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2 changes: 1 addition & 1 deletion .codespellrc
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
[codespell]
skip = .git,*.pdf,*.svg,venvs,venv,site
skip = .git,*.pdf,*.svg,venvs,venv,site,*.cast
#
# ignore-words-list =
17 changes: 17 additions & 0 deletions docs/examples/validation/bids_eeg_cbm_grouped.txt
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=== ERROR (21 issues) ===
[DANDI.NO_DANDISET_FOUND] eeg_cbm — Path is not inside a Dandiset
[BIDS.EMPTY_FILE] eeg_cbm/sub-cbm001/eeg/sub-cbm001_task-protmap_eeg.edf — Empty files not allowed.
[BIDS.EMPTY_FILE] eeg_cbm/sub-cbm002/eeg/sub-cbm002_task-protmap_eeg.edf — Empty files not allowed.
... and 18 more issues
=== HINT (410 issues) ===
[BIDS.README_FILE_SMALL] eeg_cbm/README — The recommended file '/README' is very small.
Please consider expanding it with additional information about the dataset.
[BIDS.JSON_KEY_RECOMMENDED] eeg_cbm/dataset_description.json — A JSON file is missing a key listed as recommended.
subCode: HEDVersion
issueMessage: Field description: If HED tags are used:
The version of the HED schema used to validate HED tags for study.
May include a single schema or a base schema and one or more library schema.
[BIDS.JSON_KEY_RECOMMENDED] eeg_cbm/dataset_description.json — A JSON file is missing a key listed as recommended.
subCode: GeneratedBy
issueMessage: Field description: Used to specify provenance of the dataset.
... and 407 more issues
72 changes: 72 additions & 0 deletions docs/examples/validation/bids_invalid_eeg_cbm.json
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[
{
"asset_paths": null,
"dandiset_path": "invalid_eeg_cbm",
"dataset_path": "invalid_eeg_cbm",
"id": "BIDS.README_FILE_MISSING",
"message": "The recommended file /README is missing.\nSee Section 03 (Modality agnostic files) of the BIDS specification.\n",
"metadata": null,
"origin": {
"standard": "BIDS",
"standard_schema_version": "1.2.1",
"standard_version": null,
"type": "VALIDATION",
"validator": "bids-validator-deno",
"validator_version": "2.4.1"
},
"path": "invalid_eeg_cbm/dataset_description.json",
"path_regex": null,
"record_version": "1",
"scope": "file",
"severity": "HINT",
"within_asset_paths": null
},
{
"asset_paths": null,
"dandiset_path": "invalid_eeg_cbm",
"dataset_path": "invalid_eeg_cbm",
"id": "BIDS.JSON_KEY_RECOMMENDED",
"message": "A JSON file is missing a key listed as recommended.\nsubCode: HEDVersion\nissueMessage: Field description: If HED tags are used:\nThe version of the HED schema used to validate HED tags for study.\nMay include a single schema or a base schema and one or more library schema.\n",
"metadata": null,
"origin": {
"standard": "BIDS",
"standard_schema_version": "1.2.1",
"standard_version": null,
"type": "VALIDATION",
"validator": "bids-validator-deno",
"validator_version": "2.4.1"
},
"path": "invalid_eeg_cbm/dataset_description.json",
"path_regex": null,
"record_version": "1",
"scope": "file",
"severity": "HINT",
"within_asset_paths": null
},
{
"asset_paths": null,
"dandiset_path": "invalid_eeg_cbm",
"dataset_path": "invalid_eeg_cbm",
"id": "BIDS.JSON_KEY_RECOMMENDED",
"message": "A JSON file is missing a key listed as recommended.\nsubCode: GeneratedBy\nissueMessage: Field description: Used to specify provenance of the dataset.\n",
"metadata": null,
"origin": {
"standard": "BIDS",
"standard_schema_version": "1.2.1",
"standard_version": null,
"type": "VALIDATION",
"validator": "bids-validator-deno",
"validator_version": "2.4.1"
},
"path": "invalid_eeg_cbm/dataset_description.json",
"path_regex": null,
"record_version": "1",
"scope": "file",
"severity": "HINT",
"within_asset_paths": null
},
{
"_truncated": true,
"omitted_count": 429
}
]
432 changes: 432 additions & 0 deletions docs/examples/validation/bids_invalid_eeg_cbm.jsonl

Large diffs are not rendered by default.

20 changes: 20 additions & 0 deletions docs/examples/validation/bids_invalid_eeg_cbm.txt
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[BIDS.README_FILE_MISSING] invalid_eeg_cbm/dataset_description.json — The recommended file /README is missing.
See Section 03 (Modality agnostic files) of the BIDS specification.
[BIDS.JSON_KEY_RECOMMENDED] invalid_eeg_cbm/dataset_description.json — A JSON file is missing a key listed as recommended.
subCode: HEDVersion
issueMessage: Field description: If HED tags are used:
The version of the HED schema used to validate HED tags for study.
May include a single schema or a base schema and one or more library schema.
[BIDS.JSON_KEY_RECOMMENDED] invalid_eeg_cbm/dataset_description.json — A JSON file is missing a key listed as recommended.
subCode: GeneratedBy
issueMessage: Field description: Used to specify provenance of the dataset.
[BIDS.JSON_KEY_RECOMMENDED] invalid_eeg_cbm/dataset_description.json — A JSON file is missing a key listed as recommended.
subCode: SourceDatasets
issueMessage: Field description: Used to specify the locations and relevant attributes of all source datasets (BIDS or not).
Valid keys in each object include `"URL"`, `"DOI"` (see
[URI](SPEC_ROOT/common-principles.md#uniform-resource-indicator)), and
`"Version"` with
[string](https://www.w3schools.com/js/js_json_datatypes.asp)
values.
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm001/eeg/sub-cbm001_task-protmap_eeg.edf — Empty files not allowed.
... and 427 more issues
67 changes: 67 additions & 0 deletions docs/examples/validation/bids_invalid_eeg_cbm.yaml
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- asset_paths: null
dandiset_path: invalid_eeg_cbm
dataset_path: invalid_eeg_cbm
id: BIDS.README_FILE_MISSING
message: "The recommended file /README is missing.\nSee Section 03 (Modality agnostic
files) of the BIDS specification.\n"
metadata: null
origin:
standard: BIDS
standard_schema_version: 1.2.1
standard_version: null
type: VALIDATION
validator: bids-validator-deno
validator_version: 2.4.1
path:
invalid_eeg_cbm/dataset_description.json
path_regex: null
record_version: '1'
scope: file
severity: HINT
within_asset_paths: null
- asset_paths: null
dandiset_path: invalid_eeg_cbm
dataset_path: invalid_eeg_cbm
id: BIDS.JSON_KEY_RECOMMENDED
message: "A JSON file is missing a key listed as recommended.\nsubCode: HEDVersion\n\
issueMessage: Field description: If HED tags are used:\nThe version of the HED
schema used to validate HED tags for study.\nMay include a single schema or a
base schema and one or more library schema.\n"
metadata: null
origin:
standard: BIDS
standard_schema_version: 1.2.1
standard_version: null
type: VALIDATION
validator: bids-validator-deno
validator_version: 2.4.1
path:
invalid_eeg_cbm/dataset_description.json
path_regex: null
record_version: '1'
scope: file
severity: HINT
within_asset_paths: null
- asset_paths: null
dandiset_path: invalid_eeg_cbm
dataset_path: invalid_eeg_cbm
id: BIDS.JSON_KEY_RECOMMENDED
message: "A JSON file is missing a key listed as recommended.\nsubCode: GeneratedBy\n\
issueMessage: Field description: Used to specify provenance of the dataset.\n"
metadata: null
origin:
standard: BIDS
standard_schema_version: 1.2.1
standard_version: null
type: VALIDATION
validator: bids-validator-deno
validator_version: 2.4.1
path:
invalid_eeg_cbm/dataset_description.json
path_regex: null
record_version: '1'
scope: file
severity: HINT
within_asset_paths: null
- _truncated: true
omitted_count: 429
22 changes: 22 additions & 0 deletions docs/examples/validation/bids_invalid_errors_only.txt
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[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm001/eeg/sub-cbm001_task-protmap_eeg.edf — Empty files not allowed.
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm002/eeg/sub-cbm002_task-protmap_eeg.edf — Empty files not allowed.
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm003/eeg/sub-cbm003_task-protmap_eeg.edf — Empty files not allowed.
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm004/eeg/sub-cbm004_task-protmap_eeg.edf — Empty files not allowed.
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm005/eeg/sub-cbm005_task-protmap_eeg.edf — Empty files not allowed.
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm006/eeg/sub-cbm006_task-protmap_eeg.edf — Empty files not allowed.
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm007/eeg/sub-cbm007_task-protmap_eeg.edf — Empty files not allowed.
