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Flb/update excel parser accroding to thermodynamics example #336

Merged
merged 72 commits into from
Jan 7, 2022
Merged

Flb/update excel parser accroding to thermodynamics example #336

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8b248fd
Added first draft of excel2onto
francescalb Nov 26, 2021
eab0472
Dummy example for make_microstructure_onto.py added.
francescalb Dec 1, 2021
e7e2df3
Added module excelparser which is used by excel2onto
francescalb Dec 1, 2021
cf035af
Merge branch 'master' into flb/close-302-excelparser
francescalb Dec 1, 2021
8db19da
Added choice for sheetname for Concepts
francescalb Dec 1, 2021
9c621c5
Merge branch 'master' of github.com:emmo-repo/EMMO-python into flb/cl…
francescalb Dec 1, 2021
dd5794a
Cleaned up dataframe to be analysed
francescalb Dec 1, 2021
7db9a8e
Added option to read base_iri from metadata
francescalb Dec 1, 2021
991278f
Added import ontologies from excel
francescalb Dec 1, 2021
ed11bcf
Try to fix documentation
francescalb Dec 2, 2021
b0d9362
Merge branch 'master' of github.com:emmo-repo/EMMO-python into flb/cl…
francescalb Dec 7, 2021
8d69516
Fixed documentation error
francescalb Dec 7, 2021
912ad2b
Added pandas to requirements
francescalb Dec 7, 2021
ce0476b
Corrected google docstring for returning Tuple with typing
francescalb Dec 7, 2021
9bd9e83
Fixed typing error
francescalb Dec 8, 2021
d746812
Added openpyxl to requirements
francescalb Dec 8, 2021
83f48b8
Added first test for adding metadata authors and contributors
francescalb Dec 8, 2021
b4f436c
Added own function for metadata
francescalb Dec 8, 2021
38199f1
Added more metadata and altLabels
francescalb Dec 8, 2021
b81fd0a
Added altLabel
francescalb Dec 8, 2021
72dd4b0
Corrected so that empty fields are not included
francescalb Dec 8, 2021
9f89d10
owlready2.Ontology->ontopy.Ontology
francescalb Dec 9, 2021
8dca4b2
parent=owl:Thing if parents missing in parser
francescalb Dec 9, 2021
a51dcb1
typo
francescalb Dec 9, 2021
091d2cb
Changed owlready.Ontology to ontopy.ontology.Ontology
francescalb Dec 9, 2021
b3b7c22
Added helper function for adding metadata
francescalb Dec 9, 2021
0e62f86
Use function for adding literals also on concepts
francescalb Dec 10, 2021
b527856
_add_literal/_parse_literal accespt pd.Series and pd.DataFrame for data
francescalb Dec 10, 2021
9209a4a
Merge branch 'master' of github.com:emmo-repo/EMMO-python into flb/cl…
francescalb Dec 10, 2021
8a59622
Added a test for the excel_parser
francescalb Dec 10, 2021
c44a63b
Corrected path in test
francescalb Dec 10, 2021
862eabe
Added creator instead of author and changed excel2onto arg to --output
francescalb Dec 10, 2021
b9ec0a1
Merge branch 'master' of github.com:emmo-repo/EMMO-python into flb/cl…
francescalb Dec 10, 2021
ee6621e
Updated excelparser ontology for comparison
francescalb Dec 10, 2021
b3db280
A first test with some hacks
francescalb Dec 22, 2021
edf16d4
Adding emmo as improted ontology in excelparser if none found.
francescalb Dec 22, 2021
a924c90
Improve warning and error messages
jesper-friis Jan 2, 2022
8292bfc
Merged master into flb/update-excel-parser-accroding-to-thermodynamic…
jesper-friis Jan 2, 2022
b251783
Corrected parsing cardinality restrictions
jesper-friis Jan 2, 2022
d4c8692
Fix serialised ontology IRI
jesper-friis Jan 2, 2022
7d8de1c
Updated the excel parser such that it works well with the latest vers…
jesper-friis Jan 3, 2022
f7cb79c
Replaced assertment with exception
jesper-friis Jan 3, 2022
a2acb24
Added force argument to excel2onto, should skip errors
francescalb Jan 3, 2022
da76852
Make sure that default base_iri is used if it is not provided by the …
jesper-friis Jan 3, 2022
e8cac94
As suggested by Francesca
jesper-friis Jan 3, 2022
2c210ab
Made real microstructure as example for excelparser and
francescalb Jan 4, 2022
01b9f68
Merge branch 'flb/update-excel-parser-accroding-to-thermodynamics_exa…
francescalb Jan 4, 2022
00c304e
Moved option for imported ontologies to separate sheet
francescalb Jan 4, 2022
f81c877
Updated test excel sheet for excelparser
francescalb Jan 4, 2022
3fdad99
Merge pull request #344 from emmo-repo/excelparser-update
francescalb Jan 4, 2022
fabc4c9
Added test for validity of concept name before proceeding in loop in
francescalb Jan 4, 2022
faa869f
Excelparser now proceeds if force is true, diregarding concepts that
francescalb Jan 4, 2022
b64c394
If missing or wrong parents, concepts are defined directly under
francescalb Jan 4, 2022
c59b53f
Added test of concept whos parent is defined later
jesper-friis Jan 4, 2022
14358c4
Work in progress: fixing not-yet-defined-parent
jesper-friis Jan 4, 2022
e037e9f
Fixed not yet defined parents
jesper-friis Jan 4, 2022
71984d2
Changed all data in conceptata to strings
francescalb Jan 4, 2022
8336fa8
Values converted to sring 'nan' are not considered when adding literal
francescalb Jan 4, 2022
addb7fe
Added som test for invalid parent
francescalb Jan 4, 2022
13fd309
Merge branch 'master' into flb/update-excel-parser-accroding-to-therm…
francescalb Jan 4, 2022
f4f217b
Merge branch 'master' into flb/update-excel-parser-accroding-to-therm…
francescalb Jan 4, 2022
8f58a2e
updated test for excelparser
francescalb Jan 5, 2022
ffff9cd
Merge branch 'flb/update-excel-parser-accroding-to-thermodynamics_exa…
francescalb Jan 5, 2022
702dc9d
Removed print
francescalb Jan 5, 2022
cfeffec
parent_name written out correctly in error msg
francescalb Jan 5, 2022
2848cfe
Merge branch 'master' into flb/update-excel-parser-accroding-to-therm…
francescalb Jan 5, 2022
abe9105
Fixed some pylit issues that resurfaced pon mergin in master
francescalb Jan 5, 2022
7298d73
Fixes, mostly documentation after review.
francescalb Jan 7, 2022
a99bee5
Fix doc-string indent
CasperWA Jan 7, 2022
83b9d85
Very minor string fix.
CasperWA Jan 7, 2022
d43bb72
Minor doc-string prettification
CasperWA Jan 7, 2022
637c35d
f-String corrections
CasperWA Jan 7, 2022
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2 changes: 1 addition & 1 deletion examples/ontology-from-excel/make_microstructure_onto.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
from ontopy.excelparser import create_ontology_from_excel
from ontopy.utils import write_catalog

ontology, catalog = create_ontology_from_excel("tool/onto.xlsx")
ontology, catalog = create_ontology_from_excel("tool/microstructure.xlsx")

ontology.save("microstructure_ontology.ttl", format="turtle", overwrite=True)
write_catalog(catalog)
Binary file added examples/ontology-from-excel/tool/microstructure.xlsx
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