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ENH: Add column definitions for channels.json #1839

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merged 5 commits into from
Nov 7, 2023
Merged

ENH: Add column definitions for channels.json #1839

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4b1b882
RF: Convert column description into a common definition
effigies Nov 3, 2023
bfa80cd
ENH: Add column definitions for channels.json
effigies Nov 3, 2023
71b88c1
force channels json to validate against both column descriptions and …
rwblair Nov 3, 2023
0718b61
columndescription in channels is describing objects as values of prop…
rwblair Nov 3, 2023
5b338ca
fix missing pattern properties in reference_frame schema
rwblair Nov 3, 2023
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2 changes: 2 additions & 0 deletions bids-validator/validators/json/json.js
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Original file line number Diff line number Diff line change
Expand Up @@ -161,6 +161,8 @@ const selectSchema = (file) => {
schema = require('./schemas/beh.json')
} else if (file.name.endsWith('_motion.json')) {
schema = require('./schemas/motion.json')
} else if (file.name.endsWith('_channels.json')) {
schema = require('./schemas/channels.json')
}
}
return schema
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47 changes: 47 additions & 0 deletions bids-validator/validators/json/schemas/channels.json
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@@ -0,0 +1,47 @@
{
"$schema": "http://json-schema.org/draft-06/schema#",
"allOf": [
{
"type": "object",
"properties": {
"reference_frame": {
"title": "Reference Frame",
"type": "object",
"properties": {
"Levels": {
"type": "object",
"patternProperties": {
"^.+$": {
"type": "object",
"properties": {
"RotationOrder": {
"description": "The sequence in which the extrinsic rotations are applied around the three axes.",
"type": "string",
"enum": ["XYZ", "XZY", "YXZ", "YZX", "ZXY", "ZYX"]
},
"RotationRule": {
"description": "The direction of rotation around each axis.",
"type": "string",
"enum": ["left-hand", "right-hand"]
},
"SpatialAxes": {
"description": "The coordinate system in which the motion data are to be interpreted. A sequence of characters from the set `{'A', 'P', 'L', 'R', 'S', 'I', '_'}` indicating the direction of each axis. For example `\"ARS\"` indicates positive values in the X, Y, Z axes are respectively anterior, right, and superior of the origin, while `\"PLI\"` indicates positive values are posterior, left, and inferior of the origin. The `\"_\"` character may be used for unused axes.",
"type": "string",
"pattern": "^[APLRSI_]{3}$"
}
}
}
}
}
}
}
}
},
{
"type": "object",
"patternProperties": {
"^.+$": { "$ref": "common_definitions.json#/definitions/ColumnDescription" }
}
}
]
}
69 changes: 68 additions & 1 deletion bids-validator/validators/json/schemas/common_definitions.json
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Original file line number Diff line number Diff line change
Expand Up @@ -122,6 +122,73 @@
"SoftwareVersions": { "type": "string" },
"TaskDescription": { "type": "string" },
"TaskName": { "type": "string", "minLength": 1 },
"TriggerChannelCount": { "type": "integer", "minimum": 0 }
"TermURL": {
"title": "TermURL",
"description": "URL pointing to a formal definition in an ontology available on the web.",
"type": "string",
"format": "uri"
},
"TriggerChannelCount": { "type": "integer", "minimum": 0 },
"ColumnDescription": {
"type": "object",
"title": "Column",
"description": "Column of a corresponding tabular file.",
"properties": {
"LongName": {
"title": "LongName",
"description": " Long (unabbreviated) name of column.",
"type": "string"
},
"Description": {
"title": "Description",
"description": "Description of the column.",
"type": "string"
},
"Units": {
"title": "Units",
"description": "Measurement units.",
"type": "string"
},
"Levels": {
"type": "object",
"title": "Levels",
"description": "For categorical variables: a dictionary of possible values (keys) and their descriptions (values).",
"patternProperties": {
"^.+$": {
"anyOf": [
{ "type": "string" },
