major re-structuring

Author: Logende

…ma-conversion-orchestrator/.dockerignore .dockerignoreschema-conversion-orchestrator/.dockerignore renamed to .dockerignore schema-conversion-orchestrator/.dockerignore renamed to .dockerignore

@@ -8,18 +8,17 @@ external_converters/node/src/
 external_converters/node/tsconfig.json
 external_converters/node/node_modules/
 
-# Standalone output/analysis scripts not used by the service
-output_*.py
-generate_diagrams.sh
-build_converters.sh
+# Standalone scripts and generated outputs not used by the service
+scripts/
+outputs/
+eval/output_schemas/
 
 # Test and dev files
 tests/
-requirements-dev.txt
+requirements/dev.txt
 
 # Docker files (not needed inside the image)
-Dockerfile
-docker-compose*.yml
+deploy/docker/
 .dockerignore
 
 # Python bytecode

.gitignore

@@ -208,16 +208,17 @@ __marimo__/
 
 # Node modules
 /node-converter/node_modules/
-/schema-conversion-orchestrator/node_modules/
+/node_modules/
 
 # Project-specific
+.DS_Store
 eval/output_schemas/
-schema-conversion-orchestrator/external_converters/node/node_modules/
+external_converters/node/node_modules/
+external_converters/java/dependency-reduced-pom.xml
+external_converters/java/original-converter.jar
+external_converters/java/converter.jar
 
 # IDEs
 .idea/
-/outputs/*
-/schema-conversion-orchestrator/external_converters/java/original-converter.jar
-/schema-conversion-orchestrator/external_converters/java/dependency-reduced-pom.xml
+/artifacts/
 /eval/conversion_matrix.png
-/schema-conversion-orchestrator/external_converters/java/converter.jar

README.md

@@ -30,28 +30,32 @@ cd universal-schema-converter
 #### Java
 
 ```bash
-cd schema-conversion-orchestrator/external_converters/java
-mvn clean package
+mvn -f external_converters/java/pom.xml clean package
 ```
 
 Result: `target/converter.jar`
 
 #### Node
 
 ```bash
-cd schema-conversion-orchestrator/external_converters/node
-npm install
-npm run build
+npm --prefix external_converters/node install
+npm --prefix external_converters/node run build
 ```
 
 Result: `dist/index.js`
 
 ### 3. Build and Run the Orchestrator
 
 ```bash
-cd schema-conversion-orchestrator
-pip install -r requirements.txt
-python3 app.py
+pip install -r requirements/runtime.txt
+PYTHONPATH=src python3 -m schema_conversion_orchestrator.app
+```
+
+From the repository root, use:
+
+```bash
+scripts/build.sh
+scripts/run.sh
 ```
 
 ### 3. Test the System
@@ -106,3 +110,6 @@ If a path fails due to a certain edge, remove all paths which include this edge
 ## 📜 License
 
 MIT License — feel free to use, contribute, and share.
+
+Third-party dependency and bundled converter notices are documented in
+[THIRD_PARTY_NOTICES.md](THIRD_PARTY_NOTICES.md).

THIRD_PARTY_NOTICES.md

@@ -0,0 +1,31 @@
+# Third-Party Notices
+
+Last reviewed: 2026-06-03.
+
+This project is licensed under [LICENSE](LICENSE). Ordinary source dependencies
+are declared in the package manager files:
+
+- Python: `requirements/runtime.txt`, `requirements/dev.txt`
+- Node: `external_converters/node/package.json`,
+  `external_converters/node/package-lock.json`
+- Java/Maven: `external_converters/java/pom.xml`
+
+This notice file is limited to third-party artifacts that are bundled, shaded,
+vendored, or otherwise easy to miss from the normal dependency declarations.
+
+## Bundled Artifacts
+
+### ROBOT
+
+`external_converters/robot/robot.jar` is bundled and used as an external Java
+process for OWL/OBO conversions.
+
+ROBOT is distributed by the OBO Library project. Public project documentation
+and the ROBOT paper report ROBOT as BSD-3-Clause licensed:
+
+- https://robot.obolibrary.org/
+- https://pmc.ncbi.nlm.nih.gov/articles/PMC6664714/
+
+Before distributing binaries or Docker images, confirm the license for the exact
+ROBOT JAR version bundled in this repository and include any required license
+text or notices with the release artifact.

build.sh

@@ -10,13 +10,14 @@ RUN apt-get update && apt-get install -y \
     && rm -rf /var/lib/apt/lists/*
 
 WORKDIR /app
+ENV PYTHONPATH=/app/src
 
 # Install Python dependencies first (layer-cached separately from app code)
-COPY requirements.txt .
+COPY requirements/runtime.txt requirements.txt
 RUN pip install --no-cache-dir -r requirements.txt
 
 # Copy Python application
-COPY *.py ./
+COPY src/ ./src/
 
 # Copy external converters (JARs, compiled Node dist, robot.jar)
 COPY external_converters/ ./external_converters/
@@ -34,4 +35,4 @@ HEALTHCHECK --interval=30s --timeout=10s --start-period=120s --retries=3 \
     CMD curl -f http://localhost:5002/health || exit 1
 
 # Use gunicorn with a single sync worker; 120 s timeout covers slow conversions
-CMD ["gunicorn", "--bind", "0.0.0.0:5002", "--workers", "1", "--timeout", "120", "wsgi:application"]
+CMD ["gunicorn", "--bind", "0.0.0.0:5002", "--workers", "1", "--timeout", "120", "schema_conversion_orchestrator.wsgi:application"]

build_subpackages.sh

@@ -10,12 +10,14 @@
 #
 # Deploy:
 #   cp .env.example .env    # edit BASE_DOMAIN and LETSENCRYPT_EMAIL
-#   docker compose -f docker-compose.https.yml up -d --build
+#   docker compose -f deploy/docker/docker-compose.https.yml up -d --build
 
 services:
   schema-converter:
     container_name: schema_converter
-    build: .
+    build:
+      context: ../..
+      dockerfile: deploy/docker/Dockerfile
     expose:
       - "5002"
     restart: unless-stopped

schema-conversion-orchestrator/Dockerfile deploy/docker/Dockerfileschema-conversion-orchestrator/Dockerfile renamed to deploy/docker/Dockerfile

@@ -7,13 +7,15 @@
 # meta-configurator/backend/docker-compose.yml.
 #
 # Deploy:
-#   docker compose up -d --build
+#   docker compose -f deploy/docker/docker-compose.yml up -d --build
 #   curl http://localhost:5002/health   # → {"status":"ok"}
 
 services:
   schema-converter:
     container_name: schema_converter
-    build: .
+    build:
+      context: ../..
+      dockerfile: deploy/docker/Dockerfile
     ports:
       - "${SCHEMA_CONVERTER_PORT:-5002}:5002"
-    restart: unless-stopped
+    restart: unless-stopped