First draft of dktk-fed and many other improvements
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README.md
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README.md
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# bridgehead
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# bridgehead
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This repository contains all information and tools to deploy a bridgehead. If you have any questions about deploying a bridgehead, please contact us.
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This repository contains all tools to deploy a bridgehead with docker. If you have any questions about deploying a bridgehead, please contact us.
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There are some prerequisites, which need to be meet befor starting a bridgehead. If you runnig a Windows or Mac OS maschine you should read starting a bridgehead. If you running a Linux maschine you can start or install a bridgehead.
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There are some prerequisites, which need to be meet before starting a bridgehead. If you running a Windows or Mac OS machine you should read starting a bridgehead. If you running a Linux machine you can start or install a bridgehead.
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## Setup
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## Setup
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Clone this repository to /srv/docker
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Clone this repository to /srv/docker/
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The first step is to copy the site.conf. It contains some configuration and secrets for your bridgehead.
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The first step is to copy the site.conf. It contains some configuration and secrets for your bridgehead.
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With cp site.dev.conf site.conf you can clone the template. You need to set the project accoriding to the which bridgehead you want to start. It's either a GBN/BBMRI-ERIC, DKTK or C4 Bridgehead.
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With cp site.dev.conf site.conf you can clone the template. You need to set the project accoriding to the which bridgehead you want to start. It's either a GBN/BBMRI-ERIC, DKTK, DKTK-FED or C4 Bridgehead.
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Each Project needs it own .env file where all the settings are located. Each Project has a template for it in there respective folder. We offer you to setup the file with and also to manage it.
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Each Project needs a .env file where all the settings are located. Each Project has a template for it in their respective folder. We offer you to setup the file with and also to manage it.
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### DKTK
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For DKTK set in the site.conf the project to "dkkt". Also you need to set many settings in the env file. For the API keys for the psuenomisation you need to contact the Mainzelliste Team.
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### GBA/BBMRI-ERIC
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For an GBN/BBMRI-ERIC deployment set the project to gbn. When you already deployed a bridgehead you can reuse the env file for it.
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### C4
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For C4 project it is similar to DKTK. Set the ldm_base_url in the configuration table to null.
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### Git repository
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### Git repository
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If you already have a git config repositpory you can clone it with
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If you already have a git config repository you can clone it with
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git submodule add -f https://"$git_username":"$git_access_token"@code.mitro.dkfz.de/scm/bd/"$site_name_lowercase"-config.git ./site-config
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git submodule add -f https://"$git_username":"$git_access_token"@code.mitro.dkfz.de/scm/bd/"$site_name_lowercase"-config.git ./site-config
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### DKTK
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For DKTK set in the site.conf the project to "dkkt". Also, you need to set many settings in the env file. For the API keys you need to contact the Mainzelliste Team.
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### DKTK-FED
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For the DKTK Federate Search put dkkt-fed in the site.conf.
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### GBA/BBMRI-ERIC
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Coming soon
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### C4
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Coming soon
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## Starting your bridgehead
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## Starting your bridgehead
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There two methods to start the bridgehead. For Windows, Linux and Mac OS you can use the start-bridgehead.sh to deploy it wit docker-compose. If will also check some other setting of your system.
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There two methods to start the bridgehead. For Windows, Linux and Mac OS you can use the start-bridgehead.sh to start it with docker-compose.
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The second methods is using the systemd management tool you start, stop and update your bridgehead.
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The second methods is using the systemd management tool you start, stop and update your bridgehead.
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Just run the install-bridgehead and thats it.
