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INCATools / kgcl

Datamodel for KGCL (Knowledge Graph Change Language)
https://w3id.org/kgcl/
MIT License
11 stars 4 forks source link

parsing rename commands take a long time #64

Closed cmungall closed 5 months ago

cmungall commented 5 months ago

runoak --profile --stacktrace -vv -i robottemplate:templates apply "rename OBI:0002516 from 'brain specimen' to 'brain sample'" -o new_templates

ncalls tottime percall cumtime percall filename:lineno(function) 1 0.000 0.000 58.273 58.273 /Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/click/core.py:1423(invoke) 1 0.000 0.000 58.273 58.273 /Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/click/core.py:732(invoke) 1 0.000 0.000 58.273 58.273 /Users/cjm/repos/ontology-access-kit/src/oaklib/cli.py:5875(apply) 1 0.000 0.000 58.227 58.227 /Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/kgcl_schema/grammar/parser.py:80(parse_statement) 1 0.000 0.000 58.223 58.223 /Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/kgcl_schema/grammar/parser.py:571(parse_rename) 1 0.000 0.000 58.222 58.222 /Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/kgcl_schema/grammar/parser.py:622(get_entity_representation) 1 0.000 0.000 58.222 58.222 /Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/kgcl_schema/grammar/parser.py:645(contract_uri) 1 0.000 0.000 58.222 58.222 /Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/kgcl_schema/grammar/parser.py:44(get_curie_converter) 1 0.001 0.001 58.222 58.222 /Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/prefixmaps/io/parser.py:28(load_converter) 1 0.001 0.001 54.505 54.505 /Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/prefixmaps/io/parser.py:35(load_multi_context) 3 1.388 0.463 54.381 18.127 /Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/prefixmaps/datamodel/context.py:147(combine) 13989 1.153 0.000 52.993 0.004 /Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/prefixmaps/datamodel/context.py:160(add_prefix) 13989 1.888 0.000 30.358 0.002 /Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/prefixmaps/datamodel/context.py:245(namespaces) 13989 16.339 0.001 28.470 0.002 /Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/prefixmaps/datamodel/context.py:253() 13989 0.302 0.000 21.465 0.002 /Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/prefixmaps/datamodel/context.py:233(prefixes) 13989 14.956 0.001 21.163 0.002 /Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/prefixmaps/datamodel/context.py:241() 192341811 18.342 0.000 18.342 0.000 {method 'lower' of 'str' objects} 1 0.000 0.000 3.716 3.716 /Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/prefixmaps/datamodel/context.py:335(as_converter) 1 0.000 0.000 3.684 3.684 /Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/curies/api.py:639(from_extended_prefix_map) 1 0.000 0.000 3.684 3.684 /Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/curies/api.py:474(init) 1 0.000 0.000 2.692 2.692 /Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/curies/api.py:373(_get_duplicate_uri_prefixes) 1 2.373 2.373 2.692 2.692 /Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/curies/api.py:374() 1 0.000 0.000 0.646 0.646 /Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/curies/api.py:382(_get_duplicate_prefixes) 1 0.386 0.386 0.646 0.646 /Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/curies/api.py:383() 1 0.000 0.000 0.344 0.344 /Users/cjm/Library/Caches/pypoetry/virtualenvs/oaklib-OeQZizwE-py3.9/lib/python3.9/site-packages/pytrie.py:115(init)

cmungall commented 5 months ago

To test, unskip

https://github.com/INCATools/ontology-access-kit/blob/8da76e19698058b43c4ae4ba2b5bcda35a1c851a/tests/test_implementations/test_robot_template.py#L55-L74