CHANGELOG_SQLITE_HF.md

Changelog: SQLite Migration & Hugging Face Spaces Deployment

Date: 2026-06-09
Branch: feature/hugging-face-deploy
Commits: fd94aa0..1cbbcaa (3 commits)

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Overview

Migrated AILIXIR from MySQL/MariaDB to SQLite and deployed the entire platform to 5 Hugging Face Spaces with GitHub-to-HF auto-sync.

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Part 1: SQLite Database Migration

Migration Fixes

4 migration files were modified to remove MySQL-specific syntax:

File	Problem	Fix
database/migrations/2026_04_20_135553_create_admets_table.php	useCurrentOnUpdate() — MySQL-only	Replaced manual timestamps with $table->timestamps()
database/migrations/2026_04_20_044726_create_screening_results_table.php	output column not nullable, causing ->change() failure	Changed json('output') to json('output')->nullable()
database/migrations/2026_04_20_055149_create_target_lookups_table.php	Same as above	Same fix
database/migrations/2026_04_21_155344_add_status_to_screening_tables.php	Used ->change() which requires MySQL-like ALTER TABLE MODIFY	Rewritten to only add status column, removed all ->change() calls

Configuration Changes

• config/database.php — SQLite connection configured with:
  • journal_mode = wal (Write-Ahead Logging for concurrent reads)
  • busy_timeout = 5000 (5 second wait on locked DB)
  • transaction_mode = IMMEDIATE (prevents "database is locked" errors)

Environment Files Updated

File	Before	After
.env.example	DB_CONNECTION=mysql + host/port/user/pass	DB_CONNECTION=sqlite, DB_DATABASE=database/ailixir.sqlite
.env.docker	Same MySQL config	Same SQLite config
docker/laravel.env	Same MySQL config	Same SQLite config

.gitignore

Added *.sqlite, *.sqlite-wal, *.sqlite-shm to prevent accidental commits of database files.

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Part 2: Docker Infrastructure Changes

Dockerfile

• PHP extension: pdo_mysql → pdo_sqlite
• System packages: Added libsqlite3-dev, supervisor
• Ports: Added EXPOSE 7860 for Hugging Face Spaces
• Database directory: Creates database/ directory during build
• Removed COPY docker/laravel.env .env (env vars now come from HF Space secrets)

docker/supervisord.conf (new)

Runs two processes in a single container for HF Spaces:

• [program:laravel] — php artisan serve --host=0.0.0.0 --port=7860
• [program:queue] — php artisan queue:work --sleep=3 --tries=3 --timeout=300

docker/entrypoint.sh

• Creates SQLite database file at runtime if it doesn't exist
• Checks RUN_MODE=hf environment variable — if set, starts supervisord instead of the default CMD
• Still supports Docker Compose mode (runs migrations, then exec's the passed CMD)

docker-compose.yml

• Removed the entire mysql: service (was MariaDB 11.4)
• Removed mysql-data volume
• Removed depends_on: mysql from laravel and queue services
• Removed DB_HOST: mysql environment overrides
• AI microservice configs remain unchanged

.env.hf (new)

Template file with all HF Space URLs pre-configured for the AI microservice URLs.

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Part 3: Hugging Face Spaces Deployment

Spaces Created (5)

Space	Type	Content
ailixir-api	Docker (Laravel)	Root repo (excludes ai_apps/, Diagrams/)
ailixir-admet	Docker (FastAPI)	ai_apps/ADMIT/admet_inference/
ailixir-drug-repurposing	Docker (FastAPI)	ai_apps/Drug Reporposing/
ailixir-chemical-rag	Docker (FastAPI)	ai_apps/chemical-rag-system/chemical-rag-system/
ailixir-generation	Docker (FastAPI)	ai_apps/generation/ (CPU-only Dockerfile)

Space Configuration

• All spaces use cpu-basic hardware (free tier)
• Port configured to 7860 in each Dockerfile
• README.md with proper YAML frontmatter added to each space
• 15-minute sleep timeout for free tier cost savings

Generation Service Adaptation

The generation service originally required NVIDIA CUDA + GPU. For HF Spaces (CPU-only), a lightweight Dockerfile was created that:

• Uses python:3.10-slim base (instead of nvidia/cuda)
• Installs only fastapi, uvicorn, pydantic, requests, rdkit
• Disables AutoDock-GPU and DeepPurpose (CPU-only)
• Provides basic molecule generation and docking scoring

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Part 4: GitHub-to-HF Auto-Sync

