Commit 6724190c authored by Vilem Ded's avatar Vilem Ded
Browse files

Merge branch 'heavy-update-schemas' into 'master'

Heavy update schemas

See merge request pinar.alper/metadata-tools!3
parents e276fa00 5c85dc12
__pycache__/
# Visual studio code
.vscode
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{
"description": "ELIXIR Luxembourg Core json schema",
"schema": {
"title": "Schema containing core attributes for any json serialisable ELIXIR Luxembourg record.",
"$schema": "http://json-schema.org/draft-04/schema#",
"type": "object",
"required": [
"source",
"name"
],
"properties": {
"source": {
"type": "string",
"format": "uri"
},
"acronym": {
"type": "string"
},
"name": {
"type": "string"
},
"description": {
"type": "string"
},
"elu_accession": {
"type": "string"
},
"elu_uuid": {
"type": "string"
},
"other_external_id": {
"type": "string"
},
"contacts": {
"type": "array",
"items": {
"type": "object",
"properties": {
"first_name": {
"type": "string"
},
"last_name": {
"title": "Schema containing core attributes for any json serialisable ELIXIR Luxembourg record.",
"$schema": "http://json-schema.org/draft-04/schema#",
"type": "object",
"required": [
"source",
"name"
],
"properties": {
"source": {
"type": "string",
"format": "uri"
},
"acronym": {
"type": "string"
},
"name": {
"type": "string"
},
"description": {
"type": "string"
},
"elu_accession": {
"type": "string"
},
"elu_uuid": {
"type": "string"
},
"other_external_id": {
"type": "string"
},
"contacts": {
"type": "array",
"items": {
"type": "object",
"properties": {
"first_name": {
"type": "string"
},
"last_name": {
"type": "string"
},
"role": {
"type": "string",
"enum": [
"Principal_Investigator",
"Researcher",
"Data_Manager",
"Data_Protection_Officer",
"Legal_Representative",
"Other"
]
},
"email": {
"type": "string",
"format": "email"
},
"affiliations": {
"description": "Names of the affiliated institutions.",
"type": "array",
"minItems": 1,
"uniqueItems": true,
"items": {
"type": "string"
},
"role": {
"type": "string",
"enum": [
"Principal_Investigator",
"Researcher",
"Data_Manager",
"Data_Protection_Officer",
"Legal_Representative",
"Other"
]
},
"email": {
"type": "string",
"format": "email"
},
"affiliations": {
"type": "array",
"items": {
"type": "string"
}
}
},
"required": [
"first_name",
"last_name",
"role",
"email",
"institution"
]
}
}
},
"required": [
"first_name",
"last_name",
"role",
"email",
"affiliations"
]
}
}
}
......
{
"description": "ELIXIR Luxembourg Projects Schema",
"schema": {
"title": "A JSON Schema for describing biomedical research Projects.",
"$schema": "http://json-schema.org/draft-04/schema#",
"type": "object",
"allOf": [
{
"$ref": "https://git-r3lab.uni.lu/pinar.alper/metadata-tools/raw/master/metadata_tools/resources/elu-core.json"
"title": "A JSON Schema for describing biomedical research Projects.",
"$schema": "http://json-schema.org/draft-04/schema#",
"type": "object",
"allOf": [
{
"$ref": "https://git-r3lab.uni.lu/pinar.alper/metadata-tools/raw/master/metadata_tools/resources/elu-core.json"
}
],
"properties": {
"project": {
"description": "Name of the project the dataset belongs to.",
"type": ["string", "null"]
},
"data_declarations": {
