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osfmap updates
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- remove osf:affiliatedInstitution (use osf:affiliation instead)
- use dcterms:conformsTo to link osf registration schema
- remodel funding info (add osf:hasFunding, osf:FundingAward)
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@aaxelb
aaxelb committed Jul 31, 2023
1 parent fd91aaf commit 2c0ccc6
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Showing 6 changed files with 125 additions and 69 deletions.
55 changes: 41 additions & 14 deletions osf/metadata/osf_gathering.py
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Original file line number Diff line number Diff line change
Expand Up @@ -106,7 +106,7 @@ def osfmap_for_type(rdftype_iri: str):
DCTERMS.title: None,
DCTERMS.type: None,
OSF.affiliation: None,
OSF.funder: None,
OSF.hasFunding: None,
OSF.contains: OSF_FILE_REFERENCE,
OSF.hasRoot: OSF_OBJECT_REFERENCE,
OSF.keyword: None,
Expand Down Expand Up @@ -135,6 +135,7 @@ def osfmap_for_type(rdftype_iri: str):
OSF.Registration: {
**OSF_OBJECT,
OSF.archivedAt: None,
DCTERMS.conformsTo: None,
OSF.hasAnalyticCodeResource: OSF_OBJECT_REFERENCE,
OSF.hasDataResource: OSF_OBJECT_REFERENCE,
OSF.hasMaterialsResource: OSF_OBJECT_REFERENCE,
Expand Down Expand Up @@ -170,7 +171,7 @@ def osfmap_for_type(rdftype_iri: str):
OSF.isContainedBy: OSF_OBJECT_REFERENCE,
OSF.fileName: None,
OSF.filePath: None,
OSF.funder: None,
OSF.hasFunding: None,
OWL.sameAs: None,
},
OSF.Agent: {
Expand Down Expand Up @@ -271,7 +272,7 @@ def gather_identifiers(focus: gather.Focus):
yield (DCTERMS.identifier, str(osfguid_iri))
if hasattr(focus.dbmodel, 'get_identifier_value'):
doi = focus.dbmodel.get_identifier_value('doi')
if doi and doi.startswith('10.'): # HACK: skip malformed doi
if doi:
doi_iri = DOI[doi]
yield (OWL.sameAs, doi_iri)
yield (DCTERMS.identifier, str(doi_iri))
Expand Down Expand Up @@ -679,19 +680,32 @@ def gather_affiliated_institutions(focus):
yield (institution_iri, DCTERMS.identifier, osf_institution.identifier_domain)


@gather.er(OSF.funder)
@gather.er(OSF.hasFunding)
def gather_funding(focus):
if hasattr(focus, 'guid_metadata_record'):
for funding in focus.guid_metadata_record.funding_info:
funder_bnode = rdflib.BNode()
yield (OSF.funder, funder_bnode)
yield (funder_bnode, RDF.type, OSF.FundingReference)
yield (funder_bnode, FOAF.name, funding.get('funder_name'))
yield (funder_bnode, DCTERMS.identifier, funding.get('funder_identifier'))
yield (funder_bnode, OSF.funderIdentifierType, funding.get('funder_identifier_type'))
yield (funder_bnode, OSF.awardNumber, funding.get('award_number'))
yield (funder_bnode, OSF.awardUri, funding.get('award_uri'))
yield (funder_bnode, OSF.awardTitle, funding.get('award_title'))
for _funding in focus.guid_metadata_record.funding_info:
_award_uri = _funding.get('award_uri')
_award_ref = (
rdflib.URIRef(_award_uri)
if _award_uri
else rdflib.BNode()
)
yield (OSF.hasFunding, _award_ref)
yield (_award_ref, RDF.type, OSF.FundingAward)
if _award_uri:
yield (_award_ref, DCTERMS.identifier, _award_uri)
yield (_award_ref, DCTERMS.title, _funding.get('award_title'))
yield (_award_ref, OSF.awardNumber, _funding.get('award_number'))
_funder_uri = _funding.get('funder_identifier')
_funder_ref = (
rdflib.URIRef(_funder_uri)
if _funder_uri
else rdflib.BNode()
)
yield (_award_ref, OSF.funder, _funder_ref)
yield (_funder_ref, FOAF.name, _funding.get('funder_name'))
yield (_funder_ref, DCTERMS.identifier, _funder_uri)
yield (_funder_ref, OSF.funderIdentifierType, _funding.get('funder_identifier_type'))


@gather.er(OSF.HostingInstitution)
Expand Down Expand Up @@ -743,6 +757,19 @@ def gather_ia_url(focus):
yield (OSF.archivedAt, focus.dbmodel.ia_url)


@gather.er(
DCTERMS.conformsTo,
focustype_iris=[OSF.Registration]
)
def gather_registration_type(focus):
_reg_schema = getattr(focus.dbmodel, 'registration_schema')
if _reg_schema:
_schema_url = rdflib.URIRef(_reg_schema.absolute_api_v2_url)
yield (DCTERMS.conformsTo, _schema_url)
yield (_schema_url, DCTERMS.title, _reg_schema.name)
yield (_schema_url, DCTERMS.description, _reg_schema.description)


@gather.er(DCTERMS.publisher)
def gather_publisher(focus):
provider = getattr(focus.dbmodel, 'provider', None)
Expand Down
47 changes: 26 additions & 21 deletions osf/metadata/serializers/datacite/datacite_tree_walker.py
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Original file line number Diff line number Diff line change
Expand Up @@ -258,7 +258,7 @@ def _visit_rights(self, parent_el):
self.visit(rights_list_el, 'rights', text=name, attrib=attrib)

def _visit_affiliations(self, parent_el, focus_iri):
for institution_iri in self.basket[focus_iri:OSF.affiliatedInstitution]:
for institution_iri in self.basket[focus_iri:OSF.affiliation]:
try:
name = next(self.basket[institution_iri:FOAF.name])
except StopIteration:
Expand All @@ -284,26 +284,31 @@ def _visit_dates(self, parent_el):

def _visit_funding_references(self, parent_el):
fundrefs_el = self.visit(parent_el, 'fundingReferences', is_list=True)
for funding_ref in self.basket[OSF.funder]:
fundref_el = self.visit(fundrefs_el, 'fundingReference')
self.visit(fundref_el, 'funderName', text=next(self.basket[funding_ref:FOAF.name], ''))
self.visit(
fundref_el,
'funderIdentifier',
text=next(self.basket[funding_ref:DCTERMS.identifier], ''),
attrib={
'funderIdentifierType': next(self.basket[funding_ref:OSF.funderIdentifierType], ''),
},
)
self.visit(
fundref_el,
'awardNumber',
text=next(self.basket[funding_ref:OSF.awardNumber], ''),
attrib={
'awardURI': next(self.basket[funding_ref:OSF.awardUri], ''),
},
)
self.visit(fundref_el, 'awardTitle', text=next(self.basket[funding_ref:OSF.awardTitle], ''))
for _funding_award in self.basket[OSF.hasFunding]:
for _funder in self.basket[_funding_award:OSF.funder]:
fundref_el = self.visit(fundrefs_el, 'fundingReference')
self.visit(fundref_el, 'funderName', text=next(self.basket[_funder:FOAF.name], ''))
self.visit(
fundref_el,
'funderIdentifier',
text=next(self.basket[_funder:DCTERMS.identifier], ''),
attrib={
'funderIdentifierType': next(self.basket[_funder:OSF.funderIdentifierType], ''),
},
)
self.visit(
fundref_el,
'awardNumber',
text=next(self.basket[_funding_award:OSF.awardNumber], ''),
attrib={
'awardURI': (
str(_funding_award)
if isinstance(_funding_award, rdflib.URIRef)
else ''
)
},
)
self.visit(fundref_el, 'awardTitle', text=next(self.basket[_funding_award:DCTERMS.title], ''))

def _visit_publication_year(self, parent_el, focus_iri):
year_copyrighted = next(self.basket[focus_iri:DCTERMS.dateCopyrighted], None)
Expand Down
18 changes: 11 additions & 7 deletions osf_tests/metadata/expected_metadata_files/project_full.turtle
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Original file line number Diff line number Diff line change
Expand Up @@ -21,13 +21,7 @@
dcterms:type "Dataset" ;
owl:sameAs <https://doi.org/10.70102/FK2osf.io/w2ibb> ;
osf:contains <http://localhost:5000/w3ibb> ;
osf:funder [ a osf:FundingReference ;
dcterms:identifier "https://doi.org/10.$$$$" ;
foaf:name "Mx. Moneypockets" ;
osf:awardNumber "10000000" ;
osf:awardTitle "because reasons" ;
osf:awardUri "https://moneypockets.example/millions" ;
osf:funderIdentifierType "Crossref Funder ID" ] ;
osf:hasFunding <https://moneypockets.example/millions> ;
osf:supplements <http://localhost:5000/w4ibb> .

