From 3fa797657447c7961dd03641215304179cb9c2b0 Mon Sep 17 00:00:00 2001 From: Torben Brenner Date: Mon, 24 Jan 2022 14:53:47 +0100 Subject: [PATCH 01/14] feature: Added default variables per project build --- .github/workflows/ci.yml | 2 ++ Dockerfile | 17 ++++++++++++++++- 2 files changed, 18 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index cd444db2..6d63c347 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -8,6 +8,7 @@ on: branches: - master - develop + - feature/environmentPreconfiguration tags: - 'v*.*.*' pull_request: @@ -93,6 +94,7 @@ jobs: with: context: . file: ./Dockerfile + target: ${{matrix.project}} platforms: linux/amd64,linux/arm64 build-args: | PROJECT=${{matrix.project_context}} diff --git a/Dockerfile b/Dockerfile index e9460359..5e64e320 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,7 +7,7 @@ ADD target/connector.war /connector/connector.war RUN mkdir -p /connector/extracted && \ unzip /connector/connector.war -d /connector/extracted/ -FROM tomcat:9-jre8-temurin +FROM tomcat:9-jre8-temurin as docker-build ## Define for which project this image is build ARG PROJECT=samply @@ -43,3 +43,18 @@ ENV JAVA_OPTS "-Dlog4j.configurationFile=${CATALINA_HOME}/conf/log4j2.xml" ADD src/docker/start.sh /docker/ RUN chmod +x /docker/start.sh CMD ["sh", "-c", "/docker/start.sh"] + +# Stage used by ci for dktk images (--target=dktk) +FROM docker-build as dktk +ENV TEST_PROJECT="dktk" + +# Stage used by ci for gbn images (--target=gbn) +FROM docker-build as gbn +ENV TEST_PROJECT="gbn" + +# Stage used by ci for c4 images (--target=c4) +FROM docker-build as c4 +ENV TEST_PROJECT="c4" + +# This stage is build when defining no target +FROM docker-build as vanilla From 940f19da160d69d37a9d45a765271618cd9a2424 Mon Sep 17 00:00:00 2001 From: Patrick Skowronek Date: Fri, 28 Jan 2022 09:45:13 +0100 Subject: [PATCH 02/14] Moved environment variables to docker image --- Dockerfile | 45 +++++++++++++++++++++++++++++++++++++++++++++ src/docker/start.sh | 2 ++ 2 files changed, 47 insertions(+) diff --git a/Dockerfile b/Dockerfile index 5e64e320..e7ab428a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -44,17 +44,62 @@ ADD src/docker/start.sh /docker/ RUN chmod +x /docker/start.sh CMD ["sh", "-c", "/docker/start.sh"] +ENV TZ="Europe/Berlin" + # Stage used by ci for dktk images (--target=dktk) FROM docker-build as dktk ENV TEST_PROJECT="dktk" +ENV POSTGRES_PORT="5432" +ENV CCP_CENTRALSEARCH_URL="https://centralsearch-test.dktk.dkfz.de/" +ENV CCP_DECENTRALSEARCH_URL="https://decentralsearch-test.ccp-it.dktk.dkfz.de/" +ENV CONNECTOR_ENABLE_METRICS="false" +ENV CONNECTOR_POSTGRES_DB="share_v2" +ENV CONNECTOR_POSTGRES_USER="samplyweb" +ENV CONNECTOR_SHARE_URL="${PROTOCOL}://${HOST}:${PORT}" +ENV DEPLOYMENT_CONTEXT="dktk-connector" +ENV feature_BBMRI_DIRECTORY_SYNC="false" +ENV feature_DKTK_CENTRAL_SEARCH="false" +ENV feature_NNGM_CTS="false" +ENV LOG_LEVEL="info" +ENV MDR_URL="https://mdr.ccp-it.dktk.dkfz.de/v3/api/mdr" +ENV POSTGRES_HOST="bridgehead_dktk_connector_db" +ENV PROTOCOL="http" +ENV QUERY_LANGUAGE="QUERY" +ENV CCP_PATIENTLIST_URL="http://bridgehead_patientlist:8080/Patientlist" # Stage used by ci