Compare Computational Assets updates vs develop

.env

@@ -17,22 +17,26 @@ KEYCLOAK_CLIENT_SECRET="QJiOGn09eCEfnqAmcPP2l4vMU8grlmVQ"
 REDIRECT_URIS=http://${HOSTNAME}/docs/oauth2-redirect
 POST_LOGOUT_REDIRECT_URIS=http://${HOSTNAME}/aiod-auth/realms/aiod/protocol/openid-connect/logout
 AIOD_KEYCLOAK_PORT=8080
+REVIEWER_ROLE_NAME=review_aiod_resources
+ADMIN_ROLE_NAME=admin_aiod_resources
 
 EGICHECKINALIAS=
 
+#AIBUILDER
+AIBUILDER_API_TOKEN=""
+
 #ELASTICSEARCH
 ES_USER=elastic
 ES_PASSWORD=changeme
 ES_DISCOVERY_TYPE=single-node
-ES_ROLE="edit_aiod_resources"
 ES_JAVA_OPTS="-Xmx256m -Xms256m"
 AIOD_ES_HTTP_PORT=9200
 AIOD_ES_TRANSPORT_PORT=9300
 
 #LOGSTASH
 LS_JAVA_OPTS="-Xmx256m -Xms256m"
 AIOD_LOGSTASH_BEATS_PORT=5044
-AIOD_LOGSTASH_PORT=5000
+AIOD_LOGSTASH_PORT=5001
 AIOD_LOGSTASH_API_PORT=9600
 
 #NGINX
@@ -41,3 +45,28 @@ AIOD_NGINX_PORT=80
 #DATA STORAGE
 DATA_PATH=./data
 BACKUP_PATH=./data/backups
+
+#PROMETHEUS and GRAFANA
+AIOD_PROMETHEUS_PORT=9090
+AIOD_GRAFANA_PORT=3000
+
+# MONITORING STORAGE
+PROMETHEUS_DATA_PATH=./data/prometheus
+GRAFANA_DATA_PATH=./data/grafana
+
+# PROMETHEUS RETENTION
+PROMETHEUS_RETENTION=7d
+
+# GRAFANA DEMOS AUTH
+GF_AUTH_ANONYMOUS_ENABLED=true
+GF_AUTH_ANONYMOUS_ORG_ROLE=Viewer
+GF_SECURITY_ADMIN_PASSWORD=admin
+
+# GRAFANA
+GRAFANA_PROMETHEUS_URL=http://prometheus:9090
+
+GRAFANA_MYSQL_HOST=sqlserver
+GRAFANA_MYSQL_PORT=3306
+GRAFANA_MYSQL_DB=aiod
+GRAFANA_MYSQL_USER=root
+GRAFANA_MYSQL_PASSWORD=${MYSQL_ROOT_PASSWORD}

.github/ISSUE_TEMPLATE/bug-report.md

@@ -0,0 +1,24 @@
+---
+name: 🐛 Bug report
+about: Create a report to help us fix it!
+title: ''
+labels: bug, triage
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**Error Reference**
+Please indicate which server you were connecting to (e.g., api.aiod.eu).
+If the server provided a reference code, please provide it (a hexadecimal string, like `d47cb85f6cf64c158dbb65e1a891903f`).
+
+**To Reproduce**
+Please provide a [minimal, reproducible example](https://stackoverflow.com/help/minimal-reproducible-example). Preferably a (set of) complete queries which do not behave as expected.
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Additional context**
+Add any other context about the problem here.

.github/dependabot.yaml

@@ -7,5 +7,5 @@ updates:
     schedule:
       interval: "daily"
     # Labels on pull requests for version updates only
-    labels: 
+    labels:
       - "pip dependencies"

.github/pull_request_template.md

@@ -0,0 +1,39 @@
+<!--
+Please carefully follow the instructions of the template, as they allow for more effective reviews with fewer back-and-forth, making a smoother process for everyone.
+Prefer small, independent PRs over big monolithic ones when possible.
+If you are only looking for feedback, clearly indicate this and open it as a "draft" instead (use the green "v" button next to "create pull request").
+-->
+
+
+## Change(s)
+<!-- Briefly describe the change of this PR, if there are multiple changes, please describe them separately. -->
+Change Type: <!-- Added/Changed/Deprecated/Removed/Fixed/Security -->
+
+Change Category: <!-- Documentation/Interface/Internal/Other -->
+
+Changelog Entry: <!-- Brief description of the change, possibly followed by more details in a separate paragraph. For example: -->
+
+<!--
+Added the `contacts` field to the `AIResource` `GET` endpoints with full contact information.
+
+This field contains the full contact information of the contacts whose identifiers are currently already provided through the `contact` field.
+-->
+
+
+
+## How to Test
+<!-- Describe a way to test the change of this PR if it requires special steps beyond CI/CD. You're writing this for the reviewer. -->
+
+## Checklist
+- [ ] Tests have been added or updated to reflect the changes, or their absence is explicitly explained. <!-- For code changes -->
+- [ ] Documentation has been added or updated to reflect the changes, or their absence is explicitly explained.
+- [ ] A self-review has been conducted checking:
+  - No unintended changes have been committed.
+  - The changes in isolation seem reasonable.
+  - Anything that may be odd or unintuitive is provided with a GitHub comment explaining it (but consider if this should not be a code comment or in the documentation instead).
+- [ ] All CI checks pass before pinging a reviewer, or provide an explanation if they do not.
+- [ ] The PR title matches the changelog entry's one-line description.
+
+## Related Issues
+<!-- Provide a list of relevant issues and/or pull requests, if any. -->
+<!-- If the pull request closes and issue, specify "Closes #X" (where X is the issue number). -->

