From 40f681573756493a4101fc5329a2d49c97c32975 Mon Sep 17 00:00:00 2001
From: juarez <d.juarez@dkfz-heidelberg.de>
Date: Fri, 10 Feb 2023 12:41:26 +0100
Subject: [PATCH] Add Teiler UI and Teiler module
---
.gitignore | 2 +-
ccp/modules/teiler-compose.yml | 42 +++++
ccp/modules/teiler-setup.sh | 8 +
ccp/modules/teiler-ui-compose.yml | 260 ++++++++++++++++++++++++++++++
ccp/modules/teiler-ui-setup.sh | 7 +
ccp/vars | 2 +-
6 files changed, 319 insertions(+), 2 deletions(-)
create mode 100644 ccp/modules/teiler-compose.yml
create mode 100644 ccp/modules/teiler-setup.sh
create mode 100644 ccp/modules/teiler-ui-compose.yml
create mode 100644 ccp/modules/teiler-ui-setup.sh
diff --git a/.gitignore b/.gitignore
index a884b44..655ca90 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,7 +1,7 @@
##Ignore site configuration
.gitmodules
site-config/*
-
+.idea
## Ignore site configuration
*/docker-compose.override.yml
diff --git a/ccp/modules/teiler-compose.yml b/ccp/modules/teiler-compose.yml
new file mode 100644
index 0000000..b2c2966
--- /dev/null
+++ b/ccp/modules/teiler-compose.yml
@@ -0,0 +1,42 @@
+version: "3.7"
+
+services:
+ teiler:
+ image: docker.verbis.dkfz.de/dktk/dktk-teiler:latest
+ container_name: bridgehead-ccp-teiler
+ environment:
+ LOG_LEVEL: "INFO"
+ TEILER_API_KEY: "${TEILER_API_KEY}"
+ CROSS_ORIGINS: "https://${HOST}/ccp-teiler-root-config"
+ TEILER_DB_USER: "teiler"
+ TEILER_DB_PASSWORD: "${TEILER_DB_PASSWORD}" # Set in teiler-setup.sh
+ TEILER_DB_URL: "jdbc:postgresql://teiler-db:5432/teiler"
+ CLEAN_TEMP_FILES_CRON_EXPRESSION: "0 0 1 * * *"
+ TEMP_FILES_LIFETIME_IN_DAYS: "1"
+ CLEAN_WRITE_FILES_CRON_EXPRESSION: "0 0 2 * * *"
+ WRITE_FILES_LIFETIME_IN_DAYS: "30"
+ labels:
+ - "traefik.enable=true"
+ - "traefik.http.routers.teiler_ccp.rule=PathPrefix(`/ccp-teiler`)"
+ - "traefik.http.services.teiler_ccp.loadbalancer.server.port=8092"
+ - "traefik.http.routers.teiler_ccp.tls=true"
+ - "traefik.http.routers.teiler_ccp.middlewares=auth"
+ volumes:
+ - "teiler:/app/teiler-files"
+
+ teiler-db:
+ image: postgres:15.1-alpine
+ container_name: bridgehead-ccp-teiler-db
+ environment:
+ POSTGRES_USER: "teiler"
+ POSTGRES_PASSWORD: "${TEILER_DB_PASSWORD}" # Set in teiler-setup.sh
+ POSTGRES_DB: "teiler"
+ volumes:
+ - "teiler-db:/var/lib/postgresql/data"
+
+
+volumes:
+ teiler-db:
+ name: "teiler-db"
+ teiler:
+ name: "teiler"
diff --git a/ccp/modules/teiler-setup.sh b/ccp/modules/teiler-setup.sh
new file mode 100644
index 0000000..d651107
--- /dev/null
+++ b/ccp/modules/teiler-setup.sh
@@ -0,0 +1,8 @@
+function teilerSetup() {
+ if [ -n "$ENABLE_TEILER" ];then
+ log INFO "Teiler setup detected -- will start Teiler service."
+ OVERRIDE+=" -f ./$PROJECT/modules/teiler-compose.yml"
+ fi
+ # TODO: Generate password in another way so that not all passwords are the same?
