some more changes

Singularity

@@ -5,29 +5,24 @@ Stage: spython-base
 %environment
     MONGO_CONNECTION_STRING=mongodb://mongodb:27017/ezbids
     BRAINLIFE_AUTHENTICATION=false
+    SINGULARITY_PWD=/app/api  # Not sure this is being properly set (or at least adhered to)
     PORT=8082
-    export MONGO_CONNECTION_STRING BRAINLIFE_AUTHENTICATION PORT
+    export MONGO_CONNECTION_STRING BRAINLIFE_AUTHENTICATION PORT SINGULARITY_PWD
 
 
 %post
     mkdir -p /app
     cd /app
+
     npm install -g pm2 typescript tsc-watch
     npm install
-
-
-%files
-    . /app
 
-
-%runscript
-    # cd /app
     cd /app/api
-    exec /bin/bash "$@"
+    echo "Current working directory: $PWD"
+    ./dev.sh
 
+%files
+    . /app
 
-%startscript
-    # cd /app
-    cd /app/api
-    exec /bin/bash "$@"
-    ./dev.sh # Need this, right?
+%test
+    # curl -f http://localhost:8082/health

dev.sh

@@ -95,8 +95,8 @@ export SINGULARITY_CACHEDIR=/tmp
 
 # Approach #2: singularity-compose 
 
-# if [ ! -d $PWD/mongodb/data/db ]; then
-#     mkdir -p $PWD/mongodb/data/db
-#     chmod -R 770 $PWD/mongodb/data/db
-# fi
+if [ ! -d $PWD/mongodb/data/db ]; then
+    mkdir -p $PWD/mongodb/data/db
+    chmod -R 770 $PWD/mongodb/data/db
+fi
 singularity-compose --debug up --no-resolv

handler/Singularity

@@ -98,6 +98,7 @@ Stage: spython-base
     npm -g install pm2
 
 %environment
+    export MONGO_CONNECTION_STRING=mongodb://mongodb:27017/ezbids
     export DEBIAN_FRONTEND=noninteractive
     export FSLDIR=/usr/local/fsl
     export PATH=$PATH:$FSLDIR/bin
@@ -110,6 +111,7 @@ Stage: spython-base
 %runscript
     cd /app/handler
     exec /bin/bash "$@"
+    pm2 start handler.js --attach --watch --ignore-watch "ui **/node_modules"
 
 %startscript
     cd /app/handler

mongodb/Singularity

@@ -1,16 +1,12 @@
 Bootstrap: docker
 From: mongo:4.4.15
 
+%setup
+    mkdir -p /data/db
+
 %environment
 export HOME=/data/db
-export PWD=/
-
-%runscript
-    # mongod --dbpath $PWD/data/db
-    cd $HOME
-    exec /usr/bin/mongod "$@"
+export SINGULARITY_PWD=/
 
-%startscript
-    # mongod --dbpath $PWD/data/db
-    cd $HOME
-    exec /usr/bin/mongod "$@"
+%post
+    echo "Current working directory: $PWD"

singularity-compose.yml

@@ -48,52 +48,46 @@ instances:
         volumes:
             - ./mongodb/data/db:/data/db
         ports:
-            - "27417:27017" #for local debugging
-        # start:
-        #     options:
-        #         - fakeroot
+            - 27417:27017 #for local debugging
+        run:
+            options:
+                - fakeroot
+            command: "mongod --dbpath /data/db"
         # run:
-        #     background: true # Does this actually run things in the background? Doesn't seem to
+        #     background: true
 
+    api:  # This seemss good, just needs mongodb up and running properly
+        container_name: brainlife_ezbids-api
+        build:
+          context: .
+          options:
+            - fakeroot
+        platform: linux/amd64
+        volumes:
+            - ./api:/app/api
+            - /tmp:/tmp
+        ports:
+            - 8082:8082 #localhost runs on local browser to it needs to access api via host port
 
-    # api:
-    #     container_name: brainlife_ezbids-api
-    #     build:
-    #       context: .
-    #       options:
-    #         - fakeroot
-    #     platform: linux/amd64
-    #     volumes:
-    #         # - ./api:/app/api
-    #         - .:/app
-    #         - /tmp:/tmp
-    #     # depends_on:
-    #     #     mongodb:
-    #     #         condition: service_healthy
-    #     post:
-    #         command: ["/bin/bash", "./api/dev.sh"] # This seems to cause the npm install to freeze
-    #     ports:
-    #         - 8082:8082 #localhost runs on local browser to it needs to access api via host port
-
-    # handler:
-    #     container_name: brainlife_ezbids-handler
-    #     build:
-    #       context: ./handler
-    #       options:
-    #         - fakeroot
-    #     platform: linux/amd64
-    #     volumes:
-    #         - .:/app
-    #         - /tmp:/tmp
-    #     depends_on:
-    #         mongodb:
-    #             condition: service_healthy
-    #         api:
-    #             condition: service_healthy
-    #     environment:
-    #         MONGO_CONNECTION_STRING: mongodb://mongodb:27017/ezbids
-    #     tty: true #turn on color for bids-validator output
-    #     command: pm2 start handler.js --attach --watch --ignore-watch "ui **/node_modules"
+    handler:
+        container_name: brainlife_ezbids-handler
+        build:
+          context: ./handler
+          options:
+            - fakeroot
+        platform: linux/amd64
+        volumes:
+            - .:/app
+            - /tmp:/tmp
+        # depends_on:
+        #     mongodb:
+        #         condition: service_healthy
+        #     api:
+        #         condition: service_healthy
+        environment:
+            MONGO_CONNECTION_STRING: mongodb://mongodb:27017/ezbids
+        tty: true #turn on color for bids-validator output
+        command: pm2 start handler.js --attach --watch --ignore-watch "ui **/node_modules"
 
     # ui:
     #     container_name: brainlife_ezbids-ui