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2 Commits

Author SHA1 Message Date
408483fc54 commit to trigger the switch 2023-08-16 09:59:15 +02:00
e66b84b590 refactor: switch sites to main 2023-08-16 09:48:42 +02:00
63 changed files with 210 additions and 1591 deletions

2
.gitignore vendored
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@ -1,7 +1,7 @@
##Ignore site configuration
.gitmodules
site-config/*
.idea
## Ignore site configuration
*/docker-compose.override.yml

116
README.md
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@ -21,8 +21,7 @@ This repository is the starting point for any information and tools you will nee
- [HTTPS Access](#https-access)
- [TLS terminating proxies](#tls-terminating-proxies)
- [File structure](#file-structure)
- [BBMRI-ERIC Directory entry needed](#bbmri-eric-directory-entry-needed)
- [Loading data](#loading-data)
- [BBMRI-ERIC Directory](#bbmri-eric-directory)
4. [Things you should know](#things-you-should-know)
- [Auto-Updates](#auto-updates)
- [Auto-Backups](#auto-backups)
@ -34,10 +33,6 @@ This repository is the starting point for any information and tools you will nee
## Requirements
The data protection group at your site will probably want to know exactly what our software does with patient data, and you may need to get their approval before you are allowed to install a Bridgehead. To help you with this, we have provided some data protection concepts:
- [Germany](https://www.bbmri.de/biobanking/it/infrastruktur/datenschutzkonzept/)
### Hardware
Hardware requirements strongly depend on the specific use-cases of your network as well as on the data it is going to serve. Most use-cases are well-served with the following configuration:
@ -56,41 +51,22 @@ Ensure the following software (or newer) is installed:
- docker >= 20.10.1
- docker-compose >= 2.xx (`docker-compose` and `docker compose` are both supported).
- systemd
- curl
We recommend to install Docker(-compose) from its official sources as described on the [Docker website](https://docs.docker.com).
> 📝 Note for Ubuntu: Snap versions of Docker are not supported.
Note for Ubuntu: Please note that snap versions of Docker are not supported.
### Network
A Bridgehead communicates to all central components via outgoing HTTPS connections.
A running Bridgehead requires an outgoing HTTPS proxy to communicate with the central components.
Your site might require an outgoing proxy (i.e. HTTPS forward proxy) to connect to external servers; you should discuss this with your local systems administration. In that case, you will need to note down the URL of the proxy. If the proxy requires authentication, you will also need to make a note of its username and password. This information will be used later on during the installation process. TLS terminating proxies are also supported, see [here](#tls-terminating-proxies). Apart from the Bridgehead itself, you may also need to configure the proxy server in [git](https://gist.github.com/evantoli/f8c23a37eb3558ab8765) and [docker](https://docs.docker.com/network/proxy/).
Additionally, your site might use its own proxy. You should discuss this with your local systems administration. If a proxy is being used, you will need to note down the URL of the proxy. If it is a secure proxy, then you will also need to make a note of its username and password. This information will be used later on during the installation process.
The following URLs need to be accessible (prefix with `https://`):
* To fetch code and configuration from git repositories
* github.com
* git.verbis.dkfz.de
* To fetch docker images
* docker.verbis.dkfz.de
* Official Docker, Inc. URLs (subject to change, see [official list](https://docs.docker.com/desktop/all))
* hub.docker.com
* registry-1.docker.io
* production.cloudflare.docker.com
* To report bridgeheads operational status
* healthchecks.verbis.dkfz.de
* only for DKTK/CCP
* broker.ccp-it.dktk.dkfz.de
* only for BBMRI-ERIC
* broker.bbmri.samply.de
* gitlab.bbmri-eric.eu
* only for German Biobank Node
* broker.bbmri.de
Note that git and Docker may also need to be configured to use this proxy. This is a job for your systems administrators.
> 📝 This URL list is subject to change. Instead of the individual names, we highly recommend whitelisting wildcard domains: *.dkfz.de, github.com, *.docker.com, *.docker.io, *.samply.de, *.bbmri.de.
If there is a site firewall, this needs to be configured so that outgoing calls to the following URLs are allowed: *.dkfz.de, github.com, docker.io, *.docker.io, *.samply.de.
> 📝 Ubuntu's pre-installed uncomplicated firewall (ufw) is known to conflict with Docker, more info [here](https://github.com/chaifeng/ufw-docker).
Note for Ubuntu: Please note that the uncomplicated firewall (ufw) is known to conflict with Docker [here](https://github.com/chaifeng/ufw-docker).
## Deployment
@ -123,7 +99,7 @@ Mention:
We will set the repository up for you. We will then send you:
- A Repository Short Name (RSN). Beware: this is distinct from your site name.
- Repository URL containing the acces token eg. https://BH_Dummy:dummy_token@git.verbis.dkfz.de/<project>-bridgehead-configs/dummy.git
- Repository URL containing the acces token eg. https://BH_Dummy:dummy_token@git.verbis.dkfz.de/bbmri-bridgehead-configs/dummy.git
During the installation, your Bridgehead will download your site's configuration from GitLab and you can review the details provided to us by email.
@ -259,21 +235,6 @@ Even within your internal network, the Bridgehead enforces HTTPS for all service
All of the Bridgehead's outgoing connections are secured by transport encryption (TLS) and a Bridgehead will refuse to connect if certificate verification fails. If your local forward proxy server performs TLS termination, please place its CA certificate in `/etc/bridgehead/trusted-ca-certs` as a `.pem` file, e.g. `/etc/bridgehead/trusted-ca-certs/mylocalca.pem`. Then, all Bridgehead components will pick up this certificate and trust it for outgoing connections.
To find the certificate file, first run the following:
```
curl -v https://broker.bbmri.samply.de/v1/health
```
In the output, look out for the line:
```
successfully set certificate verify locations:
```
Here a file will be mentioned, perhaps in the directory /etc/ssl/certs. The exact location will depend on your operating system. This is the file that you need to copy.
### File structure
- `/srv/docker/bridgehead` contains this git repository with the shell scripts and *project-specific configuration*. In here, all files are identical for all sites. You should not make any changes here.
@ -286,29 +247,28 @@ Here a file will be mentioned, perhaps in the directory /etc/ssl/certs. The exac
Your Bridgehead's actual data is not stored in the above directories, but in named docker volumes, see `docker volume ls` and `docker volume inspect <volume_name>`.
### BBMRI-ERIC Directory entry needed
### BBMRI-ERIC Directory
If you run a biobank, you should be listed together with your collections with in the [Directory](https://directory.bbmri-eric.eu), a BBMRI-ERIC project that catalogs biobanks.
If you run a biobank, you should register with the [Directory](https://directory.bbmri-eric.eu), a BBMRI-ERIC project that catalogs biobanks.
To do this, contact the BBMRI-ERIC national node for the country where your biobank is based, see [the list of nodes](http://www.bbmri-eric.eu/national-nodes/).
Once you have added your biobank to the Directory you got persistent identifier (PID) for your biobank and unique identifiers (IDs) for your collections. The collection IDs are necessary for the biospecimens assigning to the collections and later in the data flows between BBMRI-ERIC tools. In case you cannot distribute all your biospecimens within collections via assigning the collection IDs, **you should choose one of your sample collections as a default collection for your biobank**. This collection will be automatically used to label any samples that have not been assigned a collection ID in your ETL process. Make a note of this default collection ID, you will need it later on in the installation process.
Once you have registered, **you should choose one of your sample collections as a default collection for your biobank**. This is the collection that will be automatically used to label any samples that have not been assigned a collection ID in your ETL process. Make a note of this ID, you will need it later on in the installation process.
### Directory sync tool
The Bridgehead's **Directory Sync** is an optional feature that keeps the Directory up to date with your local data, e.g. number of samples. Conversely, it also updates the local FHIR store with the latest contact details etc. from the Directory. You must explicitly set your country specific directory URL, username and password to enable this feature.
The Bridgehead's **Directory Sync** is an optional feature that keeps the Directory up to date with your local data, e.g. number of samples. Conversely, it also updates the local FHIR store with the latest contact details etc. from the Directory. You must explicitly set your country specific directory url, username and password to enable this feature.
Full details can be found in [directory_sync_service](https://github.com/samply/directory_sync_service).
To enable it, you will need to set these variables to the ```bbmri.conf``` file of your GitLab repository. Here is an example config:
```
### Directory sync service
DS_DIRECTORY_URL=https://directory.bbmri-eric.eu
DS_DIRECTORY_USER_NAME=your_directory_username
DS_DIRECTORY_USER_PASS=qwdnqwswdvqHBVGFR9887
DS_TIMER_CRON="0 22 * * *"
```
You must contact the Directory team for your national node to find the URL, and to register as a user.
You must contact the Directory for your national node to find the URL, and to register as a user.
Additionally, you should choose when you want Directory sync to run. In the example above, this is set to happen at 10 pm every evening. You can modify this to suit your requirements. The timer specification should follow the [cron](https://crontab.guru) convention.
@ -316,32 +276,6 @@ Once you edited the gitlab config, the bridgehead will autoupdate the config wit
There will be a delay before the effects of Directory sync become visible. First, you will need to wait until the time you have specified in ```TIMER_CRON```. Second, the information will then be synchronized from your national node with the central European Directory. This can take up to 24 hours.
### Loading data
The data accessed by the federated search is held in the Bridgehead in a FHIR store (we use Blaze).
You can load data into this store by using its FHIR API:
```
https://<Name of your server>/bbmri-localdatamanagement/fhir
```
The name of your server will generally be the full name of the VM that the Bridgehead runs on. You can alternatively supply an IP address.
The FHIR API uses basic auth. You can find the credentials in `/etc/bridgehead/<project>.local.conf`.
Note that if you don't have a DNS certificate for the Bridgehead, you will need to allow an insecure connection. E.g. with curl, use the `-k` flag.
The storage space on your hard drive will depend on the number of FHIR resources that you intend to generate. This will be the sum of the number of patients/subjects, the number of samples, the number of conditions/diseases and the number of observations. As a general rule of thumb, you can assume that each resource will consume about 2 kilobytes of disk space.
For more information on Blaze performance, please refer to [import performance](https://github.com/samply/blaze/blob/master/docs/performance/import.md).
#### ETL for BBMRI and GBA
Normally, you will need to build your own ETL to feed the Bridgehead. However, there is one case where a short cut might be available:
- If you are using CentraXX as a BIMS and you have a FHIR-Export License, then you can employ standard mapping scripts that access the CentraXX-internal data structures and map the data onto the BBMRI FHIR profile. It may be necessary to adjust a few parameters, but this is nonetheless significantly easier than writing your own ETL.
You can find the profiles for generating FHIR in [Simplifier](https://simplifier.net/bbmri.de/~resources?category=Profile).
## Things you should know
### Auto-Updates
@ -385,28 +319,8 @@ Installation under WSL ought to work, but we have not tested this.
### Docker Daemon Proxy Configuration
Docker has a background daemon, responsible for downloading images and starting them. Sometimes, proxy configuration from your system won't carry over and it will fail to download images. In that case, you'll need to configure the proxy inside the system unit of docker by creating the file `/etc/systemd/system/docker.service.d/proxy.conf` with the following content:
Docker has a background daemon, responsible for downloading images and starting them. Sometimes, proxy configuration from your system won't carry over and it will fail to download images. In that case, configure the proxy for this daemon as described in the [official documentation](https://docs.docker.com).
``` ini
[Service]
Environment="HTTP_PROXY=http://proxy.example.com:3128"
Environment="HTTPS_PROXY=https://proxy.example.com:3128"
Environment="NO_PROXY=localhost,127.0.0.1,some-local-docker-registry.example.com,.corp"
```
After saving the configuration file, you'll need to reload the system daemon for the changes to take effect:
``` shell
sudo systemctl daemon-reload
```
and restart the docker daemon:
``` shell
sudo systemctl restart docker
```
For more information, please consult the [official documentation](https://docs.docker.com/config/daemon/systemd/#httphttps-proxy).
### Monitoring

