Merge pull request #78 from apdavison/improve-regression-tests

Run regression tests with both "v4" and "latest"

Author: Raphael-Gazzotti

pipeline/src/base.py

@@ -161,7 +161,7 @@ def validate(self, ignore=None):
 
         Returns a dict containing information about any validation failures.
         """
-        return self._validate(ignore=ignore)
+        return dict(self._validate(ignore=ignore))
 
     def _validate(self, ignore=None, seen=None):
         # this is implemented as an internal method so that the

pipeline/src/properties.py

@@ -131,7 +131,7 @@ def validate(self, value, ignore=None, seen=None):
                             if isinstance(item, Link):
                                 item_type = f"value contains a link to {item.allowed_types}"
                             else:
-                                item_type = f"value contains {type(item)}"
+                                item_type = f"value contains {type(item).__name__}"
                             failures["type"].append(
                                 f"{self.name}: Expected {', '.join(t.__name__ for t in self.types)}, " + item_type
                             )
@@ -166,7 +166,7 @@ def validate(self, value, ignore=None, seen=None):
                     if isinstance(value, Link):
                         value_type = f"value contains a link to {value.allowed_types}"
                     else:
-                        value_type = f"value contains {type(value)}"
+                        value_type = f"value contains {type(value).__name__}"
                     failures["type"].append(
                         f"{self.name}: Expected {', '.join(t.__name__ for t in self.types)}, " + value_type
                     )

pipeline/tests/test_regressions.py

@@ -1,39 +1,45 @@
 from datetime import date
 import json
 import os
+
+import pytest
+
 from openminds import Collection, IRI
-from openminds.v4 import core as omcore
+import openminds.latest
+import openminds.v4
 from utils import build_fake_node
 
 
-def test_issue_0002():
+@pytest.mark.parametrize("om", [openminds.latest, openminds.v4])
+def test_issue_0002(om):
     # https://github.com/openMetadataInitiative/openMINDS_Python/issues/2
     # @type should not be given as a list but as a string
 
-    node = build_fake_node(omcore.Person)
+    node = build_fake_node(om.core.Person)
     data = node.to_jsonld()
     assert data["@type"] == "https://openminds.om-i.org/types/Person"
 
 
-def test_issue_0003():
+@pytest.mark.parametrize("om", [openminds.latest, openminds.v4])
+def test_issue_0003(om):
     # https://github.com/openMetadataInitiative/openMINDS_Python/issues/3
     # validate() does not complain about direct entries that should be lists
 
     # we address this by always wrapping a single item in a list in such cases
 
-    some_file = omcore.File(
+    some_file = om.core.File(
         iri=IRI("http://example.com/some_file.txt"),
         name="some_file.txt",
     )
 
-    node1 = omcore.FileArchive(
+    node1 = om.core.FileArchive(
         iri=IRI("http://example.com/archive.zip"),
-        format=omcore.ContentType(name="application/zip"),
+        format=om.core.ContentType(name="application/zip"),
         source_data=[some_file],  # multiple=True, min_items=1
     )
-    node2 = omcore.FileArchive(
+    node2 = om.core.FileArchive(
         iri=IRI("http://example.com/archive.zip"),
-        format=omcore.ContentType(name="application/zip"),
+        format=om.core.ContentType(name="application/zip"),
         source_data=some_file,  # multiple=True, min_items=1
     )
     # on export, a single item should be wrapped in a list, where the property expects an array
@@ -59,14 +65,15 @@ def test_issue_0003():
     )
 
 
-def test_issue0005():
+@pytest.mark.parametrize("om", [openminds.latest, openminds.v4])
+def test_issue0005(om):
     # https://github.com/openMetadataInitiative/openMINDS_Python/issues/5
     # validate() does not complain about list/tuple entries that should be a direct single entry
-    uni1 = omcore.Organization(full_name="University of This Place")
-    person = omcore.Person(
+    uni1 = om.core.Organization(full_name="University of This Place")
+    person = om.core.Person(
         given_name="A",
         family_name="Professor",
-        affiliations=[omcore.Affiliation(member_of=uni1, end_date=(2023, 9, 30))],
+        affiliations=[om.core.Affiliation(member_of=uni1, end_date=(2023, 9, 30))],
     )
     failures = person.validate()
     assert len(failures) == 1
@@ -76,16 +83,17 @@ def test_issue0005():
     assert len(failures) == 0
 
 
-def test_issue0007():
+@pytest.mark.parametrize("om", [openminds.latest, openminds.v4])
+def test_issue0007(om):
     # https://github.com/openMetadataInitiative/openMINDS_Python/issues/7
     # Instances of embedded types with value type "array" are not correctly resolved for saving and causing an error.
 
