Add config and build scripts (#1)

* Add config

* Add Makefile, Dockerfile and docker-compose.yml

* Add build workflow and readme

.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@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
+
+      - 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

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+FROM tomcat:9.0-jdk11-temurin
+
+ENV TZ=Europe/Stockholm
+
+RUN mkdir -p /data/ala-hub/config
+
+COPY sbdi/data/config/charts.json /data/ala-hub/config/charts.json
+COPY sbdi/data/config/grouped_facets_default.json /data/ala-hub/config/grouped_facets_default.json
+
+COPY build/libs/ala-hub-*-plain.war $CATALINA_HOME/webapps/ROOT.war

Makefile

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+run:
+	./gradlew bootRun
+
+run-docker:
+	./gradlew clean build
+	docker compose build --no-cache
+	docker compose up --detach
+
+release:
+	../sbdi-install/utils/make-release.sh

docker-compose.yml

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+version: '3.8'
+
+services:
+
+  ala-hub:
+    image: sbdi/ala-hub-dev
+    build:
+      context: .
+    ports:
+      - 8080:8080
+    volumes:
+      - ./sbdi/data/config/ala-hub-config.properties:/data/ala-hub/config/ala-hub-config.properties

sbdi/README.md

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+# Ala-hub
+
+## Setup
+
+Create data directory at `/data/ala-hub` and populate as below (it is easiest to symlink the config files to the ones in this repo):
+```
+mats@xps-13:/data/ala-hub$ tree
+.
+└── config
+    ├── ala-hub-config.properties -> /home/mats/src/biodiversitydata-se/ala-hub/sbdi/data/config/ala-hub-config.properties
+    ├── charts.json -> /home/mats/src/biodiversitydata-se/ala-hub/sbdi/data/config/charts.json
+    └── grouped_facets_default.json -> /home/mats/src/biodiversitydata-se/ala-hub/sbdi/data/config/grouped_facets_default.json
+```
+
+## 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/ala-hub (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/ala-hub-config.properties

