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[ENH] Allow plus signs in labels #1926

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Merged
merged 16 commits into from
Feb 25, 2025
Merged

[ENH] Allow plus signs in labels #1926

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0afce3c
Allow plus signs in labels.
tsalo Sep 20, 2024
e32984c
Update test_rules.py
tsalo Sep 20, 2024
97de148
Remove self from CODEOWNERS.
tsalo Sep 20, 2024
8400bc6
Update formats.yaml
tsalo Sep 20, 2024
aa9c73c
Merge branch 'master' into plus-sign-labels
tsalo Sep 23, 2024
a950d08
Update src/schema/objects/formats.yaml
tsalo Sep 23, 2024
7ba5e39
[DATALAD RUNCMD] Replace more of label regexes present in various spo…
yarikoptic Sep 23, 2024
1481dc6
Adjust (or replace) mentionings of alphanumeric as now would include …
yarikoptic Sep 23, 2024
d692608
Allow for + in the paths, which can include labels
yarikoptic Sep 23, 2024
a096cba
Fix regex for `_run` index in a test_validator.py
yarikoptic Sep 30, 2024
45643a5
Merge remote-tracking branch 'upstream/master' into plus-sign-labels
effigies Jan 14, 2025
304f0de
Update src/appendices/entity-table.md
effigies Jan 14, 2025
e076d05
fix(test): Run is an index, not a label
effigies Jan 14, 2025
abce472
Merge branch 'master' into plus-sign-labels
effigies Jan 23, 2025
f551f7d
Merge branch 'master' into plus-sign-labels
tsalo Feb 10, 2025
75924cf
Merge branch 'master' into plus-sign-labels
tsalo Feb 24, 2025
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4 changes: 2 additions & 2 deletions CODEOWNERS
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Original file line number Diff line number Diff line change
Expand Up @@ -16,5 +16,5 @@
/src/derivatives/diffusion-derivatives.md @francopestilli @oesteban @Lestropie

# The schema
/src/schema/ @tsalo @erdalkaraca
/tools/schemacode/ @tsalo @erdalkaraca
/src/schema/ @erdalkaraca
/tools/schemacode/ @erdalkaraca
9 changes: 7 additions & 2 deletions src/schema/objects/formats.yaml
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Expand Up @@ -9,8 +9,13 @@ index:
label:
display_name: Label
description: |
Freeform labels without special characters.
pattern: '[0-9a-zA-Z]+'
Free-form labels with alphanumeric and plus (+) characters.

Plus signs MAY be used to concatenate multiple applicable labels,
but no relationship is established by a partial match.
In particular, the inheritance principle does not connect files
containing "ent-X+Y" and "ent-X" or "ent-Y".
pattern: '[0-9a-zA-Z+]+'
# Metadata types
boolean:
display_name: Boolean
Expand Down
8 changes: 4 additions & 4 deletions tools/schemacode/bidsschematools/tests/test_rules.py
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Expand Up @@ -18,8 +18,8 @@ def test_entity_rule(schema_obj):
nii_rule = rules._entity_rule(rule, schema_obj)
assert nii_rule == {
"regex": (
r"sub-(?P<subject>[0-9a-zA-Z]+)/"
r"(?:ses-(?P<session>[0-9a-zA-Z]+)/)?"
r"sub-(?P<subject>[0-9a-zA-Z+]+)/"
r"(?:ses-(?P<session>[0-9a-zA-Z+]+)/)?"
r"(?P<datatype>anat)/"
r"(?(subject)sub-(?P=subject)_)"
r"(?(session)ses-(?P=session)_)"
Expand Down Expand Up @@ -50,8 +50,8 @@ def test_entity_rule(schema_obj):
json_rule = rules._entity_rule(rule, schema_obj)
assert json_rule == {
"regex": (
r"(?:sub-(?P<subject>[0-9a-zA-Z]+)/)?"
r"(?:ses-(?P<session>[0-9a-zA-Z]+)/)?"
r"(?:sub-(?P<subject>[0-9a-zA-Z+]+)/)?"
r"(?:ses-(?P<session>[0-9a-zA-Z+]+)/)?"
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I am afraid that is not all ... I will push a few commits on that end in a few minutes (I hope you don't mind).
Some other might need adjustment and I even start feeling that we might need to come up with some term (like "literal" but there might be better) to encompass "alphanumeric" and +.

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@yarikoptic Note this is a regression test that shows the specific output of a specific synthetic rule.

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my comment is not really about this test -- I meant that changes in this PR (just this test) aren't sufficient. pushed now

r"(?:(?P<datatype>anat)/)?"
r"(?(subject)sub-(?P=subject)_)"
r"(?(session)ses-(?P=session)_)"
Expand Down