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@ -1,6 +1,6 @@
version: "3.7"
# This includes only the shared persistence for BBMRI-ERIC and GBN. Federation components are included as modules, see ccp vars.
# This includes only the shared persistence for BBMRI-ERIC and GBN. Federation components are included as modules, see vars.
services:
blaze:
@ -8,9 +8,8 @@ services:
container_name: bridgehead-bbmri-blaze
environment:
BASE_URL: "http://bridgehead-bbmri-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
JAVA_TOOL_OPTIONS: "-Xmx4g"
LOG_LEVEL: "debug"
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "blaze-data:/app/data"

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@ -1,5 +1,3 @@
version: "3.7"
services:
directory_sync_service:
image: "docker.verbis.dkfz.de/cache/samply/directory_sync_service"

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@ -0,0 +1,50 @@
version: "3.7"
services:
dnpm-beam-proxy:
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
container_name: bridgehead-dnpm-beam-proxy
environment:
BROKER_URL: ${DNPM_BROKER_URL}
PROXY_ID: ${DNPM_PROXY_ID}
APP_dnpm-connect_KEY: ${DNPM_BEAM_SECRET_SHORT}
PRIVKEY_FILE: /run/secrets/proxy.pem
ALL_PROXY: http://forward_proxy:3128
TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs
ROOTCERT_FILE: /conf/root.crt.pem
secrets:
- proxy.pem
depends_on:
- "forward_proxy"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/ccp/root-new.crt.pem:/conf/root.crt.pem:ro
dnpm-beam-connect:
depends_on: [ dnpm-beam-proxy ]
image: docker.verbis.dkfz.de/cache/samply/beam-connect:dnpm
container_name: bridgehead-dnpm-beam-connect
environment:
PROXY_URL: http://dnpm-beam-proxy:8081
PROXY_APIKEY: ${DNPM_BEAM_SECRET_SHORT}
APP_ID: dnpm-connect.${DNPM_PROXY_ID}
DISCOVERY_URL: "./conf/central_targets.json"
LOCAL_TARGETS_FILE: "./conf/connect_targets.json"
HTTP_PROXY: http://forward_proxy:3128
HTTPS_PROXY: http://forward_proxy:3128
NO_PROXY: dnpm-beam-proxy,dnpm-backend
RUST_LOG: ${RUST_LOG:-info}
volumes:
- /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
- /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
labels:
- "traefik.enable=true"
- "traefik.http.routers.dnpm-connect.rule=PathPrefix(`/dnpm-connect`)"
- "traefik.http.middlewares.dnpm-connect-strip.stripprefix.prefixes=/dnpm-connect"
- "traefik.http.routers.dnpm-connect.middlewares=dnpm-connect-strip"
- "traefik.http.services.dnpm-connect.loadbalancer.server.port=8062"
- "traefik.http.routers.dnpm-connect.tls=true"
secrets:
proxy.pem:
file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

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@ -0,0 +1,13 @@
#!/bin/bash
if [ -n "${ENABLE_DNPM}" ]; then
log INFO "DNPM setup detected (Beam.Connect) -- will start Beam and Beam.Connect for DNPM."
OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose.yml"
# Set variables required for Beam-Connect
DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
DNPM_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
DNPM_BROKER_ID="broker.ccp-it.dktk.dkfz.de"
DNPM_BROKER_URL="https://${DNPM_BROKER_ID}"
DNPM_PROXY_ID="${SITE_ID}.${DNPM_BROKER_ID}"
fi

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@ -2,7 +2,7 @@ version: "3.7"
services:
focus-eric:
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
image: docker.verbis.dkfz.de/cache/samply/focus:main
container_name: bridgehead-focus-eric
environment:
API_KEY: ${ERIC_FOCUS_BEAM_SECRET_SHORT}
@ -32,5 +32,5 @@ services:
- "forward_proxy"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/bbmri/modules/${ERIC_ROOT_CERT}.root.crt.pem:/conf/root.crt.pem:ro
- /srv/docker/bridgehead/bbmri/modules/eric.root.crt.pem:/conf/root.crt.pem:ro

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@ -4,23 +4,8 @@ if [ "${ENABLE_ERIC}" == "true" ]; then
log INFO "BBMRI-ERIC setup detected -- will start services for BBMRI-ERIC."
OVERRIDE+=" -f ./$PROJECT/modules/eric-compose.yml"
# The environment needs to be defined in /etc/bridgehead
case "$ENVIRONMENT" in
"production")
export ERIC_BROKER_ID=broker.bbmri.samply.de
export ERIC_ROOT_CERT=eric
;;
"test")
export ERIC_BROKER_ID=broker-test.bbmri-test.samply.de
export ERIC_ROOT_CERT=eric.test
;;
*)
report_error 6 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
export ERIC_BROKER_ID=broker.bbmri.samply.de
export ERIC_ROOT_CERT=eric
;;
esac
# Set required variables
ERIC_BROKER_ID=broker.bbmri.samply.de
ERIC_BROKER_URL=https://${ERIC_BROKER_ID}
ERIC_PROXY_ID=${SITE_ID}.${ERIC_BROKER_ID}
ERIC_FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"

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@ -1,20 +0,0 @@
-----BEGIN CERTIFICATE-----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-----END CERTIFICATE-----

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@ -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"

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@ -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

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@ -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.

View File

@ -2,7 +2,7 @@ version: "3.7"
services:
focus-gbn:
image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
image: docker.verbis.dkfz.de/cache/samply/focus:main
container_name: bridgehead-focus-gbn
environment:
API_KEY: ${GBN_FOCUS_BEAM_SECRET_SHORT}
@ -32,5 +32,5 @@ services:
- "forward_proxy"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/bbmri/modules/${GBN_ROOT_CERT}.root.crt.pem:/conf/root.crt.pem:ro
- /srv/docker/bridgehead/bbmri/modules/gbn.root.crt.pem:/conf/root.crt.pem:ro

View File

@ -4,25 +4,10 @@ if [ "${ENABLE_GBN}" == "true" ]; then
log INFO "GBN setup detected -- will start services for German Biobank Node."
OVERRIDE+=" -f ./$PROJECT/modules/gbn-compose.yml"
# The environment needs to be defined in /etc/bridgehead
case "$ENVIRONMENT" in
"production")
export GBN_BROKER_ID=broker.bbmri.de
export GBN_ROOT_CERT=gbn
;;
"test")
export GBN_BROKER_ID=broker.test.bbmri.de
export GBN_ROOT_CERT=gbn.test
;;
*)
report_error 6 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
export GBN_BROKER_ID=broker.bbmri.de
export GBN_ROOT_CERT=gbn
;;
esac
# Set required variables
GBN_BROKER_ID='#TODO#'
GBN_BROKER_URL=https://${GBN_BROKER_ID}
GBN_PROXY_ID=${SITE_ID}.${GBN_BROKER_ID}
GBN_FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
GBN_SUPPORT_EMAIL=feedback@germanbiobanknode.de
GBN_SUPPORT_EMAIL=todo@verbis.dkfz.de
fi

View File

@ -1,20 +1 @@
-----BEGIN CERTIFICATE-----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-----END CERTIFICATE-----
#TODO#

View File

@ -1,20 +0,0 @@
-----BEGIN CERTIFICATE-----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-----END CERTIFICATE-----

View File

@ -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: "bbmri-qb"
EXPORTER_DEFAULT_TEMPLATE_ID: "bbmri"
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

View File

@ -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

View File

@ -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.

View File

@ -7,18 +7,6 @@
FOCUS_RETRY_COUNT=32
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
OIDC_USER_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})"
OIDC_ADMIN_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_Verwalter"
OIDC_PRIVATE_CLIENT_ID=${SITE_ID}-private
OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public
# Use "test-realm-01" for testing
OIDC_REALM="${OIDC_REALM:-master}"
OIDC_URL="https://login.verbis.dkfz.de"
OIDC_ISSUER_URL="${OIDC_URL}/realms/${OIDC_REALM}"
OIDC_GROUP_CLAIM="groups"
POSTGRES_TAG=15.6-alpine
for module in $PROJECT/modules/*.sh
do
log DEBUG "sourcing $module"
@ -26,7 +14,7 @@ do
done
SUPPORT_EMAIL=$ERIC_SUPPORT_EMAIL
BROKER_URL_FOR_PREREQ="${ERIC_BROKER_URL:-$GBN_BROKER_URL}"
BROKER_URL_FOR_PREREQ=$ERIC_BROKER_URL
if [ -n "$GBN_SUPPORT_EMAIL" ]; then
SUPPORT_EMAIL=$GBN_SUPPORT_EMAIL

View File

@ -50,8 +50,6 @@ loadVars() {
source /etc/bridgehead/$PROJECT.local.conf || fail_and_report 1 "Found /etc/bridgehead/$PROJECT.local.conf but failed to import"
fi
fetchVarsFromVaultByFile /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "Unable to fetchVarsFromVaultByFile"
setHostname
optimizeBlazeMemoryUsage
[ -e ./$PROJECT/vars ] && source ./$PROJECT/vars
set +a
@ -66,23 +64,7 @@ loadVars() {
OVERRIDE+=" -f ./$PROJECT/docker-compose.override.yml"
fi
detectCompose
setupProxy
# Set some project-independent default values
: ${ENVIRONMENT:=production}
case "$ENVIRONMENT" in
"production")
export FOCUS_TAG=main
;;
"test")
export FOCUS_TAG=develop
;;
*)
report_error 7 "Environment \"$ENVIRONMENT\" is unknown. Assuming production. FIX THIS!"
export FOCUS_TAG=main
;;
esac
setHostname
}
case "$ACTION" in
@ -90,14 +72,11 @@ case "$ACTION" in
loadVars
hc_send log "Bridgehead $PROJECT startup: Checking requirements ..."
checkRequirements
sync_secrets
hc_send log "Bridgehead $PROJECT startup: Requirements checked out. Now starting bridgehead ..."
exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE up --abort-on-container-exit
;;
stop)
loadVars
# Kill stale secret-sync instances if present
docker kill $(docker ps -q --filter ancestor=docker.verbis.dkfz.de/cache/samply/secret-sync-local) 2>/dev/null || true
# HACK: This is temporarily to properly shut down false bridgehead instances (bridgehead-ccp instead ccp)
$COMPOSE -p bridgehead-$PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE down
exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE down
@ -106,11 +85,6 @@ case "$ACTION" in
bk_is_running
exit $?
;;
logs)
loadVars
shift 2
exec $COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE logs -f $@
;;
update)
loadVars
exec ./lib/update-bridgehead.sh $PROJECT

View File

@ -6,9 +6,7 @@ services:
container_name: bridgehead-ccp-blaze
environment:
BASE_URL: "http://bridgehead-ccp-blaze:8080"
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
JAVA_TOOL_OPTIONS: "-Xmx4g"
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "blaze-data:/app/data"
@ -21,7 +19,7 @@ services:
- "traefik.http.routers.blaze_ccp.tls=true"
focus:
image: docker.verbis.dkfz.de/cache/samply/focus:0.4.4
image: docker.verbis.dkfz.de/cache/samply/focus:main
container_name: bridgehead-focus
environment:
API_KEY: ${FOCUS_BEAM_SECRET_SHORT}
@ -30,7 +28,7 @@ services:
BLAZE_URL: "http://bridgehead-ccp-blaze:8080/fhir/"
BEAM_PROXY_URL: http://beam-proxy:8081
RETRY_COUNT: ${FOCUS_RETRY_COUNT}
EPSILON: 0.28
OBFUSCATE: "no"
depends_on:
- "beam-proxy"
- "blaze"