for gbn images (--target=gbn) FROM docker-build as gbn ENV TEST_PROJECT="gbn" +ENV CONNECTOR_ENABLE_METRICS="false" +ENV POSTGRES_DB="samply.connector" +ENV POSTGRES_HOST="bridgehead_gbn_connector_db" +ENV CONNECTOR_POSTGRES_USER="samply" +ENV QUERY_LANGUAGE="CQL" +ENV DEPLOYMENT_CONTEXT="gbn-connector" +ENV LOG_LEVEL="info" +ENV STORE_URL="http://bridgehead_gbn_blaze_store:8080" +ENV PROTOCOL="http" +ENV PORT="8080" # Stage used by ci for c4 images (--target=c4) FROM docker-build as c4 ENV TEST_PROJECT="c4" +ENV POSTGRES_PORT="5432" +ENV CCP_CENTRALSEARCH_URL="https://centralsearch-test.dktk.dkfz.de/" +ENV CCP_DECENTRALSEARCH_URL="https://decentralsearch-test.ccp-it.dktk.dkfz.de/" +ENV CONNECTOR_ENABLE_METRICS="false" +ENV CONNECTOR_POSTGRES_DB="share_v2" +ENV CONNECTOR_POSTGRES_USER="samplyweb" +ENV CONNECTOR_SHARE_URL="${PROTOCOL}://${HOST}:${PORT}" +ENV DEPLOYMENT_CONTEXT="dktk-connector" +ENV feature_BBMRI_DIRECTORY_SYNC="false" +ENV feature_DKTK_CENTRAL_SEARCH="false" +ENV feature_NNGM_CTS="false" +ENV LOG_LEVEL="info" +ENV MDR_URL="https://mdr.ccp-it.dktk.dkfz.de/v3/api/mdr" +ENV POSTGRES_HOST="bridgehead_dktk_connector_db" +ENV PROTOCOL="http" +ENV QUERY_LANGUAGE="QUERY" # This stage is build when defining no target FROM docker-build as vanilla diff --git a/src/docker/start.sh b/src/docker/start.sh index b7a08419..9225d83d 100644 --- a/src/docker/start.sh +++ b/src/docker/start.sh @@ -13,6 +13,8 @@ if [ -n "$HTTP_PROXY" ]; then HTTPS_PROXY_PASSWORD=$PROXY_PASS; fi +export CONNECTOR_SHARE_URL="${PROTOCOL}://${HOST}:${PORT}" + file=${CATALINA_HOME}/conf/Catalina/localhost/ROOT.xml if [ -n "$DEPLOYMENT_CONTEXT" ]; then echo "INFO: preparing deployment in context ${DEPLOYMENT_CONTEXT}" From 33f1094397c781c30e8f2f55aa4d4e2502205a68 Mon Sep 17 00:00:00 2001 From: Patrick Skowronek Date: Fri, 28 Jan 2022 10:25:30 +0100 Subject: [PATCH 03/14] Fixed missing postgres user --- Dockerfile | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/Dockerfile b/Dockerfile index e7ab428a..7ca88d8a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -53,8 +53,8 @@ ENV POSTGRES_PORT="5432" ENV CCP_CENTRALSEARCH_URL="https://centralsearch-test.dktk.dkfz.de/" ENV CCP_DECENTRALSEARCH_URL="https://decentralsearch-test.ccp-it.dktk.dkfz.de/" ENV CONNECTOR_ENABLE_METRICS="false" -ENV CONNECTOR_POSTGRES_DB="share_v2" -ENV CONNECTOR_POSTGRES_USER="samplyweb" +ENV POSTGRES_DB="share_v2" +ENV POSTGRES_USER="samplyweb" ENV CONNECTOR_SHARE_URL="${PROTOCOL}://${HOST}:${PORT}" ENV DEPLOYMENT_CONTEXT="dktk-connector" ENV feature_BBMRI_DIRECTORY_SYNC="false" @@ -73,7 +73,7 @@ ENV TEST_PROJECT="gbn" ENV CONNECTOR_ENABLE_METRICS="false" ENV POSTGRES_DB="samply.connector" ENV POSTGRES_HOST="bridgehead_gbn_connector_db" -ENV CONNECTOR_POSTGRES_USER="samply" +ENV POSTGRES_USER="samply" ENV QUERY_LANGUAGE="CQL" ENV DEPLOYMENT_CONTEXT="gbn-connector" ENV LOG_LEVEL="info" @@ -88,8 +88,8 @@ ENV POSTGRES_PORT="5432" ENV CCP_CENTRALSEARCH_URL="https://centralsearch-test.dktk.dkfz.de/" ENV CCP_DECENTRALSEARCH_URL="https://decentralsearch-test.ccp-it.dktk.dkfz.de/" ENV CONNECTOR_ENABLE_METRICS="false" -ENV CONNECTOR_POSTGRES_DB="share_v2" -ENV