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Update isajson schema to draft 07 #11

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Update isajson schema to draft 07 #11

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286172b
replace @id uri formats with uri-reference format
HLWeil Nov 28, 2022
23d4226
make date fields accept date format in addition to date-time format
HLWeil Nov 28, 2022
bf02a22
make date fields oneOf between date and date-time
HLWeil Dec 19, 2022
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4 changes: 2 additions & 2 deletions source/_static/isajson/assay_schema.json
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
"$schema": "http://json-schema.org/draft-07/schema#",
"title": "Assay JSON Schema",
"name": "Assay JSON Schema",
"description": "JSON Schema describing an Assay",
Expand All @@ -9,7 +9,7 @@
},
"type": "object",
"properties": {
"@id": { "type": "string", "format": "uri" },
"@id": { "type": "string", "format": "uri-reference" },
"comments" : {
"type": "array",
"items": {
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4 changes: 2 additions & 2 deletions source/_static/isajson/comment_schema.json
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@@ -1,10 +1,10 @@
{
"$schema": "http://json-schema.org/draft-04/schema",
"$schema": "http://json-schema.org/draft-07/schema",
"title": "ISA comment schema - it corresponds to ISA Comment[] construct",
"description": "JSON-schema representing a comment in the ISA model",
"type": "object",
"properties": {
"@id": { "type": "string", "format": "uri" },
"@id": { "type": "string", "format": "uri-reference" },
"name": {
"type": "string"
},
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4 changes: 2 additions & 2 deletions source/_static/isajson/data_schema.json
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@@ -1,10 +1,10 @@
{
"$schema": "http://json-schema.org/draft-04/schema",
"$schema": "http://json-schema.org/draft-07/schema",
"title": "ISA data schema",
"description": "JSON-schema representing a data file in the ISA model",
"type": "object",
"properties": {
"@id": { "type": "string", "format": "uri" },
"@id": { "type": "string", "format": "uri-reference" },
"name": {
"type": "string"
},
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4 changes: 2 additions & 2 deletions source/_static/isajson/factor_schema.json
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@@ -1,11 +1,11 @@
{
"$schema": "http://json-schema.org/draft-04/schema",
"$schema": "http://json-schema.org/draft-07/schema",
"title": "ISA factor schema",
"name": "ISA factor schema",
"description": "JSON-schema representing a factor value in the ISA model",
"type": "object",
"properties": {
"@id": { "type": "string", "format": "uri" },
"@id": { "type": "string", "format": "uri-reference" },
"factorName": {
"type": "string"
},
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4 changes: 2 additions & 2 deletions source/_static/isajson/factor_value_schema.json
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@@ -1,10 +1,10 @@
{
"$schema": "http://json-schema.org/draft-04/schema",
"$schema": "http://json-schema.org/draft-07/schema",
"title": "ISA factor value schema",
"description": "JSON-schema representing a factor value in the ISA model",
"type": "object",
"properties": {
"@id": { "type": "string", "format": "uri" },
"@id": { "type": "string", "format": "uri-reference" },
"category" : {
"$ref": "factor_schema.json#"
},
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30 changes: 26 additions & 4 deletions source/_static/isajson/investigation_schema.json
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@@ -1,16 +1,38 @@
{
"$schema": "http://json-schema.org/draft-04/schema",
"$schema": "http://json-schema.org/draft-07/schema",
"title" : "ISA investigation schema",
"description" : "JSON-schema representing an investigation in the ISA model",
"type" : "object",
"properties" : {
"@id": { "type": "string", "format": "uri" },
"@id": { "type": "string", "format": "uri-reference" },
"filename": { "type" : "string"},
"identifier" : { "type" : "string" },
"title" : { "type" : "string"},
"description" : { "type" : "string"},
"submissionDate" : { "type" : "string", "format" : "date-time"},
"publicReleaseDate" : { "type" : "string", "format" : "date-time"},
"submissionDate" : {
"type": "string",
"oneOf": [
{
"format": "date-time"
},
{
"format": "date"
}
]

},
"publicReleaseDate" :{
"type": "string",
"oneOf": [
{
"format": "date-time"
},
{
"format": "date"
}
]