+ TEILER_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
+}
diff --git a/ccp/modules/teiler-ui-compose.yml b/ccp/modules/teiler-ui-compose.yml
new file mode 100644
index 0000000..5bdc6b2
--- /dev/null
+++ b/ccp/modules/teiler-ui-compose.yml
@@ -0,0 +1,260 @@
+version: "3.7"
+
+############################################ Keycloak
+login-db:
+ image: "postgres:15.1"
+ container_name: bridgehead-login-db
+ environment:
+ POSTGRES_USER: "keycloak"
+ POSTGRES_PASSWORD: "${KEYCLOAK_DB_PASSWORD}" # Set in teiler-setup.sh
+ POSTGRES_DB: "keycloak"
+ volumes:
+ - "login-db:/var/lib/postgresql/data"
+
+login:
+ #image: "jboss/keycloak:16.1.1"
+ image: docker.verbis.dkfz.de/dktk/dktk-keycloak:latest
+ container_name: bridgehead-login
+ environment:
+ KEYCLOAK_USER: "admin"
+ KEYCLOAK_PASSWORD: "${KEYCLOAK_ADMIN_PASSWORD}"
+ DB_PASSWORD: "${KEYCLOAK_DB_PASSWORD}" # Set in teiler-setup.sh
+ labels:
+ - "traefik.enable=true"
+ - "traefik.http.routers.login.rule=PathPrefix(`/login`)"
+ - "traefik.http.services.login.loadbalancer.server.port=8080"
+ - "traefik.http.routers.login.tls=true"
+ depends_on:
+ - login-db
+
+############################################ Teiler-UI
+teiler-root-config:
+ image: samply/teiler-root-config:developer
+ container_name: bridgehead-teiler-root-config
+ labels:
+ - "traefik.enable=true"
+ - "traefik.http.routers.teiler_root_config_ccp.rule=PathPrefix(`/ccp-teiler-root-config`)"
+ - "traefik.http.services.teiler_root_config_ccp.loadbalancer.server.port=9000"
+ - "traefik.http.routers.teiler_root_config_ccp.tls=true"
+ environment:
+ TEILER_CORE_URL: "https://${HOST}/ccp-teiler-core"
+ TEILER_UI_URL: "https://${HOST}/ccp-teiler-ui"
+ DEFAULT_LANGUAGE: "de"
+
+teiler-ui:
+ image: samply/teiler-ui:developer
+ container_name: bridgehead-teiler-ui
+# ports:
+# - 4200:80
+ labels:
+ - "traefik.enable=true"
+ - "traefik.http.routers.teiler_ui_ccp.rule=PathPrefix(`/ccp-teiler-ui`)"
+ - "traefik.http.services.teiler_ui_ccp.loadbalancer.server.port=80"
+ - "traefik.http.routers.teiler_ui_ccp.tls=true"
+ environment:
+ DEFAULT_LANGUAGE: "DE"
+ TEILER_CORE_URL: "https://${HOST}/ccp-teiler-core"
+ KEYCLOAK_URL: "https://${HOST}/login"
+ KEYCLOAK_REALM: "teiler-ui"
+ KEYCLOAK_CLIENT_ID: "teiler-ui"
+ TEILER_ADMIN_NAME: "${OPERATOR_FIRST_NAME} ${OPERATOR_LAST_NAME}"
+ TEILER_ADMIN_EMAIL: "${OPERATOR_EMAIL}"
+ TEILER_ADMIN_PHONE: "${OPERATOR_PHONE}"
+ TEILER_PROJECT: "${PROJECT}"
+
+teiler-core:
+ image: samply/teiler-core:developer
+ container_name: bridgehead-teiler
+ volumes:
+ - "/etc/bridgehead/ccp.conf:/app/ccp.conf"
+ labels:
+ - "traefik.enable=true"
+ - "traefik.http.routers.teiler_core_ccp.rule=PathPrefix(`/ccp-teiler-core`)"
+ - "traefik.http.services.teiler_core_ccp.loadbalancer.server.port=8085"
+ - "traefik.http.routers.teiler_core_ccp.tls=true"
+ environment:
+ LOG_LEVEL: "INFO"
+ APPLICATION_PORT: "8085"
