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WIP: Feature/environment preconfiguration #148

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3fa7976
feature: Added default variables per project build
torbrenner Jan 24, 2022
940f19d
Moved environment variables to docker image
patrick-skowronek Jan 28, 2022
33f1094
Fixed missing postgres user
patrick-skowronek Jan 28, 2022
fe350fa
Add missing MDR to gbn and correct POSTGres PW
patrick-skowronek Jan 28, 2022
8444f1c
Add missing id-manager url to dktk
patrick-skowronek Feb 9, 2022
7f937f7
Added missing Var
patrick-skowronek Mar 1, 2022
a8c2ac2
Merge remote-tracking branch 'origin/release-7.6.1' into feature/envi…
patrick-skowronek Mar 1, 2022
86ab7fa
Added config for forward proxy
patrick-skowronek Apr 6, 2022
50ff886
Fixed naming of services
patrick-skowronek Apr 7, 2022
2d50708
Added NNGM Docker image
patrick-skowronek Apr 14, 2022
7a77ac2
Merge branch 'master' into feature/environmentPreconfiguration
patrick-skowronek Apr 25, 2022
8518457
Changed nngm profile due to no ldm needed
patrick-skowronek Apr 25, 2022
13125ce
Build nngm image as dktk
patrick-skowronek Apr 26, 2022
6332019
finalized nngm docker image
patrick-skowronek Apr 27, 2022
c2a8050
Merge branch 'master' into feature/environmentPreconfiguration
patrick-skowronek Apr 27, 2022
3d7be07
Update Dockerfile
patrick-skowronek May 23, 2022
ae38f93
Fixed Blaze URL for GBN
Jun 2, 2022
3d8f9b0
Merge pull request #177 from samply/feature/environmentPreconfigurati…
DavidCroftDKFZ Jul 6, 2022
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5 changes: 5 additions & 0 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@ on:
branches:
- master
- develop
- feature/environmentPreconfiguration
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@alexanderkiel alexanderkiel Feb 9, 2022

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This is not needed. If you file a PR, the branch will be build.

tags:
- 'v*.*.*'
pull_request:
Expand All @@ -30,6 +31,9 @@ jobs:
- project: c4
project_context: dktk
maven_profile: dktk
- project: nngm
project_context: dktk
maven_profile: dktk
services:
postgres:
image: postgres
Expand Down Expand Up @@ -93,6 +97,7 @@ jobs:
with:
context: .
file: ./Dockerfile
target: ${{matrix.project}}
platforms: linux/amd64,linux/arm64
build-args: |
PROJECT=${{matrix.project_context}}
Expand Down
109 changes: 108 additions & 1 deletion Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -43,3 +43,110 @@ 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"]

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 POSTGRES_DB="share_v2"
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 LOG_LEVEL="info"
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 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)
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_USER="samply"
ENV QUERY_LANGUAGE="CQL"
ENV DEPLOYMENT_CONTEXT="gbn-connector"
ENV LOG_LEVEL="info"
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"
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
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 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 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 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"
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 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"
ENV QUERY_LANGUAGE="CQL"
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"
ENV NNGM_MAINZELLISTE_URL="https://test.verbis.dkfz.de/nngm/mainzelliste"


# This stage is build when defining no target
FROM docker-build as vanilla
4 changes: 3 additions & 1 deletion src/docker/start.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -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 ${DEPLOYMENT_CONTEXT}"
Expand All @@ -25,7 +27,7 @@ sed -i "s/{postgres-host}/${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"
Expand Down