From bbda99254fadc62040628a7efe5b9e84e7d11137 Mon Sep 17 00:00:00 2001 From: Pierre Delpy <75260699+PierreDelpy@users.noreply.github.com> Date: Tue, 17 Mar 2026 15:54:25 +0100 Subject: [PATCH 01/13] feature: add osiris2fhir in cce and minor fixes (#374) --- cce/modules/osiris2fhir-setup.sh | 6 ++++++ pscc/modules/osiris2fhir-compose.yml | 4 +++- pscc/modules/osiris2fhir-setup.sh | 2 +- 3 files changed, 10 insertions(+), 2 deletions(-) create mode 100644 cce/modules/osiris2fhir-setup.sh diff --git a/cce/modules/osiris2fhir-setup.sh b/cce/modules/osiris2fhir-setup.sh new file mode 100644 index 0000000..ce1d6d7 --- /dev/null +++ b/cce/modules/osiris2fhir-setup.sh @@ -0,0 +1,6 @@ +#!/bin/bash +if [ -n "$ENABLE_OSIRIS2FHIR" ]; then + log INFO "OSIRIS2FHIR-REST setup detected -- will start osiris2fhir module." + OVERRIDE+=" -f ./pscc/modules/osiris2fhir-compose.yml" + LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)" +fi \ No newline at end of file diff --git a/pscc/modules/osiris2fhir-compose.yml b/pscc/modules/osiris2fhir-compose.yml index a5fbffb..6b346d9 100644 --- a/pscc/modules/osiris2fhir-compose.yml +++ b/pscc/modules/osiris2fhir-compose.yml @@ -1,8 +1,10 @@ services: osiris2fhir: container_name: bridgehead-osiris2fhir - image: docker.verbis.dkfz.de/ccp/osiris2fhir:${SITE_ID} + image: docker.verbis.dkfz.de/ccp/osiris2fhir environment: + FHIR_PROFILE: ${PROJECT:-pscc} + LOG_LEVEL: ${LOG_LEVEL:-INFO} SALT: ${LOCAL_SALT} labels: - "traefik.enable=true" diff --git a/pscc/modules/osiris2fhir-setup.sh b/pscc/modules/osiris2fhir-setup.sh index 852a3a8..ce1d6d7 100644 --- a/pscc/modules/osiris2fhir-setup.sh +++ b/pscc/modules/osiris2fhir-setup.sh @@ -1,6 +1,6 @@ #!/bin/bash if [ -n "$ENABLE_OSIRIS2FHIR" ]; then - log INFO "oBDS2FHIR-REST setup detected -- will start osiris2fhir module." + log INFO "OSIRIS2FHIR-REST setup detected -- will start osiris2fhir module." OVERRIDE+=" -f ./pscc/modules/osiris2fhir-compose.yml" LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)" fi \ No newline at end of file From 71b25fe49041c97fb38bc172538228668a218860 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Radovan=20Tom=C3=A1=C5=A1ik?= Date: Tue, 7 Apr 2026 12:48:29 +0200 Subject: [PATCH 02/13] feat: add Data Quality Agent configuration and setup (#373) * feat: add Data Quality Agent configuration and setup * fix: correct environment variable name in Data Quality Agent configuration * feat: update Data Quality Agent configuration and setup instructions * feat: update Data Quality Agent setup and documentation * feat: add volume configuration for agent data in Data Quality Agent compose file * feat: update volume configuration for Data Quality Agent in compose file * Update README.md Co-authored-by: Tobias Kussel --------- Co-authored-by: Tobias Kussel --- README.md | 27 ++++++++++++++++++++ bbmri/modules/data-quality-agent-compose.yml | 23 +++++++++++++++++ bbmri/modules/data-quality-agent-setup.sh | 7 +++++ versions/acceptance | 3 ++- versions/prod | 3 ++- versions/test | 1 + 6 files changed, 62 insertions(+), 2 deletions(-) create mode 100644 bbmri/modules/data-quality-agent-compose.yml create mode 100644 bbmri/modules/data-quality-agent-setup.sh diff --git a/README.md b/README.md index d0e462a..0574acc 100644 --- a/README.md +++ b/README.md @@ -27,6 +27,7 @@ This repository is the starting point for any information and tools you will nee - [Teiler (Frontend)](#teiler-frontend) - [Data Exporter Service](#data-exporter-service) - [Data Quality Report](#data-quality-report) + - [Data Quality Agent](#data-quality-agent) 4. [Things you should know](#things-you-should-know) - [Auto-Updates](#auto-updates) - [Auto-Backups](#auto-backups) @@ -424,6 +425,32 @@ ENABLE_EXPORTER=true ``` [For further information](docs/exporter.md) +### Data Quality Agent + +The Data Quality Agent is an optional module that periodically evaluates the quality of FHIR data stored in Blaze. It generates local data quality reports accessible via the Bridgehead web interface. + +To enable the service, set the following variable in your `.conf` file: + +```bash +ENABLE_DATA_QUALITY_AGENT=true +``` + +#### Sharing Data Quality Reports (recommended) + +We encourage sharing your data quality reports with the central BBMRI-ERIC quality dashboard. The reports contain only aggregated, non-patient-identifiable statistics and help the network to monitor and improve overall data quality. However, quality reporting is completely optional and opt-in. + +To opt in, additionally set the following variables in your `.conf` file: + +```bash +DATA_QUALITY_SERVER_URL=https://quality-dashboard.bbmri-eric.eu +DATA_QUALITY_SERVER_NAME=Central Data Quality Server of BBMRI +``` + +If these variables are not set, the Data Quality Agent will still run and generate local reports, but no data will be shared externally. + +Reports are accessible at `https:///bbmri-data-quality-agent` (default credentials are admin:admin, please change it after first login!!). + +[Official documentation](https://fdqf.bbmri-eric.eu/user/deployment.html) ## Things you should know ### Auto-Updates diff --git a/bbmri/modules/data-quality-agent-compose.yml b/bbmri/modules/data-quality-agent-compose.yml new file mode 100644 index 0000000..443bec8 --- /dev/null +++ b/bbmri/modules/data-quality-agent-compose.yml @@ -0,0 +1,23 @@ +version: "3.7" + +services: + data-quality-agent: + image: ghcr.io/bbmri-cz/data-quality-server:${DATA_QUALITY_AGENT_TAG} + container_name: bridgehead-bbmri-data-quality-agent + environment: + APP_SETTING_FHIR_URL: http://bridgehead-bbmri-blaze:8080/fhir + REPORTING_SERVER_URL: ${DATA_QUALITY_SERVER_URL} + REPORTING_SERVER_NAME: ${DATA_QUALITY_SERVER_NAME} + labels: + - "traefik.enable=true" + - "traefik.http.routers.data_quality_agent_bbmri.rule=PathPrefix(`/bbmri-data-quality-agent`)" + - "traefik.http.services.data_quality_agent_bbmri.loadbalancer.server.port=8082" + - "traefik.http.routers.data_quality_agent_bbmri.tls=true" + - "traefik.http.middlewares.data_quality_agent_bbmri_strip.stripprefix.prefixes=/bbmri-data-quality-agent" + - "traefik.http.routers.data_quality_agent_bbmri.middlewares=data_quality_agent_bbmri_strip,auth" + depends_on: + - "blaze" + volumes: + - /var/cache/bridgehead/bbmri/agent-db:/app/data + - /etc/localtime:/etc/localtime:ro + - /etc/timezone:/etc/timezone:ro diff --git a/bbmri/modules/data-quality-agent-setup.sh b/bbmri/modules/data-quality-agent-setup.sh new file mode 100644 index 0000000..f0a0e84 --- /dev/null +++ b/bbmri/modules/data-quality-agent-setup.sh @@ -0,0 +1,7 @@ +#!