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Fix outdated prefix map #297

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merged 6 commits into from
Aug 4, 2022
Merged

Fix outdated prefix map #297

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a9395dc
Fix outdated prefix map
matentzn Aug 3, 2022
c899171
first stab at getting context.
hrshdhgd Aug 3, 2022
da12580
reformatted
hrshdhgd Aug 3, 2022
967c2b9
fixed test
hrshdhgd Aug 4, 2022
0faa581
gettign schema path from constants.py
hrshdhgd Aug 4, 2022
0578959
Merge branch 'master' into fix-prefix-map-outdated
hrshdhgd Aug 4, 2022
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6 changes: 5 additions & 1 deletion sssom/context.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,11 @@
import uuid
from typing import Optional

from linkml.generators.jsonldcontextgen import ContextGenerator

from sssom.constants import SCHEMA_YAML

from .external_context import sssom_external_context
from .internal_context import sssom_context
from .typehints import Metadata, MetadataType, PrefixMap

# HERE = pathlib.Path(__file__).parent.resolve()
Expand All @@ -26,6 +29,7 @@ def get_jsonld_context():

:return: JSON-LD context
"""
sssom_context = ContextGenerator(SCHEMA_YAML).serialize()
return json.loads(sssom_context, strict=False)


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165 changes: 0 additions & 165 deletions sssom/internal_context.py
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2 changes: 1 addition & 1 deletion tests/test_parsers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -98,7 +98,7 @@ def test_parse_obographs(self):
write_table(msdf, file)
self.assertEqual(
len(msdf.df),
9878,
9876,
f"{self.obographs_file} has the wrong number of mappings.",
)

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