From 68a788767a62fc42ccdf76782c511b7e6453adb7 Mon Sep 17 00:00:00 2001 From: Mallory Freeberg Date: Fri, 15 Dec 2017 15:54:03 +0000 Subject: [PATCH 1/3] Extended file extension types allowed in file.json --- json_schema/file.json | 21 ++++++++++++++++----- 1 file changed, 16 insertions(+), 5 deletions(-) diff --git a/json_schema/file.json b/json_schema/file.json index d8ebb7779..b516d05ef 100644 --- a/json_schema/file.json +++ b/json_schema/file.json @@ -1,5 +1,5 @@ { - "description": "Information about the data files produced from single cells.", + "description": "Information about the data files produced from single cells and results files produced from analysis workflows.", "title": "file", "required": [ "filename" @@ -13,19 +13,30 @@ "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json" }, "filename": { - "pattern": "^.*.fastq$|^.*.fastq.gz$|^.*.jpg$|^.*.jpeg$|^.*.tiff$|^.*.png$", + "pattern": "^.*.fastq$|^.*.fastq.gz$|^.*.jpg$|^.*.jpeg$|^.*.tiff$|^.*.png$|^.*.txt$|^.*.bam$|^.*.cram$|^.*.gtf$|^.*.fq$|^.*.fq.gz$|^.*.tar$|^.*.interval_list$|^.*.tsv$|^.*.csv$", "type": "string", - "description": "A filename for a data file. Must have a valid extension." + "description": "A filename for a data or results file. Must have a valid extension." }, "file_format": { "enum": [ "fastq", "fastq.gz", + "fq", + "fq.gz", "tiff", "jpg", - "png" + "png", + "txt", + "bam", + "cram", + "jpeg", + "gtf", + "tar", + "interval_list", + "tsv", + "csv" ], - "description": "The format that the data file is in. Must be one of: fastq, fastq.gz, tiff, jpg, png." + "description": "The format that the data file is in. Must be one of: fastq, fastq.gz, tiff, jpg, jpeg, png, txt, bam, cram, gtf, tar, tsv, csv." } } } \ No newline at end of file From e35a3d51354de066ef2289d5fb1a8addc2a86805 Mon Sep 17 00:00:00 2001 From: Mallory Freeberg Date: Fri, 15 Dec 2017 15:56:09 +0000 Subject: [PATCH 2/3] Updated URL to patch 4.6.1 --- json_schema/analysis.json | 202 ++++++++++++------------ json_schema/analysis_bundle.json | 38 ++--- json_schema/assay.json | 56 +++---- json_schema/assay_bundle.json | 68 ++++---- json_schema/barcode.json | 48 +++--- json_schema/cell_suspension.json | 36 ++--- json_schema/contact.json | 66 ++++---- json_schema/core.json | 36 ++--- json_schema/death.json | 44 +++--- json_schema/donor.json | 152 +++++++++--------- json_schema/enrichment.json | 48 +++--- json_schema/file.json | 60 +++---- json_schema/imaging.json | 64 ++++---- json_schema/immortalized_cell_line.json | 62 ++++---- json_schema/ingest.json | 40 ++--- json_schema/ontology.json | 16 +- json_schema/organoid.json | 14 +- json_schema/primary_cell_line.json | 40 ++--- json_schema/project.json | 112 ++++++------- json_schema/project_bundle.json | 38 ++--- json_schema/protocol.json | 54 +++---- json_schema/publication.json | 38 ++--- json_schema/rna.json | 84 +++++----- json_schema/sample.json | 130 +++++++-------- json_schema/sample_bundle.json | 50 +++--- json_schema/seq.json | 130 +++++++-------- json_schema/single_cell.json | 34 ++-- json_schema/specimen_from_organism.json | 30 ++-- json_schema/state_of_specimen.json | 58 +++---- json_schema/submission.json | 100 ++++++------ json_schema/well.json | 38 ++--- 31 files changed, 993 insertions(+), 993 deletions(-) diff --git a/json_schema/analysis.json b/json_schema/analysis.json index adb41dfb1..029e31f58 100644 --- a/json_schema/analysis.json +++ b/json_schema/analysis.json @@ -1,188 +1,188 @@ { - "title": "analysis", + "title": "analysis", "required": [ - "timestamp_start_utc", - "timestamp_stop_utc", - "computational_method", - "input_bundles", - "reference_bundle", - "analysis_id", - "analysis_run_type", - "metadata_schema", - "tasks", - "inputs", - "outputs", + "timestamp_start_utc", + "timestamp_stop_utc", + "computational_method", + "input_bundles", + "reference_bundle", + "analysis_id", + "analysis_run_type", + "metadata_schema", + "tasks", + "inputs", + "outputs", "core" - ], - "additionalProperties": true, + ], + "additionalProperties": true, "definitions": { "task": { - "additionalProperties": false, + "additionalProperties": false, "required": [ - "name", - "start_time", - "stop_time", - "disk_size", - "docker_image", - "cpus", - "memory", + "name", + "start_time", + "stop_time", + "disk_size", + "docker_image", + "cpus", + "memory", "zone" - ], - "type": "object", + ], + "type": "object", "properties": { "disk_size": { "type": "string" - }, + }, "name": { "type": "string" - }, + }, "zone": { "type": "string" - }, + }, "log_err": { "type": "string" - }, + }, "start_time": { - "type": "string", + "type": "string", "format": "date-time" - }, + }, "cpus": { "type": "integer" - }, + }, "log_out": { "type": "string" - }, + }, "stop_time": { - "type": "string", + "type": "string", "format": "date-time" - }, + }, "memory": { "type": "string" - }, + }, "docker_image": { "type": "string" } } - }, + }, "parameter": { - "additionalProperties": false, + "additionalProperties": false, "required": [ - "name", + "name", "value" - ], - "type": "object", + ], + "type": "object", "properties": { "checksum": { "type": "string" - }, + }, "name": { "type": "string" - }, + }, "value": { "type": "string" } } - }, + }, "file": { - "additionalProperties": false, + "additionalProperties": false, "required": [ - "name", - "file_path", + "name", + "file_path", "format" - ], - "type": "object", + ], + "type": "object", "properties": { "checksum": { "type": "string" - }, + }, "file_path": { "type": "string" - }, - "format": { - "type": "string" - }, + }, "name": { "type": "string" + }, + "format": { + "type": "string" } } } - }, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", + }, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "inputs": { "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/analysis.json#/definitions/parameter" - }, - "type": "array", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/analysis.json#/definitions/parameter" + }, + "type": "array", "description": "Input parameters used in the pipeline run, these can be files or string values (settings)." - }, + }, "reference_bundle": { - "type": "string", + "type": "string", "description": "Bundle containing the reference used in running the pipeline." - }, + }, "tasks": { "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/analysis.json#/definitions/task" - }, - "type": "array", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/analysis.json#/definitions/task" + }, + "type": "array", "description": "Descriptions of tasks in the workflow." - }, + }, "description": { - "type": "string", + "type": "string", "description": "A general description of the analysis." - }, + }, "timestamp_stop_utc": { - "type": "string", - "format": "date-time", - "description": "Terminal stop time of the full pipeline." - }, + "type": "string", + "description": "Terminal stop time of the full pipeline.", + "format": "date-time" + }, "input_bundles": { "items": { "type": "string" - }, - "type": "array", + }, + "type": "array", "description": "The input bundles used in this analysis run." - }, + }, "outputs": { "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/analysis.json#/definitions/file" - }, - "type": "array", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/analysis.json#/definitions/file" + }, + "type": "array", "description": "Output generated by the pipeline run." - }, - "analysis_id": { - "type": "string", - "description": "A unique ID for this analysis." - }, + }, + "name": { + "type": "string", + "description": "A short, descriptive name for the analysis that need not be unique." + }, "computational_method": { - "type": "string", + "type": "string", "description": "A URI to a versioned workflow and versioned execution environment in a GA4GH-compliant repository." - }, + }, "timestamp_start_utc": { - "type": "string", - "format": "date-time", - "description": "Initial start time of the full pipeline." - }, + "type": "string", + "description": "Initial start time of the full pipeline.", + "format": "date-time" + }, "core": { - "description": "Type and schema for this object.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json" - }, + "description": "Type and schema for this object.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/core.json" + }, "analysis_run_type": { "enum": [ - "run", + "run", "copy-forward" - ], - "type": "string", + ], + "type": "string", "description": "Indicator of whether the analysis actually ran or was just copied forward as an optimization." - }, + }, "metadata_schema": { - "type": "string", + "type": "string", "description": "The version of the metadata schemas used for the json files." - }, - "name": { - "type": "string", - "description": "A short, descriptive name for the analysis that need not be unique." + }, + "analysis_id": { + "type": "string", + "description": "A unique ID for this analysis." } } } \ No newline at end of file diff --git a/json_schema/analysis_bundle.json b/json_schema/analysis_bundle.json index 8d8339fb5..3e330445b 100644 --- a/json_schema/analysis_bundle.json +++ b/json_schema/analysis_bundle.json @@ -2,31 +2,31 @@ "definitions": { "analysis_ingest": { "required": [ - "hca_ingest", - "content", + "hca_ingest", + "content", "core" - ], - "type": "object", + ], + "type": "object", "properties": { "content": { - "type": "object", - "description": "Analysis content", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/analysis.json" - }, + "type": "object", + "description": "Analysis content", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/analysis.json" + }, "core": { - "description": "Type and schema for this object.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json" - }, + "description": "Type and schema for this object.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/core.json" + }, "hca_ingest": { - "type": "object", - "description": "core fields added by HCA ingest service", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ingest.json" + "type": "object", + "description": "core fields added by HCA ingest service", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/ingest.json" } } } - }, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", - "description": "A schema for a analysis bundle", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/analysis_bundle.json#/definitions/analysis_ingest" + }, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", + "description": "A schema for a analysis bundle", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/analysis_bundle.json#/definitions/analysis_ingest" } \ No newline at end of file diff --git a/json_schema/assay.json b/json_schema/assay.json index 84290c5ac..45aef1fdc 100644 --- a/json_schema/assay.json +++ b/json_schema/assay.json @@ -1,45 +1,45 @@ { - "description": "An assay contains information relevant to how a sample (in vitro) was converted into digital information (in silico).", - "title": "assay", + "description": "An assay contains information relevant to how a sample (in vitro) was converted into digital information (in silico).", + "title": "assay", "required": [ - "core", + "core", "assay_id" - ], - "additionalProperties": false, - "definitions": {}, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", + ], + "additionalProperties": false, + "definitions": {}, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "core": { - "description": "Type and schema for this object.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json" - }, + "description": "Type and schema for this object.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/core.json" + }, "name": { - "type": "string", + "type": "string", "description": "A short, descriptive name for the assay that need not be unique." - }, + }, "seq": { - "description": "Information about how a cDNA sample was sequenced.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/seq.json" - }, + "description": "Information about how a cDNA sample was sequenced.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/seq.json" + }, "rna": { - "description": "Information about how RNA was converted to cDNA.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/rna.json" - }, + "description": "Information about how RNA was converted to cDNA.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/rna.json" + }, "single_cell": { - "description": "Information on single-cell aspects of an assay.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/single_cell.json" - }, + "description": "Information on single-cell aspects of an assay.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/single_cell.json" + }, "imaging": { - "description": "Information on image based RNA quantification assays", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/imaging.json" - }, + "description": "Information on image based RNA quantification assays", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/imaging.json" + }, "assay_id": { - "type": "string", + "type": "string", "description": "A unique ID for this assay." - }, + }, "description": { - "type": "string", + "type": "string", "description": "A general description of the assay." } } diff --git a/json_schema/assay_bundle.json b/json_schema/assay_bundle.json index 5045bd908..482f5c8ff 100644 --- a/json_schema/assay_bundle.json +++ b/json_schema/assay_bundle.json @@ -2,49 +2,49 @@ "definitions": { "assay_ingest": { "required": [ - "hca_ingest", - "content", + "hca_ingest", + "content", "core" - ], - "type": "object", + ], + "type": "object", "properties": { - "content": { - "type": "object", - "description": "Assay content", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/assay.json" - }, - "derivation_protocols": { - "items": { - "description": "An array of protocols used in derivation of this sample.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/protocol.json" - }, - "type": "array" - }, - "hca_ingest": { - "type": "object", - "description": "core fields added by HCA ingest service", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ingest.json" - }, "has_input": { - "type": "string", + "type": "string", "description": "The sample that this assay was performed on." - }, + }, + "core": { + "description": "Type and schema for this object.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/core.json" + }, + "content": { + "type": "object", + "description": "Assay content", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/assay.json" + }, "has_output": { "items": { "type": "string" - }, - "type": "array", + }, + "type": "array", "description": "The files that were generated from this assay." - }, - "core": { - "description": "Type and schema for this object.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json" + }, + "derivation_protocols": { + "items": { + "description": "An array of protocols used in derivation of this sample.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/protocol.json" + }, + "type": "array" + }, + "hca_ingest": { + "type": "object", + "description": "core fields added by HCA ingest service", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/ingest.json" } } } - }, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", - "description": "A schema for an assay bundle", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/assay_bundle.json#/definitions/assay_ingest" + }, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", + "description": "A schema for an assay bundle", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/assay_bundle.json#/definitions/assay_ingest" } \ No newline at end of file diff --git a/json_schema/barcode.json b/json_schema/barcode.json index 635f69114..96fb99d5a 100644 --- a/json_schema/barcode.json +++ b/json_schema/barcode.json @@ -1,38 +1,38 @@ { - "description": "This object describes where a particular type of barcode is in a read.", - "title": "barcode", + "description": "This object describes where a particular type of barcode is in a read.", + "title": "barcode", "required": [ - "offset", - "size", + "offset", + "size", "read" - ], - "additionalProperties": false, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", + ], + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "read": { "enum": [ - "Read 1", - "Read 2", - "i7 Index", + "Read 1", + "Read 2", + "i7 Index", "i5 Index" - ], + ], "description": "The read that the barcode is found in. Should be one of Read 1, Read 2, i7 Index, or i5 Index." - }, - "offset": { - "minimum": 0, - "type": "integer", - "description": "Offset in read of barcode. 0 for beginning of read.", + }, + "size": { + "minimum": 0, + "type": "integer", + "description": "Size of barcode in nucleotides.", "maximum": 50 - }, + }, "white_list_file": { - "type": "string", + "type": "string", "description": "Name of file containing legitimate barcode sequences. Unused for randomly generated barcodes." - }, - "size": { - "minimum": 0, - "type": "integer", - "description": "Size of barcode in nucleotides.", + }, + "offset": { + "minimum": 0, + "type": "integer", + "description": "Offset in read of barcode. 0 for beginning of read.", "maximum": 50 } } diff --git a/json_schema/cell_suspension.json b/json_schema/cell_suspension.json index f1a58645e..966d66bac 100644 --- a/json_schema/cell_suspension.json +++ b/json_schema/cell_suspension.json @@ -1,31 +1,31 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "description": "Information about the cell suspension derived from the collected or cultured specimen", + "$schema": "http://json-schema.org/draft-04/schema#", + "title": "cell_suspension", + "description": "Information about the cell suspension derived from the collected or cultured specimen", "properties": { "well": { - "description": "Information about wells in a plate or chip used for single-cell isolation.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/well.json" - }, + "description": "Information about wells in a plate or chip used for single-cell isolation.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/well.json" + }, "target_cell_type": { "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology_json/cell_type_ontology.json" - }, - "type": "array", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/ontology_json/cell_type_ontology.json" + }, + "type": "array", "description": "Cell types present in the suspension." - }, + }, "total_estimated_cells": { - "minimum": 0.1, - "type": "number", - "description": "Total estimated number of cells in sample. May be 1 for well-based assays.", + "minimum": 0.1, + "type": "number", + "description": "Total estimated number of cells in sample. May be 1 for well-based assays.", "maximum": 1000000000.0 - }, + }, "enrichment": { "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/enrichment.json" - }, - "type": "array", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/enrichment.json" + }, + "type": "array", "description": "How sample was enriched for specific cell type(s)." } - }, - "title": "cell_suspension" + } } \ No newline at end of file diff --git a/json_schema/contact.json b/json_schema/contact.json index 3de8e4b8d..20ee9b5e2 100644 --- a/json_schema/contact.json +++ b/json_schema/contact.json @@ -1,51 +1,51 @@ { - "description": "contact schema generate by tagSchemaToJson from contact", - "title": "contact", + "description": "contact schema generate by tagSchemaToJson from contact", + "title": "contact", "required": [ - "name", + "name", "email" - ], - "additionalProperties": false, - "definitions": {}, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", + ], + "additionalProperties": false, + "definitions": {}, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { - "country": { - "description": "Name of country where contact works.", - "type": "string" - }, "country_division": { - "description": "Name of state, province, canton, or other country subdivision where contact works.", - "type": "string" - }, + "type": "string", + "description": "Name of state, province, canton, or other country subdivision where contact works." + }, "city": { - "type": "string", + "type": "string", "description": "Name of city where contact works." - }, + }, "name": { - "type": "string", + "type": "string", "description": "The contact's name. Should be in the format first, middle, last name. Middle can be initial or left blank. e.g. John,D,Doe or Jane,,Smith" - }, - "email": { - "pattern": "^.