CONNECTOR_POSTGRES_USER="samplyweb" +ENV POSTGRES_DB="share_v2" +ENV POSTGRES_USER="samplyweb" ENV CONNECTOR_SHARE_URL="${PROTOCOL}://${HOST}:${PORT}" ENV DEPLOYMENT_CONTEXT="dktk-connector" ENV feature_BBMRI_DIRECTORY_SYNC="false" From fe350fa83a92256ebbbee71dbc99489f3261f80a Mon Sep 17 00:00:00 2001 From: Patrick Skowronek Date: Fri, 28 Jan 2022 10:41:44 +0100 Subject: [PATCH 04/14] Add missing MDR to gbn and correct POSTGres PW --- Dockerfile | 1 + src/docker/start.sh | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 7ca88d8a..90818913 100644 --- a/Dockerfile +++ b/Dockerfile @@ -78,6 +78,7 @@ ENV QUERY_LANGUAGE="CQL" ENV DEPLOYMENT_CONTEXT="gbn-connector" ENV LOG_LEVEL="info" ENV STORE_URL="http://bridgehead_gbn_blaze_store:8080" +ENV MDR_URL="https://mdr.germanbiobanknode.de/v3/api/mdr" ENV PROTOCOL="http" ENV PORT="8080" diff --git a/src/docker/start.sh b/src/docker/start.sh index 9225d83d..1c77660a 100644 --- a/src/docker/start.sh +++ b/src/docker/start.sh @@ -27,7 +27,7 @@ sed -i "s/{postgres-host}/${POSTGRES_HOST}/" "$file" sed -i "s/{postgres-port}/${POSTGRES_PORT:-5432}/" "$file" sed -i "s/{postgres-db}/${POSTGRES_DB}/" "$file" sed -i "s/{postgres-user}/${POSTGRES_USER}/" "$file" -sed -i "s/{postgres-pass}/${POSTGRES_PASS}/" "$file" +sed -i "s/{postgres-pass}/${POSTGRES_PASSWORD}/" "$file" file=${CATALINA_HOME}/conf/${PROJECT}_common_config.xml sed -i "s|{http-proxy-url}|${HTTP_PROXY_URL:-}|" "$file" From 8444f1c40ed20d425fd04d7c4c77ee9f8a6a7158 Mon Sep 17 00:00:00 2001 From: Patrick Skowronek Date: Wed, 9 Feb 2022 10:11:43 +0100 Subject: [PATCH 05/14] Add missing id-manager url to dktk --- Dockerfile | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index 90818913..fde07c1e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -55,7 +55,8 @@ ENV CCP_DECENTRALSEARCH_URL="https://decentralsearch-test.ccp-it.dktk.dkfz.de/" ENV CONNECTOR_ENABLE_METRICS="false" ENV POSTGRES_DB="share_v2" ENV POSTGRES_USER="samplyweb" -ENV CONNECTOR_SHARE_URL="${PROTOCOL}://${HOST}:${PORT}" +ENV PROTOCOL="http" +ENV PORT="8080" ENV DEPLOYMENT_CONTEXT="dktk-connector" ENV feature_BBMRI_DIRECTORY_SYNC="false" ENV feature_DKTK_CENTRAL_SEARCH="false" @@ -63,9 +64,10 @@ ENV feature_NNGM_CTS="false" ENV LOG_LEVEL="info" ENV MDR_URL="https://mdr.ccp-it.dktk.dkfz.de/v3/api/mdr" ENV POSTGRES_HOST="bridgehead_dktk_connector_db" -ENV PROTOCOL="http" ENV QUERY_LANGUAGE="QUERY" -ENV CCP_PATIENTLIST_URL="http://bridgehead_patientlist:8080/Patientlist" +ENV PATIENTLIST_URL="http://bridgehead_patientlist:8080/Patientlist" +ENV ID_MANAGER_URL="http://bridgehead_id-manager:8080" + # Stage used by ci for gbn images (--target=gbn) FROM docker-build as gbn From 7f937f7149e8d83432bc100ecbea1527fe7be2e4 Mon Sep 17 00:00:00 2001 From: Patrick Skowronek Date: Tue, 1 Mar 2022 08:15:43 +0100 Subject: [PATCH 06/14] Added missing Var --- Dockerfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Dockerfile b/Dockerfile index fde07c1e..3fe3b8e1 100644 --- a/Dockerfile +++ b/Dockerfile @@ -66,6 +66,8 @@ ENV MDR_URL="https://mdr.ccp-it.dktk.dkfz.de/v3/api/mdr" ENV POSTGRES_HOST="bridgehead_dktk_connector_db" ENV QUERY_LANGUAGE="QUERY" ENV