From 64db5ad5b7522bacd5cbd54293da772429bf8860 Mon Sep 17 00:00:00 2001
From: Yannick Marcon <yannick.marcon@obiba.org>
Date: Wed, 8 May 2024 20:51:19 +0200
Subject: [PATCH] fix: apply the mongo settings properly #10

---
 bin/first_run.sh   | 23 +++++++++++++++++++++++
 bin/start.sh       | 20 +++++++-------------
 docker-compose.yml | 17 +++++++++++------
 3 files changed, 41 insertions(+), 19 deletions(-)

diff --git a/bin/first_run.sh b/bin/first_run.sh
index 1cfcfa3..e145b89 100644
--- a/bin/first_run.sh
+++ b/bin/first_run.sh
@@ -36,6 +36,29 @@ anonympw=$(echo -n $MICA_ANONYMOUS_PASSWORD | xargs java -jar /usr/share/mica2/t
 cat $MICA_HOME/conf/shiro.ini | sed -e "s/^anonymous\s*=.*/anonymous=$anonympw/" > /tmp/shiro.ini && \
     mv /tmp/shiro.ini $MICA_HOME/conf/shiro.ini
 
+# Configure MongoDB
+if [ -n "$MONGODB_URI" ]
+then
+	sed s,localhost:27017/mica,$MONGODB_URI,g $MICA_HOME/conf/application.yml > /tmp/application.yml
+	mv -f /tmp/application.yml $MICA_HOME/conf/application.yml
+elif [ -n "$MONGO_HOST" ]
+	then
+  MGP=27017
+	if [ -n "$MONGO_PORT" ]
+	then
+		MGP=$MONGO_PORT
+	fi
+	MGURI="$MONGO_HOST:$MGP"
+	if [ -n "$MONGO_USER" ] && [ -n "$MONGO_PASSWORD" ]
+	then
+		MGURI="$MONGO_USER:$MONGO_PASSWORD@$MGURI/$MONGO_DB?authSource=admin"
+	else
+		MGURI="$MGURI/$MONGO_DB"
+	fi
+	sed s,localhost:27017/mica,$MGURI,g $MICA_HOME/conf/application.yml > /tmp/application.yml
+	mv -f /tmp/application.yml $MICA_HOME/conf/application.yml
+fi
+
 # Configure Opal
 if [ -n "$OPAL_HOST" ]
 	then
diff --git a/bin/start.sh b/bin/start.sh
index 170a64b..07ed413 100644
--- a/bin/start.sh
+++ b/bin/start.sh
@@ -27,19 +27,13 @@ if [ -e /opt/mica/bin/first_run.sh ]
     mv /opt/mica/bin/first_run.sh /opt/mica/bin/first_run.sh.done
 fi
 
-if [ -z $MONGODB_URI ]
-then
-  #https://docs.spring.io/spring-boot/docs/1.5.6.RELEASE/reference/html/boot-features-external-config.html#boot-features-external-config
-  # According to spring documentation ENV vars have precede before application.yaml properties, so we just set the value instead of fiddling with the yml file
-  if [ -n "$MONGO_USERNAME" ] && [ -n "$MONGO_PASSWORD" ]
-  then
-    export SPRING_DATA_MONGODB_URI=mongodb://$MONGO_USERNAME:$MONGO_PASSWORD@${MONGO_HOST:-mongo}:${MONGO_PORT:-27017}/${MONGO_DB:-mica}?authSource=admin
-  else
-    export SPRING_DATA_MONGODB_URI=mongodb://${MONGO_HOST:-mongo}:${MONGO_PORT:-27017}/${MONGO_DB:-mica}
-  fi
-else
-export SPRING_DATA_MONGODB_URI=$MONGODB_URI
-fi
+# Wait for MongoDB to be ready
+if [ -n "$MONGO_HOST" ]
+	then
+	until curl -i http://$MONGO_HOST:$MONGO_PORT/mica &> /dev/null
+	do
+  		sleep 1
+	done
 
 # Start mica
 /usr/share/mica2/bin/mica2
diff --git a/docker-compose.yml b/docker-compose.yml
index 012246b..1c34bce 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -1,4 +1,3 @@
-version: '3'
 services:
         mica:
                 image: obiba/mica
@@ -13,17 +12,17 @@ services:
                         - MONGO_HOST=mongo
                         - MONGO_PORT=27017
                         - MONGO_DB=mica
-#                       - MONGO_USERNAME=mica
-#                       - MONGO_PASSWORD=${MICA_ADMINISTRATOR_PASSWORD}
+                        - MONGO_USER=${MONGO_USER:-obiba}
+                        - MONGO_PASSWORD=${MONGO_PASSWORD:-password}
                         - OPAL_URL=http://opal:8080
                         - AGATE_URL=http://agate:8081
                 volumes:
                         - /tmp/mica:/srv
         mongo:
                 image: mongo:6.0
-#                environment:
-#                        - MONGO_INITDB_ROOT_USERNAME=mica
-#                        - MONGO_INITDB_ROOT_PASSWORD=${MICA_ADMINISTRATOR_PASSWORD}
+                environment:
+                        - MONGO_INITDB_ROOT_USERNAME=${MONGO_USER:-obiba}
+                        - MONGO_INITDB_ROOT_PASSWORD=${MONGO_PASSWORD:-password}
         opal:
                 image: obiba/opal
                 ports:
@@ -34,6 +33,9 @@ services:
                         - OPAL_ADMINISTRATOR_PASSWORD=password
                         - MONGO_HOST=mongo
                         - MONGO_PORT=27017
+                        - MONGO_USER=${MONGO_USER:-obiba}
+                        - MONGO_PASSWORD=${MONGO_PASSWORD:-password}
+                        - MONGODATA_DATABASE=opal
                         - AGATE_URL=http://agate:8081
                 volumes:
                         - /tmp/opal:/srv
@@ -47,6 +49,9 @@ services:
                         - AGATE_ADMINISTRATOR_PASSWORD=password
                         - MONGO_HOST=mongo
                         - MONGO_PORT=27017
+                        - MONGO_DB=agate
+                        - MONGO_USER=${MONGO_USER:-obiba}
+                        - MONGO_PASSWORD=${MONGO_PASSWORD:-password}
                         - RECAPTCHA_SITE_KEY=6Lfo7gYTAAAAAOyl8_MHuH-AVBzRDtpIuJrjL3Pb
                         - RECAPTCHA_SECRET_KEY=6Lfo7gYTAAAAADym-vSDvPBeBCXaxIprA0QXLk_b
                 volumes: