Skip to content

Commit

Permalink
bodc: updated file uri & subject label
Browse files Browse the repository at this point in the history
  • Loading branch information
@0einstein0
0einstein0 committed Jan 31, 2025
1 parent 340ce04 commit 4a674ac
Show file tree
Hide file tree
Showing 3 changed files with 42 additions and 40 deletions.
2 changes: 1 addition & 1 deletion invenio_vocabularies/config.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -196,7 +196,7 @@ def is_edmo(val):
)
"""Subject GEMET file download link."""

VOCABULARIES_SUBJECTS_BODC_PUV_FILE_URL = "http://vocab.nerc.ac.uk/collection/P01/current/?_profile=nvs&_mediatype=application/rdf+xml"
VOCABULARIES_SUBJECTS_BODC_PUV_FILE_URL = "http://vocab.nerc.ac.uk/collection/P02/current/?_profile=nvs&_mediatype=application/rdf+xml"
"""Subject BODC-PUV file download link."""

VOCABULARIES_AFFILIATIONS_EDMO_COUNTRY_MAPPING = {
Expand Down
10 changes: 8 additions & 2 deletions invenio_vocabularies/contrib/subjects/bodc/datastreams.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -78,8 +78,14 @@ def _transform_entry(self, subject, rdf_graph):
else:
raise TransformerError(f"No id found for: {subject}")

alt_labels = [obj for obj in subject_data.get(str(self.skos_core.altLabel), [])]
subject_text = str(alt_labels[0]) if alt_labels else ""
pref_labels = [
obj for obj in subject_data.get(str(self.skos_core.prefLabel), [])
]

if not pref_labels:
raise TransformerError(f"No preferred label found for subject: {subject}")

subject_text = str(pref_labels[0])
definition = str(subject_data.get(str(self.skos_core.definition), [None])[0])

return {
Expand Down
70 changes: 33 additions & 37 deletions tests/contrib/subjects/bodc/test_subjects_bodc_datastream.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,45 +20,39 @@

