feature: enable pscc bh within cce project

bridgehead

@@ -35,6 +35,9 @@ case "$PROJECT" in
 	cce)
 		#nothing extra to do
 		;;
+	pscc)
+		#nothing extra to do
+		;;
 	itcc)
 		#nothing extra to do
 		;;

cce/modules/pscc-compose.yml

@@ -0,0 +1,65 @@
+version: "3.7"
+
+services:
+  blaze-pscc:
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
+    container_name: bridgehead-pscc-blaze
+    environment:
+      BASE_URL: "http://bridgehead-pscc-blaze:8080"
+      JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
+      DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
+      DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
+      CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
+      ENFORCE_REFERENTIAL_INTEGRITY: "false"
+    volumes:
+      - "blaze-data-pscc:/app/data"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.blaze_pscc.rule=PathPrefix(`/pscc-localdatamanagement`)"
+      - "traefik.http.middlewares.pscc_b_strip.stripprefix.prefixes=/pscc-localdatamanagement"
+      - "traefik.http.services.blaze_pscc.loadbalancer.server.port=8080"
+      - "traefik.http.routers.blaze_pscc.middlewares=pscc_b_strip"
+      - "traefik.http.routers.blaze_pscc.tls=true"
+
+  focus-pscc:
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
+    container_name: bridgehead-pscc-focus
+    environment:
+      API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
+      BEAM_APP_ID_LONG: focus.${PROXY_ID_PSCC}
+      PROXY_ID: ${PROXY_ID_PSCC}
+      BLAZE_URL: "http://bridgehead-pscc-blaze:8080/fhir/"
+      BEAM_PROXY_URL: http://beam-proxy-pscc:8081
+      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
+      EPSILON: 0.28
+      ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
+    depends_on:
+      - "beam-proxy"
+      - "blaze"
+
+  beam-proxy-pscc:
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
+    container_name: bridgehead-pscc-beam-proxy
+    environment:
+      BROKER_URL: ${BROKER_URL_PSCC}
+      PROXY_ID: ${PROXY_ID_PSCC}
+      APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
+      PRIVKEY_FILE: /run/secrets/proxy.pem
+      ALL_PROXY: http://forward_proxy:3128
+      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
+      ROOTCERT_FILE: /conf/root.crt.pem
+    secrets:
+      - proxy.pem
+    depends_on:
+      - "forward_proxy"
+    volumes:
+      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
+      - /srv/docker/bridgehead/pscc/root.crt.pem:/conf/root.crt.pem:ro
+
+
+volumes:
+  blaze-data-pscc:
+
+secrets:
+  proxy.pem:
+    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

cce/modules/pscc-setup.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+if [ -n "$ENABLE_PSCC" ];then
+  OVERRIDE+=" -f ./$PROJECT/modules/pscc-compose.yml"
+fi

cce/vars

@@ -1,6 +1,9 @@
 BROKER_ID=test-no-real-data.broker.samply.de
+BROKER_ID_PSCC=test-no-real-data.broker.samply.de
 BROKER_URL=https://${BROKER_ID}
+BROKER_URL_PSCC=https://${BROKER_ID}
 PROXY_ID=${SITE_ID}.${BROKER_ID}
+PROXY_ID_PSCC=${SITE_ID}.${BROKER_ID_PSCC}
 FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
 FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
 SUPPORT_EMAIL=manoj.waikar@dkfz-heidelberg.de

ccp/queries_to_cache.conf

@@ -1,2 +1,3 @@
 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
-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+ORGANOID_DASHBOARD_PUBLIC

lib/prepare-system.sh

@@ -55,6 +55,9 @@ case "$PROJECT" in
 	cce)
 		site_configuration_repository_middle="git.verbis.dkfz.de/cce-sites/"
 		;;
+	pscc)
+		site_configuration_repository_middle="git.verbis.dkfz.de/pscc-sites/"
+		;;
 	itcc)
 		site_configuration_repository_middle="git.verbis.dkfz.de/itcc-sites/"
         ;;

