feat(viz-backend): add endpoints

Author: glichtner

apps/viz-backend/app/database.py

@@ -1,7 +1,7 @@
 from urllib.parse import quote
 
 from settings import config
-from sqlalchemy import create_engine, event
+from sqlalchemy import MetaData, Table, create_engine, event
 from sqlalchemy.engine.interfaces import DBAPIConnection
 from sqlalchemy.ext.declarative import declarative_base
 from sqlalchemy.orm import sessionmaker
@@ -46,3 +46,78 @@ def set_timezone(
 SessionLocal = sessionmaker(autocommit=False, autoflush=False, bind=engine)
 
 Base = declarative_base()
+
+metadata = MetaData()
+
+
+def reflect_tables() -> dict[str, Table]:
+    """
+    Reflect tables and views from the specified schemas.
+    Returns dynamically reflected tables.
+    """
+    result_schema = config.omop.result_schema  # Schema for result views
+    data_schema = config.omop.data_schema  # Schema for data tables
+
+    interval_result = Table(
+        "interval_result", metadata, autoload_with=engine, schema=result_schema
+    )
+    full_day_coverage = Table(
+        "full_day_coverage", metadata, autoload_with=engine, schema=result_schema
+    )
+    partial_day_coverage = Table(
+        "partial_day_coverage", metadata, autoload_with=engine, schema=result_schema
+    )
+    criterion = Table("criterion", metadata, autoload_with=engine, schema=result_schema)
+
+    concept = Table("concept", metadata, autoload_with=engine, schema=data_schema)
+    person = Table("person", metadata, autoload_with=engine, schema=data_schema)
+    measurement = Table(
+        "measurement", metadata, autoload_with=engine, schema=data_schema
+    )
+    visit_occurrence = Table(
+        "visit_occurrence", metadata, autoload_with=engine, schema=data_schema
+    )
+    drug_exposure = Table(
+        "drug_exposure", metadata, autoload_with=engine, schema=data_schema
+    )
+    observation = Table(
+        "observation", metadata, autoload_with=engine, schema=data_schema
+    )
+    condition_occurrence = Table(
+        "condition_occurrence", metadata, autoload_with=engine, schema=data_schema
+    )
+    procedure_occurrence = Table(
+        "procedure_occurrence", metadata, autoload_with=engine, schema=data_schema
+    )
+
+    return {
+        "interval_result": interval_result,
+        "full_day_coverage": full_day_coverage,
+        "partial_day_coverage": partial_day_coverage,
+        "criterion": criterion,
+        "concept": concept,
+        "person": person,
+        "measurement": measurement,
+        "visit_occurrence": visit_occurrence,
+        "drug_exposure": drug_exposure,
+        "observation": observation,
+        "condition_occurrence": condition_occurrence,
+        "procedure_occurrence": procedure_occurrence,
+    }
+
+
+# Reflect tables and expose them
+tables = reflect_tables()
+interval_result = tables["interval_result"]
+full_day_coverage = tables["full_day_coverage"]
+partial_day_coverage = tables["partial_day_coverage"]
+criterion = tables["criterion"]
+
+concept = tables["concept"]
+person = tables["person"]
+measurement = tables["measurement"]
+visit_occurrence = tables["visit_occurrence"]
+drug_exposure = tables["drug_exposure"]
+observation = tables["observation"]
+condition_occurrence = tables["condition_occurrence"]
+procedure_occurrence = tables["procedure_occurrence"]