From 133c1e990b766a09a7a0f4fd1fdabec82d5225a8 Mon Sep 17 00:00:00 2001 From: karan-palan Date: Tue, 2 Sep 2025 18:36:37 +0530 Subject: [PATCH] fix(schemas): autofix linting issues of biomaterial_core.json Signed-off-by: karan-palan --- .../core/biomaterial/biomaterial_core.json | 176 +++++++++--------- 1 file changed, 85 insertions(+), 91 deletions(-) diff --git a/json_schema/core/biomaterial/biomaterial_core.json b/json_schema/core/biomaterial/biomaterial_core.json index 5ba53012..6ca1e6fc 100644 --- a/json_schema/core/biomaterial/biomaterial_core.json +++ b/json_schema/core/biomaterial/biomaterial_core.json @@ -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" } + } }