VALID_XML_DATA = bytes(
"""<?xml version="1.0" encoding="UTF-8"?><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:dc="http://purl.org/dc/terms/" xmlns:dce="http://purl.org/dc/elements/1.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:grg="http://www.isotc211.org/schemas/grg/" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:void="http://rdfs.org/ns/void#" xmlns:pav="http://purl.org/pav/" xmlns:prov="https://www.w3.org/ns/prov#" xmlns:reg="http://purl.org/linked-data/registry#" xmlns:cpm="http://purl.org/voc/cpm#" xmlns:qudt="https://qudt.org/2.1/schema/qudt#" xmlns:semapv="http://w3id.org/semapv/vocab/" xmlns:iop="https://w3id.org/iadopt/ont#" xmlns:sssom="https://w3id.org/sssom/schema/" xmlns:puv="https://w3id.org/env/puv#">
<skos:Collection rdf:about="http://vocab.nerc.ac.uk/collection/P01/current/">
<skos:prefLabel>BODC Parameter Usage Vocabulary</skos:prefLabel>
<dc:title>BODC Parameter Usage Vocabulary</dc:title>
<skos:altLabel>BODC PUV</skos:altLabel>
<dc:alternative>BODC PUV</dc:alternative>
<dc:description>Terms built using the BODC parameter semantic model designed to describe individual measured phenomena. May be used to mark up sets of data such as a NetCDF array or spreadsheet column. Units must be specified when using a P01 code. The P06 unit that is linked to individual P01 in the NVS is the one used in BODC's systems but external users can use any appropriate units.</dc:description>
<dc:license rdf:resource="https://creativecommons.org/licenses/by/4.0/"/>
<skos:member>
<skos:Concept xml:base="http://vocab.nerc.ac.uk/collection/P01/current/SAGEMSFM/" rdf:about="http://vocab.nerc.ac.uk/collection/P01/current/SAGEMSFM/">
<dc:identifier>SDN:P01::SAGEMSFM</dc:identifier>
<dce:identifier>SDN:P01::SAGEMSFM</dce:identifier>
<dc:date>2008-10-16 16:27:06.0</dc:date>
<skos:notation>SDN:P01::SAGEMSFM</skos:notation>
<skos:prefLabel xml:lang="en">14C age of Foraminiferida (ITIS: 44030: WoRMS 22528) [Subcomponent: tests] in sediment by picking and accelerator mass spectrometry</skos:prefLabel>
<skos:altLabel>AMSSedAge</skos:altLabel>
<skos:definition xml:lang="en">Accelerated mass spectrometry on picked tests</skos:definition>
<owl:versionInfo>1</owl:versionInfo>
<pav:hasCurrentVersion rdf:resource="http://vocab.nerc.ac.uk/collection/P01/current/SAGEMSFM/1/"/>
<pav:version>1</pav:version>
<pav:authoredOn>2008-10-16 16:27:06.0</pav:authoredOn>
<skos:note xml:lang="en">accepted</skos:note>
<owl:deprecated>false</owl:deprecated>
<iop:hasMatrix rdf:resource="http://vocab.nerc.ac.uk/collection/S21/current/S21S022/"/>
<skos:related rdf:resource="http://vocab.nerc.ac.uk/collection/P06/current/UYBP/"/>
<skos:broader rdf:resource="http://vocab.nerc.ac.uk/collection/S25/current/BE002325/"/>
<skos:broader rdf:resource="http://vocab.nerc.ac.uk/collection/S26/current/MAT00136/"/>
<void:inDataset rdf:resource="http://vocab.nerc.ac.uk/.well-known/void"/>
</skos:Concept>
</skos:member>
</skos:Collection>
<rdf:Description rdf:about="http://vocab.nerc.ac.uk/collection/P02/current/QDMD/">
<pav:authoredOn>2008-08-15 10:07:03.0</pav:authoredOn>
<pav:hasCurrentVersion rdf:resource="http://vocab.nerc.ac.uk/collection/P02/current/QDMD/1/"/>
<dce:identifier>SDN:P02::QDMD</dce:identifier>
<pav:version>1</pav:version>
<skos:broader rdf:resource="http://vocab.nerc.ac.uk/collection/C47/current/IN6_1_2/"/>
<skos:broader rdf:resource="http://vocab.nerc.ac.uk/collection/P22/current/19/"/>
<rdf:type rdf:resource="http://www.w3.org/2004/02/skos/core#Concept"/>
<skos:definition xml:lang="en">Parameters quantifying the amount of liquids (e.g. ship's ballast) or solids (e.g. dredge spoil) deposited into the water column as a result of man's activities</skos:definition>
<void:inDataset rdf:resource="http://vocab.nerc.ac.uk/.well-known/void"/>
<owl:deprecated>false</owl:deprecated>
<skos:note xml:lang="en">accepted</skos:note>
<dc:identifier>SDN:P02::QDMD</dc:identifier>
<skos:prefLabel xml:lang="en">Quantity of material dumped</skos:prefLabel>
<owl:versionInfo>1</owl:versionInfo>
<dc:date>2008-08-15 10:07:03.0</dc:date>
<skos:altLabel>Amount_dumped</skos:altLabel>
<skos:inScheme rdf:resource="http://vocab.nerc.ac.uk/scheme/EDMED_DCAT_THEMES/current/"/>
<skos:notation>SDN:P02::QDMD</skos:notation>
<skos:broader rdf:resource="http://vocab.nerc.ac.uk/collection/D01/current/D0100001/"/>
<skos:broader rdf:resource="http://vocab.nerc.ac.uk/collection/L19/current/005/"/>
<skos:broader rdf:resource="http://vocab.nerc.ac.uk/collection/P03/current/H001/"/>
<skos:broader rdf:resource="http://vocab.nerc.ac.uk/collection/P05/current/007/"/>
</rdf:Description>
</rdf:RDF>""",
encoding="utf-8",
)

INVALID_XML_DATA = bytes(
"""<?xml version="1.0" encoding="UTF-8"?><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:skos="http://www.w3.org/2004/02/skos/core#">
<skos:Collection rdf:about="http://vocab.nerc.ac.uk/collection/P01/current/">
<skos:Collection rdf:about="http://vocab.nerc.ac.uk/collection/P02/current/">
<skos:member>
<skos:Concept rdf:about="http://vocab.nerc.ac.uk/collection/P01/current/SAGEMSFM/">
<skos:Concept rdf:about="http://vocab.nerc.ac.uk/collection/P02/current/QDMD/">
<skos:prefLabel>Invalid Data</skos:prefLabel>
<!-- No skos:notation present -->
</skos:Concept>
Expand All @@ -73,17 +67,19 @@
def expected_from_rdf():
return [
{
"id": "SDN:P01::SAGEMSFM",
"id": "SDN:P02::QDMD",
"scheme": "BODC-PUV",
"subject": "AMSSedAge",
"subject": "Quantity of material dumped",
"title": {
"en": "14c age of foraminiferida (itis: 44030: worms 22528) [subcomponent: tests] in sediment by picking and accelerator mass spectrometry",
"en": "Quantity of material dumped",
},
"props": {
"definition": "Parameters quantifying the amount of liquids (e.g. ship's ballast) or solids (e.g. dredge spoil) deposited into the water column as a result of man's activities"
},
"props": {"definition": "Accelerated mass spectrometry on picked tests"},
"identifiers": [
{
"scheme": "url",
"identifier": "http://vocab.nerc.ac.uk/collection/P01/current/SAGEMSFM/",
"identifier": "http://vocab.nerc.ac.uk/collection/P02/current/QDMD/",
}
],
}
Expand Down

0 comments on commit 4a674ac

Please sign in to comment.