feat: initialize rust backend with axum server, seaorm models, and project scaffolding

.gitignore

@@ -0,0 +1,17 @@
+# BACKEND
+target/
+Cargo.lock
+config.yaml
+backend/data/zhealth.db
+backend/data/zhealth.db-wal
+backend/data/zhealth.db-shm
+
+# FRONTEND
+
+# AI
+
+# OS
+.DS_Store
+
+# IDE
+.vscode/

Makefile

@@ -0,0 +1,72 @@
+# zhealth Makefile
+# Run `make help` to see available commands
+
+.PHONY: help dev build release lint typecheck test clean serve
+
+# Default target
+help:
+	@echo "Available commands:"
+	@echo "  make dev       - Start development servers"
+	@echo "  make build     - Build for development"
+	@echo "  make release   - Build optimized production bundle"
+	@echo "  make lint      - Run linters (Clippy + ESLint)"
+	@echo "  make typecheck - Type checking (Rust + TypeScript)"
+	@echo "  make test      - Run all tests"
+	@echo "  make serve     - Serve production build locally"
+	@echo "  make clean     - Clean build artifacts"
+
+# Backend commands
+.PHONY: backend-dev backend-build backend-release backend-lint backend-test
+
+backend-dev:
+	cd backend && cargo run
+
+backend-build:
+	cd backend && cargo build
+
+backend-release:
+	cd backend && cargo build --release
+
+backend-lint:
+	cd backend && cargo clippy -- -D warnings
+
+backend-test:
+	cd backend && cargo test
+
+# Frontend commands (placeholder for when frontend is set up)
+.PHONY: frontend-dev frontend-build frontend-release frontend-lint frontend-test
+
+frontend-dev:
+	@echo "Frontend not yet configured"
+
+frontend-build:
+	@echo "Frontend not yet configured"
+
+frontend-release:
+	@echo "Frontend not yet configured"
+
+frontend-lint:
+	@echo "Frontend not yet configured"
+
+frontend-test:
+	@echo "Frontend not yet configured"
+
+# Combined commands
+dev: backend-dev
+
+build: backend-build frontend-build
+
+release: backend-release frontend-release
+
+lint: backend-lint frontend-lint
+
+typecheck: backend-lint frontend-lint
+
+test: backend-test frontend-test
+
+serve:
+	cd backend && cargo run --release
+
+clean:
+	cd backend && cargo clean
+	@echo "Cleaned backend artifacts"

PROJECT_MGMT/coding_standards.md

@@ -89,12 +89,17 @@ paths:
   database: "./data/zhealth.db"
   logs: "./logs"
 
+logging:
+  level: "info"  # trace | debug | info | warn | error
+
 auth:
-  jwt_secret: "${JWT_SECRET}"  # Loaded from env
-  token_expiry_hours: 24
+  session_secret: "${SESSION_SECRET}"  # Loaded from env
+  session_expiry_hours: 24
+  cookie_name: "zhealth_session"
 
 ai:
   provider: "gemini"  # gemini | openai | anthropic
+  model: "gemini-3-flash-preview"
   api_key: "${AI_API_KEY}"
 ```
 

PROJECT_MGMT/phased_approach.md

@@ -10,7 +10,7 @@
 ## Phase 2: API & Core Auth
 
 - API Development with Axum.
-- Implementation of Auth logic (JWT, Middleware, RBAC enforcement).
+- Implementation of Auth logic (Session-based, Middleware, RBAC enforcement).
 - Frontend Development (Vite + React + TS) - Initial Layout.
 
 ## Phase 3: Integration

backend/Cargo.toml

@@ -0,0 +1,43 @@
+[package]
+name = "zhealth-backend"
+version = "0.1.0"
+edition = "2024"
+
+[[bin]]
+name = "zhealth"
+path = "src/main.rs"
+
+[dependencies]
+# Web Framework
+axum = "0.8"
+tokio = { version = "1", features = ["full"] }
+tower = "0.5"
+tower-http = { version = "0.6", features = ["cors", "trace"] }
+
+# Database
+sea-orm = { version = "1.1", features = ["sqlx-sqlite", "runtime-tokio-rustls", "macros"] }
+
+# Serialization
+serde = { version = "1", features = ["derive"] }
+serde_yaml = "0.9"
+
+# Auth
+argon2 = "0.5"
+rand = "0.8"
+
+# Time
+chrono = { version = "0.4", features = ["serde"] }
+
+# Logging
+tracing = "0.1"
+tracing-subscriber = { version = "0.3", features = ["env-filter"] }
+
+# Error handling
+thiserror = "2"
+anyhow = "1"
+
+# Regex for config env expansion
+regex = "1"
+
+# CLI
+argh = "0.1"

backend/sample.config.yaml

@@ -0,0 +1,25 @@
+# Sample Configuration for zhealth-backend
+# Copy this to config.yaml and update values as needed.
+# Secrets should be loaded from environment variables using ${VAR_NAME} syntax.
+
+server:
+  host: "127.0.0.1"
+  port: 3000
+
+paths:
+  database: "./data/zhealth.db"
+  logs: "./logs"
+
+logging:
+  level: "info"  # Options: trace | debug | info | warn | error
+
+auth:
+  session_secret: "${SESSION_SECRET}"
+  session_expiry_hours: 24
+  cookie_name: "zhealth_session"
+  cookie_secure: false  # Set to true in production with HTTPS
+
+ai:
+  provider: "gemini"  # Options: gemini | openai | anthropic
+  model: "gemini-3-flash-preview"
+  api_key: "${AI_API_KEY}"

backend/src/cli.rs

@@ -0,0 +1,33 @@
+//! CLI definition using argh.
+
+use argh::FromArgs;
+
+/// zhealth: AI-powered health management platform
+#[derive(FromArgs)]
+pub struct Args {
+    #[argh(subcommand)]
+    pub command: Command,
+}
+
+#[derive(FromArgs)]
+#[argh(subcommand)]
+pub enum Command {
+    Serve(ServeCommand),
+    Migrate(MigrateCommand),
+    Version(VersionCommand),
+}
+
+/// Start the server (runs migrations first)
+#[derive(FromArgs)]
+#[argh(subcommand, name = "serve")]
+pub struct ServeCommand {}
+
+/// Run database migrations only
+#[derive(FromArgs)]
+#[argh(subcommand, name = "migrate")]
+pub struct MigrateCommand {}
+
+/// Show version information
+#[derive(FromArgs)]
+#[argh(subcommand, name = "version")]
+pub struct VersionCommand {}

backend/src/config.rs

@@ -0,0 +1,71 @@
+//! Configuration loading and parsing.
+
+use serde::Deserialize;
+use std::fs;
+use std::path::Path;
+
+#[derive(Debug, Deserialize)]
+pub struct Config {
+    pub server: ServerConfig,
+    pub paths: PathsConfig,
+    pub logging: LoggingConfig,
+    pub auth: AuthConfig,
+    pub ai: AiConfig,
+}
+
+#[derive(Debug, Deserialize)]
+pub struct ServerConfig {
+    pub host: String,
+    pub port: u16,
+}
+
+#[derive(Debug, Deserialize)]
+pub struct PathsConfig {
+    pub database: String,
+    pub logs: String,
+}
+
+#[derive(Debug, Deserialize)]
+pub struct LoggingConfig {
+    pub level: String,
+}
+
+#[derive(Debug, Deserialize)]
+pub struct AuthConfig {
+    pub session_secret: String,
+    pub session_expiry_hours: u32,
+    pub cookie_name: String,
+    pub cookie_secure: bool,
+}
+
+#[derive(Debug, Deserialize)]
+pub struct AiConfig {
+    pub provider: String,
+    pub model: String,
+    pub api_key: String,
+}
+
+impl Config {
+    /// Load configuration from a YAML file.
+    pub fn load<P: AsRef<Path>>(path: P) -> anyhow::Result<Self> {
+        let content = fs::read_to_string(path)?;
+        // Expand environment variables in the format ${VAR_NAME}
+        let expanded = expand_env_vars(&content);
+        let config: Config = serde_yaml::from_str(&expanded)?;
+        Ok(config)
+    }
+}
+
+/// Expand environment variables in the format ${VAR_NAME}.
+fn expand_env_vars(content: &str) -> String {
+    let mut result = content.to_string();
+    let re = regex::Regex::new(r"\$\{([^}]+)\}").unwrap();
+
+    for cap in re.captures_iter(content) {
+        let var_name = &cap[1];
+        let var_value = std::env::var(var_name).unwrap_or_default();
+        result = result.replace(&cap[0], &var_value);
+    }
+
+    result
+}

backend/src/db.rs

@@ -0,0 +1,42 @@
+//! Database connection and migrations.
+
+use sea_orm::{ConnectionTrait, Database, DatabaseConnection, DbBackend, DbErr, Schema, Statement};
+use sea_orm::sea_query::SqliteQueryBuilder;
+
+use crate::config::Config;
+use crate::models::bio::{biomarker_entry, biomarker_type};
+use crate::models::user::{session, user};
+
+/// Connect to the SQLite database.
+pub async fn connect(config: &Config) -> Result<DatabaseConnection, DbErr> {
+    let db_path = &config.paths.database;
+
+    // Ensure the data directory exists
+    if let Some(parent) = std::path::Path::new(db_path).parent() {
+        std::fs::create_dir_all(parent).ok();
+    }
+
+    let db_url = format!("sqlite:{}?mode=rwc", db_path);
+    Database::connect(&db_url).await
+}
+
+/// Run migrations to create tables if they don't exist.
+pub async fn run_migrations(db: &DatabaseConnection) -> Result<(), DbErr> {
+    let schema = Schema::new(DbBackend::Sqlite);
+
+    // Create table statements
+    let statements = vec![
+        schema.create_table_from_entity(user::Entity),
+        schema.create_table_from_entity(session::Entity),
+        schema.create_table_from_entity(biomarker_type::Entity),
+        schema.create_table_from_entity(biomarker_entry::Entity),
+    ];
+
+    for mut stmt in statements {
+        let sql = stmt.if_not_exists().to_string(SqliteQueryBuilder);
+        db.execute(Statement::from_string(DbBackend::Sqlite, sql))
+            .await?;
+    }
+
+    Ok(())
+}

backend/src/main.rs

@@ -0,0 +1,75 @@
+mod cli;
+mod config;
+mod db;
+mod models;
+
+use axum::{routing::get, Router};
+use std::net::SocketAddr;
+use tracing_subscriber::{layer::SubscriberExt, util::SubscriberInitExt};
+
+use cli::{Args, Command};
+
+const VERSION: &str = env!("CARGO_PKG_VERSION");
+
+#[tokio::main]
+async fn main() -> anyhow::Result<()> {
+    let args: Args = argh::from_env();
+
+    match args.command {
+        Command::Version(_) => {
+            println!("zhealth {}", VERSION);
+        }
+        Command::Migrate(_) => {
+            let config = config::Config::load("config.yaml")?;
+            init_logging(&config);
+            
+            tracing::info!("Running migrations...");
+            let db = db::connect(&config).await?;
+            db::run_migrations(&db).await?;
+            tracing::info!("Migrations complete.");
+        }
+        Command::Serve(_) => {
+            let config = config::Config::load("config.yaml")?;
+            init_logging(&config);
+
+            // Run migrations first
+            tracing::info!("Running migrations...");
+            let db = db::connect(&config).await?;
+            db::run_migrations(&db).await?;
+            tracing::info!("Migrations complete.");
+
+            // Start server
+            tracing::info!("Starting zhealth-backend...");
+            let app = Router::new()
+                .route("/", get(root))
+                .route("/health", get(health_check));
+
+            let addr: SocketAddr = format!("{}:{}", config.server.host, config.server.port)
+                .parse()
+                .expect("Invalid server address");
+
+            tracing::info!("Listening on http://{}", addr);
+
+            let listener = tokio::net::TcpListener::bind(addr).await?;
+            axum::serve(listener, app).await?;
+        }
+    }
+
+    Ok(())
+}
+
+fn init_logging(config: &config::Config) {
+    let log_level = config.logging.level.parse().unwrap_or(tracing::Level::INFO);
+    tracing_subscriber::registry()
+        .with(tracing_subscriber::fmt::layer())
+        .with(tracing_subscriber::filter::LevelFilter::from_level(log_level))
+        .init();
+}
+
+async fn root() -> &'static str {
+    "zhealth API"
+}
+
+async fn health_check() -> &'static str {
+    "OK"
+}

backend/src/models/bio/biomarker_entry.rs

@@ -0,0 +1,56 @@
+//! BiomarkerEntry entity - user-logged biomarker values.
+
+use sea_orm::entity::prelude::*;
+use serde::{Deserialize, Serialize};
+
+#[derive(Clone, Debug, PartialEq, DeriveEntityModel, Serialize, Deserialize)]
+#[sea_orm(table_name = "biomarker_entries")]
+pub struct Model {
+    #[sea_orm(primary_key)]
+    pub id: i32,
+
+    pub user_id: i32,
+    pub biomarker_type_id: i32,
+
+    /// The measured value
+    pub value: f64,
+
+    /// Date when the measurement was taken
+    pub measured_at: Date,
+
+    #[sea_orm(column_type = "Text", nullable)]
