Restructuring

.gitignore

@@ -2,6 +2,8 @@
 db/
 neo4j-data/
 neo4j-data-new/
+observability/
+logs/
 
 # Ignore Gradle project-specific cache directory
 nbproject
@@ -233,7 +235,7 @@ Temporary Items
 ### Gradle ###
 .gradle
 **/build/
-!src/**/build/
+!idoris/**/build/
 
 # Ignore Gradle GUI configuration
 gradle-app.setting
@@ -258,3 +260,4 @@ gradle-app.setting
 *.hprof
 
 # End of https://www.toptal.com/developers/gitignore/api/intellij+all,macos,java,gradle,webstorm+all,git!/.idea/!/db/
+*/build

README.md

@@ -4,18 +4,6 @@
 
 IDORIS is an **Integrated Data Type and Operations Registry with Inheritance System**.
 
-## Cloning this repository
-
-This repository includes files that are stored using Git LFS.
-Please install Git LFS before cloning this repository.
-For more information, see https://git-lfs.com/.
-Then execute the following command to clone this repository:
-
-```
-git lfs install
-git lfs clone https://github.com/maximiliani/idoris.git
-```
-
 ## Installation of Neo4j
 
 IDORIS relies on the Neo4j graph database.
@@ -49,7 +37,7 @@ For macOS, you can install it using Homebrew: ```brew install openjdk@21```.
 
 For Fedora, you can install it using DNF: ```sudo dnf install java-21```.
 
-Configure the [application.properties](src/main/resources/application.properties) file to contain the Neo4j API
+Configure the [application.properties](idoris/main/resources/application.properties) file to contain the Neo4j API
 credentials.
 
 ```
@@ -58,7 +46,8 @@ logging.level.root=INFO
 spring.neo4j.uri=bolt://localhost:7687
 spring.neo4j.authentication.username=neo4j
 spring.neo4j.authentication.password=superSecret
-spring.data.rest.basePath=/api
+# Base path for all REST endpoints
+server.servlet.context-path=/api
 server.port=8095
 idoris.validation-level=info
 idoris.validation-policy=strict
@@ -71,3 +60,11 @@ When Neo4j is running, start IDORIS with the following command:
 ```
 
 You can access the IDORIS API at http://localhost:8095/api.
+
+### API Documentation
+
+IDORIS provides comprehensive API documentation using OpenAPI/Swagger. You can access the API documentation
+at http://localhost:8095/swagger-ui.html when the application is running.
+
+All endpoints support HATEOAS (Hypermedia as the Engine of Application State) and return HAL (Hypertext Application
+Language) responses, making the API self-discoverable.

