fix: resolve DB bootstrap issues on fresh installations

.env

@@ -3,6 +3,10 @@ DATABASE_PORT=3306
 MYSQL_ROOT_PASSWORD=password
 DATABASE_NAME=specify
 
+# This allows for a destructive reset of the database if it is not empty but contains no legacy Specify schema.
+# For production environments, it is recommended to set this to false to prevent accidental data loss.
+ALLOW_DB_RESET=false
+
 # The following are database users with specific roles and privileges. 
 # If the migrator and app user are not defined, the system will use the master user credentials.
 # See documenation https://discourse.specifysoftware.org/t/new-blank-database-creation-database-user-levels/3023

docker-compose.yml

@@ -25,8 +25,6 @@ services:
     environment:
       - MYSQL_ROOT_PASSWORD=${MYSQL_ROOT_PASSWORD}
       - MYSQL_DATABASE=${DATABASE_NAME}
-      - MYSQL_USER=${MASTER_NAME}
-      - MYSQL_PASSWORD=${MASTER_PASSWORD}
 
   specify7:
     container_name: specify7
@@ -35,7 +33,6 @@ services:
       target: run-development
     command: ve/bin/python manage.py runserver 0.0.0.0:8000
     init: true
-    restart: unless-stopped
     depends_on:
       # It seems like there was a race condition on the the
       # webpack-output volume. I suspect if this container mounts it

docker-entrypoint.sh

@@ -9,11 +9,13 @@ if [ "$1" = 've/bin/gunicorn' ] || [ "$1" = 've/bin/python' ]; then
   rsync -a --delete specifyweb/frontend/static/ /volumes/static-files/frontend-static
   cd /opt/specify7
   echo "Applying Django migrations."
-  set +e
-  ./sp7_db_setup_check.sh # Setup db users and run mirgations
-  # ve/bin/python manage.py base_specify_migration
-  # ve/bin/python manage.py migrate
-  ve/bin/python manage.py run_key_migration_functions # Uncomment if you want the key migration functions to run on startup.
-  set -e
+  if ./sp7_db_setup_check.sh; then
+    # sp7_db_setup_check.sh intentionally runs manage.py base_specify_migration and manage.py migrate;
+    # only manage.py run_key_migration_functions is invoked here afterward.
+    ve/bin/python manage.py run_key_migration_functions # Runs after sp7_db_setup_check.sh succeeds.
+  else
+    echo "Database setup failed; skipping startup migrations."
+    exit 1
+  fi
 fi
 exec "$@"

sp7_db_setup_check.sh

@@ -124,6 +124,12 @@ fi
 DB_EXISTS=$(mariadb -h "$DB_HOST" -P "$DB_PORT" -u "$MASTER_USER_NAME" --password="$MASTER_USER_PASSWORD" \
   -sse "SELECT COUNT(*) FROM information_schema.schemata WHERE schema_name = '$DB_NAME';")
 
+LEGACY_SCHEMA_EXISTS=0
+if [[ "$DB_EXISTS" -ne 0 ]]; then
+  LEGACY_SCHEMA_EXISTS=$(mariadb -h "$DB_HOST" -P "$DB_PORT" -u "$MASTER_USER_NAME" --password="$MASTER_USER_PASSWORD" \
+    -sse "SELECT COUNT(*) FROM information_schema.tables WHERE table_schema = '$DB_NAME' AND table_name = 'specifyuser';")
+fi
+
 if [[ "$DB_EXISTS" -eq 0 ]]; then
   echo "Creating database '$DB_NAME'..."
   echo "Executing: mariadb -h \"$DB_HOST\" -P \"$DB_PORT\" -u \"$MASTER_USER_NAME\" --password=\"<hidden>\" -e \"CREATE DATABASE \`$DB_NAME\`;\""
@@ -134,6 +140,41 @@ if [[ "$DB_EXISTS" -eq 0 ]]; then
     echo "Error: Failed to create database."
     exit 1
   fi
+elif [[ "$LEGACY_SCHEMA_EXISTS" -eq 0 ]]; then
+  echo "Database '$DB_NAME' exists but does not contain a Specify schema."
+
+  # Check whether the database is truly empty. If it is empty, proceed with initial setup. 
+  # If it's non-empty, require explicit opt-in via ALLOW_DB_RESET=true to perform a destructive reset.
+  if ! DB_TABLE_COUNT=$(mariadb -N -B -h "$DB_HOST" -P "$DB_PORT" \
+        -u "$MASTER_USER_NAME" --password="$MASTER_USER_PASSWORD" \
+        -sse "SELECT COUNT(*) FROM information_schema.tables WHERE table_schema = '$DB_NAME';"); then
+    echo "Error: Failed to count tables in '$DB_NAME'."
+    exit 1
+  fi
+  if [[ -z "$DB_TABLE_COUNT" ]]; then
+    echo "Error: Empty response when counting tables in '$DB_NAME'."
+    exit 1
+  fi
+
+  if [[ "$DB_TABLE_COUNT" -eq 0 ]]; then
+    echo "Database '$DB_NAME' is empty; proceeding with initial setup."
+    NEW_DATABASE_CREATED=1
+  else
+    if [[ "${ALLOW_DB_RESET:-}" == "true" ]]; then
+      echo "Resetting non-empty database '$DB_NAME' because ALLOW_DB_RESET=true was set."
+      if ! mariadb -h "$DB_HOST" -P "$DB_PORT" -u "$MASTER_USER_NAME" --password="$MASTER_USER_PASSWORD" \
+           -e "DROP DATABASE \`$DB_NAME\`; CREATE DATABASE \`$DB_NAME\`;"; then
+        echo "Error: Failed to reset database."
+        exit 1
+      fi
+      NEW_DATABASE_CREATED=1
+    else
+      echo "Error: Database '$DB_NAME' exists but lacks the Specify schema and is not empty."
+      echo "If you want to allow a destructive reset, set ALLOW_DB_RESET=true in your environment before starting."
+      echo "Otherwise restore a proper Specify database or delete the database entirely to start fresh."
+      exit 1
+    fi
+  fi
 else
   echo "Database '$DB_NAME' already exists."
 fi
@@ -423,11 +464,11 @@ echo "New app user created: $([[ "$NEW_APP_USER_CREATED" -eq 1 ]] && echo True |
 echo "--------------------------------------------------"
 
 # Run the base_specify_migration script
-if [[ "$NEW_DATABASE_CREATED" -eq 0 ]]; then
+if [[ "$LEGACY_SCHEMA_EXISTS" -eq 1 ]]; then
   echo "Existing database detected."
   ve/bin/python manage.py base_specify_migration --use-override --database=${MIGRATION_DB_ALIAS}
 else
-  echo "New database detected."
+  echo "Blank or newly created database detected."
   ve/bin/python manage.py base_specify_migration --database=${MIGRATION_DB_ALIAS}
 fi