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+# Grails settings
+grails.serverURL=http://localhost:8080
+grails.resources.work.dir=/data/ala-hub/cache
+
+
+
+# CAS Config
+serverName=http://localhost:8080
+security.cas.casServerName=https://auth.biodiversitydata.se
+security.cas.appServerName=http://localhost:8080
+security.cas.casServerUrlPrefix=https://auth.biodiversitydata.se/cas
+security.cas.casServerLoginUrl=https://auth.biodiversitydata.se/cas/login
+security.cas.casServerLogoutUrl=https://auth.biodiversitydata.se/cas/logout
+security.cas.loginUrl=https://auth.biodiversitydata.se/cas/login
+security.cas.logoutUrl=https://auth.biodiversitydata.se/cas/logout
+security.cas.uriFilterPattern=/admin.*,/alaAdmin.*,/download.*
+security.cas.authenticateOnlyIfLoggedInFilterPattern=/occurrences/*,/explore/your-area,/query,/proxy/download/*,
+security.cas.bypass=false
+disableCAS=false
+
+server.address=localhost
+server.port=8080
+server.servlet.contextPath=
+# Default Locale
+defaultLocale=en
+
+# Legacy CAS properties
+casProperties=casServerLoginUrl,serverName,centralServer,casServerName,uriFilterPattern,uriExclusionFilterPattern,authenticateOnlyIfLoggedInFilterPattern,casServerLoginUrlPrefix,gateway,casServerUrlPrefix,contextPath
+uriFilterPattern=/admin*,/alaAdmin*,/download*
+uriExclusionFilterPattern=/occurrences/shapeUpload,/images.*,/css.*,/js.*,.*json,/help/.*
+authenticateOnlyIfLoggedInFilterPattern=/occurrences/*,/explore/your-area,/query,/proxy/download/*
+casServerName=https://auth.biodiversitydata.se
+casServerUrlPrefix=https://auth.biodiversitydata.se/cas
+casServerLoginUrl=https://auth.biodiversitydata.se/cas/login
+casServerLogoutUrl=https://auth.biodiversitydata.se/cas/logout
+
+# Data Quality settings
+dataquality.enabled=false
+dataquality.baseUrl=https://dataquality.ala.org.au/
+dataquality.learnmore_link=
+dataquality.apiKey=
+dataquality.warningOn=
+dataquality.disableAllFiltersByDefault=false
+dataquality.expandFiltersByDefault=true
+
+# App settings
+organisation.baseUrl=https://biodiversitydata.se
+
+# skin
+skin.homeUrl=https://tools.biodiversitydata.se
+skin.layout=ala
+skin.favicon=https://static.biodiversitydata.se/favicon.ico
+skin.fluidLayout=true
+skin.orgNameLong=Swedish Biodiversity Data Infrastructure
+skin.orgNameShort=SBDI
+skin.attribution=
+skin.useAlaBie=true
+skin.useAlaSpatialPortal=trye
+skin.useAlaImageService=true
+skin.taxaLinks.baseUrl=https://species.biodiversitydata.se/species/
+skin.dataQualityLink.show=true
+skin.dataQualityLink.url=
+skin.dataQualityLink.text=not set
+skin.exploreUrl=
+supportEmail=support@biodiversitydata.se
+
+images.images.metadataUrl=
+bie.baseUrl=https://species.biodiversitydata.se
+bieService.baseUrl=https://species.biodiversitydata.se/ws
+bie.searchPath=/search
+biocache.apiKey=bee2bf23-c554-41dc-8b18-363c59949ad7
+biocache.queryContext=
+biocache.baseUrl=https://records.biodiversitydata.se/ws
+biocache.url=https://records.biodiversitydata.se
+biocacheServiceUrl=https://records.biodiversitydata.se/ws
+# bicoacheServicesUrl maintained for backwards compatibility with < biocache_hubs 5.0
+biocacheServicesUrl=https://records.biodiversitydata.se/ws
+biocache.downloads.extra=
+biocache.ajax.useProxy=false
+biocache.groupedFacetsUrl=
+biocache.indexedFieldsUrl=https://records.biodiversitydata.se/ws/index/fields
+collectory.baseUrl=https://collections.biodiversitydata.se
+collections.baseUrl=https://collections.biodiversitydata.se
+collectory.resources=https://collections.biodiversitydata.se/public/resources.json
+spatial.baseUrl=https://spatial.biodiversitydata.se
+spatial.baseURL=https://spatial.biodiversitydata.se
+layersservice.baseUrl=https://spatial.biodiversitydata.se/ws
