ci: added docker compose config for running tests

Dockerfile

@@ -0,0 +1,25 @@
+# SPDX-FileCopyrightText: 2024 Stichting Health-RI
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
+FROM ckan/ckan-dev:2.10
+
+WORKDIR /opt
+
+RUN  pip install -e 'git+https://github.com/ckan/[email protected]#egg=ckanext-scheming[requirements]'
+RUN  pip install -e 'git+https://github.com/ckan/[email protected]#egg=ckanext-harvest[requirements]'
+RUN  pip install -e 'git+https://github.com/ckan/[email protected]#egg=ckanext-dcat[requirements]'
+RUN  pip install -r https://raw.githubusercontent.com/ckan/ckanext-dcat/v1.5.1/requirements.txt
+
+COPY . /opt/fdp
+WORKDIR /opt/fdp
+
+RUN pip install -r requirements.txt
+RUN pip install -r dev-requirements.txt
+RUN pip install --upgrade pytest-rerunfailures
+
+RUN python3 setup.py develop
+# Replace default path to CKAN core config file with the one on the container
+RUN sed -i -e 's/use = config:.*/use = config:\/srv\/app\/src\/ckan\/test-core.ini/' test.ini
+
+CMD ./ckanext/fairdatapoint/tests/run_tests.sh

README.md

@@ -5,7 +5,6 @@ SPDX-FileContributor: 2024 Stichting Health-RI
 SPDX-License-Identifier: CC-BY-4.0
 -->
 
-
 [![REUSE status](https://api.reuse.software/badge/github.com/GenomicDataInfrastructure/gdi-userportal-ckanext-fairdatapoint)](https://api.reuse.software/info/github.com/GenomicDataInfrastructure/gdi-userportal-ckanext-fairdatapoint)
 [![Tests](https://github.com/GenomicDataInfrastructure/gdi-userportal-ckanext-fairdatapoint/actions/workflows/test.yml/badge.svg)](https://github.com/GenomicDataInfrastructure/gdi-userportal-ckanext-fairdatapoint/actions/workflows/test.yml)
 [![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=GenomicDataInfrastructure_gdi-userportal-ckanext-fairdatapoint&metric=alert_status)](https://sonarcloud.io/summary/new_code?id=GenomicDataInfrastructure_gdi-userportal-ckanext-fairdatapoint)
@@ -14,21 +13,21 @@ SPDX-License-Identifier: CC-BY-4.0
 [![GitHub contributors](https://img.shields.io/github/contributors/GenomicDataInfrastructure/gdi-userportal-ckanext-fairdatapoint)](https://github.com/GenomicDataInfrastructure/gdi-userportal-ckanext-fairdatapoint/graphs/contributors)
 [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](code_of_conduct.md)
 
-
 # ckanext-fairdatapoint
 
 CKAN harvester for [FAIR Data Point](https://www.fairdatapoint.org/). Contains a harvester for FAIR data points. In the future, the FAIR data point API might be supported by this extension too.
 
 ## Stages
 
 The harvester runs in three stages. Each of these stages can be modified.
+
  1. Gather stage. The gather stage uses the FairDataPointRecordProvider which implements the IRecordProvider interface to create a list of identifiers of the objects which should be included in the harvest. In case of a FAIR data point, this list includes catalogs and datasets. In the future, collections could be added;
  2. Fetch stage. The fetch stage downloads the actual source data. In this phase, additional data from other sources may be included to better suit the DCAT profile as expected by CKAN;
- 3. Import stage. The import stage does the actual import. How the RDF from the FAIR data point is mapped to CKAN packages and resources is determined by so-called application profiles. In case of a FAIR data point which uses custom fields, a profile must be created. A profile can be defined as a Python class in the ckanext.fairdatapoint.profiles.py file. The new profile must be registered in the [ckan.rdf.profiles] section of setup.py. What profile is being used for a particular is determined by the harvester configuration. 
+ 3. Import stage. The import stage does the actual import. How the RDF from the FAIR data point is mapped to CKAN packages and resources is determined by so-called application profiles. In case of a FAIR data point which uses custom fields, a profile must be created. A profile can be defined as a Python class in the ckanext.fairdatapoint.profiles.py file. The new profile must be registered in the [ckan.rdf.profiles] section of setup.py. What profile is being used for a particular is determined by the harvester configuration.
 
 ``
 {
-	"profiles": "fairdatapoint_dcat_ap"
+ "profiles": "fairdatapoint_dcat_ap"
 }
 ``
 
@@ -46,7 +45,6 @@ ckan --config=<full path to CKAN ini-file> search-index rebuild
 
 For more information got to [GDI harvester information](https://genomicdatainfrastructure.github.io/gdi-userportal-docs/docs/ckan/harvester/)
 
-
 ## Requirements
 
 Compatibility with core CKAN versions:
@@ -55,7 +53,6 @@ Compatibility with core CKAN versions:
 |-----------------|-------------|
 | 2.10            | tested      |
 
-
 ## Installation
 
 **TODO:** Add any additional install steps to the list below.
@@ -70,10 +67,10 @@ To install gdi-userportal-ckanext-fairdatapoint:
 
