From 760d599b7cd40f657ecbbe73aa43000ceef6d81c Mon Sep 17 00:00:00 2001 From: Patrick Skowronek Date: Thu, 10 Oct 2024 12:56:36 +0200 Subject: [PATCH 1/9] Add CCP-PPI --- ccp/docker-compose.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/ccp/docker-compose.yml b/ccp/docker-compose.yml index fcabc9bd..01b5aadf 100644 --- a/ccp/docker-compose.yml +++ b/ccp/docker-compose.yml @@ -57,6 +57,11 @@ services: - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro - /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro + ccp-patient-project-identificator: + image: samply/ccp-patient-project-identificator + environment: + MAINZELLISTE_APIKEY: ${MAINZELLISTE_APIKEY} + SITE_NAME: ${SITE_NAME} volumes: blaze-data: From 8e7fe6851eefa3407d045d9d77cc666a651204ca Mon Sep 17 00:00:00 2001 From: Patrick Skowronek Date: Thu, 10 Oct 2024 13:11:43 +0200 Subject: [PATCH 2/9] fix: use correct mainzelliste api key --- ccp/docker-compose.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/ccp/docker-compose.yml b/ccp/docker-compose.yml index 01b5aadf..7318942f 100644 --- a/ccp/docker-compose.yml +++ b/ccp/docker-compose.yml @@ -59,8 +59,9 @@ services: ccp-patient-project-identificator: image: samply/ccp-patient-project-identificator + container_name: bridgehead-ccp-patient-project-identificator environment: - MAINZELLISTE_APIKEY: ${MAINZELLISTE_APIKEY} + MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY} SITE_NAME: ${SITE_NAME} volumes: From 23981062bb44c6f2b84d90809e88f4b50e382c1e Mon Sep 17 00:00:00 2001 From: Patrick Skowronek Date: Thu, 10 Oct 2024 13:27:24 +0200 Subject: [PATCH 3/9] Move ppi to id-management --- ccp/docker-compose.yml | 7 ------- ccp/modules/id-management-compose.yml | 7 +++++++ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/ccp/docker-compose.yml b/ccp/docker-compose.yml index 7318942f..f46615dd 100644 --- a/ccp/docker-compose.yml +++ b/ccp/docker-compose.yml @@ -57,13 +57,6 @@ services: - /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro - /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro - ccp-patient-project-identificator: - image: samply/ccp-patient-project-identificator - container_name: bridgehead-ccp-patient-project-identificator - environment: - MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY} - SITE_NAME: ${SITE_NAME} - volumes: blaze-data: diff --git a/ccp/modules/id-management-compose.yml b/ccp/modules/id-management-compose.yml index ce0a58a4..704646de 100644 --- a/ccp/modules/id-management-compose.yml +++ b/ccp/modules/id-management-compose.yml @@ -101,5 +101,12 @@ services: forward_proxy: condition: service_healthy + ccp-patient-project-identificator: + image: samply/ccp-patient-project-identificator + container_name: bridgehead-ccp-patient-project-identificator + environment: + MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY} + SITE_NAME: ${SITE_NAME} + volumes: patientlist-db-data: From 26712d3567225e8c5071456f7120ca94b326d7d0 Mon Sep 17 00:00:00 2001 From: davidmscholz <130749829+davidmscholz@users.noreply.github.com> Date: Wed, 30 Oct 2024 15:21:15 +0100 Subject: [PATCH 4/9] feat: add and set FOCUS_ENDPOINT_TYPE to support fhir2sql (#244) * add and set FOCUS_ENDPOINT_TYPE Co-authored-by: Jan <59206115+Threated@users.noreply.github.com> --------- Co-authored-by: davidmscholz Co-authored-by: Jan <59206115+Threated@users.noreply.github.com> --- ccp/docker-compose.yml | 1 + ccp/modules/fhir2sql-setup.sh | 1 + 2 files changed, 2 insertions(+) diff --git a/ccp/docker-compose.yml b/ccp/docker-compose.yml index 2e4e139f..e63f5a57 100644 --- a/ccp/docker-compose.yml +++ b/ccp/docker-compose.yml @@ -33,6 +33,7 @@ services: RETRY_COUNT: ${FOCUS_RETRY_COUNT} EPSILON: 0.28 QUERIES_TO_CACHE: '/queries_to_cache.conf' + ENDPOINT_TYPE: ${FOCUS_ENDPOINT_TYPE:-blaze} volumes: - /srv/docker/bridgehead/ccp/queries_to_cache.conf:/queries_to_cache.conf depends_on: diff --git a/ccp/modules/fhir2sql-setup.sh b/ccp/modules/fhir2sql-setup.sh index 64fa7c08..8c9a72b8 100644 --- a/ccp/modules/fhir2sql-setup.sh +++ b/ccp/modules/fhir2sql-setup.sh @@ -4,4 +4,5 @@ if [ "$ENABLE_FHIR2SQL" == true ]; then log INFO "Dashboard setup detected -- will start Dashboard backend and FHIR2SQL service." OVERRIDE+=" -f ./$PROJECT/modules/fhir2sql-compose.yml" DASHBOARD_DB_PASSWORD="$(generate_simple_password 'fhir2sql')" + FOCUS_ENDPOINT_TYPE="blaze-and-sql" fi From 52c24ee6faa9d02c36aa838fb636c2dca2f6b1e9 Mon Sep 17 00:00:00 2001 From: Jan <59206115+Threated@users.noreply.github.com> Date: Tue, 5 Nov 2024 13:34:36 +0100 Subject: [PATCH 5/9] fix(fhir2sql): add the postgres connection string to focus (#245) --- ccp/modules/fhir2sql-compose.