Migrated TransFAIR start logic from launch file to docker-compose

The start-up logic for TransFAIR is specific to the ECDC/EHDS2 Bridgehead,
and did not belong in the TransFAIR repo. This commit fixes that.

It also honours the change of the TransFAIR branch name for this
project, "ehds2".

README.md

@@ -102,6 +102,12 @@ To get the right Beam certificate for your setup, you will need to edit the foll
 - bbmri/modules/ehds2.root.crt.pem
 - bbmri/modules/ehds2.test.root.crt.pem
 
+You will also need to edit:
+
+./bbmri/modules/ehds2-setup.sh
+
+and set the broker address correctly for your site.
+
 When you first start the Bridgehead, it will clone two extra repositories into /srv/docker, namely, focus and transfair. It will automatically build local images of these repositories for you. These components have the following functionality that has been customized for ECDC:
 
 - *focus.* This component is responsible for completing the CQL that is used for running queries against the Blaze FHIR store. It uses a set of templates for doing this. Extra templates have been written for the ECDC use case.

bbmri/modules/ehds2-compose.yml

@@ -46,26 +46,30 @@ services:
       #WRITE_BUNDLES_TO_FILE: "true"
       AMR_FILE_PATH: "/app/data"
     restart: on-failure
-    #command: sh -c "sleep 60 && rm -rf /app/test/* && ([ ! -f "/app/lock" && ] && java -jar transFAIR.jar && touch "/app/lock) && tail -f /dev/null"
+    # The start up logic for TransFAIR is kind of complicated for the ECDC/EHDS2
-    #command: sh -c "sleep 60 && rm -rf /app/test/* && java -jar transFAIR.jar && tail -f /dev/null"
+    # pilot. This is because we only want to run it if 1. there are source data
-    #command: sh -c "echo listing /app/data && ls -la /app/data && /app/launch.sh"
+    # files to be transformed and 2. if there is no lock file. We also need to
-    #command: sh -c "echo listing /app/data && ls -la /app/data && [ "$(ls -A /app/data)" ] && [ ! -f "/app/data/lock" ] && /app/launch.sh & tail -f /dev/null"
+    # wait for Blaze to start, TransFAIR does not check for this. And finally,
-    #command: sh -c "echo listing /app/data && ls -la /app/data && [ ! -z "$(ls -A /app/data)" ] && [ ! -f "/app/data/lock" ] && /app/launch.sh & tail -f /dev/null"
+    # once TransFAIR has finished loading data, a lock file is created, to stop
-    #command: bash -c "echo listing /app/data && ls -la /app/data && [ ! -z "$(ls -A /app/data)" ] && [ ! -f "/app/data/lock" ] && /app/launch.sh & tail -f /dev/null"
+    # a time-consuming repeat run.
-    #command: bash -c "echo listing /app/data && ls -la /app/data && [ ! -f "/app/data/lock" ] && /app/launch.sh & tail -f /dev/null"
+    command: bash -c " \
-    #command: bash -c "echo listing /app/data && ls -la /app/data && [ ! -z "$(find /app/data -mindepth 1 -maxdepth 1)" ] && [ ! -f "/app/data/lock" ] && /app/launch.sh & tail -f /dev/null"
+             echo listing /app/data && \
-    #command: bash -c "echo listing /app/data && ls -la /app/data && [ ! -z $(ls -A /app/data) ] && [ ! -f /app/data/lock ] && /app/launch.sh & tail -f /dev/null"
+             ls -la /app/data && \
-    #command: bash -c "echo listing /app/data && ls -la /app/data && [ ! -f /app/data/lock ] && /app/launch.sh & tail -f /dev/null" # works!
+             [ -f /app/data/*.[cC][sS][vV] ] && \
-    #command: bash -c "echo listing /app/data && ls -la /app/data && [ ! -z `ls -A /app/data` ] && [ ! -f /app/data/lock ] && /app/launch.sh & tail -f /dev/null"
+             [ ! -f /app/data/lock ] && \
-    #command: bash -c "echo listing /app/data && ls -la /app/data && [ -f /app/data/*.csv ] && [ ! -f /app/data/lock ] && /app/launch.sh & tail -f /dev/null" # works!
+             ( \
-    command: bash -c "echo listing /app/data && ls -la /app/data && [ -f /app/data/*.[cC][sS][vV] ] && [ ! -f /app/data/lock ] && /app/launch.sh & tail -f /dev/null"
+                 echo 'Wait for Blaze to finish initializing' ; \
-    #command: sh -c "echo listing /app/data && ls -la /app/data && [ ! -z $(ls -A /app/data) ] && [ ! -f /app/data/lock ] && /app/launch.sh & tail -f /dev/null"
+                 sleep 60 ; \
-    #command: sh -c "rm -rf /app/test/* && java -jar transFAIR.jar"
+                 echo 'Remove old output files' ; \
+                 rm -rf /app/test/* ; \
+                 cd /app ; \
+                 echo 'Run TransFAIR' ; \
+                 java -jar transFAIR.jar ; \
+                 echo 'Touching lock file' ; \
+                 touch /app/data/lock \
+             ) & tail -f /dev/null"
+    # If you put .csv files into ./../ecdc/data, TransFAIR will try to process them.
     volumes:
-      #- /home/gerhard/Projects/EHDS2/PrototypeSpring2024/test/:/app/test/
-      #- /home/gerhard/Projects/EHDS2/PrototypeSpring2024/Data/:/app/data/
-      #- ../ecdc/test:/app/test/
-      #- ../ecdc/data:/app/data/
       - ../../ecdc/test:/app/test/
       - ../../ecdc/data:/app/data/
 

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 main_ecdc_amt_prototype
+    clone_repo_if_nonexistent https://github.com/samply/transFAIR.git $base_dir/transfair ehds2
 }
 
 function clone_focus_if_nonexistent() {