ontology

ontology_platform/vendored/ontocast/docker/README.md

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+# Triple Store Configuration
+
+OntoCast supports multiple triple store backends for storing and managing RDF data. This guide covers the setup and configuration of supported triple stores.
+
+---
+
+## Overview
+
+OntoCast supports the following triple store backends:
+
+1. **Apache Fuseki** (Recommended) - Native RDF triple store with SPARQL support
+2. **Neo4j with n10s plugin** - Graph database with RDF capabilities
+3. **Filesystem** - Local file-based storage (fallback)
+
+When multiple triple stores are configured, OntoCast uses the following priority order:
+1. Fuseki (if `FUSEKI_URI` and `FUSEKI_AUTH` are set)
+2. Neo4j (if `NEO4J_URI` and `NEO4J_AUTH` are set)
+3. Filesystem (default fallback)
+
+---
+
+## Environment Variables
+
+Configure your triple store connection using environment variables in your main `.env` file:
+
+```bash
+# Fuseki Configuration (Preferred)
+FUSEKI_URI=http://localhost:3032/test
+FUSEKI_AUTH=admin/abc123-qwe
+
+# Neo4j Configuration (Alternative)
+NEO4J_URI=bolt://localhost:7689
+NEO4J_AUTH=neo4j/test!passfortesting
+```
+
+---
+
+## Apache Fuseki Setup
+
+Sample configurations are provided here: [ontocast/docker](https://github.com/growgraph/ontocast/tree/main/docker).
+
+**1. Prepare the environment file:**
+```bash
+cd docker/fuseki
+cp .env.example .env
+# Edit with your values
+```
+
+**Example `docker/fuseki/.env.example`:**
+```bash
+IMAGE_VERSION=secoresearch/fuseki:5.1.0
+SPEC=test
+CONTAINER_NAME="${SPEC}.fuseki"
+STORE_FOLDER="$HOME/tmp/${CONTAINER_NAME}"
+TS_PORT=3032
+TS_PASSWORD="abc123-qwe"
+TS_USERNAME="admin"
+UID=1000
+GID=1000
+```
+
+**2. Start/Stop Fuseki:**
+```bash
+# Start
+cd docker/fuseki
+docker compose --env-file .env up fuseki -d
+
+# Stop
+# (use the container name from your .env, e.g. test.fuseki)
+docker compose stop test.fuseki
+```
+
+**3. Access Fuseki:**
+- Web interface: http://localhost:3032
+- Default dataset: `/test`
+- SPARQL endpoint: http://localhost:3032/test/sparql
+
+---
+
+## Neo4j with n10s Plugin Setup
+
+**1. Prepare the environment file:**
+```bash
+cd docker/neo4j
+cp .env.example .env
+# Edit with your values
+```
+
+**Example `docker/neo4j/.env.example`:**
+```bash
+IMAGE_VERSION=neo4j:5.20
+SPEC=test
+CONTAINER_NAME="${SPEC}.sem.neo4j"
+NEO4J_PORT=7476
+NEO4J_BOLT_PORT=7689
+STORE_FOLDER="$HOME/tmp/${CONTAINER_NAME}"
+NEO4J_PLUGINS='["apoc", "graph-data-science", "n10s"]'
+NEO4J_AUTH="neo4j/test!passfortesting"
+```
+
+**2. Start/Stop Neo4j:**
+```bash
+# Start
+cd docker/neo4j
+docker compose --env-file .env up neo4j -d
+
+# Stop
+docker compose stop neo4j
+```
+
+**3. Access Neo4j:**
+- Browser: http://localhost:7476
+- Username: `neo4j`
+- Password: `test!passfortesting`
+- Bolt: bolt://localhost:7689
+
+---
+
+## Filesystem Storage (Fallback)
+
+If neither Fuseki nor Neo4j is configured, OntoCast will store ontologies and facts as Turtle files in the working directory.
+
+**No setup required.**
+
+---
+
+## Triple Store Comparison
+
+| Feature | Fuseki | Neo4j + n10s | Filesystem |
+|---------|--------|--------------|------------|
+| **RDF Native** | ✅ Yes | ⚠️ Via plugin | ✅ Yes |
+| **SPARQL** | ✅ Full 1.1 | ❌ Limited | ❌ No |
+| **Setup Complexity** | ✅ Simple | ⚠️ Moderate | ✅ Very Simple |
+| **Visualization** | ⚠️ Basic | ✅ Excellent | ❌ None |
+| **Production Ready** | ✅ Yes | ✅ Yes | ❌ No |
+
+---
+
+## Best Practices
+
+- Use **Filesystem** for quick setup and testing.
+- Use **Fuseki** for RDF-focused or production deployments.
+- Use **Neo4j** if you need advanced graph analytics or visualization.
+- Monitor triple store performance and logs.
+- Backup your data regularly.
+
+---
+
+## Troubleshooting
+
+### Fuseki
+```bash
+# Check if Fuseki is running
+curl http://localhost:3032/$/ping
+
+# Restart Fuseki
+docker compose restart fuseki
+```
+
+### Neo4j
+```bash
+# Check if Neo4j is running
+curl http://localhost:7476
+
+# Check n10s plugin
+cypher-shell -u neo4j -p test!passfortesting "CALL n10s.graphconfig.show()"
+```
+
+### Common Problems
+- **Connection Refused**: Triple store not running
+- **Authentication Failed**: Incorrect credentials
+- **Dataset Not Found**: Dataset not created in Fuseki
+- **Plugin Not Loaded**: n10s plugin not installed in Neo4j

