prov:qualifiedAttribution metadata [ENG-6185]

CenterForOpenScience · Oct 25, 2024 · 16d0a72 · 16d0a72
1 parent 2819c75
commit 16d0a72
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Showing 9 changed files with 103 additions and 10 deletions.
diff --git a/osf/metadata/osf_gathering.py b/osf/metadata/osf_gathering.py
@@ -21,6 +21,7 @@
     OSF,
     OSFIO,
     OWL,
+    PROV,
     RDF,
     ROR,
     SKOS,
@@ -31,7 +32,10 @@
 )
 from osf.metrics.reports import PublicItemUsageReport
 from osf.metrics.utils import YearMonth
-from osf.utils import workflows as osfworkflows
+from osf.utils import (
+    workflows as osfworkflows,
+    permissions as osfpermissions,
+)
 from osf.utils.outcomes import ArtifactTypes
 from website import settings as website_settings
 
@@ -129,6 +133,7 @@ def pls_get_magic_metadata_basket(osf_item) -> gather.Basket:
         DCTERMS.creator: OSF_AGENT_REFERENCE,
     },
     OWL.sameAs: None,
+    PROV.qualifiedAttribution: None,
 }
 
 OSFMAP = {
@@ -252,6 +257,11 @@ def pls_get_magic_metadata_basket(osf_item) -> gather.Basket:
     ArtifactTypes.PAPERS: OSF.hasPapersResource,
     ArtifactTypes.SUPPLEMENTS: OSF.hasSupplementalResource,
 }
+OSF_CONTRIBUTOR_ROLES = {
+    osfpermissions.READ: OSF['readonly-contributor'],
+    osfpermissions.WRITE: OSF['write-contributor'],
+    osfpermissions.ADMIN: OSF['admin-contributor'],
+}
 
 BEPRESS_SUBJECT_SCHEME_URI = 'https://bepress.com/reference_guide_dc/disciplines/'
 BEPRESS_SUBJECT_SCHEME_TITLE = 'bepress Digital Commons Three-Tiered Taxonomy'
@@ -886,6 +896,19 @@ def gather_agents(focus):
     # TODO: preserve order via rdflib.Seq
 
 
+@gather.er(PROV.qualifiedAttribution)
+def gather_qualified_attributions(focus):
+    _contributor_set = getattr(focus.dbmodel, 'contributor_set', None)
+    if _contributor_set is not None:
+        for _contributor in _contributor_set.filter(visible=True).select_related('user'):
+            _osfrole_ref = OSF_CONTRIBUTOR_ROLES.get(_contributor.permission)
+            if _osfrole_ref is not None:
+                _attribution_ref = rdflib.BNode()
+                yield (PROV.qualifiedAttribution, _attribution_ref)
+                yield (_attribution_ref, PROV.agent, OsfFocus(_contributor.user))
+                yield (_attribution_ref, DCAT.hadRole, _osfrole_ref)
+
+
 @gather.er(OSF.affiliation)
 def gather_affiliated_institutions(focus):
     if hasattr(focus.dbmodel, 'get_affiliated_institutions'):   # like OSFUser

diff --git a/osf/metadata/rdfutils.py b/osf/metadata/rdfutils.py
@@ -23,6 +23,7 @@
 RDF = rdflib.Namespace('http://www.w3.org/1999/02/22-rdf-syntax-ns#')   # "resource description framework"
 SKOS = rdflib.Namespace('http://www.w3.org/2004/02/skos/core#')         # "simple knowledge organization system"
 DCAT = rdflib.Namespace('http://www.w3.org/ns/dcat#')                   # "data catalog (vocabulary)"
+PROV = rdflib.Namespace('http://www.w3.org/ns/prov#')                   # "provenance"
 # non-standard namespace for datacite terms (resolves to datacite docs)
 DATACITE = rdflib.Namespace('https://schema.datacite.org/meta/kernel-4/#')
 
@@ -38,6 +39,7 @@
     'skos': SKOS,
     'dcmitype': DCMITYPE,
     'dcat': DCAT,
+    'prov': PROV,
 }
 
 

diff --git a/osf_tests/metadata/expected_metadata_files/preprint_basic.turtle b/osf_tests/metadata/expected_metadata_files/preprint_basic.turtle
@@ -3,6 +3,7 @@
 @prefix foaf: <http://xmlns.com/foaf/0.1/> .
 @prefix osf: <https://osf.io/vocab/2022/> .
 @prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix prov: <http://www.w3.org/ns/prov#> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix skos: <http://www.w3.org/2004/02/skos/core#> .
 
