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More annotation tweaks: remove unused ids, use rdf:li #353

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Merged
Parent: Added segment picking from faces
merged 2 commits into from
Apr 29, 2024
Merged

More annotation tweaks: remove unused ids, use rdf:li #353

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6c5ae6e
chore: remove ruff linter pre-commit hook
sanjayankur31 Apr 29, 2024
afbde92
feat(annotations): make annotations comply with NeuroML/LEMS requirem…
sanjayankur31 Apr 29, 2024
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2 changes: 0 additions & 2 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,4 @@ repos:
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.4.1
hooks:
- id: ruff
args: [ --exit-zero ]
- id: ruff-format
15 changes: 14 additions & 1 deletion pyneuroml/annotations.py
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Expand Up @@ -7,6 +7,7 @@
Copyright 2024 NeuroML contributors
"""

import re
import logging
import pprint
import typing
Expand Down Expand Up @@ -369,8 +370,20 @@ def create_annotation(
# indent
if indent > 0:
annotation = textwrap.indent(annotation, " " * indent)
# remove xml header

# xml issues
if "xml" in serialization_format:
# replace rdf:_1 etc with rdf:li
# our LEMS definitions only know rdf:li
# https://github.com/RDFLib/rdflib/issues/1374#issuecomment-885656850
rdfli_pattern = re.compile(r"\brdf:_\d+\b")
annotation = rdfli_pattern.sub("rdf:li", annotation)

# remove nodeids for rdflib BNodes: these aren't required
rdfbnode_pattern = re.compile(r' rdf:nodeID="\S+"')
annotation = rdfbnode_pattern.sub("", annotation)

# remove xml header, not used when embedding into other NeuroML files
if xml_header is False:
annotation = annotation[annotation.find(">") + 1 :]

Expand Down