"type": "array",
"items": {
"$ref": "#/definitions/elu:data"
}
],
"properties": {
"project": {
"type": "string"
},
"data_declarations": {
"type": "array",
"items": {
"$ref": "#/definitions/elu:data"
}
},
"storages": {
"type": "array",
"items": {
"$ref": "#/definitions/elu:storage"
},
"storages": {
"type": "array",
"items": {
"$ref": "#/definitions/elu:storage"
}
},
"transfers": {
"type": "array",
"items": {
"$ref": "#/definitions/elu:transfer"
}
}
},
"definitions": {
"elu:storage": {
"type": "object",
"properties": {
"platform": {"type": "string"},
"location": {"type": "string"},
"accesses": {
"type": "array",
"items": {
"type": "string"
}
}
},
"transfers": {
"type": "array",
"items": {
"$ref": "#/definitions/elu:transfer"
}
},
"elu:transfer": {
"type": "object",
"properties": {
"partner": {"type": "string"},
"transfer_details": {"type": ["string", "null"]},
"transfer_date": {
"type": ["string", "null"],
"pattern": "^[0-9]{4}-[0-9]{2}-[0-9]{2}$"
}
}
},
"definitions": {
"elu:storage": {
"type": "object",
"properties": {
"platform": "string",
"location": "string",
"accesses": {
"type": "array",
"items": {
"type": "string"
}
}
"elu:data": {
"type": "object",
"properties": {
"title": {
"type": "string"
},
"elu:transfer": {
"type": "object",
"properties": {
"partner": "string",
"transfer_details": "string",
"transfer_date": {
"type": "string",
"pattern": "^[0-9]{4}-[0-9]{2}-[0-9]{2}$"
}
}
},
"elu:data": {
"type": "object",
"properties": {
"title": {
"type": "string"
},
"use_restrictions": {
"type": "array",
"items": {
"type": "object",
"properties": {
"ga4gh_code": {
"type": "string",
"enum": [
"NRES",
"GRU(CC)",
"HMB(CC)",
"DS-[XX](CC)",
"POA",
"RS-[XX]",
"RUO",
"NMDS",
"GSO",
"NPU",
"PUB",
"COL-[XX]",
"RTN",
"IRB",
"GS-[XX]",
"MOR-[XX]",
"TS-[XX]",
"US",
"PS",
"IS"
]
},
"note": {
"type": "string"
}
},
"required": [
"ga4gh_code",
"note"
]
}
},
"data_types": {
"type": "array",
"items": {
"use_restrictions": {
"type": "array",
"items": {
"type": "object",
"properties": {
"ga4gh_code": {
"type": "string",
"enum": [
"Omics_data",
"Genotype_data",
"Whole_genome_sequencing",
"Exome_sequencing",
"Genomics_variant_array",
"RNASeq",
"Genetic_and_derived_genetic_data",
"Transcriptome_array",
"Methylation_array",
"MicroRNA_array",
"Metabolomics",
"Metagenomics",
"Proteomics",
"Other_omics_data",
"Clinical_Imaging",
"Cell_Imaging",
"Human_subject_data",
"Clinical_data",
"Lifestyle_data",
"Socio_Economic_Data",
"Environmental_Data",
"Other_Phenotype_data",
"Other"
"NRES",
"GRU(CC)",
"HMB(CC)",
"DS-[XX](CC)",
"POA",
"RS-[XX]",
"RUO",
"NMDS",
"GSO",
"NPU",
"PUB",
"COL-[XX]",
"RTN",
"IRB",
"GS-[XX]",
"MOR-[XX]",
"TS-[XX]",
"US",
"PS",
"IS"
]
},
"data_type_notes": {
"note": {
"type": "string"
},
"access_category": {
"type": "string",
"enum": [
"open-access",
"controlled-access"
]
},
"subjects_category": {
"type": "array",
"items": {
"type": "string",
"enum": [
"cases",
"controls",
"cases_and_controls"
]
}
},
"de_identification": {
"type": "string",
"enum": [
"anonymized",
"pseudonymized"
]
},
"consent_status": {
"type": "string",
"enum": [
"heterogeneous",
"homogeneous"
]
},
"has_special_subjects": {
"type": "boolean"
},
"special_subjects_description": {
"type": "string"
},
"embargo_date": {
"type": "string",
"pattern": "^[0-9]{4}-[0-9]{2}-[0-9]{2}$"
},
"storage_end_date": {
"type": "string",
"pattern": "^[0-9]{4}-[0-9]{2}-[0-9]{2}$"
},
"storage_duration_criteria": {
"type": "string",
"pattern": "^[0-9]{4}-[0-9]{2}-[0-9]{2}$"
}
},
"required": [
"ga4gh_code",
"note"
]
}
},
"data_types": {
"type": "array",
"items": {
"type": "string",
"enum": [
"ATAC-seq",
"Biometric_data",
"ChIP-seq",
"Samples",
"Disease status",
"Ethnic_origin",
"Imaging",
"Omics_data",
"Genotype_data",
"Whole_genome_sequencing",
"Exome_sequencing",
"Genomics_variant_array",
"RNASeq",
"Genetic_and_derived_genetic_data",
"Transcriptome_array",
"Methylation_array",
"MicroRNA_array",
"Metabolomics",
"Metagenomics",
"Metatranscriptomics",
"Metaproteomics",
"Single_Cell_RNAseq",
"Proteomics",
"Other_omics_data",
"Clinical_Imaging",
"Cell_Imaging",
"Human_subject_data",
"Clinical_data",
"Lifestyle_data",
"Socio_Economic_Data",
"Environmental_Data",
"Other_Phenotype_data",
"Other"
]
},
"data_type_notes": {
"type": "string"
},
"access_category": {
"type": "string",
"enum": [
"open-access",
"controlled-access"
]
},
"subjects_category": {
"type": "array",
"items": {
"type": "string",
"enum": [
"cases",
"controls",
"cases_and_controls"
]
}
},
"de_identification": {
"type": "string",
"enum": [
"anonymized",
"pseudonymized"
]
},
"consent_status": {
"type": "string",
"enum": [
"heterogeneous",
"homogeneous"
]
},
"has_special_subjects": {
"type": "boolean"
},
"special_subjects_description": {
"type": "string"
},
"embargo_date": {
"type": "string",
"pattern": "^[0-9]{4}-[0-9]{2}-[0-9]{2}$"
},
"storage_end_date": {
"type": "string",
"pattern": "^[0-9]{4}-[0-9]{2}-[0-9]{2}$"
},
"storage_duration_criteria": {
"type": "string",
"pattern": "^[0-9]{4}-[0-9]{2}-[0-9]{2}$"
}
}
}
......
{
"description": "ELIXIR Luxembourg Partner Schema",
"title": "A JSON Schema for describing partners institutes.",
"$schema": "http://json-schema.org/draft-04/schema#",
"type": "object",
"allOf": [{
"$ref": "#/definitions/elu:partner"
}],
"definitions": {
"elu:partner": {
"type": "object",
"allOf": [
{
"$ref": "https://git-r3lab.uni.lu/pinar.alper/metadata-tools/raw/master/metadata_tools/resources/elu-core.json"
}
],
"properties": {
"is_clinical": {
"type": "boolean"
},
"geo_category": {
"type": "string",
"enum": [
"National",
"EU",
"Non_EU",
"International"
]
},
"sector_category": {
"type": "string",
"enum": [
"PUBLIC",
"PRIVATE_P",
"PRIVATE_NP"
]
},
"address": {
"type": ["string", "null"]
},
"country_code":{
"title": "ISO 3166-1 Alpha-2 Country code",
"type": ["string", "null"],
"pattern": "^[A-Z]{2}$"
}
}
}
}
}
{
"description": "ELIXIR Luxembourg Partner Schema",
"schema": {
"title": "A JSON Schema for describing partners institutes.",
"$schema": "http://json-schema.org/draft-04/schema#",
"type": "array",
"items": {
"$ref": "#/definitions/elu:partner"
},
"definitions": {
"elu:partner": {
"type": "object",
"allOf": [
{
"$ref": "https://git-r3lab.uni.lu/pinar.alper/metadata-tools/raw/master/metadata_tools/resources/elu-core.json"
}
],
"properties": {
"is_clinical": {
"type": "boolean"
},
"geo_category": {
"type": "string",
"enum": [
"National",