/bin/bash + +if [ "$ENABLE_DATA_QUALITY_AGENT" == "true" ]; then + log INFO "Data Quality Agent setup detected -- will start data-quality-agent service." + OVERRIDE+=" -f ./$PROJECT/modules/data-quality-agent-compose.yml" +fi + diff --git a/versions/acceptance b/versions/acceptance index 89d509e..10fb37e 100644 --- a/versions/acceptance +++ b/versions/acceptance @@ -3,4 +3,5 @@ BEAM_TAG=develop BLAZE_TAG=0.32 POSTGRES_TAG=15.13-alpine TEILER_DASHBOARD_TAG=develop -MTBA_TAG=develop \ No newline at end of file +MTBA_TAG=develop +DATA_QUALITY_AGENT_TAG=latest diff --git a/versions/prod b/versions/prod index 7f6642d..29e7c5b 100644 --- a/versions/prod +++ b/versions/prod @@ -3,4 +3,5 @@ BEAM_TAG=main BLAZE_TAG=0.32 POSTGRES_TAG=15.13-alpine TEILER_DASHBOARD_TAG=main -MTBA_TAG=main \ No newline at end of file +MTBA_TAG=main +DATA_QUALITY_AGENT_TAG=0.1 diff --git a/versions/test b/versions/test index b1a3a40..10fb37e 100644 --- a/versions/test +++ b/versions/test @@ -4,3 +4,4 @@ BLAZE_TAG=0.32 POSTGRES_TAG=15.13-alpine TEILER_DASHBOARD_TAG=develop MTBA_TAG=develop +DATA_QUALITY_AGENT_TAG=latest From 7a8664a636ea5d6c0b5a6ec4faf771cd902fdd47 Mon Sep 17 00:00:00 2001 From: Jan <59206115+Threated@users.noreply.github.com> Date: Fri, 10 Apr 2026 11:38:28 +0200 Subject: [PATCH 03/13] fix project check in secret_sync_gitlab_token (#378) --- lib/functions.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/functions.sh b/lib/functions.sh index 520d86a..3a5cfe4 100644 --- a/lib/functions.sh +++ b/lib/functions.sh @@ -337,7 +337,7 @@ function sync_secrets() { } function secret_sync_gitlab_token() { - if [[ "$PROJECT" != "dktk" && "$PROJECT" != "bbmri" ]]; then + if [[ "$PROJECT" != "ccp" && "$PROJECT" != "bbmri" ]]; then log "INFO" "Not running Secret Sync for project minimal" return fi From 2b7e3ef3a18073372e9c85e4f7f420953cb683d6 Mon Sep 17 00:00:00 2001 From: Patrick Skowronek <86347677+patrick-skowronek@users.noreply.github.com> Date: Mon, 11 May 2026 11:35:32 +0200 Subject: [PATCH 04/13] fix: replace old dpc link (#384) --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 0574acc..03a1b63 100644 --- a/README.md +++ b/README.md @@ -42,7 +42,7 @@ This repository is the starting point for any information and tools you will nee The data protection officer at your site will probably want to know exactly what our software does with patient data, and you may need to get their approval before you are allowed to install a Bridgehead. To help you with this, we have provided some data protection concepts: -- [Germany](https://www.bbmri.de/biobanking/it/infrastruktur/datenschutzkonzept/) +- [Germany](https://www.netzwerk-universitaetsmedizin.de/plattformen/gbn/biobanking/it/infrastruktur/datenschutzkonzept) ### Hardware From cbf75f632f3f268676d03e12ecbeb1f4cdec9b3e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Radovan=20Tom=C3=A1=C5=A1ik?= Date: Mon, 11 May 2026 12:55:44 +0200 Subject: [PATCH 05/13] Fix image reference for data-quality-agent service (#381) --- bbmri/modules/data-quality-agent-compose.