Refactor server into routers and add database backend

.gitignore

@@ -142,6 +142,7 @@ vite.config.ts.timestamp-*
 *~
 .venv/
 venv/
+__pycache__/
 
 # Visual Studio Code
 .vscode/

backend/auth.py

@@ -0,0 +1,19 @@
+################################################################################
+## Copyright 2025 Lawrence Livermore National Security, LLC. and Binghamton University.
+## See the top-level LICENSE file for details.
+##
+## SPDX-License-Identifier: Apache-2.0
+################################################################################
+
+from fastapi import Header, HTTPException, status
+from typing import Optional
+
+
+async def get_forwarded_user(x_forwarded_user: Optional[str] = Header(None, alias="X-Forwarded-User")) -> str:
+    """Extract authenticated user from X-Forwarded-User header"""
+    if not x_forwarded_user:
+        raise HTTPException(
+            status_code=status.HTTP_401_UNAUTHORIZED,
+            detail="Missing X-Forwarded-User header. Authentication required.",
+        )
+    return x_forwarded_user

backend/database/engine.py

@@ -0,0 +1,51 @@
+################################################################################
+## Copyright 2025 Lawrence Livermore National Security, LLC. and Binghamton University.
+## See the top-level LICENSE file for details.
+##
+## SPDX-License-Identifier: Apache-2.0
+##########################################################################
+
+from sqlalchemy.ext.asyncio import create_async_engine, AsyncSession, async_sessionmaker
+from sqlalchemy.exc import OperationalError
+from sqlalchemy.orm import declarative_base
+import os
+
+if "MARIADB_HOST" not in os.environ:
+    engine = AsyncSessionLocal = None
+else:
+    DB_USER = os.getenv("MARIADB_USER", "user")
+    DB_PASSWORD = os.getenv("MARIADB_PASSWORD", "password")
+    DB_HOST = os.getenv("MARIADB_HOST", "localhost")
+    DB_PORT = os.getenv("MARIADB_PORT", "8080")
+    DATABASE_URL = f"mysql+aiomysql://{DB_USER}:{DB_PASSWORD}@{DB_HOST}:{DB_PORT}"
+
+    try:
+        engine = create_async_engine(
+            DATABASE_URL,
+            echo=True,
+            pool_size=10,
+            max_overflow=20,
+            pool_pre_ping=True,
+            pool_recycle=3600,
+        )
+
+        AsyncSessionLocal = async_sessionmaker(engine, class_=AsyncSession, expire_on_commit=False)
+    except OperationalError:
+        engine = AsyncSessionLocal = None
+
+Base = declarative_base()
+
+
+async def get_db():
+    if AsyncSessionLocal is None:
+        yield None
+        return
+    async with AsyncSessionLocal() as session:
+        try:
+            yield session
+            await session.commit()
+        except Exception:
+            await session.rollback()
+            raise
+        finally:
+            await session.close()

backend/database/models.py

@@ -0,0 +1,71 @@
+################################################################################
+## Copyright 2025 Lawrence Livermore National Security, LLC. and Binghamton University.
+## See the top-level LICENSE file for details.
+##
+## SPDX-License-Identifier: Apache-2.0
+################################################################################
+
+from sqlalchemy import Column, String, DateTime, Boolean, ForeignKey, Index, Text, JSON, Float
+from sqlalchemy.orm import relationship, Mapped, mapped_column
+from datetime import datetime
+from typing import Optional
+from backend.database.engine import Base
+
+
+class Project(Base):
+    __tablename__ = "projects"
+
+    id: Mapped[str] = mapped_column(String(255), primary_key=True)
+    user: Mapped[str] = mapped_column(String(255), nullable=False, index=True)
+    name: Mapped[str] = mapped_column(String(255), nullable=False)
+    created_at: Mapped[datetime] = mapped_column(DateTime, default=datetime.utcnow, nullable=False)
+    last_modified: Mapped[datetime] = mapped_column(
+        DateTime, default=datetime.utcnow, onupdate=datetime.utcnow, nullable=False
+    )
+
+    experiments: Mapped[list["Experiment"]] = relationship(
+        "Experiment", back_populates="project", cascade="all, delete-orphan"
+    )
+
+    __table_args__ = (Index("idx_user_last_modified", "user", "last_modified"),)
+
+
+class Experiment(Base):
+    __tablename__ = "experiments"
+
+    id: Mapped[str] = mapped_column(String(255), primary_key=True)
+    project_id: Mapped[str] = mapped_column(String(255), ForeignKey("projects.id", ondelete="CASCADE"), nullable=False)
+    user: Mapped[str] = mapped_column(String(255), nullable=False, index=True)
+    name: Mapped[str] = mapped_column(String(255), nullable=False)
+    created_at: Mapped[datetime] = mapped_column(DateTime, default=datetime.utcnow, nullable=False)
+    last_modified: Mapped[datetime] = mapped_column(
+        DateTime, default=datetime.utcnow, onupdate=datetime.utcnow, nullable=False
+    )
+    is_running: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
+
+    # System state fields
+    smiles: Mapped[Optional[str]] = mapped_column(Text, nullable=True)
+    problem_type: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
+    problem_name: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
+    system_prompt: Mapped[Optional[str]] = mapped_column(Text, nullable=True)
+    problem_prompt: Mapped[Optional[str]] = mapped_column(Text, nullable=True)
+    property_type: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
+    custom_property_name: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
+    custom_property_desc: Mapped[Optional[str]] = mapped_column(Text, nullable=True)
+    custom_property_ascending: Mapped[Optional[bool]] = mapped_column(Boolean, nullable=True)
+
+    # Complex JSON fields for nested data structures
+    tree_nodes: Mapped[Optional[str]] = mapped_column(JSON, nullable=True)
+    edges: Mapped[Optional[str]] = mapped_column(JSON, nullable=True)
+    metrics_history: Mapped[Optional[str]] = mapped_column(JSON, nullable=True)
+    visible_metrics: Mapped[Optional[str]] = mapped_column(JSON, nullable=True)
+    graph_state: Mapped[Optional[str]] = mapped_column(JSON, nullable=True)
+    auto_zoom: Mapped[Optional[bool]] = mapped_column(Boolean, nullable=True)
+    sidebar_state: Mapped[Optional[str]] = mapped_column(JSON, nullable=True)
+
+    # Experiment context
+    experiment_context: Mapped[Optional[str]] = mapped_column(Text, nullable=True)
+
+    project: Mapped["Project"] = relationship("Project", back_populates="experiments")
+
+    __table_args__ = (Index("idx_user_project", "user", "project_id"),)