View File

@ -1,18 +0,0 @@
version: "3.7"
services:
adt2fhir-rest:
container_name: bridgehead-adt2fhir-rest
image: docker.verbis.dkfz.de/ccp/adt2fhir-rest:main
environment:
IDTYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
MAINZELLISTE_APIKEY: ${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
SALT: ${LOCAL_SALT}
restart: always
labels:
- "traefik.enable=true"
- "traefik.http.routers.adt2fhir-rest.rule=PathPrefix(`/adt2fhir-rest`)"
- "traefik.http.middlewares.adt2fhir-rest_strip.stripprefix.prefixes=/adt2fhir-rest"
- "traefik.http.services.adt2fhir-rest.loadbalancer.server.port=8080"
- "traefik.http.routers.adt2fhir-rest.tls=true"
- "traefik.http.routers.adt2fhir-rest.middlewares=adt2fhir-rest_strip,auth"

View File

@ -1,13 +0,0 @@
#!/bin/bash
function adt2fhirRestSetup() {
if [ -n "$ENABLE_ADT2FHIR_REST" ]; then
log INFO "ADT2FHIR-REST setup detected -- will start adt2fhir-rest API."
if [ ! -n "$IDMANAGER_LOCAL_PATIENTLIST_APIKEY" ]; then
log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
exit 1;
fi
OVERRIDE+=" -f ./$PROJECT/modules/adt2fhir-rest-compose.yml"
LOCAL_SALT="$(echo \"local-random-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
fi
}

View File

@ -1,171 +0,0 @@
version: "3.7"
services:
rstudio:
container_name: bridgehead-rstudio
image: docker.verbis.dkfz.de/ccp/dktk-rstudio:latest
environment:
#DEFAULT_USER: "rstudio" # This line is kept for informational purposes
PASSWORD: "${RSTUDIO_ADMIN_PASSWORD}" # It is required, even if the authentication is disabled
DISABLE_AUTH: "true" # https://rocker-project.org/images/versioned/rstudio.html#how-to-use
HTTP_RELATIVE_PATH: "/rstudio"
ALL_PROXY: "http://forward_proxy:3128" # https://rocker-project.org/use/networking.html
labels:
- "traefik.enable=true"
- "traefik.http.routers.rstudio_ccp.rule=PathPrefix(`/rstudio`)"
- "traefik.http.services.rstudio_ccp.loadbalancer.server.port=8787"
- "traefik.http.middlewares.rstudio_ccp_strip.stripprefix.prefixes=/rstudio"
- "traefik.http.routers.rstudio_ccp.tls=true"
- "traefik.http.routers.rstudio_ccp.middlewares=oidcAuth,rstudio_ccp_strip"
networks:
- rstudio
opal:
container_name: bridgehead-opal
image: docker.verbis.dkfz.de/ccp/dktk-opal:latest
labels:
- "traefik.enable=true"
- "traefik.http.routers.opal_ccp.rule=PathPrefix(`/opal`)"
- "traefik.http.services.opal_ccp.loadbalancer.server.port=8080"
- "traefik.http.routers.opal_ccp.tls=true"
links:
- opal-rserver
- opal-db
environment:
JAVA_OPTS: "-Xms1G -Xmx8G -XX:+UseG1GC -Dhttps.proxyHost=forward_proxy -Dhttps.proxyPort=3128"
# OPAL_ADMINISTRATOR_USER: "administrator" # This line is kept for informational purposes
OPAL_ADMINISTRATOR_PASSWORD: "${OPAL_ADMIN_PASSWORD}"
POSTGRESDATA_HOST: "opal-db"
POSTGRESDATA_DATABASE: "opal"
POSTGRESDATA_USER: "opal"
POSTGRESDATA_PASSWORD: "${OPAL_DB_PASSWORD}"
ROCK_HOSTS: "opal-rserver:8085"
APP_URL: "https://${HOST}/opal"
APP_CONTEXT_PATH: "/opal"
OPAL_PRIVATE_KEY: "/run/secrets/opal-key.pem"
OPAL_CERTIFICATE: "/run/secrets/opal-cert.pem"
OIDC_URL: "${OIDC_URL}"
OIDC_REALM: "${OIDC_REALM}"
OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}"
OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}"
TOKEN_MANAGER_PASSWORD: "${TOKEN_MANAGER_OPAL_PASSWORD}"
EXPORTER_PASSWORD: "${EXPORTER_OPAL_PASSWORD}"
BEAM_APP_ID: token-manager.${PROXY_ID}
BEAM_SECRET: ${TOKEN_MANAGER_SECRET}
BEAM_DATASHIELD_PROXY: request-manager
volumes:
- "/var/cache/bridgehead/ccp/opal-metadata-db:/srv" # Opal metadata
secrets:
- opal-cert.pem
- opal-key.pem
opal-db:
container_name: bridgehead-opal-db
image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
environment:
POSTGRES_PASSWORD: "${OPAL_DB_PASSWORD}" # Set in datashield-setup.sh
POSTGRES_USER: "opal"
POSTGRES_DB: "opal"
volumes:
- "/var/cache/bridgehead/ccp/opal-db:/var/lib/postgresql/data" # Opal project data (imported from exporter)
opal-rserver:
container_name: bridgehead-opal-rserver
image: docker.verbis.dkfz.de/ccp/dktk-rserver # datashield/rock-base + dsCCPhos
tmpfs:
- /srv
beam-connect:
image: docker.verbis.dkfz.de/cache/samply/beam-connect:develop
container_name: bridgehead-datashield-connect
environment:
PROXY_URL: "http://beam-proxy:8081"
TLS_CA_CERTIFICATES_DIR: /run/secrets
APP_ID: datashield-connect.${SITE_ID}.${BROKER_ID}
PROXY_APIKEY: ${DATASHIELD_CONNECT_SECRET}
DISCOVERY_URL: "./map/central.json"
LOCAL_TARGETS_FILE: "./map/local.json"
NO_AUTH: "true"
secrets:
- opal-cert.pem
depends_on:
- beam-proxy
volumes:
- /tmp/bridgehead/opal-map/:/map/:ro
networks:
- default
- rstudio
traefik:
labels:
- "traefik.http.middlewares.oidcAuth.forwardAuth.address=http://oauth2-proxy:4180/"
- "traefik.http.middlewares.oidcAuth.forwardAuth.trustForwardHeader=true"
- "traefik.http.middlewares.oidcAuth.forwardAuth.authResponseHeaders=X-Auth-Request-Access-Token,Authorization"
networks:
- default
- rstudio
forward_proxy:
networks:
- default
- rstudio
beam-proxy:
environment:
APP_datashield-connect_KEY: ${DATASHIELD_CONNECT_SECRET}
APP_token-manager_KEY: ${TOKEN_MANAGER_SECRET}
# TODO: Allow users of group /DataSHIELD and OIDC_USER_GROUP at the same time:
# Maybe a solution would be (https://oauth2-proxy.github.io/oauth2-proxy/configuration/oauth_provider):
# --allowed-groups=/DataSHIELD,OIDC_USER_GROUP
oauth2-proxy:
image: docker.verbis.dkfz.de/cache/oauth2-proxy/oauth2-proxy:latest
container_name: bridgehead-oauth2proxy
command: >-
--allowed-group=DataSHIELD
--oidc-groups-claim=${OIDC_GROUP_CLAIM}
--auth-logging=true
--whitelist-domain=${HOST}
--http-address="0.0.0.0:4180"
--reverse-proxy=true
--upstream="static://202"
--email-domain="*"
--cookie-name="_BRIDGEHEAD_oauth2"
--cookie-secret="${OAUTH2_PROXY_SECRET}"
--cookie-expire="12h"
--cookie-secure="true"
--cookie-httponly="true"
#OIDC settings
--provider="keycloak-oidc"
--provider-display-name="VerbIS Login"
--client-id="${OIDC_PRIVATE_CLIENT_ID}"
--client-secret="${OIDC_CLIENT_SECRET}"
--redirect-url="https://${HOST}${OAUTH2_CALLBACK}"
--oidc-issuer-url="${OIDC_ISSUER_URL}"
--scope="openid email profile"
--code-challenge-method="S256"
--skip-provider-button=true
#X-Forwarded-Header settings - true/false depending on your needs
--pass-basic-auth=true
--pass-user-headers=false
--pass-access-token=false
labels:
- "traefik.enable=true"
- "traefik.http.routers.oauth2_proxy.rule=Host(`${HOST}`) && PathPrefix(`/oauth2`, `/oauth2/callback`)"
- "traefik.http.services.oauth2_proxy.loadbalancer.server.port=4180"
- "traefik.http.routers.oauth2_proxy.tls=true"
environment:
http_proxy: "http://forward_proxy:3128"
https_proxy: "http://forward_proxy:3128"
depends_on:
forward_proxy:
condition: service_healthy
secrets:
opal-cert.pem:
file: /tmp/bridgehead/opal-cert.pem
opal-key.pem:
file: /tmp/bridgehead/opal-key.pem
networks:
rstudio:

