
Removed docker specific folder.

Dockerfile

@@ -1,62 +1,65 @@
-# Build stage for Java classes
-FROM hbpmip/java-base-build:3.6.0-jdk-11-0 as java-build-env
+#######################################################
+# Build the spring boot maven project
+#######################################################
+FROM maven:3.8.5-openjdk-11 as mvn-build-env
 
-COPY pom.xml /project/
+ENV CODE_PATH="/opt/code"
+WORKDIR $CODE_PATH
 
-RUN cp /usr/share/maven/ref/settings-docker.xml /root/.m2/settings.xml \
-    && mvn clean compile test
+COPY pom.xml $CODE_PATH
 
-COPY src/ /project/src/
+RUN mvn clean compile test
 
-# Repeating the file copy works better. I dunno why.
-RUN cp /usr/share/maven/ref/settings-docker.xml /root/.m2/settings.xml \
-    && mvn clean package
+COPY src/ $CODE_PATH/src
 
-FROM hbpmip/java-base:11.0.1-1
+RUN mvn clean package
 
-RUN apt-get update && apt-get install -y --no-install-recommends curl jq
-RUN rm -rf /var/lib/apt/lists/* /tmp/*
+#######################################################
+# Setup the running container
+#######################################################
+FROM openjdk:11.0.15-jdk
+MAINTAINER Thanasis Karampatsis <tkarabatsis@athenarc.gr>
 
-COPY docker/config/application.tmpl /opt/portal/config/application.tmpl
-COPY docker/README.md docker/run.sh /opt/portal/
+#######################################################
+# Setting up timezone
+#######################################################
+ENV TZ=Etc/GMT
+RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
 
-RUN addgroup portal \
-    && adduser --system --disabled-password --uid 1000 --ingroup portal portal \
-    && chmod +x /opt/portal/run.sh \
-    && ln -s /opt/portal/run.sh /run.sh \
-    && chown -R portal:portal /opt/portal
+#######################################################
+# Setting up env variables and workdir
+#######################################################
+ENV APP_CONFIG_TEMPLATE="/opt/config/application.tmpl" \
+    APP_CONFIG_LOCATION="/opt/config/application.yml" \
+    SPRING_CONFIG_LOCATION="file:/opt/config/application.yml"
 
-COPY --from=java-build-env /project/target/portal-backend.jar /usr/share/jars/
+WORKDIR /opt
 
-ARG BUILD_DATE
-ARG VCS_REF
-ARG VERSION
 
-USER portal
-ENV APP_NAME="Portal backend" \
-    APP_TYPE="Spring" \
-    VERSION=$VERSION \
-    BUILD_DATE=$BUILD_DATE \
-    CONTEXT_PATH="/services" \
-    BUGSNAG_KEY="dff301aa15eb795a6d8b22b600586f77"
+#######################################################
+# Install dockerize
+#######################################################
+ENV DOCKERIZE_VERSION v0.6.1
+RUN wget https://github.com/jwilder/dockerize/releases/download/$DOCKERIZE_VERSION/dockerize-alpine-linux-amd64-$DOCKERIZE_VERSION.tar.gz \
+    && tar -C /usr/local/bin -xzvf dockerize-alpine-linux-amd64-$DOCKERIZE_VERSION.tar.gz \
+    && rm dockerize-alpine-linux-amd64-$DOCKERIZE_VERSION.tar.gz
 
-WORKDIR /home/portal
-ENTRYPOINT ["/run.sh"]
 
-EXPOSE 8080
+#######################################################
+# Prepare the spring boot application files
+#######################################################
+COPY /config/application.tmpl $APP_CONFIG_TEMPLATE
+COPY --from=mvn-build-env /opt/code/target/portal-backend.jar /usr/share/jars/
+
+
+#######################################################
+# Volume for the backend config files
+#######################################################
+VOLUME /opt/portal/api
 
+
+ENTRYPOINT ["sh", "-c", "dockerize -template $APP_CONFIG_TEMPLATE:$APP_CONFIG_LOCATION java -Daeron.term.buffer.length -jar /usr/share/jars/portal-backend.jar"]
+EXPOSE 8080
 HEALTHCHECK --start-period=60s CMD curl -v --silent http://localhost:8080/services/actuator/health 2>&1 | grep UP
 
-LABEL org.label-schema.build-date=$BUILD_DATE \
-      org.label-schema.name="hbpmip/portal-backend" \
-      org.label-schema.description="Spring backend for the MIP portal" \
-      org.label-schema.url="https://mip.humanbrainproject.eu" \
-      org.label-schema.vcs-type="git" \
-      org.label-schema.vcs-url="https://github.com/HBPMedical/portal-backend" \
-      org.label-schema.vcs-ref=$VCS_REF \
-      org.label-schema.version="$VERSION" \
-      org.label-schema.vendor="LREN CHUV" \
-      org.label-schema.license="AGPLv3" \
-      org.label-schema.docker.dockerfile="Dockerfile" \
-      org.label-schema.memory-hint="2048" \
-      org.label-schema.schema-version="1.0"
+

LICENSE

@@ -1,7 +1,7 @@
 Original developer’s Attribution Information
 ____________________________________________
 
-Attribution Copyright Notice: © 2016-2017 LREN CHUV.
+Attribution Copyright Notice: © 2016-2022 LREN CHUV.
 Attribution Phrase: Powered by the Medical Informatics Platform of the Human Brain Project
 Attribution URL: https://mip.humanbrainproject.eu
 

README.md

@@ -1,45 +1,44 @@
 [![CHUV](https://img.shields.io/badge/CHUV-LREN-AF4C64.svg)](https://www.unil.ch/lren/en/home.html) [![License](https://img.shields.io/badge/license-AGPL--3.0-blue.svg)](https://www.gnu.org/licenses/agpl-3.0.html)
 [![DockerHub](https://img.shields.io/badge/docker-hbpmip%2Fportal--backend-008bb8.svg)](https://hub.docker.com/r/hbpmip/portal-backend/)
-[![Codacy Badge](https://api.codacy.com/project/badge/Grade/05ba08087da24b3980475f88e1a591b7)](https://www.codacy.com/app/hbp-mip/portal-backend?utm_source=github.com&utm_medium=referral&utm_content=LREN-CHUV/portal-backend&utm_campaign=Badge_Grade)
-[![CircleCI](https://circleci.com/gh/LREN-CHUV/portal-backend/tree/master.svg?style=svg)](https://circleci.com/gh/LREN-CHUV/portal-backend/tree/master)
 
 # Backend for the MIP portal
 
-## Usage
-
-* Build a versioned image: `./build.sh`
-* Build and test an image: `./test.sh`
+## DEV Deployment
+To run the backend using an IDE for development, such as IntelliJ, you need a running instance of PostgreSQL.
 
 ## Deployment (using a Docker image)
+Build the image: ` docker build -t hbpmip/portal-backend:latest .`
 
-* See the [documentation for hbpmip/portal-backend Docker image](./docker/README.md)
-
-## Build
-
-Run: `./build.sh`
-
-## Publish on Docker Hub
-
-Run: `./publish.sh`
+To use this image, you need a running instance of PostgreSQL and to configure the software using the following environment variables.
 
-## License
+#### LOG LEVELS ###
+* LOG_LEVEL: log level for the developer added logs. Default is "ERROR".
+* LOG_LEVEL_FRAMEWORK: log level for all the framework logs. Default is "ERROR".
 
-Copyright © 2016-2017 LREN CHUV
+#### AUTHENTICATION ###
+* AUTHENTICATION: true for production, false for development.
 
-Licensed under the GNU Affero General Public License, Version 3.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
+#### DATABASE CONFIGURATION ###
+* PORTAL_DB_URL: JDBC URL to connect to the portal database, default value is "jdbc:postgresql://127.0.0.1:5432/portal".
+* PORTAL_DB_SCHEMA: Database schema, default value is "public".
+* PORTAL_DB_USER: User to use when connecting to the portal database, default value is "postgres".
+* PORTAL_DB_PASSWORD: Password to use when connecting to the portal database.
 
-   [https://www.gnu.org/licenses/agpl-3.0.html](https://www.gnu.org/licenses/agpl-3.0.html)
+#### EXTERNAL SERVICES ###
+* MIPENGINE_URL: URL to MIPENGINE server. Default is "http://localhost:5000" .
+* EXAREME_URL: URL to Exareme server. Default is "http://localhost:9090" .
+* GALAXY_URL: URL to Workflow server. Default is "http://localhost:8090/" .
+* GALAXY_API_KEY: The api key to authorize galaxy requests.
+* GALAXY_USERNAME: The username of galaxy user to be able to embed the frame.
+* GALAXY_PASSWORD: The password of galaxy user.
 
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
+#### KEYCLOAK ###
+* KEYCLOAK_AUTH_URL: Keycloak authentication URL.
+* KEYCLOAK_REALM: Keycloak realm user for authentication.
+* KEYCLOAK_CLIENT_ID: The keycloak client id.
+* KEYCLOAK_CLIENT_SECRET: The keycloak secret to be able to authenticate.
 
 # Acknowledgements
 
 This work has been funded by the European Union Seventh Framework Program (FP7/2007­2013) under grant agreement no. 604102 (HBP)
 
-This work is part of SP8 of the Human Brain Project (SGA1).