.github/workflows/dockerized-tests.yml

@@ -1,8 +1,8 @@
 name: Docker - build, test, push
 
 # This workflow will build docker image and run tests inside the container.
-# This workflow is only executed if there is pull request with change in pyproject.toml dependencies, 
-# or in Dockerfile, or in docker workflow. 
+# This workflow is only executed if there is pull request with change in pyproject.toml dependencies,
+# or in Dockerfile, or in docker workflow.
 
 on:
   pull_request:
@@ -17,8 +17,8 @@ on:
 
   release:
     types: [published]
-      
-  # allows to manually start a workflow run from the GitHub UI or using the GitHub API.    
+
+  # allows to manually start a workflow run from the GitHub UI or using the GitHub API.
   workflow_dispatch:
     inputs:
       push-image:

.github/workflows/docs.yml

@@ -0,0 +1,33 @@
+name: docs - build, deploy
+on:
+  push:
+    branches:
+      - main
+      - develop
+permissions:
+  contents: write
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # fetch full git history for mkdocs-git-revision-date-localized-plugin.
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
+      - uses: actions/cache@v4
+        with:
+          key: mkdocs-material-${{ env.cache_id }}
+          path: .cache
+          restore-keys: |
+            mkdocs-material-
+      # We need to install not just the doc dependencies but also the package itself
+      # since it has the docs/tools/asset_type_replacer plugin.
+      - run: python -m pip install -e ".[docs]"
+      - run: python -m mkdocs gh-deploy --force

.github/workflows/pytest-tests.yml

@@ -1,12 +1,12 @@
 # This workflow will install Python dependencies, run tests and pre-commit hook with a single version of Python
 # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
 
-name:  Run Unit Test via Pytest 
+name:  Run Unit Test via Pytest
 
 on:
   pull_request:
     branches: [ "develop" ]
-  # allows to manually start a workflow run from the GitHub UI or using the GitHub API. 
+  # allows to manually start a workflow run from the GitHub UI or using the GitHub API.
   workflow_dispatch:
 
 permissions:
@@ -21,15 +21,15 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python-version }} 
+    - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v3
       with:
-        python-version: ${{ matrix.python-version }}  
+        python-version: ${{ matrix.python-version }}
     - name: Setup Python virtual environment
       run: |
         python3.11 -m venv venv
         source venv/bin/activate
-        
+
     - name: Install dependencies
       run: |
         source venv/bin/activate
@@ -40,8 +40,3 @@ jobs:
       run: |
         source venv/bin/activate
         pre-commit run --all
-
-
-
-
-

.gitignore

@@ -14,7 +14,7 @@ logstash/config/pipeline
 logstash/config/sql
 
 
-# MacOS 
+# MacOS
 .DS_Store
 
 # Byte-compiled / optimized / DLL files

.pre-commit-config.yaml

@@ -1,13 +1,30 @@
 
 repos:
-  - repo: https://github.com/psf/black
-    rev: 22.12.0
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0  # Use the ref you want to point at
     hooks:
-      - id: black
+      - id: no-commit-to-branch
+      - id: check-added-large-files
+      - id: check-illegal-windows-names
+      - id: trailing-whitespace
+      - id: mixed-line-ending
+      - id: end-of-file-fixer
+      - id: check-executables-have-shebangs
+      - id: debug-statements
+      - id: check-json
+      - id: check-toml
+      - id: check-yaml
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+      - id: codespell
+        files: "(docs|.github/ISSUE_TEMPLATE)/.*"
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.1
+    rev: v0.9.7
     hooks:
-      - id: ruff  # only do linting for security for now
+      - id: ruff
+        args: [ --fix ]
+      - id: ruff-format
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v0.991
     hooks:
@@ -19,19 +36,11 @@ repos:
           - types-pytz
           - types-requests
           - types-setuptools
-  - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
-    hooks:
-      - id: flake8
-        name: flake8 src
-        files: src/.*
-        additional_dependencies:
-          - flake8-print==5.0.0
   - repo: local
     hooks:
       - id: pytest-check
         name: pytest-check
-        entry: pytest src/tests
+        entry: pytest src/tests --versions 'latest'
         language: system
         pass_filenames: false
         exclude: ".*.md"

Dockerfile

@@ -23,4 +23,4 @@ COPY ./src /app
 RUN groupadd -r apprunner && \
    useradd -mg apprunner apprunner \
    && chown -R apprunner:apprunner /app
-USER apprunner:apprunner
+USER apprunner:apprunner

alembic/alembic/README

@@ -1 +1 @@
-Generic single-database configuration.
+Generic single-database configuration.

alembic/alembic/versions/0a23b40cc09c_extend_max_length_of_text_in_note.py

@@ -1,10 +1,11 @@
 """Extend max length of text in note
 
 Revision ID: 0a23b40cc09c
-Revises: 
+Revises:
 Create Date: 2024-08-29 11:37:20.827291
 
 """
+
 from typing import Sequence, Union
 
 from alembic import op

alembic/alembic/versions/0f2fe1324047_non_nullable_date_modified_and_date_created.py

@@ -5,6 +5,7 @@
 Create Date: 2024-10-31 16:37:23.196383
 
 """
+
 from typing import Sequence, Union
 
 from alembic import op