ontology_platform/vendored/ontocast/docker/__init__.py

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+"""Docker configurations for OntoCast.
+
+This package contains Docker configurations for running OntoCast
+dependencies, including triple store databases and other services.
+
+Available configurations:
+- neo4j: Neo4j database with n10s plugin
+- fuseki: Apache Fuseki triple store server
+"""

ontology_platform/vendored/ontocast/docker/fuseki/.env.example

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+IMAGE_VERSION=secoresearch/fuseki:5.1.0
+SPEC=ontocast
+CONTAINER_NAME="${SPEC}.fuseki"
+TS_PORT=3032
+TS_PASSWORD="abc123-qwe"
+TS_USERNAME="admin"

ontology_platform/vendored/ontocast/docker/fuseki/docker-compose.yml

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+services:
+    fuseki:
+        image: ${IMAGE_VERSION}
+        user: "${UID}:${GID}"
+        restart: "no"
+        profiles: ["${CONTAINER_NAME}"]
+        ports:
+        -   "${TS_PORT}:3030"
+        container_name: ${CONTAINER_NAME}
+        volumes:
+        -   fuseki_data:/fuseki
+        environment:
+        -   ADMIN_PASSWORD=${TS_PASSWORD}
+volumes:
+    fuseki_data:
+        driver: local

ontology_platform/vendored/ontocast/docker/neo4j/.env.example

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+IMAGE_VERSION=neo4j:5.21.0
+SPEC=ontocast
+CONTAINER_NAME="${SPEC}.neo4j"
+NEO4J_PORT=7476
+NEO4J_BOLT_PORT=7689
+NEO4J_PLUGINS='["n10s"]'
+NEO4J_AUTH="neo4j/test!passfortesting"

ontology_platform/vendored/ontocast/docker/neo4j/docker-compose.yml

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+services:
+    neo4j:
+        image: ${IMAGE_VERSION}
+        restart: "no"
+        profiles: ["${CONTAINER_NAME}"]
+        ports:
+        -   "${NEO4J_PORT}:7474"
+        -   "${NEO4J_BOLT_PORT}:7687"
+        container_name: ${CONTAINER_NAME}
+        volumes:
+        -   neo4j_data:/data
+        -   neo4j_plugins:/plugins
+        -   neo4j_logs:/logs
+        environment:
+        -   NEO4J_ACCEPT_LICENSE_AGREEMENT=yes
+        -   NEO4J_AUTH=${NEO4J_AUTH}
+        -   NEO4J_PLUGINS=${NEO4J_PLUGINS}
+        -   NEO4J_dbms_security_procedures_unrestricted=n10s.*
+        -   NEO4J_dbms_security_procedures_allowlist=n10s.*
+volumes:
+    neo4j_data:
+        driver: local
+    neo4j_plugins:
+        driver: local
+    neo4j_logs:
+        driver: local

ontology_platform/vendored/ontocast/docker/qdrant/.env.example

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+IMAGE_VERSION=qdrant/qdrant:v1.16.3
+SPEC=ontocast
+CONTAINER_NAME="${SPEC}.qdrant"
+QDRANT_HTTP_PORT=6333
+QDRANT_GRPC_PORT=6334
+QDRANT_API_KEY="abc123-qwe"
+QDRANT_LOG_LEVEL=INFO

ontology_platform/vendored/ontocast/docker/qdrant/docker-compose.yml

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+services:
+    qdrant:
+        image: ${IMAGE_VERSION}
+        restart: "no"
+        profiles: ["${CONTAINER_NAME}"]
+        ports:
+        -   "${QDRANT_HTTP_PORT}:6333"
+        -   "${QDRANT_GRPC_PORT}:6334"
+        container_name: ${CONTAINER_NAME}
+        volumes:
+        -   qdrant_data:/qdrant/storage
+        environment:
+        -   QDRANT__SERVICE__API_KEY=${QDRANT_API_KEY}
+        -   QDRANT__LOG_LEVEL=${QDRANT_LOG_LEVEL}
+
+volumes:
+    qdrant_data:
+        driver: local