Add config and build scripts (#1)

* Add default ala config template

* Update config from production

* Add config files from ala-install

* Update configs from prod

* Update config. Add Makefile, docker-compose and Dockerfile

* Add build workflow and readme

* Removed log4j.xml

* Update config

* Update docker compose

.github/workflows/build.yml

@@ -0,0 +1,59 @@
+name: Build
+
+on:
+  push:
+    branches:
+      - '*'
+    tags:
+      - '*'
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout project sources
+        uses: actions/checkout@v4
+
+      - name: Setup Java
+        uses: actions/setup-java@v3
+        with:
+          java-version: '11'
+          distribution: 'temurin'
+
+      - name: Setup Gradle
+        uses: gradle/gradle-build-action@v2
+
+      - name: Run build with Gradle Wrapper
+        run: ./gradlew build -x test
+
+      - name: Upload war
+        uses: actions/upload-artifact@v3
+        with:
+          name: package
+          path: build/libs
+
+      - name: Log in to the Container registry
+        if: github.event_name == 'push' && contains(github.ref, 'refs/tags/')
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        if: github.event_name == 'push' && contains(github.ref, 'refs/tags/')
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ghcr.io/${{ github.repository }}
+
+      - name: Build and push Docker image
+        if: github.event_name == 'push' && contains(github.ref, 'refs/tags/')
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

Dockerfile

@@ -0,0 +1,29 @@
+FROM tomcat:9.0-jdk11-temurin
+
+ENV TZ=Europe/Stockholm
+
+RUN mkdir -p  \
+    /data/biocache/config \
+    /data/biocache/heatmap \
+    /data/biocache/tmp \
+	/data/biocache-load \
+	/data/biocache-media \
+	/data/biocache-upload \
+	/data/biocache-delete \
+	/data/biocache-download/tmp \
+    /data/cache \
+    /data/offline/exports \
+    /data/logger-client/config
+
+COPY sbdi/data/config/*.json /data/biocache/config/
+COPY sbdi/data/config/*.xml /data/biocache/config/
+COPY sbdi/data/config/*.html /data/biocache/config/
+
+COPY build/libs/biocache-service-*.war $CATALINA_HOME/webapps/ws.war
+
+ENV DOCKERIZE_VERSION v0.7.0
+
+RUN apt-get update \
+    && apt-get install -y wget \
+    && wget -O - https://github.com/jwilder/dockerize/releases/download/$DOCKERIZE_VERSION/dockerize-linux-amd64-$DOCKERIZE_VERSION.tar.gz | tar xzf - -C /usr/local/bin \
+    && apt-get autoremove -yqq --purge wget && rm -rf /var/lib/apt/lists/*

Makefile

@@ -0,0 +1,14 @@
+run:
+	docker compose up cassandra solr --detach
+	./gradlew bootRun
+
+# Change cassandra and solr connections in biocache-config.properties for this to work
+# Replace localhost with cassandra and solr respectively
+# Also, the service may fail on startup if cassandra isn't ready. Just restart the service if that happens.
+run-docker:
+	./gradlew clean build -x test
+	docker compose build --no-cache
+	docker compose up --detach
+
+release:
+	../sbdi-install/utils/make-release.sh

docker-compose.yml

@@ -0,0 +1,40 @@
+version: '3.8'
+
+services:
+
+  cassandra:
+    image: cassandra:3.11
+    environment:
+      MAX_HEAP_SIZE: 128M
+      HEAP_NEWSIZE: 24M
+    ports:
+      - 9042:9042
+    volumes:
+      - db_cassandra:/var/lib/cassandra
+
+  solr:
+    image: ghcr.io/biodiversitydata-se/biocache-solr:1.0.0
+    #image: sbdi/biocache-solr-dev
+    environment:
+      SOLR_HEAP: 4g
+      SOLR_OPTS: "-Dlog4j2.formatMsgNoLookups=true"
+    #build:
+    #  context: ../biocache-solr
+    ports:
+      - "8983:8983"
+    volumes:
+      - data_solr:/var/solr
+
+  biocache-service:
+    image: sbdi/biocache-service-dev
+    build:
+      context: .
+    ports:
+      - 8080:8080
+    volumes:
+      - ./sbdi/data/config/biocache-config.properties:/data/biocache/config/biocache-config.properties
+      - ./sbdi/data/config/logger-client.properties:/data/logger-client/config/logger-client.properties
+
+volumes:
+  db_cassandra:
+  data_solr:

