Add config files and build scripts (#1)

* Added config file

* Add Makefile and docker-compose.yml

* Add Dockerfile

* Remove noise from logs

* Changed jdbc driver

* Add README, make-release and build workflow. Tweaked Docker file

.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@v3
+
+      - 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
+
+      - 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@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        if: github.event_name == 'push' && contains(github.ref, 'refs/tags/')
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ghcr.io/${{ github.repository }}
+
+      - name: Build and push Docker image
+        if: github.event_name == 'push' && contains(github.ref, 'refs/tags/')
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

Dockerfile

@@ -0,0 +1,12 @@
+FROM tomcat:9.0-jdk11-temurin
+
+RUN mkdir -p /data/logger/config
+
+COPY build/libs/logger-service-*-plain.war $CATALINA_HOME/webapps/ROOT.war
+
+ENV DOCKERIZE_VERSION v0.7.0
+
+RUN apt-get update \
+    && apt-get install -y wget \
+    && wget -O - https://github.com/jwilder/dockerize/releases/download/$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 +1,13 @@
+run:
+	docker compose up --detach mysqldb
+	./gradlew bootRun
+
+# You need to change dataSource.url in logger-config.properties
+# to use 'mysqldb' instead of '127.0.0.1' for this to work
+run-docker:
+	./gradlew build
+	docker compose build --no-cache
+	docker compose up --detach
+
+release:
+	@./sbdi/make-release.sh

docker-compose.yml

@@ -0,0 +1,33 @@
+services:
+
+  mysqldb:
+    image: mysql:5.7
+    volumes:
+      - db_data_logger:/var/lib/mysql
+    environment:
+      MYSQL_ALLOW_EMPTY_PASSWORD: 1
+      MYSQL_DATABASE: logger
+      MYSQL_USER: logger
+      MYSQL_PASSWORD: logger
+    ports:
+      - 3306:3306
+
+  logger:
+    depends_on:
+      - mysqldb
+    image: sbdi/logger-dev
+    build:
+      context: .
+    ports:
+      - 8080:8080
+    volumes:
+      - ./sbdi/data/config/logger-config.properties:/data/logger/config/logger-config.properties
+
+volumes:
+  db_data_logger:
+#  db_data_logger_prod:
+#    driver: local
+#    driver_opts:
+#      type: none
+#      o: bind
+#      device: "/home/mats/Documents/sbdi/logger/db_data_logger"

grails-app/conf/logback.xml

@@ -11,6 +11,14 @@
         </encoder>
     </appender>
 
+    <!-- SBDI: this is to get rid of noise in the logs -->
+    <logger name="org.grails.config.NavigableMap" level="ERROR">
+        <appender-ref ref="STDOUT" />
+    </logger>
+    <logger name="org.hibernate.orm.deprecation" level="ERROR">
+        <appender-ref ref="STDOUT" />
+    </logger>
+
     <root level="warn">
         <appender-ref ref="STDOUT" />
     </root>

sbdi/README.md

@@ -0,0 +1,35 @@
+# Logger
+
+## Setup
+
+### Config and data directory
+Create data directory at `/data/logger` and populate as below (it is easiest to symlink the config files to the ones in this repo):
+```
+mats@xps-13:/data/logger$ tree
+.
+└── config
+    └── logger-config.properties -> /home/mats/src/biodiversitydata-se/logger-service/sbdi/data/config/logger-config.properties
+```
+
+### Database
+An empty database will be created the first time the application starts. You can then export the database from production using `mysqldump` and import it.
+
+## Usage
+Run locally:
+```
+make run
+```
+
+Build and run in Docker (using Tomcat). This requires a small change in the config file to work. See comment in Makefile.
+```
+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/logger (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/logger-config.properties

@@ -0,0 +1,58 @@
+# CAS Config
+security.cas.appServerName=http://localhost:8080
+security.cas.loginUrl=https://auth.biodiversitydata.se/cas/login
+security.cas.logoutUrl=https://auth.biodiversitydata.se/cas/logout
+gateway=false
+security.cas.adminRole=ROLE_ADMIN
+disableCAS=false
+security.cas.casServerName=https://auth.biodiversitydata.se
+security.cas.casServerUrlPrefix=https://auth.biodiversitydata.se/cas
+security.cas.authCookieName=
+#security.cas.authenticateOnlyIfLoggedInFilterPattern=/,/apps,/category
+security.cas.bypass=false
+userDetails.url = https://auth.biodiversitydata.se/userdetails/
+
+# Legacy CAS properties
+casProperties=casServerLoginUrl,serverName,centralServer,casServerName,uriFilterPattern,uriExclusionFilter,authenticateOnlyIfLoggedInFilterPattern,casServerLoginUrlPrefix,gateway,casServerUrlPrefix,contextPath
+casServerName=https://auth.biodiversitydata.se
+casServerUrlPrefix=https://auth.biodiversitydata.se
+casServerLoginUrl=https://auth.biodiversitydata.se/login
+
+ala.admin.systemMessage.path=/data/logger/config
+
+# Grails config
+serverURL=http://localhost:8080
+grails.serverURL=http://localhost:8080
+serverName=http://localhost:8080
+contextPath=
+
+# Data Source properties
+dataSource.dbCreate=none
+dataSource.driverClassName=com.mysql.cj.jdbc.Driver
+#dataSource.dialect=org.hibernate.dialect.MySQL8Dialect
+dataSource.url=jdbc\:mysql\://127.0.0.1/logger?autoReconnect=true&connectTimeout=0&useUnicode=true&characterEncoding=UTF-8&useSSL=false&serverTimezone=Europe/Stockholm
+dataSource.username=logger
+dataSource.password=logger
+
+# Header and footer
+headerAndFooter.baseURL=https://static.biodiversitydata.se
+headerAndFooter.version=2
+ala.baseURL=https://biodiversitydata.se
+bie.baseURL=https://species.biodiversitydata.se
+bie.searchPath=/search
+collectoryUrl=https://collections.biodiversitydata.se
+
+#skin.layout=
+skin.orgNameLong=Swedish Biodiversity Data Infrastructure
+skin.orgNameShort = SBDI
+skin.orgSupportEmail=gbif@nrm.se
+privacyPolicy=
+
+#oidc related
+security.cas.enabled=true
+security.oidc.enabled=false
+security.oidc.clientId=
+security.oidc.secret=
+security.oidc.discoveryUri=
+security.jwt.enabled=false
+security.jwt.discoveryUri=

sbdi/make-release.sh

@@ -0,0 +1,33 @@
+#!/bin/bash
+
+# Get the last GitHub tag version
+last_tag=$(git describe --tags --abbrev=0)
+
+major=$(echo "$last_tag" | cut -d. -f1)
+minor=$(echo "$last_tag" | cut -d. -f2)
+patch=$(echo "$last_tag" | cut -d. -f3)
+
+new_patch=$((patch + 1))
+
+echo
+read -p "Current version: $last_tag. Enter the new version (or press Enter for $major.$minor.$new_patch): " new_version_input
+
+if [ -z "$new_version_input" ]; then
+    new_version="$major.$minor.$new_patch"
+else
+    new_version="$new_version_input"
+fi
+
+# Validate the new version format (assuming it follows semantic versioning)
+if ! [[ "$new_version" =~ ^[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
+    echo "Invalid version format. Please use semantic versioning (e.g., 1.2.3)."
+    exit 1
+fi
+
+echo "Updating to version $new_version"
+
+# Create a new tag
+git tag "$new_version"
+git push origin "$new_version"
+
+echo "Tag $new_version created and pushed."