Merge pull request #89 from GenomicDataInfrastructure/dcat-2.2.0

feat: integrate Health DCAT file on top of DCAT-AP 3 profile

Author: hcvdwerf

.github/workflows/test.yml

@@ -14,7 +14,8 @@ jobs:
       # The CKAN version tag of the Solr and Postgres containers should match
       # the one of the container the tests run on.
       # You can switch this base image with a custom image tailored to your project
-      image: openknowledge/ckan-dev:2.10
+      image: ckan/ckan-dev:2.11-py3.10
+      options: --user root
     services:
       solr:
         image: ckan/ckan-solr:2.11-solr9
@@ -42,15 +43,16 @@ jobs:
         pip install -r requirements.txt
         pip install -r dev-requirements.txt
         pip install --upgrade pytest-rerunfailures
-        pip install -e 'git+https://github.com/CivityNL/[email protected]#egg=ckanext-scheming[requirements]'
+        pip install -e 'git+https://github.com/CivityNL/[email protected]-1#egg=ckanext-scheming[requirements]'
         pip install -e 'git+https://github.com/ckan/[email protected]#egg=ckanext-harvest[requirements]'
-        pip install -e 'git+https://github.com/ckan/ckanext-dcat.git@v2.1.0#egg=ckanext-dcat[requirements]'
-        pip install -r https://raw.githubusercontent.com/ckan/ckanext-dcat/v2.1.0/requirements.txt
+        pip install -e 'git+https://github.com/ckan/ckanext-dcat.git@v2.2.0#egg=ckanext-dcat[requirements]'
+        pip install -r https://raw.githubusercontent.com/ckan/ckanext-dcat/v2.2.0/requirements.txt
         python3 setup.py develop
     - name: Setup extension
       run: |
         sed -i -e 's/use = config:.*/use = config:\/srv\/app\/src\/ckan\/test-core.ini/' test.ini
         ckan -c test.ini db init
+        ckan -c test.ini db pending-migrations --apply
     - name: Run tests
       run: |
         pytest --ckan-ini=test.ini --cov=ckanext.fairdatapoint --disable-warnings ckanext/fairdatapoint 

README.md

@@ -115,8 +115,8 @@ 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]'
-pip install -e 'git+https://github.com/ckan/ckanext-dcat.git@v2.1.0#egg=ckanext-dcat'
-pip install -r https://raw.githubusercontent.com/ckan/ckanext-dcat/v2.1.0/requirements.txt
+pip install -e 'git+https://github.com/ckan/ckanext-dcat.git@v2.2.0#egg=ckanext-dcat'
+pip install -r https://raw.githubusercontent.com/ckan/ckanext-dcat/v2.2.0/requirements.txt
 ```
 
 ## Tests

ckanext/fairdatapoint/profiles.py

@@ -16,7 +16,7 @@
 from dateutil.parser import ParserError
 from rdflib import DCAT, DCTERMS, FOAF, Namespace, URIRef
 
-from ckanext.dcat.profiles import EuropeanDCATAP3Profile
+from ckanext.dcat.profiles import EuropeanHealthDCATAPProfile
 from ckanext.fairdatapoint.labels import PACKAGE_REPLACE_FIELDS
 
 log = logging.getLogger(__name__)
@@ -56,7 +56,7 @@ def validate_tags(values_list: List[Dict]) -> List:
     return tags
 
 
-class FAIRDataPointDCATAPProfile(EuropeanDCATAP3Profile):
+class FAIRDataPointDCATAPProfile(EuropeanHealthDCATAPProfile):
     """
     An RDF profile for FAIR data points
     """

ckanext/fairdatapoint/tests/test_processors.py

@@ -53,7 +53,7 @@ def test_fdp_record_converter_dataset_dict(self):
                                 license_id="", identifier="27866022694497978",
                                 has_version=[
                                     "https://repo.metadatacenter.org/template-instances/2836bf1c-76e9-44e7-a65e-80e9ca63025a"],
-                                contact=[{'email': '', 'identifier': 'https://orcid.org/0000-0002-4348-707X', 'name': 'N.K. De Vries','uri': ''}
+                                contact=[{'email': '', 'identifier': 'https://orcid.org/0000-0002-4348-707X', 'name': 'N.K. De Vries','uri': '', 'url': ''}
                                 ], creator=[{'email': '', 'identifier': '', 'name': '', 'type': '', 'uri': 'https://orcid.org/0000-0002-0180-3636', 'url': ''}],
                                 publisher=[{'email': '','identifier': '','name': '','type': '','uri': 'https://opal.health-ri.nl/pub', 'url': ''}],
                                 temporal_start='2020-01-01', temporal_end='2025-12-31')

requirements.txt

@@ -3,7 +3,6 @@
 # SPDX-License-Identifier: AGPL-3.0-only
 
 rdflib~=7.1.0
-six~=1.16.0
 setuptools~=70.3.0
 nose~=1.3.7
 requests~=2.32.3

test.ini

@@ -9,15 +9,15 @@ smtp_server = localhost
 error_email_from = ckan@localhost
 
 [app:main]
-scheming.dataset_schemas = ckanext.dcat.schemas:dcat_ap_full.yaml ckanext.fairdatapoint:tests/test_data/scheming/schemas/gdi_userportal.yaml
+scheming.dataset_schemas = ckanext.dcat.schemas:health_dcat_ap.yaml ckanext.fairdatapoint:tests/test_data/scheming/schemas/gdi_userportal.yaml
 scheming.presets = ckanext.scheming:presets.json ckanext.dcat.schemas:presets.yaml ckanext.fairdatapoint:tests/test_data/scheming/presets/gdi_presets.yaml
 scheming.dataset_fallback = false
 use = config:../../src/ckan/test-core.ini
 
 # Insert any custom config settings to be used when running your extension's
 # tests here. These will override the one defined in CKAN core's test-core.ini
 ckan.plugins = dcat scheming_datasets fairdatapoint
-ckanext.dcat.rdf.profiles = euro_dcat_ap_3 euro_dcat_ap_scheming fairdatapoint_dcat_ap
+ckanext.dcat.rdf.profiles = euro_health_dcat_ap euro_dcat_ap_3 euro_dcat_ap_scheming fairdatapoint_dcat_ap
 
 # Logging configuration
 [loggers]