5 GitHub Actions Workflows

File	Triggers	Syncs
.github/workflows/sync-hf-backend.yml	Push to main/develop (excl. ai_apps/)	Whole repo → ailixir-api
.github/workflows/sync-hf-admet.yml	Push to ai_apps/ADMIT/admet_inference/	Subdir → ailixir-admet
.github/workflows/sync-hf-drug-repurposing.yml	Push to ai_apps/Drug Reporposing/	Subdir → ailixir-drug-repurposing
.github/workflows/sync-hf-chemical-rag.yml	Push to ai_apps/chemical-rag-system/	Subdir → ailixir-chemical-rag
.github/workflows/sync-hf-generation.yml	Push to ai_apps/generation/	Subdir → ailixir-generation

Each workflow:

1. Clones the target HF Space repo
2. Rsyncs the relevant files (excluding .git, __pycache__, etc.)
3. Commits with the GitHub commit SHA
4. Pushes to HF Space

GitHub Actions Workflow Updates

• api-tests.yml — Removed MySQL wait loop and health check; removed MySQL log collection
• integration-test.yml — Same changes across all 4 job definitions

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Part 5: Files Modified/Created Summary

Modified (15 files)

.config/database.php
.env.docker
.env.example
.gitignore
Dockerfile
docker-compose.yml
docker/entrypoint.sh
docker/laravel.env
.github/workflows/api-tests.yml
.github/workflows/integration-test.yml
database/migrations/2026_04_20_044726_create_screening_results_table.php
database/migrations/2026_04_20_055149_create_target_lookups_table.php
database/migrations/2026_04_20_135553_create_admets_table.php
database/migrations/2026_04_21_155344_add_status_to_screening_tables.php
database/ailixir.sqlite (new, empty)

Created (9 files)

.env.hf
docker/supervisord.conf
.github/workflows/sync-hf-backend.yml
.github/workflows/sync-hf-admet.yml
.github/workflows/sync-hf-drug-repurposing.yml
.github/workflows/sync-hf-chemical-rag.yml
.github/workflows/sync-hf-generation.yml
HF_SPACES_GUIDE.md (this file)
CHANGELOG_SQLITE_HF.md (this file)

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Architecture Diagram

┌─────────────────────────────────────────────────────────┐
│                    GitHub Repository                      │
│                     RottenShadow/                         │
│                   AILIXIR_BackEnd                         │
└────────────────────┬────────────────────────────────────┘
                     │ Push triggers
                     ▼
       ┌─────────────────────────────┐
       │   GitHub Actions (5 WFs)    │
       │   Auto-sync to HF Spaces    │
       └─────────────┬───────────────┘
                     │
     ┌───────────────┼───────────────────────┐
     │               │                       │
     ▼               ▼                       ▼
┌──────────┐  ┌──────────┐  ┌──────────┐  ┌──────────┐  ┌──────────┐
│ailixir-  │  │ailixir-  │  │ailixir-  │  │ailixir-  │  │ailixir-  │
│api       │  │admet     │  │drug-     │  │chemical- │  │generation│
│(Laravel) │  │(ADMET)   │  │repurpos. │  │rag       │  │(Molec.   │
│SQLite    │  │          │  │          │  │          │  │Gen.)     │
└────┬─────┘  └──────────┘  └──────────┘  └──────────┘  └──────────┘
     │
     │  HTTP proxying to AI microservices
      ├──→ https://shdwRow-ailixir-admet.hf.space
     ├──→ https://RottenShadow-ailixir-drug-repurposing.hf.space
     ├──→ https://RottenShadow-ailixir-chemical-rag.hf.space
      └──→ https://shdwRow-ailixir-generation.hf.space

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Remaining Steps (Manual)

1. Set HF tokens as GitHub secrets — Required for auto-sync workflows

   • Go to: https://github.com/RottenShadow/AILIXIR_BackEnd/settings/secrets/actions
   • Add secret: HF_TOKEN = YOUR_ROTTENSHADOW_TOKEN
   • Add secret: HF_TOKEN_AILIXIR = YOUR_AILIXIR_AI_TEAM_TOKEN

2. Set backend Space secrets — Required for ailixir-api to function

   • Go to: https://huggingface.co/spaces/Ailixir-AI-Team/ailixir-api/settings
   • Add all secrets listed in HF_SPACES_GUIDE.md section 3.1
   • Minimum: APP_KEY, RUN_MODE=hf, and all AI service URLs

3. Wait for builds to complete — Backend Docker image is large (~5GB) and takes 15–45 minutes to build on HF free tier

4. Verify connectivity — Test the health endpoints and ensure the backend can reach all AI services