*@.*..*$", - "type": "string", - "description": "An email address for the contact." - }, + }, + "country": { + "type": "string", + "description": "Name of country where contact works." + }, + "institution": { + "type": "string", + "description": "Name of primary institute where contact works." + }, "phone": { - "type": "string", + "type": "string", "description": "Phone number (including country code) of contact or contact's lab." - }, + }, "address": { - "type": "string", + "type": "string", "description": "Full mailing address where contact works. Should include street name and number, city, state, postal code, country." - }, + }, "laboratory": { - "type": "string", + "type": "string", "description": "Name of lab (often the PI name) within institute where contact works." - }, - "institution": { - "type": "string", - "description": "Name of primary institute where contact works." + }, + "email": { + "pattern": "^.*@.*..*$", + "type": "string", + "description": "An email address for the contact." } } } \ No newline at end of file diff --git a/json_schema/core.json b/json_schema/core.json index 32227703a..b669edcb0 100644 --- a/json_schema/core.json +++ b/json_schema/core.json @@ -1,32 +1,32 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", + "$schema": "http://json-schema.org/draft-04/schema#", "required": [ "type" - ], - "description": "Core object found in all modules.", + ], + "description": "Core object found in all modules.", "properties": { "type": { "enum": [ - "assay", - "project", - "protocol", - "sample", - "file", - "analysis", - "assay_bundle", - "sample_bundle", - "project_bundle", + "assay", + "project", + "protocol", + "sample", + "file", + "analysis", + "assay_bundle", + "sample_bundle", + "project_bundle", "analysis_bundle" - ], + ], "description": "The name of the core metadata entity type." - }, + }, "schema_url": { - "type": "string", + "type": "string", "description": "URL of JSON schema document that validates this version of this module." - }, + }, "schema_version": { - "pattern": "^...*..*$", - "type": "string", + "pattern": "^...*..*$", + "type": "string", "description": "Version number in major.minor.patch format. e.g. 3.2.4. Major version changes likely require changes to software. Minor version changes should not require software changes. Patches are just documentation changes." } } diff --git a/json_schema/death.json b/json_schema/death.json index f9a79a0a2..d2b522c7f 100644 --- a/json_schema/death.json +++ b/json_schema/death.json @@ -1,37 +1,37 @@ { - "description": "Information relating to the death of the donor", - "title": "death", + "description": "Information relating to the death of the donor", + "title": "death", "required": [ "cause_of_death" - ], - "additionalProperties": false, - "definitions": {}, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", + ], + "additionalProperties": false, + "definitions": {}, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "cause_of_death": { - "description": "Cause of death from death report for human donor, from research lab for mouse.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json" - }, + "description": "Cause of death from death report for human donor, from research lab for mouse.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/ontology.json" + }, "hardy_scale": { - "minimum": 0, - "type": "integer", - "description": "Should be integer representing: (0) ventilator case, (1) violent and fast death, (2) fast death of natural causes, (3) intermediate death, or (4) slow death.", + "minimum": 0, + "type": "integer", + "description": "Should be integer representing: (0) ventilator case, (1) violent and fast death, (2) fast death of natural causes, (3) intermediate death, or (4) slow death.", "maximum": 4 - }, + }, "cold_perfused": { - "type": "boolean", + "type": "boolean", "description": "Yes if perfused with cold fluid to help preserve tissues before heart stopped. No otherwise." - }, + }, "days_on_ventilator": { - "minimum": 0, - "type": "number", - "description": "Days on ventilator before dying.", + "minimum": 0, + "type": "number", + "description": "Days on ventilator before dying.", "maximum": 10000 - }, + }, "time_of_death": { - "type": "string", - "description": "Date and time of death on death certificate for deceased donor.", + "type": "string", + "description": "Date and time of death on death certificate for deceased donor.", "format": "date-time" } } diff --git a/json_schema/donor.json b/json_schema/donor.json index 2e6e8f9f8..9de0faf6b 100644 --- a/json_schema/donor.json +++ b/json_schema/donor.json @@ -1,124 +1,124 @@ { - "description": "Information about the donor from which a specimen was collected", - "title": "donor", + "description": "Information about the donor from which a specimen was collected", + "title": "donor", "required": [ "is_living" - ], - "additionalProperties": false, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", + ], + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "nutritional_state": { "enum": [ - "normal", - "fasting", + "normal", + "fasting", "feeding tube removed" - ], + ], "description": "Should be one of normal, fasting, or feeding tube removed." - }, + }, "is_living": { - "type": "boolean", + "type": "boolean", "description": "Should be yes if donor is living at time of sample donation. Otherwise, should be no." - }, + }, "death": { - "description": "Information about conditions of death (or info that donor was living at time of collection).", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/death.json" - }, + "description": "Information about conditions of death (or info that donor was living at time of collection).", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/death.json" + }, "genotype": { - "type": "string", + "type": "string", "description": "Genotype of donor including strain, cross, and genetic modification information. Must be in MGI format for mice." - }, + }, "weight": { - "pattern": "^[0-9]+\\.?[0-9]*-?[0-9]*\\.?[0-9]*$", - "type": "string", + "pattern": "^[0-9]+\\.?[0-9]*-?[0-9]*\\.?[0-9]*$", + "type": "string", "description": "Weight of donor, in kilograms. Can be a range separated by a hyphen." - }, - "body_mass_index": { - "minimum": 5, - "type": "number", - "description": "The body mass index of the donor.", - "maximum": 100 - }, + }, + "strain": { + "items": { + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/ontology.json" + }, + "type": "array", + "description": "The name of the mouse inbred strain. e.g. C57BL/6." + }, "alcohol_history": { - "type": "string", + "type": "string", "description": "Number of drinks consumed on a typical day." - }, + }, "age": { - "pattern": "^[0-9]+\\.?[0-9]*-?[0-9]*\\.?[0-9]*$", - "type": "string", + "pattern": "^[0-9]+\\.?[0-9]*-?[0-9]*\\.?[0-9]*$", + "type": "string", "description": "Age in age_units. For embryos, measured since fertilization. For all others, measured since birth." - }, + }, "life_stage": { "enum": [ - "adult", - "child", - "embryo", + "adult", + "child", + "embryo", "postpartum" - ], + ], "description": "Should be one of adult, child, embryo, or postpartum." - }, + }, "disease": { "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology_json/disease_ontology.json" - }, - "type": "array", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/ontology_json/disease_ontology.json" + }, + "type": "array", "description": "Short description of disease status of individual." - }, + }, "age_unit": { "enum": [ - "hour", - "day", - "week", - "year", - "hours", - "days", - "weeks", + "hour", + "day", + "week", + "year", + "hours", + "days", + "weeks", "years" - ], + ], "description": "The unit in which age is expressed. Must be one of day, week, month, or year." - }, + }, "height": { - "pattern": "^[0-9]+\\.?[0-9]*-?[0-9]*\\.?[0-9]*$", - "type": "string", + "pattern": "^[0-9]+\\.?[0-9]*-?[0-9]*\\.?[0-9]*$", + "type": "string", "description": "Height of donor, in meters. Can be a range separated by a hyphen." - }, - "strain": { - "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json" - }, - "type": "array", - "description": "The name of the mouse inbred strain. e.g. C57BL/6." - }, + }, + "body_mass_index": { + "minimum": 5, + "type": "number", + "description": "The body mass index of the donor.", + "maximum": 100 + }, "ancestry": { "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json" - }, - "type": "array", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/ontology.json" + }, + "type": "array", "description": "An array of ontology terms from EMBL-EBI's Ancestry Ontology describing ancestral groups, uncategorised ancestral groups, and population isolates." - }, + }, "smoking_history": { - "type": "string", + "type": "string", "description": "Estimated number of cigarettes smoked per day and for how many years." - }, + }, "sex": { "enum": [ - "female", - "male", - "mixed", + "female", + "male", + "mixed", "unknown" - ], + ], "description": "Sex of donor. Should be one of male, female, mixed, or unknown." - }, + }, "medication": { "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json" - }, - "type": "array", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/ontology.json" + }, + "type": "array", "description": "List of medications the donor was currently taking at time of sample donation." - }, + }, "development_stage": { - "description": "More detailed (especially for embryos) version of life_stage. e.g. \"E9\" or \"P17\" for mouse.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json" + "description": "More detailed (especially for embryos) version of life_stage. e.g. \"E9\" or \"P17\" for mouse.