Make .env file take precedence over exported vars, add a flag to make this behaviour configurable

Author: pavish

bin/mathesar

@@ -12,6 +12,7 @@ SCRIPT_NAME=$(basename "$0")
 NO_VENV=false
 FALLBACK_TO_INBUILT_DOCKER_DB=false
 SETUP_DJANGO=false
+PREFER_EXPORTED_ENV=false
 
 # Color definitions for output
 RED=$(tput setaf 1 2>/dev/null || echo "")
@@ -128,11 +129,12 @@ set_env_vars_from_file() {
       var_name="${trimmed%%=*}"
       var_value="${trimmed#*=}"
 
-      # Only export the variable if it is not already set.
+      # If PREFER_EXPORTED_ENV is true, only set from .env if variable is not already set.
+      # If PREFER_EXPORTED_ENV is false, always set from .env
       # This check uses bash parameter expansion: if the variable is not set, ${!var_name+_} is empty.
       # If it's set even when empty, it'll return a value (when empty, it'll return _).
       # `!` is required below - it denotes that the value of var_name should be used as the env variable name.
-      if [[ -z "${!var_name+_}" ]]; then
+      if [[ "${PREFER_EXPORTED_ENV}" = false ]] || [[ -z "${!var_name+_}" ]]; then
         export "$var_name"="$var_value"
       fi
     done < "${ENV_FILE}"
@@ -241,7 +243,7 @@ run_mathesar() {
     popd > /dev/null
   fi
 
-  local gunicorn_opts="config.wsgi -b 0.0.0.0:${MATHESAR_PORT}"
+  local gunicorn_opts="config.wsgi -b 0.0.0.0:${MATHESAR_PORT} --chdir ${BASE_DIR}"
   if [ "${DEBUG}" = "true" ]; then
     gunicorn_opts+=" --log-level=debug"
   fi
@@ -254,9 +256,7 @@ run_mathesar() {
   fi
 
   info "Starting gunicorn webserver..."
-  pushd "${BASE_DIR}" > /dev/null
-    exec "$gunicorn_bin" $gunicorn_opts
-  popd > /dev/null
+  exec "$gunicorn_bin" $gunicorn_opts
 }
 
 
@@ -282,6 +282,10 @@ Commands:
       Options:
         --port <port>, -p <port>    Specify the port for Mathesar's web service (default is 8000).
 
+        --prefer-exported-env, -e   Prefer existing exported environment variables over the .env file.
+                                    If this option is set and required environment variables aren't exported,
+                                    the values from the .env file will be substituted for the missing ones.
+
   version
       Show version information.
 
@@ -385,8 +389,12 @@ if [ "${COMMAND}" = "run" ]; then
           err "The --port/-p option requires an argument."
         fi
         ;;
+      --prefer-exported-env|-e)
+        PREFER_EXPORTED_ENV=true
+        shift
+        ;;
       -*)
-        # Support clubbed short options for fallback (-f), no-venv (-n), and setup-django (-s).
+        # Support clubbed short options for fallback (-f), no-venv (-n), prefer-exported-env (-e), and setup-django (-s).
         # If the option string includes any 'p' we now no longer allow clubbing.
         shortopts="${1#-}"
         if [[ "$shortopts" == *"p"* ]]; then
@@ -398,6 +406,7 @@ if [ "${COMMAND}" = "run" ]; then
             f) FALLBACK_TO_INBUILT_DOCKER_DB=true ;;
             n) NO_VENV=true ;;
             s) SETUP_DJANGO=true ;;
+            e) PREFER_EXPORTED_ENV=true ;;
             *)
               usage_err "Unknown option: -$letter"
               ;;

scripts/install.sh

@@ -508,9 +508,9 @@ update_current_shell_env() {
       fi
     fi
   elif ! . "${INSTALL_DIR}/bin/mathesar_path_source"; then
-      echo "Warning: Unable to source mathesar_path_source in the current session."
-      echo "Please run: source \"${INSTALL_DIR}/bin/mathesar_path_source\" or restart your shell"
-      return 1
+    echo "Warning: Unable to source mathesar_path_source in the current session."
+    echo "Please run: source \"${INSTALL_DIR}/bin/mathesar_path_source\" or restart your shell"
+    return 1
   fi
 
   # Re-exec the shell if interactive
@@ -613,11 +613,14 @@ configure_path() {
 
       info "Attempting to update the current shell environment..."
       if update_current_shell_env; then
-        success "Everything's ready, you can now start Mathesar by executing \"mathesar run\". Use \"mathesar help\" for more information.".
+        success "Everything's ready, you can now start Mathesar by executing \"mathesar run\"."
+        echo "Use \"mathesar help\" for more information.".
+        echo "Please restart your shell if the 'mathesar' command is not found."
       else
         echo "Unable to automatically update the current shell environment."
         echo "Please run the following command in your terminal to update your PATH:"
         echo "source \"${INSTALL_DIR}/bin/mathesar_path_source\""
+        echo "Please restart your shell if the 'mathesar' command is still not found."
       fi
     fi
   fi