docker-compose-observability.yml

@@ -0,0 +1,142 @@
+version: '3.8'
+
+services:
+  # Prometheus for metrics collection
+  prometheus:
+    image: prom/prometheus:latest
+    container_name: prometheus
+    ports:
+      - "9090:9090"
+    volumes:
+      - ./observability/prometheus/prometheus.yml:/etc/prometheus/prometheus.yml
+      - prometheus_data:/prometheus
+    command:
+      - '--config.file=/etc/prometheus/prometheus.yml'
+      - '--storage.tsdb.path=/prometheus'
+      - '--web.console.libraries=/etc/prometheus/console_libraries'
+      - '--web.console.templates=/etc/prometheus/consoles'
+      - '--web.enable-lifecycle'
+      - '--web.enable-remote-write-receiver'
+    restart: unless-stopped
+    networks:
+      - observability-network
+
+  # Mimir for scalable metrics storage
+  mimir:
+    image: grafana/mimir:latest
+    container_name: mimir
+    ports:
+      - "9009:9009"  # HTTP API
+      - "9095:9095"  # gRPC API
+      - "9093:9093"  # Alertmanager API
+    volumes:
+      #      - ./observability/mimir/mimir-config.yaml:/etc/mimir/config.yaml
+      - mimir_data:/data
+    #    command: [ "-config.file=/etc/mimir/config.yaml" ]
+    restart: unless-stopped
+    networks:
+      - observability-network
+
+  # Loki for log aggregation
+  loki:
+    image: grafana/loki:latest
+    container_name: loki
+    ports:
+      - "3100:3100"
+    volumes:
+      - ./observability/loki/loki-config.yml:/etc/loki/local-config.yaml
+      - loki_data:/loki
+    command: -config.file=/etc/loki/local-config.yaml
+    restart: unless-stopped
+    networks:
+      - observability-network
+
+  # Grafana Alloy for unified observability data collection
+  alloy:
+    image: grafana/alloy:latest
+    container_name: alloy
+    volumes:
+      - ./observability/alloy/alloy-config.alloy:/etc/alloy/config.alloy
+      - /var/log:/var/log
+      - ./logs:/logs
+      - ./observability/alloy/alloy_data:/var/lib/alloy/data
+    command: [ "run", "--storage.path=/var/lib/alloy/data", "--server.http.listen-addr=0.0.0.0:12345", "/etc/alloy/config.alloy" ]
+    restart: unless-stopped
+    ports:
+      - "4317:4317"  # OTLP gRPC
+      - "4318:4318"  # OTLP HTTP
+      - "12345:12345"  # Alloy UI
+    depends_on:
+      - loki
+      - prometheus
+    networks:
+      - observability-network
+
+  # Tempo for distributed tracing
+  tempo:
+    image: grafana/tempo:latest
+    container_name: tempo
+    command: [ "-config.file=/etc/tempo/tempo-config.yml" ]
+    user: root  # Run as root to avoid permission issues
+    volumes:
+      - ./observability/tempo/tempo-config.yml:/etc/tempo/tempo-config.yml
+      - tempo_data:/tmp/tempo
+    ports:
+      - "3200:3200"  # tempo
+      - "4319:4319"  # OTLP gRPC (changed from 4317 to avoid conflict with Alloy)
+      - "4320:4320"  # OTLP HTTP (changed from 4318 to avoid conflict with Alloy)
+      - "9411:9411"  # Zipkin
+    restart: unless-stopped
+    networks:
+      - observability-network
+
+  # Pyroscope for continuous profiling
+  pyroscope:
+    image: grafana/pyroscope:latest
+    container_name: pyroscope
+    ports:
+      - "4040:4040"  # HTTP API and UI
+    volumes:
+      #      - ./observability/pyroscope/pyroscope-config.yaml:/etc/pyroscope/config.yaml
+      - pyroscope_data:/data
+    #    command: [ "-config.file=/etc/pyroscope/config.yaml" ]
+    restart: unless-stopped
+    networks:
+      - observability-network
+
+  # Grafana for visualization
+  grafana:
+    image: grafana/grafana:latest
+    container_name: grafana
+    ports:
+      - "3000:3000"
+    volumes:
+      - ./observability/grafana/provisioning:/etc/grafana/provisioning
+      - ./observability/grafana/dashboards:/var/lib/grafana/dashboards
+      - grafana_data:/var/lib/grafana
+    environment:
+      - GF_SECURITY_ADMIN_USER=admin
+      - GF_SECURITY_ADMIN_PASSWORD=admin
+      - GF_USERS_ALLOW_SIGN_UP=false
+      - GF_INSTALL_PLUGINS=grafana-piechart-panel
+    restart: unless-stopped
+    depends_on:
+      - prometheus
+      - mimir
+      - loki
+      - tempo
+      - pyroscope
+    networks:
+      - observability-network
+
+volumes:
+  prometheus_data:
+  mimir_data:
+  loki_data:
+  tempo_data:
+  pyroscope_data:
+  grafana_data:
+
+networks:
+  observability-network:
+    driver: bridge

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 #
-# Copyright (c) 2025 Karlsruhe Institute of Technology
+# Copyright (c) 2025-2026 Karlsruhe Institute of Technology
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -15,7 +15,7 @@
 #
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.14.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-9.3.0-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME