diff --git a/cce/modules/lens-compose.yml b/cce/modules/lens-compose.yml deleted file mode 100644 index 12b95ce..0000000 --- a/cce/modules/lens-compose.yml +++ /dev/null @@ -1,33 +0,0 @@ -version: "3.7" -services: - landing: - container_name: lens_federated-search - image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID} - labels: - - "traefik.enable=true" - - "traefik.http.routers.landing.rule=PathPrefix(`/`)" - - "traefik.http.services.landing.loadbalancer.server.port=80" - - "traefik.http.routers.landing.tls=true" - - spot: - image: docker.verbis.dkfz.de/ccp-private/central-spot - environment: - BEAM_SECRET: "${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(`${HOST}`) && PathPrefix(`/backend`)" - - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend" - - "traefik.http.routers.spot.tls=true" - - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot" diff --git a/cce/modules/lens-setup.sh b/cce/modules/lens-setup.sh deleted file mode 100644 index c19dc4b..0000000 --- a/cce/modules/lens-setup.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/bash - -if [ -n "$ENABLE_LENS" ];then - OVERRIDE+=" -f ./$PROJECT/modules/lens-compose.yml" -fi \ No newline at end of file diff --git a/cce/vars b/cce/vars index 7d0c1a3..70a7c30 100644 --- a/cce/vars +++ b/cce/vars @@ -7,7 +7,7 @@ SUPPORT_EMAIL=manoj.waikar@dkfz-heidelberg.de PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem BROKER_URL_FOR_PREREQ=$BROKER_URL -for module in $PROJECT/modules/*.sh +for module in common/*.sh do log DEBUG "sourcing $module" source $module diff --git a/ccp/modules/exporter-setup.sh b/ccp/modules/exporter-setup.sh deleted file mode 100644 index 9b947a6..0000000 --- a/ccp/modules/exporter-setup.sh +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash -e - -if [ "$ENABLE_EXPORTER" == true ]; then - log INFO "Exporter setup detected -- will start Exporter service." - OVERRIDE+=" -f ./$PROJECT/modules/exporter-compose.yml" - EXPORTER_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)" - EXPORTER_API_KEY="$(echo \"This is a salt string to generate one consistent API KEY for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)" -fi diff --git a/ccp/modules/teiler-setup.sh b/ccp/modules/teiler-setup.sh deleted file mode 100644 index eed3f81..0000000 --- a/ccp/modules/teiler-setup.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash -e - -if [ "$ENABLE_TEILER" == true ];then - log INFO "Teiler setup detected -- will start Teiler services." - OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml" - TEILER_DEFAULT_LANGUAGE=DE - TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,} - add_public_oidc_redirect_url "/ccp-teiler/*" -fi diff --git a/ccp/vars b/ccp/vars index 0900914..012a963 100644 --- a/ccp/vars +++ b/ccp/vars @@ -20,7 +20,7 @@ OIDC_GROUP_CLAIM="groups" POSTGRES_TAG=15.6-alpine -for module in $PROJECT/modules/*.sh +for module in common/*.sh do log DEBUG "sourcing $module" source $module diff --git a/ccp/modules/blaze-secondary-compose.yml b/common/blaze-secondary-compose.yml similarity index 100% rename from ccp/modules/blaze-secondary-compose.yml rename to common/blaze-secondary-compose.yml diff --git a/ccp/modules/blaze-secondary-setup.sh b/common/blaze-secondary-setup.sh similarity index 82% rename from ccp/modules/blaze-secondary-setup.sh rename to common/blaze-secondary-setup.sh index 307da01..08ebc23 100644 --- a/ccp/modules/blaze-secondary-setup.sh +++ b/common/blaze-secondary-setup.sh @@ -3,7 +3,7 @@ function blazeSecondarySetup() { if [ -n "$ENABLE_SECONDARY_BLAZE" ]; then log INFO "Secondary Blaze setup detected -- will start second blaze." - OVERRIDE+=" -f ./$PROJECT/modules/blaze-secondary-compose.yml" + OVERRIDE+=" -f ./common/blaze-secondary-compose.yml" #make oBDS2FHIR ignore ID-Management and replace target Blaze PATIENTLIST_URL=" " STORE_PATH="http://blaze-secondary:8080/fhir" diff --git a/ccp/modules/datashield-compose.yml b/common/datashield-compose.yml similarity index 100% rename from ccp/modules/datashield-compose.yml rename to common/datashield-compose.yml diff --git a/ccp/modules/datashield-setup.sh b/common/datashield-setup.sh similarity index 94% rename from ccp/modules/datashield-setup.sh rename to common/datashield-setup.sh index 9692fb9..17b2ab4 100644 --- a/ccp/modules/datashield-setup.sh +++ b/common/datashield-setup.sh @@ -10,7 +10,7 @@ if [ "$ENABLE_DATASHIELD" == true ]; then add_private_oidc_redirect_url "${OAUTH2_CALLBACK}" log INFO "DataSHIELD setup detected -- will start DataSHIELD services." - OVERRIDE+=" -f ./$PROJECT/modules/datashield-compose.yml" + OVERRIDE+=" -f ./common/datashield-compose.yml" EXPORTER_OPAL_PASSWORD="$(generate_password \"exporter in Opal\")" TOKEN_MANAGER_OPAL_PASSWORD="$(generate_password \"Token Manager in Opal\")" OPAL_DB_PASSWORD="$(echo \"Opal DB\" | generate_simple_password)" @@ -23,7 +23,7 @@ if [ "$ENABLE_DATASHIELD" == true ]; then openssl req -x509 -newkey rsa:4096 -nodes -keyout /tmp/bridgehead/opal-key.pem -out /tmp/bridgehead/opal-cert.pem -days 3650 -subj "/CN=opal/C=DE" fi mkdir -p /tmp/bridgehead/opal-map - sites="$(cat ./$PROJECT/modules/datashield-sites.json)" + sites="$(cat ./common/datashield-sites.json)" echo "$sites" | docker_jq -n --args '{"sites": input | map({ "name": ., "id": ., diff --git a/common/datashield-sites.json b/common/datashield-sites.json new file mode 100644 index 0000000..600534d --- /dev/null +++ b/common/datashield-sites.json @@ -0,0 +1,15 @@ +[ + "berlin", + "muenchen-lmu", + "dresden", + "freiburg", + "muenchen-tum", + "tuebingen", + "mainz", + "frankfurt", + "essen", + "dktk-datashield-test", + "dktk-test", + "mannheim", + "central-ds-orchestrator" +] diff --git a/ccp/modules/datashield.md b/common/datashield.md similarity index 100% rename from ccp/modules/datashield.md rename to common/datashield.md diff --git a/ccp/modules/dnpm-compose.yml b/common/dnpm-compose.yml similarity index 100% rename from ccp/modules/dnpm-compose.yml rename to common/dnpm-compose.yml diff --git a/ccp/modules/dnpm-node-compose.yml b/common/dnpm-node-compose.yml similarity index 100% rename from ccp/modules/dnpm-node-compose.yml rename to common/dnpm-node-compose.yml diff --git a/ccp/modules/dnpm-node-setup.sh b/common/dnpm-node-setup.sh similarity index 96% rename from ccp/modules/dnpm-node-setup.sh rename to common/dnpm-node-setup.sh index bf8fd26..918963d 100644 --- a/ccp/modules/dnpm-node-setup.sh +++ b/common/dnpm-node-setup.sh @@ -2,7 +2,7 @@ if [ -n "${ENABLE_DNPM_NODE}" ]; then log INFO "DNPM setup detected (BwHC Node) -- will start BwHC node." - OVERRIDE+=" -f ./$PROJECT/modules/dnpm-node-compose.yml" + OVERRIDE+=" -f ./common/dnpm-node-compose.yml" # Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/.conf DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)" diff --git a/ccp/modules/dnpm-setup.sh b/common/dnpm-setup.sh similarity index 90% rename from ccp/modules/dnpm-setup.sh rename to common/dnpm-setup.sh index 9ca4767..58b60e9 100644 --- a/ccp/modules/dnpm-setup.sh +++ b/common/dnpm-setup.sh @@ -2,7 +2,7 @@ if [ -n "${ENABLE_DNPM}" ]; then log INFO "DNPM setup detected (Beam.Connect) -- will start Beam.Connect for DNPM." - OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose.yml" + OVERRIDE+=" -f ./common/dnpm-compose.yml" # Set variables required for Beam-Connect DNPM_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)" diff --git a/kr/modules/export-and-qb.curl-templates b/common/export-and-qb.curl-templates similarity index 100% rename from kr/modules/export-and-qb.curl-templates rename to common/export-and-qb.curl-templates diff --git a/ccp/modules/exporter-compose.yml b/common/exporter-compose.yml similarity index 100% rename from ccp/modules/exporter-compose.yml rename to common/exporter-compose.yml diff --git a/kr/modules/exporter-setup.sh b/common/exporter-setup.sh similarity index 91% rename from kr/modules/exporter-setup.sh rename to common/exporter-setup.sh index 9b947a6..57cad2f 100644 --- a/kr/modules/exporter-setup.sh +++ b/common/exporter-setup.sh @@ -2,7 +2,7 @@ if [ "$ENABLE_EXPORTER" == true ]; then log INFO "Exporter setup detected -- will start Exporter service." - OVERRIDE+=" -f ./$PROJECT/modules/exporter-compose.yml" + OVERRIDE+=" -f ./common/exporter-compose.yml" EXPORTER_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)" EXPORTER_API_KEY="$(echo \"This is a salt string to generate one consistent API KEY for the exporter. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 64)" fi diff --git a/ccp/modules/exporter.md b/common/exporter.md similarity index 100% rename from ccp/modules/exporter.md rename to common/exporter.md diff --git a/ccp/modules/fhir2sql-compose.yml b/common/fhir2sql-compose.yml similarity index 100% rename from ccp/modules/fhir2sql-compose.yml rename to common/fhir2sql-compose.yml diff --git a/ccp/modules/fhir2sql-setup.sh b/common/fhir2sql-setup.sh similarity index 78% rename from ccp/modules/fhir2sql-setup.sh rename to common/fhir2sql-setup.sh index 64fa7c0..4cc700a 100644 --- a/ccp/modules/fhir2sql-setup.sh +++ b/common/fhir2sql-setup.sh @@ -2,6 +2,6 @@ if [ "$ENABLE_FHIR2SQL" == true ]; then log INFO "Dashboard setup detected -- will start Dashboard backend and FHIR2SQL service." - OVERRIDE+=" -f ./$PROJECT/modules/fhir2sql-compose.yml" + OVERRIDE+=" -f ./common/fhir2sql-compose.yml" DASHBOARD_DB_PASSWORD="$(generate_simple_password 'fhir2sql')" fi diff --git a/ccp/modules/fhir2sql.md b/common/fhir2sql.md similarity index 100% rename from ccp/modules/fhir2sql.md rename to common/fhir2sql.md diff --git a/ccp/modules/id-management-compose.yml b/common/id-management-compose.yml similarity index 100% rename from ccp/modules/id-management-compose.yml rename to common/id-management-compose.yml diff --git a/ccp/modules/id-management-setup.sh b/common/id-management-setup.sh similarity index 96% rename from ccp/modules/id-management-setup.sh rename to common/id-management-setup.sh index 333b512..ed844fe 100644 --- a/ccp/modules/id-management-setup.sh +++ b/common/id-management-setup.sh @@ -3,7 +3,7 @@ function idManagementSetup() { if [ -n "$IDMANAGER_UPLOAD_APIKEY" ]; then log INFO "id-management setup detected -- will start id-management (mainzelliste & magicpl)." - OVERRIDE+=" -f ./ccp/modules/id-management-compose.yml" + OVERRIDE+=" -f ./common/id-management-compose.yml" # Auto Generate local Passwords PATIENTLIST_POSTGRES_PASSWORD="$(echo \"id-management-module-db-password-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)" diff --git a/ccp/modules/id-management.md b/common/id-management.md similarity index 100% rename from ccp/modules/id-management.md rename to common/id-management.md diff --git a/itcc/modules/lens-compose.yml b/common/lens-compose.yml similarity index 100% rename from itcc/modules/lens-compose.yml rename to common/lens-compose.yml diff --git a/common/lens-setup.sh b/common/lens-setup.sh new file mode 100644 index 0000000..e9cf41b --- /dev/null +++ b/common/lens-setup.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +if [ -n "$ENABLE_LENS" ];then + OVERRIDE+=" -f ./common/lens-compose.yml" +fi \ No newline at end of file diff --git a/ccp/modules/mtba-compose.yml b/common/mtba-compose.yml similarity index 100% rename from ccp/modules/mtba-compose.yml rename to common/mtba-compose.yml diff --git a/ccp/modules/mtba-setup.sh b/common/mtba-setup.sh similarity index 85% rename from ccp/modules/mtba-setup.sh rename to common/mtba-setup.sh index d2acbe2..f6c5728 100644 --- a/ccp/modules/mtba-setup.sh +++ b/common/mtba-setup.sh @@ -6,7 +6,7 @@ function mtbaSetup() { if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:" fi - OVERRIDE+=" -f ./$PROJECT/modules/mtba-compose.yml" + OVERRIDE+=" -f ./common/mtba-compose.yml" add_private_oidc_redirect_url "/mtba/*" fi } diff --git a/ccp/modules/mtba.md b/common/mtba.md similarity index 100% rename from ccp/modules/mtba.md rename to common/mtba.md diff --git a/ccp/modules/nngm-compose.yml b/common/nngm-compose.yml similarity index 100% rename from ccp/modules/nngm-compose.yml rename to common/nngm-compose.yml diff --git a/ccp/modules/nngm-setup.sh b/common/nngm-setup.sh similarity index 68% rename from ccp/modules/nngm-setup.sh rename to common/nngm-setup.sh index 48fc45e..aa32fe1 100644 --- a/ccp/modules/nngm-setup.sh +++ b/common/nngm-setup.sh @@ -2,5 +2,5 @@ if [ -n "$NNGM_CTS_APIKEY" ]; then log INFO "nNGM setup detected -- will start nNGM Connector." - OVERRIDE+=" -f ./$PROJECT/modules/nngm-compose.yml" + OVERRIDE+=" -f ./common/nngm-compose.yml" fi diff --git a/ccp/modules/obds2fhir-rest-compose.yml b/common/obds2fhir-rest-compose.yml similarity index 100% rename from ccp/modules/obds2fhir-rest-compose.yml rename to common/obds2fhir-rest-compose.yml diff --git a/ccp/modules/obds2fhir-rest-setup.sh b/common/obds2fhir-rest-setup.sh similarity index 88% rename from ccp/modules/obds2fhir-rest-setup.sh rename to common/obds2fhir-rest-setup.sh index 6120f31..8bdfb60 100644 --- a/ccp/modules/obds2fhir-rest-setup.sh +++ b/common/obds2fhir-rest-setup.sh @@ -7,7 +7,7 @@ function obds2fhirRestSetup() { log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:" PATIENTLIST_URL=" " fi - OVERRIDE+=" -f ./ccp/modules/obds2fhir-rest-compose.yml" + OVERRIDE+=" -f ./common/obds2fhir-rest-compose.yml" LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)" fi } diff --git a/ccp/modules/teiler-compose.yml b/common/teiler-compose.yml similarity index 100% rename from ccp/modules/teiler-compose.yml rename to common/teiler-compose.yml diff --git a/kr/modules/teiler-setup.sh b/common/teiler-setup.sh similarity index 82% rename from kr/modules/teiler-setup.sh rename to common/teiler-setup.sh index eed3f81..613b472 100644 --- a/kr/modules/teiler-setup.sh +++ b/common/teiler-setup.sh @@ -2,7 +2,7 @@ if [ "$ENABLE_TEILER" == true ];then log INFO "Teiler setup detected -- will