GenomicDataInfrastructure · brunopacheco1 · Feb 1, 2024 · Jan 31, 2024
diff --git a/.env.example b/.env.example
@@ -1,3 +1,8 @@
+# SPDX-FileCopyrightText: 2006-2023 Open Knowledge Foundation and contributors
+# SPDX-FileContributor: PNED G.I.E.
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
 # Host Ports
 CKAN_PORT_HOST=5500
 

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -1,3 +1,8 @@
+# SPDX-FileCopyrightText: 2024 PNED G.I.E.
+# SPDX-FileContributor: Stichting Health-RI
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
 name: Publish and Deploy main
 
 on:

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2024 PNED G.I.E.
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
 name: Publish release
 
 on:

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -0,0 +1,18 @@
+# SPDX-FileCopyrightText: 2024 PNED G.I.E.
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
+name: Run Tests
+
+on: push
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - uses: actions/checkout@v4
+      - name: REUSE Compliance Check
+        uses: fsfe/reuse-action@v2
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,8 @@
+# SPDX-FileCopyrightText: 2006-2023 Open Knowledge Foundation and contributors
+# SPDX-FileContributor: PNED G.I.E.
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
 # generic
 .DS_Store
 .vagrant

diff --git a/.gitmodules b/.gitmodules
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2024 PNED G.I.E.
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
 [submodule "src/ckanext-gdi-userportal"]
 	path = src/ckanext-gdi-userportal
 	url = [email protected]:GenomicDataInfrastructure/ckanext-gdi-userportal.git

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,9 @@
+<!--
+SPDX-FileCopyrightText: 2024 PNED G.I.E.
+
+SPDX-License-Identifier: CC-BY-4.0
+-->
+
 # Changelog
 
 All notable changes to this project will be documented in this file.

diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -1,3 +1,9 @@
+<!--
+SPDX-FileCopyrightText: 2024 Contributor Covenant
+SPDX-FileContributor: PNED G.I.E.
+
+SPDX-License-Identifier: CC-BY-4.0
+-->
 
 # Contributor Covenant Code of Conduct
 

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,3 +1,9 @@
+<!--
+SPDX-FileCopyrightText: 2024 PNED G.I.E.
+
+SPDX-License-Identifier: CC-BY-4.0
+-->
+
 <!-- omit in toc -->
 # Contributing to CKAN Docker GDI  User Portal
 

diff --git a/LICENSE b/LICENSE
diff --git a/LICENSES/AGPL-3.0-only.txt b/LICENSES/AGPL-3.0-only.txt
diff --git a/LICENSES/CC-BY-4.0.txt b/LICENSES/CC-BY-4.0.txt
diff --git a/README.md b/README.md
@@ -1,5 +1,13 @@
+<!--
+SPDX-FileCopyrightText: 2024 PNED G.I.E.
+
+SPDX-License-Identifier: CC-BY-4.0
+-->
+
+[![REUSE status](https://api.reuse.software/badge/github.com/GenomicDataInfrastructure/gdi-userportal-ckan-docker)](https://api.reuse.software/info/github.com/GenomicDataInfrastructure/gdi-userportal-ckan-docker)
 ![example workflow](https://github.com/GenomicDataInfrastructure/gdi-userportal-ckan-docker/actions/workflows/main.yml/badge.svg)
 ![example workflow](https://github.com/GenomicDataInfrastructure/gdi-userportal-ckan-docker/actions/workflows/release.yml/badge.svg)
+![example workflow](https://github.com/GenomicDataInfrastructure/gdi-userportal-ckan-docker/actions/workflows/test.yml/badge.svg)
 [![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=GenomicDataInfrastructure_gdi-userportal-ckan-docker&metric=alert_status)](https://sonarcloud.io/summary/new_code?id=GenomicDataInfrastructure_gdi-userportal-ckan-docker)
 [![GitHub contributors](https://img.shields.io/github/contributors/GenomicDataInfrastructure/gdi-userportal-ckan-docker)](https://github.com/GenomicDataInfrastructure/gdi-userportal-ckan-docker/graphs/contributors)
 [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](code_of_conduct.md)
@@ -68,9 +76,8 @@ more information.
 Copying and License
 -------------------
 