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/ontology.json" } } } \ No newline at end of file diff --git a/json_schema/enrichment.json b/json_schema/enrichment.json index 01a86417b..d5bbc4c07 100644 --- a/json_schema/enrichment.json +++ b/json_schema/enrichment.json @@ -1,36 +1,36 @@ { - "description": "enrichment schema generate by tagSchemaToJson from enrichment", - "title": "enrichment", + "description": "enrichment schema generate by tagSchemaToJson from enrichment", + "title": "enrichment", "required": [ "type" - ], - "additionalProperties": false, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", + ], + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { - "size_max": { - "minimum": 0.01, - "type": "number", - "description": "Maximum size passing selection, in microns.", - "maximum": 10000 - }, - "size_min": { - "minimum": 0.01, - "type": "number", - "description": "Minimum size passing selection, in microns.", - "maximum": 10000 - }, "type": { "enum": [ - "FACS", - "MACS", - "Ficoll gradient", + "FACS", + "MACS", + "Ficoll gradient", "density gradient" - ], + ], "description": "The method by which enrichment was achieved. e.g. MACS, FACS, Ficoll gradient" - }, + }, + "size_min": { + "minimum": 0.01, + "type": "number", + "description": "Minimum size passing selection, in microns.", + "maximum": 10000 + }, + "size_max": { + "minimum": 0.01, + "type": "number", + "description": "Maximum size passing selection, in microns.", + "maximum": 10000 + }, "markers": { - "type": "string", + "type": "string", "description": "Space-delimited list of markers (with +/-) used for enrichment. e.g. CD4+ CD8-" } } diff --git a/json_schema/file.json b/json_schema/file.json index b516d05ef..f3a5ef224 100644 --- a/json_schema/file.json +++ b/json_schema/file.json @@ -1,42 +1,42 @@ { - "description": "Information about the data files produced from single cells and results files produced from analysis workflows.", - "title": "file", + "description": "Information about the data files produced from single cells and results files produced from analysis workflows.", + "title": "file", "required": [ "filename" - ], - "additionalProperties": false, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", + ], + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "core": { - "description": "Type and schema for this object.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json" - }, - "filename": { - "pattern": "^.*.fastq$|^.*.fastq.gz$|^.*.jpg$|^.*.jpeg$|^.*.tiff$|^.*.png$|^.*.txt$|^.*.bam$|^.*.cram$|^.*.gtf$|^.*.fq$|^.*.fq.gz$|^.*.tar$|^.*.interval_list$|^.*.tsv$|^.*.csv$", - "type": "string", - "description": "A filename for a data or results file. Must have a valid extension." - }, + "description": "Type and schema for this object.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/core.json" + }, "file_format": { "enum": [ - "fastq", - "fastq.gz", - "fq", - "fq.gz", - "tiff", - "jpg", - "png", - "txt", - "bam", - "cram", - "jpeg", - "gtf", - "tar", - "interval_list", - "tsv", + "fastq", + "fastq.gz", + "fq", + "fq.gz", + "tiff", + "jpg", + "png", + "txt", + "bam", + "cram", + "jpeg", + "gtf", + "tar", + "interval_list", + "tsv", "csv" - ], + ], "description": "The format that the data file is in. Must be one of: fastq, fastq.gz, tiff, jpg, jpeg, png, txt, bam, cram, gtf, tar, tsv, csv." + }, + "filename": { + "pattern": "^.*.fastq$|^.*.fastq.gz$|^.*.jpg$|^.*.jpeg$|^.*.tiff$|^.*.png$|^.*.txt$|^.*.bam$|^.*.cram$|^.*.gtf$|^.*.fq$|^.*.fq.gz$|^.*.tar$|^.*.interval_list$|^.*.tsv$|^.*.csv$", + "type": "string", + "description": "A filename for a data or results file. Must have a valid extension." } } } \ No newline at end of file diff --git a/json_schema/imaging.json b/json_schema/imaging.json index b890e9749..4e4f1b1ef 100644 --- a/json_schema/imaging.json +++ b/json_schema/imaging.json @@ -1,61 +1,61 @@ { - "description": "imaging schema generate by tagSchemaToJson from imaging", - "title": "imaging", + "description": "imaging schema generate by tagSchemaToJson from imaging", + "title": "imaging", "required": [ - "field_counts", - "field_resolution", + "field_counts", + "field_resolution", "probes" - ], - "additionalProperties": false, - "definitions": {}, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", + ], + "additionalProperties": false, + "definitions": {}, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "exposure_time": { - "minimum": 1e-09, - "type": "number", - "description": "Exposure time as a floating point number in units of seconds", + "minimum": 1e-09, + "type": "number", + "description": "Exposure time as a floating point number in units of seconds", "maximum": 1000 - }, + }, "field_microns": { "items": { "type": "integer" - }, - "type": "array", + }, + "type": "array", "description": "microns covered by a field in x,y, and z. Z includes all focal planes in a single file" - }, + }, "fixation": { - "type": "string", + "type": "string", "description": "Description of fixation conditions" - }, + }, "microscope": { "enum": [ - "generic confocal", + "generic confocal", "generic two photon" - ], + ], "description": "Microscope used for imaging" - }, + }, "embedding": { - "type": "string", + "type": "string", "description": "Description of embedding conditions" - }, + }, "field_resolution": { "items": { "type": "integer" - }, - "type": "array", + }, + "type": "array", "description": "x, y, and z (number of focal planes) resolution of an individual field" - }, + }, + "probes": { + "type": "string", + "description": "A file containing information on probe sequence, genes they cover, and colors" + }, "field_counts": { "items": { "type": "integer" - }, - "type": "array", + }, + "type": "array", "description": "number of fields in x and y dimensions" - }, - "probes": { - "type": "string", - "description": "A file containing information on probe sequence, genes they cover, and colors" } } } \ No newline at end of file diff --git a/json_schema/immortalized_cell_line.json b/json_schema/immortalized_cell_line.json index 6ec7544ac..3fddefee3 100644 --- a/json_schema/immortalized_cell_line.json +++ b/json_schema/immortalized_cell_line.json @@ -1,48 +1,48 @@ { - "description": "Information about the immortalized cell line used in the sample", - "title": "immortalized_cell_line", - "additionalProperties": false, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", + "description": "Information about the immortalized cell line used in the sample", + "title": "immortalized_cell_line", + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "catalog_url": { - "type": "string", + "type": "string", "description": "The supplier catalogue URL for the cell line." - }, + }, "cell_type": { - "description": "What cell type the line was derived from. CLO ontology.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology_json/cell_type_ontology.json" - }, + "description": "What cell type the line was derived from. CLO ontology.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/ontology_json/cell_type_ontology.json" + }, "date_established": { - "type": "string", - "description": "When the cell line was established.", + "type": "string", + "description": "When the cell line was established.", "format": "date-time" - }, + }, "catalog_number": { - "type": "string", + "type": "string", "description": "The supplier catalogue number for the cell line." - }, + }, "disease": { - "description": "A disease associated with the cell line. EFO ontology.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology_json/disease_ontology.json" - }, + "description": "A disease associated with the cell line. EFO ontology.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/ontology_json/disease_ontology.json" + }, "passage_number": { - "minimum": 0, - "type": "integer", - "description": "The number of passages the cell line as been through.", + "minimum": 0, + "type": "integer", + "description": "The number of passages the cell line as been through.", "maximum": 1000 - }, - "publication": { - "description": "The publication in which the cell line creation was cited.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/publication.json" - }, + }, + "cell_cycle": { + "description": "The cell cycle phase, if known.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/ontology.json" + }, "karyotype": { - "type": "string", + "type": "string", "description": "The karyotype of the cell line." - }, - "cell_cycle": { - "description": "The cell cycle phase, if known.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json" + }, + "publication": { + "description": "The publication in which the cell line creation was cited.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/publication.json" } } } \ No newline at end of file diff --git a/json_schema/ingest.json b/json_schema/ingest.json index 56a70a2a8..24f571287 100644 --- a/json_schema/ingest.json +++ b/json_schema/ingest.json @@ -1,38 +1,38 @@ { - "additionalProperties": false, - "$schema": "http://json-schema.org/draft-04/schema#", + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", "required": [ - "document_id", + "document_id", "submissionDate" - ], - "description": "Information added or generated at ingest time.", + ], + "description": "Information added or generated at ingest time.", "properties": { "accession": { - "type": "string", + "type": "string", "description": "A unique accession for this entity, provided by the broker." - }, + }, "submissionDate": { - "type": "string", - "description": "When project was first submitted to database.", + "type": "string", + "description": "When project was first submitted to database.", "format": "date-time" - }, + }, "submitter_id": { - "type": "string", + "type": "string", "description": "ID of contact who first submitted project" - }, + }, "updateDate": { - "type": "string", - "description": "When project was last updated", + "type": "string", + "description": "When project was last updated", "format": "date-time" - }, + }, "document_id": { - "comment": "This structure supports the current ingest API. It may change in future.", - "pattern": ".{8}-.{4}-.{4}-.{4}-.{12}", - "type": "string", + "comment": "This structure supports the current ingest API. It may change in future.", + "pattern": ".{8}-.{4}-.{4}-.{4}-.{12}", + "type": "string", "description": "Identifier for document." - }, + }, "updater_id": { - "type": "string", + "type": "string", "description": "ID of contact who last updated project" } } diff --git a/json_schema/ontology.json b/json_schema/ontology.json index 65b65e367..71513c541 100644 --- a/json_schema/ontology.json +++ b/json_schema/ontology.json @@ -1,18 +1,18 @@ { - "description": "A term that may be associated with an ontology term", - "title": "ontology", + "description": "A term that may be associated with an ontology term", + "title": "ontology", "required": [ "text" - ], - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", + ], + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "text": { - "type": "string", + "type": "string", "description": "The text for the term as the user provides it." - }, + }, "ontology": { - "type": "string", + "type": "string", "description": "An optional ontology reference in format where prefix_ indicates which ontology" } } diff --git a/json_schema/organoid.json b/json_schema/organoid.json index 517f36a76..e8888d655 100644 --- a/json_schema/organoid.json +++ b/json_schema/organoid.json @@ -1,14 +1,14 @@ { - "description": "A description of an organoid sample.", - "$schema": "http://json-schema.org/draft-04/schema#", + "title": "organoid", + "$schema": "http://json-schema.org/draft-04/schema#", "required": [ "model_for_organ" - ], + ], + "description": "A description of an organoid sample.", "properties": { "model_for_organ": { - "description": "Organ that this organoid is a model system for.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json" + "description": "Organ that this organoid is a model system for.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/ontology.json" } - }, - "title": "organoid" + } } \ No newline at end of file diff --git a/json_schema/primary_cell_line.json b/json_schema/primary_cell_line.json index c1a471547..62513007b 100644 --- a/json_schema/primary_cell_line.json +++ b/json_schema/primary_cell_line.json @@ -1,32 +1,32 @@ { - "description": "Information about the primary cell line used in the sample", - "title": "primary_cell_line", - "additionalProperties": false, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", + "description": "Information about the primary cell line used in the sample", + "title": "primary_cell_line", + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "cell_type": { - "description": "The cell type that the cell line was derived from. Should be a CLO ontology.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology_json/cell_type_ontology.json" - }, + "description": "The cell type that the cell line was derived from. Should be a CLO ontology.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/ontology_json/cell_type_ontology.json" + }, "date_established": { - "type": "string", - "description": "When the cell line was established, in date-time format.", + "type": "string", + "description": "When the cell line was established, in date-time format.", "format": "date-time" - }, + }, "disease": { - "description": "Free text describing any disease association to the cell type. Should be found in EFO ontology.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology_json/disease_ontology.json" - }, + "description": "Free text describing any disease association to the cell type. Should be found in EFO ontology.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/ontology_json/disease_ontology.json" + }, "passage_number": { - "minimum": 0, - "type": "integer", - "description": "The number of passages the cell line has been through.", + "minimum": 0, + "type": "integer", + "description": "The number of passages the cell line has been through.", "maximum": 1000 - }, + }, "cell_cycle": { - "description": "The cell cycle phase if the cell line is synchronized growing cells or the phase is known.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json" + "description": "The cell cycle phase if the cell line is synchronized growing cells or the phase is known.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/ontology.json" } } } \ No newline at end of file diff --git a/json_schema/project.json b/json_schema/project.json index 20dd658c9..d13adb9c7 100644 --- a/json_schema/project.json +++ b/json_schema/project.json @@ -1,105 +1,105 @@ { - "description": "project schema generate by tagSchemaToJson from project", - "title": "project", + "description": "project schema generate by tagSchemaToJson from project", + "title": "project", "required": [ - "core", - "contributors", + "core", + "contributors", "project_id" - ], + ], "patternProperties": { "^characteristics_.*$": { - "type": "string", + "type": "string", "description": "Fields that begin with characteristics_ can contain any value, and the field name can be anything after the prefix" } - }, - "additionalProperties": false, - "definitions": {}, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", + }, + "additionalProperties": false, + "definitions": {}, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "core": { - "description": "type and schema for this object", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json" - }, + "description": "type and schema for this object", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/core.json" + }, "related_projects": { "items": { "type": "string" - }, - "type": "array", + }, + "type": "array", "description": "A list of other projects that may be logically grouped with this one." - }, + }, "name": { - "type": "string", + "type": "string", "description": "A short, descriptive name for the project that need not be unique." - }, + }, "contributors": { "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/contact.json" - }, - "type": "array", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/contact.json" + }, + "type": "array", "description": "List of people contributing to the project." - }, + }, "submitters": { "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/contact.json" - }, - "type": "array", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/contact.json" + }, + "type": "array", "description": "List of people submitting data to the project." - }, + }, "insdc_project": { - "pattern": "^[D|E|S]RP[0-9]+$", - "type": "string", + "pattern": "^[D|E|S]RP[0-9]+$", + "type": "string", "description": "An INSDC (International Nucleotide Sequence Database Collaboration) project accession. Can be from the DDBJ, EMBL-EBI, or NCBI. Accession must start with DRP, ERP, or SRP." - }, + }, "supplementary_files": { "items": { "type": "string" - }, - "type": "array", + }, + "type": "array", "description": "Project-level supplementary files. e.g. experimental design documents, lab spreadsheets, manuscripts in preparation." - }, + }, "geo_series": { - "pattern": "^GSE.*$", - "type": "string", + "pattern": "^GSE.*$", + "type": "string", "description": "An NCBI GEO series accession." - }, + }, "experimental_design": { "items": { - "description": "A short description of overall experiment type. e.g. \"single cell RNA sequencing.\"", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json" - }, + "description": "A short description of overall experiment type. e.g. \"single cell RNA sequencing.\"", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/ontology.json" + }, "type": "array" - }, + }, "publications": { "items": { - "description": "An array of publication modules.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/publication.json" - }, + "description": "An array of publication modules.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/publication.json" + }, "type": "array" - }, + }, "experimental_factor_name": { "items": { "type": "string" - }, - "type": "array", + }, + "type": "array", "description": "A list of the factors that vary between samples in the experiment. e.g. \"time since collection\", \"preservation method\"" - }, + }, "project_id": { - "type": "string", + "type": "string", "description": "A unique ID for this project." - }, + }, "array_express_investigation": { - "pattern": "^E-....-.*$", - "type": "string", + "pattern": "^E-....-.*$", + "type": "string", "description": "An EBI ArrayExpress investigation accession." - }, + }, "insdc_study": { - "pattern": "^PRJ[E|N|D][a-zA-Z][0-9]+$", - "type": "string", + "pattern": "^PRJ[E|N|D][a-zA-Z][0-9]+$", + "type": "string", "description": "An INSDC (International Nucleotide Sequence Database Collaboration) study accession. Can be from the DDBJ, EMBL-EBI, or NCBI. Accession must start with PRJE, PRJN, or PRJD" - }, + }, "description": { - "type": "string", + "type": "string", "description": "A general description of the project." } } diff --git a/json_schema/project_bundle.json b/json_schema/project_bundle.json index 27eb9afd5..7f9a73d0f 100644 --- a/json_schema/project_bundle.json +++ b/json_schema/project_bundle.json @@ -2,31 +2,31 @@ "definitions": { "project_ingest": { "required": [ - "hca_ingest", - "content", + "hca_ingest", + "content", "core" - ], - "type": "object", + ], + "type": "object", "properties": { "content": { - "type": "object", - "description": "Project content", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/project.json" - }, + "type": "object", + "description": "Project content", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/project.json" + }, "core": { - "description": "Type and schema for this object.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json" - }, + "description": "Type and schema for this object.