<http://localhost:5000/w4ibb> a osf:Preprint ;
Expand All @@ -54,6 +48,12 @@
osf:filePath "/my-file.blarg" ;
osf:isContainedBy <http://localhost:5000/w2ibb> .

<https://moneypockets.example/millions> a osf:FundingAward ;
dcterms:identifier "https://moneypockets.example/millions" ;
dcterms:title "because reasons" ;
osf:awardNumber "10000000" ;
osf:funder <https://doi.org/10.$$$$> .

<https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode> dcterms:identifier "https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode" ;
foaf:name "CC-By Attribution-NonCommercial-NoDerivatives 4.0 International" .

Expand All @@ -72,6 +72,10 @@
dcterms:type foaf:Person ;
foaf:name "Person McNamington" .

<https://doi.org/10.$$$$> dcterms:identifier "https://doi.org/10.$$$$" ;
foaf:name "Mx. Moneypockets" ;
osf:funderIdentifierType "Crossref Funder ID" .

<http://localhost:5000> a osf:Agent ;
dcterms:identifier "http://localhost:5000" ;
dcterms:type foaf:Organization ;
Expand Down
5 changes: 4 additions & 1 deletion osf_tests/metadata/expected_metadata_files/registration_basic.turtle
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
@prefix owl: <http://www.w3.org/2002/07/owl#> .

<http://localhost:5000/w5ibb> a osf:Registration ;
dcterms:conformsTo <http://localhost:8000/v2/schemas/registrations/63d3f6c7dcb7b30226be52a9/> ;
dcterms:created "2123-05-04" ;
dcterms:creator <http://localhost:5000/w1ibb> ;
dcterms:dateCopyrighted "2252" ;
Expand Down Expand Up @@ -39,4 +40,6 @@
<http://localhost:5000> a osf:Agent ;
dcterms:identifier "http://localhost:5000" ;
dcterms:type foaf:Organization ;
foaf:name "OSF" .
foaf:name "OSF" .

<http://localhost:8000/v2/schemas/registrations/63d3f6c7dcb7b30226be52a9/> dcterms:title "Open-Ended Registration" .
5 changes: 4 additions & 1 deletion osf_tests/metadata/expected_metadata_files/registration_full.turtle
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
@prefix owl: <http://www.w3.org/2002/07/owl#> .

<http://localhost:5000/w5ibb> a osf:Registration ;
dcterms:conformsTo <http://localhost:8000/v2/schemas/registrations/63d3f6c7dcb7b30226be52a9/> ;
dcterms:created "2123-05-04" ;
dcterms:creator <http://localhost:5000/w1ibb> ;
dcterms:dateCopyrighted "2250-2254" ;
Expand Down Expand Up @@ -43,4 +44,6 @@
<http://localhost:5000> a osf:Agent ;
dcterms:identifier "http://localhost:5000" ;
dcterms:type foaf:Organization ;
foaf:name "OSF" .
foaf:name "OSF" .

<http://localhost:8000/v2/schemas/registrations/63d3f6c7dcb7b30226be52a9/> dcterms:title "Open-Ended Registration" .
64 changes: 39 additions & 25 deletions osf_tests/metadata/test_osf_gathering.py
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Original file line number Diff line number Diff line change
Expand Up @@ -456,15 +456,15 @@ def test_gather_affiliated_institutions(self):
self.user__admin.add_or_update_affiliated_institution(institution)
self.project.add_affiliated_institution(institution, self.user__admin)
_assert_triples(osf_gathering.gather_affiliated_institutions(self.projectfocus), {
(self.projectfocus.iri, OSF.affiliatedInstitution, institution_iri),
(self.projectfocus.iri, OSF.affiliation, institution_iri),
(institution_iri, RDF.type, OSF.Agent),
(institution_iri, DCTERMS.type, FOAF.Organization),
(institution_iri, FOAF.name, Literal(institution.name)),
(institution_iri, DCTERMS.identifier, Literal(institution.identifier_domain)),
})
# focus: user
_assert_triples(osf_gathering.gather_affiliated_institutions(self.userfocus__admin), {
(self.userfocus__admin.iri, OSF.affiliatedInstitution, institution_iri),
(self.userfocus__admin.iri, OSF.affiliation, institution_iri),
(institution_iri, RDF.type, OSF.Agent),
(institution_iri, DCTERMS.type, FOAF.Organization),
(institution_iri, FOAF.name, Literal(institution.name)),
Expand All @@ -489,42 +489,56 @@ def test_gather_funding(self):
'award_number': '27',
},
]
bnode1 = rdflib.BNode()
bnode2 = rdflib.BNode()
_bnode1 = rdflib.BNode()
_bnode2 = rdflib.BNode()
_award_uri = URIRef('https://nih.example/award')
_funder_uri = URIRef('https://doi.org/10.fake/NIH')
_assert_triples(osf_gathering.gather_funding(self.projectfocus), {
(self.projectfocus.iri, OSF.funder, bnode1),
(bnode1, RDF.type, OSF.FundingReference),
(bnode1, FOAF.name, Literal('hooray')),
(self.projectfocus.iri, OSF.funder, bnode2),
(bnode2, RDF.type, OSF.FundingReference),
(bnode2, FOAF.name, Literal('NIH')),
(bnode2, DCTERMS.identifier, Literal('https://doi.org/10.fake/NIH')),
(bnode2, OSF.funderIdentifierType, Literal('Crossref Funder ID')),
(bnode2, OSF.awardNumber, Literal('27')),
(bnode2, OSF.awardUri, Literal('https://nih.example/award')),
(bnode2, OSF.awardTitle, Literal('big fun')),
(self.projectfocus.iri, OSF.hasFunding, _bnode1),
(_bnode1, RDF.type, OSF.FundingAward),
(_bnode1, OSF.funder, _bnode2),
(_bnode2, FOAF.name, Literal('hooray')),
(self.projectfocus.iri, OSF.hasFunding, _award_uri),
(_award_uri, RDF.type, OSF.FundingAward),
(_award_uri, DCTERMS.identifier, Literal(_award_uri)),
(_award_uri, DCTERMS.title, Literal('big fun')),
(_award_uri, OSF.awardNumber, Literal('27')),
(_award_uri, OSF.funder, _funder_uri),
(_funder_uri, FOAF.name, Literal('NIH')),
(_funder_uri, DCTERMS.identifier, Literal(_funder_uri)),
(_funder_uri, OSF.funderIdentifierType, Literal('Crossref Funder ID')),
})
# focus: registration
_assert_triples(osf_gathering.gather_funding(self.registrationfocus), set())
self.registrationfocus.guid_metadata_record.funding_info = [
{'funder_name': 'blooray'},
{
'funder_name': 'blooray',
'funder_identifier': 'https://doi.org/11.bloo',
},
]
bnode1 = rdflib.BNode()
_funder_uri = rdflib.URIRef('https://doi.org/11.bloo')
_assert_triples(osf_gathering.gather_funding(self.registrationfocus), {
(self.registrationfocus.iri, OSF.funder, bnode1),
(bnode1, RDF.type, OSF.FundingReference),
(bnode1, FOAF.name, Literal('blooray')),
(self.registrationfocus.iri, OSF.hasFunding, _bnode1),
(_bnode1, RDF.type, OSF.FundingAward),
(_bnode1, OSF.funder, _funder_uri),
(_funder_uri, DCTERMS.identifier, Literal(_funder_uri)),
(_funder_uri, FOAF.name, Literal('blooray')),
})
# focus: file
_assert_triples(osf_gathering.gather_funding(self.filefocus), set())
self.filefocus.guid_metadata_record.funding_info = [
{'funder_name': 'exray'},
{
'funder_name': 'exray',
'funder_identifier': 'https://doi.org/11.ex',
},
]
bnode1 = rdflib.BNode()
_funder_uri = rdflib.URIRef('https://doi.org/11.ex')
_assert_triples(osf_gathering.gather_funding(self.filefocus), {
(self.filefocus.iri, OSF.funder, bnode1),
(bnode1, RDF.type, OSF.FundingReference),
(bnode1, FOAF.name, Literal('exray')),
(self.filefocus.iri, OSF.hasFunding, _bnode1),
(_bnode1, RDF.type, OSF.FundingAward),
(_bnode1, OSF.funder, _funder_uri),
(_funder_uri, DCTERMS.identifier, Literal(_funder_uri)),
(_funder_uri, FOAF.name, Literal('exray')),
})

def test_gather_user_basics(self):
Expand Down

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