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[ENH] Allow plus signs in labels #1926

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[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
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10 changes: 5 additions & 5 deletions src/schema/objects/columns.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,7 @@ derived_from:
`sample-<label>` entity from which a sample is derived,
for example a slice of tissue (`sample-02`) derived from a block of tissue (`sample-01`).
type: string
pattern: ^sample-[0-9a-zA-Z]+$
pattern: ^sample-[0-9a-zA-Z+]+$
desc_id:
name: desc_id
display_name: Description Label
Expand All @@ -125,7 +125,7 @@ desc_id:
its `desc_id` column SHOULD contain all labels of the `desc` entity)
used across the entire derivative dataset.
type: string
pattern: ^desc-[0-9a-zA-Z]+$
pattern: ^desc-[0-9a-zA-Z+]+$
description:
name: description
display_name: Description
Expand Down Expand Up @@ -369,7 +369,7 @@ participant_id:
A participant identifier of the form `sub-<label>`,
matching a participant entity found in the dataset.
type: string
pattern: ^sub-[0-9a-zA-Z]+$
pattern: ^sub-[0-9a-zA-Z+]+$
placement__motion:
name: placement
display_name: Placement
Expand Down Expand Up @@ -434,7 +434,7 @@ sample_id:
A sample identifier of the form `sample-<label>`,
matching a sample entity found in the dataset.
type: string
pattern: ^sample-[0-9a-zA-Z]+$
pattern: ^sample-[0-9a-zA-Z+]+$
sample_type:
name: sample_type
display_name: Sample type
Expand Down Expand Up @@ -466,7 +466,7 @@ session_id:
A session identifier of the form `ses-<label>`,
matching a session found in the dataset.
type: string
pattern: ^ses-[0-9a-zA-Z]+$
pattern: ^ses-[0-9a-zA-Z+]+$
sex:
name: sex
display_name: Sex
Expand Down
12 changes: 10 additions & 2 deletions src/schema/objects/formats.yaml
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Expand Up @@ -9,8 +9,16 @@ 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 entities such as `<name>-x+y` with either `<name>-x` or `<name>-y`.
For example, metadata stored in a file at the root of the dataset with name `/acq-6p_T2w.json`
does not apply to files with partially matching "acquisition" entity values
such as `/sub-1/anat/sub-1_acq-6p+s2_T2w.nii`.
pattern: '[0-9a-zA-Z+]+'
# Metadata types
boolean:
display_name: Boolean
Expand Down
2 changes: 1 addition & 1 deletion src/schema/objects/metadata.yaml
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Expand Up @@ -3676,7 +3676,7 @@ TaskName:
Name of the task.
No two tasks should have the same name.
The task label included in the filename is derived from this `"TaskName"` field
by removing all non-alphanumeric characters (that is, all except those matching `[0-9a-zA-Z]`).
by removing all non-alphanumeric characters (that is, all except those matching `[0-9a-zA-Z+]`).
For example `"TaskName"` `"faces n-back"` or `"head nodding"` will correspond to task labels
`facesnback` and `headnodding`, respectively.
type: string
Expand Down
2 changes: 1 addition & 1 deletion tools/schemacode/bidsschematools/tests/data/expected_bids_validator_xs_write.log
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@

SUMMARY:
0 out of 1 files were successfully validated, using the following regular expressions:
- `.*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)anat/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_ce-(?P<ceagent>[0-9a-zA-Z]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9a-zA-Z]+))(|_part-(?P<part>(mag|phase|real|imag)))_(T1w|T2w|PDw|T2starw|FLAIR|inplaneT1|inplaneT2|PDT2|angio|T2star)\.(nii.gz|nii|json)$`
- `.*?/sub-(?P<subject>[0-9a-zA-Z+]+)/(|ses-(?P<session>[0-9a-zA-Z+]+)/)anat/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z+]+))(|_ce-(?P<ceagent>[0-9a-zA-Z+]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z+]+))(|_run-(?P<run>[0-9a-zA-Z+]+))(|_part-(?P<part>(mag|phase|real|imag)))_(T1w|T2w|PDw|T2starw|FLAIR|inplaneT1|inplaneT2|PDT2|angio|T2star)\.(nii.gz|nii|json)$`
The following files were not matched by any regex schema entry:
* `/home/chymera/.data2/datalad/000026/noncompliant/sub-EXC022/anat/sub-EXC022_ses-MRI_flip-1_VFA.nii.gz
The following mandatory regex schema entries did not match any files:
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
24 changes: 12 additions & 12 deletions tools/schemacode/bidsschematools/tests/test_validator.py
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Expand Up @@ -72,12 +72,12 @@ def test_write_report(tmp_path):

validation_result["schema_tracking"] = [
{
"regex": ".*?/sub-(?P<subject>[0-9a-zA-Z]+)/"
"(|ses-(?P<session>[0-9a-zA-Z]+)/)anat/sub-(?P=subject)"
"(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))"
"(|_ce-(?P<ceagent>[0-9a-zA-Z]+))"
"(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))"
"(|_run-(?P<run>[0-9a-zA-Z]+))"
"regex": ".*?/sub-(?P<subject>[0-9a-zA-Z+]+)/"
"(|ses-(?P<session>[0-9a-zA-Z+]+)/)anat/sub-(?P=subject)"
"(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z+]+))"
"(|_ce-(?P<ceagent>[0-9a-zA-Z+]+))"
"(|_rec-(?P<reconstruction>[0-9a-zA-Z+]+))"
"(|_run-(?P<run>[0-9a-zA-Z+]+))"
"(|_part-(?P<part>(mag|phase|real|imag)))"
"_(T1w|T2w|PDw|T2starw|FLAIR|inplaneT1|inplaneT2|PDT2|angio|T2star)"
"\\.(nii.gz|nii|json)$",
Expand All @@ -86,12 +86,12 @@ def test_write_report(tmp_path):
]
validation_result["schema_listing"] = [
{
"regex": ".*?/sub-(?P<subject>[0-9a-zA-Z]+)/"
"(|ses-(?P<session>[0-9a-zA-Z]+)/)anat/sub-(?P=subject)"
"(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))"
"(|_ce-(?P<ceagent>[0-9a-zA-Z]+))"
"(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))"
"(|_run-(?P<run>[0-9a-zA-Z]+))"
"regex": ".*?/sub-(?P<subject>[0-9a-zA-Z+]+)/"
"(|ses-(?P<session>[0-9a-zA-Z+]+)/)anat/sub-(?P=subject)"
"(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z+]+))"
"(|_ce-(?P<ceagent>[0-9a-zA-Z+]+))"
"(|_rec-(?P<reconstruction>[0-9a-zA-Z+]+))"
"(|_run-(?P<run>[0-9a-zA-Z+]+))"
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"(|_part-(?P<part>(mag|phase|real|imag)))"
"_(T1w|T2w|PDw|T2starw|FLAIR|inplaneT1|inplaneT2|PDT2|angio|T2star)"
"\\.(nii.gz|nii|json)$",
Expand Down