View File

@ -1,157 +0,0 @@
<template id="opal-ccp" source-id="blaze-store" opal-project="ccp-demo" target-id="opal" >
<container csv-filename="Patient-${TIMESTAMP}.csv" opal-table="patient" opal-entity-type="Patient">
<attribute csv-column="patient-id" opal-value-type="text" primary-key="true" val-fhir-path="Patient.id.value" anonym="Pat" op="EXTRACT_RELATIVE_ID"/>
<attribute csv-column="dktk-id-global" opal-value-type="text" val-fhir-path="Patient.identifier.where(type.coding.code = 'Global').value.value"/>
<attribute csv-column="dktk-id-lokal" opal-value-type="text" val-fhir-path="Patient.identifier.where(type.coding.code = 'Lokal').value.value" />
<attribute csv-column="geburtsdatum" opal-value-type="date" val-fhir-path="Patient.birthDate.value"/>
<attribute csv-column="geschlecht" opal-value-type="text" val-fhir-path="Patient.gender.value" />
<attribute csv-column="datum_des_letztbekannten_vitalstatus" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '75186-7').effective.value" join-fhir-path="/Observation.where(code.coding.code = '75186-7').subject.reference.value"/>
<attribute csv-column="vitalstatus" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '75186-7').value.coding.code.value" join-fhir-path="/Observation.where(code.coding.code = '75186-7').subject.reference.value"/>
<!--fehlt in ADT2FHIR--><attribute csv-column="tod_tumorbedingt" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '68343-3').value.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.value" join-fhir-path="/Observation.where(code.coding.code = '68343-3').subject.reference.value"/>
<!--fehlt in ADT2FHIR--><attribute csv-column="todesursachen" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '68343-3').value.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/JNUCS').code.value" join-fhir-path="/Observation.where(code.coding.code = '68343-3').subject.reference.value"/>
</container>
<container csv-filename="Diagnosis-${TIMESTAMP}.csv" opal-table="diagnosis" opal-entity-type="Diagnosis">
<attribute csv-column="diagnosis-id" primary-key="true" opal-value-type="text" val-fhir-path="Condition.id.value" anonym="Dia" op="EXTRACT_RELATIVE_ID"/>
<attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Condition.subject.reference.value" anonym="Pat"/>
<attribute csv-column="primaerdiagnose" opal-value-type="text" val-fhir-path="Condition.code.coding.code.value"/>
<attribute csv-column="tumor_diagnosedatum" opal-value-type="date" val-fhir-path="Condition.onset.value"/>
<attribute csv-column="primaertumor_diagnosetext" opal-value-type="text" val-fhir-path="Condition.code.text.value"/>
<attribute csv-column="version_des_icd-10_katalogs" opal-value-type="integer" val-fhir-path="Condition.code.coding.version.value"/>
<attribute csv-column="lokalisation" opal-value-type="text" val-fhir-path="Condition.bodySite.coding.where(system = 'urn:oid:2.16.840.1.113883.6.43.1').code.value"/>
<attribute csv-column="icd-o_katalog_topographie_version" opal-value-type="text" val-fhir-path="Condition.bodySite.coding.where(system = 'urn:oid:2.16.840.1.113883.6.43.1').version.value"/>
<attribute csv-column="seitenlokalisation_nach_adt-gekid" opal-value-type="text" val-fhir-path="Condition.bodySite.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/SeitenlokalisationCS').code.value"/>
</container>
<container csv-filename="Progress-${TIMESTAMP}.csv" opal-table="progress" opal-entity-type="Progress">
<!--it would be better to generate a an ID, instead of extracting the ClinicalImpression id-->
<attribute csv-column="progress-id" primary-key="true" opal-value-type="text" val-fhir-path="ClinicalImpression.id.value" anonym="Pro" op="EXTRACT_RELATIVE_ID"/>
<attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="ClinicalImpression.problem.reference.value" anonym="Dia"/>
<attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="ClinicalImpression.subject.reference.value" anonym="Pat" />
<attribute csv-column="untersuchungs-_befunddatum_im_verlauf" opal-value-type="date" val-fhir-path="ClinicalImpression.effective.value" />
<!-- just for evaluation: redundant to Untersuchungs-, Befunddatum im Verlauf-->
<attribute csv-column="datum_lokales_oder_regionaeres_rezidiv" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = 'LA4583-6').effective.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value" />
<attribute csv-column="gesamtbeurteilung_tumorstatus" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21976-6').value.coding.code.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value"/>
<attribute csv-column="lokales_oder_regionaeres_rezidiv" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = 'LA4583-6').value.coding.code.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value"/>
<attribute csv-column="lymphknoten-rezidiv" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = 'LA4370-8').value.coding.code.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value" />
<attribute csv-column="fernmetastasen" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = 'LA4226-2').value.coding.code.value" join-fhir-path="ClinicalImpression.finding.itemReference.reference.value" />
</container>
<container csv-filename="Histology-${TIMESTAMP}.csv" opal-table="histology" opal-entity-type="Histology" >
<attribute csv-column="histology-id" primary-key="true" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').id" anonym="His" op="EXTRACT_RELATIVE_ID"/>
<attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').focus.reference.value" anonym="Dia"/>
<attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').subject.reference.value" anonym="Pat" />
<attribute csv-column="histologie_datum" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '59847-4').effective.value"/>
<attribute csv-column="icd-o_katalog_morphologie_version" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').value.coding.version.value" />
<attribute csv-column="morphologie" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').value.coding.code.value"/>
<attribute csv-column="morphologie-freitext" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59847-4').value.text.value"/>
<attribute csv-column="grading" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '59542-1').value.coding.code.value" join-fhir-path="Observation.where(code.coding.code = '59847-4').hasMember.reference.value"/>
</container>
<container csv-filename="Metastasis-${TIMESTAMP}.csv" opal-table="metastasis" opal-entity-type="Metastasis" >
<attribute csv-column="metastasis-id" primary-key="true" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21907-1').id" anonym="Met" op="EXTRACT_RELATIVE_ID"/>
<attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21907-1').focus.reference.value" anonym="Dia"/>
<attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21907-1').subject.reference.value" anonym="Pat" />
<attribute csv-column="datum_fernmetastasen" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '21907-1').effective.value"/>
<attribute csv-column="fernmetastasen_vorhanden" opal-value-type="boolean" val-fhir-path="Observation.where(code.coding.code = '21907-1').value.coding.code.value"/>
<attribute csv-column="lokalisation_fernmetastasen" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21907-1').bodySite.coding.code.value"/>
</container>
<container csv-filename="TNM-${TIMESTAMP}.csv" opal-table="tnm" opal-entity-type="TNM">
<attribute csv-column="tnm-id" primary-key="true" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').id" anonym="TNM" op="EXTRACT_RELATIVE_ID"/>
<attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').focus.reference.value" anonym="Dia"/>
<attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').subject.reference.value" anonym="Pat" />
<attribute csv-column="datum_der_tnm_dokumentation_datum_befund" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').effective.value"/>
<attribute csv-column="uicc_stadium" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').value.coding.code.value"/>
<attribute csv-column="tnm-t" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21905-5' or code.coding.code = '21899-0').value.coding.code.value"/>
<attribute csv-column="tnm-n" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21906-3' or code.coding.code = '21900-6').value.coding.code.value"/>
<attribute csv-column="tnm-m" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21907-1' or code.coding.code = '21901-4').value.coding.code.value"/>
<attribute csv-column="c_p_u_preefix_t" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21905-5' or code.coding.code = '21899-0').extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-TNMcpuPraefix').value.coding.code.value"/>
<attribute csv-column="c_p_u_preefix_n" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21906-3' or code.coding.code = '21900-6').extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-TNMcpuPraefix').value.coding.code.value"/>
<attribute csv-column="c_p_u_preefix_m" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21907-1' or code.coding.code = '21901-4').extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-TNMcpuPraefix').value.coding.code.value"/>
<attribute csv-column="tnm-y-symbol" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '59479-6' or code.coding.code = '59479-6').value.coding.code.value"/>
<attribute csv-column="tnm-r-symbol" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '21983-2' or code.coding.code = '21983-2').value.coding.code.value"/>
<attribute csv-column="tnm-m-symbol" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').component.where(code.coding.code = '42030-7' or code.coding.code = '42030-7').value.coding.code.value"/>
<!--nur bei UICC, nicht in ADT2FHIR--><attribute csv-column="tnm-version" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '21908-9' or code.coding.code = '21902-2').value.coding.version.value"/>
</container>
<container csv-filename="System-Therapy-${TIMESTAMP}.csv" opal-table="system-therapy" opal-entity-type="SystemTherapy">
<attribute csv-column="system-therapy-id" primary-key="true" opal-value-type="text" val-fhir-path="MedicationStatement.id" anonym="Sys" op="EXTRACT_RELATIVE_ID"/>
<attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="MedicationStatement.reasonReference.reference.value" anonym="Dia"/>
<attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="MedicationStatement.subject.reference.value" anonym="Pat" />
<attribute csv-column="systemische_therapie_stellung_zu_operativer_therapie" opal-value-type="text" val-fhir-path="MedicationStatement.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-StellungZurOp').value.coding.code.value"/>
<attribute csv-column="intention_chemotherapie" opal-value-type="text" val-fhir-path="MedicationStatement.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-SYSTIntention').value.coding.code.value"/>
<attribute csv-column="therapieart" opal-value-type="text" val-fhir-path="MedicationStatement.category.coding.code.value"/>
<attribute csv-column="systemische_therapie_beginn" opal-value-type="date" val-fhir-path="MedicationStatement.effective.start.value"/>
<attribute csv-column="systemische_therapie_ende" opal-value-type="date" val-fhir-path="MedicationStatement.effective.end.value"/>
<attribute csv-column="systemische_therapie_protokoll" opal-value-type="text" val-fhir-path="MedicationStatement.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-SystemischeTherapieProtokoll').value.text.value"/>
<attribute csv-column="systemische_therapie_substanzen" opal-value-type="text" val-fhir-path="MedicationStatement.medication.text.value"/>
<attribute csv-column="chemotherapie" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'CH').exists().value" />
<attribute csv-column="hormontherapie" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'HO').exists().value" />
<attribute csv-column="immuntherapie" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'IM').exists().value" />
<attribute csv-column="knochenmarktransplantation" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'KM').exists().value" />
<attribute csv-column="abwartende_strategie" opal-value-type="boolean" val-fhir-path="MedicationStatement.where(category.coding.code = 'WS').exists().value" />
</container>
<container csv-filename="Surgery-${TIMESTAMP}.csv" opal-table="surgery" opal-entity-type="Surgery">
<attribute csv-column="surgery-id" primary-key="true" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').id" anonym="Sur" op="EXTRACT_RELATIVE_ID"/>
<attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').reasonReference.reference.value" anonym="Dia"/>
<attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').subject.reference.value" anonym="Pat" />
<attribute csv-column="ops-code" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').code.coding.code.value"/>
<attribute csv-column="datum_der_op" opal-value-type="date" val-fhir-path="Procedure.where(category.coding.code = 'OP').performed.value"/>
<attribute csv-column="intention_op" opal-value-type="text" val-fhir-path="Procedure.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-OPIntention').value.coding.code.value"/>
<attribute csv-column="lokale_beurteilung_resttumor" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').outcome.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/LokaleBeurteilungResidualstatusCS').code.value" />
<attribute csv-column="gesamtbeurteilung_resttumor" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'OP').outcome.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/GesamtbeurteilungResidualstatusCS').code.value" />
</container>
<container csv-filename="Radiation-Therapy-${TIMESTAMP}.csv" opal-table="radiation-therapy" opal-entity-type="RadiationTherapy">
<attribute csv-column="radiation-therapy-id" primary-key="true" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'ST').id" anonym="Rad" op="EXTRACT_RELATIVE_ID"/>
<attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'ST').reasonReference.reference.value" anonym="Dia"/>
<attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Procedure.where(category.coding.code = 'ST').subject.reference.value" anonym="Pat" />
<attribute csv-column="strahlentherapie_stellung_zu_operativer_therapie" opal-value-type="text" val-fhir-path="Procedure.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-StellungZurOp').value.coding.code.value"/>
<attribute csv-column="intention_strahlentherapie" opal-value-type="text" val-fhir-path="Procedure.extension('http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Extension-SYSTIntention').value.coding.code.value" />
<attribute csv-column="strahlentherapie_beginn" opal-value-type="date" val-fhir-path="Procedure.where(category.coding.code = 'ST').performed.start.value"/>
<attribute csv-column="strahlentherapie_ende" opal-value-type="date" val-fhir-path="Procedure.where(category.coding.code = 'ST').performed.end.value"/>
</container>
<container csv-filename="Molecular-Marker-${TIMESTAMP}.csv" opal-table="molecular-marker" opal-entity-type="MolecularMarker">
<attribute csv-column="mol-marker-id" primary-key="true" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').id" anonym="Mol" op="EXTRACT_RELATIVE_ID"/>
<attribute csv-column="diagnosis-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').focus.reference.value" anonym="Dia" />
<attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').subject.reference.value" anonym="Pat" />
<attribute csv-column="datum_der_datenerhebung" opal-value-type="date" val-fhir-path="Observation.where(code.coding.code = '69548-6').effective.value"/>
<attribute csv-column="marker" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').component.value.coding.code.value"/>
<attribute csv-column="status_des_molekularen_markers" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').value.coding.code.value" />
<attribute csv-column="zusaetzliche_alternative_dokumentation" opal-value-type="text" val-fhir-path="Observation.where(code.coding.code = '69548-6').value.text.value"/>
</container>
<container csv-filename="Sample-${TIMESTAMP}.csv" opal-table="sample" opal-entity-type="Sample">
<attribute csv-column="sample-id" primary-key="true" opal-value-type="text" val-fhir-path="Specimen.id" anonym="Sam" op="EXTRACT_RELATIVE_ID"/>
<attribute csv-column="patient-id" opal-value-type="text" val-fhir-path="Specimen.subject.reference.value" anonym="Pat" />
<attribute csv-column="entnahmedatum" opal-value-type="date" val-fhir-path="Specimen.collection.collectedDateTime.value"/>
<attribute csv-column="probenart" opal-value-type="text" val-fhir-path="Specimen.type.coding.code.value"/>
<attribute csv-column="status" opal-value-type="text" val-fhir-path="Specimen.status.code.value"/>
<attribute csv-column="projekt" opal-value-type="text" val-fhir-path="Specimen.identifier.system.value"/>
<!-- @TODO: it is still necessary to clarify whether it would not be better to take the quantity of collection.quantity -->
<attribute csv-column="menge" opal-value-type="integer" val-fhir-path="Specimen.container.specimenQuantity.value.value"/>
<attribute csv-column="einheit" opal-value-type="text" val-fhir-path="Specimen.container.specimenQuantity.unit.value"/>
<attribute csv-column="aliquot" opal-value-type="text" val-fhir-path="Specimen.parent.reference.exists().value" />
</container>
<fhir-rev-include>Observation:patient</fhir-rev-include>
<fhir-rev-include>Condition:patient</fhir-rev-include>
<fhir-rev-include>ClinicalImpression:patient</fhir-rev-include>
<fhir-rev-include>MedicationStatement:patient</fhir-rev-include>
<fhir-rev-include>Procedure:patient</fhir-rev-include>
<fhir-rev-include>Specimen:patient</fhir-rev-include>
</template>

