Update standardize_license_labels.py

util/standardize_license_labels.py

@@ -0,0 +1,76 @@
+# -*- coding: utf-8 -*-
+
+"""
+
+Run with: ``python standardize_license_labels.py``.
+
+Author: `Charles Tapley Hoyt <https://cthoyt.com>`_.
+"""
+
+import pathlib
+from typing import Union
+
+import click
+from bioregistry.license_standardizer import LICENSES
+from tqdm import tqdm
+
+HERE = pathlib.Path(__file__).parent.resolve()
+ONTOLOGY_DIRECTORY = HERE.parent.joinpath("ontology").resolve()
+
+
+def update_markdown(path: Union[str, pathlib.Path]) -> None:
+    """Update the given markdown file."""
+    with open(path) as file:
+        lines = [line.rstrip("\n") for line in file]
+
+    try:
+        idx = min(i for i, line in enumerate(lines) if line.startswith("license:"))
+    except ValueError:
+        tqdm.write(f"no license in {path}")
+        return
+
+    license_url = None
+    for i in range(1, 3):
+        line = lines[idx + i].strip()
+        if "url:" in line:
+            _, license_url = line.split(':', 1)
+
+    if license_url is None:
+        tqdm.write(f"no license URL in {path}")
+        return
+
+    new_label = LICENSES.get(license_url.strip())
+    if new_label is None:
+        tqdm.write(f"could not standardize license URL {license_url} in {path}")
+        return
+
+    license_label, license_label_idx = None, None
+    for i in range(1, 3):
+        line = lines[idx + i].strip()
+        if "label:" in line:
+            license_label_idx = idx + i
+            _, license_label = line.split(":", 1)
+
+    if license_label.replace("-", "") == new_label.replace("-", ""):
+        return
+
+    if license_label_idx is None:
+        tqdm.write(f"no license label in {path}")
+        return
+
+    with open(path, "w") as file:
+        for i, line in enumerate(lines):
+            if i == license_label_idx:
+                print(f"  label: {new_label}", file=file)
+            else:
+                print(line, file=file)
+
+
+@click.command()
+def main():
+    for path in ONTOLOGY_DIRECTORY.glob("*.md"):
+        update_markdown(path)
+
+
+if __name__ == "__main__":
+    main()