copilot-swe-agent[bot] raylim commited on
Commit
45cb0d2
·
1 Parent(s): ae3280a

Add error handling for missing tissue site CSV file

Browse files

Co-authored-by: raylim <3074310+raylim@users.noreply.github.com>

Files changed (1) hide show
  1. src/mosaic/ui/utils.py +14 -6
src/mosaic/ui/utils.py CHANGED
@@ -37,15 +37,23 @@ def get_tissue_sites():
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  """Get the list of tissue sites from the tissue site map file.
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  Returns:
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- List of tissue site names
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  """
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  global tissue_site_list
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  if tissue_site_list is None:
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- current_dir = Path(__file__).parent.parent.parent.parent
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- tissue_site_map_path = current_dir / "data" / "tissue_site_original_to_idx.csv"
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- df = pd.read_csv(tissue_site_map_path)
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- # Get unique tissue sites and sort them
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- tissue_site_list = ["Unknown"] + sorted(df["TISSUE_SITE"].unique().tolist())
 
 
 
 
 
 
 
 
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  return tissue_site_list
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  """Get the list of tissue sites from the tissue site map file.
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  Returns:
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+ List of tissue site names. Returns ["Unknown"] if the CSV file is not found.
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  """
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  global tissue_site_list
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  if tissue_site_list is None:
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+ try:
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+ current_dir = Path(__file__).parent.parent.parent.parent
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+ tissue_site_map_path = current_dir / "data" / "tissue_site_original_to_idx.csv"
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+ df = pd.read_csv(tissue_site_map_path)
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+ # Get unique tissue sites and sort them
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+ tissue_site_list = ["Unknown"] + sorted(df["TISSUE_SITE"].unique().tolist())
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+ except FileNotFoundError:
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+ gr.Warning(
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+ f"Tissue site mapping file not found at {tissue_site_map_path}. "
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+ "Only 'Unknown' option will be available for tissue site selection. "
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+ "Please ensure the data files are downloaded from the model repository."
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+ )
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+ tissue_site_list = ["Unknown"]
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  return tissue_site_list
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