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bbmri/modules/data-quality-agent-compose.yml b/bbmri/modules/data-quality-agent-compose.yml index 443bec8..272f982 100644 --- a/bbmri/modules/data-quality-agent-compose.yml +++ b/bbmri/modules/data-quality-agent-compose.yml @@ -2,7 +2,7 @@ version: "3.7" services: data-quality-agent: - image: ghcr.io/bbmri-cz/data-quality-server:${DATA_QUALITY_AGENT_TAG} + image: ghcr.io/bbmri-cz/data-quality-agent:${DATA_QUALITY_AGENT_TAG} container_name: bridgehead-bbmri-data-quality-agent environment: APP_SETTING_FHIR_URL: http://bridgehead-bbmri-blaze:8080/fhir From 47b793668ae818243b79c553b3de09ebfbbc638b Mon Sep 17 00:00:00 2001 From: Martin Jurk <96107909+Martin1088@users.noreply.github.com> Date: Tue, 12 May 2026 13:56:35 +0200 Subject: [PATCH 06/13] Feature/ml itcc (#380) * sites moved to etc itcc.comf * mainzelliste test * volume * fix image * db name chaged * ingest component test * clean up * maizelliste env db * test server ip * beam sockets * teswt socket and task * secure db and ml * refactor and patient endpoints * partner id * new refactor and encription key generation * db deleted * keyset to var/ --- itcc/docker-compose.yml | 8 ++-- itcc/modules/itcc-omics-ingest.sh | 21 ++++++++++ itcc/modules/itcc-omics-ingest.yaml | 65 ++++++++++++++++++++++++++--- itcc/vars | 3 ++ 4 files changed, 88 insertions(+), 9 deletions(-) diff --git a/itcc/docker-compose.yml b/itcc/docker-compose.yml index 49edff0..ae9e09f 100644 --- a/itcc/docker-compose.yml +++ b/itcc/docker-compose.yml @@ -2,7 +2,7 @@ version: "3.7" services: blaze: - image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG} + image: docker.verbis.dkfz.de/cache/samply/blaze:latest container_name: bridgehead-itcc-blaze environment: BASE_URL: "http://bridgehead-itcc-blaze:8080" @@ -32,7 +32,7 @@ services: BEAM_PROXY_URL: http://beam-proxy:8081 RETRY_COUNT: ${FOCUS_RETRY_COUNT} EPSILON: 0.28 - QUERIES_TO_CACHE: '/queries_to_cache.conf' + QUERIES_TO_CACHE: "/queries_to_cache.conf" ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze} volumes: - /srv/docker/bridgehead/itcc/queries_to_cache.conf:/queries_to_cache.conf:ro @@ -41,12 +41,13 @@ services: - "blaze" beam-proxy: - image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG} + image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop-sockets container_name: bridgehead-beam-proxy environment: BROKER_URL: ${BROKER_URL} PROXY_ID: ${PROXY_ID} APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT} + APP_omics-endpoint_KEY: ${FOCUS_BEAM_SECRET_SHORT} PRIVKEY_FILE: /run/secrets/proxy.pem ALL_PROXY: http://forward_proxy:3128 TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs @@ -59,7 +60,6 @@ services: - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro - /srv/docker/bridgehead/itcc/root.crt.pem:/conf/root.crt.pem:ro - volumes: blaze-data: diff --git a/itcc/modules/itcc-omics-ingest.sh b/itcc/modules/itcc-omics-ingest.sh index a078140..9d0dcb4 100644 --- a/itcc/modules/itcc-omics-ingest.sh +++ b/itcc/modules/itcc-omics-ingest.sh @@ -3,4 +3,25 @@ if [ -n "$ENABLE_OMICS" ];then OVERRIDE+=" -f ./$PROJECT/modules/itcc-omics-ingest.yaml" GENERATE_API_KEY="$(generate_simple_password 'omics')" + PATIENTLIST_POSTGRES_PASSWORD=="$(generate_simple_password 'mainzelliste')" + KEYSET=/var/bridgehead/mainzelliste/keyset_siv.json + if [ ! -f "$KEYSET" ]; then + mkdir -p "$(dirname "$KEYSET")" + KEY_ID=$(($(openssl rand -hex 4 | sed 's/^/0x/') & 0x7FFFFFFF)) + VALUE=$({ printf '\x12\x40'; openssl rand 64; } | base64 | tr -d '\n') + jq -n --argjson id "$KEY_ID" --arg value "$VALUE" '{ + primaryKeyId: $id, + key: [{ + keyData: { + typeUrl: "type.googleapis.com/google.crypto.tink.AesSivKey", + value: $value, + keyMaterialType: "SYMMETRIC" + }, + status: "ENABLED", + keyId: $id, + outputPrefixType: "TINK" + }] + }' > "$KEYSET" + chmod 600 "$KEYSET" + fi fi \ No newline at end of file diff --git a/itcc/modules/itcc-omics-ingest.yaml b/itcc/modules/itcc-omics-ingest.yaml index 8108433..74ae527 100644 --- a/itcc/modules/itcc-omics-ingest.yaml +++ b/itcc/modules/itcc-omics-ingest.yaml @@ -1,14 +1,69 @@ services: omics-endpoint: - image: ghcr.io/samply/itcc-omics-ingest:main + image: samply/itcc-omics-ingest:main environment: - - API_KEY=${GENERATE_API_KEY} - volumes: - - /var/cache/bridgehead/omics/data:/data/uploads + API_KEY: ${GENERATE_API_KEY} + BEAM_APP_ID_LONG: omics-endpoint.${PROXY_ID} + BEAM_SECRET: ${FOCUS_BEAM_SECRET_SHORT} + DWH_SOCKET_ID: ${DWH_SOCKET_ID} + DWH_TASK_ID: ${DWH_TASK_ID} + PARTNER_ID: ${SITE_ID} + ML_API_KEY: ${GENERATE_API_KEY} labels: - - "traefik.http.routers.omics.rule=Host(`${HOST}`) && PathPrefix(`/api/omics`)" + - "traefik.http.routers.omics.rule=Host(`${HOST}`) && + PathPrefix(`/api/upload`)" - "traefik.enable=true" - "traefik.http.services.omics.loadbalancer.server.port=6080" - "traefik.http.routers.omics.tls=true" - "traefik.http.middlewares.omics-stripprefix.stripprefix.prefixes=/api" - "traefik.http.routers.omics.middlewares=omics-stripprefix" + + patientlist-db: + image: postgres:${POSTGRES_TAG} + container_name: bridgehead-patientlist-db + restart: unless-stopped + environment: + POSTGRES_DB: mainzelliste + POSTGRES_USER: ${ML_DB_USER} + POSTGRES_PASSWORD: ${PATIENTLIST_POSTGRES_PASSWORD} + volumes: + - "patientlist-db-data:/var/lib/postgresql/data" + healthcheck: + test: ["CMD-SHELL", "pg_isready -U ${ML_DB_USER} -d mainzelliste"] + interval: 5s + timeout: 5s + retries: 10 + start_period: 10s + + patientlist: + image: medicalinformatics/mainzelliste:latest + container_name: bridgehead-patientlist + restart: unless-stopped + depends_on: + patientlist-db: + condition: service_healthy + environment: + ML_API_KEY: ${GENERATE_API_KEY} + ML_DB_HOST: patientlist-db + ML_DB_PORT: "5432" + ML_DB_NAME: mainzelliste + ML_DB_USER: ${ML_DB_USER} + ML_DB_PASS: ${PATIENTLIST_POSTGRES_PASSWORD} + ML_DB_DRIVER: org.postgresql.Driver + ML_DB_TYPE: postgresql + ML_LOG_LEVEL: INFO + ML_ALLOWEDREMOTEADDRESSES: "127.0.0.1,::1,172.16.0.0/12" + + secrets: + - mainzelliste.docker.conf + - source: symmetric_key + target: /etc/resources/keys/symmetric_key.json + +volumes: + patientlist-db-data: +secrets: + mainzelliste.docker.conf: + file: /etc/bridgehead/mainzelliste/mainzelliste.docker.conf + + symmetric_key: + file: /var/bridgehead/mainzelliste/keyset_siv.json diff --git a/itcc/vars b/itcc/vars index 3eee652..26fbc25 100644 --- a/itcc/vars +++ b/itcc/vars @@ -7,6 +7,9 @@ SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem BROKER_URL_FOR_PREREQ=$BROKER_URL PUBLIC_ENVIRONMENT=prod +DWH_SOCKET_ID=socket.itcc-datalake.${BROKER_ID} +DWH_TASK_ID=task.itcc-datalake.