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Fixed issue with exel2onto: not all relations are included in the gen…
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…erated ontology (#458)

* Fixed issue #457 by avoiding resetting `added_rows` for each initial iteration.

* Added an extra count for all added rows, including all loops, and fix in property error list.

* Updated ttl file to be made in accordance with correction on restrictions

* Fixed .tll files according to pylint

Co-authored-by: Francesca L. Bleken <[email protected]>
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@jesper-friis @francescalb
jesper-friis and francescalb authored Sep 8, 2022
1 parent 855ed95 commit 499a56b
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Showing 2 changed files with 49 additions and 34 deletions.
15 changes: 9 additions & 6 deletions ontopy/excelparser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -178,11 +178,13 @@ def create_ontology_from_pandas( # pylint:disable=too-many-locals,too-many-bran
"missing_parents": [],
"invalid_parents": [],
"nonadded_concepts": [],
"errors_in_properties": [],
}

onto.sync_python_names()
with onto:
remaining_rows = set(range(len(data)))
all_added_rows = []
while remaining_rows:
added_rows = set()
for index in remaining_rows:
Expand Down Expand Up @@ -327,10 +329,11 @@ def create_ontology_from_pandas( # pylint:disable=too-many-locals,too-many-bran
raise ExcelError(
f"Not able to add the following concepts: {unadded}."
)
all_added_rows.extend(added_rows)

# Add properties in a second loop

for index in added_rows:
for index in all_added_rows:
row = data.loc[index]
properties = row["Relations"]
if properties == "nan":
Expand All @@ -343,19 +346,19 @@ def create_ontology_from_pandas( # pylint:disable=too-many-locals,too-many-bran
props = properties.split(";")
for prop in props:
try:
concept.is_a.append(evaluate(onto, prop))
concept.is_a.append(evaluate(onto, prop.strip()))
except pyparsing.ParseException as exc:
warnings.warn(
f"Error in Property assignment for: {concept}. "
f"Property to be Evaluated: {prop}. "
f"Error is {exc}."
f"Error in Property assignment for: '{concept}'. "
f"Property to be Evaluated: '{prop}'. "
f"{exc}"
)
concepts_with_errors["errors_in_properties"].append(name)
except NoSuchLabelError as exc:
msg = (
f"Error in Property assignment for: {concept}. "
f"Property to be Evaluated: {prop}. "
f"Error is {exc}."
f"{exc}"
)
if force is True:
warnings.warn(msg)
Expand Down
68 changes: 40 additions & 28 deletions tests/testonto/excelparser/fromexcelonto.ttl
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Original file line number Diff line number Diff line change
@@ -1,102 +1,114 @@
@prefix : <http://emmo.info/emmo/domain/onto#> .
@prefix core: <http://www.w3.org/2004/02/skos/core#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix emmo: <http://emmo.info/emmo#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix term: <http://purl.org/dc/terms/> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .

<http://emmo.info/emmo/domain/onto> a owl:Ontology ;
term:contributor "SINTEF"@en,
dcterms:contributor "SINTEF"@en,
"SINTEF Industry"@en ;
term:creator "Francesca L. Bleken"@en,
dcterms:creator "Francesca L. Bleken"@en,
"Jesper Friis"@en,
"Sylvain Gouttebroze"@en ;
term:title "A test domain ontology"@en ;
dcterms:title "A test domain ontology"@en ;
owl:imports <https://raw.githubusercontent.com/emmo-repo/emmo-repo.github.io/master/versions/1.0.0-beta/emmo-inferred-chemistry> ;
owl:versionInfo "0.01"@en .