start Teiler services." - OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml" + OVERRIDE+=" -f ./common/teiler-compose.yml" TEILER_DEFAULT_LANGUAGE=DE TEILER_DEFAULT_LANGUAGE_LOWER_CASE=${TEILER_DEFAULT_LANGUAGE,,} add_public_oidc_redirect_url "/ccp-teiler/*" diff --git a/ccp/modules/teiler.md b/common/teiler.md similarity index 100% rename from ccp/modules/teiler.md rename to common/teiler.md diff --git a/dhki/vars b/dhki/vars index b728925..9790848 100644 --- a/dhki/vars +++ b/dhki/vars @@ -10,7 +10,7 @@ BROKER_URL_FOR_PREREQ=$BROKER_URL POSTGRES_TAG=15.6-alpine -for module in ccp/modules/*.sh +for module in common/*.sh do log DEBUG "sourcing $module" source $module diff --git a/itcc/modules/lens-setup.sh b/itcc/modules/lens-setup.sh deleted file mode 100644 index c19dc4b..0000000 --- a/itcc/modules/lens-setup.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/bash - -if [ -n "$ENABLE_LENS" ];then - OVERRIDE+=" -f ./$PROJECT/modules/lens-compose.yml" -fi \ No newline at end of file diff --git a/itcc/vars b/itcc/vars index b03403b..576890c 100644 --- a/itcc/vars +++ b/itcc/vars @@ -7,7 +7,7 @@ SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem BROKER_URL_FOR_PREREQ=$BROKER_URL -for module in $PROJECT/modules/*.sh +for module in common/*.sh do log DEBUG "sourcing $module" source $module diff --git a/kr/modules/exporter-compose.yml b/kr/modules/exporter-compose.yml deleted file mode 100644 index d5eb227..0000000 --- a/kr/modules/exporter-compose.yml +++ /dev/null @@ -1,67 +0,0 @@ -version: "3.7" - -services: - exporter: - image: docker.verbis.dkfz.de/ccp/dktk-exporter:latest - container_name: bridgehead-ccp-exporter - environment: - JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC" - LOG_LEVEL: "INFO" - EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh - CROSS_ORIGINS: "https://${HOST}" - EXPORTER_DB_USER: "exporter" - EXPORTER_DB_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh - EXPORTER_DB_URL: "jdbc:postgresql://exporter-db:5432/exporter" - HTTP_RELATIVE_PATH: "/ccp-exporter" - SITE: "${SITE_ID}" - HTTP_SERVLET_REQUEST_SCHEME: "https" - OPAL_PASSWORD: "${EXPORTER_OPAL_PASSWORD}" - labels: - - "traefik.enable=true" - - "traefik.http.routers.exporter_ccp.rule=PathPrefix(`/ccp-exporter`)" - - "traefik.http.services.exporter_ccp.loadbalancer.server.port=8092" - - "traefik.http.routers.exporter_ccp.tls=true" - - "traefik.http.middlewares.exporter_ccp_strip.stripprefix.prefixes=/ccp-exporter" - - "traefik.http.routers.exporter_ccp.middlewares=exporter_ccp_strip" - volumes: - - "/var/cache/bridgehead/ccp/exporter-files:/app/exporter-files/output" - - exporter-db: - image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG} - container_name: bridgehead-ccp-exporter-db - environment: - POSTGRES_USER: "exporter" - POSTGRES_PASSWORD: "${EXPORTER_DB_PASSWORD}" # Set in exporter-setup.sh - POSTGRES_DB: "exporter" - volumes: - # Consider removing this volume once we find a solution to save Lens-queries to be executed in the explorer. - - "/var/cache/bridgehead/ccp/exporter-db:/var/lib/postgresql/data" - - reporter: - image: docker.verbis.dkfz.de/ccp/dktk-reporter:latest - container_name: bridgehead-ccp-reporter - environment: - JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC" - LOG_LEVEL: "INFO" - CROSS_ORIGINS: "https://${HOST}" - HTTP_RELATIVE_PATH: "/ccp-reporter" - SITE: "${SITE_ID}" - EXPORTER_API_KEY: "${EXPORTER_API_KEY}" # Set in exporter-setup.sh - EXPORTER_URL: "http://exporter:8092" - LOG_FHIR_VALIDATION: "false" - HTTP_SERVLET_REQUEST_SCHEME: "https" - - # In this initial development state of the bridgehead, we are trying to have so many volumes as possible. - # However, in the first executions in the CCP sites, this volume seems to be very important. A report is - # a process that can take several hours, because it depends on the exporter. - # There is a risk that the bridgehead restarts, losing the already created export. - - volumes: - - "/var/cache/bridgehead/ccp/reporter-files:/app/reports" - labels: - - "traefik.enable=true" - - "traefik.http.routers.reporter_ccp.rule=PathPrefix(`/ccp-reporter`)" - - "traefik.http.services.reporter_ccp.loadbalancer.server.port=8095" - - "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" diff --git a/kr/modules/exporter.md b/kr/modules/exporter.md deleted file mode 100644 index 24e81b0..0000000 --- a/kr/modules/exporter.md +++ /dev/null @@ -1,15 +0,0 @@ -# Exporter and Reporter - - -## Exporter -The exporter is a REST API that exports the data of the different databases of the bridgehead in a set of tables. -It can accept different output formats as CSV, Excel, JSON or XML. It can also export data into Opal. - -## Exporter-DB -It is a database to save queries for its execution in the exporter. -The exporter manages also the different executions of the same query in through the database. - -## Reporter -This component is a plugin of the exporter that allows to create more complex Excel reports described in templates. -It is compatible with different template engines as Groovy, Thymeleaf,... -It is perfect to generate a document as our traditional CCP quality report. diff --git a/kr/modules/lens-compose.yml b/kr/modules/lens-compose.yml deleted file mode 100644 index 180dd67..0000000 --- a/kr/modules/lens-compose.yml +++ /dev/null @@ -1,33 +0,0 @@ -version: "3.7" -services: - landing: - container_name: lens_federated-search - image: docker.verbis.dkfz.de/ccp/lens:${SITE_ID} - labels: - - "traefik.enable=true" - - "traefik.http.routers.landing.rule=PathPrefix(`/`)" - - "traefik.http.services.landing.loadbalancer.server.port=80" - - "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: ${BROKER_ID} - BEAM_APP_ID: "focus" - PROJECT_METADATA: "kr_supervisors" - depends_on: - - "beam-proxy" - labels: - - "traefik.enable=true" - - "traefik.http.services.spot.loadbalancer.server.port=8080" - - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowmethods=GET,OPTIONS,POST" - - "traefik.http.middlewares.corsheaders2.headers.accesscontrolalloworiginlist=https://${HOST}" - - "traefik.http.middlewares.corsheaders2.headers.accesscontrolallowcredentials=true" - - "traefik.http.middlewares.corsheaders2.headers.accesscontrolmaxage=-1" - - "traefik.http.routers.spot.rule=Host(`${HOST}`) && PathPrefix(`/backend`)" - - "traefik.http.middlewares.stripprefix_spot.stripprefix.prefixes=/backend" - - "traefik.http.routers.spot.tls=true" - - "traefik.http.routers.spot.middlewares=corsheaders2,stripprefix_spot" diff --git a/kr/modules/lens-setup.sh b/kr/modules/lens-setup.sh deleted file mode 100644 index c19dc4b..0000000 --- a/kr/modules/lens-setup.