View File

@ -1,44 +0,0 @@
#!/bin/bash -e
if [ "$ENABLE_DATASHIELD" == true ]; then
# HACK: This only works because exporter-setup.sh and teiler-setup.sh are sourced after datashield-setup.sh
if [ -z "${ENABLE_EXPORTER}" ] || [ "${ENABLE_EXPORTER}" != "true" ]; then
log WARN "The ENABLE_EXPORTER variable is either not set or not set to 'true'."
fi
OAUTH2_CALLBACK=/oauth2/callback
OAUTH2_PROXY_SECRET="$(echo \"This is a salt string to generate one consistent encryption key for the oauth2_proxy. It is not required to be secret.\" | sha1sum | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 32)"
add_private_oidc_redirect_url "${OAUTH2_CALLBACK}"
log INFO "DataSHIELD setup detected -- will start DataSHIELD services."
OVERRIDE+=" -f ./$PROJECT/modules/datashield-compose.yml"
EXPORTER_OPAL_PASSWORD="$(generate_password \"exporter in Opal\")"
TOKEN_MANAGER_OPAL_PASSWORD="$(generate_password \"Token Manager in Opal\")"
OPAL_DB_PASSWORD="$(echo \"Opal DB\" | generate_simple_password)"
OPAL_ADMIN_PASSWORD="$(generate_password \"admin password for Opal\")"
RSTUDIO_ADMIN_PASSWORD="$(generate_password \"admin password for R-Studio\")"
DATASHIELD_CONNECT_SECRET="$(echo \"DataShield Connect\" | generate_simple_password)"
TOKEN_MANAGER_SECRET="$(echo \"Token Manager\" | generate_simple_password)"
if [ ! -e /tmp/bridgehead/opal-cert.pem ]; then
mkdir -p /tmp/bridgehead/
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)"
echo "$sites" | docker_jq -n --args '{"sites": input | map({
"name": .,
"id": .,
"virtualhost": "\(.):443",
"beamconnect": "datashield-connect.\(.).'"$BROKER_ID"'"
})}' $sites >/tmp/bridgehead/opal-map/central.json
echo "$sites" | docker_jq -n --args '[{
"external": "'"$SITE_ID"':443",
"internal": "opal:8443",
"allowed": input | map("datashield-connect.\(.).'"$BROKER_ID"'")
}]' >/tmp/bridgehead/opal-map/local.json
if [ "$USER" == "root" ]; then
chown -R bridgehead:docker /tmp/bridgehead
chmod g+wr /tmp/bridgehead/opal-map/*
chmod g+r /tmp/bridgehead/opal-key.pem
fi
add_private_oidc_redirect_url "/opal/*"
fi

View File

@ -1,14 +0,0 @@
[
"berlin",
"muenchen-lmu",
"dresden",
"freiburg",
"muenchen-tum",
"tuebingen",
"mainz",
"frankfurt",
"essen",
"dktk-datashield-test",
"dktk-test",
"mannheim"
]

View File

@ -1,28 +0,0 @@
# DataSHIELD
This module constitutes the infrastructure to run DataSHIELD within the bridghead.
For more information about DataSHIELD, please visit https://www.datashield.org/
## R-Studio
To connect to the different bridgeheads of the CCP through DataSHIELD, you can use your own R-Studio environment.
However, this R-Studio has already installed the DataSHIELD libraries and is integrated within the bridgehead.
This can save you some time for extra configuration of your R-Studio environment.
## Opal
This is the core of DataSHIELD. It is made up of Opal, a Postgres database and an R-server.
For more information about Opal, please visit https://opaldoc.obiba.org
### Opal
Opal is OBiBas core database application for biobanks.
### Opal-DB
Opal requires a database to import the data for DataSHIELD. We use a Postgres instance as database.
The data is imported within the bridgehead through the exporter.
### Opal-R-Server
R-Server to execute R scripts in DataSHIELD.
## Beam
### Beam-Connect
Beam-Connect is used to route http(s) traffic through beam to enable R-Studio to access data from other bridgeheads that have datashield enabled.
### Beam-Proxy
The usual beam proxy used for communication.

View File

@ -6,7 +6,7 @@ services:
APP_dnpm-connect_KEY: ${DNPM_BEAM_SECRET_SHORT}
dnpm-beam-connect:
depends_on: [ beam-proxy ]
image: docker.verbis.dkfz.de/cache/samply/beam-connect:develop
image: docker.verbis.dkfz.de/cache/samply/beam-connect:dnpm
container_name: bridgehead-dnpm-beam-connect
environment:
PROXY_URL: http://beam-proxy:8081
@ -16,14 +16,9 @@ services:
LOCAL_TARGETS_FILE: "./conf/connect_targets.json"
HTTP_PROXY: "http://forward_proxy:3128"
HTTPS_PROXY: "http://forward_proxy:3128"
NO_PROXY: beam-proxy,dnpm-backend,host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
NO_PROXY: beam-proxy,dnpm-backend
RUST_LOG: ${RUST_LOG:-info}
NO_AUTH: "true"
TLS_CA_CERTIFICATES_DIR: ./conf/trusted-ca-certs
extra_hosts:
- "host.docker.internal:host-gateway"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
- /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
labels:
@ -33,7 +28,3 @@ services:
- "traefik.http.routers.dnpm-connect.middlewares=dnpm-connect-strip"
- "traefik.http.services.dnpm-connect.loadbalancer.server.port=8062"
- "traefik.http.routers.dnpm-connect.tls=true"
dnpm-echo:
image: docker.verbis.dkfz.de/cache/samply/bridgehead-echo:latest
container_name: bridgehead-dnpm-echo

View File

@ -1,34 +0,0 @@
version: "3.7"
services:
dnpm-backend:
image: ghcr.io/kohlbacherlab/bwhc-backend:1.0-snapshot-broker-connector
container_name: bridgehead-dnpm-backend
environment:
- ZPM_SITE=${ZPM_SITE}
- N_RANDOM_FILES=${DNPM_SYNTH_NUM}
volumes:
- /etc/bridgehead/dnpm:/bwhc_config:ro
- ${DNPM_DATA_DIR}:/bwhc_data
labels:
- "traefik.enable=true"
- "traefik.http.routers.bwhc-backend.rule=PathPrefix(`/bwhc`)"
- "traefik.http.services.bwhc-backend.loadbalancer.server.port=9000"
- "traefik.http.routers.bwhc-backend.tls=true"
dnpm-frontend:
image: ghcr.io/kohlbacherlab/bwhc-frontend:2209
container_name: bridgehead-dnpm-frontend
links:
- dnpm-backend
environment:
- NUXT_HOST=0.0.0.0
- NUXT_PORT=8080
- BACKEND_PROTOCOL=https
- BACKEND_HOSTNAME=$HOST
- BACKEND_PORT=443
labels:
- "traefik.enable=true"
- "traefik.http.routers.bwhc-frontend.rule=PathPrefix(`/`)"
- "traefik.http.services.bwhc-frontend.loadbalancer.server.port=8080"
- "traefik.http.routers.bwhc-frontend.tls=true"

View File

@ -1,28 +0,0 @@
#!/bin/bash
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"
# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.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)"
if [ -z "${ZPM_SITE+x}" ]; then
log ERROR "Mandatory variable ZPM_SITE not defined!"
exit 1
fi
if [ -z "${DNPM_DATA_DIR+x}" ]; then
log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
exit 1
fi
DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:-0}
if grep -q 'traefik.http.routers.landing.rule=PathPrefix(`/landing`)' /srv/docker/bridgehead/minimal/docker-compose.override.yml 2>/dev/null; then
echo "Override of landing page url already in place"
else
echo "Adding override of landing page url"
if [ -f /srv/docker/bridgehead/minimal/docker-compose.override.yml ]; then
echo -e ' landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
else
echo -e 'version: "3.7"\nservices:\n landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
fi
fi
fi

View File

@ -1,15 +1,10 @@
#!/bin/bash -e
#!/bin/bash
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"
# Set variables required for Beam-Connect
DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
DNPM_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
# If the DNPM_NO_PROXY variable is set, prefix it with a comma (as it gets added to a comma separated list)
if [ -n "${DNPM_NO_PROXY}" ]; then
DNPM_ADDITIONAL_NO_PROXY=",${DNPM_NO_PROXY}"
else
DNPM_ADDITIONAL_NO_PROXY=""
fi
fi

View File

@ -1,6 +0,0 @@
# Full Excel Export
curl --location --request POST 'https://${HOST}/ccp-exporter/request?query=Patient&query-format=FHIR_PATH&template-id=ccp&output-format=EXCEL' \
--header 'x-api-key: ${EXPORT_API_KEY}'
# QB
curl --location --request POST 'https://${HOST}/ccp-reporter/generate?template-id=ccp'

View File

@ -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"

View File

@ -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

View File

@ -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.

View File

@ -1,5 +1,4 @@
version: "3.7"
services:
id-manager:
image: docker.verbis.dkfz.de/bridgehead/magicpl
@ -29,7 +28,6 @@ services:
container_name: bridgehead-patientlist
environment:
- TOMCAT_REVERSEPROXY_FQDN=${HOST}
- TOMCAT_REVERSEPROXY_SSL=true
- ML_SITE=${IDMANAGEMENT_FRIENDLY_ID}
- ML_DB_PASS=${PATIENTLIST_POSTGRES_PASSWORD}
- ML_API_KEY=${IDMANAGER_LOCAL_PATIENTLIST_APIKEY}
@ -45,7 +43,7 @@ services:
- patientlist-db
patientlist-db:
image: docker.verbis.dkfz.de/cache/postgres:${POSTGRES_TAG}
image: docker.verbis.dkfz.de/cache/postgres:15.1-alpine
container_name: bridgehead-patientlist-db
environment:
POSTGRES_USER: "mainzelliste"

View File

@ -1,4 +1,4 @@
#!/bin/bash -e
#!/bin/bash
function idManagementSetup() {
if [ -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
@ -39,7 +39,6 @@ function applySpecialCases() {
result="$1";
result="${result/Lmu/LMU}";
result="${result/Tum/TUM}";
result="${result/Dktk Test/Teststandort}";
echo "$result";
}

View File

@ -11,30 +11,22 @@ services:
ID_MANAGER_API_KEY: ${IDMANAGER_UPLOAD_APIKEY}
ID_MANAGER_PSEUDONYM_ID_TYPE: BK_${IDMANAGEMENT_FRIENDLY_ID}_L-ID
ID_MANAGER_URL: http://id-manager:8080/id-manager
PATIENT_CSV_FIRST_NAME_HEADER: ${MTBA_PATIENT_CSV_FIRST_NAME_HEADER:-FIRST_NAME}
PATIENT_CSV_LAST_NAME_HEADER: ${MTBA_PATIENT_CSV_LAST_NAME_HEADER:-LAST_NAME}
PATIENT_CSV_GENDER_HEADER: ${MTBA_PATIENT_CSV_GENDER_HEADER:-GENDER}
PATIENT_CSV_BIRTHDAY_HEADER: ${MTBA_PATIENT_CSV_BIRTHDAY_HEADER:-BIRTHDAY}
PATIENT_CSV_FIRST_NAME_HEADER: ${MTBA_PATIENT_CSV_FIRST_NAME_HEADER}
PATIENT_CSV_LAST_NAME_HEADER: ${MTBA_PATIENT_CSV_LAST_NAME_HEADER}
PATIENT_CSV_GENDER_HEADER: ${MTBA_PATIENT_CSV_GENDER_HEADER}
PATIENT_CSV_BIRTHDAY_HEADER: ${MTBA_PATIENT_CSV_BIRTHDAY_HEADER}
CBIOPORTAL_URL: http://cbioportal:8080
FILE_CHARSET: ${MTBA_FILE_CHARSET:-UTF-8}
FILE_END_OF_LINE: ${MTBA_FILE_END_OF_LINE:-LF}
CSV_DELIMITER: ${MTBA_CSV_DELIMITER:-TAB}
HTTP_RELATIVE_PATH: "/mtba"
OIDC_ADMIN_GROUP: "${OIDC_ADMIN_GROUP}"
OIDC_CLIENT_ID: "${OIDC_PRIVATE_CLIENT_ID}"
OIDC_CLIENT_SECRET: "${OIDC_CLIENT_SECRET}"
OIDC_REALM: "${OIDC_REALM}"
OIDC_URL: "${OIDC_URL}"
FILE_CHARSET: ${MTBA_FILE_CHARSET}
FILE_END_OF_LINE: ${MTBA_FILE_END_OF_LINE}
CSV_DELIMITER: ${MTBA_CSV_DELIMITER}
labels:
- "traefik.enable=true"
- "traefik.http.routers.mtba_ccp.rule=PathPrefix(`/mtba`)"
- "traefik.http.services.mtba_ccp.loadbalancer.server.port=8480"
- "traefik.http.routers.mtba_ccp.tls=true"
- "traefik.http.routers.mtba.rule=PathPrefix(`/`)"
- "traefik.http.services.mtba.loadbalancer.server.port=80"
- "traefik.http.routers.mtba.tls=true"
volumes:
- /var/cache/bridgehead/ccp/mtba/input:/app/input
- /var/cache/bridgehead/ccp/mtba/persist:/app/persist
- /tmp/bridgehead/mtba/input:/app/input
- /tmp/bridgehead/mtba/persist:/app/persist
# TODO: Include CBioPortal in Deployment ...
# NOTE: CBioPortal can't load data while the system is running. So after import of data bridgehead needs to be restarted!

