Fix inconsistent cache defaults, export bucket cache name

src/gypsum_client/__init__.py

@@ -16,6 +16,7 @@
     del version, PackageNotFoundError
 
 
+from ._utils import BUCKET_CACHE_NAME
 from .auth import access_token, set_access_token
 from .cache_directory import cache_directory
 from .clone_operations import clone_version
@@ -44,3 +45,4 @@
 from .set_operations import set_permissions, set_quota
 from .upload_api_operations import abort_upload, complete_upload, start_upload
 from .upload_file_actions import upload_directory, upload_files
+from .validate_metadata import validate_metadata

src/gypsum_client/fetch_metadata_database.py

@@ -26,7 +26,9 @@
 
 
 def fetch_metadata_database(
-    name: str = "bioconductor.sqlite3", cache_dir: str = None, overwrite: bool = False
+    name: str = "bioconductor.sqlite3",
+    cache_dir: str = cache_directory(),
+    overwrite: bool = False,
 ) -> str:
     """Fetch the SQLite database containing metadata from the gypsum backend.
 
@@ -72,7 +74,7 @@ def fetch_metadata_database(
     if cache_dir is None:
         cache_path = tempfile.NamedTemporaryFile(suffix=".sqlite3").name
     else:
-        cache_dir = os.path.join(cache_directory(cache_dir), "databases")
+        cache_dir = os.path.join(cache_dir, "databases")
 
         cache_path = os.path.join(cache_dir, name)
         if not os.path.exists(cache_path):

src/gypsum_client/fetch_metadata_schema.py

@@ -14,7 +14,7 @@
 
 def fetch_metadata_schema(
     name: str = "bioconductor/v1.json",
-    cache_dir: str = None,
+    cache_dir: str = cache_directory(),
     overwrite: bool = False,
 ) -> str:
     """Fetch a JSON schema file for metadata to be inserted into a SQLite database.
@@ -58,7 +58,7 @@ def fetch_metadata_schema(
     if cache_dir is None:
         cache_path = tempfile.mktemp(suffix=".json")
     else:
-        cache_dir = os.path.join(cache_directory(cache_dir), "schemas")
+        cache_dir = os.path.join(cache_dir, "schemas")
 
         cache_path = os.path.join(cache_dir, name)
         if not os.path.exists(cache_path):

src/gypsum_client/prepare_directory_for_upload.py

@@ -121,15 +121,13 @@ def prepare_directory_upload(
     for root, _, files in os.walk(directory):
         for name in files:
             rel_path = os.path.relpath(os.path.join(root, name), directory)
-            dest = (
-                os.readlink(os.path.join(directory, rel_path))
-                if os.path.islink(os.path.join(directory, rel_path))
-                else None
-            )
-            if not dest:
+
+            if not os.path.islink(os.path.join(directory, rel_path)):
                 out_files.append(rel_path)
                 continue
 
+            dest = os.readlink(os.path.join(directory, rel_path))
+
             if links == "never":
                 if not os.path.exists(dest):
                     raise ValueError(
@@ -140,6 +138,7 @@ def prepare_directory_upload(
 
             dest = _normalize_and_sanitize_path(dest)
             dest_components = _match_path_to_cache(dest, cache_dir)
+
             if dest_components:
                 out_links.append(
                     {
@@ -160,6 +159,7 @@ def prepare_directory_upload(
                 raise ValueError(
                     f"Cannot use a dangling link to '{dest}' as a regular upload."
                 )
+
             out_files.append(rel_path)
 
     return {"files": out_files, "links": out_links}

src/gypsum_client/resolve_links.py

@@ -21,7 +21,7 @@ def resolve_links(
     project: str,
     asset: str,
     version: str,
-    cache_dir: Optional[str] = None,
+    cache_dir: Optional[str] = cache_directory(),
     overwrite: str = False,
     url: str = rest_url(),
 ):

src/gypsum_client/save_operations.py

@@ -35,7 +35,7 @@ def save_version(
     project: str,
     asset: str,
     version: str,
-    cache_dir: Optional[str] = None,
+    cache_dir: Optional[str] = cache_directory(),
     overwrite: bool = False,
     relink: bool = True,
     concurrent: int = 1,
@@ -203,7 +203,7 @@ def save_file(
     asset: str,
     version: str,
     path: str,
-    cache_dir: Optional[str] = None,
+    cache_dir: Optional[str] = cache_directory(),
     overwrite: bool = False,
     url: str = rest_url(),
 ):