@@ -25,7 +26,9 @@
     dcat:accessService <http://localhost:5000> ;
     osf:hostingInstitution <https://cos.io/> ;
     osf:isSupplementedBy <http://localhost:5000/w2ibb> ;
-    osf:statedConflictOfInterest osf:no-conflict-of-interest .
+    osf:statedConflictOfInterest osf:no-conflict-of-interest ;
+    prov:qualifiedAttribution [ dcat:hadRole osf:admin-contributor ;
+            prov:agent <http://localhost:5000/w1ibb> ] .
 
 <http://localhost:5000> a dcterms:Agent,
         foaf:Organization ;

diff --git a/osf_tests/metadata/expected_metadata_files/preprint_full.turtle b/osf_tests/metadata/expected_metadata_files/preprint_full.turtle
@@ -3,6 +3,7 @@
 @prefix foaf: <http://xmlns.com/foaf/0.1/> .
 @prefix osf: <https://osf.io/vocab/2022/> .
 @prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix prov: <http://www.w3.org/ns/prov#> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix skos: <http://www.w3.org/2004/02/skos/core#> .
 
@@ -25,7 +26,9 @@
     dcat:accessService <http://localhost:5000> ;
     osf:hostingInstitution <https://cos.io/> ;
     osf:isSupplementedBy <http://localhost:5000/w2ibb> ;
-    osf:statedConflictOfInterest osf:no-conflict-of-interest .
+    osf:statedConflictOfInterest osf:no-conflict-of-interest ;
+    prov:qualifiedAttribution [ dcat:hadRole osf:admin-contributor ;
+            prov:agent <http://localhost:5000/w1ibb> ] .
 
 <http://localhost:5000> a dcterms:Agent,
         foaf:Organization ;

diff --git a/osf_tests/metadata/expected_metadata_files/project_basic.turtle b/osf_tests/metadata/expected_metadata_files/project_basic.turtle
@@ -3,6 +3,7 @@
 @prefix foaf: <http://xmlns.com/foaf/0.1/> .
 @prefix osf: <https://osf.io/vocab/2022/> .
 @prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix prov: <http://www.w3.org/ns/prov#> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix skos: <http://www.w3.org/2004/02/skos/core#> .
 
@@ -24,7 +25,9 @@
     dcat:accessService <http://localhost:5000> ;
     osf:contains <http://localhost:5000/w3ibb> ;
     osf:hostingInstitution <https://cos.io/> ;
-    osf:supplements <http://localhost:5000/w4ibb> .
+    osf:supplements <http://localhost:5000/w4ibb> ;
+    prov:qualifiedAttribution [ dcat:hadRole osf:admin-contributor ;
+            prov:agent <http://localhost:5000/w1ibb> ] .
 
 <http://localhost:5000/w4ibb> a osf:Preprint ;
     dcterms:created "2123-05-04" ;

diff --git a/osf_tests/metadata/expected_metadata_files/project_full.turtle b/osf_tests/metadata/expected_metadata_files/project_full.turtle
@@ -3,6 +3,7 @@
 @prefix foaf: <http://xmlns.com/foaf/0.1/> .
 @prefix osf: <https://osf.io/vocab/2022/> .
 @prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix prov: <http://www.w3.org/ns/prov#> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix skos: <http://www.w3.org/2004/02/skos/core#> .
 
@@ -30,7 +31,9 @@
     osf:hasFunding <https://moneypockets.example/millions>,
         <https://moneypockets.example/millions-more> ;
     osf:hostingInstitution <https://cos.io/> ;
-    osf:supplements <http://localhost:5000/w4ibb> .
+    osf:supplements <http://localhost:5000/w4ibb> ;
+    prov:qualifiedAttribution [ dcat:hadRole osf:admin-contributor ;
+            prov:agent <http://localhost:5000/w1ibb> ] .
 
 <http://localhost:5000/w4ibb> a osf:Preprint ;
     dcterms:created "2123-05-04" ;

diff --git a/osf_tests/metadata/expected_metadata_files/registration_basic.turtle b/osf_tests/metadata/expected_metadata_files/registration_basic.turtle
@@ -3,6 +3,7 @@
 @prefix foaf: <http://xmlns.com/foaf/0.1/> .
 @prefix osf: <https://osf.io/vocab/2022/> .
 @prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix prov: <http://www.w3.org/ns/prov#> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix skos: <http://www.w3.org/2004/02/skos/core#> .
 