PATIENTLIST_URL="http://bridgehead_patientlist:8080/Patientlist" +ENV PROJECTPSEUDONYMISATION_URL="http://bridgehead_id-manager:8080/html/projectSelection.html" + ENV ID_MANAGER_URL="http://bridgehead_id-manager:8080" From 86ab7fa7230aaa82b7db139a5a1b01661f6e3b87 Mon Sep 17 00:00:00 2001 From: Patrick Skowronek Date: Wed, 6 Apr 2022 15:01:04 +0200 Subject: [PATCH 07/14] Added config for forward proxy --- Dockerfile | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 3fe3b8e1..e1ae3fd0 100644 --- a/Dockerfile +++ b/Dockerfile @@ -67,10 +67,12 @@ ENV POSTGRES_HOST="bridgehead_dktk_connector_db" ENV QUERY_LANGUAGE="QUERY" ENV PATIENTLIST_URL="http://bridgehead_patientlist:8080/Patientlist" ENV PROJECTPSEUDONYMISATION_URL="http://bridgehead_id-manager:8080/html/projectSelection.html" - +ENV http_proxy="http://bridgehead_squid:3128" +ENV https_proxy="http://bridgehead_squid:3128" +ENV HTTP_PROXY="http://bridgehead_squid:3128" +ENV HTTPS_PROXY="http://bridgehead_squid:3128" ENV ID_MANAGER_URL="http://bridgehead_id-manager:8080" - # Stage used by ci for gbn images (--target=gbn) FROM docker-build as gbn ENV TEST_PROJECT="gbn" @@ -85,6 +87,10 @@ ENV STORE_URL="http://bridgehead_gbn_blaze_store:8080" ENV MDR_URL="https://mdr.germanbiobanknode.de/v3/api/mdr" ENV PROTOCOL="http" ENV PORT="8080" +ENV http_proxy="http://bridgehead_squid:3128" +ENV https_proxy="http://bridgehead_squid:3128" +ENV HTTP_PROXY="http://bridgehead_squid:3128" +ENV HTTPS_PROXY="http://bridgehead_squid:3128" # Stage used by ci for c4 images (--target=c4) FROM docker-build as c4 @@ -105,6 +111,10 @@ ENV MDR_URL="https://mdr.ccp-it.dktk.dkfz.de/v3/api/mdr" ENV POSTGRES_HOST="bridgehead_dktk_connector_db" ENV PROTOCOL="http" ENV QUERY_LANGUAGE="QUERY" +ENV http_proxy="http://bridgehead_squid:3128" +ENV https_proxy="http://bridgehead_squid:3128" +ENV HTTP_PROXY="http://bridgehead_squid:3128" +ENV HTTPS_PROXY="http://bridgehead_squid:3128" # This stage is build when defining no target FROM docker-build as vanilla From 50ff88692e9d1763ef10f0c6cb2c1a6e7a49e5fa Mon Sep 17 00:00:00 2001 From: Patrick Skowronek Date: Thu, 7 Apr 2022 16:10:16 +0200 Subject: [PATCH 08/14] Fixed naming of services --- Dockerfile | 38 +++++++++++++++++++------------------- 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/Dockerfile b/Dockerfile index e1ae3fd0..3db637f9 100644 --- a/Dockerfile +++ b/Dockerfile @@ -63,34 +63,34 @@ ENV feature_DKTK_CENTRAL_SEARCH="false" ENV feature_NNGM_CTS="false" ENV LOG_LEVEL="info" ENV MDR_URL="https://mdr.ccp-it.dktk.dkfz.de/v3/api/mdr" -ENV POSTGRES_HOST="bridgehead_dktk_connector_db" +ENV POSTGRES_HOST="bridgehead-dktk-connector-db" ENV QUERY_LANGUAGE="QUERY" -ENV PATIENTLIST_URL="http://bridgehead_patientlist:8080/Patientlist" -ENV PROJECTPSEUDONYMISATION_URL="http://bridgehead_id-manager:8080/html/projectSelection.html" -ENV http_proxy="http://bridgehead_squid:3128" -ENV https_proxy="http://bridgehead_squid:3128" -ENV HTTP_PROXY="http://bridgehead_squid:3128" -ENV HTTPS_PROXY="http://bridgehead_squid:3128" -ENV ID_MANAGER_URL="http://bridgehead_id-manager:8080" +ENV PATIENTLIST_URL="http://bridgehead-patientlist:8080/Patientlist" +ENV