fix: storage and directories bug

backend/src/backend/scripts.py

@@ -16,6 +16,7 @@ from common.db.models import (
 )
 from common.ids import new_ulid
 from common.storage.schemas import ServerObjectRequest
+from common.storage import build_storage_uri
 from fastapi import (
     APIRouter,
     BackgroundTasks,
@@ -89,6 +90,15 @@ def safe_directory_name(value: str) -> str:
     return name
 
 
+# Version/run artifacts are not part of the user's workspace directory tree.
+TREE_EXCLUDED_USAGE_TYPES = (
+    "version_artifact",
+    "snapshot",
+    "run_log",
+    "run_result",
+)
+
+
 def user_relative_path(context: RequestContext, child_path: str = "") -> str:
     base = f"users/{context.user.username}"
     normalized = normalize_user_path(child_path)
@@ -464,7 +474,7 @@ async def create_script_record(
         bucket_name=bucket_name,
         object_key=object_key,
         object_key_hash=hashlib.sha256(object_key.encode("utf-8")).digest(),
-        storage_uri=f"s3://{bucket_name}/{object_key}",
+        storage_uri=build_storage_uri(bucket_name, object_key),
         file_name=name,
         file_extension=PurePosixPath(jupyter_name).suffix.lower() or None,
         mime_type=mime_type,
@@ -625,6 +635,7 @@ async def get_workspace_tree(
                 StorageObjects.object_status == "available",
                 StorageObjects.is_deleted == 0,
                 StorageObjects.relative_path.like(like_prefix),
+                StorageObjects.usage_type.notin_(TREE_EXCLUDED_USAGE_TYPES),
             )
         )
     ).all()
@@ -691,18 +702,20 @@ async def list_workspace_directories(
 
     rows = (
         await session.execute(
-            select(StorageObjects.relative_path, StorageObjects.object_type).where(
+            select(StorageObjects.relative_path).where(
                 StorageObjects.workspace_id == context.workspace.workspace_id,
                 StorageObjects.object_status == "available",
                 StorageObjects.is_deleted == 0,
                 StorageObjects.relative_path.like(f"{descendant_prefix}%"),
                 ~StorageObjects.relative_path.like(f"{descendant_prefix}%/%"),
+                StorageObjects.object_type == "directory",
+                StorageObjects.usage_type.notin_(TREE_EXCLUDED_USAGE_TYPES),
             )
         )
     ).all()
 
     directories: dict[str, dict[str, Any]] = {}
-    for relative, _object_type in rows:
+    for (relative,) in rows:
         if not relative or not relative.startswith(descendant_prefix):
             continue
         suffix = relative[len(descendant_prefix) :]
@@ -720,7 +733,8 @@ async def list_workspace_directories(
         )
 
     for directory in directories.values():
-        child_prefix = f"{target_prefix}/{directory['path']}/"
+        # directory['path'] is already workspace-relative and includes the parent segment.
+        child_prefix = f"{scoped_prefix}/{directory['path']}/"
         has_children = await session.scalar(
             select(StorageObjects.storage_object_id).where(
                 StorageObjects.workspace_id == context.workspace.workspace_id,
@@ -728,6 +742,7 @@ async def list_workspace_directories(
                 StorageObjects.is_deleted == 0,
                 StorageObjects.relative_path.like(f"{child_prefix}%"),
                 ~StorageObjects.relative_path.like(f"{child_prefix}%/%"),
+                StorageObjects.usage_type.notin_(TREE_EXCLUDED_USAGE_TYPES),
             ).limit(1)
         )
         directory["has_children"] = has_children is not None

backend/src/backend/services/storage.py

@@ -47,6 +47,7 @@ from common.storage.schemas import (
     DownloadUrlRequest,
     ServerObjectRequest,
 )
+from common.storage import build_storage_uri
 
 
 # ── shared low-level helpers (module-private) ────────────────────────────
@@ -90,7 +91,7 @@ def _build_storage_object(
         bucket_name=upload.bucket_name,
         object_key=upload.object_key,
         object_key_hash=upload.object_key_hash,
-        storage_uri=f"s3://{upload.bucket_name}/{upload.object_key}",
+        storage_uri=build_storage_uri(upload.bucket_name, upload.object_key),
         file_name=safe_name,
         file_extension=PurePosixPath(safe_name).suffix.lower() or None,
         mime_type=content_type,
@@ -519,4 +520,4 @@ async def soft_delete_object(
             "trash_key": item.trash_key,
             "trash_bucket": settings.s3_trash_bucket,
         }
-    }
+    }

backend/src/backend/storage_api.py

@@ -19,7 +19,7 @@ from common.db.models import (
     Workspaces,
 )
 from common.ids import new_ulid
-from common.storage import actual_bucket_name
+from common.storage import actual_bucket_name, build_storage_uri
 from common.storage.schemas import (
     CreateUploadRequest,
     DownloadUrlRequest,
@@ -350,7 +350,7 @@ async def upload_bytes_to_session(
         bucket_name=upload.bucket_name,
         object_key=upload.object_key,
         object_key_hash=upload.object_key_hash,
-        storage_uri=f"s3://{upload.bucket_name}/{upload.object_key}",
+        storage_uri=build_storage_uri(upload.bucket_name, upload.object_key),
         file_name=file_name,
         file_extension=PurePosixPath(file_name).suffix.lower() or None,
         mime_type=upload.content_type,