sbdi/README.md

@@ -0,0 +1,54 @@
+# Biocache-service
+
+## Setup
+This service requires a rather elaborate directory and file structure in `/data/`:
+```
+mats@xps-13:/data$ tree biocache* cache offline logger-client
+biocache
+├── config
+│   ├── applicationContext.xml -> /home/mats/src/biodiversitydata-se/biocache-service/sbdi/data/config/applicationContext.xml
+│   ├── biocache-config.properties -> /home/mats/src/biodiversitydata-se/biocache-service/sbdi/data/config/biocache-config.properties
+│   ├── download-csdm-email.html -> /home/mats/src/biodiversitydata-se/biocache-service/sbdi/data/config/download-csdm-email.html
+│   ├── download-doi-email.html -> /home/mats/src/biodiversitydata-se/biocache-service/sbdi/data/config/download-doi-email.html
+│   ├── download-doi-readme.html -> /home/mats/src/biodiversitydata-se/biocache-service/sbdi/data/config/download-doi-readme.html
+│   ├── download-email.html -> /home/mats/src/biodiversitydata-se/biocache-service/sbdi/data/config/download-email.html
+│   ├── download-readme.html -> /home/mats/src/biodiversitydata-se/biocache-service/sbdi/data/config/download-readme.html
+│   ├── facets.json -> /home/mats/src/biodiversitydata-se/biocache-service/sbdi/data/config/facets.json
+│   ├── groups.json -> /home/mats/src/biodiversitydata-se/biocache-service/sbdi/data/config/groups.json
+│   ├── pipelines-field-config.json -> /home/mats/src/biodiversitydata-se/biocache-service/sbdi/data/config/pipelines-field-config.json
+│   └── subgroups.json -> /home/mats/src/biodiversitydata-se/biocache-service/sbdi/data/config/subgroups.json
+├── heatmap
+└── tmp
+biocache-delete
+biocache-download
+biocache-load
+biocache-media
+biocache-upload
+cache
+offline
+└── exports
+logger-client
+└── config
+   └── logger-client.properties -> /home/mats/src/biodiversitydata-se/biocache-service/sbdi/data/config/logger-client.properties
+```
+
+## Usage
+
+Run locally:
+```
+make run
+```
+
+Build and run in Docker (using Tomcat):
+```
+make run-docker
+```
+
+Make a release. This will create a new tag and push it. A new Docker container will be built on Github.
+```
+mats@xps-13:~/src/biodiversitydata-se/biocache-service (master *)$ make release
+
+Current version: 1.0.1. Enter the new version (or press Enter for 1.0.2): 
+Updating to version 1.0.2
+Tag 1.0.2 created and pushed.
+```

sbdi/data/config/applicationContext.xml

@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans"
+       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+       xmlns:p="http://www.springframework.org/schema/p"
+       xmlns:context="http://www.springframework.org/schema/context"
+       xmlns:jms="http://www.springframework.org/schema/jms"
+       xmlns:amq="http://activemq.apache.org/schema/core"
+       xsi:schemaLocation="http://www.springframework.org/schema/beans
+                                           http://www.springframework.org/schema/beans/spring-beans-3.0.xsd
+                                           http://www.springframework.org/schema/context
+                                           http://www.springframework.org/schema/context/spring-context-3.0.xsd
+                           http://www.springframework.org/schema/jms
+                           http://www.springframework.org/schema/jms/spring-jms.xsd
+                           http://activemq.apache.org/schema/core
+                           http://activemq.apache.org/schema/core/activemq-core.xsd">
+
+<!-- Example ActiveMQ JMS settings
+    <bean id="jmsMessageListener" class="org.ala.jms.service.JmsMessageListener" />
+         <bean id="jmsConnectionFactory" class="org.apache.activemq.ActiveMQConnectionFactory">
+                <property name="brokerURL" value="tcp://localhost:61616" />             
+                <property name="userName" value="system" />
+                <property name="password" value="manager" />
+        </bean> 
+        <bean id="pooledJmsConnectionFactory" class="org.apache.activemq.pool.PooledConnectionFactory"
+          destroy-method="stop">
+                <property name="connectionFactory" ref="jmsConnectionFactory" />
+        </beans>
+        <jms:listener-container container-type="default" 
+                                connection-factory="pooledJmsConnectionFactory"
+                                acknowledge="auto">
+                <jms:listener destination="au.org.ala.cs" ref="jmsMessageListener" />
+        </jms:listener-container>
+</beans>
+-->
+
+</beans>