@@ -23,7 +24,9 @@
     dcterms:type <https://schema.datacite.org/meta/kernel-4/#StudyRegistration> ;
     dcat:accessService <http://localhost:5000> ;
     osf:contains <http://localhost:5000/w6ibb> ;
-    osf:hostingInstitution <https://cos.io/> .
+    osf:hostingInstitution <https://cos.io/> ;
+    prov:qualifiedAttribution [ dcat:hadRole osf:admin-contributor ;
+            prov:agent <http://localhost:5000/w1ibb> ] .
 
 <http://localhost:5000/w2ibb> a osf:Project ;
     dcterms:created "2123-05-04" ;

diff --git a/osf_tests/metadata/expected_metadata_files/registration_full.turtle b/osf_tests/metadata/expected_metadata_files/registration_full.turtle
@@ -3,6 +3,7 @@
 @prefix foaf: <http://xmlns.com/foaf/0.1/> .
 @prefix osf: <https://osf.io/vocab/2022/> .
 @prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix prov: <http://www.w3.org/ns/prov#> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix skos: <http://www.w3.org/2004/02/skos/core#> .
 
@@ -23,7 +24,9 @@
     dcterms:type <https://schema.datacite.org/meta/kernel-4/#StudyRegistration> ;
     dcat:accessService <http://localhost:5000> ;
     osf:contains <http://localhost:5000/w6ibb> ;
-    osf:hostingInstitution <https://cos.io/> .
+    osf:hostingInstitution <https://cos.io/> ;
+    prov:qualifiedAttribution [ dcat:hadRole osf:admin-contributor ;
+            prov:agent <http://localhost:5000/w1ibb> ] .
 
 <http://localhost:5000/w2ibb> a osf:Project ;
     dcterms:created "2123-05-04" ;

