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Convert IRI -> CURIE using bioregistry while parse-ing a KGCL command. #6

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merged 9 commits into from
Aug 16, 2022
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Convert IRI -> CURIE using bioregistry while parse-ing a KGCL command. #6

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34a4eba
Add bioregistry, convert IRI=>CURIE during `parse`
hrshdhgd Jul 28, 2022
6d4e77f
update gitignore
hrshdhgd Jul 28, 2022
a02f5c9
get preferred prefix instead of lowercase
hrshdhgd Jul 28, 2022
814fb97
removed '<' from URI representations
hrshdhgd Aug 11, 2022
627bbd4
remove < > references
hrshdhgd Aug 11, 2022
217acad
addressed for multiple URIs in command
hrshdhgd Aug 11, 2022
8ccad9e
https://github.com/INCATools/kgcl-rdflib/issues/43
hrshdhgd Aug 11, 2022
53a8d93
tests pass and < added back
hrshdhgd Aug 16, 2022
44c8099
removed < again and tests pass
hrshdhgd Aug 16, 2022
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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -5,3 +5,4 @@ __pycache__
.pytest_cache
.idea
tmp/
tests/outputs/*
112 changes: 107 additions & 5 deletions poetry.lock
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1 change: 1 addition & 0 deletions pyproject.toml
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Expand Up @@ -14,6 +14,7 @@ readme = "README.md"
python = "^3.8"
linkml-runtime = "^1.1.24"
lark = "^1.1.2"
bioregistry = "^0.5.49"

[tool.poetry.dev-dependencies]
linkml = "^1.2.15"
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29 changes: 21 additions & 8 deletions src/kgcl_schema/grammar/parser.py
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@@ -1,20 +1,24 @@
"""KGCL parser."""
import logging
import re
import sys
from pathlib import Path
from typing import List

import click
from kgcl_schema.utils import to_json, to_rdf, to_yaml
from lark import Lark, Token

from kgcl_schema.datamodel.kgcl import (ClassCreation, EdgeCreation, EdgeDeletion,
NewSynonym, NodeAnnotationChange, NodeCreation,
from bioregistry import parse_iri, get_preferred_prefix, curie_to_str
from kgcl_schema.datamodel.kgcl import (Change, ClassCreation, EdgeCreation,
EdgeDeletion, NewSynonym,
NodeAnnotationChange, NodeCreation,
NodeDeepening, NodeDeletion, NodeMove,
NodeObsoletion, NodeRename, NodeShallowing,
NodeUnobsoletion, PlaceUnder, PredicateChange,
RemovedNodeFromSubset, RemoveUnder, Change, Session)
NodeObsoletion, NodeRename,
NodeShallowing, NodeUnobsoletion,
PlaceUnder, PredicateChange,
RemovedNodeFromSubset, RemoveUnder,
Session)
from kgcl_schema.datamodel.ontology_model import Edge
from kgcl_schema.utils import to_json, to_rdf, to_yaml
from lark import Lark, Token


def id_generator():
Expand Down Expand Up @@ -54,6 +58,15 @@ def parse_statement(input: str) -> Change:

Return an instantiated dataclass object from model.kgcl_schema.
"""
regex = r'<http[s]?://(?:[a-zA-Z]|[0-9]|[$-_@.&+]|[!*\(\),]|(?:%[0-9a-fA-F][0-9a-fA-F]))+'
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uri = re.findall(regex, input)
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if uri:
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# curie = curie_from_iri(uri[0].replace("<", "").replace(">",""))
pref, i = parse_iri(uri[0].replace("<", "").replace(">",""))
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pref = get_preferred_prefix(pref)
curie = curie_to_str(pref, i)
input = input.replace(uri[0], curie)
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Beter use https://github.com/cthoyt/curies

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(but dont sweat it)


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It seems very hacky to replace URIs with CURIEs just so the KGCL parser works. Why is that necessary?

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When adding synonyms, apparently only CURIEs are expected and ehnce the conversion from URI => CURIE. Just a judgement call, there could be a better way of handling this. Ideas?

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I dont know how that parser works, but if CURIES are expected, wouldn't it be better to make sure the input is "valid kgcl" using a validator and not trying to hack anything? The user can be forced to provide CURIEs if that is what the spec wants..

In any case, I would for sure factor out the method def replace_uris_with_curies_in_kgcl_command(input) into its how, document it etc. Not convinced this is great but if its necessary to be parseable than so be it.

tree = kgcl_parser.parse(input)
id = "kgcl_change_id_" + str(next(id_gen))

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6 changes: 3 additions & 3 deletions tests/cases.py
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Expand Up @@ -124,10 +124,10 @@
#f"create node {NEW_TERM_URI} 'foo'",
TODO_TOKEN,
NodeCreation(id=UID,
node_id=NEW_TERM_URI, ## TODO: remove this
about_node=NEW_TERM_URI,
node_id=NEW_TERM, ## TODO: remove this
about_node=NEW_TERM,
name="'foo'",
about_node_representation='uri'),
about_node_representation='curie'),
None
),
(
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