-    person = omcore.Person(given_name="A", family_name="Professor", id="_:001")
-    uni1 = omcore.Organization(full_name="University of This Place", id="_:002")
-    uni2 = omcore.Organization(full_name="University of That Place", id="_:003")
+    person = om.core.Person(given_name="A", family_name="Professor", id="_:001")
+    uni1 = om.core.Organization(full_name="University of This Place", id="_:002")
+    uni2 = om.core.Organization(full_name="University of That Place", id="_:003")
     person.affiliations = [
-        omcore.Affiliation(member_of=uni1),
-        omcore.Affiliation(member_of=uni2),
+        om.core.Affiliation(member_of=uni1),
+        om.core.Affiliation(member_of=uni2),
     ]
 
     actual = person.to_jsonld(include_empty_properties=False, embed_linked_nodes=False, with_context=True)
@@ -149,17 +157,18 @@ def test_issue0007():
     assert saved_data == expected_saved_data
 
 
-def test_issue0008():
+@pytest.mark.parametrize("om", [openminds.latest, openminds.v4])
+def test_issue0008(om):
     # https://github.com/openMetadataInitiative/openMINDS_Python/issues/8
     # The instance of linked types in instances of embedded types are integrated as embedded not linked
     # (example: person -> affiliations (embedded) -> organization (linked))
 
-    uni1 = omcore.Organization(full_name="University of This Place", id="_:001")
-    person = omcore.Person(
+    uni1 = om.core.Organization(full_name="University of This Place", id="_:001")
+    person = om.core.Person(
         id="_:002",
         given_name="A",
         family_name="Professor",
-        affiliations=[omcore.Affiliation(member_of=uni1, end_date=date(2023, 9, 30))],
+        affiliations=[om.core.Affiliation(member_of=uni1, end_date=date(2023, 9, 30))],
     )
     actual = person.to_jsonld(include_empty_properties=False, embed_linked_nodes=False, with_context=True)
     expected = {
@@ -179,14 +188,15 @@ def test_issue0008():
     assert actual == expected
 
 
-def test_issue0026():
+@pytest.mark.parametrize("om", [openminds.latest, openminds.v4])
+def test_issue0026(om):
     # https://github.com/openMetadataInitiative/openMINDS_Python/issues/26
     # When reading a JSON-LD file, the attributes of LinkedMetadata nodes
     # inside EmbeddedMetadata nodes are not set properly
 
-    uni1 = omcore.Organization(full_name="University of This Place", id="_:uthisp")
-    person = omcore.Person(
-        given_name="A", family_name="Professor", affiliations=[omcore.Affiliation(member_of=uni1)], id="_:ap"
+    uni1 = om.core.Organization(full_name="University of This Place", id="_:uthisp")
+    person = om.core.Person(
+        given_name="A", family_name="Professor", affiliations=[om.core.Affiliation(member_of=uni1)], id="_:ap"
     )
 
     c = Collection(person)
@@ -196,57 +206,59 @@ def test_issue0026():
     output_paths = c.save("issue0026.jsonld", individual_files=False, include_empty_properties=False)
 
     new_collection = Collection()
-    new_collection.load(*output_paths)
+    new_collection.load(*output_paths, version=om.__name__.split(".")[1])
     os.remove("issue0026.jsonld")
 
-    person_again = [item for item in new_collection if isinstance(item, omcore.Person)][0]
+    person_again = [item for item in new_collection if isinstance(item, om.core.Person)][0]
     assert len(person_again.affiliations) == 1
     assert person_again.affiliations[0].member_of.full_name == "University of This Place"
 
 
-def test_issue0023():
+@pytest.mark.parametrize("om", [openminds.latest, openminds.v4])
+def test_issue0023(om):
     # https://github.com/openMetadataInitiative/openMINDS_Python/issues/23
     # If a user adds an instance/node to a collection, and then later adds linked types to the instance,
     # currently that is not added to the collection
 
-    uni1 = omcore.Organization(full_name="University of This Place", id="_:uthisp")
-    person = omcore.Person(
-        given_name="A", family_name="Professor", affiliations=[omcore.Affiliation(member_of=uni1)], id="_:ap"
+    uni1 = om.core.Organization(full_name="University of This Place", id="_:uthisp")
+    person = om.core.Person(
+        given_name="A", family_name="Professor", affiliations=[om.core.Affiliation(member_of=uni1)], id="_:ap"
     )
-    dv = omcore.DatasetVersion(full_name="The name of the dataset version", custodians=[person], id="_:dv")
+    dv = om.core.DatasetVersion(full_name="The name of the dataset version", custodians=[person], id="_:dv")
 
     c = Collection(dv)
 