+layersservice.url=https://spatial.biodiversitydata.se/ws
+# userDetails.url is not used by the hubs but by the ala-auth plugin
+userDetails.url=https://auth.biodiversitydata.se/userdetails/
+# userdetails.baseUrl is used by the hubs
+userdetails.baseUrl=https://auth.biodiversitydata.se/userdetails
+doiService.baseUrl=https://doi.ala.org.au
+logger.baseUrl=https://logger.biodiversitydata.se/service
+loggerURL=https://logger.biodiversitydata.se/service
+sightings.baseUrl=
+
+# Image viewer
+image.baseUrl=https://images.biodiversitydata.se
+images.baseUrl=https://images.biodiversitydata.se
+images.viewerUrl=https://images.biodiversitydata.se/image/viewer?imageId=
+images.metadataUrl=https://images.biodiversitydata.se/image/details?imageId=
+alwaysshow.imagetab=false
+
+#spatial.params=&dynamic=true&ws=http%3A%2F%2Fsandbox.ala.org.au%2Fhubs-webapp&bs=http%3A%2F%2Fsandbox.ala.org.au%2Fbiocache-service
+spatial.params=
+
+# ROLE for access to sensitive records
+clubRoleForHub=
+
+# URL for data quality checks
+dataQualityChecksUrl=https://docs.google.com/spreadsheet/pub?key=0AjNtzhUIIHeNdHJOYk1SYWE4dU1BMWZmb2hiTjlYQlE&single=true&gid=0&output=csv'
+
+# Default view for search results
+defaultListView=
+
+# dwc values to exclude from occurrence record pages
+dwc.exclude=dataHubUid,dataProviderUid,institutionUid,year,month,day,modified,left,right,provenance,preferredFlag,outlierForLayers,speciesGroups,associatedMedia,images,userQualityAssertion,speciesHabitats,duplicationType,taxonomicIssues,subspeciesID,nameMatchMetric,sounds
+
+# Explore your area defaults
+exploreYourArea.lat=62.38663
+exploreYourArea.lng=16.32130
+exploreYourArea.location=Sweden
+
+# Table display
+table.displayDynamicProperties=true
+
+# Facet configuration
+facets.limit=100
+facets.customOrder=
+facets.defaultColourBy=basis_of_record
+facets.includeDynamicFacets=false
+facets.exclude=state
+facets.hide=
+facets.include=
+# facets cached affects the advanced search. Please include indexed fields that are used in drop downs
+facets.cached=species_group,species_subgroup,country,institution_uid,collection_uid,data_resource_uid,institution_name,collection_name,data_resource
+facets.defaultSelected=basis_of_record,taxon_name,institution_name,collection_name,data_resource,year
+facets.max=16
+
+# Mapping
+map.cloudmade.key=BC9A493B41014CAABB98F0471D759707
+map.defaultLatitude=62.38663
+map.defaultLongitude=16.32130
+map.defaultZoom=4
+map.defaultFacetMapColourBy=basis_of_record
+map.pointColour=df4a21
+map.zoomOutsideScopedRegion=true
+map.height=600
+geocode.region=SE
+
+map.minimal.url=https://cartodb-basemaps-{s}.global.ssl.fastly.net/light_all/{z}/{x}/{y}.png
+map.overlay.url=https://spatial.biodiversitydata.se/geoserver/gwc/service/wms
+
+mapdownloads.baseLayers.states.name=lan
+mapdownloads.baseLayers.states.i18nCode=baselayer.states
+mapdownloads.baseLayers.states.displayName=States & Provinces
+
+# Google API key
+google.apikey=AIzaSyAJDtEeoy7Sc9pij2TAoVnmTwA34Q-2VHk
+
+# authorised roles
+authorise.roles=
+
+# alerts and myannotation settings
+alerts.myannotation.enabled=false
+alerts.baseUrl=
+alerts.apiKey=
+
+# misc
+speciesList.baseURL=https://lists.biodiversitydata.se
+speciesListToolUrl=https://lists.biodiversitydata.se/speciesListItem/list/
+advancedTaxaField=taxa
+
+# australia specific list paths
+#stateConservationListPath.NewSouthWales=/speciesListItem/list/dr650
+#stateConservationListPath.AustralianCapitalTerritory=/speciesListItem/list/dr649
+#stateConservationListPath.Queensland=/speciesListItem/list/dr652
+#stateConservationListPath.Victoria=/speciesListItem/list/dr655
+#stateConservationListPath.WesternAustralia=/speciesListItem/list/dr2201
+#stateConservationListPath.SouthAustralia=/speciesListItem/list/dr653
