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Fixes issue with punning that made the ontology non-DL #391

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merged 2 commits into from
Jul 11, 2023
Merged

Fixes issue with punning that made the ontology non-DL #391

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4e5b3c1
Added OWL integrity testing for internal modules
jmillanacosta Jul 11, 2023
7d17e08
Removes citesAsAuthority
jmillanacosta Jul 11, 2023
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2 changes: 1 addition & 1 deletion config/aopo.iris
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Original file line number Diff line number Diff line change
Expand Up @@ -3,4 +3,4 @@
+(http://aopkb.org/aop_ontology#AopEntity):http://aopkb.org/aop_ontology#AdverseOutcome AO
+(http://aopkb.org/aop_ontology#AopEntity):http://aopkb.org/aop_ontology#KeyEvent AO
+(http://aopkb.org/aop_ontology#AopEntity):http://aopkb.org/aop_ontology#MolecularInitiatingEvent MIE

-:http://purl.org/spar/cito/citesAsAuthority
1 change: 1 addition & 0 deletions config/clo.iris
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Expand Up @@ -4,3 +4,4 @@
+(http://purl.obolibrary.org/obo/CL_0000003):http://purl.obolibrary.org/obo/CL_1001603 lung macrophage
+(http://purl.obolibrary.org/obo/CL_0000000):http://purl.obolibrary.org/obo/CL_0001034 cell in vitro
+(http://purl.obolibrary.org/obo/CL_0001034):http://purl.obolibrary.org/obo/CL_0000010 cultured cell (including cell lines)
-:http://purl.org/spar/cito/citesAsAuthority
1 change: 1 addition & 0 deletions config/pato.iris
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Expand Up @@ -19,3 +19,4 @@
+(http://purl.obolibrary.org/obo/PATO_0000068):http://purl.obolibrary.org/obo/PATO_0002632 secondary
+(http://purl.obolibrary.org/obo/BFO_0000019):http://purl.obolibrary.org/obo/PATO_0000150 texture
+(http://purl.obolibrary.org/obo/PATO_0000150):http://purl.obolibrary.org/obo/PATO_0002012 coating
-:http://purl.org/spar/cito/citesAsAuthority
1 change: 1 addition & 0 deletions config/uberon.iris
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Expand Up @@ -3,3 +3,4 @@
+(http://purl.obolibrary.org/obo/UBERON_0000062):http://purl.obolibrary.org/obo/UBERON_0002530 gland
+(http://purl.obolibrary.org/obo/UBERON_0002530):http://purl.obolibrary.org/obo/UBERON_0006925 digestive system gland;digestive gland
+(http://purl.obolibrary.org/obo/UBERON_0001062):http://purl.obolibrary.org/obo/UBERON_0000479 tissue
-:http://purl.org/spar/cito/citesAsAuthority
13 changes: 12 additions & 1 deletion scripts/src/tests/test_owl_integrity.py
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Expand Up @@ -29,7 +29,16 @@ def test_owl_file_integrity(self):
for version in config['versions']:
file = os.path.join(self.repo_path, f'enanomapper{version}.owl')
self.assertTrue(self.is_owl_file_valid(file), f"Invalid eNanoMapper ontology OWL file: enanomapper{version}.owl")

internal = os.listdir('internal')
internal_dev = os.listdir('internal-dev')
for i in internal:
if 'OWL'.casefold() in i:
file = os.path.join(self.repo_path, 'internal', i)
self.assertTrue(self.is_owl_file_valid(file), f"Invalid eNanoMapper internal module OWL file: {i}")
for i in internal_dev:
if 'OWL'.casefold() in i:
file = os.path.join(self.repo_path, 'internal-dev', i)
self.assertTrue(self.is_owl_file_valid(file), f"Invalid eNanoMapper internal-dev module OWL file: {i}")
def load_configuration(self):
"""Load the configuration from the YAML file and return it as a dictionary."""

Expand All @@ -44,6 +53,7 @@ def is_owl_file_valid(self, file_path):
Returns:
bool: True if the file is valid, False otherwise.
"""

try:
graph = Graph()
graph.parse(file_path, format='xml')
Expand All @@ -53,5 +63,6 @@ def is_owl_file_valid(self, file_path):
return False



if __name__ == '__main__':
unittest.main()