feat: copy markdown utility

pixi.toml

@@ -17,6 +17,7 @@ update-download-map = "python -c 'from src.fetch_articles.article_downloader imp
 download-articles = "python -m src.fetch_articles.article_downloader"
 download-data = "gdown --fuzzy https://drive.google.com/file/d/1qtQWvi0x_k5_JofgrfsgkWzlIdb6isr9/view && unzip autogkb-data.zip && rm autogkb-data.zip"
 setup-repo = "pixi install && pixi run download-data"
+copy-markdown = "python -m src.copy_markdown"
 
 [dependencies]
 seaborn = ">=0.13.2,<0.14"

src/copy_markdown.py

@@ -0,0 +1,34 @@
+from typing import List
+import os
+import shutil
+from loguru import logger
+from pathlib import Path
+
+"""
+Pass in a list of PMCIDs and have those files copied to a new folder
+"""
+
+
+def copy_markdown(pmcids: List[str]) -> None:
+    succesful = 0
+    for pmcid in pmcids:
+        try:
+            source_file = Path("data") / "articles" / f"{pmcid}.md"
+            destination = Path("data") / "extractions" / "markdown"
+            os.makedirs(destination, exist_ok=True)
+            shutil.copy2(source_file, destination / f"{pmcid}.md")
+            succesful += 1
+        except Exception as e:
+            logger.error(e)
+    logger.info(
+        f"Copied {succesful}/{len(pmcids)} markdown to data/extractions/markdown"
+    )
+
+
+def main():
+    pmcids = ["PMC4737107", "PMC5712579", "PMC5728534", "PMC5749368", "PMC11730665"]
+    copy_markdown(pmcids=pmcids)
+
+
+if __name__ == "__main__":
+    main()