${BROKER_ID} +ML_DB_USER=mainzelliste for module in $PROJECT/modules/*.sh do From 112be2a2d663d52d0d1e9638ca5700c01239e23a Mon Sep 17 00:00:00 2001 From: Pierre Delpy <75260699+PierreDelpy@users.noreply.github.com> Date: Fri, 22 May 2026 12:58:17 +0200 Subject: [PATCH 07/13] Fix/pscc lens local (#385) * fix: deployment of local pscc lens instance --- pscc/modules/lens-compose.yml | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/pscc/modules/lens-compose.yml b/pscc/modules/lens-compose.yml index 4571c7b..f5ef163 100644 --- a/pscc/modules/lens-compose.yml +++ b/pscc/modules/lens-compose.yml @@ -2,7 +2,9 @@ version: "3.7" services: lens: container_name: lens-federated-search - image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID} + image: docker.verbis.dkfz.de/ccp/lens:pscc + environment: + PUBLIC_SPOT_URL: https://${HOST}/prod labels: - "traefik.http.services.lens.loadbalancer.server.port=3000" - "traefik.enable=true" @@ -11,7 +13,6 @@ services: spot: image: samply/rustyspot:latest - platform: linux/amd64 environment: HTTP_PROXY: ${HTTP_PROXY_URL} HTTPS_PROXY: ${HTTPS_PROXY_URL} @@ -37,4 +38,8 @@ services: - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/prod`)" - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/prod" - "traefik.http.routers.spot.tls=true" - - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot,auth" \ No newline at end of file + - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot,auth" + + beam-proxy: + environment: + APP_spot_KEY: ${FOCUS_BEAM_SECRET_SHORT} \ No newline at end of file From 4211528f563ced414f7a764e5b30df5652b5cfe4 Mon Sep 17 00:00:00 2001 From: afigueroaDkfz <146178090+afigueroaDkfz@users.noreply.github.com> Date: Tue, 26 May 2026 16:16:06 +0200 Subject: [PATCH 08/13] fix: make url dynamic based on host configuration (#386) --- itcc/modules/lens-compose.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/itcc/modules/lens-compose.yml b/itcc/modules/lens-compose.yml index 5a5b78c..a548cde 100644 --- a/itcc/modules/lens-compose.yml +++ b/itcc/modules/lens-compose.yml @@ -7,6 +7,7 @@ services: HOST: "0.0.0.0" BIND_ADDR: "0.0.0.0:3000" PUBLIC_ENVIRONMENT: ${PUBLIC_ENVIRONMENT} + PUBLIC_SPOT_URL: https://${HOST}/prod labels: - "traefik.enable=true" - "traefik.http.routers.itcc.rule=Host(`${HOST}`) && PathPrefix(`/`)" From e3a8cf790c11f5525b98e6e05d0d28ca95d2a130 Mon Sep 17 00:00:00 2001 From: Enola Knezevic <115070135+enola-dkfz@users.noreply.github.com> Date: Fri, 29 May 2026 15:28:04 +0200 Subject: [PATCH 09/13] use latest blaze in test (#387) --- versions/test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/versions/test b/versions/test index 10fb37e..648e371 100644 --- a/versions/test +++ b/versions/test @@ -1,6 +1,6 @@ FOCUS_TAG=develop BEAM_TAG=develop -BLAZE_TAG=0.32 +BLAZE_TAG=latest POSTGRES_TAG=15.13-alpine TEILER_DASHBOARD_TAG=develop MTBA_TAG=develop From 54291c06f789223bced47c1956f7aea2563abcf0 Mon Sep 17 00:00:00 2001 From: Tobias Kussel Date: Tue, 2 Jun 2026 15:03:35 +0200 Subject: [PATCH 10/13] =?UTF-8?q?Fix=20spelling=20of=20'Charite'=20to=20'C?= =?UTF-8?q?harit=C3=A9'=20in=20DNPM=20targets=20(#389)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- minimal/modules/dnpm-central-targets.