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/ccp/modules/fhir2sql-compose.yml b/ccp/modules/fhir2sql-compose.yml index 7733787d..1230e898 100644 --- a/ccp/modules/fhir2sql-compose.yml +++ b/ccp/modules/fhir2sql-compose.yml @@ -23,3 +23,7 @@ services: POSTGRES_DB: "dashboard" volumes: - "/var/cache/bridgehead/ccp/dashboard-db:/var/lib/postgresql/data" + + focus: + environment: + POSTGRES_CONNECTION_STRING: "postgresql://dashboard:${DASHBOARD_DB_PASSWORD}@dashboard-db/dashboard" \ No newline at end of file From 967e45624e79d2649882c91b09874efb40dcc726 Mon Sep 17 00:00:00 2001 From: djuarezgf <46350150+djuarezgf@users.noreply.github.com> Date: Tue, 5 Nov 2024 15:46:00 +0100 Subject: [PATCH 6/9] Add exporter configuration to focus (#249) --- ccp/modules/exporter-compose.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/ccp/modules/exporter-compose.yml b/ccp/modules/exporter-compose.yml index d5eb2274..af4c67bc 100644 --- a/ccp/modules/exporter-compose.yml +++ b/ccp/modules/exporter-compose.yml @@ -65,3 +65,8 @@ services: - "traefik.http.routers.reporter_ccp.tls=true" - "traefik.http.middlewares.reporter_ccp_strip.stripprefix.prefixes=/ccp-reporter" - "traefik.http.routers.reporter_ccp.middlewares=reporter_ccp_strip" + + focus: + environment: + EXPORTER_URL: "http://exporter:8092" + AUTH_HEADER: "${EXPORTER_API_KEY}" From 122ff16bb18084954d20780244032b7a7370dd18 Mon Sep 17 00:00:00 2001 From: patrickskowronekdkfz <86347677+patrickskowronekdkfz@users.noreply.github.com> Date: Tue, 12 Nov 2024 09:58:17 +0100 Subject: [PATCH 7/9] fix: use verbis cache image instead of docker-hub (#250) --- ccp/modules/id-management-compose.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ccp/modules/id-management-compose.yml b/ccp/modules/id-management-compose.yml index 704646de..b7c3f61c 100644 --- a/ccp/modules/id-management-compose.yml +++ b/ccp/modules/id-management-compose.yml @@ -102,7 +102,7 @@ services: condition: service_healthy ccp-patient-project-identificator: - image: samply/ccp-patient-project-identificator + image: docker.verbis.dkfz.de/cache/samply/ccp-patient-project-identificator container_name: bridgehead-ccp-patient-project-identificator environment: MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY} From 45aefd24e52003a40aa50d9c29aae3d97ec98fce Mon Sep 17 00:00:00 2001 From: Enola Knezevic <115070135+enola-dkfz@users.noreply.github.com> Date: Fri, 6 Dec 2024 11:27:38 +0100 Subject: [PATCH 8/9] renamed exporter API key to EXPORTER_API_KEY (#252) --- ccp/modules/exporter-compose.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ccp/modules/exporter-compose.yml b/ccp/modules/exporter-compose.yml index af4c67bc..10ae89ff 100644 --- a/ccp/modules/exporter-compose.yml +++ b/ccp/modules/exporter-compose.yml @@ -69,4 +69,4 @@ services: focus: environment: EXPORTER_URL: "http://exporter:8092" - AUTH_HEADER: "${EXPORTER_API_KEY}" + EXPORTER_API_KEY: "${EXPORTER_API_KEY}" From e3510363ad2a2eb22ad686c4fb2e7cb346e8d2e4 Mon Sep 17 00:00:00 2001 From: patrickskowronekdkfz <86347677+patrickskowronekdkfz@users.noreply.github.com> Date: Tue, 10 Dec 2024 17:18:07 +0100 Subject: [PATCH 9/9] fix: remove credentials from git remote, if update fails (#253) Signed-off-by: Patrick Skowronek --- lib/update-bridgehead.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/lib/update-bridgehead.sh b/lib/update-bridgehead.sh index 44655b16..56afb17b 100755 --- a/lib/update-bridgehead.sh +++ b/lib/update-bridgehead.sh @@ -58,7 +58,8 @@ for DIR in /etc/bridgehead $(pwd); do OUT=$(retry 5 git -c http.proxy=$HTTPS_PROXY_FULL_URL -c https.proxy=$HTTPS_PROXY_FULL_URL -C $DIR fetch 2>&1 && retry 5 git -c http.proxy=$HTTPS_PROXY_FULL_URL -c https.proxy=$HTTPS_PROXY_FULL_URL -C $DIR pull 2>&1) fi if [ $? -ne 0 ]; then - report_error log "Unable to update git $DIR: $OUT" + OUT_SAN=$(echo $OUT | sed -E 's|://[^:]+:[^@]+@|://credentials@|g') + report_error log "Unable to update git $DIR: $OUT_SAN" fi new_git_hash="$(git -C $DIR rev-parse --verify HEAD)"