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Fix serialised ontology iri #341

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merged 4 commits into from
Jan 5, 2022
+8 −11
Merged

Fix serialised ontology iri #341

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6fc5842
Corrected parsing cardinality restrictions
jesper-friis Jan 2, 2022
1221496
Fix serialised ontology IRI
jesper-friis Jan 2, 2022
95c9dbe
Merge branch 'master' into fix-serialised-ontology-iri
CasperWA Jan 3, 2022
9e06713
Merge branch 'master' into fix-serialised-ontology-iri
jesper-friis Jan 5, 2022
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19 changes: 8 additions & 11 deletions ontopy/excelparser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
import pyparsing
import pandas as pd
import ontopy
from ontopy import World, get_ontology
from ontopy import World
from ontopy.utils import NoSuchLabelError
from ontopy.manchester import evaluate
import owlready2 # pylint: disable=C0411
Expand Down Expand Up @@ -64,10 +64,7 @@ def create_ontology_from_pandas( # pylint: disable=too-many-locals,too-many-bra
data = data.astype({"prefLabel": "str"})

# Make new ontology
world = World()
onto = world.get_ontology(base_iri)

onto, catalog = get_metadata_from_dataframe(metadata, onto)
onto, catalog = get_metadata_from_dataframe(metadata, base_iri)

# base_iri from metadata if it exists and base_iri_from_metadata
if not base_iri_from_metadata:
Expand Down Expand Up @@ -155,17 +152,14 @@ def create_ontology_from_pandas( # pylint: disable=too-many-locals,too-many-bra

def get_metadata_from_dataframe( # pylint: disable=too-many-locals,too-many-branches,too-many-statements
metadata: pd.DataFrame,
onto: owlready2.Ontology = None,
base_iri: str,
base_iri_from_metadata: bool = True,
catalog: dict = None,
) -> Tuple[ontopy.ontology.Ontology, dict]:
"""
Populate ontology with metada from pd.DataFrame
Create ontology with metadata from pd.DataFrame
"""

if onto is None:
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onto = get_ontology()

# base_iri from metadata if it exists and base_iri_from_metadata
if base_iri_from_metadata:
try:
Expand All @@ -175,10 +169,13 @@ def get_metadata_from_dataframe( # pylint: disable=too-many-locals,too-many-bra
"More than one Ontology IRI given. The first was chosen."
)
base_iri = base_iris[0] + "#"
onto.base_iri = base_iri
except (TypeError, ValueError, AttributeError):
pass

# Make new ontology
world = World()
onto = world.get_ontology(base_iri)

# Get imported ontologies from metadata
try:
imported_ontology_paths = _parse_literal(
Expand Down