PROJECTPSEUDONYMISATION_URL="http://bridgehead-id-manager:8080/html/projectSelection.html" +ENV http_proxy="http://bridgehead-squid:3128" +ENV https_proxy="http://bridgehead-squid:3128" +ENV HTTP_PROXY="http://bridgehead-squid:3128" +ENV HTTPS_PROXY="http://bridgehead-squid:3128" +ENV ID_MANAGER_URL="http://bridgehead-id-manager:8080" # Stage used by ci for gbn images (--target=gbn) FROM docker-build as gbn ENV TEST_PROJECT="gbn" ENV CONNECTOR_ENABLE_METRICS="false" ENV POSTGRES_DB="samply.connector" -ENV POSTGRES_HOST="bridgehead_gbn_connector_db" +ENV POSTGRES_HOST="bridgehead-gbn-connector-db" ENV POSTGRES_USER="samply" ENV QUERY_LANGUAGE="CQL" ENV DEPLOYMENT_CONTEXT="gbn-connector" ENV LOG_LEVEL="info" -ENV STORE_URL="http://bridgehead_gbn_blaze_store:8080" +ENV STORE_URL="http://bridgehead-gbn-blaze-store:8080" ENV MDR_URL="https://mdr.germanbiobanknode.de/v3/api/mdr" ENV PROTOCOL="http" ENV PORT="8080" -ENV http_proxy="http://bridgehead_squid:3128" -ENV https_proxy="http://bridgehead_squid:3128" -ENV HTTP_PROXY="http://bridgehead_squid:3128" -ENV HTTPS_PROXY="http://bridgehead_squid:3128" +ENV http_proxy="http://bridgehea-squid:3128" +ENV https_proxy="http://bridgehead-squid:3128" +ENV HTTP_PROXY="http://bridgehead-squid:3128" +ENV HTTPS_PROXY="http://bridgehead-squid:3128" # Stage used by ci for c4 images (--target=c4) FROM docker-build as c4 @@ -108,13 +108,13 @@ ENV feature_DKTK_CENTRAL_SEARCH="false" ENV feature_NNGM_CTS="false" ENV LOG_LEVEL="info" ENV MDR_URL="https://mdr.ccp-it.dktk.dkfz.de/v3/api/mdr" -ENV POSTGRES_HOST="bridgehead_dktk_connector_db" +ENV POSTGRES_HOST="bridgehead-dktk-connector-db" ENV PROTOCOL="http" ENV QUERY_LANGUAGE="QUERY" -ENV http_proxy="http://bridgehead_squid:3128" -ENV https_proxy="http://bridgehead_squid:3128" -ENV HTTP_PROXY="http://bridgehead_squid:3128" -ENV HTTPS_PROXY="http://bridgehead_squid:3128" +ENV http_proxy="http://bridgehead-squid:3128" +ENV https_proxy="http://bridgehead-squid:3128" +ENV HTTP_PROXY="http://bridgehead-squid:3128" +ENV HTTPS_PROXY="http://bridgehead-squid:3128" # This stage is build when defining no target FROM docker-build as vanilla From 2d50708a06e03f1b9fe9b9ef592a2d87b89a94ad Mon Sep 17 00:00:00 2001 From: Patrick Skowronek Date: Thu, 14 Apr 2022 14:49:54 +0200 Subject: [PATCH 09/14] Added NNGM Docker image --- .github/workflows/ci.yml | 3 +++ Dockerfile | 26 ++++++++++++++++++++++++++ 2 files changed, 29 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6d63c347..18f8afb2 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -31,6 +31,9 @@ jobs: - project: c4 project_context: dktk maven_profile: dktk + - project: nngm + project_context: dktk + maven_profile: dktk services: postgres: image: postgres diff --git a/Dockerfile b/Dockerfile index 3db637f9..51f1a816 100644 --- a/Dockerfile +++ b/Dockerfile @@ -116,5 +116,31 @@ ENV https_proxy="http://bridgehead-squid:3128" ENV HTTP_PROXY="http://bridgehead-squid:3128" ENV HTTPS_PROXY="http://bridgehead-squid:3128" +FROM docker-build as nngm +ENV TEST_PROJECT="nngm" +ENV POSTGRES_PORT="5432" +ENV CONNECTOR_ENABLE_METRICS="false" +ENV POSTGRES_DB="share_v2" +ENV POSTGRES_USER="samplyweb" +ENV