Merge branch 'issue-95-take2' of https://github.com/cancervariants/fusor

into issue-95-take2
cancervariants · Jul 29, 2024 · f00ddb2 · f00ddb2
2 parents c664b77 + 8fd8d3f
commit f00ddb2
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Showing 2 changed files with 3 additions and 7 deletions.
diff --git a/src/fusor/fusor.py b/src/fusor/fusor.py
@@ -569,11 +569,10 @@ def _normalized_gene(
         gene_norm_resp = self.gene_normalizer.normalize(query)
         if gene_norm_resp.match_type:
             gene = gene_norm_resp.gene
-            # remove normalize.gene from id (ex; 'normalize.gene.hgnc:1097' -> 'hgnc:1097')
-            gene_id = gene_norm_resp.normalized_id.replace("normalize.gene.", "")
-            gene.id = gene_id
+            gene_id = gene_norm_resp.normalized_id
             if use_minimal_gene:
                 return Gene(id=gene_id, label=gene.label), None
+            gene.id = gene_id
             return gene, None
         return None, f"gene-normalizer unable to normalize {query}"
 

diff --git a/src/fusor/models.py b/src/fusor/models.py
@@ -442,10 +442,7 @@ def _fetch_gene_id(
         :param alt_field: the field to fetch the gene from, if it is not called "gene" (ex: associatedGene instead)
         :return: gene ID if gene is defined
         """
-        if alt_field:
-            gene_info = cls._access_object_attr(obj, alt_field)
-        else:
-            gene_info = cls._access_object_attr(obj, "gene")
+        gene_info = cls._access_object_attr(obj, alt_field if alt_field else "gene")
         if gene_info:
             gene_id = cls._access_object_attr(gene_info, "id")
             if gene_id: