From 286172bfdc0d3a57538ff9bd6418c34940520b49 Mon Sep 17 00:00:00 2001 From: Heinrich Lukas Weil Date: Mon, 28 Nov 2022 14:49:54 +0100 Subject: [PATCH 1/3] replace @id uri formats with uri-reference format --- source/_static/isajson/assay_schema.json | 4 ++-- source/_static/isajson/comment_schema.json | 4 ++-- source/_static/isajson/data_schema.json | 4 ++-- source/_static/isajson/factor_schema.json | 4 ++-- source/_static/isajson/factor_value_schema.json | 4 ++-- source/_static/isajson/investigation_schema.json | 4 ++-- source/_static/isajson/material_attribute_schema.json | 4 ++-- source/_static/isajson/material_attribute_value_schema.json | 4 ++-- source/_static/isajson/material_schema.json | 4 ++-- source/_static/isajson/ontology_annotation_schema.json | 4 ++-- source/_static/isajson/ontology_source_reference_schema.json | 2 +- source/_static/isajson/person_schema.json | 4 ++-- source/_static/isajson/process_parameter_value_schema.json | 2 +- source/_static/isajson/process_schema.json | 4 ++-- source/_static/isajson/protocol_parameter_schema.json | 4 ++-- source/_static/isajson/protocol_schema.json | 4 ++-- source/_static/isajson/publication_schema.json | 2 +- source/_static/isajson/sample_schema.json | 4 ++-- source/_static/isajson/source_schema.json | 4 ++-- source/_static/isajson/study_schema.json | 4 ++-- 20 files changed, 37 insertions(+), 37 deletions(-) diff --git a/source/_static/isajson/assay_schema.json b/source/_static/isajson/assay_schema.json index f716da1..4735912 100644 --- a/source/_static/isajson/assay_schema.json +++ b/source/_static/isajson/assay_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", + "$schema": "http://json-schema.org/draft-06/schema#", "title": "Assay JSON Schema", "name": "Assay JSON Schema", "description": "JSON Schema describing an Assay", @@ -9,7 +9,7 @@ }, "type": "object", "properties": { - "@id": { "type": "string", "format": "uri" }, + "@id": { "type": "string", "format": "uri-reference" }, "comments" : { "type": "array", "items": { diff --git a/source/_static/isajson/comment_schema.json b/source/_static/isajson/comment_schema.json index 1ff9c12..08cbda1 100644 --- a/source/_static/isajson/comment_schema.json +++ b/source/_static/isajson/comment_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-04/schema", + "$schema": "http://json-schema.org/draft-06/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" }, diff --git a/source/_static/isajson/data_schema.json b/source/_static/isajson/data_schema.json index dad2085..bf5dbc7 100644 --- a/source/_static/isajson/data_schema.json +++ b/source/_static/isajson/data_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-04/schema", + "$schema": "http://json-schema.org/draft-06/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" }, diff --git a/source/_static/isajson/factor_schema.json b/source/_static/isajson/factor_schema.json index cb3f960..cec3b9f 100644 --- a/source/_static/isajson/factor_schema.json +++ b/source/_static/isajson/factor_schema.json @@ -1,11 +1,11 @@ { - "$schema": "http://json-schema.org/draft-04/schema", + "$schema": "http://json-schema.org/draft-06/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" }, diff --git a/source/_static/isajson/factor_value_schema.json b/source/_static/isajson/factor_value_schema.json index 5a42725..7549444 100644 --- a/source/_static/isajson/factor_value_schema.json +++ b/source/_static/isajson/factor_value_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-04/schema", + "$schema": "http://json-schema.org/draft-06/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" : { "$ref": "factor_schema.json#" }, diff --git a/source/_static/isajson/investigation_schema.json b/source/_static/isajson/investigation_schema.json index d039db2..14100d6 100644 --- a/source/_static/isajson/investigation_schema.json +++ b/source/_static/isajson/investigation_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-04/schema", + "$schema": "http://json-schema.org/draft-06/schema", "title" : "ISA investigation schema", "description" : "JSON-schema representing an investigation in the ISA model", "type" : "object", "properties" : { - "@id": { "type": "string", "format": "uri" }, + "@id": { "type": "string", "format": "uri-reference" }, "filename": { "type" : "string"}, "identifier" : { "type" : "string" }, "title" : { "type" : "string"}, diff --git a/source/_static/isajson/material_attribute_schema.json b/source/_static/isajson/material_attribute_schema.json index 4b6d0f9..bf24771 100644 --- a/source/_static/isajson/material_attribute_schema.json +++ b/source/_static/isajson/material_attribute_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-04/schema", + "$schema": "http://json-schema.org/draft-06/schema", "title" : "ISA material attribute schema", "description" : "JSON-schema representing a characteristics category (what appears between the brackets in Charactersitics[]) in the ISA model", "type" : "object", "properties" : { - "@id": { "type": "string", "format": "uri" }, + "@id": { "type": "string", "format": "uri-reference" }, "characteristicType": { "$ref": "ontology_annotation_schema.json#" } diff --git a/source/_static/isajson/material_attribute_value_schema.json b/source/_static/isajson/material_attribute_value_schema.json index 479f6e6..0f64f45 100644 --- a/source/_static/isajson/material_attribute_value_schema.json +++ b/source/_static/isajson/material_attribute_value_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-04/schema", + "$schema": "http://json-schema.org/draft-06/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" : { "$ref": "material_attribute_schema.json#" }, diff --git a/source/_static/isajson/material_schema.json b/source/_static/isajson/material_schema.json index e84d19c..db1c9f0 100644 --- a/source/_static/isajson/material_schema.json +++ b/source/_static/isajson/material_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-04/schema", + "$schema": "http://json-schema.org/draft-06/schema", "title" : "ISA material node schema", "description" : "JSON-schema representing a material node in the ISA model, which is not a source or a sample (as they have specific schemas) - this will correspond to 'Extract Name', 'Labeled Extract Name'", "type" : "object", "properties" : { - "@id": { "type": "string", "format": "uri" }, + "@id": { "type": "string", "format": "uri-reference" }, "name" : { "type" : "string" }, "type": { "type": "string", diff --git a/source/_static/isajson/ontology_annotation_schema.json b/source/_static/isajson/ontology_annotation_schema.json index 083e7d2..a183338 100644 --- a/source/_static/isajson/ontology_annotation_schema.json +++ b/source/_static/isajson/ontology_annotation_schema.json @@ -1,11 +1,11 @@ { - "$schema": "http://json-schema.org/draft-04/schema", + "$schema": "http://json-schema.org/draft-06/schema", "title" : "ISA ontology reference schema", "name" : "ISA ontology reference schema", "description" : "JSON-schema representing an ontology reference or annotation in the ISA model (for fields that are required to be ontology annotations)", "type" : "object", "properties" : { - "@id": { "type": "string", "format": "uri" }, + "@id": { "type": "string", "format": "uri-reference" }, "annotationValue": { "anyOf": [ { "type": "string" }, diff --git a/source/_static/isajson/ontology_source_reference_schema.json b/source/_static/isajson/ontology_source_reference_schema.json index 8dff468..4828d93 100644 --- a/source/_static/isajson/ontology_source_reference_schema.json +++ b/source/_static/isajson/ontology_source_reference_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-04/schema", + "$schema": "http://json-schema.org/draft-06/schema", "title" : "ISA ontology source reference schema", "name" : "ISA ontology source reference schema", "description" : "JSON-schema representing an ontology reference in the ISA model", diff --git a/source/_static/isajson/person_schema.json b/source/_static/isajson/person_schema.json index 389860e..2a65554 100644 --- a/source/_static/isajson/person_schema.json +++ b/source/_static/isajson/person_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-04/schema", + "$schema": "http://json-schema.org/draft-06/schema", "title" : "ISA person schema", "description" : "JSON-schema representing a person in the ISA model", "type" : "object", "properties" : { - "@id": { "type": "string", "format": "uri" }, + "@id": { "type": "string", "format": "uri-reference" }, "lastName" : { "type" : "string"}, "firstName" : { "type" : "string"}, "midInitials" : { "type" : "string" }, diff --git a/source/_static/isajson/process_parameter_value_schema.json