:EMMO_0264be35-e8ad-5b35-a1a3-84b37bde22d1 a owl:Class ;
emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "Temporal pattern occurring in a time interval"@en ;
emmo:EMMO_b432d2d5_25f4_4165_99c5_5935a7763c1a "Light house during one night"@en ;
rdfs:subClassOf :EMMO_138590b8-3333-515d-87ab-717aac8434e6,
rdfs:subClassOf [ a owl:Restriction ;
owl:onProperty emmo:EMMO_e1097637_70d2_4895_973f_2396f04fa204 ;
owl:someValuesFrom emmo:EMMO_d4f7d378_5e3b_468a_baa1_a7e98358cda7 ],
:EMMO_138590b8-3333-515d-87ab-717aac8434e6,
:EMMO_4b32833e-0833-56a7-903c-28a6a8191fe8 ;
core:prefLabel "FiniteTemporalPattern"@en .
skos:prefLabel "FiniteTemporalPattern"@en .

:EMMO_1c81f1eb-8b94-5e74-96de-1aeacbdb5b93 a owl:Class ;
emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "The boundary of a grain"@en ;
rdfs:subClassOf :EMMO_472ed27e-ce08-53cb-8453-56ab363275c4 ;
core:prefLabel "GrainBoundary"@en .
skos:prefLabel "GrainBoundary"@en .

:EMMO_6920d08f-b1e4-5789-9778-f75f4514ef46 a owl:Class ;
emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "NEED elucidation"@en ;
rdfs:subClassOf owl:Thing ;
core:prefLabel "SpatioTemporalBoundary"@en .
skos:prefLabel "SpatioTemporalBoundary"@en .

:EMMO_76b2eb15-3ab7-52b3-ade2-755aa390d63e a owl:Class ;
emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "Spatial pattern localized in a volume of space"@en ;
emmo:EMMO_b432d2d5_25f4_4165_99c5_5935a7763c1a "Textured surface after etching"@en ;
rdfs:subClassOf :EMMO_4b32833e-0833-56a7-903c-28a6a8191fe8,
rdfs:subClassOf [ a owl:Restriction ;
owl:onProperty emmo:EMMO_17e27c22_37e1_468c_9dd7_95e137f73e7f ;
owl:someValuesFrom :EMMO_472ed27e-ce08-53cb-8453-56ab363275c4 ],
[ a owl:Restriction ;
owl:onProperty emmo:EMMO_e1097637_70d2_4895_973f_2396f04fa204 ;
owl:someValuesFrom emmo:EMMO_f1a51559_aa3d_43a0_9327_918039f0dfed ],
:EMMO_4b32833e-0833-56a7-903c-28a6a8191fe8,
:EMMO_5f50f77e-f321-53e3-af76-fe5b0a347479 ;
core:prefLabel "FiniteSpatialPattern"@en .
skos:prefLabel "FiniteSpatialPattern"@en .

:EMMO_b04965e6-a9bb-591f-8f8a-1adcb2c8dc39 a owl:Class ;
rdfs:subClassOf emmo:EMMO_21f56795_ee72_4858_b571_11cfaa59c1a8 ;
core:prefLabel "1"@en .
skos:prefLabel "1"@en .

:EMMO_e0b20a22-7e6f-5c81-beca-35bc5358e11b a owl:Class ;
emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "NEED elucidation"@en ;
rdfs:subClassOf :EMMO_4b32833e-0833-56a7-903c-28a6a8191fe8,
:EMMO_9fa9ca88-2891-538a-a8dd-ccb8a08b9890 ;
core:prefLabel "FiniteSpatioTemporalPattern"@en .
skos:prefLabel "FiniteSpatioTemporalPattern"@en .

:EMMO_e633d033-2af6-5f04-a706-dab826854fb1 a owl:Class ;
emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "The boundary of a subgrain"@en ;
rdfs:subClassOf owl:Thing ;
core:prefLabel "SubgrainBoundary"@en .
skos:prefLabel "SubgrainBoundary"@en .

:EMMO_f8ad57d3-6cb5-5628-99e6-eb5915bece3a a owl:Class ;
rdfs:subClassOf owl:Thing ;
core:prefLabel "SubSubgrainBoundary"@en .
skos:prefLabel "SubSubgrainBoundary"@en .

:EMMO_138590b8-3333-515d-87ab-717aac8434e6 a owl:Class ;
emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "Pattern with only temporal aspect"@en ;
emmo:EMMO_b432d2d5_25f4_4165_99c5_5935a7763c1a "Voltage in AC plug"@en ;
rdfs:subClassOf owl:Thing ;
core:prefLabel "TemporalPattern"@en .
skos:prefLabel "TemporalPattern"@en .

:EMMO_5f50f77e-f321-53e3-af76-fe5b0a347479 a owl:Class ;
emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "Spatial pattern without regular temporal variations"@en ;
emmo:EMMO_b432d2d5_25f4_4165_99c5_5935a7763c1a "Infinite grid"@en ;
rdfs:subClassOf :EMMO_9fa9ca88-2891-538a-a8dd-ccb8a08b9890 ;
skos:prefLabel "SpatialPattern"@en .

:EMMO_1b2bfe71-5da9-5c46-b137-be45c3e3f9c3 a owl:Class ;
emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "NEED elucidation"@en ;
rdfs:subClassOf emmo:EMMO_649bf97b_4397_4005_90d9_219755d92e34 ;
core:prefLabel "Boundary"@en .
skos:prefLabel "Boundary"@en .

:EMMO_472ed27e-ce08-53cb-8453-56ab363275c4 a owl:Class ;
emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 " "@en ;
rdfs:subClassOf :EMMO_1b2bfe71-5da9-5c46-b137-be45c3e3f9c3 ;
core:prefLabel "SpatialBoundary"@en .

:EMMO_5f50f77e-f321-53e3-af76-fe5b0a347479 a owl:Class ;
emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "Spatial pattern without regular temporal variations"@en ;
emmo:EMMO_b432d2d5_25f4_4165_99c5_5935a7763c1a "Infinite grid"@en ;
rdfs:subClassOf :EMMO_9fa9ca88-2891-538a-a8dd-ccb8a08b9890 ;
core:prefLabel "SpatialPattern"@en .
skos:prefLabel "SpatialBoundary"@en .

:EMMO_9fa9ca88-2891-538a-a8dd-ccb8a08b9890 a owl:Class ;
emmo:EMMO_21ae69b4_235e_479d_8dd8_4f756f694c1b "A"@en,
"Just"@en,
"Test"@en ;
emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "NEED elucidation"@en ;
rdfs:subClassOf :EMMO_cd254842-c697-55f6-917d-9805c77b9187 ;
core:prefLabel "SpatioTemporalPattern"@en .
skos:prefLabel "SpatioTemporalPattern"@en .

:EMMO_cd254842-c697-55f6-917d-9805c77b9187 a owl:Class ;
emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "everything that can be perceived or measured"@en ;
rdfs:comment " this definition is much broader than definition of pattern such as \"the regular and repeated way in which something happens or is\""@en,
"a pattern is defined from a contrast"@en ;
rdfs:subClassOf emmo:EMMO_649bf97b_4397_4005_90d9_219755d92e34 ;
core:prefLabel "Pattern"@en .
skos:prefLabel "Pattern"@en .

:EMMO_4b32833e-0833-56a7-903c-28a6a8191fe8 a owl:Class ;
emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "Pattern occuring within a boundary in the 4D space"@en ;
rdfs:comment "Every physical patterns are FinitePattern"@en ;
rdfs:subClassOf :EMMO_cd254842-c697-55f6-917d-9805c77b9187 ;
core:prefLabel "FinitePattern"@en .
rdfs:subClassOf [ a owl:Restriction ;
owl:onProperty emmo:EMMO_17e27c22_37e1_468c_9dd7_95e137f73e7f ;
owl:someValuesFrom :EMMO_1b2bfe71-5da9-5c46-b137-be45c3e3f9c3 ],
:EMMO_cd254842-c697-55f6-917d-9805c77b9187 ;
skos:prefLabel "FinitePattern"@en .

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