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/core.json" + }, "hca_ingest": { - "type": "object", - "description": "core fields added by HCA ingest service", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ingest.json" + "type": "object", + "description": "core fields added by HCA ingest service", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/ingest.json" } } } - }, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", - "description": "A schema for a project bundle", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/project_bundle.json#/definitions/project_ingest" + }, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", + "description": "A schema for a project bundle", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/project_bundle.json#/definitions/project_ingest" } \ No newline at end of file diff --git a/json_schema/protocol.json b/json_schema/protocol.json index 12be851db..c5f595fa2 100644 --- a/json_schema/protocol.json +++ b/json_schema/protocol.json @@ -1,47 +1,47 @@ { - "description": "protocol schema generate by tagSchemaToJson from protocol", - "title": "protocol", + "description": "protocol schema generate by tagSchemaToJson from protocol", + "title": "protocol", "required": [ - "core", - "protocol_id", + "core", + "protocol_id", "type" - ], - "additionalProperties": false, - "definitions": {}, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", + ], + "additionalProperties": false, + "definitions": {}, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "core": { - "description": "type and schema for this object", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json" - }, + "description": "type and schema for this object", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/core.json" + }, "retail_name": { - "type": "string", + "type": "string", "description": "The retail name of the kit used. e.g SureCell WTA 3' Library Prep Kit" - }, + }, "description": { - "type": "string", + "type": "string", "description": "A general description of the protocol." - }, + }, "protocol_id": { - "type": "string", + "type": "string", "description": "A unique ID for this protocol." - }, + }, "batch_number": { - "type": "string", + "type": "string", "description": "The batch of kit used." - }, + }, "pdf": { - "pattern": "^.*.pdf$", - "type": "string", + "pattern": "^.*.pdf$", + "type": "string", "description": "A filename of a PDF containing the details of the protocol." - }, + }, "type": { - "description": "The type of protocol. Ideally an EFO term.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json" - }, + "description": "The type of protocol. Ideally an EFO term.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/ontology.json" + }, "name": { - "type": "string", + "type": "string", "description": "A short, descriptive name for the protocol that need not be unique." } } diff --git a/json_schema/publication.json b/json_schema/publication.json index 2c7f51c67..087571d87 100644 --- a/json_schema/publication.json +++ b/json_schema/publication.json @@ -1,36 +1,36 @@ { - "description": "A publication contains information about a journal article, book, web page or other external available documentation on a project", - "title": "publication", + "description": "A publication contains information about a journal article, book, web page or other external available documentation on a project", + "title": "publication", "required": [ - "authors", + "authors", "title" - ], - "additionalProperties": false, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", + ], + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "url": { - "type": "string", + "type": "string", "description": "A URL, preferably not behind a paywall, for the publication." - }, + }, + "title": { + "type": "string", + "description": "The full title of the publication." + }, "pmid": { - "type": "integer", + "type": "integer", "description": "A PubMed ID of the publication, if available. e.g. 27565351" - }, + }, "doi": { - "type": "string", + "type": "string", "description": "The publication digital object identifier (doi), if available. e.g. 10.1016/j.cell.2016.07.054" - }, + }, "authors": { "items": { "type": "string" - }, - "type": "array", + }, + "type": "array", "description": "A list of authors associated with the publication. Names can be in any format but must be separated by ||." - }, - "title": { - "type": "string", - "description": "The full title of the publication." } } } \ No newline at end of file diff --git a/json_schema/rna.json b/json_schema/rna.json index 48d650484..52d5ac7d0 100644 --- a/json_schema/rna.json +++ b/json_schema/rna.json @@ -1,72 +1,72 @@ { - "description": "Information about how RNA was converted to cDNA for sequencing.", - "title": "rna", + "description": "Information about how RNA was converted to cDNA for sequencing.", + "title": "rna", "required": [ - "end_bias", - "library_construction", + "end_bias", + "library_construction", "strand" - ], - "additionalProperties": false, - "definitions": {}, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", + ], + "additionalProperties": false, + "definitions": {}, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "spike_in_dilution": { - "minimum": 1, - "type": "integer", - "description": "Dilution of RNA spike-in.", + "minimum": 1, + "type": "integer", + "description": "Dilution of RNA spike-in.", "maximum": 1000000 - }, + }, "library_protocol": { - "pattern": "^P-....-.*$", - "type": "string", + "pattern": "^P-....-.*$", + "type": "string", "description": "RNA preparation protocol" - }, + }, "spike_in": { "enum": [ "ERCC" - ], + ], "description": "Name of RNA spike-in kit. e.g. ERCC." - }, + }, "end_bias": { "enum": [ - "three_prime_end", - "three_prime_bias", - "five_prime_end", - "five_prime_bias", + "three_prime_end", + "three_prime_bias", + "five_prime_end", + "five_prime_bias", "none" - ], + ], "description": "The type of end bias the library has. Must be one of 3' bias, 5' bias, 3' end, 5' end, or none." - }, + }, "primer": { "enum": [ - "poly-dT", + "poly-dT", "random" - ], + ], "description": "Primer used for cDNA synthesis from RNA. Must be either poly-dT or random." - }, + }, "strand": { "enum": [ - "both", + "both", "first" - ], + ], "description": "Single stranded?" - }, + }, "library_construction": { "enum": [ - "unknown", - "CEL-seq", - "SMARTer Ultra Low RNA Kit", - "modified smart-seq2", - "smart-seq2", - "QUARTZ-Seq", - "10x_v2", - "drop-seq", - "inDrop", - "10x_v1", - "SMARTer cDNA synthesis kit", + "unknown", + "CEL-seq", + "SMARTer Ultra Low RNA Kit", + "modified smart-seq2", + "smart-seq2", + "QUARTZ-Seq", + "10x_v2", + "drop-seq", + "inDrop", + "10x_v1", + "SMARTer cDNA synthesis kit", "TruSeq Stranded Total RNA Library Prep" - ], + ], "description": "The general approach for sequencing library construction. e.g. Smart-seq, Drop-seq, 10x." } } diff --git a/json_schema/sample.json b/json_schema/sample.json index 6414f1889..61e5351b7 100644 --- a/json_schema/sample.json +++ b/json_schema/sample.json @@ -4,123 +4,123 @@ "required": [ "donor" ] - }, + }, { "required": [ "immortalized_cell_line" ] - }, + }, { "required": [ "cell_suspension" ] - }, + }, { "required": [ "organoid" ] - }, + }, { "required": [ "primary_cell_line" ] - }, + }, { "required": [ "specimen_from_organism" ] } - ], - "description": "A sample contains information on the biosample that was sequenced or imaged. This includes donor, body part, and anything that comes between removing the sample from a donor and the assay.", - "title": "sample", + ], + "description": "A sample contains information on the biosample that was sequenced or imaged. This includes donor, body part, and anything that comes between removing the sample from a donor and the assay.", "allOf": [ { "required": [ - "sample_id", - "core", + "sample_id", + "core", "ncbi_taxon_id" ] } - ], + ], + "title": "sample", "patternProperties": { "^characteristics_.*$": { - "type": "string", + "type": "string", "description": "Fields that begin with characteristics_ can contain any value, and the field name can be anything after the prefix." } - }, - "additionalProperties": false, - "$schema": "http://json-schema.org/draft-04/schema#", + }, + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", "properties": { "core": { - "description": "Type and schema for this object.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json" - }, + "description": "Type and schema for this object.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/core.json" + }, + "sample_accessions": { + "additionalProperties": false, + "type": "object", + "description": "One or more accession numbers from a standard archive.", + "properties": { + "insdc_sample": { + "pattern": "^[D|E|S]RS[0-9]+$", + "type": "string", + "description": "An INSDC (International Nucleotide Sequence Database Collaboration) sample accession. Can be from the DDBJ, EMBL-EBI, or NCBI. Accession must start with DRS, ERS, or SRS." + }, + "biosd_sample": { + "pattern": "^SAM(D|N|E([AG]?))[0-9]+$", + "type": "string", + "description": "A DDBJ, NCBI, or EBI BioSample ID. Accessions must start with SAMD, SAMN, or SAME." + } + } + }, "immortalized_cell_line": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/immortalized_cell_line.json" - }, + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/immortalized_cell_line.json" + }, "description": { - "type": "string", + "type": "string", "description": "A general description of the sample." - }, + }, "cell_suspension": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/cell_suspension.json" - }, + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/cell_suspension.json" + }, "specimen_from_organism": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/specimen_from_organism.json" - }, + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/specimen_from_organism.json" + }, "genus_species": { - "description": "Scientific binomial name of donor species. e.g. Homo sapiens.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json" - }, + "description": "Scientific binomial name of donor species. e.g. Homo sapiens.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/ontology.json" + }, "supplementary_files": { "items": { "type": "string" - }, - "type": "array", + }, + "type": "array", "description": "A list of filenames of sample-level supplementary files." - }, - "name": { - "type": "string", - "description": "A short, descriptive name for the sample that need not be unique." - }, + }, "ncbi_taxon_id": { - "type": "integer", + "type": "integer", "description": "A taxonomy ID (taxonID) from NCBI." - }, + }, "derived_from": { - "comment": "This field is primarily required for spreadsheet based submissions", - "type": "string", + "comment": "This field is primarily required for spreadsheet based submissions", + "type": "string", "description": "If this sample is derived from another sample e.g. a tissue or donor, enter the sample_id for the sample this was derived from" - }, + }, "sample_id": { - "type": "string", + "type": "string", "description": "A unique ID for this sample." - }, + }, "donor": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/donor.json" - }, + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/donor.json" + }, "primary_cell_line": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/primary_cell_line.json" - }, + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/primary_cell_line.json" + }, "organoid": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/organoid.json" - }, - "sample_accessions": { - "additionalProperties": false, - "type": "object", - "description": "One or more accession numbers from a standard archive.", - "properties": { - "biosd_sample": { - "pattern": "^SAM(D|N|E([AG]?))[0-9]+$", - "type": "string", - "description": "A DDBJ, NCBI, or EBI BioSample ID. Accessions must start with SAMD, SAMN, or SAME." - }, - "insdc_sample": { - "pattern": "^[D|E|S]RS[0-9]+$", - "type": "string", - "description": "An INSDC (International Nucleotide Sequence Database Collaboration) sample accession. Can be from the DDBJ, EMBL-EBI, or NCBI. Accession must start with DRS, ERS, or SRS." - } - } + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/organoid.json" + }, + "name": { + "type": "string", + "description": "A short, descriptive name for the sample that need not be unique." } } } \ No newline at end of file diff --git a/json_schema/sample_bundle.json b/json_schema/sample_bundle.json index f52e8d8fd..94afcad60 100644 --- a/json_schema/sample_bundle.json +++ b/json_schema/sample_bundle.json @@ -2,47 +2,47 @@ "definitions": { "sample_ingest": { "required": [ - "hca_ingest", + "hca_ingest", "content" - ], - "type": "object", + ], + "type": "object", "properties": { "content": { - "type": "object", - "description": "Sample content", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/sample.json" - }, + "type": "object", + "description": "Sample content", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/sample.json" + }, "derivation_protocols": { "items": { - "description": "An array of protocols used in derivation of this sample.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/protocol.json" - }, + "description": "An array of protocols used in derivation of this sample.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/protocol.json" + }, "type": "array" - }, + }, "hca_ingest": { - "type": "object", - "description": "core fields added by HCA ingest service", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ingest.json" - }, + "type": "object", + "description": "core fields added by HCA ingest service", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/ingest.json" + }, "derived_from": { - "type": "string", + "type": "string", "description": "The sample that this sample was derived from." } } } - }, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", - "description": "A schema for a sample bundle", + }, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", + "description": "A schema for a sample bundle", "properties": { "core": { - "description": "Type and schema for this object.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/core.json" - }, + "description": "Type and schema for this object.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/core.json" + }, "samples": { "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/sample_bundle.json#/definitions/sample_ingest" - }, + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/sample_bundle.json#/definitions/sample_ingest" + }, "type": "array" } } diff --git a/json_schema/seq.json b/json_schema/seq.json index 522b0e2b7..6f7e95930 100644 --- a/json_schema/seq.json +++ b/json_schema/seq.json @@ -1,121 +1,121 @@ { - "description": "Information about how a sample was sequenced.", - "title": "seq", + "description": "Information about how a sample was sequenced.", + "title": "seq", "required": [ - "instrument_model", - "instrument_platform", - "lanes", - "molecule", + "instrument_model", + "instrument_platform", + "lanes", + "molecule", "paired_ends" - ], - "additionalProperties": false, + ], + "additionalProperties": false, "definitions": { "lanes": { "items": { - "additionalProperties": false, + "additionalProperties": false, "required": [ "r1" - ], - "type": "object", + ], + "type": "object", "properties": { "i1": { - "type": "string", + "type": "string", "description": "A barcode index file. Often index off of first read." - }, + }, "i2": { - "type": "string", + "type": "string", "description": "A barcode index file. Often index off of second read." - }, + }, "number": { - "type": "number", + "type": "number", "description": "Which lane number" - }, + }, "r2": { - "type": "string", + "type": "string", "description": "File name of second read in paired-end read assay." - }, + }, "r1": { - "type": "string", + "type": "string", "description": "File name of first read in paired-end read sequencing assay, or only read for unpaired." } - }, + }, "title": "A sequencing lane." - }, - "type": "array", + }, + "type": "array", "title": "lane array" } - }, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", + }, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "paired_ends": { - "type": "boolean", + "type": "boolean", "description": "Was a paired-end sequencing strategy used? Must be either yes or no." - }, + }, "lanes": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/seq.json#/definitions/lanes" - }, + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/seq.json#/definitions/lanes" + }, "insdc_run": { "items": { - "pattern": "^[D|E|S]RR[0-9]+$", + "pattern": "^[D|E|S]RR[0-9]+$", "type": "string" - }, - "type": "array", + }, + "type": "array", "description": "An INSDC (International Nucleotide Sequence Database Collaboration) run accession. Accession must start with DRR, ERR, or SRR." - }, + }, "local_machine_name": { - "type": "string", + "type": "string", "description": "Local name for the particular machine on which the sample was sequenced." - }, + }, "molecule": { "enum": [ - "polyA RNA", - "total RNA", + "polyA RNA", + "total RNA", "genomic DNA" - ], + ], "description": "Specific type of molecule sequenced. e.g. total RNA, genomic DNA, polyA RNA." - }, + }, "instrument_model": { "enum": [ - "HiSeq 2000", - "HiSeq 2500", - "HiSeq 4000", - "MiSeq", - "NextSeq 500", + "HiSeq 2000", + "HiSeq 2500", + "HiSeq 4000", + "MiSeq", + "NextSeq 500", "Sequel" - ], + ], "description": "The model of the sequencer used. e.g. HiSeq 2000, Sequel." - }, + }, "umi_barcode": { - "description": "Information about unique molecular identifier (UMI) barcode sequences.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/barcode.json" - }, + "description": "Information about unique molecular identifier (UMI) barcode sequences.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/barcode.json" + }, "library_protocol": { - "pattern": "^P-....-.*$", - "type": "string", + "pattern": "^P-....-.*$", + "type": "string", "description": "DNA sequencing library preparation protocol." - }, + }, "insdc_experiment": { - "pattern": "^[D|E|S]RX[0-9]+$", - "type": "string", + "pattern": "^[D|E|S]RX[0-9]+$", + "type": "string", "description": "An INSDC (International Nucleotide Sequence Database Collaboration) experiment accession. Accession must start with DRX, ERX, or SRX." - }, + }, "instrument_platform": { "enum": [ - "Illumina", - "Ion Torrent", + "Illumina", + "Ion Torrent", "Pacific Biosciences" - ], + ], "description": "The sequencing platform used. e.g. Illumina, Ion Torrent, Pacific Biosciences." - }, + }, "library_construction": { "enum": [ - "Nextera XT", - "TruSeq", - "modified Nextera XT", - "10x_v2", + "Nextera XT", + "TruSeq", + "modified Nextera XT", + "10x_v2", "10x_v1" - ], + ], "description": "How the DNA sequencing library was prepared. e.g. Nextera XT, TrueSeq." } } diff --git a/json_schema/single_cell.json b/json_schema/single_cell.json index 175096cd2..84eb8c643 100644 --- a/json_schema/single_cell.json +++ b/json_schema/single_cell.json @@ -1,28 +1,28 @@ { - "description": "Contains information on single cell aspects of an assay.", - "title": "single_cell", + "description": "Contains information on single cell aspects of an assay.", + "title": "single_cell", "required": [ "cell_handling" - ], - "additionalProperties": false, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", + ], + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "cell_barcode": { - "description": "Information about cell identifier barcode.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/barcode.json" - }, + "description": "Information about cell identifier barcode.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/barcode.json" + }, "cell_handling": { "enum": [ - "10x_v2", - "FACS", - "Fluidigm C1", - "drop-seq", - "inDrop", - "mouth pipette", - "bulk", + "10x_v2", + "FACS", + "Fluidigm C1", + "drop-seq", + "inDrop", + "mouth pipette", + "bulk", "10x_v1" - ], + ], "description": "How cells are separated. e.g. FACS, drop-seq, 10x_v2, Fluidigm C1." } } diff --git a/json_schema/specimen_from_organism.json b/json_schema/specimen_from_organism.json index 84dc5be44..10e106759 100644 --- a/json_schema/specimen_from_organism.json +++ b/json_schema/specimen_from_organism.json @@ -1,25 +1,25 @@ { - "description": "Information about the specimen that was extracted from the donor organism.", - "title": "specimen_from_organism", + "description": "Information about the specimen that was extracted from the donor organism.", + "title": "specimen_from_organism", "required": [ - "body_part", + "body_part", "organ" - ], - "additionalProperties": false, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", + ], + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "body_part": { - "description": "A more detailed position within the body than the term given in the organ field.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology_json/body_part_ontology.json" - }, + "description": "A more detailed position within the body than the term given in the organ field.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/ontology_json/body_part_ontology.json" + }, "state_of_specimen": { - "description": "State of body_part at collection and how it was preserved after removal.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/state_of_specimen.json" - }, + "description": "State of body_part at collection and how it was preserved after removal.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/state_of_specimen.json" + }, "organ": { - "description": "The organ that the sample came from. e.g. liver, spleen. Blood and connective tissue count as organs.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/ontology.json" + "description": "The organ that the sample came from. e.g. liver, spleen. Blood and connective tissue count as organs.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/ontology.json" } } } \ No newline at end of file diff --git a/json_schema/state_of_specimen.json b/json_schema/state_of_specimen.json index 37017f8a5..c6d231027 100644 --- a/json_schema/state_of_specimen.json +++ b/json_schema/state_of_specimen.json @@ -1,53 +1,53 @@ { - "description": "State of body part at collection and how it was preserved after removal and/or cell enrichment", - "title": "state_of_specimen", - "additionalProperties": false, - "definitions": {}, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", + "description": "State of body part at collection and how it was preserved after removal and/or cell enrichment", + "title": "state_of_specimen", + "additionalProperties": false, + "definitions": {}, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "ischemic_time": { - "minimum": 0, - "type": "integer", - "description": "Duration of time, in seconds, that the body part had insufficient blood supply.", + "minimum": 0, + "type": "integer", + "description": "Duration of time, in seconds, that the body part had insufficient blood supply.", "maximum": 1000000 - }, + }, "gross_image": { "items": { - "pattern": "^.*.jpg$|^.*.jpeg$|^.*.tiff$|^.*.png$", + "pattern": "^.*.jpg$|^.*.jpeg$|^.*.tiff$|^.*.png$", "type": "string" - }, - "type": "array", + }, + "type": "array", "description": "List of filenames of photographs of body part without magnification. Must be of format JPEG, TIFF, or PNG." - }, + }, "postmortem_interval": { - "minimum": 0, - "type": "integer", - "description": "Duration of time, in seconds, between when death is declared and when the tissue is preserved or processed.", + "minimum": 0, + "type": "integer", + "description": "Duration of time, in seconds, between when death is declared and when the tissue is preserved or processed.", "maximum": 1000000 - }, + }, "gross_description": { - "type": "string", + "type": "string", "description": "Color, size, and other aspects of specimen as visible to naked eye." - }, + }, "autolysis_score": { "enum": [ - "none", - "mild", + "none", + "mild", "moderate" - ], + ], "description": "State of tissue breakdown due to self-digestion. Must be one of: none, mild, moderate." - }, + }, "microscopic_image": { "items": { - "pattern": "^.*.jpg$|^.*.jpeg$|^.*.tiff$|^.*.png$", + "pattern": "^.*.jpg$|^.*.jpeg$|^.*.tiff$|^.*.png$", "type": "string" - }, - "type": "array", + }, + "type": "array", "description": "List of filenames of photographs of body part under microscope. Must be of format JPEG, TIFF, or PNG." - }, + }, "microscopic_description": { - "type": "string", + "type": "string", "description": "How the sample looks under the microscope and how it compares with normal cells." } } diff --git a/json_schema/submission.json b/json_schema/submission.json index a93e5cf31..1ee2ab1b7 100644 --- a/json_schema/submission.json +++ b/json_schema/submission.json @@ -1,87 +1,87 @@ { - "title": "submission", + "title": "submission", "required": [ - "transfer_service_version", + "transfer_service_version", "submitted_files" - ], - "additionalProperties": false, + ], + "additionalProperties": false, "definitions": { - "transfer_service_version": { - "additionalProperties": false, - "type": "string" - }, "submitted_files": { - "additionalProperties": false, + "additionalProperties": false, "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/submission.json#/definitions/file" - }, + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/submission.json#/definitions/file" + }, "type": "array" - }, + }, + "transfer_service_version": { + "additionalProperties": false, + "type": "string" + }, "file": { - "additionalProperties": false, + "additionalProperties": false, "required": [ - "name", - "content_type", - "size", - "id", + "name", + "content_type", + "size", + "id", "checksums" - ], - "type": "object", + ], + "type": "object", "properties": { + "id": { + "type": "string", + "description": "URI of the Data Storage System file resource that describes this file" + }, "checksums": { "required": [ - "s3etag", - "sha1", - "sha256", + "s3etag", + "sha1", + "sha256", "crc32" - ], - "type": "object", + ], + "type": "object", "properties": { "crc32": { - "type": "string", + "type": "string", "description": "CRC-32 checksum of this file" - }, + }, "sha256": { - "type": "string", + "type": "string", "description": "SHA-256 checksum of this file" - }, + }, "s3etag": { - "type": "string", + "type": "string", "description": "S3 ETAG checksum of this file" - }, + }, "sha1": { - "type": "string", + "type": "string", "description": "SHA-1 checksum of this file" } } - }, - "size": { - "type": "integer", - "description": "Length of file in bytes" - }, + }, "name": { - "type": "string", + "type": "string", "description": "Name of the file" - }, + }, "content_type": { - "type": "string", + "type": "string", "description": "type of file e.g hca-sample-json, hca-assay-json, hca-rnaseq-fastq-gz" - }, - "id": { - "type": "string", - "description": "URI of the Data Storage System file resource that describes this file" + }, + "size": { + "type": "integer", + "description": "Length of file in bytes" } } } - }, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", + }, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { - "transfer_service_version": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/submission.json#/definitions/transfer_service_version" - }, "submitted_files": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.0/json_schema/submission.json#/definitions/submitted_files" + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/submission.json#/definitions/submitted_files" + }, + "transfer_service_version": { + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/submission.json#/definitions/transfer_service_version" } } } \ No newline at end of file diff --git a/json_schema/well.json b/json_schema/well.json index 9b2c9b2dc..c97f57ae0 100644 --- a/json_schema/well.json +++ b/json_schema/well.json @@ -1,34 +1,34 @@ { - "description": "This describes the well inside the plate or fluidics chip where sample came from.", - "title": "well", - "additionalProperties": false, - "$schema": "http://json-schema.org/draft-04/schema#", - "type": "object", + "description": "This describes the well inside the plate or fluidics chip where sample came from.", + "title": "well", + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "plate": { - "type": "string", + "type": "string", "description": "An ID for the plate that the well is located on." - }, + }, + "row": { + "type": "string", + "description": "Well row in plate." + }, "quality": { "enum": [ - "OK", - "control, 2-cell well", - "control, empty well", + "OK", + "control, 2-cell well", + "control, empty well", "low quality cell" - ], + ], "description": "Note on how good cell looks if imaged in well before sequencing." - }, + }, "col": { - "type": "string", + "type": "string", "description": "Well column in plate." - }, + }, "name": { - "type": "string", + "type": "string", "description": "A name for the well. Should be unique for the plate" - }, - "row": { - "type": "string", - "description": "Well row in plate." } } } \ No newline at end of file From e8fefa343cf3c1051426a975f56ba0ed6764719d Mon Sep 17 00:00:00 2001 From: Mallory Freeberg Date: Fri, 15 Dec 2017 16:10:17 +0000 Subject: [PATCH 3/3] Removed requirement of file extensions for files in file.json. --- json_schema/file.json | 24 +++--------------------- 1 file changed, 3 insertions(+), 21 deletions(-) diff --git a/json_schema/file.json b/json_schema/file.json index f3a5ef224..f47731760 100644 --- a/json_schema/file.json +++ b/json_schema/file.json @@ -13,29 +13,11 @@ "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/core.json" }, "file_format": { - "enum": [ - "fastq", - "fastq.gz", - "fq", - "fq.gz", - "tiff", - "jpg", - "png", - "txt", - "bam", - "cram", - "jpeg", - "gtf", - "tar", - "interval_list", - "tsv", - "csv" - ], - "description": "The format that the data file is in. Must be one of: fastq, fastq.gz, tiff, jpg, jpeg, png, txt, bam, cram, gtf, tar, tsv, csv." + "description": "The format that the data file is in. Must be one of: fastq, fastq.gz, tiff, jpg, jpeg, png, txt, bam, cram, gtf, tar, tsv, csv.", + "type": "string" }, "filename": { - "pattern": "^.*.fastq$|^.*.fastq.gz$|^.*.jpg$|^.*.jpeg$|^.*.tiff$|^.*.png$|^.*.txt$|^.*.bam$|^.*.cram$|^.*.gtf$|^.*.fq$|^.*.fq.gz$|^.*.tar$|^.*.interval_list$|^.*.tsv$|^.*.csv$", - "type": "string", + "type": "string", "description": "A filename for a data or results file. Must have a valid extension." } }