b/source/_static/isajson/process_parameter_value_schema.json index 17375a8..51037d0 100644 --- a/source/_static/isajson/process_parameter_value_schema.json +++ b/source/_static/isajson/process_parameter_value_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-04/schema", + "$schema": "http://json-schema.org/draft-06/schema", "title" : "ISA process parameter value schema", "description" : "JSON-schema representing a Parameter Value (associated with a Protocol REF) in the ISA model", "type" : "object", diff --git a/source/_static/isajson/process_schema.json b/source/_static/isajson/process_schema.json index 35b6889..b498a01 100644 --- a/source/_static/isajson/process_schema.json +++ b/source/_static/isajson/process_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-04/schema", + "$schema": "http://json-schema.org/draft-06/schema", "title": "ISA process or protocol application schema, corresponds to 'Protocol REF' columns in the study and assay files", "description": "JSON-schema representing a protocol application in the ISA model", "type": "object", "properties": { - "@id": { "type": "string", "format": "uri" }, + "@id": { "type": "string", "format": "uri-reference" }, "name": { "type": "string" }, diff --git a/source/_static/isajson/protocol_parameter_schema.json b/source/_static/isajson/protocol_parameter_schema.json index bfbbe2d..c86cb96 100644 --- a/source/_static/isajson/protocol_parameter_schema.json +++ b/source/_static/isajson/protocol_parameter_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-04/schema", + "$schema": "http://json-schema.org/draft-06/schema", "title" : "ISA protocol parameter schema", "description" : "JSON-schema representing a parameter for a protocol (category declared in the investigation file) in the ISA model", "type" : "object", "properties" : { - "@id": { "type": "string", "format": "uri" }, + "@id": { "type": "string", "format": "uri-reference" }, "parameterName": { "$ref": "ontology_annotation_schema.json#" } diff --git a/source/_static/isajson/protocol_schema.json b/source/_static/isajson/protocol_schema.json index 8ada017..6ae7ab7 100644 --- a/source/_static/isajson/protocol_schema.json +++ b/source/_static/isajson/protocol_schema.json @@ -1,11 +1,11 @@ { - "$schema": "http://json-schema.org/draft-04/schema", + "$schema": "http://json-schema.org/draft-06/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": { diff --git a/source/_static/isajson/publication_schema.json b/source/_static/isajson/publication_schema.json index 1718331..0ecfc7c 100644 --- a/source/_static/isajson/publication_schema.json +++ b/source/_static/isajson/publication_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-04/schema", + "$schema": "http://json-schema.org/draft-06/schema", "title" : "ISA investigation schema", "name" : "ISA investigation schema", "description" : "JSON-schema representing an investigation in the ISA model", diff --git a/source/_static/isajson/sample_schema.json b/source/_static/isajson/sample_schema.json index afcffd8..57e9a62 100644 --- a/source/_static/isajson/sample_schema.json +++ b/source/_static/isajson/sample_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-04/schema", + "$schema": "http://json-schema.org/draft-06/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", diff --git a/source/_static/isajson/source_schema.json b/source/_static/isajson/source_schema.json index 5e3a60b..654b43c 100644 --- a/source/_static/isajson/source_schema.json +++ b/source/_static/isajson/source_schema.json @@ -1,9 +1,9 @@ { - "$schema": "http://json-schema.org/draft-04/schema", + "$schema": "http://json-schema.org/draft-06/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", diff --git a/source/_static/isajson/study_schema.json b/source/_static/isajson/study_schema.json index 1ce3b01..82494b4 100644 --- a/source/_static/isajson/study_schema.json +++ b/source/_static/isajson/study_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", + "$schema": "http://json-schema.org/draft-06/schema#", "title": "Study JSON Schema", "description": "JSON Schema describing an Study", "@context": { @@ -8,7 +8,7 @@ }, "type": "object", "properties": { - "@id": { "type": "string", "format": "uri" }, + "@id": { "type": "string", "format": "uri-reference" }, "filename" : { "type" : "string"}, "identifier" : { "type" : "string" }, "title" : { "type" : "string"}, From 