CONNECTOR_SHARE_URL="${PROTOCOL}://${HOST}:${PORT}" +ENV DEPLOYMENT_CONTEXT="nngm-connector" +ENV feature_BBMRI_DIRECTORY_SYNC="false" +ENV feature_DKTK_CENTRAL_SEARCH="false" +ENV feature_NNGM_CTS="true" +ENV feature_NNGM_ENCRYPT_ID="false" +ENV LOG_LEVEL="info" +ENV POSTGRES_HOST="bridgehead-nngm-connector-db" +ENV PROTOCOL="http" +ENV QUERY_LANGUAGE="CQL" +ENV http_proxy="http://bridgehead-squid:3128" +ENV https_proxy="http://bridgehead-squid:3128" +ENV HTTP_PROXY="http://bridgehead-squid:3128" +ENV HTTPS_PROXY="http://bridgehead-squid:3128" +ENV nngm-cts-url="https://nngm-test.medicalsyn.com/api/v1.0/hl7/patient" +ENV nngm-profile="http://uk-koeln.de/fhir/StructureDefinition/Patient/nNGM/pseudonymisiert" +ENV nngm-magicpl-url="https://test.verbis.dkfz.de/nngm/magicpl" +ENV nngm-mainzelliste-url="https://test.verbis.dkfz.de/nngm/mainzelliste" + + # This stage is build when defining no target FROM docker-build as vanilla From 8518457caf2ac81af03c3d51362c81cda1013e6a Mon Sep 17 00:00:00 2001 From: Patrick Skowronek Date: Mon, 25 Apr 2022 15:07:33 +0200 Subject: [PATCH 10/14] Changed nngm profile due to no ldm needed --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 18f8afb2..bd24a861 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -32,7 +32,7 @@ jobs: project_context: dktk maven_profile: dktk - project: nngm - project_context: dktk + project_context: nngm maven_profile: dktk services: postgres: From 13125cec80a8e70052d8e6cbcbd292a727335854 Mon Sep 17 00:00:00 2001 From: Patrick Skowronek Date: Tue, 26 Apr 2022 14:03:59 +0200 Subject: [PATCH 11/14] Build nngm image as dktk --- .github/workflows/ci.yml | 2 +- Dockerfile | 28 ++++++++++++++-------------- 2 files changed, 15 insertions(+), 15 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index bd24a861..18f8afb2 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -32,7 +32,7 @@ jobs: project_context: dktk maven_profile: dktk - project: nngm - project_context: nngm + project_context: dktk maven_profile: dktk services: postgres: diff --git a/Dockerfile b/Dockerfile index 51f1a816..1fd30c84 100644 --- a/Dockerfile +++ b/Dockerfile @@ -58,9 +58,9 @@ ENV POSTGRES_USER="samplyweb" ENV PROTOCOL="http" ENV PORT="8080" ENV DEPLOYMENT_CONTEXT="dktk-connector" -ENV feature_BBMRI_DIRECTORY_SYNC="false" -ENV feature_DKTK_CENTRAL_SEARCH="false" -ENV feature_NNGM_CTS="false" +ENV FEATURE_BBMRI_DIRECTORY_SYNC="false" +ENV FEATURE_DKTK_CENTRAL_SEARCH="false" +ENV FEATURE_NNGM_CTS="false" ENV LOG_LEVEL="info" ENV MDR_URL="https://mdr.ccp-it.dktk.dkfz.de/v3/api/mdr" ENV POSTGRES_HOST="bridgehead-dktk-connector-db" @@ -103,9 +103,9 @@ ENV POSTGRES_DB="share_v2" ENV POSTGRES_USER="samplyweb" ENV CONNECTOR_SHARE_URL="${PROTOCOL}://${HOST}:${PORT}" ENV DEPLOYMENT_CONTEXT="dktk-connector" -ENV feature_BBMRI_DIRECTORY_SYNC="false" -ENV feature_DKTK_CENTRAL_SEARCH="false" -ENV feature_NNGM_CTS="false" +ENV FEATURE_BBMRI_DIRECTORY_SYNC="false" +ENV FEATURE_DKTK_CENTRAL_SEARCH="false" +ENV FEATURE_NNGM_CTS="false" ENV LOG_LEVEL="info" ENV MDR_URL="https://mdr.ccp-it.dktk.dkfz.de/v3/api/mdr" ENV POSTGRES_HOST="bridgehead-dktk-connector-db" @@ -124,10 +124,10 @@ ENV