+    pub notes: Option<String>,
+
+    pub created_at: DateTime,
+}
+
+#[derive(Copy, Clone, Debug, EnumIter, DeriveRelation)]
+pub enum Relation {
+    #[sea_orm(
+        belongs_to = "crate::models::user::user::Entity",
+        from = "Column::UserId",
+        to = "crate::models::user::user::Column::Id"
+    )]
+    User,
+
+    #[sea_orm(
+        belongs_to = "super::biomarker_type::Entity",
+        from = "Column::BiomarkerTypeId",
+        to = "super::biomarker_type::Column::Id"
+    )]
+    BiomarkerType,
+}
+
+impl Related<crate::models::user::user::Entity> for Entity {
+    fn to() -> RelationDef {
+        Relation::User.def()
+    }
+}
+
+impl Related<super::biomarker_type::Entity> for Entity {
+    fn to() -> RelationDef {
+        Relation::BiomarkerType.def()
+    }
+}
+
+impl ActiveModelBehavior for ActiveModel {}

backend/src/models/bio/biomarker_type.rs

@@ -0,0 +1,43 @@
+//! BiomarkerType entity - the knowledge base of available biomarkers.
+
+use sea_orm::entity::prelude::*;
+use serde::{Deserialize, Serialize};
+
+#[derive(Clone, Debug, PartialEq, DeriveEntityModel, Serialize, Deserialize)]
+#[sea_orm(table_name = "biomarker_types")]
+pub struct Model {
+    #[sea_orm(primary_key)]
+    pub id: i32,
+
+    #[sea_orm(unique)]
+    pub name: String,
+
+    /// Category: lipid_panel, metabolic, vitamins, hormones, etc.
+    pub category: String,
+
+    /// Unit of measurement: mg/dL, mmol/L, ng/mL, etc.
+    pub unit: String,
+
+    /// Lower bound of normal reference range
+    pub reference_min: Option<f64>,
+
+    /// Upper bound of normal reference range
+    pub reference_max: Option<f64>,
+
+    #[sea_orm(column_type = "Text", nullable)]
+    pub description: Option<String>,
+}
+
+#[derive(Copy, Clone, Debug, EnumIter, DeriveRelation)]
+pub enum Relation {
+    #[sea_orm(has_many = "super::biomarker_entry::Entity")]
+    Entries,
+}
+
+impl Related<super::biomarker_entry::Entity> for Entity {
+    fn to() -> RelationDef {
+        Relation::Entries.def()
+    }
+}
+
+impl ActiveModelBehavior for ActiveModel {}

backend/src/models/bio/mod.rs

@@ -0,0 +1,7 @@
+//! Biomarker entities for health data tracking.
+
+pub mod biomarker_entry;
+pub mod biomarker_type;
+
+pub use biomarker_entry::Entity as BiomarkerEntry;
+pub use biomarker_type::Entity as BiomarkerType;

backend/src/models/mod.rs

@@ -0,0 +1,7 @@
+//! Database models for zhealth.
+
+pub mod bio;
+pub mod user;
+
+pub use bio::{BiomarkerEntry, BiomarkerType};
+pub use user::{Session, User};

backend/src/models/user/mod.rs

@@ -0,0 +1,7 @@
+//! User and session entities for authentication.
+
+pub mod session;
+pub mod user;
+
+pub use session::Entity as Session;
+pub use user::Entity as User;

backend/src/models/user/session.rs

@@ -0,0 +1,33 @@
+//! Session entity for cookie-based authentication.
+
+use sea_orm::entity::prelude::*;
+use serde::{Deserialize, Serialize};
+
+#[derive(Clone, Debug, PartialEq, Eq, DeriveEntityModel, Serialize, Deserialize)]
+#[sea_orm(table_name = "sessions")]
+pub struct Model {
+    #[sea_orm(primary_key, auto_increment = false)]
+    pub id: String,
+
+    pub user_id: i32,
+    pub expires_at: DateTime,
+    pub created_at: DateTime,
+}
+
+#[derive(Copy, Clone, Debug, EnumIter, DeriveRelation)]
+pub enum Relation {
+    #[sea_orm(
+        belongs_to = "super::user::Entity",
+        from = "Column::UserId",
+        to = "super::user::Column::Id"
+    )]
+    User,
+}
+
+impl Related<super::user::Entity> for Entity {
+    fn to() -> RelationDef {
+        Relation::User.def()
+    }
+}
+
+impl ActiveModelBehavior for ActiveModel {}

backend/src/models/user/user.rs

@@ -0,0 +1,37 @@
+//! User entity for authentication.
+
+use sea_orm::entity::prelude::*;
+use serde::{Deserialize, Serialize};
+
+#[derive(Clone, Debug, PartialEq, Eq, DeriveEntityModel, Serialize, Deserialize)]
+#[sea_orm(table_name = "users")]
+pub struct Model {
+    #[sea_orm(primary_key)]
+    pub id: i32,
+
+    #[sea_orm(unique)]
+    pub username: String,
+
+    #[sea_orm(column_type = "Text")]
+    pub password_hash: String,
+
+    #[sea_orm(unique)]
+    pub email: String,
+
+    pub created_at: DateTime,
+    pub updated_at: DateTime,
+}
+
+#[derive(Copy, Clone, Debug, EnumIter, DeriveRelation)]
+pub enum Relation {
+    #[sea_orm(has_many = "super::session::Entity")]
+    Sessions,
+}
+
+impl Related<super::session::Entity> for Entity {
+    fn to() -> RelationDef {
+        Relation::Sessions.def()
+    }
+}
+
+impl ActiveModelBehavior for ActiveModel {}