23d4226f5827ee432b9ab7a7d83bc19ecdfbb951 Mon Sep 17 00:00:00 2001 From: Heinrich Lukas Weil Date: Mon, 28 Nov 2022 15:47:35 +0100 Subject: [PATCH 2/3] make date fields accept date format in addition to date-time format --- source/_static/isajson/assay_schema.json | 2 +- source/_static/isajson/comment_schema.json | 2 +- source/_static/isajson/data_schema.json | 2 +- source/_static/isajson/factor_schema.json | 2 +- .../_static/isajson/factor_value_schema.json | 2 +- .../_static/isajson/investigation_schema.json | 28 +++++++++++++++++-- .../isajson/material_attribute_schema.json | 2 +- .../material_attribute_value_schema.json | 2 +- source/_static/isajson/material_schema.json | 2 +- .../isajson/ontology_annotation_schema.json | 2 +- .../ontology_source_reference_schema.json | 2 +- source/_static/isajson/person_schema.json | 2 +- .../process_parameter_value_schema.json | 2 +- source/_static/isajson/process_schema.json | 12 ++++++-- .../isajson/protocol_parameter_schema.json | 2 +- source/_static/isajson/protocol_schema.json | 2 +- .../_static/isajson/publication_schema.json | 2 +- source/_static/isajson/sample_schema.json | 2 +- source/_static/isajson/source_schema.json | 2 +- source/_static/isajson/study_schema.json | 28 +++++++++++++++++-- 20 files changed, 77 insertions(+), 25 deletions(-) diff --git a/source/_static/isajson/assay_schema.json b/source/_static/isajson/assay_schema.json index 4735912..e224fe4 100644 --- a/source/_static/isajson/assay_schema.json +++ b/source/_static/isajson/assay_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-06/schema#", + "$schema": "http://json-schema.org/draft-07/schema#", "title": "Assay JSON Schema", "name": "Assay JSON Schema", "description": "JSON Schema describing an Assay", diff --git a/source/_static/isajson/comment_schema.json b/source/_static/isajson/comment_schema.json index 08cbda1..73be862 100644 --- a/source/_static/isajson/comment_schema.json +++ b/source/_static/isajson/comment_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-06/schema", + "$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", diff --git a/source/_static/isajson/data_schema.json b/source/_static/isajson/data_schema.json index bf5dbc7..9ea4bfa 100644 --- a/source/_static/isajson/data_schema.json +++ b/source/_static/isajson/data_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-06/schema", + "$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", diff --git a/source/_static/isajson/factor_schema.json b/source/_static/isajson/factor_schema.json index cec3b9f..50fe895 100644 --- a/source/_static/isajson/factor_schema.json +++ b/source/_static/isajson/factor_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-06/schema", + "$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", diff --git a/source/_static/isajson/factor_value_schema.json b/source/_static/isajson/factor_value_schema.json index 7549444..a16342a 100644 --- a/source/_static/isajson/factor_value_schema.json +++ b/source/_static/isajson/factor_value_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-06/schema", + "$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", diff --git a/source/_static/isajson/investigation_schema.json b/source/_static/isajson/investigation_schema.json index 14100d6..91dcf2c 100644 --- a/source/_static/isajson/investigation_schema.json +++ b/source/_static/isajson/investigation_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-06/schema", + "$schema": "http://json-schema.org/draft-07/schema", "title" : "ISA investigation schema", "description" : "JSON-schema representing an investigation in the ISA model", "type" : "object", @@ -9,8 +9,30 @@ "identifier" : { "type" : "string" }, "title" : { "type" : "string"}, "description" : { "type" : "string"}, - "submissionDate" : { "type" : "string", "format" : "date-time"}, - "publicReleaseDate" : { "type" : "string", "format" : "date-time"}, + "submissionDate" : { + "type": "string", + "anyOf": [ + { + "format": "date-time" + }, + { + "format": "date" + } + ] + + }, + "publicReleaseDate" :{ + "type": "string", + "anyOf": [ + { + "format": "date-time" + }, + { + "format": "date" + } + ] + + }, "ontologySourceReferences" : { "type" : "array", "items" : { diff --git a/source/_static/isajson/material_attribute_schema.json