add updated 'start_up.sh' script for streamline-emr docker image

This modified script replaces adds a wait condition on startup before attempting
to interact with the database. This is done with 'mariadb-admin ping' run in a
loop at 1s intervals, ultimately timing out after 30s if unsuccessful. Other
minor updates to the script print additional info the docker logs during
startup.

docker/Dockerfile.streamline-emr.arm64

@@ -1 +1,2 @@
 FROM streamlinehealth/streamline:signalytic
+COPY ./start_up.sh /var/www/html/start_up.sh

docker/start_up.sh

@@ -0,0 +1,84 @@
+#! /bin/sh
+
+# Required script variables 
+APP_NAME=${APP_NAME:-'streamline'}
+export MYSQL_DATABASE=${DB_DATABASE:-'streamline'}
+export MYSQL_USER=${DB_USERNAME:-'root'}
+export MYSQL_PASSWORD=${DB_PASSWORD:-'streamline'}
+export MYSQL_ROOT_PASSWORD=${DB_ROOT_PASSWORD:-'streamline'}
+
+# execute run.sh script for MySQL initialisation
+chmod +x .docker/mysql/mysql-init.sh
+
+# run the MariaDB initialization script
+echo "[info] running mariadb init script"
+./.docker/mysql/mysql-init.sh
+
+if [ $? -eq 0 ]; then
+
+    echo "[info] waiting for DB to start..."
+    for i in $(seq 1 30); do
+        mariadb-admin ping -u $MYSQL_USER -p$MYSQL_PASSWORD &>/dev/null
+        if [ $? -eq 0 ]; then
+          echo "[info] DB ready"
+          break
+        fi
+        sleep 1
+    done
+    mariadb-admin ping -u $MYSQL_USER -p$MYSQL_PASSWORD
+    if [ $? -ne 0 ]; then
+      echo "[info] timed out waiting for DB"
+      exit 1
+    fi
+
+    echo "[info] MySQL server started. checking for '$MYSQL_DATABASE' database. "
+
+    mysql -u $MYSQL_USER -p$MYSQL_PASSWORD -e "use streamline;"
+
+    # Guard condition to re-check existence of database schema
+    # If it doesnt exist, create it and import streamline_initial.sql file
+    if [ $? -eq 1 ]; then
+
+        mysql -u $MYSQL_USER -p$MYSQL_PASSWORD -e "CREATE DATABASE $MYSQL_DATABASE;"
+
+        if [ $? -eq 0 ]; then
+            echo "[info] Database: $MYSQL_DATABASE created."
+
+            mysql -u $MYSQL_USER -p$MYSQL_PASSWORD $MYSQL_DATABASE < ./.docker/mysql/scripts/streamline_initial.sql
+            if [ $? -eq 0 ]; then
+                echo "[info] populated database."
+            else
+                echo "[error] database not populated."
+            fi
+
+        else
+            echo "[error] database not created."
+        fi
+
+    else
+        echo "[info] Database: $MYSQL_DATABASE exists. "
+    fi
+
+    echo "[info] starting $APP_NAME ..."
+
+    echo "[info] artisan migrate"
+    php /var/www/html/artisan migrate
+    echo "[info] migrate result: $?"
+
+    echo "[info] seed: PermissionTableSeeder"
+    php /var/www/html/artisan db:seed --class=PermissionTableSeeder
+    echo "[info] seed result: $?"
+
+    echo "[info] seed: PermissionsCategoryTableSeeder"
+    php /var/www/html/artisan db:seed --class=PermissionsCategoryTableSeeder
+    echo "[info] seed result: $?"
+
+    echo "serving app..."
+    php /var/www/html/artisan serve --host=0.0.0.0 --port=80
+
+else
+    echo "[error] MariaDB server couldnt be started."
+
+    # terminate script if database isnt running
+    exit 1;
+fi