fix: normalize path (#283)

changelog.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## Unreleased
+
+### Fixed
+- Fix `edsnlp.utils.file_system.normalize_fs_path` file system detection not working correctly
+
 ## v0.11.1 (2024-04-02)
 
 ### Added

edsnlp/utils/file_system.py

@@ -42,24 +42,21 @@ def normalize_fs_path(
     filesystem: Optional[FileSystem],
     path: Union[str, Path],
 ) -> Tuple[AbstractFileSystem, str]:
-    path = str(path)
+    has_protocol = isinstance(path, str) and "://" in path
 
-    if filesystem is None or (isinstance(path, str) and "://" in path):
-        path = (
-            os.path.abspath(path)
-            if isinstance(path, Path) or "://" in path
-            else f"file://{os.path.abspath(path)}"
-        )
-        inferred_fs, fs_path = pyarrow.fs.FileSystem.from_uri(path)
+    # We need to detect the fs from the path
+    if filesystem is None or has_protocol:
+        uri: str = path if has_protocol else f"file://{os.path.abspath(path)}"
+        inferred_fs, fs_path = pyarrow.fs.FileSystem.from_uri(uri)
         filesystem = filesystem or inferred_fs
         assert inferred_fs.type_name == filesystem.type_name, (
             f"Protocol {inferred_fs.type_name} in path does not match "
             f"filesystem {filesystem.type_name}"
         )
-        path = fs_path
+        path = fs_path  # path without protocol
 
     return (
         ArrowFSWrapper(filesystem)
         if isinstance(filesystem, pyarrow.fs.FileSystem)
         else filesystem
-    ), path
+    ), str(path)

tests/data/test_parquet.py

@@ -1,3 +1,4 @@
+import os
 from pathlib import Path
 
 import pyarrow.dataset
@@ -242,7 +243,7 @@ def test_read_to_parquet(blank_nlp, tmpdir):
     fs = pyarrow.fs.LocalFileSystem()
     doc = list(
         edsnlp.data.read_parquet(
-            input_dir,
+            input_dir.relative_to(os.getcwd()),
             converter="omop",
             span_attributes=["etat", "assertion"],
             doc_attributes=["context_var"],