b/source/_static/isajson/material_attribute_schema.json index bf24771..1210aca 100644 --- a/source/_static/isajson/material_attribute_schema.json +++ b/source/_static/isajson/material_attribute_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-06/schema", + "$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", diff --git a/source/_static/isajson/material_attribute_value_schema.json b/source/_static/isajson/material_attribute_value_schema.json index 0f64f45..4733d34 100644 --- a/source/_static/isajson/material_attribute_value_schema.json +++ b/source/_static/isajson/material_attribute_value_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-06/schema", + "$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", diff --git a/source/_static/isajson/material_schema.json b/source/_static/isajson/material_schema.json index db1c9f0..7608220 100644 --- a/source/_static/isajson/material_schema.json +++ b/source/_static/isajson/material_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-06/schema", + "$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", diff --git a/source/_static/isajson/ontology_annotation_schema.json b/source/_static/isajson/ontology_annotation_schema.json index a183338..b915147 100644 --- a/source/_static/isajson/ontology_annotation_schema.json +++ b/source/_static/isajson/ontology_annotation_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-06/schema", + "$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)", diff --git a/source/_static/isajson/ontology_source_reference_schema.json b/source/_static/isajson/ontology_source_reference_schema.json index 4828d93..ba4e517 100644 --- a/source/_static/isajson/ontology_source_reference_schema.json +++ b/source/_static/isajson/ontology_source_reference_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-06/schema", + "$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", diff --git a/source/_static/isajson/person_schema.json b/source/_static/isajson/person_schema.json index 2a65554..045ef1d 100644 --- a/source/_static/isajson/person_schema.json +++ b/source/_static/isajson/person_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-06/schema", + "$schema": "http://json-schema.org/draft-07/schema", "title" : "ISA person schema", "description" : "JSON-schema representing a person in the ISA model", "type" : "object", diff --git a/source/_static/isajson/process_parameter_value_schema.json b/source/_static/isajson/process_parameter_value_schema.json index 51037d0..1096e58 100644 --- a/source/_static/isajson/process_parameter_value_schema.json +++ b/source/_static/isajson/process_parameter_value_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-06/schema", + "$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", diff --git a/source/_static/isajson/process_schema.json b/source/_static/isajson/process_schema.json index b498a01..2ce9836 100644 --- a/source/_static/isajson/process_schema.json +++ b/source/_static/isajson/process_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-06/schema", + "$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", @@ -22,7 +22,15 @@ }, "date": { "type": "string", - "format": "date-time" + "anyOf": [ + { + "format": "date-time" + }, + { + "format": "date" + } + ] + }, "previousProcess" : { "$ref" : "process_schema.json#" diff --git a/source/_static/isajson/protocol_parameter_schema.json b/source/_static/isajson/protocol_parameter_schema.json index c86cb96..6e8d5c5 100644 --- a/source/_static/isajson/protocol_parameter_schema.json +++ b/source/_static/isajson/protocol_parameter_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-06/schema", + "$schema": "http://json-schema.org/draft-07/schema", "title" : "ISA protocol parameter schema", "description" : "JSON-schema representing a parameter for a protocol (category declared in the investigation file) in the ISA model", "type" : "object", diff --git a/source/_static/isajson/protocol_schema.json b/source/_static/isajson/protocol_schema.json index 6ae7ab7..7d934ee 100644 --- a/source/_static/isajson/protocol_schema.json +++ b/source/_static/isajson/protocol_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-06/schema", + "$schema": "http://json-schema.org/draft-08/schema", "title": "ISA protocol schema", "name": "ISA protocol schema", "description": "JSON-schema representing a protocol in the ISA