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apdavison wants to merge 5 commits into from
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Save schema version in JSON-LD files #75

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b362df7
Include schema version in JSON-LD files
apdavison Nov 13, 2025
1bfb67d
more consistent formatting
apdavison Nov 17, 2025
3383b94
Change prefix for https://schema.org/ from "s" to "schema"
apdavison Nov 17, 2025
cd084d4
Merge branch 'pipeline' into save-schema-version
apdavison Nov 17, 2025
7838ec1
we are merging into a branch that uses openminds.v4 within test_regre…
apdavison Nov 17, 2025
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14 changes: 10 additions & 4 deletions pipeline/src/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -68,11 +68,14 @@ def to_jsonld(self, include_empty_properties=True, embed_linked_nodes=True, with
"""

data = {"@type": self.type_}
if isinstance(self, LinkedMetadata):
data["s:schemaVersion"] = self.schema_version
if with_context:
if self.type_.startswith("https://openminds.ebrains.eu/"):
data["@context"] = {"@vocab": "https://openminds.ebrains.eu/vocab/"}
else:
data["@context"] = {"@vocab": "https://openminds.om-i.org/props/"}
data["@context"]["s"] = "https://schema.org/"
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@Raphael-Gazzotti Raphael-Gazzotti Nov 17, 2025

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Minor point, but the prefix 'schema' is the most commonly used for schema.org.

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@apdavison apdavison Nov 17, 2025

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ok, I'll make that change

if hasattr(self, "id") and self.id:
data["@id"] = self.id
for property in self.__class__.properties:
Expand Down Expand Up @@ -122,6 +125,10 @@ def from_jsonld(cls, data, ignore_unexpected_keys=False):
"""
data_copy = data.copy()
context = data_copy.pop("@context", None)
schema_version = data_copy.pop("s:schemaVersion", None)
# todo: also handle an expanded key, i.e., "https://schema.org/schemaVersion"
# todo: check major part of schema_version against self.schema_version
# i.e. v4.1 and v4.0 would be ok, v5.0 and v4.0 would not
type_ = data_copy.pop("@type")
if isinstance(type_, list) and len(type_) == 1:
type_ = type_[0]
Expand All @@ -138,7 +145,7 @@ def from_jsonld(cls, data, ignore_unexpected_keys=False):
else:
# todo: implement or import a function that does a full JSON-LD expansion
# not just this special case
expanded_path = f"{cls.context['@vocab']}{property.path}"
expanded_path = f"{cls.context['@vocab']}{property.path}"
if expanded_path in data_copy:
value = data_copy.pop(expanded_path)
found = True
Expand Down Expand Up @@ -268,9 +275,8 @@ def __init__(self, identifier, allowed_types=None):
self.allowed_types = allowed_types

def to_jsonld(self):
return {
"@id": self.identifier
}
return {"@id": self.identifier}


class IRI:
"""
Expand Down
14 changes: 10 additions & 4 deletions pipeline/src/collection.py
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Expand Up @@ -93,7 +93,10 @@ def save(self, path, individual_files=False, include_empty_properties=False):
if node.type_.startswith("https://openminds.ebrains.eu/"):
data_context = {"@vocab": "https://openminds.ebrains.eu/vocab/"}
else:
data_context = {"@vocab": "https://openminds.om-i.org/props/"}
data_context = {
"@vocab": "https://openminds.om-i.org/props/"
}
data_context["s"] = "https://schema.org/"

for linked_node in node.links:
self._add_node(linked_node)
Expand Down Expand Up @@ -169,12 +172,15 @@ def load(self, *paths):
data = json.load(fp)
if "@graph" in data:
if data["@context"]["@vocab"].startswith("https://openminds.ebrains.eu/"):
version = "v3"
default_version = "v3"
else:
version = "latest"
default_version = "v4"
for item in data["@graph"]:
if "@type" in item:
cls = lookup_type(item["@type"], version=version)
version = default_version
if "s:schemaVersion" in item: # todo: expand this using the context
version = item["s:schemaVersion"]
cls = lookup_type(item["@type"], version=version.split(".")[0])
node = cls.from_jsonld(item)
else:
# allow links to metadata instances outside this collection
Expand Down
8 changes: 7 additions & 1 deletion pipeline/tests/test_collections.py
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Original file line number Diff line number Diff line change
Expand Up @@ -96,17 +96,22 @@ def test_collection_sort_by_id():
os.remove("test_collection_sort_by_id.jsonld")

expected_saved_data = {
"@context": {"@vocab": "https://openminds.om-i.org/props/"},
"@context": {
"@vocab": "https://openminds.om-i.org/props/",
"s": "https://schema.org/",
},
"@graph": [
{
"@id": "_:001",
"@type": "https://openminds.om-i.org/types/Organization",
"fullName": "University of That Place",
"s:schemaVersion": "latest"
},
{
"@id": "_:002",
"@type": "https://openminds.om-i.org/types/Organization",
"fullName": "University of This Place",
"s:schemaVersion": "latest"
},
{
"@id": "_:004",
Expand All @@ -117,6 +122,7 @@ def test_collection_sort_by_id():
],
"familyName": "Professor",
"givenName": "A",
"s:schemaVersion": "latest"
},
],
}
Expand Down
2 changes: 2 additions & 0 deletions pipeline/tests/test_instantiation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -104,8 +104,10 @@ def test_link():
expected = {
"@context": {
"@vocab": "https://openminds.om-i.org/props/",
"s": "https://schema.org/"
},
"@type": "https://openminds.om-i.org/types/DatasetVersion",
"s:schemaVersion": "v4.0",
"studyTarget": [
{
"@id": "https://openminds.om-i.org/instances/species/musMusculus",
Expand Down
31 changes: 26 additions & 5 deletions pipeline/tests/test_regressions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
import json
import os
from openminds import Collection, IRI
from openminds.latest import core as omcore
import openminds.v4.core as omcore
from utils import build_fake_node


Expand Down Expand Up @@ -38,18 +38,24 @@ def test_issue_0003():
)
# on export, a single item should be wrapped in a list, where the property expects an array
expected = {
"@context": {"@vocab": "https://openminds.om-i.org/props/"},
"@context": {
"@vocab": "https://openminds.om-i.org/props/",
"s": "https://schema.org/"
},
"@type": "https://openminds.om-i.org/types/FileArchive",
"IRI": "http://example.com/archive.zip",
"format": {
"@type": "https://openminds.om-i.org/types/ContentType",
"name": "application/zip",
"s:schemaVersion": "v4.0",
},
"s:schemaVersion": "v4.0",
"sourceData": [
{
"@type": "https://openminds.om-i.org/types/File",
"IRI": "http://example.com/some_file.txt",
"name": "some_file.txt",
"s:schemaVersion": "v4.0",
}
],
}
Expand Down Expand Up @@ -90,11 +96,15 @@ def test_issue0007():

actual = person.to_jsonld(include_empty_properties=False, embed_linked_nodes=False, with_context=True)
expected = {
"@context": {"@vocab": "https://openminds.om-i.org/props/"},
"@context": {
"@vocab": "https://openminds.om-i.org/props/",
"s": "https://schema.org/"
},
"@id": "_:001",
"@type": "https://openminds.om-i.org/types/Person",
"familyName": "Professor",
"givenName": "A",
"s:schemaVersion": "v4.0",
"affiliation": [
{
"@type": "https://openminds.om-i.org/types/Affiliation",
Expand All @@ -105,6 +115,7 @@ def test_issue0007():
"memberOf": {"@id": "_:003"},
},
],

}
assert actual == expected

Expand All @@ -116,7 +127,10 @@ def test_issue0007():
saved_data = json.load(fp)
os.remove("issue0007.jsonld")
expected_saved_data = {
"@context": {"@vocab": "https://openminds.om-i.org/props/"},
"@context": {
"@vocab": "https://openminds.om-i.org/props/",
"s": "https://schema.org/"
},
"@graph": [
{
"@id": "_:001",
Expand All @@ -133,16 +147,19 @@ def test_issue0007():
],
"familyName": "Professor",
"givenName": "A",
"s:schemaVersion": "v4.0",
},
{
"@id": "_:002",
"@type": "https://openminds.om-i.org/types/Organization",
"fullName": "University of This Place",
"s:schemaVersion": "v4.0",
},
{
"@id": "_:003",
"@type": "https://openminds.om-i.org/types/Organization",
"fullName": "University of That Place",
"s:schemaVersion": "v4.0",
},
],
}
Expand All @@ -163,7 +180,10 @@ def test_issue0008():
)
actual = person.to_jsonld(include_empty_properties=False, embed_linked_nodes=False, with_context=True)
expected = {
"@context": {"@vocab": "https://openminds.om-i.org/props/"},
"@context": {
"@vocab": "https://openminds.om-i.org/props/",
"s": "https://schema.org/"
},
"@id": "_:002",
"@type": "https://openminds.om-i.org/types/Person",
"affiliation": [
Expand All @@ -175,6 +195,7 @@ def test_issue0008():
],
"familyName": "Professor",
"givenName": "A",
"s:schemaVersion": "v4.0",
}
assert actual == expected

Expand Down