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feat: use project overarching vars #239

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4446f9b
feat: use project overarching vars
Oct 15, 2024
022d6e9
to squash
Oct 15, 2024
2b391a5
minor fix
Oct 15, 2024
5f5e626
minor fix
Oct 15, 2024
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2 changes: 1 addition & 1 deletion bbmri/docker-compose.yml
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Expand Up @@ -4,7 +4,7 @@ version: "3.7"

services:
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-bbmri-blaze
environment:
BASE_URL: "http://bridgehead-bbmri-blaze:8080"
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1 change: 1 addition & 0 deletions bbmri/vars
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Expand Up @@ -7,6 +7,7 @@
FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem

source vars
for module in $PROJECT/modules/*.sh
do
log DEBUG "sourcing $module"
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2 changes: 1 addition & 1 deletion bridgehead
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Expand Up @@ -64,7 +64,7 @@ loadVars() {
fetchVarsFromVaultByFile /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "Unable to fetchVarsFromVaultByFile"
setHostname
optimizeBlazeMemoryUsage
[ -e ./$PROJECT/vars ] && source ./$PROJECT/vars
[ -e ./$PROJECT/vars ] && source ./$PROJECT/vars ./vars
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TKussel marked this conversation as resolved.
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@Threated Threated Oct 15, 2024 •
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I think the source of ./vars should happen before the more specific project vars so that they can override the default and get set regardless of project vars existing or not

set +a

OVERRIDE=${OVERRIDE:=""}
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2 changes: 1 addition & 1 deletion cce/docker-compose.yml
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Expand Up @@ -2,7 +2,7 @@ version: "3.7"

services:
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-cce-blaze
environment:
BASE_URL: "http://bridgehead-cce-blaze:8080"
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1 change: 1 addition & 0 deletions cce/vars
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Expand Up @@ -7,6 +7,7 @@ SUPPORT_EMAIL=manoj.waikar@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BROKER_URL_FOR_PREREQ=$BROKER_URL

source vars
for module in $PROJECT/modules/*.sh
do
log DEBUG "sourcing $module"
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2 changes: 1 addition & 1 deletion ccp/docker-compose.yml
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Expand Up @@ -2,7 +2,7 @@ version: "3.7"

services:
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-ccp-blaze
environment:
BASE_URL: "http://bridgehead-ccp-blaze:8080"
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5 changes: 3 additions & 2 deletions ccp/modules/blaze-secondary-compose.yml
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Expand Up @@ -2,13 +2,14 @@ version: "3.7"

services:
blaze-secondary:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-ccp-blaze-secondary
environment:
BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080"
JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
ENFORCE_REFERENTIAL_INTEGRITY: "false"
volumes:
- "blaze-secondary-data:/app/data"
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3 changes: 1 addition & 2 deletions ccp/vars
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Expand Up @@ -18,8 +18,7 @@ OIDC_URL="https://login.verbis.dkfz.de"
OIDC_ISSUER_URL="${OIDC_URL}/realms/${OIDC_REALM}"
OIDC_GROUP_CLAIM="groups"

POSTGRES_TAG=15.6-alpine

source vars
for module in $PROJECT/modules/*.sh
do
log DEBUG "sourcing $module"
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4 changes: 2 additions & 2 deletions dhki/docker-compose.yml
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Expand Up @@ -2,7 +2,7 @@ version: "3.7"

services:
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-dhki-blaze
environment:
BASE_URL: "http://bridgehead-dhki-blaze:8080"
Expand Down Expand Up @@ -39,7 +39,7 @@ services:
- "blaze"

beam-proxy:
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
container_name: bridgehead-beam-proxy
environment:
BROKER_URL: ${BROKER_URL}
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3 changes: 1 addition & 2 deletions dhki/vars
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Expand Up @@ -8,8 +8,7 @@ PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem

BROKER_URL_FOR_PREREQ=$BROKER_URL

POSTGRES_TAG=15.6-alpine

source vars
for module in ccp/modules/*.sh
do
log DEBUG "sourcing $module"
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2 changes: 1 addition & 1 deletion itcc/docker-compose.yml
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Expand Up @@ -2,7 +2,7 @@ version: "3.7"

services:
blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-itcc-blaze
environment:
BASE_URL: "http://bridgehead-itcc-blaze:8080"
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1 change: 1 addition & 0 deletions itcc/vars
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Expand Up @@ -7,6 +7,7 @@ SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BROKER_URL_FOR_PREREQ=$BROKER_URL

source vars
for module in $PROJECT/modules/*.sh
do
log DEBUG "sourcing $module"
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4 changes: 2 additions & 2 deletions kr/docker-compose.yml
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Expand Up @@ -6,7 +6,7 @@ services:
replicas: 0 #deactivate landing page

blaze:
image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
container_name: bridgehead-kr-blaze
environment:
BASE_URL: "http://bridgehead-kr-blaze:8080"
Expand Down Expand Up @@ -40,7 +40,7 @@ services:
- "blaze"

beam-proxy:
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
container_name: bridgehead-beam-proxy
environment:
BROKER_URL: ${BROKER_URL}
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15 changes: 0 additions & 15 deletions kr/modules/exporter.md
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This file was deleted.

19 changes: 0 additions & 19 deletions kr/modules/teiler.md
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This file was deleted.

1 change: 1 addition & 0 deletions kr/vars
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
BROKER_URL_FOR_PREREQ=$BROKER_URL

source vars
for module in $PROJECT/modules/*.sh
do
log DEBUG "sourcing $module"
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6 changes: 3 additions & 3 deletions lib/functions.sh
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Expand Up @@ -170,11 +170,11 @@ optimizeBlazeMemoryUsage() {
available_system_memory_chunks=$((BLAZE_MEMORY_CAP / 1000))
if [ $available_system_memory_chunks -eq 0 ]; then
log WARN "Only ${BLAZE_MEMORY_CAP} system memory available for Blaze. If your Blaze stores more than 128000 fhir ressources it will run significally slower."
export BLAZE_RESOURCE_CACHE_CAP=128000;
export BLAZE_CQL_CACHE_CAP=32;
export BLAZE_RESOURCE_CACHE_CAP=128000
export BLAZE_CQL_CACHE_CAP=32
else
export BLAZE_RESOURCE_CACHE_CAP=$((available_system_memory_chunks * 312500))
export BLAZE_CQL_CACHE_CAP=$((($system_memory_in_mb/4)/16));
export BLAZE_CQL_CACHE_CAP=$((($system_memory_in_mb/4)/16))
fi
fi
}
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6 changes: 3 additions & 3 deletions lib/prepare-system.sh
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Expand Up @@ -57,9 +57,9 @@ case "$PROJECT" in
;;
itcc)
site_configuration_repository_middle="git.verbis.dkfz.de/itcc-sites/"
;;
dhki)
site_configuration_repository_middle="git.verbis.dkfz.de/dhki/"
;;
dhki)
site_configuration_repository_middle="git.verbis.dkfz.de/dhki/"
;;
kr)
site_configuration_repository_middle="git.verbis.dkfz.de/krebsregister-sites/"
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2 changes: 1 addition & 1 deletion lib/prerequisites.sh
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Expand Up @@ -67,7 +67,7 @@ fi
log INFO "Checking network access ($BROKER_URL_FOR_PREREQ) ..."

source "${CONFIG_DIR}${PROJECT}".conf
source ${PROJECT}/vars
source ${PROJECT}/vars vars

if [ "${PROJECT}" != "minimal" ]; then
set +e
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2 changes: 2 additions & 0 deletions minimal/vars
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@@ -1,3 +1,5 @@

source vars
for module in $PROJECT/modules/*.sh
do
log DEBUG "sourcing $module"
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2 changes: 2 additions & 0 deletions vars
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@TKussel TKussel Oct 15, 2024

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BEAM_TAG is missing?

@PierreDelpy PierreDelpy Oct 15, 2024

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BEAM_TAG gets exported here https://github.com/samply/bridgehead/blob/develop/bridgehead#L90

@TKussel TKussel Oct 15, 2024

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I'm not too happy about having different places where the tags are set, but we can tackle that in the future as it touches the Environment topic.

Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
BLAZE_TAG=0.28
POSTGRES_TAG=15.6-alpine