 2. Clone the source and install it on the virtualenv
 
-    git clone https://github.com/GenomicDataInfrastructure/gdi-userportal-ckanext-fairdatapoint.git
+    git clone <https://github.com/GenomicDataInfrastructure/gdi-userportal-ckanext-fairdatapoint.git>
     cd gdi-userportal-ckanext-fairdatapoint
     pip install -e .
-	pip install -r requirements.txt
+ pip install -r requirements.txt
 
 3. Add `fairdatapoint` to the `ckan.plugins` setting in your CKAN
    config file (by default the config file is located at
@@ -83,17 +80,15 @@ To install gdi-userportal-ckanext-fairdatapoint:
 
      sudo service apache2 reload
 
-
 ## Config settings
 
 None at present
 
 **TODO:** Document any optional config settings here. For example:
 
-	# The minimum number of hours to wait before re-checking a resource
-	# (optional, default: 24).
-	ckanext.fairdatapoint.some_setting = some_default_value
-
+ # The minimum number of hours to wait before re-checking a resource
+ # (optional, default: 24).
+ ckanext.fairdatapoint.some_setting = some_default_value
 
 ## Developer installation
 
@@ -107,6 +102,7 @@ do:
 
 Fairdatapoint plugin depends on `ckanext-scheming`, `ckanext-harvester` and `ckanext-dcat`. Make sure these are installed,
 otherwise run:
+
 ```commandline
 pip install -e 'git+https://github.com/ckan/[email protected]#egg=ckanext-scheming[requirements]'
 pip install -e 'git+https://github.com/ckan/[email protected]#egg=ckanext-harvest[requirements]'
@@ -116,8 +112,7 @@ pip install -r https://raw.githubusercontent.com/ckan/ckanext-dcat/v1.5.1/requir
 
 ## Tests
 
-To run the tests go to [GDI harvester test information](https://genomicdatainfrastructure.github.io/gdi-userportal-docs/docs/ckan/extension-local-setup-and-testing/)
-
+To run the tests, run `docker compose build && docker-compose -f docker-compose.yml up --abort-on-container-exit --exit-code-from ckan-test && docker-compose rm -fsv`
 
 ## Releasing a new version of ckanext-fairdatapoint
 
@@ -152,7 +147,9 @@ If ckanext-fairdatapoint should be available on PyPI you can follow these steps
        git push --tags
 
 ## License
+
 This work is licensed under multiple licenses. Because keeping this section up-to-date is challenging, here is a brief summary as of January 2024:
+
 - All original source code is licensed under [AGPL](./LICENSES/AGPL-3.0-only.txt).
 - All documentation is licensed under [CC-BY-4.0](./LICENSES/CC-BY-4.0.txt).
 - Some configuration and data files are licensed under [CC-BY-4.0](./LICENSES/CC-BY-4.0.txt).

ckanext/fairdatapoint/tests/run_tests.sh

@@ -0,0 +1,14 @@
+#!/bin/sh
+
+# SPDX-FileCopyrightText: 2024 Stichting Health-RI
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
+# Initialize database
+ckan -c test.ini db init
+
+# Run tests
+pytest --ckan-ini=test.ini --cov=ckanext.fairdatapoint --disable-warnings ckanext/fairdatapoint
+
+# Generate coverage report
+coverage xml -o coverage.xml

docker-compose.yml

@@ -0,0 +1,57 @@
+# SPDX-FileCopyrightText: 2024 Stichting Health-RI
+#
+# SPDX-License-Identifier: AGPL-3.0-only
+
+services:
+  solr:
+    image: ckan/ckan-solr:2.10-solr9
+    # SOLR has very annoying log output from the health check
+    logging:
+      driver: none
+    healthcheck:
+      test: [ "CMD-SHELL", "curl -f http://localhost:8983/solr/ckan/admin/ping | grep \"OK\" || exit 1" ]
+      interval: 30s
+      timeout: 30s
+      retries: 5
+      start_period: 5s
+
+  postgres:
+    image: ckan/ckan-postgres-dev:2.11
+    environment:
+      POSTGRES_USER: postgres
+      POSTGRES_PASSWORD: postgres
+      POSTGRES_DB: postgres
+    healthcheck:
+      test: [ "CMD", "pg_isready" ]
+      interval: 10s
+      timeout: 5s
+      retries: 5
+      start_period: 5s
+
+  redis:
+    image: redis:7
+    healthcheck:
+      test: [ "CMD", "redis-cli", "ping" ]
+      interval: 10s
+      timeout: 30s
+      retries: 5
+      start_period: 3s
+
+  ckan-test:
+    platform: linux/amd64
+    build:
+      context: ./
+      dockerfile: Dockerfile
+    depends_on:
+      postgres:
+        condition: service_healthy
+      solr:
+        condition: service_healthy
+      redis:
+        condition: service_healthy
+    environment:
+      CKAN_SQLALCHEMY_URL: postgresql://ckan_default:pass@postgres/ckan_test
+      CKAN_DATASTORE_WRITE_URL: postgresql://datastore_write:pass@postgres/datastore_test
+      CKAN_DATASTORE_READ_URL: postgresql://datastore_read:pass@postgres/datastore_test
+      CKAN_SOLR_URL: http://solr:8983/solr/ckan
+      CKAN_REDIS_URL: redis://redis:6379/1