✨Add support for local source files (#156)

Signed-off-by: zethson <[email protected]>
Co-authored-by: Lukas Heumos <[email protected]>

bionty/base/dev/_io.py

@@ -1,4 +1,5 @@
 import os
+import shutil
 from pathlib import Path
 from typing import Union
 
@@ -48,6 +49,10 @@ def url_download(
     Raises:
         HttpError: If the request response is not 200 and OK.
     """
+    if url.startswith("file://"):
+        url = url.split("file://")[-1]
+        shutil.copy(url, localpath)
+        return localpath
     try:
         response = requests.get(url, stream=True, allow_redirects=True, **kwargs)
         response.raise_for_status()

tests/dev/test_io.py

@@ -1,3 +1,4 @@
+import tempfile
 from pathlib import Path
 
 import pytest
@@ -20,3 +21,23 @@ def test_url_download(local):
 
     downloaded_path = Path(url_download(url=url, localpath=localpath))
     assert downloaded_path.exists()
+
+
+def test_local_file():
+    with tempfile.TemporaryDirectory() as temp_dir:
+        local_file = Path(temp_dir) / "test.txt"
+        target_file = Path(temp_dir) / "downloaded.txt"
+        test_content = "temporary file"
+
+        local_file.write_text(test_content)
+        assert local_file.exists(), "Test file was not created"
+
+        downloaded_path = Path(
+            url_download(url=f"file://{local_file}", localpath=target_file)
+        )
+
+        assert downloaded_path.exists(), "Downloaded file not found"
+        assert downloaded_path.read_text() == test_content, "Content mismatch"
+
+        if downloaded_path.exists():
+            downloaded_path.unlink()