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm008/eeg/sub-cbm008_task-protmap_eeg.edf — Empty files not allowed.
[BIDS.NIFTI_HEADER_UNREADABLE] invalid_eeg_cbm/sub-cbm011/sub-cbm011_scans.nii — We were unable to parse header data from this NIfTI file. Please ensure it is not corrupted or mislabeled.
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm009/eeg/sub-cbm009_task-protmap_eeg.edf — Empty files not allowed.
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm010/eeg/sub-cbm010_task-protmap_eeg.edf — Empty files not allowed.
[BIDS.EXTENSION_MISMATCH] invalid_eeg_cbm/sub-cbm011/sub-cbm011_scans.nii — Extension used by file does not match allowed extensions for its suffix
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm011/eeg/sub-cbm011_task-protmap_eeg.edf — Empty files not allowed.
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm012/eeg/sub-cbm012_task-protmap_eeg.edf — Empty files not allowed.
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm013/eeg/sub-cbm013_task-protmap_eeg.edf — Empty files not allowed.
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm014/eeg/sub-cbm014_task-protmap_eeg.edf — Empty files not allowed.
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm015/eeg/sub-cbm015_task-protmap_eeg.edf — Empty files not allowed.
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm016/eeg/sub-cbm016_task-protmap_eeg.edf — Empty files not allowed.
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm017/eeg/sub-cbm017_task-protmap_eeg.edf — Empty files not allowed.
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm018/eeg/sub-cbm018_task-protmap_eeg.edf — Empty files not allowed.
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm019/eeg/sub-cbm019_task-protmap_eeg.edf — Empty files not allowed.
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm020/eeg/sub-cbm020_task-protmap_eeg.edf — Empty files not allowed.
17 changes: 17 additions & 0 deletions docs/examples/validation/bids_invalid_grouped_severity.txt
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=== HINT (410 issues) ===
[BIDS.README_FILE_MISSING] invalid_eeg_cbm/dataset_description.json — The recommended file /README is missing.
See Section 03 (Modality agnostic files) of the BIDS specification.
[BIDS.JSON_KEY_RECOMMENDED] invalid_eeg_cbm/dataset_description.json — A JSON file is missing a key listed as recommended.
subCode: HEDVersion
issueMessage: Field description: If HED tags are used:
The version of the HED schema used to validate HED tags for study.
May include a single schema or a base schema and one or more library schema.
[BIDS.JSON_KEY_RECOMMENDED] invalid_eeg_cbm/dataset_description.json — A JSON file is missing a key listed as recommended.
subCode: GeneratedBy
issueMessage: Field description: Used to specify provenance of the dataset.
... and 407 more issues
=== ERROR (22 issues) ===
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm001/eeg/sub-cbm001_task-protmap_eeg.edf — Empty files not allowed.
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm002/eeg/sub-cbm002_task-protmap_eeg.edf — Empty files not allowed.
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm003/eeg/sub-cbm003_task-protmap_eeg.edf — Empty files not allowed.
... and 19 more issues
43 changes: 43 additions & 0 deletions docs/examples/validation/bids_invalid_grouped_severity_id.txt
Original file line number Diff line number Diff line change
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=== HINT (410 issues) ===
=== BIDS.README_FILE_MISSING (1 issue) ===
[BIDS.README_FILE_MISSING] invalid_eeg_cbm/dataset_description.json — The recommended file /README is missing.
See Section 03 (Modality agnostic files) of the BIDS specification.
=== BIDS.JSON_KEY_RECOMMENDED (3 issues) ===
[BIDS.JSON_KEY_RECOMMENDED] invalid_eeg_cbm/dataset_description.json — A JSON file is missing a key listed as recommended.
subCode: HEDVersion
issueMessage: Field description: If HED tags are used:
The version of the HED schema used to validate HED tags for study.
May include a single schema or a base schema and one or more library schema.
[BIDS.JSON_KEY_RECOMMENDED] invalid_eeg_cbm/dataset_description.json — A JSON file is missing a key listed as recommended.
subCode: GeneratedBy
issueMessage: Field description: Used to specify provenance of the dataset.
... and 1 more issue
=== BIDS.SIDECAR_KEY_RECOMMENDED (360 issues) ===
[BIDS.SIDECAR_KEY_RECOMMENDED] invalid_eeg_cbm/sub-cbm001/eeg/sub-cbm001_task-protmap_eeg.edf — A data file's JSON sidecar is missing a key listed as recommended.
subCode: Manufacturer
issueMessage: Field description: Manufacturer of the equipment that produced the measurements.