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version: "3.7"
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services:
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traefik:
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container_name: bridgehead_traefik
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image: traefik:2.4
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command:
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- --api.insecure=true
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- --entrypoints.web.address=:80
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- --entrypoints.web-secure.address=:443
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- --providers.docker=true
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ports:
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- 80:80
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- 443:443
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- 8080:8080
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volumes:
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- /var/run/docker.sock:/var/run/docker.sock:ro
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- ../auth/:/auth
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extra_hosts:
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- "host.docker.internal:host-gateway"
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landing:
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container_name: bridgehead_landingpage
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image: nginx:stable
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volumes:
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- ../landing/:/usr/share/nginx/html
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labels:
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- "traefik.enable=true"
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- "traefik.http.routers.landing.rule=PathPrefix(`/`)"
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- "traefik.http.services.landing.loadbalancer.server.port=80"
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blaze:
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image: "samply/blaze:0.15"
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container_name: bridgehead_dktk_blaze
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environment:
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BASE_URL: "http://blaze:8080"
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JAVA_TOOL_OPTIONS: "-Xmx4g"
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LOG_LEVEL: "debug"
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ENFORCE_REFERENTIAL_INTEGRITY: "false"
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volumes:
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- "blaze-data:/app/data"
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labels:
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- "traefik.enable=true"
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- "traefik.http.middlewares.test-auth.basicauth.usersfile=/auth/dktk"
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- "traefik.http.routers.blaze_dktk.rule=PathPrefix(`/dktk-localdatamanagement`)"
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- "traefik.http.middlewares.dktk_b_strip.stripprefix.prefixes=/dktk-localdatamanagement"
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- "traefik.http.services.blaze_dktk.loadbalancer.server.port=8080"
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- "traefik.http.routers.blaze_dktk.middlewares=dktk_b_strip,test-auth"
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# dktk-fed-search-share:
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# image: "ghcr.io/samply/dktk-fed-search-share:pr-1"
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# container_name: bridgehead_dktk_share
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# environment:
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# APP_BASE_URL: "http://dktk-fed-search-share:8080"
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# APP_STORE_URL: "http://blaze:8080/fhir"
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# APP_BROKER_BASEURL: "http://e260-serv-11.inet.dkfz-heidelberg.de:8080/broker/rest/searchbroker"
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# APP_BROKER_MAIL: "foo@bar.de"
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# APP_STORE_BASEURL: "http://bridgehead_dktk_blaze:8080/fhir"
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# SPRING_DATASOURCE_URL: "jdbc:postgresql://dktk-fed-search-share-db:5432/dktk-fed-search-share"
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# JAVA_TOOL_OPTIONS: "-Xmx1g"
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# http_proxy: "http://www-int2.inet.dkfz-heidelberg.de:3128"
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# https_proxy: "http://www-int2.inet.dkfz-heidelberg.de:3128"
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# HTTP_PROXY: "http://www-int2.inet.dkfz-heidelberg.de:3128"
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# HTTPS_PROXY: "http://www-int2.inet.dkfz-heidelberg.de:3128"
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# depends_on:
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# - dktk-fed-search-share-db
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# - blaze
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# labels:
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# - "traefik.enable=true"
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# - "traefik.http.routers.dktk-fed-search.rule=PathPrefix(`/dktk-connector`)"
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# - "traefik.http.services.dktk-fed-search.loadbalancer.server.port=8080"
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# dktk-fed-search-share-db:
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# image: "postgres:14"
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# environment:
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# POSTGRES_USER: "dktk-fed-search-share"
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# POSTGRES_PASSWORD: "dktk-fed-search-share"
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# POSTGRES_DB: "dktk-fed-search-share"
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# volumes:
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# - "dktk-fed-search-share-db-data:/var/lib/postgresql/data"
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volumes:
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blaze-data:
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# dktk-fed-search-share-db-data:
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environment:
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environment:
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STORE_URL: ${STORE_URL}
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STORE_URL: ${STORE_URL}
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POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
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POSTGRES_PASSWORD: ${CONNECTOR_POSTGRES_PASS}
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PATIENTLIST_URL: "http://bridgehead_patientlist:8080"
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PROJECTPSEUDONYMISATION_URL: "http://bridgehead_dktk_idmanager:8080/ID-Manager/html/projectSelection.html"
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volumes:
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volumes:
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- "connector_logs:/usr/local/tomcat/logs"
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- "connector_logs:/usr/local/tomcat/logs"
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depends_on:
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depends_on:
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<html lang="en">
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<head>
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<meta charset="utf-8">
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<meta name="viewport" content="width=device-width, initial-scale=1">
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<meta name="description" content="">
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<title>Bridgehead Overview</title>
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<!-- Bootstrap core CSS -->
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<link href="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/css/bootstrap.min.css" rel="stylesheet"
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integrity="sha384-1BmE4kWBq78iYhFldvKuhfTAU6auU8tT94WrHftjDbrCEXSU1oBoqyl2QvZ6jIW3" crossorigin="anonymous">
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<script src="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/js/bootstrap.bundle.min.js"
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integrity="sha384-ka7Sk0Gln4gmtz2MlQnikT1wXgYsOg+OMhuP+IlRH9sENBO0LRn5q+8nbTov4+1p"
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crossorigin="anonymous"></script>
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</head>
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<body>
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<div class="alert alert-danger" role="alert">
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For updating the Bridgehead your action is requiered. This message is shown when the update of one of your
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componentes need action to complete. This is a breaking change.
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</div>
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<div class="alert alert-warning">
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There is a componente update for your bridgehead. Please run the updater
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</div>
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<div class="alert alert-success">
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Your Bridgehead was updated!
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</div>
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<div class="container px-4 py-5" id="featured-3">
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<h2 class="pb-2 border-bottom">Bridgehead</h2>
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<div class="accordion" id="accordionExample">
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<div class="accordion-item">
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<h2 class="accordion-header" id="headingOne">
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<button class="accordion-button" type="button" data-bs-toggle="collapse" data-bs-target="#collapseOne"
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aria-expanded="true" aria-controls="collapseOne">
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Projects
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</button>
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</h2>
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<div id="collapseOne" class="accordion-collapse collapse show" aria-labelledby="headingOne"
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data-bs-parent="#accordionExample">
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<div class="accordion-body">
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<div class="row g-4 py-5 row-cols-1 row-cols-lg-3">
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<div class="feature col">
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<div class="feature-icon">
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<img src="GBN_CMYK_schwarz.svg" class="img-fluid img-thumbnail">
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</div>
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<h4>GBA/GBN</h4>
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<p>GBN bringt Biobanken und Forscher*innen zusammen, damit Erkenntnisse über die Erkrankung gewonnen und
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Therapien entwickelt werden können.</p>
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</div>
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<div class="feature col">
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<div class="feature-icon">
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<img src="Logo_DKTK_neu_.jpg" class="img-fluid img-thumbnail">
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</div>
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<h4>CCP-IT</h4>
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<p>Das Deutsche Konsortium für Translationale Krebsforschung ist eine Initiative der Bundesregierung zur
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Förderung der medizinische Krebsforschung.</p>
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</div>
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<div class="feature col">
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<div class="feature-icon">
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<img
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src="https://www.nngm.de/wp-content/themes/nNGM/assets/images/new_icons/logo-nngm-nationales-netzwerk-genomische-medizin-lungenkrebs.svg"
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class="img-fluid img-thumbnail">
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</div>
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<h4>Nationales Netzwerk Genomische Medizin (nNGM)</h4>
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<p>Über ein bundesweites Netzwerk sollen in Deutschland künftig alle Patienten mit fortgeschrittenem
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Lungenkrebs Zugang zu molekularer Diagnostik und innovativen Therapien erhalten. Dafür schließen sich
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20 Netzwerkzentren im „nationalen Netzwerk Genomische Medizin (nNGM) Lungenkrebs“ zusammen – darunter
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alle 13 onkologischen Spitzenzentren, die aktuell von der Deutschen Krebshilfe gefördert werden. </p>
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</div>
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</div>
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</div>
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</div>
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</div>
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</div>
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<div>
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<h2>Components</h2>
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<h3>Central</h3>
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<table class="table">
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<thead>
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<tr>
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<th>Group</th>
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<th>Service</th>
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<th>Status</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td>CCP-IT</td>
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<td><a href="patientlist.ccp-it.dktk.dkfz.de">Zentrale Patientenliste</td>
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<td>✓</td>
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</tr>
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<tr>
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<td>CCP-IT</td>
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<td><a href="decentralsearch.ccp-it.dktk.dkfz.de">Dezentrale Suche</td>
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<td>✓</td>
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</tr>
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<tr>
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<td>CCP-IT</td>
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<td><a href="centralsearch.ccp-it.dktk.dkfz.de">Zentrale Suche</td>
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<td>✓</td>
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</tr>
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<tr>
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<td>CCP-IT</td>
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<td><a href="deployment.ccp-it.dktk.dkfz.de">Deployment-Server</td>
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<td>✓</td>
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</tr>
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<tr>
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<td>CCP-IT</td>
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<td><a href="dktk-kne.kgu.de">Zentraler Kontrollnummernerzeuger</td>
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<td>✓</td>
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</tr>
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<tr>
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<td>GBA</td>
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<td><a href="https://samplelocator.bbmri.de/icd10">GBA-ICD10</td>
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<td>✓</td>
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</tr>
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<tr>
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<td>GBA</td>
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<td><a href="auth.dev.germanbiobanknode.de">GBA-Auth</td>
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<td>✓</td>
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</tr>
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<tr>
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<td>GBA</td>
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<td><a href="mdr.germanbiobanknode.de">GBA-MDR</td>
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<td>✓</td>
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</tr>
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<tr>
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<td>GBA</td>
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<td><a href="samplelocator.bbmri.de">GBA-Suchbroker</td>
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<td>✓</td>
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</tr>
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</tbody>
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</table>
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</div>
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<div>
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<h3>Local</h3>
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<table class="table">
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<thead>
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<tr>
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<th>Project</th>
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<th>Services</th>
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<th>Status</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td>Monitoring Proxy</td>
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<td><a href="http://e260-serv-05:8080/">Traefik</a></td>
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<td>✓</td>
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</tr>
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<tr>
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<td>Monitoring Resources</td>
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|
||||||
<td><a href="http://e260-serv-05:8080/grafana">Granfana</a></td>
|
|
||||||
<td>✓</td>
|
|
||||||
</tr>
|
|
||||||
<tr>
|
|
||||||
<td>GBA</td>
|
|
||||||
<td><a href="http://e260-serv-05/gbn-connector/">Connector</a></td>
|
|
||||||
<td>✓</td>
|
|
||||||
</tr>
|
|
||||||
<tr>
|
|
||||||
<td>GBA</td>
|
|
||||||
<td><a href="http://e260-serv-05/gbn-localdatamanagement/fhir">LDM: Blaze</a></td>
|
|
||||||
<td>✓</td>
|
|
||||||
</tr>
|
|
||||||
<tr>
|
|
||||||
<td>DKTK</td>
|
|
||||||
<td><a href="http://e260-serv-05/dktk-connector/">Connector</a></td>
|
|
||||||
<td>✓</td>
|
|
||||||
</tr>
|
|
||||||
<tr>
|
|
||||||
<td>DKTK</td>
|
|
||||||
<td><a href="">CentraXX</a></td>
|
|
||||||
<td>✓</td>
|
|
||||||
</tr>
|
|
||||||
<tr>
|
|
||||||
<td>Idmanagement</td>
|
|
||||||
<td><a href="http://e260-serv-05/ID-Manager/">ID-Manager</a></td>
|
|
||||||
<td>✓</td>
|
|
||||||
</tr>
|
|
||||||
<tr>
|
|
||||||
<td>Idmanagement</td>
|
|
||||||
<td><a href="http://e260-serv-05/Patientenlist/">Patientenliste</a></td>
|
|
||||||
<td>✓</td>
|
|
||||||
</tr>
|
|
||||||
<tr>
|
|
||||||
<td>C4</td>
|
|
||||||
<td><a href="http://e260-serv-05/c4-connector/">Connector</a></td>
|
|
||||||
<td>✓</td>
|
|
||||||
</tr>
|
|
||||||
<tr>
|
|
||||||
<td>C4</td>
|
|
||||||
<td><a href="http://e260-serv-05/c4-localdatamanagement/">LDM: Samply Store</a></td>
|
|
||||||
<td>✓</td>
|
|
||||||
</tr>
|
|
||||||
</tbody>
|
|
||||||
</table>
|
|
||||||
</div>
|
|
||||||
</body>
|
|
||||||
|
|
||||||
</html>
|
|
||||||
|
|
@ -0,0 +1,88 @@
|
||||||
|
#!/bin/bash
|
||||||
|
|
||||||
|
cat > ../landing/index.html <<EOL
|
||||||
|
<html lang="en">
|
||||||
|
|
||||||
|
<head>
|
||||||
|
<meta charset="utf-8">
|
||||||
|
<meta name="viewport" content="width=device-width, initial-scale=1">
|
||||||
|
<meta name="description" content="">
|
||||||
|
<title>Bridgehead Overview</title>
|
||||||
|
<!-- Bootstrap core CSS -->
|
||||||
|
<link href="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/css/bootstrap.min.css" rel="stylesheet"
|
||||||
|
integrity="sha384-1BmE4kWBq78iYhFldvKuhfTAU6auU8tT94WrHftjDbrCEXSU1oBoqyl2QvZ6jIW3" crossorigin="anonymous">
|
||||||
|
<script src="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/js/bootstrap.bundle.min.js"
|
||||||
|
integrity="sha384-ka7Sk0Gln4gmtz2MlQnikT1wXgYsOg+OMhuP+IlRH9sENBO0LRn5q+8nbTov4+1p"
|
||||||
|
crossorigin="anonymous"></script>
|
||||||
|
|
||||||
|
</head>
|
||||||
|
|
||||||
|
<body>
|
||||||
|
|
||||||
|
<nav class="navbar navbar-light" style="background-color: #aad7f6;">
|
||||||
|
<h2 class="pb-2 border-bottom">Bridgehead ${site_name}</h2>
|
||||||
|
</nav>
|
||||||
|
<div class="container px-4 py-5" id="featured-3">
|
||||||
|
<div>
|
||||||
|
<h2>Components</h2>
|
||||||
|
<h3>Central</h3>
|
||||||
|
<table class="table">
|
||||||
|
<thead class="thead-dark">
|
||||||
|
<tr>
|
||||||
|
<th style="width: 50%">Group</th>
|
||||||
|
<th style="width: 50%">Service</th>
|
||||||
|
</tr>
|
||||||
|
</thead>
|
||||||
|
<tbody>
|
||||||
|
<tr>
|
||||||
|
<td>CCP-IT</td>
|
||||||
|
<td><a href="https://patientlist.ccp-it.dktk.dkfz.de">Zentrale Patientenliste</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td>CCP-IT</td>
|
||||||
|
<td><a href="https://decentralsearch.ccp-it.dktk.dkfz.de">Dezentrale Suche</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td>CCP-IT</td>
|
||||||
|
<td><a href="https://centralsearch.ccp-it.dktk.dkfz.de">Zentrale Suche</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td>CCP-IT</td>
|
||||||
|
<td><a href="https://deployment.ccp-it.dktk.dkfz.de">Deployment-Server</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td>CCP-IT</td>
|
||||||
|
<td><a href="https://dktk-kne.kgu.de">Zentraler Kontrollnummernerzeuger</td>
|
||||||
|
</tr>
|
||||||
|
</tbody>
|
||||||
|
</table>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div>
|
||||||
|
<h3>Local</h3>
|
||||||
|
<table class="table">
|
||||||
|
<thead class="thead-dark">
|
||||||
|
<tr>
|
||||||
|
<th style="width: 50%">Project</th>
|
||||||
|
<th style="width: 50%">Services</th>
|
||||||
|
</tr>
|
||||||
|
</thead>
|
||||||
|
<tbody>
|
||||||
|
<tr>
|
||||||
|
<td>Bridgehead</td>
|
||||||
|
<td>Reverse Proxy <a href="http://e260-serv-05:8080/">Traefik</a></td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td>DKTK</td>
|
||||||
|
<td><a href="http://e260-serv-05/dktk-localdatamanagement/fhir/">Blaze</a></td>
|
||||||
|
</tr>
|
||||||
|
</tbody>
|
||||||
|
</table>
|
||||||
|
</div>
|
||||||
|
<footer class="footer mt-auto py-3 ">
|
||||||
|
<a href="https://dktk.dkfz.de/"><img src="https://www.oncoray.de/fileadmin/files/bilder_gruppen/DKTK/Logo_DKTK_neu_2016.jpg" height="10%" width="30%"></a> DKTK 2022
|
||||||
|
</footer>
|
||||||
|
</body>
|
||||||
|
|
||||||
|
</html>
|
||||||
|
EOL
|
||||||
|
|
@ -4,7 +4,7 @@
|
||||||
## Check if user is a su
|
## Check if user is a su
|
||||||
echo "Welcome to the starting a bridgehead. We will get your instance up and running in no time"
|
echo "Welcome to the starting a bridgehead. We will get your instance up and running in no time"
|
||||||
echo "First we will check if all prerequisites are met ..."
|
echo "First we will check if all prerequisites are met ..."
|
||||||
prerequisites="git docker docker-compose"
|
prerequisites="git docker docker-compose cat"
|
||||||
for prerequisite in $prerequisites; do
|
for prerequisite in $prerequisites; do
|
||||||
$prerequisite --version 2>&1
|
$prerequisite --version 2>&1
|
||||||
is_available=$?
|
is_available=$?
|
||||||
|
|
|
||||||
|
|
@ -9,6 +9,8 @@ if ! lib/prerequisites.sh; then
|
||||||
fi
|
fi
|
||||||
source site.conf
|
source site.conf
|
||||||
|
|
||||||
|
./lib/generate.sh
|
||||||
|
|
||||||
log "Starting bridgehead"
|
log "Starting bridgehead"
|
||||||
|
|
||||||
docker-compose -f ${project}/docker-compose.yml --env-file site-config/${project}.env up -d
|
docker-compose -f ${project}/docker-compose.yml --env-file site-config/${project}.env up -d
|
||||||
|
|
|
||||||
|
|
@ -6,3 +6,5 @@ source site.conf
|
||||||
log "Stopping bridgehead"
|
log "Stopping bridgehead"
|
||||||
|
|
||||||
docker-compose -f ${project}/docker-compose.yml --env-file site-config/${project}.env down
|
docker-compose -f ${project}/docker-compose.yml --env-file site-config/${project}.env down
|
||||||
|
|
||||||
|
rm landing/index.html
|
||||||
Loading…
Reference in New Issue