Add eFP/ePlant gene ID validation, microarray probeset support, and m…

api/models/efp_schemas.py

@@ -181,7 +181,7 @@ def _schema(species: str, charset: str = "latin1") -> DatabaseSpec:
     ("root_Schaefer_lab", "root Schaefer lab"),
     ("rpatel", "rpatel"),
     ("seed_db", "seed db"),
-    ("seedcoat", "oat"),
+    ("seedcoat", "arabidopsis seedcoat"),
     ("selaginella", "selaginella"),
     ("shoot_apex", "arabidopsis"),
     ("silique", "arabidopsis"),

api/resources/gene_expression.py

@@ -1,26 +1,12 @@
-"""
-Reena Obmina | BCB330 Project 2025-2026 | University of Toronto
-
-REST endpoint for gene expression queries across all eFP databases.
-
-Routes: GET /gene_expression/expression/<database>/<gene_id>
-
-All gene IDs are validated by species before reaching the query layer.
-Probeset conversion is applied automatically for microarray databases.
-"""
 from flask_restx import Namespace, Resource
 from markupsafe import escape
 
 from api.services.efp_data import query_efp_database_dynamic
 from api.utils.bar_utils import BARUtils
 from api.utils.gene_id_utils import (
-    CROSS_SPECIES_DATABASES,
     DATABASE_SPECIES,
-    PROBESET_DATABASES,
-    convert_gene_to_probeset,
-    is_probeset_id,
-    normalize_gene_id,
-    validate_gene_id,
+    GeneIdUtils,
+    DATABASE_EFP_PROJECT,
 )
 
 gene_expression = Namespace(
@@ -46,38 +32,21 @@
 )
 class GeneExpression(Resource):
     def get(self, database, gene_id):
-        """Retrieve expression values for a gene from a given eFP database.
-        """
+        """Retrieve expression values for a gene from a given eFP database."""
         database = str(escape(database))
         gene_id = str(escape(gene_id))
 
-        # 1. Resolve database species and expected input species.
-        #    Cross-species databases (e.g. phelipanche) accept an Arabidopsis AGI
-        #    even though the database itself belongs to a different species.
         species = DATABASE_SPECIES.get(database)
         if species is None:
             return BARUtils.error_exit(f"Unknown database '{database}'"), 400
-        input_species = CROSS_SPECIES_DATABASES.get(database, species)
 
-        # 2. If the caller already supplied a probeset ID, use it directly
-        if is_probeset_id(gene_id):
+        if GeneIdUtils.is_probeset_id(gene_id):
             query_id = gene_id
         else:
-            # 3. Validate gene ID format against the expected input species regex
-            if not validate_gene_id(gene_id, input_species):
-                return BARUtils.error_exit(f"Invalid {input_species} gene ID: '{gene_id}'"), 400
-
-            # 4. Normalise (e.g. strip maize transcript suffix _T##)
-            gene_id = normalize_gene_id(gene_id, species)
-
-            # 5. Microarray / non-direct databases need gene ID -> probeset conversion
-            if database in PROBESET_DATABASES:
-                probeset, err = convert_gene_to_probeset(gene_id, species, database)
-                if err:
-                    return BARUtils.error_exit(err), 404
-                query_id = probeset
-            else:
-                query_id = gene_id
+            if not GeneIdUtils.validate_gene_for_database(gene_id, database):
+                label = DATABASE_EFP_PROJECT.get(database) or species or database
+                return BARUtils.error_exit(f"Invalid gene ID for {label}: '{gene_id}'"), 400
+            query_id = GeneIdUtils.normalize_gene_id(gene_id, species)
 
         result = query_efp_database_dynamic(database, query_id)
 

api/utils/efp_utils.py

@@ -57,12 +57,12 @@ def is_efp_input_valid(efp, view, mode, gene_1, gene_2=None):
 
         # Maybe this part could be improved
         if efp == "efp_arabidopsis":
-            # Validate gene ids
-            if not BARUtils.is_arabidopsis_gene_valid(gene_1):
+            # Accept AGI format (AT1G01010) or microarray probeset IDs (267643_at)
+            if not BARUtils.is_efp_gene_valid(gene_1, "efp_arabidopsis"):
                 return False, "Gene 1 is invalid."
 
             if mode == "Compare":
-                if not BARUtils.is_arabidopsis_gene_valid(gene_2):
+                if not BARUtils.is_efp_gene_valid(gene_2, "efp_arabidopsis"):
                     return False, "Gene 2 is invalid."
 
         if efp == "efp_arachis":