diff --git a/osf_tests/metadata/test_osf_gathering.py b/osf_tests/metadata/test_osf_gathering.py
@@ -17,6 +17,7 @@
     DCMITYPE,
     DOI,
     OWL,
+    PROV,
     RDF,
     SKOS,
     checksum_iri,
@@ -40,12 +41,13 @@ def setUpTestData(cls):
             external_identity={'ORCID': {'1234-4321-5678-8765': 'VERIFIED'}},
         )
         cls.user__readonly = factories.UserFactory(
-            external_identity={'ORCID': {'1234-4321-6789-9876': 'CREATE'}},
+            external_identity={'ORCID': {'1234-4321-6789-9876': 'CREATE'}},  # unverified orcid
             social={
                 'profileWebsites': ['http://mysite.example', 'http://myothersite.example/foo'],
                 'baiduScholar': 'blarg',
             },
         )
+        cls.user__invisible = factories.UserFactory()
         # cedar metadata template
         cls.cedar_template = factories.CedarMetadataTemplateFactory(
             cedar_id='https://repo.metadatacenter.org/templates/this-is-a-cedar-id',
@@ -58,7 +60,8 @@ def setUpTestData(cls):
         cls.project.add_addon('box', auth=None)
         cls.project.add_addon('gitlab', auth=None)
         cls.project.add_contributor(cls.user__readwrite, permissions=permissions.WRITE)
-        cls.project.add_contributor(cls.user__readonly, permissions=permissions.READ, visible=False)
+        cls.project.add_contributor(cls.user__readonly, permissions=permissions.READ)
+        cls.project.add_contributor(cls.user__invisible, permissions=permissions.WRITE, visible=False)
         cls.component = factories.ProjectFactory(parent=cls.project, creator=cls.user__admin, is_public=True)
         cls.sibcomponent = factories.ProjectFactory(parent=cls.project, creator=cls.user__admin, is_public=True)
         cls.subcomponent = factories.ProjectFactory(parent=cls.component, creator=cls.user__admin, is_public=True)
@@ -95,7 +98,8 @@ def setUpTestData(cls):
             is_public=True,
         )
         cls.preprint.add_contributor(cls.user__readwrite, permissions=permissions.WRITE)
-        cls.preprint.add_contributor(cls.user__readonly, permissions=permissions.READ, visible=False)
+        cls.preprint.add_contributor(cls.user__readonly, permissions=permissions.READ)
+        cls.preprint.add_contributor(cls.user__invisible, permissions=permissions.WRITE, visible=False)
         cls.registration_cedar_record = factories.CedarMetadataRecordFactory(
             template=cls.cedar_template,
             is_published=True,
@@ -530,11 +534,19 @@ def test_gather_agents(self):
         assert_triples(osf_gathering.gather_agents(self.projectfocus), {
             (self.projectfocus.iri, DCTERMS.creator, self.userfocus__admin),
             (self.projectfocus.iri, DCTERMS.creator, self.userfocus__readwrite),
+            (self.projectfocus.iri, DCTERMS.creator, self.userfocus__readonly),
         })
         # focus: registration
         assert_triples(osf_gathering.gather_agents(self.registrationfocus), {
             (self.registrationfocus.iri, DCTERMS.creator, self.userfocus__admin),
             (self.registrationfocus.iri, DCTERMS.creator, self.userfocus__readwrite),
+            (self.registrationfocus.iri, DCTERMS.creator, self.userfocus__readonly),
+        })
+        # focus: preprint
+        assert_triples(osf_gathering.gather_agents(self.preprintfocus), {
+            (self.preprintfocus.iri, DCTERMS.creator, self.userfocus__admin),
+            (self.preprintfocus.iri, DCTERMS.creator, self.userfocus__readwrite),
+            (self.preprintfocus.iri, DCTERMS.creator, self.userfocus__readonly),
         })
         # focus: file
         assert_triples(osf_gathering.gather_agents(self.filefocus), set())
@@ -823,3 +835,41 @@ def test_gather_storage_region(self):
             (self.preprintfocus.iri, OSF.storageRegion, _default_region_ref),
             (_default_region_ref, SKOS.prefLabel, Literal('United States', lang='en')),
         })
+
+    def test_gather_qualified_attributions(self):
+        _attribution_admin = rdflib.BNode()
+        _attribution_readwrite = rdflib.BNode()
+        _attribution_readonly = rdflib.BNode()
+        assert_triples(osf_gathering.gather_qualified_attributions(self.projectfocus), {
+            (self.projectfocus.iri, PROV.qualifiedAttribution, _attribution_admin),
+            (_attribution_admin, PROV.agent, self.userfocus__admin),
+            (_attribution_admin, DCAT.hadRole, OSF['admin-contributor']),
+            (self.projectfocus.iri, PROV.qualifiedAttribution, _attribution_readwrite),
+            (_attribution_readwrite, PROV.agent, self.userfocus__readwrite),
+            (_attribution_readwrite, DCAT.hadRole, OSF['write-contributor']),
+            (self.projectfocus.iri, PROV.qualifiedAttribution, _attribution_readonly),
+            (_attribution_readonly, PROV.agent, self.userfocus__readonly),
+            (_attribution_readonly, DCAT.hadRole, OSF['readonly-contributor']),
+        })
+        assert_triples(osf_gathering.gather_qualified_attributions(self.registrationfocus), {
+            (self.registrationfocus.iri, PROV.qualifiedAttribution, _attribution_admin),
+            (_attribution_admin, PROV.agent, self.userfocus__admin),
+            (_attribution_admin, DCAT.hadRole, OSF['admin-contributor']),
+            (self.registrationfocus.iri, PROV.qualifiedAttribution, _attribution_readwrite),
+            (_attribution_readwrite, PROV.agent, self.userfocus__readwrite),
+            (_attribution_readwrite, DCAT.hadRole, OSF['write-contributor']),
+            (self.registrationfocus.iri, PROV.qualifiedAttribution, _attribution_readonly),
+            (_attribution_readonly, PROV.agent, self.userfocus__readonly),
+            (_attribution_readonly, DCAT.hadRole, OSF['readonly-contributor']),
+        })
+        assert_triples(osf_gathering.gather_qualified_attributions(self.preprintfocus), {
+            (self.preprintfocus.iri, PROV.qualifiedAttribution, _attribution_admin),
+            (_attribution_admin, PROV.agent, self.userfocus__admin),
+            (_attribution_admin, DCAT.hadRole, OSF['admin-contributor']),
+            (self.preprintfocus.iri, PROV.qualifiedAttribution, _attribution_readwrite),
+            (_attribution_readwrite, PROV.agent, self.userfocus__readwrite),
+            (_attribution_readwrite, DCAT.hadRole, OSF['write-contributor']),
+            (self.preprintfocus.iri, PROV.qualifiedAttribution, _attribution_readonly),
+            (_attribution_readonly, PROV.agent, self.userfocus__readonly),
+            (_attribution_readonly, DCAT.hadRole, OSF['readonly-contributor']),
+        })