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fix(schemas): autofix linting issues of biomaterial_core.json #1627

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fix(schemas): autofix linting issues of biomaterial_core.json #1627

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176 changes: 85 additions & 91 deletions json_schema/core/biomaterial/biomaterial_core.json
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Original file line number Diff line number Diff line change
@@ -1,94 +1,88 @@
{
"$schema": "http://json-schema.org/draft-07/schema#",
"description": "Information about any biological material that was generated/used in the project including everything from a whole organism to subcellular components.",
"additionalProperties": false,
"required": [
"biomaterial_id",
"ncbi_taxon_id"
],
"title": "Biomaterial core",
"name": "biomaterial_core",
"type": "object",
"properties": {
"describedBy": {
"description": "The URL reference to the schema.",
"type": "string",
"pattern" : "^(http|https)://schema.(.*?)humancellatlas.org/core/biomaterial/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/biomaterial_core"
},
"schema_version": {
"description": "The version number of the schema in major.minor.patch format.",
"type": "string",
"pattern": "^\\d+\\.\\d+\\.\\d+$",
"example": "4.6.1"
},
"biomaterial_id":{
"description": "A unique ID for the biomaterial.",
"type": "string",
"user_friendly": "Biomaterial ID"
},
"biomaterial_name": {
"description": "A short, descriptive name for the biomaterial that need not be unique.",
"type": "string",
"user_friendly": "Biomaterial name"
},
"biomaterial_description": {
"description": "A general description of the biomaterial.",
"type": "string",
"user_friendly": "Biomaterial description"
},
"ncbi_taxon_id" : {
"description": "A taxonomy ID (taxonID) from NCBI.",
"type" : "array",
"items":{
"type": "integer"
},
"user_friendly": "NCBI taxon ID",
"example": 9606
},
"genotype": {
"description": "Genotype of the biomaterial.",
"type": "string",
"user_friendly": "Genotype",
"example": "DRB1 0401 protective allele; HLA-B*3901 allele"
},
"supplementary_files": {
"description": "A list of filenames of biomaterial-level supplementary files.",
"type": "array",
"items": {
"type": "string"
},
"user_friendly": "Supplementary files",
"example": "sample_site_image.jpg"
},
"biosamples_accession": {
"description": "A BioSamples accession.",
"type": "string",
"pattern": "^SAM(D|N|E([AG]?))[0-9]+$",
"user_friendly": "BioSamples accession",
"example": "SAMN00000000",
"guidelines": "Enter accession if sample has been archived. Accession can be from the DDBJ, NCBI, or EMBL-EBI and must start with SAMD, SAMN, or SAME, respectively."
},
"insdc_sample_accession": {
"description": "An International Nucleotide Sequence Database Collaboration (INSDC) sample accession.",
"type": "string",
"pattern": "^[DES]RS[0-9]+$",
"user_friendly": "INSDC sample accession",
"example": "SRS0000000",
"guidelines": "Enter accession if sample has been archived. Accession can be from the DDBJ, NCBI, or EMBL-EBI and must start with DRS, SRS, or ERS, respecitvely."
},
"HDBR_accession": {
"description": "A Human Developmental Biology Resource (HDBR) sample accession.",
"type": "string",
"pattern": "(^[0-9]{5})(,\\s[0-9]{1,},\\s[a-zA-Z]+$){0,1}",
"user_friendly": "HDBR accession",
"example": "34526; 14758, 2, liver",
"guidelines": "Enter accession if sample has been obtained from the Human Developmental Biology Resource (HDBR)."
},
"timecourse": {
"description": "Information relating to a timecourse associated with this biomaterial.",
"type": "object",
"$ref": "module/biomaterial/timecourse.json",
"user_friendly": "Timecourse"
}
"$schema": "http://json-schema.org/draft-07/schema#",
"description": "Information about any biological material that was generated/used in the project including everything from a whole organism to subcellular components.",
"additionalProperties": false,
"required": [ "biomaterial_id", "ncbi_taxon_id" ],
"title": "Biomaterial core",
"x-name": "biomaterial_core",
"type": "object",
"properties": {
"describedBy": {
"description": "The URL reference to the schema.",
"type": "string",
"pattern": "^(http|https)://schema.(.*?)humancellatlas.org/core/biomaterial/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/biomaterial_core"
},
"schema_version": {
"description": "The version number of the schema in major.minor.patch format.",
"type": "string",
"pattern": "^\\d+\\.\\d+\\.\\d+$",
"x-example": "4.6.1"
},
"biomaterial_id": {
"description": "A unique ID for the biomaterial.",
"type": "string",
"x-user_friendly": "Biomaterial ID"
},
"biomaterial_name": {
"description": "A short, descriptive name for the biomaterial that need not be unique.",
"type": "string",
"x-user_friendly": "Biomaterial name"
},
"biomaterial_description": {
"description": "A general description of the biomaterial.",
"type": "string",
"x-user_friendly": "Biomaterial description"
},
"ncbi_taxon_id": {
"description": "A taxonomy ID (taxonID) from NCBI.",
"type": "array",
"items": {
"type": "integer"
},
"x-user_friendly": "NCBI taxon ID",
"x-example": 9606
},
"genotype": {
"description": "Genotype of the biomaterial.",
"type": "string",
"x-user_friendly": "Genotype",
"x-example": "DRB1 0401 protective allele; HLA-B*3901 allele"
},
"supplementary_files": {
"description": "A list of filenames of biomaterial-level supplementary files.",
"type": "array",
"items": {
"type": "string"
},
"x-user_friendly": "Supplementary files",
"x-example": "sample_site_image.jpg"
},
"biosamples_accession": {
"description": "A BioSamples accession.",
"type": "string",
"pattern": "^SAM(D|N|E([AG]?))[0-9]+$",
"x-user_friendly": "BioSamples accession",
"x-example": "SAMN00000000",
"x-guidelines": "Enter accession if sample has been archived. Accession can be from the DDBJ, NCBI, or EMBL-EBI and must start with SAMD, SAMN, or SAME, respectively."
},
"insdc_sample_accession": {
"description": "An International Nucleotide Sequence Database Collaboration (INSDC) sample accession.",
"type": "string",
"pattern": "^[DES]RS[0-9]+$",
"x-user_friendly": "INSDC sample accession",
"x-example": "SRS0000000",
"x-guidelines": "Enter accession if sample has been archived. Accession can be from the DDBJ, NCBI, or EMBL-EBI and must start with DRS, SRS, or ERS, respecitvely."
},
"HDBR_accession": {
"description": "A Human Developmental Biology Resource (HDBR) sample accession.",
"type": "string",
"pattern": "(^[0-9]{5})(,\\s[0-9]{1,},\\s[a-zA-Z]+$){0,1}",
"x-user_friendly": "HDBR accession",
"x-example": "34526; 14758, 2, liver",
"x-guidelines": "Enter accession if sample has been obtained from the Human Developmental Biology Resource (HDBR)."
},
"timecourse": {
"$ref": "module/biomaterial/timecourse.json"
}
}
}