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bridgehead
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Deal with multiple data files, update repos 

The check for the presence of data in the TransFAIR updating function
only worked for single CSV files. Tis commit corrects that.

Now also do a git pull on the various repos, to keep things up to date.
This commit is contained in:
DavidCroftDKFZ 2024-07-12 11:07:06 +02:00
parent 70aca8e99c
commit 153f654397
2 changed files with 7 additions and 3 deletions
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2
bridgehead
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@ -89,6 +89,8 @@ case "$ACTION" in
loadVars
hc_send log "Bridgehead $PROJECT startup: Checking requirements ..."
checkRequirements
# Note: changes to "bridgehead" script will only take effect after next start.
git pull
# Local versions of focus and transfair are needed by EHDS2
clone_focus_if_nonexistent ${BASE}/..
build_focus ${BASE}/..

8
lib/functions.sh
View File

@ -282,10 +282,11 @@ function build_transfair() {
# We only take the touble to build transfair if:
#
# 1. There is no data lock file (which means that no ETL has yet been run) and
# 2. There is data available.
if [ -f ../ecdc/data/*.[cC][sS][vV] ] && [ ! -f ../ecdc/data/lock ]; then
# 1. There is data available (any CSV files) and
# 2. There is no data lock file (which means that no ETL has yet been run).
if ls ../ecdc/data/*.[cC][sS][vV] 1> /dev/null 2>&1 && [ ! -f ../ecdc/data/lock ]; then
cd $base_dir/transfair
git pull
docker build --progress=plain -t samply/transfair --no-cache .
cd -
fi
@ -295,6 +296,7 @@ function build_focus() {
local base_dir="$1"
cd $base_dir/focus
git pull
docker build --progress=plain -f DockerfileWithBuild -t samply/focus --no-cache .
cd -
}