pscc/docker-compose.yml

@@ -0,0 +1,65 @@
+version: "3.7"
+
+services:
+  blaze:
+    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
+    container_name: bridgehead-pscc-blaze
+    environment:
+      BASE_URL: "http://bridgehead-pscc-blaze:8080"
+      JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
+      DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
+      DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
+      CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
+      ENFORCE_REFERENTIAL_INTEGRITY: "false"
+    volumes:
+      - "blaze-data:/app/data"
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.blaze_pscc.rule=PathPrefix(`/pscc-localdatamanagement`)"
+      - "traefik.http.middlewares.pscc_b_strip.stripprefix.prefixes=/pscc-localdatamanagement"
+      - "traefik.http.services.blaze_pscc.loadbalancer.server.port=8080"
+      - "traefik.http.routers.blaze_pscc.middlewares=pscc_b_strip"
+      - "traefik.http.routers.blaze_pscc.tls=true"
+
+  focus:
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
+    container_name: bridgehead-focus
+    environment:
+      API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
+      BEAM_APP_ID_LONG: focus.${PROXY_ID}
+      PROXY_ID: ${PROXY_ID}
+      BLAZE_URL: "http://bridgehead-pscc-blaze:8080/fhir/"
+      BEAM_PROXY_URL: http://beam-proxy:8081
+      RETRY_COUNT: ${FOCUS_RETRY_COUNT}
+      EPSILON: 0.28
+      ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze}
+    depends_on:
+      - "beam-proxy"
+      - "blaze"
+
+  beam-proxy:
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
+    container_name: bridgehead-beam-proxy
+    environment:
+      BROKER_URL: ${BROKER_URL}
+      PROXY_ID: ${PROXY_ID}
+      APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
+      PRIVKEY_FILE: /run/secrets/proxy.pem
+      ALL_PROXY: http://forward_proxy:3128
+      TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
+      ROOTCERT_FILE: /conf/root.crt.pem
+    secrets:
+      - proxy.pem
+    depends_on:
+      - "forward_proxy"
+    volumes:
+      - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
+      - /srv/docker/bridgehead/pscc/root.crt.pem:/conf/root.crt.pem:ro
+
+
+volumes:
+  blaze-data:
+
+secrets:
+  proxy.pem:
+    file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

pscc/modules/lens-compose.yml

@@ -0,0 +1,34 @@
+version: "3.7"
+services:
+  landing:
+    container_name: lens_federated-search
+    image: docker.verbis.dkfz.de/dashboard/pscc-explorer
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.landing.rule=PathPrefix(`/`)"
+      - "traefik.http.services.landing.loadbalancer.server.port=5173"
+      - "traefik.http.routers.landing.middlewares=auth"
+      - "traefik.http.routers.landing.tls=true"
+
+#  spot:
+#    image: docker.verbis.dkfz.de/ccp-private/central-spot
+#    environment:
+#      BEAM_SECRET: "${FOCUS_BEAM_SECRET_SHORT}"
+#      BEAM_URL: http://beam-proxy:8081
+#      BEAM_PROXY_ID: ${SITE_ID}
+#      BEAM_BROKER_ID: ${BROKER_ID}
+#      BEAM_APP_ID: "focus"
+#      PROJECT_METADATA: "cce_supervisors"
+#    depends_on:
+#      - "beam-proxy"
+#    labels:
+#      - "traefik.enable=true"
+#      - "traefik.http.services.spot.loadbalancer.server.port=8080"
+#      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
+#      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}"
+#      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true"
+#      - "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1"
+#      - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)"
+#      - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend"
+#      - "traefik.http.routers.spot.tls=true"
+#      - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot"

pscc/modules/lens-setup.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+if [ -n "$ENABLE_LENS" ];then
+  OVERRIDE+=" -f ./$PROJECT/modules/lens-compose.yml"
+fi

pscc/root.crt.pem

@@ -0,0 +1,20 @@
+-----BEGIN CERTIFICATE-----
+MIIDNTCCAh2gAwIBAgIUW34NEb7bl0+Ywx+I1VKtY5vpAOowDQYJKoZIhvcNAQEL
+BQAwFjEUMBIGA1UEAxMLQnJva2VyLVJvb3QwHhcNMjQwMTIyMTMzNzEzWhcNMzQw
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+AXXNJqQ88djrKs5MDXS8RIjS/cu2ayuLaYDe+BzVmUXNA0Vt9nZGdaz63SLLcjpU
+fNSxBfKbwmf7s30AK8Cnfj9q4W/BlBeVizUHQsg1+RQpDIdMrRQrwkXv8mfLw+w5
+3oaXNW6W/8KpBp/H8TBZ6myl6jCbeR3T8EMXBwipMGop/1zkbF01i98Xpqmhx2+l
+n+80ofPsSspOo5XmgCZym8CD/m/oFHmjcvOfpOCvDh4PZ+i37pmbSlCYoMpla3u/
+7MJMP5lugfLBYNDN2p+V4KbHP/cApCDT5UWLOeAWjgiZQtHH5ilDeYqEc1oPjyJt
+Rtup0MTxSJtN
+-----END CERTIFICATE-----

pscc/vars

@@ -0,0 +1,14 @@
+BROKER_ID=test-no-real-data.broker.samply.de
+BROKER_URL=https://${BROKER_ID}
+PROXY_ID=${SITE_ID}.${BROKER_ID}
+FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
+FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
+SUPPORT_EMAIL=denis.koether@dkfz-heidelberg.de
+PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
+BROKER_URL_FOR_PREREQ=$BROKER_URL
+
+for module in $PROJECT/modules/*.sh
+do
+    log DEBUG "sourcing $module"
+    source $module
+done