code cleanup

Singularity

@@ -3,12 +3,10 @@ From: node:16
 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 SINGULARITY_PWD
-
+    export MONGO_CONNECTION_STRING=mongodb://mongodb:27017/ezbids
+    export BRAINLIFE_AUTHENTICATION=false
+    export SINGULARITY_PWD=/app/api  # Not sure this is being properly set (or at least adhered to)
+    export PORT=8082
 
 %post
     mkdir -p /app

dev.sh

@@ -39,35 +39,52 @@ npm run prepare-husky
 export SINGULARITY_DISABLE_CACHE=true
 export SINGULARITY_CACHEDIR=/tmp
 
-# Approach #1: singularity (individual .sif files)
+# # Approach #1: singularity (individual .sif files)
 
 # # Helpful commentary on mongodb container build with Singularity: https://stackoverflow.com/questions/70746228/singularity-mongodb-container-in-background-mode
-# if [ ! -d $PWD/mongodb/data/db ]; then
-#   mkdir -p $PWD/mongodb/data/db
-#   chmod -R 770 $PWD/mongodb/data/db
+# # 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 ]; then
+#   mkdir -p $PWD/mongodb/data
+#   chmod -R 770 $PWD/mongodb/data
 # fi
 
+
 # if [ ! -f $PWD/mongodb/mongodb.sif ]; then # Will eventually be redundant and can remove
-#     echo "building mongodb"
 #     # build image
-#     singularity build           \
+#     singularity build      \
 #       --arch "amd64"            \
 #       --fakeroot                \
 #       --disable-cache           \
 #       $PWD/mongodb/mongodb.sif  \
 #       $PWD/mongodb/Singularity
 
-#     # start the container instance
-#     singularity instance start  \
-#       --fakeroot                \
-#       --bind $PWD/mongodb/data/db:/data/db \
-#       $PWD/mongodb/mongodb.sif  \
-#       brainlife_ezbids-mongodb
+#     # # start the container instance
+#     # singularity instance start                  \
+#     #   --fakeroot                                \
+#     #   --bind $PWD/mongodb/data:/data/db         \
+#     #   --net                                     \
+#     #   --network-args "portmap=27417:27017/tcp"  \
+#     #   --network-args "IP=0.0.0.0"               \
+#     #   $PWD/mongodb/mongodb.sif                  \
+#     #   brainlife_ezbids-mongodb
+
+#     # run the container instance
+#     singularity run                        \
+#       --fakeroot                                \
+#       --bind $PWD/mongodb/data:/data/db         \
+#       --net                                     \
+#       --network-args "portmap=27417:27017/tcp"  \
+#       $PWD/mongodb/mongodb.sif
+
+#       # --network-args "IP=127.0.0.1"             \
+#       # --hostname brainlife_ezbids-mongodb       \
+
+#     # DEBUG singularity instance start --bind /home/ubuntu/dlevitas/brainlife/ezbids/mongodb/data:/data/db --net --network-args "portmap=27417:27017/tcp" --network-args "IP=10.22.0.2" --hostname mongodb1 --writable-tmpfs /home/ubuntu/dlevitas/brainlife/ezbids/mongodb/mongodb.sif mongodb1 
 
-
-#       # --net \
-#       # --network-args "portmap=27417:27017/tcp"  \
-#       # --bind $PWD/data/db:/data/db \  # Might not need this if mongodb/Singularity contains a %files section
 #     # singularity run instance://brainlife_ezbids-mongodb # This seems to run mongodb in the foreground, meaning can't move on to building other containers.
 # fi
 
@@ -95,9 +112,9 @@ 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 down
 singularity-compose --debug up --no-resolv

mongodb/Singularity

@@ -2,11 +2,21 @@ Bootstrap: docker
 From: mongo:4.4.15
 
 %setup
-    mkdir -p /data/db
+    # mkdir -p /data/db
+    if [ ! -d $PWD/data ]; then
+        mkdir -p $PWD/data
+    fi
+    echo "Setup working directory: $PWD"
 
 %environment
 export HOME=/data/db
 export SINGULARITY_PWD=/
 
 %post
     echo "Current working directory: $PWD"
+
+%runscript # Unsure if this section is necessary (doesn't seem like it)
+    exec /usr/bin/mongod "$@"
+
+%startscript # Unsure if this section is necessary (doesn't seem like it)
+    exec /usr/bin/mongod "$@"

singularity-compose.yml

@@ -1,109 +1,73 @@
 version: "2.0"
 
 instances:
-    # mongodb: # ORIGINAL
-    #     container_name: brainlife_ezbids-mongodb
-    #     image: docker://mongo:4.4.15
-    #     platform: linux/amd64
-    #     volumes:
-    #         - /tmp:/tmp
-    #     ports:
-    #         - 27417:27017 #for local debugging
-    #     post:
-    #         command:
-    #             - "mongod --dbpath /tmp"
-
-    # mongodb:  # NEW BUT STILL BAD
-    #     container_name: brainlife_ezbids-mongodb
-    #     build:
-    #         context: ./mongodb
-    #         options:
-    #             - fakeroot
-    #     platform: linux/amd64
-    #     # volumes:
-    #     #     - ./data/db:/data/db
-    #     post:
-    #         command: [ "/bin/bash", "./mongodb/mongodb_setup.sh"]
-    #     ports:
-    #         - 27417:27017 #for local debugging
-
-    # mongodb:  # THIRD ATTEMPT
-    #     container_name: brainlife_ezbids-mongodb
-    #     image: docker://mongo:4.4.15
-    #     platform: linux/amd64
-    #     volumes:
-    #         - ./data/db:/data/db
-    #     ports:
-    #         - 27417:27017 #for local debugging
-    #     # run:
-    #     #     background: true # Does this actually run things in the background? Doesn't seem to
-
-    mongodb:  # FOURTH ATTEMPT
+    mongodb:
         container_name: brainlife_ezbids-mongodb
         build:
             context: ./mongodb
             options:
                 - fakeroot
         platform: linux/amd64
         volumes:
-            - ./mongodb/data/db:/data/db
+            - ./mongodb/data:/data/db
         network:
             options:
                 - fakeroot
-            # enable: true
-            # allocate_ip: true
+            enable: true
+            allocate_ip: true
             args:
                 - portmap=27417:27017/tcp
                 - IP=127.0.0.1
         ports:
-            - 27417:27017 #for local debugging
+            - 27417:27017 # for local debugging
         run:  # start results in errors
+            background: true
             options:
                 - fakeroot
-            command: mongod --dbpath /data/db
+            command: mongod --dbpath /data/db --port=27017 # command: mongod --dbpath /data/db --bind_ip_all --logpath /data/db/mongod.log --fork
 
-    # 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:  # 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
 
-    # 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
-    #     # tty: true #turn on color for bids-validator output
-    #     run:
-    #         options:
-    #             - fakeroot
-    #            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
+        # tty: true # don't think this works with Singularity
+        run:
+            options:
+                - fakeroot
+            command: pm2 start handler.js --attach --watch --ignore-watch "ui **/node_modules"
 
-    # ui:
-    #     container_name: brainlife_ezbids-ui
-    #     build:
-    #       context: ./ui
-    #       options:
-    #         - fakeroot
-    #     platform: linux/amd64
-    #     volumes:
-    #         - ./ui/src:/ui/src #don't copy node_modules which might be compiled for mac (vite won't work)
-    #     ports:
-    #         - 3000:3000 #vite wants to be exposed on the host for HMR?
+    ui:
+        container_name: brainlife_ezbids-ui
+        build:
+          context: ./ui
+          options:
+            - fakeroot
+        platform: linux/amd64
+        volumes:
+            - ./ui/src:/ui/src # don't copy node_modules which might be compiled for mac (vite won't work)
+        ports:
+            - 3000:3000 # vite wants to be exposed on the host for HMR?