Fix allele state

tests/fixtures/validators.yml

@@ -3,6 +3,7 @@ amino_acid_substitution:
     - query: BRAF V600E
     - query: NP_004324.2:p.Val600Glu
     - query: NP_005219.2:p.Thr790Met
+    - query: EGFR Leu858Arg
   should_not_match:
     - query: NP_004324.2:p.Val600000000000Glu
     - query: NP_004324.2:p.Glu600Val

variant/validators/polypeptide_sequence_variant_base.py

@@ -96,16 +96,17 @@ def get_vrs_allele(self, sequence_id, s) -> dict:
         )
 
         state = models.SequenceState(sequence=s.alt_protein)
+        state_dict = state.as_dict()
+        if len(state_dict['sequence']) == 3:
+            for one, three in \
+                    self._amino_acid_cache._amino_acid_code_conversion.items():
+                if three == state_dict['sequence']:
+                    state.sequence = one
+
         allele = models.Allele(location=seq_location,
                                state=state)
         allele['_id'] = ga4gh_identify(allele)
-        allele = allele.as_dict()
-        if len(allele['state']['sequence']) == 3:
-            for one, three in \
-                    self._amino_acid_cache._amino_acid_code_conversion:
-                if three == allele['state']['sequence']:
-                    allele['state']['sequence'] = one
-        return allele
+        return allele.as_dict()
 
     def get_hgvs_expr(self, classification) -> str:
         """Return HGVS expression for a classification.