View File

@ -1,13 +1,13 @@
#!/bin/bash -e
#!/bin/bash
function mtbaSetup() {
if [ -n "$ENABLE_MTBA" ];then
log INFO "MTBA setup detected -- will start MTBA Service and CBioPortal."
if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
log ERROR "Missing ID-Management Module! Fix this by setting up ID Management:"
exit 1;
fi
OVERRIDE+=" -f ./$PROJECT/modules/mtba-compose.yml"
add_private_oidc_redirect_url "/mtba/*"
fi
# TODO: Check if ID-Management Module is activated!
if [ -n "$ENABLE_MTBA" ];then
log INFO "MTBA setup detected -- will start MTBA Service and CBioPortal."
if [ ! -n "$IDMANAGER_UPLOAD_APIKEY" ]; then
log ERROR "Detected MTBA Module configuration but ID-Management Module seems not to be configured!"
exit 1;
fi
OVERRIDE+=" -f ./$PROJECT/modules/mtba-compose.yml"
fi
}

View File

@ -1,6 +0,0 @@
# Molecular Tumor Board Alliance (MTBA)
In this module, the genetic data to import is stored in a directory (/tmp/bridgehead/mtba/input). A process checks
regularly if there are files in the directory. The files are pseudonomized when the IDAT is provided. The files are
combined with clinical data of the blaze and imported in cBioPortal. On the other hand, this files are also imported in
Blaze.

View File

@ -1,5 +1,4 @@
version: "3.7"
volumes:
nngm-rest:
@ -22,6 +21,9 @@ services:
- "traefik.http.routers.connector.middlewares=connector_strip,auth-nngm"
volumes:
- nngm-rest:/var/log
traefik:
labels:
- "traefik.http.middlewares.auth-nngm.basicauth.users=${NNGM_AUTH}"

View File

@ -1,6 +1,8 @@
#!/bin/bash -e
#!/bin/bash
if [ -n "$NNGM_CTS_APIKEY" ]; then
log INFO "nNGM setup detected -- will start nNGM Connector."
OVERRIDE+=" -f ./$PROJECT/modules/nngm-compose.yml"
fi
function nngmSetup() {
if [ -n "$NNGM_CTS_APIKEY" ]; then
log INFO "nNGM setup detected -- will start nNGM Connector."
OVERRIDE+=" -f ./$PROJECT/modules/nngm-compose.yml"
fi
}

View File

@ -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

View File

@ -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

View File

@ -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.

20
ccp/root-new.crt.pem Normal file
View File

@ -0,0 +1,20 @@
-----BEGIN CERTIFICATE-----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-----END CERTIFICATE-----

View File

@ -8,17 +8,6 @@ PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BROKER_URL_FOR_PREREQ=$BROKER_URL
OIDC_USER_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})"
OIDC_ADMIN_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_Verwalter"
OIDC_PRIVATE_CLIENT_ID=${SITE_ID}-private
OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public
# Use "test-realm-01" for testing
OIDC_REALM="${OIDC_REALM:-master}"
OIDC_URL="https://login.verbis.dkfz.de"
OIDC_ISSUER_URL="${OIDC_URL}/realms/${OIDC_REALM}"
OIDC_GROUP_CLAIM="groups"
POSTGRES_TAG=15.6-alpine
for module in $PROJECT/modules/*.sh
do
@ -27,5 +16,5 @@ do
done
idManagementSetup
nngmSetup
mtbaSetup
adt2fhirRestSetup

View File

@ -9,33 +9,6 @@ detectCompose() {
fi
}
setupProxy() {
### Note: As the current data protection concepts do not allow communication via HTTP,
### we are not setting a proxy for HTTP requests.
local http="no"
local https="no"
if [ $HTTPS_PROXY_URL ]; then
local proto="$(echo $HTTPS_PROXY_URL | grep :// | sed -e 's,^\(.*://\).*,\1,g')"
local fqdn="$(echo ${HTTPS_PROXY_URL/$proto/})"
local hostport=$(echo $HTTPS_PROXY_URL | sed -e "s,$proto,,g" | cut -d/ -f1)
HTTPS_PROXY_HOST="$(echo $hostport | sed -e 's,:.*,,g')"
HTTPS_PROXY_PORT="$(echo $hostport | sed -e 's,^.*:,:,g' -e 's,.*:\([0-9]*\).*,\1,g' -e 's,[^0-9],,g')"
if [[ ! -z "$HTTPS_PROXY_USERNAME" && ! -z "$HTTPS_PROXY_PASSWORD" ]]; then
local proto="$(echo $HTTPS_PROXY_URL | grep :// | sed -e 's,^\(.*://\).*,\1,g')"
local fqdn="$(echo ${HTTPS_PROXY_URL/$proto/})"
HTTPS_PROXY_FULL_URL="$(echo $proto$HTTPS_PROXY_USERNAME:$HTTPS_PROXY_PASSWORD@$fqdn)"
https="authenticated"
else
HTTPS_PROXY_FULL_URL=$HTTPS_PROXY_URL
https="unauthenticated"
fi
fi
log INFO "Configuring proxy servers: $http http proxy (we're not supporting unencrypted comms), $https https proxy"
export HTTPS_PROXY_HOST HTTPS_PROXY_PORT HTTPS_PROXY_FULL_URL
}
exitIfNotRoot() {
if [ "$EUID" -ne 0 ]; then
log "ERROR" "Please run as root"
@ -53,7 +26,7 @@ checkOwner(){
}
printUsage() {
echo "Usage: bridgehead start|stop|logs|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
echo "Usage: bridgehead start|stop|is-running|update|install|uninstall|adduser|enroll PROJECTNAME"
echo "PROJECTNAME should be one of ccp|bbmri"
}
@ -76,7 +49,7 @@ fetchVarsFromVault() {
set +e
PASS=$(BW_MASTERPASS="$BW_MASTERPASS" BW_CLIENTID="$BW_CLIENTID" BW_CLIENTSECRET="$BW_CLIENTSECRET" docker run --rm -e BW_MASTERPASS -e BW_CLIENTID -e BW_CLIENTSECRET -e http_proxy docker.verbis.dkfz.de/cache/samply/bridgehead-vaultfetcher:latest $@)
PASS=$(BW_MASTERPASS="$BW_MASTERPASS" BW_CLIENTID="$BW_CLIENTID" BW_CLIENTSECRET="$BW_CLIENTSECRET" docker run --rm -e BW_MASTERPASS -e BW_CLIENTID -e BW_CLIENTSECRET -e http_proxy samply/bridgehead-vaultfetcher $@)
RET=$?
if [ $RET -ne 0 ]; then
@ -155,28 +128,6 @@ setHostname() {
fi
}
# This function optimizes the usage of memory through blaze, according to the official performance tuning guide:
# https://github.com/samply/blaze/blob/master/docs/tuning-guide.md
# Short summary of the adjustments made:
# - set blaze memory cap to a quarter of the system memory
# - set db block cache size to a quarter of the system memory
# - limit resource count allowed in blaze to 1,25M per 4GB available system memory
optimizeBlazeMemoryUsage() {
if [ -z "$BLAZE_MEMORY_CAP" ]; then
system_memory_in_mb=$(LC_ALL=C free -m | grep 'Mem:' | awk '{print $2}');
export BLAZE_MEMORY_CAP=$(($system_memory_in_mb/4));
fi
if [ -z "$BLAZE_RESOURCE_CACHE_CAP" ]; then
available_system_memory_chunks=$((BLAZE_MEMORY_CAP / 1000))
if [ $available_system_memory_chunks -eq 0 ]; then
log WARN "Only ${BLAZE_MEMORY_CAP} system memory available for Blaze. If your Blaze stores more than 128000 fhir ressources it will run significally slower."
export BLAZE_RESOURCE_CACHE_CAP=128000;
else
export BLAZE_RESOURCE_CACHE_CAP=$((available_system_memory_chunks * 312500))
fi
fi
}
# Takes 1) The Backup Directory Path 2) The name of the Service to be backuped
# Creates 3 Backups: 1) For the past seven days 2) For the current month and 3) for each calendar week
createEncryptedPostgresBackup(){
@ -237,7 +188,7 @@ function do_enroll_inner {
PARAMS+="--admin-email $SUPPORT_EMAIL"
fi
docker run --rm -v /etc/bridgehead/pki:/etc/bridgehead/pki docker.verbis.dkfz.de/cache/samply/beam-enroll:latest --output-file $PRIVATEKEYFILENAME --proxy-id $MANUAL_PROXY_ID $PARAMS
docker run --rm -ti -v /etc/bridgehead/pki:/etc/bridgehead/pki samply/beam-enroll:latest --output-file $PRIVATEKEYFILENAME --proxy-id $MANUAL_PROXY_ID $PARAMS
chmod 600 $PRIVATEKEYFILENAME
}
@ -261,128 +212,3 @@ add_basic_auth_user() {
log DEBUG "Saving clear text credentials in $FILE. If wanted, delete them manually."
sed -i "/^$NAME/ s|$|\n# User: $USER\n# Password: $PASSWORD|" $FILE
}
OIDC_PUBLIC_REDIRECT_URLS=${OIDC_PUBLIC_REDIRECT_URLS:-""}
OIDC_PRIVATE_REDIRECT_URLS=${OIDC_PRIVATE_REDIRECT_URLS:-""}
# Add a redirect url to the public oidc client of the bridgehead
function add_public_oidc_redirect_url() {
if [[ $OIDC_PUBLIC_REDIRECT_URLS == "" ]]; then
OIDC_PUBLIC_REDIRECT_URLS+="$(generate_redirect_urls $1)"
else
OIDC_PUBLIC_REDIRECT_URLS+=",$(generate_redirect_urls $1)"
fi
}
# Add a redirect url to the private oidc client of the bridgehead
function add_private_oidc_redirect_url() {
if [[ $OIDC_PRIVATE_REDIRECT_URLS == "" ]]; then
OIDC_PRIVATE_REDIRECT_URLS+="$(generate_redirect_urls $1)"
else
OIDC_PRIVATE_REDIRECT_URLS+=",$(generate_redirect_urls $1)"
fi
}
function sync_secrets() {
local delimiter=$'\x1E'
local secret_sync_args=""
if [[ $OIDC_PRIVATE_REDIRECT_URLS != "" ]]; then
secret_sync_args="OIDC:OIDC_CLIENT_SECRET:private;$OIDC_PRIVATE_REDIRECT_URLS"
fi
if [[ $OIDC_PUBLIC_REDIRECT_URLS != "" ]]; then
if [[ $secret_sync_args == "" ]]; then
secret_sync_args="OIDC:OIDC_PUBLIC:public;$OIDC_PUBLIC_REDIRECT_URLS"
else
secret_sync_args+="${delimiter}OIDC:OIDC_PUBLIC:public;$OIDC_PUBLIC_REDIRECT_URLS"
fi
fi
if [[ $secret_sync_args == "" ]]; then
return
fi
if [ "${ENABLE_ERIC}" == "true" ]; then
BROKER_ROOT_CERT=/srv/docker/bridgehead/bbmri/$ERIC_ROOT_CERT.crt.pem
PROXY_ID=$ERIC_PROXY_ID
BROKER_ID=$ERIC_BROKER_ID
elif [ "${ENABLE_GBN}" == "true" ]; then
BROKER_ROOT_CERT=/srv/docker/bridgehead/bbmri/$GBN_ROOT_CERT.crt.pem
PROXY_ID=$GBN_PROXY_ID
BROKER_ID=$GBN_BROKER_ID
elif [ "${PROJECT}" == "ccp"]; then
BROKER_ROOT_CERT=/srv/docker/bridgehead/ccp/root.crt.pem
else
fail_and_report 1 "Could not start secret sync as the configuration does not seem to use beam"
fi
local broker_url="https://$BROKER_ID"
mkdir -p /var/cache/bridgehead/secrets/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/secrets/'. Please run sudo './bridgehead install $PROJECT' again."
touch /var/cache/bridgehead/secrets/oidc
docker run --rm \
-v /var/cache/bridgehead/secrets/oidc:/usr/local/cache \
-v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
-v $BROKER_ROOT_CERT:/run/secrets/root.crt.pem:ro \
-v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
-e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
-e NO_PROXY=localhost,127.0.0.1 \
-e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
-e PROXY_ID=$PROXY_ID \
-e BROKER_URL=$broker_url \
-e OIDC_PROVIDER=secret-sync-central.oidc-client-enrollment.$BROKER_ID \
-e SECRET_DEFINITIONS=$secret_sync_args \
docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
set -a # Export variables as environment variables
source /var/cache/bridgehead/secrets/*
set +a # Export variables in the regular way
}
capitalize_first_letter() {
input="$1"
capitalized="$(tr '[:lower:]' '[:upper:]' <<< ${input:0:1})${input:1}"
echo "$capitalized"
}
# Generate a string of ',' separated string of redirect urls relative to $HOST.
# $1 will be appended to the url
# If the host looks like dev-jan.inet.dkfz-heidelberg.de it will generate urls with dev-jan and the original $HOST as url Authorities
function generate_redirect_urls(){
local redirect_urls="https://${HOST}$1"
local host_without_proxy="$(echo "$HOST" | cut -d '.' -f1)"
# Only append second url if its different and the host is not an ip address
if [[ "$HOST" != "$host_without_proxy" && ! "$HOST" =~ ^[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
redirect_urls+=",https://$host_without_proxy$1"
fi
echo "$redirect_urls"
}
# This password contains at least one special char, a random number and a random upper and lower case letter
generate_password(){
local seed_text="$1"
local seed_num=$(awk 'BEGIN{FS=""} NR==1{print $10}' /etc/bridgehead/pki/${SITE_ID}.priv.pem | od -An -tuC)
local nums="1234567890"
local n=$(echo "$seed_num" | awk '{print $1 % 10}')
local random_digit=${nums:$n:1}
local n=$(echo "$seed_num" | awk '{print $1 % 26}')
local upper="ABCDEFGHIJKLMNOPQRSTUVWXYZ"
local lower="abcdefghijklmnopqrstuvwxyz"
local random_upper=${upper:$n:1}
local random_lower=${lower:$n:1}
local n=$(echo "$seed_num" | awk '{print $1 % 8}')
local special='@#$%^&+='
local random_special=${special:$n:1}
local combined_text="This is a salt string to generate one consistent password for ${seed_text}. It is not required to be secret."
local main_password=$(echo "${combined_text}" | sha1sum | openssl pkeyutl -sign -inkey "/etc/bridgehead/pki/${SITE_ID}.priv.pem" 2> /dev/null | base64 | head -c 26 | sed 's/\//A/g')
echo "${main_password}${random_digit}${random_upper}${random_lower}${random_special}"
}
# This password only contains alphanumeric characters
generate_simple_password(){
local seed_text="$1"
local combined_text="This is a salt string to generate one consistent password for ${seed_text}. It is not required to be secret."
echo "${combined_text}" | sha1sum | openssl pkeyutl -sign -inkey "/etc/bridgehead/pki/${SITE_ID}.priv.pem" 2> /dev/null | base64 | head -c 26 | sed 's/[+\/]/A/g'
}
docker_jq() {
docker run --rm -i docker.verbis.dkfz.de/cache/jqlang/jq:latest "$@"
}