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/minimal/modules/dnpm-central-targets.json b/minimal/modules/dnpm-central-targets.json index 5469da0..9b28c37 100644 --- a/minimal/modules/dnpm-central-targets.json +++ b/minimal/modules/dnpm-central-targets.json @@ -49,7 +49,7 @@ "beamconnect": "dnpm-connect.dnpm-bridge.broker.ccp-it.dktk.dkfz.de" }, { - "id": "Charite", + "id": "Charité", "name": "Berlin", "virtualhost": "charite.dnpm.de", "beamconnect": "dnpm-connect.berlin-test.broker.ccp-it.dktk.dkfz.de" From b7a8646e917708de240da6f591f9e99acc6198e7 Mon Sep 17 00:00:00 2001 From: Enola Knezevic <115070135+enola-dkfz@users.noreply.github.com> Date: Wed, 17 Jun 2026 13:24:32 +0200 Subject: [PATCH 11/13] latest blaze in acceptance and 1.8 in production (#388) --- versions/acceptance | 2 +- versions/prod | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/versions/acceptance b/versions/acceptance index 10fb37e..648e371 100644 --- a/versions/acceptance +++ b/versions/acceptance @@ -1,6 +1,6 @@ FOCUS_TAG=develop BEAM_TAG=develop -BLAZE_TAG=0.32 +BLAZE_TAG=latest POSTGRES_TAG=15.13-alpine TEILER_DASHBOARD_TAG=develop MTBA_TAG=develop diff --git a/versions/prod b/versions/prod index 29e7c5b..a336e12 100644 --- a/versions/prod +++ b/versions/prod @@ -1,6 +1,6 @@ FOCUS_TAG=main BEAM_TAG=main -BLAZE_TAG=0.32 +BLAZE_TAG=1.8 POSTGRES_TAG=15.13-alpine TEILER_DASHBOARD_TAG=main MTBA_TAG=main From f549f95b2c677c9aa571bf51337452584d2baf1a Mon Sep 17 00:00:00 2001 From: Enola Knezevic <115070135+enola-dkfz@users.noreply.github.com> Date: Mon, 29 Jun 2026 11:16:57 +0200 Subject: [PATCH 12/13] added CQL_FLAVOUR (#391) --- bbmri/modules/eric-compose.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/bbmri/modules/eric-compose.yml b/bbmri/modules/eric-compose.yml index e6ed044..65eb6b6 100644 --- a/bbmri/modules/eric-compose.yml +++ b/bbmri/modules/eric-compose.yml @@ -12,6 +12,7 @@ services: BEAM_PROXY_URL: http://beam-proxy-eric:8081 RETRY_COUNT: ${FOCUS_RETRY_COUNT} OBFUSCATE_BBMRI_ERIC_WAY: "true" + CQL_FLAVOUR: "${FOCUS_CQL_FLAVOUR}" depends_on: - "beam-proxy-eric" - "blaze" From d7c01594de360304ebbe3f897b213e5033e30b2b Mon Sep 17 00:00:00 2001 From: Tim Schumacher Date: Tue, 30 Jun 2026 15:28:25 +0200 Subject: [PATCH 13/13] Don't use wildcard in sudoers to support sudo-rs (#392) --- lib/install-bridgehead.sh | 1 - lib/update-bridgehead.sh | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/lib/install-bridgehead.sh b/lib/install-bridgehead.sh index f712153..2e2ec69 100755 --- a/lib/install-bridgehead.sh +++ b/lib/install-bridgehead.sh @@ -21,7 +21,6 @@ Cmnd_Alias BRIDGEHEAD${PROJECT^^} = \\ /bin/systemctl start bridgehead@${PROJECT}.service, \\ /bin/systemctl stop bridgehead@${PROJECT}.service, \\ /bin/systemctl restart bridgehead@${PROJECT}.service, \\ - /bin/systemctl restart bridgehead@*.service, \\ /bin/chown -R bridgehead /etc/bridgehead /srv/docker/bridgehead, \\ /usr/bin/chown -R bridgehead /etc/bridgehead /srv/docker/bridgehead diff --git a/lib/update-bridgehead.sh b/lib/update-bridgehead.sh index 8ae3bde..cf846db 100755 --- a/lib/update-bridgehead.sh +++ b/lib/update-bridgehead.sh @@ -98,7 +98,7 @@ if [ $git_updated = "true" ] || [ $docker_updated = "true" ]; then RES="Updates detected, now restarting bridgehead:\n$CHANGES" log "INFO" "$RES" hc_send log "$RES" - sudo /bin/systemctl restart bridgehead@*.service + sudo /bin/systemctl restart bridgehead@${PROJECT}.service else RES="Nothing updated, nothing to restart." log "INFO" "$RES"