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/bash - -if [ -n "$ENABLE_LENS" ];then - OVERRIDE+=" -f ./$PROJECT/modules/lens-compose.yml" -fi \ No newline at end of file diff --git a/kr/modules/obds2fhir-rest-compose.yml b/kr/modules/obds2fhir-rest-compose.yml deleted file mode 100644 index f201e23..0000000 --- a/kr/modules/obds2fhir-rest-compose.yml +++ /dev/null @@ -1,20 +0,0 @@ -version: "3.7" - -services: - obds2fhir-rest: - container_name: bridgehead-obds2fhir-rest - image: docker.verbis.dkfz.de/ccp/obds2fhir-rest:main - environment: - IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID - MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY} - SALT: ${LOCAL_SALT} - KEEP_INTERNAL_ID: ${KEEP_INTERNAL_ID:-false} - MAINZELLISTE_URL: ${PATIENTLIST_URL:-http://patientlist:8080/patientlist} - restart: always - labels: - - "traefik.enable=true" - - "traefik.http.routers.obds2fhir-rest.rule=PathPrefix(`/obds2fhir-rest`) || PathPrefix(`/adt2fhir-rest`)" - - "traefik.http.middlewares.obds2fhir-rest_strip.stripprefix.prefixes=/obds2fhir-rest,/adt2fhir-rest" - - "traefik.http.services.obds2fhir-rest.loadbalancer.server.port=8080" - - "traefik.http.routers.obds2fhir-rest.tls=true" - - "traefik.http.routers.obds2fhir-rest.middlewares=obds2fhir-rest_strip,auth" diff --git a/kr/modules/obds2fhir-rest-setup.sh b/kr/modules/obds2fhir-rest-setup.sh deleted file mode 100644 index 677ea63..0000000 --- a/kr/modules/obds2fhir-rest-setup.sh +++ /dev/null @@ -1,13 +0,0 @@ -#!/bin/bash - -function obds2fhirRestSetup() { - if [ -n "$ENABLE_OBDS2FHIR_REST" ]; then - log INFO "oBDS2FHIR-REST setup detected -- will start obds2fhir-rest module." - if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then - log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:" - PATIENTLIST_URL=" " - fi - OVERRIDE+=" -f ./$PROJECT/modules/obds2fhir-rest-compose.yml" - LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)" - fi -} diff --git a/kr/modules/teiler-compose.yml b/kr/modules/teiler-compose.yml deleted file mode 100644 index f415ee9..0000000 --- a/kr/modules/teiler-compose.yml +++ /dev/null @@ -1,81 +0,0 @@ -version: "3.7" - -services: - - teiler-orchestrator: - image: docker.verbis.dkfz.de/cache/samply/teiler-orchestrator:latest - container_name: bridgehead-teiler-orchestrator - labels: - - "traefik.enable=true" - - "traefik.http.routers.teiler_orchestrator_ccp.rule=PathPrefix(`/ccp-teiler`)" - - "traefik.http.services.teiler_orchestrator_ccp.loadbalancer.server.port=9000" - - "traefik.http.routers.teiler_orchestrator_ccp.tls=true" - - "traefik.http.middlewares.teiler_orchestrator_ccp_strip.stripprefix.prefixes=/ccp-teiler" - - "traefik.http.routers.teiler_orchestrator_ccp.middlewares=teiler_orchestrator_ccp_strip" - environment: - TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend" - TEILER_DASHBOARD_URL: "https://${HOST}/ccp-teiler-dashboard" - DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE_LOWER_CASE}" - HTTP_RELATIVE_PATH: "/ccp-teiler" - - teiler-dashboard: - image: docker.verbis.dkfz.de/cache/samply/teiler-dashboard:develop - container_name: bridgehead-teiler-dashboard - labels: - - "traefik.enable=true" - - "traefik.http.routers.teiler_dashboard_ccp.rule=PathPrefix(`/ccp-teiler-dashboard`)" - - "traefik.http.services.teiler_dashboard_ccp.loadbalancer.server.port=80" - - "traefik.http.routers.teiler_dashboard_ccp.tls=true" - - "traefik.http.middlewares.teiler_dashboard_ccp_strip.stripprefix.prefixes=/ccp-teiler-dashboard" - - "traefik.http.routers.teiler_dashboard_ccp.middlewares=teiler_dashboard_ccp_strip" - environment: - DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}" - TEILER_BACKEND_URL: "https://${HOST}/ccp-teiler-backend" - OIDC_URL: "${OIDC_URL}" - OIDC_REALM: "${OIDC_REALM}" - OIDC_CLIENT_ID: "${OIDC_PUBLIC_CLIENT_ID}" - OIDC_TOKEN_GROUP: "${OIDC_GROUP_CLAIM}" - TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}" - TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}" - TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}" - TEILER_PROJECT: "${PROJECT}" - EXPORTER_API_KEY: "${EXPORTER_API_KEY}" - TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler" - TEILER_DASHBOARD_HTTP_RELATIVE_PATH: "/ccp-teiler-dashboard" - TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler" - TEILER_USER: "${OIDC_USER_GROUP}" - TEILER_ADMIN: "${OIDC_ADMIN_GROUP}" - REPORTER_DEFAULT_TEMPLATE_ID: "ccp-qb" - EXPORTER_DEFAULT_TEMPLATE_ID: "ccp" - - - teiler-backend: - image: docker.verbis.dkfz.de/ccp/dktk-teiler-backend:latest - container_name: bridgehead-teiler-backend - labels: - - "traefik.enable=true" - - "traefik.http.routers.teiler_backend_ccp.rule=PathPrefix(`/ccp-teiler-backend`)" - - "traefik.http.services.teiler_backend_ccp.loadbalancer.server.port=8085" - - "traefik.http.routers.teiler_backend_ccp.tls=true" - - "traefik.http.middlewares.teiler_backend_ccp_strip.stripprefix.prefixes=/ccp-teiler-backend" - - "traefik.http.routers.teiler_backend_ccp.middlewares=teiler_backend_ccp_strip" - environment: - LOG_LEVEL: "INFO" - APPLICATION_PORT: "8085" - APPLICATION_ADDRESS: "${HOST}" - DEFAULT_LANGUAGE: "${TEILER_DEFAULT_LANGUAGE}" - CONFIG_ENV_VAR_PATH: "/run/secrets/ccp.conf" - TEILER_ORCHESTRATOR_HTTP_RELATIVE_PATH: "/ccp-teiler" - TEILER_ORCHESTRATOR_URL: "https://${HOST}/ccp-teiler" - TEILER_DASHBOARD_DE_URL: "https://${HOST}/ccp-teiler-dashboard/de" - TEILER_DASHBOARD_EN_URL: "https://${HOST}/ccp-teiler-dashboard/en" - CENTRAX_URL: "${CENTRAXX_URL}" - HTTP_PROXY: "http://forward_proxy:3128" - ENABLE_MTBA: "${ENABLE_MTBA}" - ENABLE_DATASHIELD: "${ENABLE_DATASHIELD}" - secrets: - - ccp.conf - -secrets: - ccp.conf: - file: /etc/bridgehead/ccp.conf diff --git a/kr/modules/teiler.md b/kr/modules/teiler.md deleted file mode 100644 index 51e94e4..0000000 --- a/kr/modules/teiler.md +++ /dev/null @@ -1,19 +0,0 @@ -# Teiler -This module orchestrates the different microfrontends of the bridgehead as a single page application. - -## Teiler Orchestrator -Single SPA component that consists on the root HTML site of the single page application and a javascript code that -gets the information about the microfrontend calling the teiler backend and is responsible for registering them. With the -resulting mapping, it can initialize, mount and unmount the required microfrontends on the fly. - -The microfrontends run independently in different containers and can be based on different frameworks (Angular, Vue, React,...) -This microfrontends can run as single alone but need an extension with Single-SPA (https://single-spa.js.org/docs/ecosystem). -There are also available three templates (Angular, Vue, React) to be directly extended to be used directly in the teiler. - -## Teiler Dashboard -It consists on the main dashboard and a set of embedded services. -### Login -user and password in ccp.local.conf - -## Teiler Backend -In this component, the microfrontends are configured. diff --git a/kr/vars b/kr/vars index d4e5a27..c3f5153 100644 --- a/kr/vars +++ b/kr/vars @@ -7,7 +7,7 @@ SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem BROKER_URL_FOR_PREREQ=$BROKER_URL -for module in $PROJECT/modules/*.sh +for module in common/*.sh do log DEBUG "sourcing $module" source $module