     # even though we add uni2 and the repository after creating the collection,
     # they should be included when we save the collection.
-    uni2 = omcore.Organization(full_name="University of That Place", id="_:uthatp")
-    person.affiliations.append(omcore.Affiliation(member_of=uni2))
-    dv.repository = omcore.FileRepository(iri="http://example.com", id="_:fr")
+    uni2 = om.core.Organization(full_name="University of That Place", id="_:uthatp")
+    person.affiliations.append(om.core.Affiliation(member_of=uni2))
+    dv.repository = om.core.FileRepository(iri="http://example.com", id="_:fr")
 
     output_paths = c.save("issue0023.jsonld", individual_files=False, include_empty_properties=False)
 
     new_collection = Collection()
-    new_collection.load(*output_paths)
+    new_collection.load(*output_paths, version=om.__name__.split(".")[1])
     os.remove("issue0023.jsonld")
 
-    dv_again = [item for item in new_collection if isinstance(item, omcore.DatasetVersion)][0]
-    assert isinstance(dv_again.repository, omcore.FileRepository)
+    dv_again = [item for item in new_collection if isinstance(item, om.core.DatasetVersion)][0]
+    assert isinstance(dv_again.repository, om.core.FileRepository)
     assert dv_again.repository.iri.value == "http://example.com"
     assert len(dv_again.custodians[0].affiliations) == 2
     assert dv_again.custodians[0].affiliations[0].member_of.full_name == "University of This Place"
     assert dv_again.custodians[0].affiliations[1].member_of.full_name == "University of That Place"
 
 
-def test_issue0056():
+@pytest.mark.parametrize("om", [openminds.latest, openminds.v4])
+def test_issue0056(om):
     # https://github.com/openMetadataInitiative/openMINDS_Python/issues/56
     # Since we are permissive on object creation, serialization to JSON-LD should work
     # even if the object gives validation failures.
     # However, under some circumstances, to_jsonld() produces a data structure
     # that cannot be saved as a JSON string.
-    dataset = omcore.Dataset(
+    dataset = om.core.Dataset(
         digital_identifier=[
-            omcore.DOI(identifier="abc"),
-            omcore.DOI(identifier="def")
+            om.core.DOI(identifier="abc"),
+            om.core.DOI(identifier="def")
         ]
     )
     failures = dataset.validate(ignore=["required"])
@@ -256,17 +268,35 @@ def test_issue0056():
     json.dumps(data)  # this should not raise an Exception
 
 
-def test_issue0073():
+@pytest.mark.parametrize("om", [openminds.v4])
+def test_issue0073a(om):
     # https://github.com/openMetadataInitiative/openMINDS_Python/issues/73
     # Infinite recursion in validate()
-    ds1 = omcore.DatasetVersion(
+    ds1 = om.core.DatasetVersion(
         short_name="ds1",
         is_alternative_version_of=None
     )
-    ds2 = omcore.DatasetVersion(
+    ds2 = om.core.DatasetVersion(
         short_name="ds2",
         is_alternative_version_of=ds1
     )
     ds1.is_alternative_version_of = ds2
 
     failures = ds1.validate()
+
+
+@pytest.mark.parametrize("om", [openminds.latest])
+def test_issue0073b(om):
+    # https://github.com/openMetadataInitiative/openMINDS_Python/issues/73
+    # Infinite recursion in validate()
+    ds1 = om.core.DatasetVersion(
+        short_name="ds1",
+        is_variant_of=None
+    )
+    ds2 = om.core.DatasetVersion(
+        short_name="ds2",
+        is_variant_of=ds1
+    )
+    ds1.is_variant_of = ds2
+
+    failures = ds1.validate()

pipeline/tests/test_validation.py

@@ -0,0 +1,27 @@
+import openminds.v4 as om
+
+
+def test_invalid_type():
+    # invalid: type
+    mouse = om.controlled_terms.Species.mus_musculus
+    dsv = om.core.DatasetVersion(accessibility=mouse)
+    assert dsv.validate(ignore=["required"]) == {
+        "type": ["accessibility: Expected ProductAccessibility, value contains Species"]
+    }
+
+    # valid
+    dsv = om.core.DatasetVersion(study_targets=[mouse])
+    assert dsv.validate(ignore=["required"]) == {}
+
+    # invalid: doubly-nested list
+    dsv = om.core.DatasetVersion(study_targets=[[mouse]])
+    assert "value contains list" in dsv.validate(ignore=["required"])["type"][0]
+
+
+def test_required():
+    p = om.core.Person()
+    assert p.validate() == {
+        "required": [
+            "given_name is required, but was not provided",
+        ]
+    }