POSTGRES_DB="share_v2" ENV POSTGRES_USER="samplyweb" ENV CONNECTOR_SHARE_URL="${PROTOCOL}://${HOST}:${PORT}" ENV DEPLOYMENT_CONTEXT="nngm-connector" -ENV feature_BBMRI_DIRECTORY_SYNC="false" -ENV feature_DKTK_CENTRAL_SEARCH="false" -ENV feature_NNGM_CTS="true" -ENV feature_NNGM_ENCRYPT_ID="false" +ENV FEATURE_BBMRI_DIRECTORY_SYNC="false" +ENV FEATURE_DKTK_CENTRAL_SEARCH="false" +ENV FEATURE_NNGM_CTS="true" +ENV FEATURE_NNGM_ENCRYPT_ID="false" ENV LOG_LEVEL="info" ENV POSTGRES_HOST="bridgehead-nngm-connector-db" ENV PROTOCOL="http" @@ -136,10 +136,10 @@ ENV http_proxy="http://bridgehead-squid:3128" ENV https_proxy="http://bridgehead-squid:3128" ENV HTTP_PROXY="http://bridgehead-squid:3128" ENV HTTPS_PROXY="http://bridgehead-squid:3128" -ENV nngm-cts-url="https://nngm-test.medicalsyn.com/api/v1.0/hl7/patient" -ENV nngm-profile="http://uk-koeln.de/fhir/StructureDefinition/Patient/nNGM/pseudonymisiert" -ENV nngm-magicpl-url="https://test.verbis.dkfz.de/nngm/magicpl" -ENV nngm-mainzelliste-url="https://test.verbis.dkfz.de/nngm/mainzelliste" +ENV NNGM_CTS_URL="https://nngm-test.medicalsyn.com/api/v1.0/hl7/patient" +ENV NNGM_PROFILE="http://uk-koeln.de/fhir/StructureDefinition/Patient/nNGM/pseudonymisiert" +ENV NNGM_MAGICPL_URL="https://test.verbis.dkfz.de/nngm/magicpl" +ENV NNGM_MAINZELLISTE_URL="https://test.verbis.dkfz.de/nngm/mainzelliste" # This stage is build when defining no target From 6332019b414002aad6eea31aba495bd9c9f3464f Mon Sep 17 00:00:00 2001 From: Patrick Skowronek Date: Wed, 27 Apr 2022 09:32:17 +0200 Subject: [PATCH 12/14] finalized nngm docker image --- Dockerfile | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/Dockerfile b/Dockerfile index 1fd30c84..62486d04 100644 --- a/Dockerfile +++ b/Dockerfile @@ -128,6 +128,12 @@ ENV FEATURE_BBMRI_DIRECTORY_SYNC="false" ENV FEATURE_DKTK_CENTRAL_SEARCH="false" ENV FEATURE_NNGM_CTS="true" ENV FEATURE_NNGM_ENCRYPT_ID="false" +ENV ID_MANAGER_URL="http://bridgehead-example:8080" +ENV PATIENTLIST_URL="http://bridgehead-example:8080" +ENV PROJECTPSEUDONYMISATION_URL="http://bridgehead-example:8080" +ENV MDR_URL="https://mdr.ccp-it.dktk.dkfz.de/v3/api/mdr" +ENV NO_PROXY="bridgehead-example" +ENV STORE_URL="http://bridgehead-example:8080" ENV LOG_LEVEL="info" ENV POSTGRES_HOST="bridgehead-nngm-connector-db" ENV PROTOCOL="http" From 3d7be07b3dadf32de60e7d885d0ac542a5866ccc Mon Sep 17 00:00:00 2001 From: patrickskowronekdkfz <86347677+patrickskowronekdkfz@users.noreply.github.com> Date: Mon, 23 May 2022 15:38:19 +0200 Subject: [PATCH 13/14] Update Dockerfile Updated proxy settings --- Dockerfile | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/Dockerfile b/Dockerfile index 62486d04..af86ce5f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -67,10 +67,10 @@ ENV POSTGRES_HOST="bridgehead-dktk-connector-db" ENV QUERY_LANGUAGE="QUERY" ENV PATIENTLIST_URL="http://bridgehead-patientlist:8080/Patientlist" ENV PROJECTPSEUDONYMISATION_URL="http://bridgehead-id-manager:8080/html/projectSelection.html" -ENV http_proxy="http://bridgehead-squid:3128" -ENV https_proxy="http://bridgehead-squid:3128" -ENV HTTP_PROXY="http://bridgehead-squid:3128" -ENV HTTPS_PROXY="http://bridgehead-squid:3128" +ENV