Deleted some unused files, renamed efp proxy to gene_expression

Author: rmobmina

api/Archive/embryo_efp_feb_6_2025_dump.sql

@@ -146,7 +146,7 @@ def create_app():
     from api.resources.efp_image import efp_image
     from api.resources.fastpheno import fastpheno
     from api.resources.llama3 import llama3
-    from api.resources.efp_proxy import efp_proxy_ns
+    from api.resources.efp_gene_expression import gene_expression
 
     bar_api.add_namespace(gene_information)
     bar_api.add_namespace(rnaseq_gene_expression)
@@ -161,7 +161,7 @@ def create_app():
     bar_api.add_namespace(efp_image)
     bar_api.add_namespace(fastpheno)
     bar_api.add_namespace(llama3)
-    bar_api.add_namespace(efp_proxy_ns)
+    bar_api.add_namespace(gene_expression)
     bar_api.init_app(bar_app)
     return bar_app
 

api/Archive/sample_data_results.csv

@@ -234,6 +234,44 @@ def _schema(species: str, charset: str = "latin1") -> DatabaseSpec:
     ("willow", "willow"),
 ]
 
+# databases that store Affymetrix/microarray probeset IDs instead of gene identifiers.
+# For Arabidopsis databases in this set, the API will auto-convert AGI → probeset
+# via the at_agi_lookup service before querying expression data.
+_PROBESET_DBS = {
+    # Arabidopsis microarray databases (Affymetrix ATH1 chip, need AGI→probeset lookup)
+    "affydb",
+    "arabidopsis_ecotypes",
+    "atgenexp",
+    "atgenexp_hormone",
+    "atgenexp_pathogen",
+    "atgenexp_plus",
+    "atgenexp_stress",
+    "guard_cell",
+    "hnahal",
+    "lateral_root_initiation",
+    "light_series",
+    "meristem_db",
+    "meristem_db_new",
+    "root",
+    "rohan",
+    "rpatel",
+    "seed_db",
+    # Non-Arabidopsis microarray databases (probeset IDs, no AGI lookup needed)
+    "barley_mas",
+    "barley_rma",
+    "human_developmental",
+    "human_developmental_SpongeLab",
+    "human_diseased",
+    "maize_gdowns",
+    "medicago_mas",
+    "medicago_rma",
+    "poplar",
+    "rice_mas",
+    "rice_rma",
+    "triticale",
+    "triticale_mas",
+}
+
 # databases that use utf8mb4 charset (all others default to latin1)
 _UTF8MB4 = {
     "actinidia_bud_development", "actinidia_flower_fruit_development",
@@ -281,7 +319,10 @@ def _schema(species: str, charset: str = "latin1") -> DatabaseSpec:
 # fmt: on
 
 SIMPLE_EFP_DATABASE_SCHEMAS: Dict[str, DatabaseSpec] = {
-    n: _schema(s, "utf8mb4" if n in _UTF8MB4 else "latin1")
+    n: {
+        **_schema(s, "utf8mb4" if n in _UTF8MB4 else "latin1"),
+        **({"identifier_type": "probeset"} if n in _PROBESET_DBS else {}),
+    }
     for n, s in _SPECS
 }
 

api/__init__.py

@@ -0,0 +1,64 @@
+from flask_restx import Namespace, Resource
+from markupsafe import escape
+
+from api import db
+from api.models.annotations_lookup import AtAgiLookup
+from api.services.efp_data import query_efp_database_dynamic, DYNAMIC_DATABASE_SCHEMAS
+
+gene_expression = Namespace(
+    'Gene Expression',
+    description='Gene expression data from BAR eFP databases',
+    path='/gene_expression',
+)
+
+
+@gene_expression.route("/expression/<string:database>/<string:gene_id>")
+@gene_expression.doc(
+    description="Retrieve gene expression values from a specified eFP database."
+)
+@gene_expression.param(
+    "gene_id",
+    "Gene ID (AGI format like AT1G01010 or probeset like 261585_at)",
+    _in="path",
+    default="AT1G01010",
+)
+@gene_expression.param(
+    "database",
+    "Database name (e.g., sample_data, klepikova, single_cell)",
+    _in="path",
+    default="klepikova",
+)
+class GeneExpression(Resource):
+    def get(self, database, gene_id):
+
+        database = escape(database)
+        gene_id = escape(gene_id)
+
+        upper_id = gene_id.upper()
+        is_agi = upper_id.startswith("AT") and "G" in upper_id
+
+        # for databases that store probeset IDs, convert AGI to probeset via at_agi_lookup
+        schema = DYNAMIC_DATABASE_SCHEMAS.get(str(database))
+        if schema and is_agi and schema.get("identifier_type") == "probeset":
+            subquery = (
+                db.select(AtAgiLookup.probeset)
+                .where(AtAgiLookup.agi == upper_id)
+                .order_by(AtAgiLookup.date.desc())
+                .limit(1)
+                .subquery()
+            )
+            sq_query = db.session.query(subquery)
+            if sq_query.count() > 0:
+                gene_id = sq_query[0][0]
+            else:
+                return {"success": False, "error": f"No probeset found for {gene_id}", "error_code": 404}, 404
+
+        result = query_efp_database_dynamic(database, gene_id, sample_ids=None)
+
+        if result["success"]:
+            return result
+        else:
+            return result, result.get("error_code", 500)
+
+
+gene_expression.add_resource(GeneExpression, '/expression/<string:database>/<string:gene_id>')