View File

@ -47,8 +47,8 @@ function hc_send(){
if [ -n "$2" ]; then
MSG="$2\n\nDocker stats:\n$UPTIME"
echo -e "$MSG" | https_proxy=$HTTPS_PROXY_FULL_URL curl --max-time 5 -A "$USER_AGENT" -s -o /dev/null -X POST --data-binary @- "$HCURL"/"$1" || log WARN "Monitoring failed: Unable to send data to $HCURL/$1"
echo -e "$MSG" | https_proxy=$HTTPS_PROXY_URL curl --max-time 5 -A "$USER_AGENT" -s -o /dev/null -X POST --data-binary @- "$HCURL"/"$1" || log WARN "Monitoring failed: Unable to send data to $HCURL/$1"
else
https_proxy=$HTTPS_PROXY_FULL_URL curl --max-time 5 -A "$USER_AGENT" -s -o /dev/null "$HCURL"/"$1" || log WARN "Monitoring failed: Unable to send data to $HCURL/$1"
https_proxy=$HTTPS_PROXY_URL curl --max-time 5 -A "$USER_AGENT" -s -o /dev/null "$HCURL"/"$1" || log WARN "Monitoring failed: Unable to send data to $HCURL/$1"
fi
}

View File

@ -89,9 +89,6 @@ elif [[ "$DEV_MODE" == "DEV" ]]; then
fi
chown -R bridgehead /etc/bridgehead /srv/docker/bridgehead
mkdir -p /tmp/bridgehead /var/cache/bridgehead
chown -R bridgehead:docker /tmp/bridgehead /var/cache/bridgehead
chmod -R g+wr /var/cache/bridgehead /tmp/bridgehead
log INFO "System preparation is completed and configuration is present."

View File

@ -14,7 +14,7 @@ checkOwner /etc/bridgehead bridgehead || exit 1
## Check if user is a su
log INFO "Checking if all prerequisites are met ..."
prerequisites="git docker curl"
prerequisites="git docker"
for prerequisite in $prerequisites; do
$prerequisite --version 2>&1
is_available=$?
@ -67,30 +67,29 @@ log INFO "Checking network access ($BROKER_URL_FOR_PREREQ) ..."
source /etc/bridgehead/${PROJECT}.conf
source ${PROJECT}/vars
if [ "${PROJECT}" != "minimal" ]; then
set +e
SERVERTIME="$(https_proxy=$HTTPS_PROXY_FULL_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
RET=$?
set -e
if [ $RET -ne 0 ]; then
log WARN "Unable to connect to Samply.Beam broker at $BROKER_URL_FOR_PREREQ. Please check your proxy settings.\nThe currently configured proxy was \"$HTTPS_PROXY_URL\". This error is normal when using proxy authentication."
log WARN "Unable to check clock skew due to previous error."
else
log INFO "Checking clock skew ..."
set +e
SERVERTIME="$(https_proxy=$HTTPS_PROXY_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
RET=$?
set -e
if [ $RET -ne 0 ]; then
log WARN "Unable to connect to Samply.Beam broker at $BROKER_URL_FOR_PREREQ. Please check your proxy settings.\nThe currently configured proxy was \"$HTTPS_PROXY_URL\". This error is normal when using proxy authentication."
log WARN "Unable to check clock skew due to previous error."
else
log INFO "Checking clock skew ..."
SERVERTIME_AS_TIMESTAMP=$(date --date="$SERVERTIME" +%s)
MYTIME=$(date +%s)
SKEW=$(($SERVERTIME_AS_TIMESTAMP - $MYTIME))
SKEW=$(echo $SKEW | awk -F- '{print $NF}')
SYNCTEXT="For example, consider entering a correct NTP server (e.g. your institution's Active Directory Domain Controller in /etc/systemd/timesyncd.conf (option NTP=) and restart systemd-timesyncd."
if [ $SKEW -ge 300 ]; then
report_error 5 "Your clock is not synchronized (${SKEW}s off). This will cause Samply.Beam's certificate will fail. Please setup time synchronization. $SYNCTEXT"
exit 1
elif [ $SKEW -ge 60 ]; then
log WARN "Your clock is more than a minute off (${SKEW}s). Consider syncing to a time server. $SYNCTEXT"
fi
fi
SERVERTIME_AS_TIMESTAMP=$(date --date="$SERVERTIME" +%s)
MYTIME=$(date +%s)
SKEW=$(($SERVERTIME_AS_TIMESTAMP - $MYTIME))
SKEW=$(echo $SKEW | awk -F- '{print $NF}')
SYNCTEXT="For example, consider entering a correct NTP server (e.g. your institution's Active Directory Domain Controller in /etc/systemd/timesyncd.conf (option NTP=) and restart systemd-timesyncd."
if [ $SKEW -ge 300 ]; then
report_error 5 "Your clock is not synchronized (${SKEW}s off). This will cause Samply.Beam's certificate will fail. Please setup time synchronization. $SYNCTEXT"
exit 1
elif [ $SKEW -ge 60 ]; then
log WARN "Your clock is more than a minute off (${SKEW}s). Consider syncing to a time server. $SYNCTEXT"
fi
fi
checkPrivKey() {
if [ -e /etc/bridgehead/pki/${SITE_ID}.priv.pem ]; then
log INFO "Success - private key found."
@ -101,7 +100,7 @@ checkPrivKey() {
return 0
}
if [[ "$@" =~ "noprivkey" || "${PROJECT}" != "minimal" ]]; then
if [[ "$@" =~ "noprivkey" ]]; then
log INFO "Skipping check for private key for now."
else
checkPrivKey || exit 1

