Merge pull request #127 from gyorilab/safer-prefix-index

Improve safety of NER build
gyorilab · Feb 6, 2024 · 24cfa02 · 24cfa02
2 parents e4be647 + 7b72202
commit 24cfa02
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diff --git a/gilda/grounder.py b/gilda/grounder.py
@@ -111,7 +111,11 @@ def __init__(
     def _build_prefix_index(self):
         prefix_index = defaultdict(set)
         for norm_term in self.entries:
+            if not norm_term:
+                continue
             parts = norm_term.split()
+            if not parts:
+                continue
             prefix_index[parts[0]].add(len(parts))
         self.prefix_index = dict(prefix_index)
 

diff --git a/gilda/term.py b/gilda/term.py
@@ -52,6 +52,8 @@ def __init__(self, norm_text, text, db, id, entry_name, status, source,
                  organism=None, source_db=None, source_id=None):
         if not text:
             raise ValueError('Text for Term cannot be empty')
+        if not norm_text.strip():
+            raise ValueError('Normalized text for Term cannot be empty')
         self.norm_text = norm_text
         self.text = text
         self.db = db