Skip to content

Use latest pre-release of the SSSOM schema. #625

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
gouttegd merged 2 commits into from
Oct 8, 2025
Merged

Use latest pre-release of the SSSOM schema. #625

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
eb80efc
Use latest pre-release of the SSSOM schema.
gouttegd Oct 8, 2025
ac9ba4a
Use SSSOMSchemaView() when needing to get the list of mapping slots.
gouttegd Oct 8, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
92 changes: 61 additions & 31 deletions poetry.lock
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 1 addition & 1 deletion pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ dependencies = [
"linkml-runtime>=1.7.5",
"linkml>1.7.10",
"pandas>1.0.3",
"sssom-schema==1.0.0",
"sssom-schema==1.1.0a2",
"sparqlwrapper>=2.0.0",
"validators>=0.20.0",
"deprecation>=2.1.0",
Expand Down
6 changes: 1 addition & 5 deletions src/sssom/util.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,6 @@
import numpy as np
import pandas as pd
import validators
import yaml
from curies import Converter, ReferenceTuple
from jsonschema import ValidationError
from linkml_runtime.linkml_model.types import Uriorcurie
Expand Down Expand Up @@ -61,7 +60,6 @@
PREDICATE_MODIFIER,
PREDICATE_MODIFIER_NOT,
RDFS_SUBCLASS_OF,
SCHEMA_YAML,
SEMAPV,
SKOS_BROAD_MATCH,
SKOS_CLOSE_MATCH,
Expand Down Expand Up @@ -1209,9 +1207,7 @@ def inject_metadata_into_df(msdf: MappingSetDataFrame) -> MappingSetDataFrame:
# TODO add this into the "standardize" function introduced in
# https://github.com/mapping-commons/sssom-py/pull/438
# TODO Check if 'k' is a valid 'slot' for 'mapping' [sssom.yaml]
with SCHEMA_YAML.open() as file:
schema = yaml.safe_load(file)
slots = schema["classes"]["mapping"]["slots"]
slots = SSSOMSchemaView().mapping_slots
for k, v in msdf.metadata.items():
if k not in msdf.df.columns and k in slots:
if k == MAPPING_SET_ID:
Expand Down
Loading