-This material is copyright (c) 2006-2023 Open Knowledge Foundation and contributors.
-
-It is open and licensed under the GNU Affero General Public License (AGPL) v3.0
-whose full text may be found at:
+This work is licensed under multiple licences. Here is a brief summary as of January 2024:
 
-http://www.fsf.org/licensing/licenses/agpl-3.0.html
+- All original source code is licensed under [AGPL-3.0-only](./LICENSES/AGPL-3.0-only.txt), copyright (c) 2006-2023 Open Knowledge Foundation and contributors.
+- All documentation is licensed under [CC-BY-4.0](./LICENSES/CC-BY-4.0.txt).
+- For more accurate information, check the individual files.
diff --git a/_http/ckan.http b/_http/ckan.http
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2024 PNED G.I.E.
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
 GET http://localhost:5500/api/action/scheming_package_show?type=dataset&id=5eedc478-87b2-4947-8a9a-c90437440079
 
 ###

diff --git a/_http/mock_catalogue.http b/_http/mock_catalogue.http
@@ -1 +1,5 @@
+# SPDX-FileCopyrightText: 2024 PNED G.I.E.
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
 GET http://localhost:8001/catalogue.ttl
diff --git a/ckan/Dockerfile b/ckan/Dockerfile
@@ -1,3 +1,8 @@
+# SPDX-FileCopyrightText: 2006-2023 Open Knowledge Foundation and contributors
+# SPDX-FileContributor: PNED G.I.E.
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
 FROM ckan/ckan-base:2.10.3
 
 # Install any extensions needed by your CKAN instance

diff --git a/ckan/Dockerfile.dev b/ckan/Dockerfile.dev
@@ -1,3 +1,8 @@
+# SPDX-FileCopyrightText: 2006-2023 Open Knowledge Foundation and contributors
+# SPDX-FileContributor: PNED G.I.E.
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
 FROM ckan/ckan-dev:2.10.3
 
 RUN  pip3 install -e git+https://github.com/ckan/[email protected]#egg=ckanext-dcat && \

diff --git a/ckan/docker-entrypoint.d/README.md b/ckan/docker-entrypoint.d/README.md
@@ -1,3 +1,9 @@
+<!--
+SPDX-FileCopyrightText: 2006-2023 Open Knowledge Foundation and contributors
+
+SPDX-License-Identifier: AGPL-3.0-only
+-->
+
 Use scripts in this folder to run extra initialization steps in your custom CKAN images.
 Any file with `.sh` or `.py` extension will be executed just after the main initialization
 script (`prerun.py`) is executed and just before the web server and supervisor processes are

diff --git a/ckan/docker-entrypoint.d/setup_scheming.sh b/ckan/docker-entrypoint.d/setup_scheming.sh
@@ -1,5 +1,9 @@
 #!/bin/bash
 
+# SPDX-FileCopyrightText: 2024 PNED G.I.E.
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
 # Update the config file with each extension config-options
 echo "[ckanext-scheming] Setting up config-options"
 ckan config-tool $CKAN_INI -s app:main \

diff --git a/ckan/patches/00_test_test.patch b/ckan/patches/00_test_test.patch
@@ -1 +1,5 @@
+# SPDX-FileCopyrightText: 2006-2023 Open Knowledge Foundation and contributors
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
 test
diff --git a/ckan/setup/prerun.py b/ckan/setup/prerun.py
@@ -1,3 +1,8 @@
+# SPDX-FileCopyrightText: 2006-2023 Open Knowledge Foundation and contributors
+# SPDX-FileContributor: PNED G.I.E.
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
 import os
 import sys
 import subprocess

diff --git a/ckan/setup/start_ckan.sh.override b/ckan/setup/start_ckan.sh.override
@@ -1,5 +1,9 @@
 #!/bin/sh
 
