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Add HCA Metadata v4.6.1 #7

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1 change: 1 addition & 0 deletions DEPENDENCIES
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Expand Up @@ -46,6 +46,7 @@ geojson-1-0-2 https://github.com/geojson/schema v1.0.2
geojson-1-0-1 https://github.com/geojson/schema v1.0.1
geojson-1-0-0 https://github.com/geojson/schema v1.0.0
hca-metadata-5-0-0 https://github.com/HumanCellAtlas/metadata-schema 5.0.0
hca-metadata-4-6-1 https://github.com/HumanCellAtlas/metadata-schema 4.6.1
dats-1-0-0 https://github.com/datatagsuite/schema 1.0.0
fhir https://github.com/FHIR/packages b401fbd45566006a21243a9b88f1391e32b1ed40
asyncapi https://github.com/asyncapi/spec-json-schemas v6.8.1
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4 changes: 4 additions & 0 deletions configuration.json
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Expand Up @@ -389,6 +389,10 @@
"base": "https://schema.humancellatlas.org",
"path": "./vendor/hca-metadata-5-0-0/json_schema"
},
"humancellatlas/metadata/v4.6.1": {
"base": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema",
"path": "./vendor/hca-metadata-4-6-1/json_schema"
},
"dats/v1.0.0": {
"base": "https://w3id.org/dats/schema",
"path": "./vendor/dats-1-0-0"
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14 changes: 14 additions & 0 deletions vendor/hca-metadata-4-6-1.mask
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docs/
examples/
json_schema/README.md
json_schema_extensions/
schema_test_files/
src/
.travis.yml
changelog.md
contributing.md
README.md
requirements.txt
json_meta_schema/
schema_tests/
spreadsheet/
188 changes: 188 additions & 0 deletions vendor/hca-metadata-4-6-1/json_schema/analysis.json
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{
"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",
"core"
],
"additionalProperties": true,
"definitions": {
"task": {
"additionalProperties": false,
"required": [
"name",
"start_time",
"stop_time",
"disk_size",
"docker_image",
"cpus",
"memory",
"zone"
],
"type": "object",
"properties": {
"disk_size": {
"type": "string"
},
"name": {
"type": "string"
},
"zone": {
"type": "string"
},
"log_err": {
"type": "string"
},
"start_time": {
"type": "string",
"format": "date-time"
},
"cpus": {
"type": "integer"
},
"log_out": {
"type": "string"
},
"stop_time": {
"type": "string",
"format": "date-time"
},
"memory": {
"type": "string"
},
"docker_image": {
"type": "string"
}
}
},
"parameter": {
"additionalProperties": false,
"required": [
"name",
"value"
],
"type": "object",
"properties": {
"checksum": {
"type": "string"
},
"name": {
"type": "string"
},
"value": {
"type": "string"
}
}
},
"file": {
"additionalProperties": false,
"required": [
"name",
"file_path",
"format"
],
"type": "object",
"properties": {
"checksum": {
"type": "string"
},
"file_path": {
"type": "string"
},
"name": {
"type": "string"
},
"format": {
"type": "string"
}
}
}
},
"$schema": "http://json-schema.org/draft-04/schema#",
"type": "object",
"properties": {
"inputs": {
"items": {
"$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",
"description": "Bundle containing the reference used in running the pipeline."
},
"tasks": {
"items": {
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/analysis.json#/definitions/task"
},
"type": "array",
"description": "Descriptions of tasks in the workflow."
},
"description": {
"type": "string",
"description": "A general description of the analysis."
},
"timestamp_stop_utc": {
"type": "string",
"description": "Terminal stop time of the full pipeline.",
"format": "date-time"
},
"input_bundles": {
"items": {
"type": "string"
},
"type": "array",
"description": "The input bundles used in this analysis run."
},
"outputs": {
"items": {
"$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."
},
"name": {
"type": "string",
"description": "A short, descriptive name for the analysis that need not be unique."
},
"computational_method": {
"type": "string",
"description": "A URI to a versioned workflow and versioned execution environment in a GA4GH-compliant repository."
},
"timestamp_start_utc": {
"type": "string",
"description": "Initial start time of the full pipeline.",
"format": "date-time"
},
"core": {
"description": "Type and schema for this object.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/core.json"
},
"analysis_run_type": {
"enum": [
"run",
"copy-forward"
],
"type": "string",
"description": "Indicator of whether the analysis actually ran or was just copied forward as an optimization."
},
"metadata_schema": {
"type": "string",
"description": "The version of the metadata schemas used for the json files."
},
"analysis_id": {
"type": "string",
"description": "A unique ID for this analysis."
}
}
}
32 changes: 32 additions & 0 deletions vendor/hca-metadata-4-6-1/json_schema/analysis_bundle.json
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{
"definitions": {
"analysis_ingest": {
"required": [
"hca_ingest",
"content",
"core"
],
"type": "object",
"properties": {
"content": {
"type": "object",
"description": "Analysis content",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/analysis.json"
},
"core": {
"description": "Type and schema for this object.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/core.json"
},
"hca_ingest": {
"type": "object",
"description": "core fields added by HCA ingest service",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/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/4.6.1/json_schema/analysis_bundle.json#/definitions/analysis_ingest"
}
46 changes: 46 additions & 0 deletions vendor/hca-metadata-4-6-1/json_schema/assay.json
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{
"description": "An assay contains information relevant to how a sample (in vitro) was converted into digital information (in silico).",
"title": "assay",
"required": [
"core",
"assay_id"
],
"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/4.6.1/json_schema/core.json"
},
"name": {
"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.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/seq.json"
},
"rna": {
"description": "Information about how RNA was converted to cDNA.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/rna.json"
},
"single_cell": {
"description": "Information on single-cell aspects of an assay.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/single_cell.json"
},
"imaging": {
"description": "Information on image based RNA quantification assays",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.6.1/json_schema/imaging.json"
},
"assay_id": {
"type": "string",
"description": "A unique ID for this assay."
},
"description": {
"type": "string",
"description": "A general description of the assay."
}
}
}
50 changes: 50 additions & 0 deletions vendor/hca-metadata-4-6-1/json_schema/assay_bundle.json
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{
"definitions": {
"assay_ingest": {
"required": [
"hca_ingest",
"content",
"core"
],
"type": "object",
"properties": {
"has_input": {
"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",
"description": "The files that were generated from this assay."
},
"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/4.6.1/json_schema/assay_bundle.json#/definitions/assay_ingest"
}
39 changes: 39 additions & 0 deletions vendor/hca-metadata-4-6-1/json_schema/barcode.json
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{
"description": "This object describes where a particular type of barcode is in a read.",
"title": "barcode",
"required": [
"offset",
"size",
"read"
],
"additionalProperties": false,
"$schema": "http://json-schema.org/draft-04/schema#",
"type": "object",
"properties": {
"read": {
"enum": [
"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."
},
"size": {
"minimum": 0,
"type": "integer",
"description": "Size of barcode in nucleotides.",
"maximum": 50
},
"white_list_file": {
"type": "string",
"description": "Name of file containing legitimate barcode sequences. Unused for randomly generated barcodes."
},
"offset": {
"minimum": 0,
"type": "integer",
"description": "Offset in read of barcode. 0 for beginning of read.",
"maximum": 50
}
}
}
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