+#stateConservationListPath.NorthernTerritory=/speciesListItem/list/dr651
+#stateConservationListPath.Tasmania=/speciesListItem/list/dr654
+
+# Header and footer
+headerAndFooter.baseURL=https://static.biodiversitydata.se
+headerAndFooter.version=2
+
+ala.baseURL=https://biodiversitydata.se
+bie.baseURL=https://species.biodiversitydata.se
+privacyPolicy=https://docs.biodiversitydata.se/sbdi-data/sbdi-atlas-terms-of-use/privacy-policy/
+
+# Only used by the mdba hub
+ecodata.baseURL=
+pdfgen.baseURL=http://pdfgen.ala.org.au
+webservice.apiKey=bee2bf23-c554-41dc-8b18-363c59949ad7
+mdba.basinChampions=
+mdba.regions=
+
+#Used by Preferred Species
+bieApiKey=c311ae5d-4a87-4702-88f2-7373dd2e2e4d
+speciesList.preferredSpeciesListDruid=
+speciesList.preferredListName=
+allowedImageEditingRoles=ROLE_ADMIN
+
+# mdba config
+specieslist.baseUrl=https://lists.biodiversitydata.se/ws
+
+# Downloads
+useDownloadPlugin=True
+downloads.indexedDownloadUrl=https://records.biodiversitydata.se/ws/occurrences/offline/download
+downloads.checklistDownloadUrl=https://records.biodiversitydata.se/ws/occurrences/facets/download
+downloads.indexedFieldsUrl=https://records.biodiversitydata.se/ws/index/fields
+downloads.fieldguideDownloadUrl=
+fieldguide.url=
+downloads.staticDownloadsUrl=
+downloads.termsOfUseUrl=https://docs.biodiversitydata.se/sbdi-data/sbdi-atlas-terms-of-use
+downloads.defaultDownloadFormat=dwc
+downloads.dwcExtraFields=data_resource_uid
+#downloads.dwcExtraFields=data_resource_uid,materialSampleID,sampleSizeUnit,sampleSizeValue,organismQuantity,organismQuantityType
+downloads.legacy.defaultFields=id,data_resource_uid,data_resource,license,catalogue_number,taxon_concept_lsid,raw_taxon_name,raw_common_name,taxon_name,rank,common_name,kingdom,phylum,class,order,family,genus,species,subspecies,institution_code,collection_code,locality,raw_latitude,raw_longitude,raw_datum,latitude,longitude,datum,coordinate_precision,coordinate_uncertainty,country,state,cl959,min_elevation_d,max_elevation_d,min_depth_d,max_depth_d,individual_count,recorded_by,year,month,day,verbatim_event_date,basis_of_record,raw_basis_of_record,sex,preparations,information_withheld,data_generalizations,outlier_layer,taxonomic_kosher,geospatial_kosher
+#downloads.legacy.defaultFields=id,data_resource_uid,data_resource,license,catalogue_number,taxon_concept_lsid,raw_taxon_name,raw_common_name,taxon_name,rank,common_name,kingdom,phylum,class,order,family,genus,species,subspecies,institution_code,collection_code,locality,raw_latitude,raw_longitude,raw_datum,latitude,longitude,coordinate_precision,coordinate_uncertainty,country,state,cl959,min_elevation_d,max_elevation_d,min_depth_d,max_depth_d,individual_count,recorded_by,year,month,day,verbatim_event_date,basis_of_record,raw_basis_of_record,sex,preparations,information_withheld,data_generalizations,outlier_layer,taxonomic_kosher,geospatial_kosher,materialSampleID,sampleSizeUnit,sampleSizeValue,organismQuantity,organismQuantityType
+downloads.customSections.misc=qualityAssertions,miscellaneousFields
+
+# Maximum download limit without 'largeDownloadRole' permission
+maxDownloadRecords=
+
+# The CAS role to use for large downloads
+largeDownloadRole=ROLE_LARGE_DOWNLOAD
+
+userCharts=false
+
+doi.mintDoi=false
+endpoints.enabled=false
+
+# 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=
+security.jwt.clientId=
+
+
+#websevice jwt
+webservice.jwt=false
+webservice.jwt-scopes=
+webservice.client-id=
+webservice.client-secret=
+
+info.app.description=Swedish Biodiversity Data Infrastructure
+
+#events cofig
+events.enabled=false
+events.graphql=
+events.eventUrl=
+userdetails.url=https://auth.biodiversitydata.se/userdetails