fix paths

GenomicDataInfrastructure · Jan 4, 2024 · 3be98ce · 3be98ce
1 parent 0d7ab6e
commit 3be98ce
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Showing 3 changed files with 17 additions and 18 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -49,6 +49,5 @@ jobs:
 
         ckan -c test.ini db init
     - name: Run tests
-      working-directory: ckanext-fairdatapoint
       run: pytest --ckan-ini=test.ini --cov=ckanext.fairdatapoint --disable-warnings ckanext/fairdatapoint
 
diff --git a/ckanext/fairdatapoint/tests/test_processors.py b/ckanext/fairdatapoint/tests/test_processors.py
@@ -1,18 +1,20 @@
 import pytest
+from pathlib import Path
 from unittest.mock import patch
 from rdflib import Graph
 from ckanext.fairdatapoint.harvesters.domain.fair_data_point_record_to_package_converter import (
     FairDataPointRecordToPackageConverter)
 
+TEST_DATA_DIRECTORY = Path(Path(__file__).parent.resolve(), "test_data")
+
 
 @pytest.mark.ckan_config("ckan.plugins", "scheming_datasets")
 @pytest.mark.usefixtures("with_plugins")
 class TestProcessors:
     @patch("ckanext.fairdatapoint.processors.FairDataPointRDFParser.datasets")
     def test_fdp_record_converter_dataset(self, parser_datasets):
         fdp_record_to_package = FairDataPointRecordToPackageConverter(profile="fairdatapoint_dcat_ap")
-        data = Graph().parse("./ckanext-fairdatapoint/ckanext/fairdatapoint/tests/test_data/"
-                             "Project_27866022694497978_out.ttl").serialize()
+        data = Graph().parse(Path(TEST_DATA_DIRECTORY, "Project_27866022694497978_out.ttl")).serialize()
         fdp_record_to_package.record_to_package(guid="catalog=https://covid19initiatives.health-ri.nl/p/"
                                                      "ProjectOverview?focusarea=http://purl.org/zonmw/generic/10006;"
                                                      "dataset=https://covid19initiatives.health-ri.nl/p/Project/"
@@ -23,17 +25,15 @@ def test_fdp_record_converter_dataset(self, parser_datasets):
     @patch("ckanext.fairdatapoint.processors.FairDataPointRDFParser.catalogs")
     def test_fdp_record_converter_catalog(self, parser_catalogs):
         fdp_record_to_package = FairDataPointRecordToPackageConverter(profile="fairdatapoint_dcat_ap")
-        data = Graph().parse(
-            "./ckanext-fairdatapoint/ckanext/fairdatapoint/tests/test_data/fdp_catalog.ttl").serialize()
+        data = Graph().parse(Path(TEST_DATA_DIRECTORY, "fdp_catalog.ttl")).serialize()
         fdp_record_to_package.record_to_package(
             guid="catalog=https://fair.healthinformationportal.eu/catalog/1c75c2c9-d2cc-44cb-aaa8-cf8c11515c8d",
             record=data)
         assert parser_catalogs.called
 
     def test_fdp_record_converter_dataset_dict(self):
         fdp_record_to_package = FairDataPointRecordToPackageConverter(profile="fairdatapoint_dcat_ap")
-        data = Graph().parse("./ckanext-fairdatapoint/ckanext/fairdatapoint/tests/test_data/"
-                             "Project_27866022694497978_out.ttl").serialize()
+        data = Graph().parse(Path(TEST_DATA_DIRECTORY, "Project_27866022694497978_out.ttl")).serialize()
         actual_dataset = fdp_record_to_package.record_to_package(
             guid="catalog=https://covid19initiatives.health-ri.nl/p/ProjectOverview?focusarea="
                  "http://purl.org/zonmw/generic/10006;"
@@ -61,8 +61,7 @@ def test_fdp_record_converter_dataset_dict(self):
 
     def test_fdp_record_converter_catalog_dict(self):
         fdp_record_to_package = FairDataPointRecordToPackageConverter(profile="fairdatapoint_dcat_ap")
-        data = Graph().parse(
-            "./ckanext-fairdatapoint/ckanext/fairdatapoint/tests/test_data/fdp_catalog.ttl").serialize()
+        data = Graph().parse(Path(TEST_DATA_DIRECTORY, "fdp_catalog.ttl")).serialize()
         actual = fdp_record_to_package.record_to_package(
             guid="catalog=https://fair.healthinformationportal.eu/catalog/1c75c2c9-d2cc-44cb-aaa8-cf8c11515c8d",
             record=data)

diff --git a/ckanext/fairdatapoint/tests/test_record_provider.py b/ckanext/fairdatapoint/tests/test_record_provider.py
@@ -1,9 +1,11 @@
 import pytest
 import requests_mock
+from pathlib import Path
 from pytest_mock import class_mocker, mocker
 from rdflib import Graph, URIRef
 from ckanext.fairdatapoint.harvesters.domain.fair_data_point_record_provider import FairDataPointRecordProvider
 
