download: allow non-url characters in filenames

strips control characters from urls such that spaces and such are allowed in filenames coming from Zenodo

changelog.md

@@ -15,6 +15,7 @@
 * Added improved printing of calibrations performed with `Pylake`.
 * Added parameter `titles` to customize title of each subplot in [`Kymo.plot_with_channels()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.kymo.Kymo.html#lumicks.pylake.kymo.Kymo.plot_with_channels).
 * Added [`KymoTrack.sample_from_channel()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.kymotracker.kymotrack.KymoTrack.html#lumicks.pylake.kymotracker.kymotrack.KymoTrack.sample_from_channel) to downsample channel data to the time points of a kymotrack.
+* Added support for file names with spaces in [`lk.download_from_doi()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.download_from_doi.html#lumicks.pylake.download_from_doi).
 
 ## v1.5.2 | 2024-07-24
 

lumicks/pylake/file_download.py

@@ -2,17 +2,42 @@
 import json
 import hashlib
 import urllib.error
-from urllib.parse import urljoin
+from urllib.parse import quote, urljoin, urlparse
 from urllib.request import urlopen
 
 from tqdm.auto import tqdm
 
 __all__ = ["download_from_doi"]
 
 
+def strip_control_characters(url_str) -> str:
+    """Strips control characters from a URL
+
+    Parameters
+    ----------
+    url_str : str
+        URL to encode
+
+    Raises
+    ------
+    ValueError
+        if the URL does not contain a scheme (e.g. https) or net location
+    """
+    url = urlparse(url_str)
+
+    if not url.scheme or not url.netloc:
+        raise ValueError(f"Invalid URL provided: {url}")
+
+    base_url = url.scheme + "://" + url.netloc + quote(url.path)
+    return base_url + "?" + quote(url.query) if url.query else base_url
+
+
 def get_url_from_doi(doi):
     """Obtains a Zenodo record from the DOI (e.g. 10.5281/zenodo.#)"""
     url = doi if doi.startswith("http") else urljoin("https://doi.org/", doi)
+
+    url = strip_control_characters(url)
+
     try:
         with urlopen(url) as response:
             return response.url
@@ -23,7 +48,8 @@ def get_url_from_doi(doi):
 def download_record_metadata(record_number):
     """Download specific Zenodo record metadata"""
     zenodo_url = "https://zenodo.org/api/records/"
-    with urlopen(urljoin(zenodo_url, str(record_number))) as response:
+
+    with urlopen(strip_control_characters(urljoin(zenodo_url, str(record_number)))) as response:
         if response.status == 200:
             return json.loads(response.read())
         else:
@@ -46,6 +72,8 @@ def download_file(url, target_path, download_path, show_progress=True, block_siz
     block_size : int
         Block size to use when downloading
     """
+    url = strip_control_characters(url)
+
     with urlopen(url) as response:
         size_bytes = int(response.headers.get("Content-Length", 0))
 

lumicks/pylake/tests/test_file_download.py

@@ -5,9 +5,37 @@
     get_url_from_doi,
     download_from_doi,
     download_record_metadata,
+    strip_control_characters,
 )
 
 
+@pytest.mark.parametrize(
+    "url, url_ref",
+    [
+        ("https://zenodo.org/api/records/13880274", "https://zenodo.org/api/records/13880274"),
+        ("https://zenodo.org/api/records/test?yes", "https://zenodo.org/api/records/test?yes"),
+        ("https://zenodo.org/api/test?yes no", "https://zenodo.org/api/test?yes%20no"),
+        ("https://zenodo.org/api/test?yes>no", "https://zenodo.org/api/test?yes%3Eno"),
+        (
+            "https://zenodo.org/space bar/test?yes>no",
+            "https://zenodo.org/space%20bar/test?yes%3Eno",
+        ),
+        (
+            "https://zenodo.org/api/records/13880274/files/20220203-165412 Marker 0.85_NotOscillate.h5/content",
+            "https://zenodo.org/api/records/13880274/files/20220203-165412%20Marker%200.85_NotOscillate.h5/content",
+        ),
+    ],
+)
+def test_strip_control_characters_url(url, url_ref):
+    assert strip_control_characters(url) == url_ref
+
+
+@pytest.mark.parametrize("invalid_url", ["https:://", "zenodo.org"])
+def test_invalid_url(invalid_url):
+    with pytest.raises(ValueError, match="Invalid URL provided"):
+        strip_control_characters(invalid_url)
+
+
 @pytest.mark.preflight
 def test_grab_record():
     assert get_url_from_doi("10.5281/zenodo.4247279") == "https://zenodo.org/records/4247279"