[BIDS.SIDECAR_KEY_RECOMMENDED] invalid_eeg_cbm/sub-cbm001/eeg/sub-cbm001_task-protmap_eeg.edf — A data file's JSON sidecar is missing a key listed as recommended.
subCode: ManufacturersModelName
issueMessage: Field description: Manufacturer's model name of the equipment that produced the measurements.
... and 358 more issues
=== BIDS.TSV_ADDITIONAL_COLUMNS_UNDEFINED (40 issues) ===
[BIDS.TSV_ADDITIONAL_COLUMNS_UNDEFINED] invalid_eeg_cbm/sub-cbm001/eeg/sub-cbm001_task-protmap_events.tsv — A TSV file has extra columns which are not defined in its associated JSON sidecar
subCode: value
[BIDS.TSV_ADDITIONAL_COLUMNS_UNDEFINED] invalid_eeg_cbm/sub-cbm001/eeg/sub-cbm001_task-protmap_events.tsv — A TSV file has extra columns which are not defined in its associated JSON sidecar
subCode: sample
... and 38 more issues
=== BIDS.EEG_CHANNEL_COUNT_MISMATCH (6 issues) ===
[BIDS.EEG_CHANNEL_COUNT_MISMATCH] invalid_eeg_cbm/sub-cbm015/eeg/sub-cbm015_task-protmap_eeg.edf — The EEGChannelCount metadata does not match the number of channels
with type EEG in the associated channels.tsv file.
[BIDS.EEG_CHANNEL_COUNT_MISMATCH] invalid_eeg_cbm/sub-cbm016/eeg/sub-cbm016_task-protmap_eeg.edf — The EEGChannelCount metadata does not match the number of channels
with type EEG in the associated channels.tsv file.
... and 4 more issues
=== ERROR (22 issues) ===
=== BIDS.EMPTY_FILE (20 issues) ===
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm001/eeg/sub-cbm001_task-protmap_eeg.edf — Empty files not allowed.
[BIDS.EMPTY_FILE] invalid_eeg_cbm/sub-cbm002/eeg/sub-cbm002_task-protmap_eeg.edf — Empty files not allowed.
... and 18 more issues
=== BIDS.NIFTI_HEADER_UNREADABLE (1 issue) ===
[BIDS.NIFTI_HEADER_UNREADABLE] invalid_eeg_cbm/sub-cbm011/sub-cbm011_scans.nii — We were unable to parse header data from this NIfTI file. Please ensure it is not corrupted or mislabeled.
=== BIDS.EXTENSION_MISMATCH (1 issue) ===
[BIDS.EXTENSION_MISMATCH] invalid_eeg_cbm/sub-cbm011/sub-cbm011_scans.nii — Extension used by file does not match allowed extensions for its suffix
4 changes: 4 additions & 0 deletions docs/examples/validation/nwb_000027.jsonl
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@@ -0,0 +1,4 @@
{"asset_paths": null, "dandiset_path": null, "dataset_path": null, "id": "DANDI.NO_DANDISET_FOUND", "message": "Path is not inside a Dandiset", "metadata": null, "origin": {"standard": "DANDI-LAYOUT", "standard_schema_version": null, "standard_version": null, "type": "VALIDATION", "validator": "dandi", "validator_version": "0+unknown"}, "path": "000027", "path_regex": null, "record_version": "1", "scope": "dandiset", "severity": "ERROR", "within_asset_paths": null}
{"asset_paths": null, "dandiset_path": null, "dataset_path": null, "id": "pynwb.GENERIC", "message": "error: nwb_version '2.0b' is not a proper semantic version. See http://semver.org", "metadata": null, "origin": {"standard": null, "standard_schema_version": null, "standard_version": null, "type": "VALIDATION", "validator": "dandi", "validator_version": "0+unknown"}, "path": "sub-RAT123/sub-RAT123.nwb", "path_regex": null, "record_version": "1", "scope": "file", "severity": "ERROR", "within_asset_paths": null}
{"asset_paths": null, "dandiset_path": "sub-RAT123", "dataset_path": "' separator, e.g., 'P1D/P3D' for an age range somewhere from 1 to 3 days. If you cannot specify the upper bound of the range, you may leave the right side blank, e.g., 'P90Y/' means 90 years old or older.", "metadata": null, "origin": {"standard": null, "standard_schema_version": null, "standard_version": null, "type": "VALIDATION", "validator": "nwbinspector", "validator_version": ""}, "path": "sub-RAT123/sub-RAT123.nwb", "path_regex": null, "record_version": "1", "scope": "file", "severity": "ERROR", "within_asset_paths": {"sub-RAT123/sub-RAT123.nwb": "/general/subject"}}