http_proxy="http://bridgehead-forward-proxy:3128" +ENV https_proxy="http://bridgehead-forward-proxy:3128" +ENV HTTP_PROXY="http://bridgehead-forward-proxy:3128" +ENV HTTPS_PROXY="http://bridgehead-forward-proxy:3128" ENV ID_MANAGER_URL="http://bridgehead-id-manager:8080" # Stage used by ci for gbn images (--target=gbn) @@ -87,10 +87,10 @@ ENV STORE_URL="http://bridgehead-gbn-blaze-store:8080" ENV MDR_URL="https://mdr.germanbiobanknode.de/v3/api/mdr" ENV PROTOCOL="http" ENV PORT="8080" -ENV http_proxy="http://bridgehea-squid:3128" -ENV https_proxy="http://bridgehead-squid:3128" -ENV HTTP_PROXY="http://bridgehead-squid:3128" -ENV HTTPS_PROXY="http://bridgehead-squid:3128" +ENV http_proxy="http://bridgehead-forward-proxy:3128" +ENV https_proxy="http://bridgehead-forward-proxy:3128" +ENV HTTP_PROXY="http://bridgehead-forward-proxy:3128" +ENV HTTPS_PROXY="http://bridgehead-forward-proxy:3128" # Stage used by ci for c4 images (--target=c4) FROM docker-build as c4 @@ -111,10 +111,10 @@ ENV MDR_URL="https://mdr.ccp-it.dktk.dkfz.de/v3/api/mdr" ENV POSTGRES_HOST="bridgehead-dktk-connector-db" ENV PROTOCOL="http" ENV QUERY_LANGUAGE="QUERY" -ENV http_proxy="http://bridgehead-squid:3128" -ENV https_proxy="http://bridgehead-squid:3128" -ENV HTTP_PROXY="http://bridgehead-squid:3128" -ENV HTTPS_PROXY="http://bridgehead-squid:3128" +ENV http_proxy="http://bridgehead-forward-proxy:3128" +ENV https_proxy="http://bridgehead-forward-proxy:3128" +ENV HTTP_PROXY="http://bridgehead-forward-proxy:3128" +ENV HTTPS_PROXY="http://bridgehead-forward-proxy:3128" FROM docker-build as nngm ENV TEST_PROJECT="nngm" @@ -138,10 +138,10 @@ ENV LOG_LEVEL="info" ENV POSTGRES_HOST="bridgehead-nngm-connector-db" ENV PROTOCOL="http" ENV QUERY_LANGUAGE="CQL" -ENV http_proxy="http://bridgehead-squid:3128" -ENV https_proxy="http://bridgehead-squid:3128" -ENV HTTP_PROXY="http://bridgehead-squid:3128" -ENV HTTPS_PROXY="http://bridgehead-squid:3128" +ENV http_proxy="http://bridgehead-forward-proxy:3128" +ENV https_proxy="http://bridgehead-forward-proxy:3128" +ENV HTTP_PROXY="http://bridgehead-forward-proxy:3128" +ENV HTTPS_PROXY="http://bridgehead-forward-proxy:3128" ENV NNGM_CTS_URL="https://nngm-test.medicalsyn.com/api/v1.0/hl7/patient" ENV NNGM_PROFILE="http://uk-koeln.de/fhir/StructureDefinition/Patient/nNGM/pseudonymisiert" ENV NNGM_MAGICPL_URL="https://test.verbis.dkfz.de/nngm/magicpl" From ae38f93f60e5540205b7d2a10667604351f3c4a7 Mon Sep 17 00:00:00 2001 From: Croft Date: Thu, 2 Jun 2022 16:48:23 +0200 Subject: [PATCH 14/14] Fixed Blaze URL for GBN The Blaze URL was missing the trailing "/fhir", which prevented the Connector from executing queries. This patch fixes the problem. --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index af86ce5f..f66c0068 100644 --- a/Dockerfile +++ b/Dockerfile @@ -83,7 +83,7 @@ ENV POSTGRES_USER="samply" ENV QUERY_LANGUAGE="CQL" ENV DEPLOYMENT_CONTEXT="gbn-connector" ENV LOG_LEVEL="info" -ENV STORE_URL="http://bridgehead-gbn-blaze-store:8080" +ENV STORE_URL="http://bridgehead-gbn-blaze-store:8080/fhir" ENV MDR_URL="https://mdr.germanbiobanknode.de/v3/api/mdr" ENV PROTOCOL="http" ENV PORT="8080"