tests should pass now

Author: rmobmina

api/resources/gene_information.py

@@ -100,11 +100,16 @@ def post(self):
 
         if len(rows) > 0:
             for row in rows:
-                if row.agi in data_items.keys():
-                    data_items[row.agi].append(row.agi)
+                normalized_agi = BARUtils.normalize_arabidopsis_gene(row.agi)
+                alias_value = row.alias
+                if BARUtils.is_arabidopsis_gene_valid(alias_value):
+                    alias_value = BARUtils.normalize_arabidopsis_gene(alias_value)
+
+                if normalized_agi in data_items.keys():
+                    data_items[normalized_agi].append(normalized_agi)
                 else:
-                    data_items[row.agi] = []
-                    data_items[row.agi].append(row.alias)
+                    data_items[normalized_agi] = []
+                    data_items[normalized_agi].append(alias_value)
 
             for gene in data_items.keys():
                 data.append({"gene": gene, "aliases": data_items[gene]})

api/resources/microarray_gene_expression.py

@@ -5,6 +5,7 @@
 from api.models.efp_dynamic import SIMPLE_EFP_SAMPLE_MODELS
 from api.utils.bar_utils import BARUtils
 from api.utils.world_efp_utils import WorldeFPUtils
+from sqlalchemy import func
 import json
 
 # Pull the dynamic model so this resource stays in sync with the schema catalog
@@ -33,7 +34,7 @@ def get(self, species="", gene_id=""):
             return BARUtils.error_exit("Invalid species")
         subquery = (
             db.select(AtAgiLookup.probeset)
-            .where(AtAgiLookup.agi == gene_id)
+            .where(func.lower(AtAgiLookup.agi) == gene_id.lower())
             .order_by(AtAgiLookup.date.desc())
             .limit(1)
             .subquery()

api/utils/bar_utils.py

@@ -33,6 +33,16 @@ def is_arabidopsis_gene_valid(gene):
         else:
             return False
 
+    @staticmethod
+    def normalize_arabidopsis_gene(gene):
+        """Return Arabidopsis gene in canonical case (At1g01010)."""
+        if not gene:
+            return gene
+        lowered = gene.lower()
+        if re.search(r"^at[12345cm]g\d{5}.?\d?$", lowered):
+            return "At" + lowered[2:]
+        return gene
+
     @staticmethod
     def is_grape_gene_valid(gene):
         """This function verifies if grape gene is valid: VIT_00s0120g00060