+ DEFAULT_LANGUAGE: "DE"
+ CONFIG_ENV_VAR_PATH: "/app/ccp.conf"
+ TEILER_CONFIG_UPDATER_CRON: "0 1 * * * *"
+ TEILER_ROOT_CONFIG_URL: "https://${HOST}/ccp-teiler-root-config"
+ TEILER_UI_DE_URL: "https://${HOST}/ccp-teiler-ui/de"
+ TEILER_UI_EN_URL: "https://${HOST}/ccp-teiler-ui/en"
+ TEILER_APP1_NAME: "config"
+# TEILER_APP2_NAME: "quality-report"
+ TEILER_APP3_NAME: "keycloak"
+ TEILER_APP3_TITLE: "Keycloak"
+ TEILER_APP4_DESCRIPTION_EN: "Authentication site"
+ TEILER_APP4_DESCRIPTION_DE: "Authentifizierungsseite"
+ TEILER_APP4_SOURCEURL: "https://${HOST}/login/auth/"
+ TEILER_APP4_ROLES: "TEILER_ADMIN"
+ TEILER_APP4_ISACTIVATED: "true"
+ TEILER_APP4_ICONSOURCEURL: "https://upload.wikimedia.org/wikipedia/commons/2/29/Keycloak_Logo.png"
+ TEILER_APP4_ORDER: "5"
+ TEILER_APP4_ISEXTERNALLINK: "true"
+ TEILER_APP4_ISLOCAL: "true"
+# TEILER_APP5_NAME: "pgadmin"
+# TEILER_APP5_TITLE: "PgAdmin"
+# TEILER_APP5_DESCRIPTION: "Database Management"
+# TEILER_APP5_SOURCEURL: "http://localhost:5000"
+# TEILER_APP5_ROLES: "TEILER_ADMIN"
+# TEILER_APP5_ISACTIVATED: "true"
+# TEILER_APP5_ICONSOURCEURL: "https://user-images.githubusercontent.com/24623425/36042969-f87531d4-0d8a-11e8-9dee-e87ab8c6a9e3.png"
+# TEILER_APP5_ORDER: "6"
+# TEILER_APP5_ISEXTERNALLINK: "true"
+# TEILER_APP5_ISLOCAL: "true"
+ TEILER_APP6_NAME: "ldm"
+ TEILER_APP6_TITLE_EN: "Local data management"
+ TEILER_APP6_TITLE_DE: "Lokales Datenmanagement"
+ TEILER_APP6_DESCRIPTION_EN: "Local Data Management"
+ TEILER_APP6_DESCRIPTION_DE: "Lokales Datenmanagement"
+ TEILER_APP6_SOURCEURL: "${CENTRAXX_URL}"
+ TEILER_APP6_ROLES: "TEILER_PUBLIC"
+ TEILER_APP6_ISACTIVATED: "${IS_DKTK_SITE}"
+ TEILER_APP6_ICONCLASS: "bi bi-server"
+ TEILER_APP6_ORDER: "7"
+ TEILER_APP6_ISEXTERNALLINK: "true"
+ TEILER_APP6_ISLOCAL: "true"
+ TEILER_APP7_NAME: "id-manager"
+ TEILER_APP7_TITLE: "ID-Manager"
+ TEILER_APP7_DESCRIPTION: "ID Manager"
+ TEILER_APP7_SOURCEURL: "https://${HOST}/id-manager/index.html"
+ TEILER_APP7_ROLES: "TEILER_PUBLIC"
+ TEILER_APP7_ISACTIVATED: "true"
+ TEILER_APP7_ICONCLASS: "bi bi-person-bounding-box"
+ TEILER_APP7_ORDER: "8"
+ TEILER_APP7_ISEXTERNALLINK: "true"
+ TEILER_APP7_ISLOCAL: "true"
+ TEILER_APP8_NAME: "patient-list"
+ TEILER_APP8_TITLE_EN: "Patient List"
+ TEILER_APP8_TITLE_DE: "Patientenliste"
+ TEILER_APP8_DESCRIPTION_EN: "Patient List"
+ TEILER_APP8_DESCRIPTION_DE: "Patientenliste"
+ TEILER_APP8_SOURCEURL: "https://${HOST}/patientlist"
+ TEILER_APP8_ROLES: "TEILER_PUBLIC"
+ TEILER_APP8_ISACTIVATED: "true"
+ TEILER_APP8_ICONCLASS: "bi bi-person-rolodex"
+ TEILER_APP8_ORDER: "9"
+ TEILER_APP8_ISEXTERNALLINK: "true"
+ TEILER_APP8_ISLOCAL: "true"
+ TEILER_APP9_NAME: "project-pseudonymisation"
+ TEILER_APP9_TITLE_EN: "Project Pseudonymisation"
+ TEILER_APP9_TITLE_DE: "Projectpseudonymisierung"
+ TEILER_APP9_DESCRIPTION_EN: "Project Pseudonymisation"
+ TEILER_APP9_DESCRIPTION_DE: "Projectpseudonymisierung"
+ TEILER_APP9_SOURCEURL: "https://${HOST}/id-manager/html/projectSelection.html"
+ TEILER_APP9_ROLES: "TEILER_PUBLIC"
+ TEILER_APP9_ISACTIVATED: "true"
+ TEILER_APP9_ICONCLASS: "bi bi-person-lines-fill"
+ TEILER_APP9_ORDER: "10"
+ TEILER_APP9_ISEXTERNALLINK: "true"
+ TEILER_APP9_ISLOCAL: "true"
+ TEILER_APP10_NAME: "federated-search"
+ TEILER_APP10_TITLE: "Lens"
+ TEILER_APP10_DESCRIPTION_EN: "Federated Search"
+ TEILER_APP10_DESCRIPTION_DE: "Föderierte Suche"
+ TEILER_APP10_SOURCEURL: "https://demo.lens.samply.de/"
+ TEILER_APP10_ROLES: "TEILER_PUBLIC"
+ TEILER_APP10_ISACTIVATED: "true"
+ TEILER_APP10_ICONCLASS: "bi bi-search"
+ TEILER_APP10_ORDER: "13"
+ TEILER_APP10_ISEXTERNALLINK: "true"
+ TEILER_APP10_ISLOCAL: "false"
+ TEILER_APP11_NAME: "central-patient-list"
+ TEILER_APP11_TITLE_EN: "Central Patient List"
+ TEILER_APP11_TITLE_DE: "Zentrale Patientenliste"
+ TEILER_APP11_DESCRIPTION_EN: "Central Patient List"
+ TEILER_APP11_DESCRIPTION_DE: "Zentrale Patientenliste"
+ TEILER_APP11_SOURCEURL: "https://patientlist.ccp-it.dktk.dkfz.de/"
+ TEILER_APP11_ROLES: "TEILER_PUBLIC"
+ TEILER_APP11_ISACTIVATED: "true"
+ TEILER_APP11_ICONCLASS: "bi bi-person-rolodex"
+ TEILER_APP11_ORDER: "14"
+ TEILER_APP11_ISEXTERNALLINK: "true"
+ TEILER_APP11_ISLOCAL: "false"
+ TEILER_APP12_NAME: "central id-manager"
+ TEILER_APP12_TITLE_EN: "Central ID-Manager"
+ TEILER_APP12_TITLE_DE: "Zentraler ID-Manager"
+ TEILER_APP12_DESCRIPTION_EN: "Central ID Manager"
+ TEILER_APP12_DESCRIPTION_DE: "Zentraler ID-Manager"
+ TEILER_APP12_SOURCEURL: "https://dktk-kne.kgu.de/"
+ TEILER_APP12_ROLES: "TEILER_PUBLIC"
+ TEILER_APP12_ISACTIVATED: "true"
+ TEILER_APP12_ICONCLASS: "bi bi-person-bounding-box"
+ TEILER_APP12_ORDER: "15"
+ TEILER_APP12_ISEXTERNALLINK: "true"
+ TEILER_APP12_ISLOCAL: "false"
+ # TODO: Icinga to be replaced by Zabbix
+ TEILER_APP13_NAME: "monitoring"
+ TEILER_APP13_TITLE: "Icinga"
+ TEILER_APP13_DESCRIPTION: "Icinga Monitoring"
+ TEILER_APP13_SOURCEURL: "https://monitor.vmitro.de/icingaweb2/dashboard"
+ TEILER_APP13_ROLES: "TEILER_ADMIN"
+ TEILER_APP13_ISACTIVATED: "true"
+ TEILER_APP13_ICONSOURCEURL: "https://images.ctfassets.net/o7xu9whrs0u9/QmL67mCGdRQ8PBcuKHGnF/858c0aee95762f59d67b25073f9483c2/icinga-logo.png"
+ TEILER_APP13_ORDER: "16"
+ TEILER_APP13_ISEXTERNALLINK: "true"
+ TEILER_APP13_ISLOCAL: "false"
+# TEILER_APP14_NAME: "function-tests"
+# TEILER_APP15_NAME: "event-log"
+ TEILER_APP16_NAME: "active-inquiries"
+ TEILER_APP16_BACKENDURL: "https://${HOST}/ccp-teiler"
+ TEILER_APP17_NAME: "archived-inquiries"
+ TEILER_APP17_BACKENDURL: "https://${HOST}/ccp-teiler"
+ TEILER_APP18_NAME: "failed-inquiries"
+ TEILER_APP18_BACKENDURL: "https://${HOST}/ccp-teiler"
+ TEILER_APP19_NAME: "inquiry"
+ TEILER_APP19_INMENU: "false"
+# TEILER_APP20_NAME: "cbioportal"
+# TEILER_APP20_TITLE: "cBioportal"
+# TEILER_APP20_DESCRIPTION: "Interactive exploration of multidimensional cancer genomics data sets"
+# TEILER_APP20_SOURCEURL: "http://localhost:8082"
+# TEILER_APP20_ROLES: "TEILER_USER"
+# TEILER_APP20_ISACTIVATED: "true"
+# TEILER_APP20_ICONSOURCEURL: "https://docs.cbioportal.org/images/cbio-logo.png"
+# TEILER_APP20_ORDER: "17"
+# TEILER_APP20_ISEXTERNALLINK: "true"
+# TEILER_APP20_ISLOCAL: "true"
+# TEILER_APP21_NAME: "mtba-bp"
+# TEILER_APP21_TITLE: "MTBA-BP"
+# TEILER_APP21_DESCRIPTION: "MTBA Camunda Business Process"
+# TEILER_APP21_SOURCEURL: "http://localhost:8480"
+# TEILER_APP21_ROLES: "TEILER_ADMIN"
+# TEILER_APP21_ISACTIVATED: "true"
+# TEILER_APP21_ICONSOURCEURL: "https://camunda.com/wp-content/uploads/2020/05/logo-camunda-black.svg"
+# TEILER_APP21_ORDER: "18"
+# TEILER_APP21_ISEXTERNALLINK: "true"
+# TEILER_APP21_ISLOCAL: "true"
+ TEILER_APP22_NAME: "dialog-quali"
+ TEILER_APP22_INMENU: "false"
+ TEILER_APP23_NAME: "dialog-uploads"
+ TEILER_APP23_INMENU: "false"
+ TEILER_APP24_NAME: "inquiry-dialog"
+ TEILER_APP24_INMENU: "false"
+ TEILER_APP25_NAME: "dialog-tests"
+ TEILER_APP25_INMENU: "false"
+# TEILER_APP26_NAME: "opal"
+# TEILER_APP26_TITLE: "Opal"
+# TEILER_APP26_DESCRIPTION: "Opal is OBiBa’s core database application for biobanks."
+# TEILER_APP26_SOURCEURL: "http://localhost:8880"
+# TEILER_APP26_ROLES: "TEILER_USER"
+# TEILER_APP26_ISACTIVATED: "true"
+# TEILER_APP26_ICONSOURCEURL: "https://www.obiba.org/assets/themes/bootstrap/img/obiba-logo-small.png"
+# TEILER_APP26_ORDER: "19"
+# TEILER_APP26_ISEXTERNALLINK: "true"
+# TEILER_APP26_ISLOCAL: "true"
+# TEILER_APP27_NAME: "rstudio"
+# TEILER_APP27_TITLE: "R Studio"
+# TEILER_APP27_DESCRIPTION: "RStudio is an integrated development environment (IDE) for R and Python."
+# TEILER_APP27_SOURCEURL: "http://localhost:8787"
+# TEILER_APP27_ROLES: "TEILER_USER"
+# TEILER_APP27_ISACTIVATED: "true"
+# TEILER_APP27_ICONSOURCEURL: "https://rstudio.com/wp-content/uploads/2018/10/RStudio-Logo-Flat.png"
+# TEILER_APP27_ORDER: "20"
+# TEILER_APP27_ISEXTERNALLINK: "true"
+# TEILER_APP27_ISLOCAL: "true"
+
+volumes:
+ login-db:
+ name: "login-db"
diff --git a/ccp/modules/teiler-ui-setup.sh b/ccp/modules/teiler-ui-setup.sh
new file mode 100644
index 0000000..c1f3933
--- /dev/null
+++ b/ccp/modules/teiler-ui-setup.sh
@@ -0,0 +1,7 @@
+function teilerUiSetup() {
+ if [ -n "$ENABLE_TEILER" ];then
+ log INFO "Teiler-UI setup detected -- will start Teiler-UI services."
+ OVERRIDE+=" -f ./$PROJECT/modules/teiler-ui-compose.yml"
+ fi
+ KEYCLOAK_DB_PASSWORD="$(echo \"This is a salt string to generate one consistent password. It is not required to be secret.\" | openssl rsautl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
+}
diff --git a/ccp/vars b/ccp/vars
index 0c80e8a..6f572af 100644
--- a/ccp/vars
+++ b/ccp/vars
@@ -17,4 +17,4 @@ done
idManagementSetup
nngmSetup
-mtbaSetup
\ No newline at end of file
+mtbaSetup