model", diff --git a/source/_static/isajson/publication_schema.json b/source/_static/isajson/publication_schema.json index 0ecfc7c..a74be36 100644 --- a/source/_static/isajson/publication_schema.json +++ b/source/_static/isajson/publication_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-06/schema", + "$schema": "http://json-schema.org/draft-07/schema", "title" : "ISA investigation schema", "name" : "ISA investigation schema", "description" : "JSON-schema representing an investigation in the ISA model", diff --git a/source/_static/isajson/sample_schema.json b/source/_static/isajson/sample_schema.json index 57e9a62..cb30844 100644 --- a/source/_static/isajson/sample_schema.json +++ b/source/_static/isajson/sample_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-06/schema", + "$schema": "http://json-schema.org/draft-07/schema", "title" : "ISA sample schema", "description" : "JSON-schema representing a sample in the ISA model. A sample represents a major output resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.", "type": "object", diff --git a/source/_static/isajson/source_schema.json b/source/_static/isajson/source_schema.json index 654b43c..4f717c7 100644 --- a/source/_static/isajson/source_schema.json +++ b/source/_static/isajson/source_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-06/schema", + "$schema": "http://json-schema.org/draft-07/schema", "title" : "ISA source schema", "description" : "JSON-schema representing a source in the ISA model. Sources are considered as the starting biological material used in a study.", "properties" : { diff --git a/source/_static/isajson/study_schema.json b/source/_static/isajson/study_schema.json index 82494b4..f2625a1 100644 --- a/source/_static/isajson/study_schema.json +++ b/source/_static/isajson/study_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-06/schema#", + "$schema": "http://json-schema.org/draft-07/schema#", "title": "Study JSON Schema", "description": "JSON Schema describing an Study", "@context": { @@ -13,8 +13,30 @@ "identifier" : { "type" : "string" }, "title" : { "type" : "string"}, "description" : { "type" : "string"}, - "submissionDate" : { "type" : "string", "format" : "date-time"}, - "publicReleaseDate" : { "type" : "string", "format" : "date-time"}, + "submissionDate" : { + "type": "string", + "anyOf": [ + { + "format": "date-time" + }, + { + "format": "date" + } + ] + + }, + "publicReleaseDate" : { + "type": "string", + "anyOf": [ + { + "format": "date-time" + }, + { + "format": "date" + } + ] + + }, "publications" : { "type" : "array", "items" : { From bf02a22796f5e202c20c69d6b54a6f651980b91d Mon Sep 17 00:00:00 2001 From: Heinrich Lukas Weil Date: Tue, 20 Dec 2022 00:33:59 +0100 Subject: [PATCH 3/3] make date fields oneOf between date and date-time --- source/_static/isajson/investigation_schema.json | 4 ++-- source/_static/isajson/process_schema.json | 2 +- source/_static/isajson/study_schema.json | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/source/_static/isajson/investigation_schema.json b/source/_static/isajson/investigation_schema.json index 91dcf2c..8a4acae 100644 --- a/source/_static/isajson/investigation_schema.json +++ b/source/_static/isajson/investigation_schema.json @@ -11,7 +11,7 @@ "description" : { "type" : "string"}, "submissionDate" : { "type": "string", - "anyOf": [ + "oneOf": [ { "format": "date-time" }, @@ -23,7 +23,7 @@ }, "publicReleaseDate" :{ "type": "string", - "anyOf": [ + "oneOf": [ { "format": "date-time" }, diff --git a/source/_static/isajson/process_schema.json b/source/_static/isajson/process_schema.json index 2ce9836..bef05ca 100644 --- a/source/_static/isajson/process_schema.json +++ b/source/_static/isajson/process_schema.json @@ -22,7 +22,7 @@ }, "date": { "type": "string", - "anyOf": [ + "oneOf": [ { "format": "date-time" }, diff --git a/source/_static/isajson/study_schema.json b/source/_static/isajson/study_schema.json index f2625a1..eb4b0d4 100644 --- a/source/_static/isajson/study_schema.json +++ b/source/_static/isajson/study_schema.json @@ -15,7 +15,7 @@ "description" : { "type" : "string"}, "submissionDate" : { "type": "string", - "anyOf": [ + "oneOf": [ { "format": "date-time" }, @@ -27,7 +27,7 @@ }, "publicReleaseDate" : { "type": "string", - "anyOf": [ + "oneOf": [ { "format": "date-time" },