From e309dc495ae9d363a371038634b238d4df27e01c Mon Sep 17 00:00:00 2001 From: Gerhard Salvini Date: Tue, 18 Jun 2024 15:28:37 +0200 Subject: [PATCH] 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. --- bbmri/modules/ehds2-compose.yml | 6 +++--- lib/functions.sh | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/bbmri/modules/ehds2-compose.yml b/bbmri/modules/ehds2-compose.yml index 1af183d..bd717bb 100644 --- a/bbmri/modules/ehds2-compose.yml +++ b/bbmri/modules/ehds2-compose.yml @@ -56,11 +56,11 @@ services: command: bash -c " \ echo listing /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 ] && \ ( \ echo 'Wait for Blaze to finish initializing' ; \ - sleep 60 ; \ + sleep 300 ; \ echo 'Remove old output files' ; \ rm -rf /app/test/* ; \ cd /app ; \ @@ -78,5 +78,5 @@ services: test-data-loader: container_name: 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" diff --git a/lib/functions.sh b/lib/functions.sh index 03b6868..b4a8c9b 100644 --- a/lib/functions.sh +++ b/lib/functions.sh @@ -267,7 +267,7 @@ function clone_repo_if_nonexistent() { function clone_transfair_if_nonexistent() { 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() {