+# SPDX-FileCopyrightText: 2006-2023 Open Knowledge Foundation and contributors
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
 # Add ckan.datapusher.api_token to the CKAN config file (updated with corrected value later)
 ckan config-tool $CKAN_INI ckan.datapusher.api_token=xxx
 

diff --git a/ckan/setup/start_ckan_development.sh.override b/ckan/setup/start_ckan_development.sh.override
@@ -1,5 +1,9 @@
 #!/bin/sh
 
+# SPDX-FileCopyrightText: 2006-2023 Open Knowledge Foundation and contributors
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
 # Install any local extensions in the src_extensions volume
 echo "Looking for local extensions to install..."
 echo "Extension dir contents:"

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -1,3 +1,8 @@
+# SPDX-FileCopyrightText: 2006-2023 Open Knowledge Foundation and contributors
+# SPDX-FileContributor: PNED G.I.E.
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
 version: "3"
 
 volumes:

diff --git a/keycloak/Dockerfile b/keycloak/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2024 PNED G.I.E.
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
 # First stage: Install curl
 FROM registry.access.redhat.com/ubi9 AS ubi-micro-build
 RUN mkdir -p /mnt/rootfs

diff --git a/keycloak/realms/ckan-realm.json.license b/keycloak/realms/ckan-realm.json.license
@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: 2024 PNED G.I.E.
+
+SPDX-License-Identifier: AGPL-3.0-only
diff --git a/postgresql/Dockerfile b/postgresql/Dockerfile
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: 2006-2023 Open Knowledge Foundation and contributors
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
 FROM postgres:12-alpine
 
 # Include extra setup scripts (eg datastore)

diff --git a/postgresql/docker-entrypoint-initdb.d/.gitattributes b/postgresql/docker-entrypoint-initdb.d/.gitattributes
@@ -1 +1,5 @@
+# SPDX-FileCopyrightText: 2006-2023 Open Knowledge Foundation and contributors
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
 *.sh text eol=lf
diff --git a/postgresql/docker-entrypoint-initdb.d/1_create_ckandb.sh b/postgresql/docker-entrypoint-initdb.d/1_create_ckandb.sh
@@ -1,4 +1,10 @@
 #!/bin/bash
+
+# SPDX-FileCopyrightText: 2006-2023 Open Knowledge Foundation and contributors
+# SPDX-FileContributor: PNED G.I.E.
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
 set -e
 
 psql -v ON_ERROR_STOP=1 --username "$POSTGRES_USER" <<-EOSQL

diff --git a/postgresql/docker-entrypoint-initdb.d/2_create_keycloakdb.sh b/postgresql/docker-entrypoint-initdb.d/2_create_keycloakdb.sh
@@ -1,4 +1,9 @@
 #!/bin/bash
+
+# SPDX-FileCopyrightText: 2024 PNED G.I.E.
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
 set -e
 
 echo "Creating $KC_DB_NAME for $KC_DB_USERNAME"

diff --git a/postgresql/docker-entrypoint-initdb.d/3_setup_test_databases.sh b/postgresql/docker-entrypoint-initdb.d/3_setup_test_databases.sh
@@ -1,4 +1,10 @@
 #!/bin/bash
+
+# SPDX-FileCopyrightText: 2006-2023 Open Knowledge Foundation and contributors
+# SPDX-FileContributor: PNED G.I.E.
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
 set -e
 
 psql -v ON_ERROR_STOP=1 --username "$POSTGRES_USER" <<-EOSQL
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		SPDX-FileCopyrightText: 2024 PNED G.I.E.

		SPDX-License-Identifier: AGPL-3.0-only