View File

@ -30,7 +30,7 @@ source $CONFFILE
assertVarsNotEmpty SITE_ID || fail_and_report 1 "Update failed: SITE_ID empty"
export SITE_ID
checkOwner /srv/docker/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /srv/docker/bridgehead"
checkOwner . bridgehead || fail_and_report 1 "Update failed: Wrong permissions in $(pwd)"
checkOwner /etc/bridgehead bridgehead || fail_and_report 1 "Update failed: Wrong permissions in /etc/bridgehead"
CREDHELPER="/srv/docker/bridgehead/lib/gitpassword.sh"
@ -50,12 +50,12 @@ for DIR in /etc/bridgehead $(pwd); do
git -C $DIR config credential.helper "$CREDHELPER"
fi
old_git_hash="$(git -C $DIR rev-parse --verify HEAD)"
if [ -z "$HTTPS_PROXY_FULL_URL" ]; then
if [ -z "$HTTP_PROXY_URL" ]; then
log "INFO" "Git is using no proxy!"
OUT=$(retry 5 git -C $DIR fetch 2>&1 && retry 5 git -C $DIR pull 2>&1)
else
log "INFO" "Git is using proxy ${HTTPS_PROXY_URL} from ${CONFFILE}"
OUT=$(retry 5 git -c http.proxy=$HTTPS_PROXY_FULL_URL -c https.proxy=$HTTPS_PROXY_FULL_URL -C $DIR fetch 2>&1 && retry 5 git -c http.proxy=$HTTPS_PROXY_FULL_URL -c https.proxy=$HTTPS_PROXY_FULL_URL -C $DIR pull 2>&1)
log "INFO" "Git is using proxy ${HTTP_PROXY_URL} from ${CONFFILE}"
OUT=$(retry 5 git -c http.proxy=$HTTP_PROXY_URL -c https.proxy=$HTTPS_PROXY_URL -C $DIR fetch 2>&1 && retry 5 git -c http.proxy=$HTTP_PROXY_URL -c https.proxy=$HTTPS_PROXY_URL -C $DIR pull 2>&1)
fi
if [ $? -ne 0 ]; then
report_error log "Unable to update git $DIR: $OUT"
@ -80,13 +80,19 @@ for DIR in /etc/bridgehead $(pwd); do
log "INFO" "You can review all changes on the repository with $git_repository_url/compare?from=$old_git_hash&to=$new_git_hash"
fi
git_updated="true"
if [ "$DIR" == "/srv/docker/bridgehead" ]; then
git -C "$DIR" checkout main
REPORT_BRANCH_NAME=$(git -C "$DIR" branch --show-current)
REPORT_STATUS_CHECK=$(git -C "$DIR" status --porcelain)
report_error 7 "MAINTENANCE: Switched Branch to main, you are now on branch $REPORT_BRANCH_NAME \n see status \n $REPORT_STATUS_CHECK"
fi
fi
done
# Check docker updates
log "INFO" "Checking for updates to running docker images ..."
docker_updated="false"
for IMAGE in $($COMPOSE -p $PROJECT -f ./minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE config | grep "image:" | sed -e 's_^.*image: \(.*\).*$_\1_g; s_\"__g'); do
for IMAGE in $(cat $PROJECT/docker-compose.yml ${OVERRIDE//-f/} minimal/docker-compose.yml | grep -v "^#" | grep "image:" | sed -e 's_^.*image: \(.*\).*$_\1_g; s_\"__g'); do
log "INFO" "Checking for Updates of Image: $IMAGE"
if docker pull $IMAGE | grep "Downloaded newer image"; then
CHANGE="Image $IMAGE updated."
@ -116,7 +122,7 @@ if [ -n "${BACKUP_DIRECTORY}" ]; then
mkdir -p "$BACKUP_DIRECTORY"
chown -R "$BACKUP_DIRECTORY" bridgehead;
fi
checkOwner "$BACKUP_DIRECTORY" bridgehead || fail_and_report 1 "Automatic maintenance failed: Wrong permissions for backup directory $BACKUP_DIRECTORY"
checkOwner "$BACKUP_DIRECTORY" bridgehead || fail_and_report 1 "Automatic maintenance failed: Wrong permissions for backup directory $(pwd)"
# Collect all container names that contain '-db'
BACKUP_SERVICES="$(docker ps --filter name=-db --format "{{.Names}}" | tr "\n" "\ ")"
log INFO "Performing automatic maintenance: Creating Backups for $BACKUP_SERVICES";

View File

@ -35,20 +35,17 @@ services:
image: docker.verbis.dkfz.de/cache/samply/bridgehead-forward-proxy:latest
environment:
HTTPS_PROXY: ${HTTPS_PROXY_URL}
HTTPS_PROXY_USERNAME: ${HTTPS_PROXY_USERNAME}
HTTPS_PROXY_PASSWORD: ${HTTPS_PROXY_PASSWORD}
USERNAME: ${HTTPS_PROXY_USERNAME}
PASSWORD: ${HTTPS_PROXY_PASSWORD}
tmpfs:
- /var/log/squid
- /var/spool/squid
volumes:
- /etc/bridgehead/trusted-ca-certs:/docker/custom-certs/:ro
healthcheck:
# Wait 1s before marking this service healthy. Required for the oauth2-proxy to talk to the OIDC provider on startup which will fail if the forward proxy is not started yet.
test: ["CMD", "sleep", "1"]
landing:
container_name: bridgehead-landingpage
image: docker.verbis.dkfz.de/cache/samply/bridgehead-landingpage:main
image: docker.verbis.dkfz.de/cache/samply/bridgehead-landingpage:master
labels:
- "traefik.enable=true"
- "traefik.http.routers.landing.rule=PathPrefix(`/`)"
@ -58,3 +55,5 @@ services:
HOST: ${HOST}
PROJECT: ${PROJECT}
SITE_NAME: ${SITE_NAME}

View File

@ -1,2 +0,0 @@
OIDC_USER_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})"
OIDC_ADMIN_GROUP="DKTK_CCP_$(capitalize_first_letter ${SITE_ID})_Verwalter"

View File

@ -1,7 +0,0 @@
OIDC_PRIVATE_CLIENT_ID=${SITE_ID}-private
OIDC_PUBLIC_CLIENT_ID=${SITE_ID}-public
# Use "test-realm-01" for testing
OIDC_REALM="${OIDC_REALM:-master}"
OIDC_URL="https://login.verbis.dkfz.de"
OIDC_ISSUER_URL="${OIDC_URL}/realms/${OIDC_REALM}"
OIDC_GROUP_CLAIM="groups"

View File

@ -18,11 +18,11 @@ services:
- "forward_proxy"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /srv/docker/bridgehead/ccp/root.crt.pem:/conf/root.crt.pem:ro
- /srv/docker/bridgehead/ccp/root-new.crt.pem:/conf/root.crt.pem:ro
dnpm-beam-connect:
depends_on: [ dnpm-beam-proxy ]
image: docker.verbis.dkfz.de/cache/samply/beam-connect:develop
image: docker.verbis.dkfz.de/cache/samply/beam-connect:dnpm
container_name: bridgehead-dnpm-beam-connect
environment:
PROXY_URL: http://dnpm-beam-proxy:8081
@ -32,14 +32,9 @@ services:
LOCAL_TARGETS_FILE: "./conf/connect_targets.json"
HTTP_PROXY: http://forward_proxy:3128
HTTPS_PROXY: http://forward_proxy:3128
NO_PROXY: dnpm-beam-proxy,dnpm-backend, host.docker.internal${DNPM_ADDITIONAL_NO_PROXY}
NO_PROXY: dnpm-beam-proxy,dnpm-backend
RUST_LOG: ${RUST_LOG:-info}
NO_AUTH: "true"
TLS_CA_CERTIFICATES_DIR: ./conf/trusted-ca-certs
extra_hosts:
- "host.docker.internal:host-gateway"
volumes:
- /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro
- /etc/bridgehead/dnpm/local_targets.json:/conf/connect_targets.json:ro
- /etc/bridgehead/dnpm/central_targets.json:/conf/central_targets.json:ro
labels:
@ -50,10 +45,6 @@ services:
- "traefik.http.services.dnpm-connect.loadbalancer.server.port=8062"
- "traefik.http.routers.dnpm-connect.tls=true"
dnpm-echo:
image: docker.verbis.dkfz.de/cache/samply/bridgehead-echo:latest
container_name: bridgehead-dnpm-echo
secrets:
proxy.pem:
file: /etc/bridgehead/pki/${SITE_ID}.priv.pem

View File

@ -1,34 +0,0 @@
version: "3.7"
services:
dnpm-backend:
image: ghcr.io/kohlbacherlab/bwhc-backend:1.0-snapshot-broker-connector
container_name: bridgehead-dnpm-backend
environment:
- ZPM_SITE=${ZPM_SITE}
- N_RANDOM_FILES=${DNPM_SYNTH_NUM}
volumes:
- /etc/bridgehead/dnpm:/bwhc_config:ro
- ${DNPM_DATA_DIR}:/bwhc_data
labels:
- "traefik.enable=true"
- "traefik.http.routers.bwhc-backend.rule=PathPrefix(`/bwhc`)"
- "traefik.http.services.bwhc-backend.loadbalancer.server.port=9000"
- "traefik.http.routers.bwhc-backend.tls=true"
dnpm-frontend:
image: ghcr.io/kohlbacherlab/bwhc-frontend:2209
container_name: bridgehead-dnpm-frontend
links:
- dnpm-backend
environment:
- NUXT_HOST=0.0.0.0
- NUXT_PORT=8080
- BACKEND_PROTOCOL=https
- BACKEND_HOSTNAME=$HOST
- BACKEND_PORT=443
labels:
- "traefik.enable=true"
- "traefik.http.routers.bwhc-frontend.rule=PathPrefix(`/`)"
- "traefik.http.services.bwhc-frontend.loadbalancer.server.port=8080"
- "traefik.http.routers.bwhc-frontend.tls=true"

View File

@ -1,28 +0,0 @@
#!/bin/bash
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"
# Set variables required for BwHC Node. ZPM_SITE is assumed to be set in /etc/bridgehead/<project>.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)"
if [ -z "${ZPM_SITE+x}" ]; then
log ERROR "Mandatory variable ZPM_SITE not defined!"
exit 1
fi
if [ -z "${DNPM_DATA_DIR+x}" ]; then
log ERROR "Mandatory variable DNPM_DATA_DIR not defined!"
exit 1
fi
DNPM_SYNTH_NUM=${DNPM_SYNTH_NUM:-0}
if grep -q 'traefik.http.routers.landing.rule=PathPrefix(`/landing`)' /srv/docker/bridgehead/minimal/docker-compose.override.yml 2>/dev/null; then
echo "Override of landing page url already in place"
else
echo "Adding override of landing page url"
if [ -f /srv/docker/bridgehead/minimal/docker-compose.override.yml ]; then
echo -e ' landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
else
echo -e 'version: "3.7"\nservices:\n landing:\n labels:\n - "traefik.http.routers.landing.rule=PathPrefix(`/landing`)"' >> /srv/docker/bridgehead/minimal/docker-compose.override.yml
fi
fi
fi

View File

@ -5,18 +5,9 @@ if [ -n "${ENABLE_DNPM}" ]; then
OVERRIDE+=" -f ./$PROJECT/modules/dnpm-compose.yml"
# Set variables required for Beam-Connect
DNPM_APPLICATION_SECRET="$(echo \"This is a salt string to generate one consistent password for DNPM. It is not required to be secret.\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
DNPM_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
DNPM_BROKER_ID="broker.ccp-it.dktk.dkfz.de"
DNPM_BROKER_URL="https://${DNPM_BROKER_ID}"
if [ -z ${BROKER_URL_FOR_PREREQ+x} ]; then
BROKER_URL_FOR_PREREQ=$DNPM_BROKER_URL
log DEBUG "No Broker for clock check set; using $DNPM_BROKER_URL"
fi
DNPM_PROXY_ID="${SITE_ID}.${DNPM_BROKER_ID}"
# If the DNPM_NO_PROXY variable is set, prefix it with a comma (as it gets added to a comma separated list)
if [ -n "${DNPM_NO_PROXY}" ]; then
DNPM_ADDITIONAL_NO_PROXY=",${DNPM_NO_PROXY}"
else
DNPM_ADDITIONAL_NO_PROXY=""
fi
fi

View File

@ -1,29 +0,0 @@
version: "3.7"
volumes:
nngm-rest:
services:
connector:
container_name: bridgehead-connector
image: docker.verbis.dkfz.de/ccp/nngm-rest:main
environment:
CTS_MAGICPL_API_KEY: ${NNGM_MAGICPL_APIKEY}
CTS_API_KEY: ${NNGM_CTS_APIKEY}
CRYPT_KEY: ${NNGM_CRYPTKEY}
#CTS_MAGICPL_SITE: ${SITE_ID}TODO
restart: always
labels:
- "traefik.enable=true"
- "traefik.http.routers.connector.rule=PathPrefix(`/nngm-connector`)"
- "traefik.http.middlewares.connector_strip.stripprefix.prefixes=/nngm-connector"
- "traefik.http.services.connector.loadbalancer.server.port=8080"
- "traefik.http.routers.connector.tls=true"
- "traefik.http.routers.connector.middlewares=connector_strip,auth-nngm"
volumes:
- nngm-rest:/var/log
traefik:
labels:
- "traefik.http.middlewares.auth-nngm.basicauth.users=${NNGM_AUTH}"

View File

@ -1,6 +0,0 @@
#!/bin/bash
if [ -n "$NNGM_CTS_APIKEY" ]; then
log INFO "nNGM setup detected -- will start nNGM Connector."
OVERRIDE+=" -f ./$PROJECT/modules/nngm-compose.yml"
fi