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Updated URLs to 4.2.0.
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@malloryfreeberg
malloryfreeberg committed Dec 5, 2017
1 parent 15d2f42 commit afe2cc0
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272 changes: 136 additions & 136 deletions json_schema/analysis.json
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Original file line number Diff line number Diff line change
@@ -1,155 +1,155 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
"additionalProperties": true,
"title": "analysis",
"required": [
"timestamp_start_utc",
"timestamp_stop_utc",
"computational_method",
"input_bundles",
"reference_bundle",
"analysis_id",
"analysis_run_type",
"metadata_schema",
"tasks",
"inputs",
"outputs"
],
"additionalProperties": true,
"definitions": {
"task": {
"additionalProperties": false,
"required": [
"name",
"start_time",
"stop_time",
"log",
"disk_size",
"docker_image",
"cpus",
"memory",
"zone"
],
"type": "object",
"properties": {
"disk_size": "string",
"name": "string",
"zone": "string",
"log_err": "uri",
"start_time": "date-time",
"cpus": "int",
"log_out": "uri",
"stop_time": "date-time",
"memory": "string",
"docker_image": "string"
}
},
"parameter": {
"additionalProperties": false,
"required": [
"name",
"value"
],
"type": "object",
"properties": {
"checksum": "string",
"name": "string",
"value": "string"
}
},
"file": {
"additionalProperties": false,
"required": [
"checksum",
"file_path",
"format"
],
"type": "object",
"properties": {
"checksum": "string",
"file_path": "uri",
"format": "string"
}
}
},
"$schema": "http://json-schema.org/draft-04/schema#",
"type": "object",
"properties": {
"tasks": {
"description": "Descriptions of tasks in the workflow.",
"type": "array",
"inputs": {
"items": {
"type": {
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/analysis.json#/definitions/task"
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/analysis.json#/definitions/parameter"
}
}
},
"analysis_id": {
"description": "A unique ID for this analysis.",
"type": "number"
},
"name": {
"description": "A short, descriptive name for the analysis that need not be unique.",
"type": "string"
},
"description": {
"description": "A general description of the analysis.",
"type": "string"
},
"computational_method": {
"description": "A URI to a versioned workflow and versioned execution environment in a GA4GH-compliant repository.",
"type": "uri"
},
"outputs": {
},
"type": "array",
"description": "Input parameters used in the pipeline run, these can be files or string values (settings)."
},
"reference_bundle": {
"type": "uri",
"description": "Bundle containing the reference used in running the pipeline."
},
"tasks": {
"items": {
"type": {
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/analysis.json#/definitions/file"
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/analysis.json#/definitions/task"
}
},
"description": "Output generated by the pipeline run.",
"type": "array"
},
},
"type": "array",
"description": "Descriptions of tasks in the workflow."
},
"description": {
"type": "string",
"description": "A general description of the analysis."
},
"timestamp_stop_utc": {
"type": "date-time",
"description": "Terminal stop time of the full pipeline."
},
"input_bundles": {
"items": {
"type": "uri"
},
"description": "The input bundles used in this analysis run.",
"type": "array"
},
"timestamp_stop_utc": {
"type": "date-time",
"description": "Terminal stop time of the full pipeline."
},
"metadata_schema": {
"description": "The version of the metadata schemas used for the json files.",
"type": "string"
},
"timestamp_start_utc": {
"description": "Initial start time of the full pipeline.",
"type": "date-time"
},
"inputs": {
},
"type": "array",
"description": "The input bundles used in this analysis run."
},
"outputs": {
"items": {
"type": {
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/analysis.json#/definitions/parameter"
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/analysis.json#/definitions/file"
}
},
"type": "array",
"description": "Input parameters used in the pipeline run, these can be files or string values (settings)."
},
},
"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": "uri",
"description": "A URI to a versioned workflow and versioned execution environment in a GA4GH-compliant repository."
},
"timestamp_start_utc": {
"type": "date-time",
"description": "Initial start time of the full pipeline."
},
"core": {
"description": "Type and schema for this object.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/core.json"
},
"analysis_run_type": {
"enum": [
"run",
"run",
"copy-forward"
],
"description": "Indicator of whether the analysis actually ran or was just copied forward as an optimization.",
"type": "string"
},
"reference_bundle": {
"description": "Bundle containing the reference used in running the pipeline.",
"type": "uri"
},
"core": {
"description": "Type and schema for this object.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/core.json"
}
},
"type": "object",
"definitions": {
"file": {
"additionalProperties": false,
"required": [
"checksum",
"file_path",
"format"
],
"properties": {
"format": "string",
"file_path": "uri",
"checksum": "string"
},
"type": "object"
},
"task": {
"properties": {
"start_time": "date-time",
"stop_time": "date-time",
"name": "string",
"log_err": "uri",
"log_out": "uri",
"disk_size": "string",
"docker_image": "string",
"cpus": "int",
"memory": "string",
"zone": "string"
},
"required": [
"name",
"start_time",
"stop_time",
"log",
"disk_size",
"docker_image",
"cpus",
"memory",
"zone"
],
"additionalProperties": false,
"type": "object"
},
"parameter": {
"additionalProperties": false,
"required": [
"name",
"value"
],
"properties": {
"checksum": "string",
"value": "string",
"name": "string"
},
"type": "object"
],
"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": "number",
"description": "A unique ID for this 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"
]
}
}
76 changes: 38 additions & 38 deletions json_schema/assay.json
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Original file line number Diff line number Diff line change
@@ -1,46 +1,46 @@
{
"$schema": "http://json-schema.org/draft-04/schema#",
"additionalProperties": false,
"definitions": {},
"description": "An assay contains information relevant to how a sample (in vitro) was converted into digital information (in silico).",
"description": "An assay contains information relevant to how a sample (in vitro) was converted into digital information (in silico).",
"title": "assay",
"required": [
"core",
"assay_id"
],
"additionalProperties": false,
"definitions": {},
"$schema": "http://json-schema.org/draft-04/schema#",
"type": "object",
"properties": {
"core": {
"description": "Type and schema for this object.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/core.json"
},
"assay_id": {
"description": "A unique ID for this assay.",
"type": "string"
},
"description": "Type and schema for this object.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/core.json"
},
"name": {
"description": "A short, descriptive name for the assay that need not be unique.",
"type": "string"
},
"description": {
"description": "A general description of the assay.",
"type": "string"
},
"imaging": {
"description": "Information on image based RNA quantification assays",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/imaging.json"
},
"rna": {
"description": "Information about how RNA was converted to cDNA.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/rna.json"
},
"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.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/seq.json"
},
"description": "Information about how a cDNA sample was sequenced.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/seq.json"
},
"rna": {
"description": "Information about how RNA was converted to cDNA.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/rna.json"
},
"single_cell": {
"description": "Information on single-cell aspects of an assay.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/single_cell.json"
"description": "Information on single-cell aspects of an assay.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/single_cell.json"
},
"imaging": {
"description": "Information on image based RNA quantification assays",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/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."
}
},
"required": [
"core",
"assay_id"
],
"title": "assay",
"type": "object"
}
}
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