},
"ontologySourceReferences" : {
"type" : "array",
"items" : {
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4 changes: 2 additions & 2 deletions source/_static/isajson/material_attribute_schema.json
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@@ -1,10 +1,10 @@
{
"$schema": "http://json-schema.org/draft-04/schema",
"$schema": "http://json-schema.org/draft-07/schema",
"title" : "ISA material attribute schema",
"description" : "JSON-schema representing a characteristics category (what appears between the brackets in Charactersitics[]) in the ISA model",
"type" : "object",
"properties" : {
"@id": { "type": "string", "format": "uri" },
"@id": { "type": "string", "format": "uri-reference" },
"characteristicType": {
"$ref": "ontology_annotation_schema.json#"
}
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4 changes: 2 additions & 2 deletions source/_static/isajson/material_attribute_value_schema.json
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@@ -1,10 +1,10 @@
{
"$schema": "http://json-schema.org/draft-04/schema",
"$schema": "http://json-schema.org/draft-07/schema",
"title" : "ISA material attribute schema",
"description" : "JSON-schema representing a material attribute (or characteristic) value in the ISA model",
"type" : "object",
"properties" : {
"@id": { "type": "string", "format": "uri" },
"@id": { "type": "string", "format": "uri-reference" },
"category" : {
"$ref": "material_attribute_schema.json#"
},
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4 changes: 2 additions & 2 deletions source/_static/isajson/material_schema.json
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{
"$schema": "http://json-schema.org/draft-04/schema",
"$schema": "http://json-schema.org/draft-07/schema",
"title" : "ISA material node schema",
"description" : "JSON-schema representing a material node in the ISA model, which is not a source or a sample (as they have specific schemas) - this will correspond to 'Extract Name', 'Labeled Extract Name'",
"type" : "object",
"properties" : {
"@id": { "type": "string", "format": "uri" },
"@id": { "type": "string", "format": "uri-reference" },
"name" : { "type" : "string" },
"type": {
"type": "string",
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4 changes: 2 additions & 2 deletions source/_static/isajson/ontology_annotation_schema.json
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@@ -1,11 +1,11 @@
{
"$schema": "http://json-schema.org/draft-04/schema",
"$schema": "http://json-schema.org/draft-07/schema",
"title" : "ISA ontology reference schema",
"name" : "ISA ontology reference schema",
"description" : "JSON-schema representing an ontology reference or annotation in the ISA model (for fields that are required to be ontology annotations)",
"type" : "object",
"properties" : {
"@id": { "type": "string", "format": "uri" },
"@id": { "type": "string", "format": "uri-reference" },
"annotationValue": {
"anyOf": [
{ "type": "string" },
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2 changes: 1 addition & 1 deletion source/_static/isajson/ontology_source_reference_schema.json
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@@ -1,5 +1,5 @@
{
"$schema": "http://json-schema.org/draft-04/schema",
"$schema": "http://json-schema.org/draft-07/schema",
"title" : "ISA ontology source reference schema",
"name" : "ISA ontology source reference schema",
"description" : "JSON-schema representing an ontology reference in the ISA model",
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4 changes: 2 additions & 2 deletions source/_static/isajson/person_schema.json
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@@ -1,10 +1,10 @@
{
"$schema": "http://json-schema.org/draft-04/schema",
"$schema": "http://json-schema.org/draft-07/schema",
"title" : "ISA person schema",
"description" : "JSON-schema representing a person in the ISA model",
"type" : "object",
"properties" : {
"@id": { "type": "string", "format": "uri" },
"@id": { "type": "string", "format": "uri-reference" },
"lastName" : { "type" : "string"},
"firstName" : { "type" : "string"},
"midInitials" : { "type" : "string" },
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2 changes: 1 addition & 1 deletion source/_static/isajson/process_parameter_value_schema.json
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{
"$schema": "http://json-schema.org/draft-04/schema",
"$schema": "http://json-schema.org/draft-07/schema",
"title" : "ISA process parameter value schema",
"description" : "JSON-schema representing a Parameter Value (associated with a Protocol REF) in the ISA model",
"type" : "object",
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14 changes: 11 additions & 3 deletions source/_static/isajson/process_schema.json
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@@ -1,10 +1,10 @@
{
"$schema": "http://json-schema.org/draft-04/schema",
"$schema": "http://json-schema.org/draft-07/schema",
"title": "ISA process or protocol application schema, corresponds to 'Protocol REF' columns in the study and assay files",
"description": "JSON-schema representing a protocol application in the ISA model",
"type": "object",
"properties": {
"@id": { "type": "string", "format": "uri" },
"@id": { "type": "string", "format": "uri-reference" },
"name": {
"type": "string"
},
Expand All @@ -22,7 +22,15 @@
},
"date": {
"type": "string",
"format": "date-time"
"oneOf": [
{
"format": "date-time"
},
{
"format": "date"
}
]