{
"type": "object",
"properties": {
"Description": { "type": "string" },
"TermURL": { "$ref": "#/definitions/TermURL" }
}
}
]
}
}
},
"TermURL": { "$ref": "#/definitions/TermURL" },
"HED": {
"anyOf": [
{
"type": "object",
"title": "HED",
"description": "For categorical variables: a dictionary of possible values (keys) and their HED strings (values).",
"patternProperties": {
"^.+$": {
"type": "string"
}
}
},
{
"type": "string",
"title": "HED",
"description": "For value variables: a string with a single '#' character where the cell value is to be interpolated."
}
]
}
}
}
}
}
72 changes: 1 addition & 71 deletions bids-validator/validators/json/schemas/data_dictionary.json
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Original file line number Diff line number Diff line change
@@ -1,76 +1,6 @@
{
"type": "object",
"patternProperties": {
"^.+$": {
"type": "object",
"title": "Column",
"description": "Column of a corresponding tabular file.",
"properties": {
"LongName": {
"title": "LongName",
"description": " Long (unabbreviated) name of column.",
"type": "string"
},
"Description": {
"title": "Description",
"description": "Description of the column.",
"type": "string"
},
"Units": {
"title": "Units",
"description": "Measurement units.",
"type": "string"
},
"Levels": {
"type": "object",
"title": "Levels",
"description": "For categorical variables: a dictionary of possible values (keys) and their descriptions (values).",
"patternProperties": {
"^.+$": {
"anyOf": [
{ "type": "string" },
{
"type": "object",
"properties": {
"Description": { "type": "string" },
"TermURL": {
"title": "TermURL",
"description": "URL pointing to a formal definition in an ontology available on the web.",
"type": "string",
"format": "uri"
}
}
}
]
}
}
},
"TermURL": {
"title": "TermURL",
"description": "URL pointing to a formal definition in an ontology available on the web.",
"type": "string",
"format": "uri"
},
"HED": {
"anyOf": [
{
"type": "object",
"title": "HED",
"description": "For categorical variables: a dictionary of possible values (keys) and their HED strings (values).",
"patternProperties": {
"^.+$": {
"type": "string"
}
}
},
{
"type": "string",
"title": "HED",
"description": "For value variables: a string with a single '#' character where the cell value is to be interpolated."
}
]
}
}
}
"^.+$": { "$ref": "common_definitions.json#/definitions/ColumnDescription" }
}
}
66 changes: 1 addition & 65 deletions bids-validator/validators/json/schemas/events.json
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Original file line number Diff line number Diff line change
@@ -1,71 +1,7 @@
{
"type": "object",
"patternProperties": {
"^.+$": {
"type": "object",
"title": "Column",
"description": "Column of a corresponding tabular file.",
"properties": {
"LongName": {
"title": "LongName",
"description": " Long (unabbreviated) name of column.",
"type": "string"
},
"Description": {
"title": "Description",
"description": "Description of the column.",
"type": "string"
},
"Units": {
"title": "Units",
"description": "Measurement units.",
"type": "string"
},
"Levels": {
"type": "object",
"title": "Levels",
"description": "For categorical variables: a dictionary of possible values (keys) and their descriptions (values).",
"patternProperties": {
"^.+$": {
"anyOf": [
{ "type": "string" },
{
"type": "object",
"properties": {
"Description": { "type": "string" },
"TermURL": {
"title": "TermURL",
"description": "URL pointing to a formal definition in an ontology available on the web.",
"type": "string",
"format": "uri"
}
}
}
]
}
}
},
"HED": {
"anyOf": [
{
"type": "object",
"title": "HED",
"description": "For categorical variables: a dictionary of possible values (keys) and their HED strings (values).",
"patternProperties": {
"^.+$": {
"type": "string"
}
}
},
{
"type": "string",
"title": "HED",
"description": "For value variables: a string with a single '#' character where the cell value is to be interpolated."
}
]
}
}
}
"^.+$": { "$ref": "common_definitions.json#/definitions/ColumnDescription" }
},
"properties": {
"StimulusPresentation": {
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