backend/database/schemas.py

@@ -0,0 +1,109 @@
+################################################################################
+## Copyright 2025 Lawrence Livermore National Security, LLC. and Binghamton University.
+## See the top-level LICENSE file for details.
+##
+## SPDX-License-Identifier: Apache-2.0
+################################################################################
+
+from pydantic import BaseModel, Field
+from datetime import datetime
+from typing import List, Optional, Any
+
+
+class ExperimentBase(BaseModel):
+    name: str
+
+
+class ExperimentCreate(ExperimentBase):
+    pass
+
+
+class ExperimentUpdate(BaseModel):
+    name: Optional[str] = None
+    is_running: Optional[bool] = None
+
+    # System state fields
+    smiles: Optional[str] = None
+    problem_type: Optional[str] = Field(None, alias="problemType")
+    problem_name: Optional[str] = Field(None, alias="problemName")
+    system_prompt: Optional[str] = Field(None, alias="systemPrompt")
+    problem_prompt: Optional[str] = Field(None, alias="problemPrompt")
+    property_type: Optional[str] = Field(None, alias="propertyType")
+    custom_property_name: Optional[str] = Field(None, alias="customPropertyName")
+    custom_property_desc: Optional[str] = Field(None, alias="customPropertyDesc")
+    custom_property_ascending: Optional[bool] = Field(None, alias="customPropertyAscending")
+
+    # Complex nested data (stored as JSON)
+    tree_nodes: Optional[Any] = Field(None, alias="treeNodes")
+    edges: Optional[Any] = None
+    metrics_history: Optional[Any] = Field(None, alias="metricsHistory")
+    visible_metrics: Optional[Any] = Field(None, alias="visibleMetrics")
+    graph_state: Optional[Any] = Field(None, alias="graphState")
+    auto_zoom: Optional[bool] = Field(None, alias="autoZoom")
+    sidebar_state: Optional[Any] = Field(None, alias="sidebarState")
+
+    # Experiment context
+    experiment_context: Optional[str] = Field(None, alias="experimentContext")
+
+    class Config:
+        populate_by_name = True
+
+
+class Experiment(ExperimentBase):
+    id: str
+    project_id: str = Field(..., alias="projectId")
+    user: str
+    created_at: datetime = Field(..., alias="createdAt")
+    last_modified: datetime = Field(..., alias="lastModified")
+    is_running: Optional[bool] = Field(None, alias="isRunning")
+
+    # System state fields
+    smiles: Optional[str] = None
+    problem_type: Optional[str] = Field(None, alias="problemType")
+    problem_name: Optional[str] = Field(None, alias="problemName")
+    system_prompt: Optional[str] = Field(None, alias="systemPrompt")
+    problem_prompt: Optional[str] = Field(None, alias="problemPrompt")
+    property_type: Optional[str] = Field(None, alias="propertyType")
+    custom_property_name: Optional[str] = Field(None, alias="customPropertyName")
+    custom_property_desc: Optional[str] = Field(None, alias="customPropertyDesc")
+    custom_property_ascending: Optional[bool] = Field(None, alias="customPropertyAscending")
+
+    # Complex nested data
+    tree_nodes: Optional[Any] = Field(None, alias="treeNodes")
+    edges: Optional[Any] = None
+    metrics_history: Optional[Any] = Field(None, alias="metricsHistory")
+    visible_metrics: Optional[Any] = Field(None, alias="visibleMetrics")
+    graph_state: Optional[Any] = Field(None, alias="graphState")
+    auto_zoom: Optional[bool] = Field(None, alias="autoZoom")
+    sidebar_state: Optional[Any] = Field(None, alias="sidebarState")
+
+    # Experiment context
+    experiment_context: Optional[str] = Field(None, alias="experimentContext")
+
+    class Config:
+        from_attributes = True
+        populate_by_name = True
+
+
+class ProjectBase(BaseModel):
+    name: str
+
+
+class ProjectCreate(ProjectBase):
+    pass
+
+
+class ProjectUpdate(ProjectBase):
+    pass
+
+
+class Project(ProjectBase):
+    id: str
+    user: str
+    created_at: datetime = Field(..., alias="createdAt")
+    last_modified: datetime = Field(..., alias="lastModified")
+    experiments: List[Experiment] = []
+
+    class Config:
+        from_attributes = True
+        populate_by_name = True