{"asset_paths": null, "dandiset_path": "sub-RAT123", "dataset_path": "tmp/tmp.YcS3RheKVl/ds000027/sub-RAT123/sub-RAT123.nwb", "path_regex": null, "record_version": "1", "scope": "file", "severity": "ERROR", "within_asset_paths": {"sub-RAT123/sub-RAT123.nwb": "/general/subject"}}
4 changes: 4 additions & 0 deletions docs/examples/validation/nwb_000027.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
[DANDI.NO_DANDISET_FOUND] 000027 — Path is not inside a Dandiset
[pynwb.GENERIC] sub-RAT123/sub-RAT123.nwb — error: nwb_version '2.0b' is not a proper semantic version. See http://semver.org
[NWBI.check_subject_age] sub-RAT123/sub-RAT123.nwb — Subject age, '12 mo', does not follow ISO 8601 duration format, e.g. 'P2Y' for 2 years or 'P23W' for 23 weeks. You may also specify a range using a '/' separator, e.g., 'P1D/P3D' for an age range somewhere from 1 to 3 days. If you cannot specify the upper bound of the range, you may leave the right side blank, e.g., 'P90Y/' means 90 years old or older.
[NWBI.check_subject_weight] sub-RAT123/sub-RAT123.nwb — Subject weight '2 lbs' does not follow the expected form '[numeric] [unit]'. For example, '2.3 kg'. Without a unit, the weight is ambiguous. Valid units are: 'kg', 'g', 'mg', 'ug', 'μg', 'ng', 'pg'.
5 changes: 5 additions & 0 deletions docs/examples/validation/nwb_000027_grouped.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
=== ERROR (4 issues) ===
[DANDI.NO_DANDISET_FOUND] 000027 — Path is not inside a Dandiset
[pynwb.GENERIC] sub-RAT123/sub-RAT123.nwb — error: nwb_version '2.0b' is not a proper semantic version. See http://semver.org
[NWBI.check_subject_age] sub-RAT123/sub-RAT123.nwb — Subject age, '12 mo', does not follow ISO 8601 duration format, e.g. 'P2Y' for 2 years or 'P23W' for 23 weeks. You may also specify a range using a '/' separator, e.g., 'P1D/P3D' for an age range somewhere from 1 to 3 days. If you cannot specify the upper bound of the range, you may leave the right side blank, e.g., 'P90Y/' means 90 years old or older.
[NWBI.check_subject_weight] sub-RAT123/sub-RAT123.nwb — Subject weight '2 lbs' does not follow the expected form '[numeric] [unit]'. For example, '2.3 kg'. Without a unit, the weight is ambiguous. Valid units are: 'kg', 'g', 'mg', 'ug', 'μg', 'ng', 'pg'.
14 changes: 14 additions & 0 deletions docs/examples/validation/nwb_000027_summary.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
[DANDI.NO_DANDISET_FOUND] 000027 — Path is not inside a Dandiset
[pynwb.GENERIC] sub-RAT123/sub-RAT123.nwb — error: nwb_version '2.0b' is not a proper semantic version. See http://semver.org
[NWBI.check_subject_age] sub-RAT123/sub-RAT123.nwb — Subject age, '12 mo', does not follow ISO 8601 duration format, e.g. 'P2Y' for 2 years or 'P23W' for 23 weeks. You may also specify a range using a '/' separator, e.g., 'P1D/P3D' for an age range somewhere from 1 to 3 days. If you cannot specify the upper bound of the range, you may leave the right side blank, e.g., 'P90Y/' means 90 years old or older.
[NWBI.check_subject_weight] sub-RAT123/sub-RAT123.nwb — Subject weight '2 lbs' does not follow the expected form '[numeric] [unit]'. For example, '2.3 kg'. Without a unit, the weight is ambiguous. Valid units are: 'kg', 'g', 'mg', 'ug', 'μg', 'ng', 'pg'.
--- Validation Summary ---
Total issues: 4
By severity:
ERROR: 4
By validator:
dandi: 2
nwbinspector: 2
By standard:
N/A: 3
DANDI-LAYOUT: 1
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