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bridgehead
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Improved docker-compose for transFAIR 

In particular, corrected the code for detecting CSV files in the data directory.
The old code could not handle more than one CSV file.
This commit is contained in:
Gerhard Salvini 2024-06-18 15:28:37 +02:00
parent 53cdd49fd7
commit e309dc495a
2 changed files with 4 additions and 4 deletions
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6
bbmri/modules/ehds2-compose.yml
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@ -56,11 +56,11 @@ services:
command: bash -c " \ command: bash -c " \
echo listing /app/data && \ echo listing /app/data && \
ls -la /app/data && \ ls -la /app/data && \
[ -f /app/data/*.[cC][sS][vV] ] && \ ls /app/data/*.[cC][sS][vV] 1> /dev/null 2>&1 && \
[ ! -f /app/data/lock ] && \ [ ! -f /app/data/lock ] && \
( \ ( \
echo 'Wait for Blaze to finish initializing' ; \ echo 'Wait for Blaze to finish initializing' ; \
sleep 60 ; \ sleep 300 ; \
echo 'Remove old output files' ; \ echo 'Remove old output files' ; \
rm -rf /app/test/* ; \ rm -rf /app/test/* ; \
cd /app ; \ cd /app ; \
@ -78,5 +78,5 @@ services:
test-data-loader: test-data-loader:
container_name: test-data-loader container_name: test-data-loader
image: samply/test-data-loader image: samply/test-data-loader
command: sh -c "sleep 300 && echo Listing all resources in FHIR store && blazectl --server http://bridgehead-bbmri-blaze:8080/fhir count-resources && tail -f /dev/null" command: sh -c "sleep 400 && echo Listing all resources in FHIR store && blazectl --server http://bridgehead-bbmri-blaze:8080/fhir count-resources && tail -f /dev/null"

2
lib/functions.sh
View File

@ -267,7 +267,7 @@ function clone_repo_if_nonexistent() {
function clone_transfair_if_nonexistent() { function clone_transfair_if_nonexistent() {
local base_dir="$1" local base_dir="$1"
clone_repo_if_nonexistent https://github.com/samply/transFAIR.git $base_dir/transfair ehds2 clone_repo_if_nonexistent https://github.com/samply/transFAIR.git $base_dir/transfair ehds2_develop
} }
function clone_focus_if_nonexistent() { function clone_focus_if_nonexistent() {