Merge pull request #1 from biodiversitydata-se/sbdi-dev

Add config files and scripts

.github/workflows/build.yml

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+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 -x integrationTest
+
+      - 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

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+FROM tomcat:9.0-jdk11-temurin
+
+ENV TZ=Europe/Stockholm
+
+RUN mkdir -p  \
+    /data/spatial-service/config \
+    /data/spatial-data
+
+COPY build/libs/spatial-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

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+run:
+	docker compose up --detach postgis geoserver
+	./gradlew bootRun
+
+# In spatial-service-config-yml you need to change dataSource.url to 'postgis'
+# and geoserver.url to 'geoserver:8079' for this to work
+run-docker:
+	./gradlew war
+	docker compose build --no-cache
+	docker compose up --detach
+
+release:
+	@./sbdi/make-release.sh

docker-compose.yml

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+version: '3.7'
+
+services:
+
+  geoserver:
+    image: ghcr.io/biodiversitydata-se/geoserver:1.0.0
+    #image: sbdi/geoserver-dev
+    #build:
+    #  context: ../geoserver
+    environment:
+      JAVA_OPTS: -Xmx2g -Xms128m -Xss512k -Djava.awt.headless=true
+      TZ: Europe/Stockholm
+    env_file: ./docker/env/geoserver/.envgeoserver
+    volumes:
+      - /data/geoserver_data_dir:/data/geoserver_data_dir
+      - /data/spatial-data:/data/spatial-data
+    ports:
+      - "8079:8080"
+
+  postgis:
+    image: postgis/postgis:13-3.4
+    environment:
+      POSTGRES_USER: postgres
+      POSTGRES_PASSWORD: postgres
+      POSTGRES_HOST_AUTH_METHOD: md5
+      TZ: Europe/Stockholm
+    ports:
+      - "5432:5432"
+    volumes:
+      - db_data_spatial-service:/var/lib/postgresql/data
+      - ./docker/env/postgis/layersdb.sql:/docker-entrypoint-initdb.d/layersdb.sql
+
+  spatial-service:
+    image: sbdi/spatial-service-dev
+    build:
+      context: .
+    ports:
+      - "8080:8080"
+    volumes:
+      - ./sbdi/data/config/spatial-service-config.yml:/data/spatial-service/config/spatial-service-config.yml
+
+volumes:
+  db_data_spatial-service:

sbdi/README.md

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+# Spatial-service
+
+## Setup
+
+### Config and data directory
+Create data directory at `/data/spatial-service` and populate as below (it is easiest to symlink the config files to the ones in this repo):
+```
+mats@xps-13:/data/spatial-service$ tree 
+.
+└── config
+    └── spatial-service-config.yml -> /home/mats/src/biodiversitydata-se/spatial-service/sbdi/data/config/spatial-service-config.yml
+```
+
+You'll also need to create the directories `/data/spatial-data` and `/data/geoserver_data_dir`. 
+
+### Database
+An empty database will be created the first time the application starts. You can then export the database from production and import it.
+
+### GeoServer
+By default the development configuration will use a local GeoServer running at http://localhost:8079/geoserver. Alternatively you can use the production GeoServer (for read-only). Change `geoserver.url` to https://spatial.biodiversitydata.se/geoserver.
+
+## 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/spatial-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/spatial-service-config.yml

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+#
+# au.org.ala.spatial.service config
+#
+data:
+  dir: '/data/spatial-data'
+geoserver:
+  url: 'http://localhost:8079/geoserver'
+  #url: 'https://spatial.biodiversitydata.se/geoserver'
+  username: 'admin'
+  password: 'geoserver'
+  canDeploy: true
+# To use a remote geoserver instance, set geoserver.remote.geoserver_data_dir to the geoserver_data_dir path on the
+# remote server. This will cause layer files to be copied to geoserver_data_dir/data/
+#  remote:
+  geoserver_data_dir: "/data/geoserver_data_dir"
+
+shpResolutions: [0.5, 0.25, 0.1, 0.05]
+grdResolutions: [0.5, 0.25, 0.1, 0.05, 0.01]
+
+biocacheServiceUrl: "https://records.biodiversitydata.se/ws"
+biocacheUrl: "https://records.biodiversitydata.se"
+openstreetmap:
+  url: "https://tile.openstreetmap.org"
+
+slave.enable: true
+service.enable: true
+
+batch_sampling_passwords: ""
+batch_sampling_points_limit: 1000000
+batch_sampling_fields_limit: 1000
+
+---
+#
+# au.org.ala.spatial.slave config
+#
+spatialService.url: "http://localhost:8080/ws"
+shp2pgsql.path: "/usr/bin/shp2pgsql"
+gdal.dir: "/usr/bin/"
+gdm.dir: "/data/spatial-data/modelling/gdm/DoGdm"
+
+aloc.xmx: "6G"
+aloc.threads: 4
+maxent.mx: "1G"
+maxent.threads: 4
+
+sampling.threads: 4
+
+slaveKey: ""
+serviceKey: ""
+
+# time between pushing status updates to the master for a task
+statusTime: 3000
+retryCount: 10
+retryTime: 30000
+
+#
+#  CAS SETTINGS
+#
+#  NOTE: Some of these will be ignored if default_config exists
+security:
+  cas:
+    appServerName: http://localhost:8080
+    casServerName: https://auth.biodiversitydata.se
+    casServerUrlPrefix: https://auth.biodiversitydata.se/cas
+    loginUrl: https://auth.biodiversitydata.se/cas/login
+    logoutUrl: https://auth.biodiversitydata.se/cas/logout
+    enabled: true
+    bypass: false
+    disableCAS: false
+    gateway: false
+  apikey:
+    check:
+      serviceUrl:  https://auth.biodiversitydata.se/apikey/ws/check?apikey={0}
+  oidc:
+    enabled: false
+  jwt:
+    enabled: false
+
+
+auth.admin_role: ROLE_ADMIN
+app.http.header.userId: X-ALA-userId
+
+headerAndFooter:
+  baseURL: "https://static.biodiversitydata.se"
+  version: "2"
+
+ala.baseURL: https://biodiversitydata.se
+bie.baseURL: https://species.biodiversitydata.se
+bie.searchPath: '/search'
+
+records.url: https://archives.ala.org.au/archives/exports/lat_lon_taxon.zip
+
+api_key:
+lists.url: https://lists.biodiversitydata.se
+collections.url: https://collections.biodiversitydata.se
+sandboxHubUrl:
+sandboxBiocacheServiceUrl:
+phyloServiceUrl:
+
+spatialHubUrl: https://spatial.biodiversitydata.se
+
+gazField: ""
+userObjectsField: ""
+
+#apiKeyCheckUrlTemplate: "https://auth.ala.org.au/apikey/ws/check?apikey={0}"
+spatialService.remote: ""
+
+journalmap.api_key:
+journalmap.url: https://www.journalmap.org/
+
+# For side by side installation with layers-service, analysis-service
+#legacy.workingdir: '/data/ala/data/alaspatial/'
+
+#legacy.enabled: true
+
+#legacy compatability type
+#"link" = link legacy files into new locations
+#"copy" = copy legacy files into new locations
+#"move" = move legacy files into new locations
+#legacy.type="link"
+
+#legacy.ANALYSIS_LAYER_FILES_PATH: '/data/ala/data/layers/analysis/'
+#legacy.LAYER_FILES_PATH: '/data/ala/data/layers/ready'
+#legacy.ALASPATIAL_OUTPUT_PATH: '/data/ala/runtime/output'
+
+grails.plugin.elfinder.rootDir: '/data/spatial-service'
+
+i18n.override.dir: '/data/spatial-service/config/i81n/'
+
+
+#layers-store config
+
+#Threads created for each batch intersection and each individual shape file
+#layers_store.BATCH_THREAD_COUNT: 3
+
+#Set LAYER_INDEX_URL to use REMOVE layer intersections.
+#layers_store.LAYER_INDEX_URL: https://spatial.ala.org.au/layers-service
+
+#Use local layer files for sampling or the /intersect/batch service provided by LAYER_INDEX_URL
+#layers_store.LOCAL_SAMPLING: false
+layers_store.LOCAL_SAMPLING: true
+
+# Set intersect config reload time in ms
+#layers_store.CONFIG_RELOAD_WAIT: 12000000
+
+#Comma separated shape file fields to preload, or 'all'
+#layers_store.PRELOADED_SHAPE_FILES: all
+#layers_store.PRELOADED_SHAPE_FILES: cl22,cl20
+
+# Grid intersection buffer size in bytes.  Must be multiple of 64.
+# Only applies to grids > 80MB.
+# layers_store.GRID_BUFFER_SIZE=4096
+#layers_store.GRID_BUFFER_SIZE: 40960
+
+# Number of GridCacheReader objects to open.
+#layers_store.GRID_CACHE_READER_COUNT: 5
+
+# layers_store ingestion
+#layers_store.CAN_INGEST_LAYERS: false
+#layers_store.CAN_UPDATE_LAYER_DISTANCES: false
+#layers_store.CAN_UPDATE_GRID_CACHE: false
+#layers_store.CAN_GENERATE_ANALYSIS_FILES: false
+#layers_store.CAN_INTERSECT_LAYERS: false
+#layers_store.CAN_GENRATE_THUMBNAILS: false
+
+#layers_store.FIELD_STYLES: true
+
+layers_store.GEONETWORK_URL: 'https://spatial.biodiversitydata.se/geonetwork'
+
+distributions.cache.dir: "/data/spatial-service/mapCache/"
+distributions.geoserver.image.url: "/ALA/wms?service=WMS&version=1.1.0&request=GetMap&sld=https://fish.ala.org.au/data/dist.sld&layers=ALA:aus1,ALA:Distributions&styles=&bbox=109,-47,157,-7&srs=EPSG:4326&format=image/png&width=400&height=400&viewparams=s:"
+
+dataSource:
+    url: 'jdbc:postgresql://localhost/layersdb'
+    username: layers
+    password: layers
+
+grails.serverURL: http://localhost:8080/ws
+grails.app.context: /ws
+
+skin.layout: main
+skin.fluidLayout: false
+skin.orgNameLong: Swedish Biodiversity Data Infrastructure
+skin.orgNameShort: SBDI
+skin.favicon: https://static.biodiversitydata.se/favicon.ico
+skin.homeUrl: https://tools.biodiversitydata.se
+
+grails.controllers.upload.maxFileSize: 2097152000
+grails.controllers.upload.maxRequestSize: 2097152000
+
+# Needed for map exports
+google:
+  apikey: "AIzaSyAJDtEeoy7Sc9pij2TAoVnmTwA34Q-2VHk"
+
+logging:
+  level:
+    root: INFO
+
+userdetails:
+    baseUrl: "https://auth.biodiversitydata.se/userdetails"
+
+# ala-auth-plugin conf
+userDetails:
+    url: "https://auth.biodiversitydata.se/userdetails"