+TEST_DATA_DIRECTORY = Path(Path(__file__).parent.resolve(), "test_data")
 
 TEST_CAT_IDS_DICT = {
             "catalog=https://fair.healthinformationportal.eu/catalog/1c75c2c9-d2cc-44cb-aaa8-cf8c11515c8d":
@@ -24,7 +26,7 @@
 def get_graph_by_id(*args, **kwargs):
     file_id = args[0]
     file_id = "_".join(file_id.split("/")[-2:])
-    path_to_file = f"./ckanext-fairdatapoint/ckanext/fairdatapoint/tests/test_data/{file_id}.ttl"
+    path_to_file = Path(TEST_DATA_DIRECTORY, f"{file_id}.ttl")
     graph = Graph().parse(path_to_file)
     return graph
 
@@ -34,9 +36,9 @@ class TestRecordProvider:
 
     @pytest.mark.parametrize("fdp_response_file,expected",
                          [
-                             ("./ckanext/fairdatapoint/tests/test_data/root_fdp_response.ttl",
+                             (Path(TEST_DATA_DIRECTORY, "root_fdp_response.ttl"),
                               TEST_CAT_IDS_DICT.keys()),
-                             ("./ckanext/fairdatapoint/tests/test_data/root_fdp_response_no_catalogs.ttl",
+                             (Path(TEST_DATA_DIRECTORY, "root_fdp_response_no_catalogs.ttl"),
                               dict().keys())
                           ])
     def test_get_record_ids(self, mocker, fdp_response_file, expected):
@@ -66,8 +68,8 @@ def test_get_record_by_id(self, mocker):
                 "dataset=https://fair.healthinformationportal.eu/dataset/898ca4b8-197b-4d40-bc81-d9cd88197670")
         fdp_get_graph.side_effect = get_graph_by_id
         actual = self.fdp_record_provider.get_record_by_id(guid)
-        expected = Graph().parse(f"./ckanext-fairdatapoint/ckanext/fairdatapoint/tests/test_data/"
-                                 f"dataset_898ca4b8-197b-4d40-bc81-d9cd88197670.ttl").serialize()
+        expected = Graph().parse(
+            Path(TEST_DATA_DIRECTORY, "dataset_898ca4b8-197b-4d40-bc81-d9cd88197670.ttl")).serialize()
         assert actual == expected
 
     def test_get_record_by_id_distr(self, mocker):
@@ -79,8 +81,8 @@ def test_get_record_by_id_distr(self, mocker):
                 "dataset=https://health-ri.sandbox.semlab-leiden.nl/dataset/d7129d28-b72a-437f-8db0-4f0258dd3c25")
         fdp_get_graph.side_effect = get_graph_by_id
         actual = self.fdp_record_provider.get_record_by_id(guid)
-        expected = Graph().parse("./ckanext-fairdatapoint/ckanext/fairdatapoint/tests/test_data/"
-                                 "dataset_d7129d28-b72a-437f-8db0-4f0258dd3c25_out.ttl").serialize()
+        expected = Graph().parse(
+            Path(TEST_DATA_DIRECTORY, "dataset_d7129d28-b72a-437f-8db0-4f0258dd3c25_out.ttl")).serialize()
         assert actual == expected
 
     def test_orcid_call(self, mocker):
@@ -96,7 +98,6 @@ def test_orcid_call(self, mocker):
                     "dataset=https://covid19initiatives.health-ri.nl/p/Project/27866022694497978")
             fdp_get_graph.side_effect = get_graph_by_id
             actual = self.fdp_record_provider.get_record_by_id(guid)
-            expected = Graph().parse("./ckanext-fairdatapoint/ckanext/fairdatapoint/tests/test_data/"
-                                     "Project_27866022694497978_out.ttl").serialize()
+            expected = Graph().parse(Path(TEST_DATA_DIRECTORY, "Project_27866022694497978_out.ttl")).serialize()
             assert mock.called
             assert actual == expected