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12 Commits

Author SHA1 Message Date
Torben Brenner
70df0cded0 fix: use RECEIVER_PROXY_ID instead of $1 2025-09-09 08:43:04 +02:00
Torben Brenner
f17ff3fcd8 fix: added missing -f arg 2025-09-09 08:43:04 +02:00
Torben Brenner
c23ef2f251 fix: don't attach to network use project instead 2025-09-09 08:43:04 +02:00
Torben Brenner
4b4dab0fec fix: add beam-send to project network 2025-09-09 08:43:04 +02:00
Torben Brenner
7717b0c528 fix: make a persistent send secret per bridgehead 2025-09-09 08:43:04 +02:00
Torben Brenner
6195f698dc refactor: beam file send is only an executable command 2025-09-09 08:43:04 +02:00
Torben Brenner
b64d848760 feat: added commands for beam-file send mode 2025-09-09 08:43:04 +02:00
Torben Brenner
ae738aa98f fix: pass outdir path as separate token 2025-09-09 08:43:04 +02:00
Torben Brenner
efb381246f fix: added quotes to data directory option 2025-09-09 08:43:04 +02:00
Torben Brenner
3d336bf233 fix: now properly reading variables for the check 2025-09-09 08:43:04 +02:00
Torben Brenner
c9a6a03628 prototype: module for beam-file 2025-09-09 08:42:53 +02:00
Tim Schumacher
8a35785a24 feat: add scout module (#339) 2025-09-02 13:23:34 +02:00
8 changed files with 108 additions and 2 deletions

View File

@@ -176,6 +176,13 @@ case "$ACTION" in
;;
postRun | postUpdate)
;;
send-file)
loadVars
log "WARNING" "Your are about to send a file to another bridgehead in your network!"
read -p "Please name the bridgehead you want to send the file to (proxy-id): " RECEIVER_PROXY_ID
read -p "Continue? (Y/N): " confirm && [[ $confirm == [yY] || $confirm == [yY][eE][sS] ]] || exit 1
exec $COMPOSE -p $PROJECT -f ./modules/beam-file-compose.yml --profile beam-file-sender run beam-file-sender send --to beamfile.$RECEIVER_PROXY_ID /data/outfile
;;
*)
printUsage
exit 1

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@@ -45,6 +45,7 @@ services:
BROKER_URL: ${BROKER_URL}
PROXY_ID: ${PROXY_ID}
APP_focus_KEY: ${FOCUS_BEAM_SECRET_SHORT}
APP_beamfilesend_KEY: ${BEAM_FILE_SEND_SECRET}
PRIVKEY_FILE: /run/secrets/proxy.pem
ALL_PROXY: http://forward_proxy:3128
TLS_CA_CERTIFICATES_DIR: /conf/trusted-ca-certs

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@@ -5,6 +5,7 @@ FOCUS_BEAM_SECRET_SHORT="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | h
FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
SUPPORT_EMAIL=support-ccp@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BEAM_FILE_SEND_SECRET="$(echo \"beam-file-send-salt\" | openssl pkeyutl -sign -inkey /etc/bridgehead/pki/${SITE_ID}.priv.pem | base64 | head -c 30)"
BROKER_URL_FOR_PREREQ=$BROKER_URL
@@ -23,4 +24,6 @@ do
source $module
done
transfairSetup
transfairSetup
scoutSetup
beamFileSetup

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@@ -0,0 +1,35 @@
# NOTE: Current implementation is restricted to a bridgehead only being able to either upload or download data
services:
beam-file-sender:
image: samply/beam-file:${BEAM_FILE_TAG}
container_name: bridgehead-beam-file-sender
environment:
- BEAM_ID=beamfilesend.${PROXY_ID}
- BEAM_SECRET=${BEAM_FILE_SEND_SECRET}
- BEAM_URL=http://beam-proxy:8081
- BIND_ADDR=0.0.0.0:8085
- API_KEY=${BEAM_FILE_API_KEY}
# Only uncomment if your are sure what to do
# ports:
# - 8085:8085
volumes:
- /var/cache/bridgehead/beam-file-out/:/data
profiles: ["beam-file-sender"]
beam-file-receiver:
image: samply/beam-file:${BEAM_FILE_TAG}
container_name: bridgehead-beam-file-receiver
environment:
- BEAM_ID=beamfile.${PROXY_ID}
- BEAM_SECRET=${BEAM_FILE_SECRET}
- BEAM_URL=http://beam-proxy:8081
- API_KEY=${BEAM_FILE_API_KEY}
command: ["receive", "save", "--outdir", "/data"]
volumes:
- /var/cache/bridgehead/beam-file/:/data
profiles: ["beam-file-receiver"]
beam-proxy:
environment:
APP_beamfile_KEY: ${BEAM_FILE_SECRET}
profiles: ["beam-file-receiver"]

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@@ -0,0 +1,11 @@
#!/bin/bash -e
function beamFileSetup() {
if [ -n "$ENABLE_BEAM_FILE_RECEIVER" ]; then
echo "Starting beam file in receiver mode"
OVERRIDE+=" -f ./modules/beam-file-compose.yml --profile beam-file-receiver"
BEAM_FILE_SECRET="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
BEAM_FILE_API_KEY="$(cat /proc/sys/kernel/random/uuid | sed 's/[-]//g' | head -c 20)"
log INFO "Beam File in Receiver Mode available uses ApiKey ${BEAM_FILE_API_KEY}"
fi
}

40
modules/scout-compose.yml Normal file
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@@ -0,0 +1,40 @@
volumes:
scout-blaze-data:
services:
traefik:
labels:
- "traefik.http.middlewares.additional-users-auth.basicauth.users=${SCOUT_BASIC_AUTH_USERS}"
scout-blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-scout-blaze
environment:
BASE_URL: "http://bridgehead-scout-blaze:8080"
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "scout-blaze-data:/app/data"
labels:
- "traefik.enable=true"
- "traefik.http.routers.scout-blaze.rule=PathPrefix(`/scout-blaze`)"
- "traefik.http.middlewares.scout-blaze-stripprefix.stripprefix.prefixes=/scout-blaze"
- "traefik.http.services.scout-blaze.loadbalancer.server.port=8080"
- "traefik.http.routers.scout-blaze.middlewares=scout-blaze-stripprefix,additional-users-auth"
- "traefik.http.routers.scout-blaze.tls=true"
scout:
image: samply/scout:main
container_name: bridgehead-scout
configs:
- scout.toml
labels:
- "traefik.enable=true"
- "traefik.http.routers.scout.rule=PathPrefix(`/scout`)"
- "traefik.http.services.scout.loadbalancer.server.port=8080"
- "traefik.http.routers.scout.middlewares=additional-users-auth"
- "traefik.http.routers.scout.tls=true"
configs:
scout.toml:
content: |
fhir_base_url = "http://scout-blaze:8080/fhir"

8
modules/scout-setup.sh Normal file
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@@ -0,0 +1,8 @@
#!/bin/bash -e
function scoutSetup() {
if [[ -n "$ENABLE_SCOUT" && -n "$SCOUT_BASIC_AUTH_USERS" ]]; then
echo "Starting scout."
OVERRIDE+=" -f ./modules/scout-compose.yml"
fi
}

View File

@@ -3,4 +3,5 @@ BEAM_TAG=develop
BLAZE_TAG=main
POSTGRES_TAG=15.13-alpine
TEILER_DASHBOARD_TAG=develop
MTBA_TAG=develop
MTBA_TAG=develop
BEAM_FILE_TAG=task-based-files