},
"previousProcess" : {
"$ref" : "process_schema.json#"
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4 changes: 2 additions & 2 deletions source/_static/isajson/protocol_parameter_schema.json
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@@ -1,10 +1,10 @@
{
"$schema": "http://json-schema.org/draft-04/schema",
"$schema": "http://json-schema.org/draft-07/schema",
"title" : "ISA protocol parameter schema",
"description" : "JSON-schema representing a parameter for a protocol (category declared in the investigation file) in the ISA model",
"type" : "object",
"properties" : {
"@id": { "type": "string", "format": "uri" },
"@id": { "type": "string", "format": "uri-reference" },
"parameterName": {
"$ref": "ontology_annotation_schema.json#"
}
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4 changes: 2 additions & 2 deletions source/_static/isajson/protocol_schema.json
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@@ -1,11 +1,11 @@
{
"$schema": "http://json-schema.org/draft-04/schema",
"$schema": "http://json-schema.org/draft-08/schema",
"title": "ISA protocol schema",
"name": "ISA protocol schema",
"description": "JSON-schema representing a protocol in the ISA model",
"type": "object",
"properties": {
"@id": { "type": "string", "format": "uri" },
"@id": { "type": "string", "format": "uri-reference" },
"comments" : {
"type": "array",
"items": {
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2 changes: 1 addition & 1 deletion source/_static/isajson/publication_schema.json
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@@ -1,5 +1,5 @@
{
"$schema": "http://json-schema.org/draft-04/schema",
"$schema": "http://json-schema.org/draft-07/schema",
"title" : "ISA investigation schema",
"name" : "ISA investigation schema",
"description" : "JSON-schema representing an investigation in the ISA model",
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4 changes: 2 additions & 2 deletions source/_static/isajson/sample_schema.json
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@@ -1,10 +1,10 @@
{
"$schema": "http://json-schema.org/draft-04/schema",
"$schema": "http://json-schema.org/draft-07/schema",
"title" : "ISA sample schema",
"description" : "JSON-schema representing a sample in the ISA model. A sample represents a major output resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.",
"type": "object",
"properties" : {
"@id": { "type": "string", "format": "uri" },
"@id": { "type": "string", "format": "uri-reference" },
"name" : { "type" : "string" },
"characteristics" : {
"type" : "array",
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4 changes: 2 additions & 2 deletions source/_static/isajson/source_schema.json
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@@ -1,9 +1,9 @@
{
"$schema": "http://json-schema.org/draft-04/schema",
"$schema": "http://json-schema.org/draft-07/schema",
"title" : "ISA source schema",
"description" : "JSON-schema representing a source in the ISA model. Sources are considered as the starting biological material used in a study.",
"properties" : {
"@id": { "type": "string", "format": "uri" },
"@id": { "type": "string", "format": "uri-reference" },
"name" : { "type" : "string" },
"characteristics" : {
"type" : "array",
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30 changes: 26 additions & 4 deletions source/_static/isajson/study_schema.json
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@@ -1,5 +1,5 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
"$schema": "http://json-schema.org/draft-07/schema#",
"title": "Study JSON Schema",
"description": "JSON Schema describing an Study",
"@context": {
Expand All @@ -8,13 +8,35 @@
},
"type": "object",
"properties": {
"@id": { "type": "string", "format": "uri" },
"@id": { "type": "string", "format": "uri-reference" },
"filename" : { "type" : "string"},
"identifier" : { "type" : "string" },
"title" : { "type" : "string"},
"description" : { "type" : "string"},
"submissionDate" : { "type" : "string", "format" : "date-time"},
"publicReleaseDate" : { "type" : "string", "format" : "date-time"},
"submissionDate" : {
"type": "string",
"oneOf": [
{
"format": "date-time"
},
{
"format": "date"
}
]

},
"publicReleaseDate" : {
"type": "string",
"oneOf": [
{
"format": "date-time"
},
{
"format": "date"
}
]

},
"publications" : {
"type" : "array",
"items" : {
Expand Down