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Merge pull request #97 from HumanCellAtlas/v4.5.0-minorRelease
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V4.5.0 minor release
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@daniwelter
daniwelter authored Dec 13, 2017
2 parents 1c26aab + 64802c2 commit f73bcd5
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44 changes: 22 additions & 22 deletions json_schema/analysis.json
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Expand Up @@ -32,36 +32,36 @@
"type": "object",
"properties": {
"disk_size": {
"type" : "string"
"type": "string"
},
"name": {
"type" : "string"
"type": "string"
},
"zone": {
"type" : "string"
"type": "string"
},
"log_err": {
"type" : "string"
"type": "string"
},
"start_time":{
"start_time": {
"type": "string",
"format": "date-time"
},
"cpus": {
"type" : "integer"
"type": "integer"
},
"log_out":{
"type" : "string"
"log_out": {
"type": "string"
},
"stop_time": {
"type": "string",
"format": "date-time"
},
"memory":{
"type" : "string"
"memory": {
"type": "string"
},
"docker_image":{
"type" : "string"
"docker_image": {
"type": "string"
}
}
},
Expand All @@ -74,13 +74,13 @@
"type": "object",
"properties": {
"checksum": {
"type" : "string"
"type": "string"
},
"name": {
"type" : "string"
"type": "string"
},
"value": {
"type" : "string"
"type": "string"
}
}
},
Expand All @@ -94,13 +94,13 @@
"type": "object",
"properties": {
"checksum": {
"type" : "string"
"type": "string"
},
"file_path": {
"type" : "string"
"type": "string"
},
"format": {
"type" : "string"
"type": "string"
}
}
}
Expand All @@ -110,7 +110,7 @@
"properties": {
"inputs": {
"items": {
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/analysis.json#/definitions/parameter"
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/analysis.json#/definitions/parameter"
},
"type": "array",
"description": "Input parameters used in the pipeline run, these can be files or string values (settings)."
Expand All @@ -121,7 +121,7 @@
},
"tasks": {
"items": {
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/analysis.json#/definitions/task"
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/analysis.json#/definitions/task"
},
"type": "array",
"description": "Descriptions of tasks in the workflow."
Expand All @@ -144,7 +144,7 @@
},
"outputs": {
"items": {
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/analysis.json#/definitions/file"
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/analysis.json#/definitions/file"
},
"type": "array",
"description": "Output generated by the pipeline run."
Expand All @@ -164,7 +164,7 @@
},
"core": {
"description": "Type and schema for this object.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/core.json"
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/core.json"
},
"analysis_run_type": {
"enum": [
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32 changes: 32 additions & 0 deletions json_schema/analysis_bundle.json
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@@ -0,0 +1,32 @@
{
"definitions": {
"analysis_ingest": {
"required": [
"hca_ingest",
"content",
"core"
],
"type": "object",
"properties": {
"content": {
"type": "object",
"description": "Analysis content",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/analysis.json"
},
"core": {
"description": "Type and schema for this object.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/core.json"
},
"hca_ingest": {
"type": "object",
"description": "core fields added by HCA ingest service",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ingest.json"
}
}
}
},
"$schema": "http://json-schema.org/draft-04/schema#",
"type": "object",
"description": "A schema for a analysis bundle",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/analysis_bundle.json#/definitions/analysis_ingest"
}
56 changes: 28 additions & 28 deletions json_schema/assay.json
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@@ -1,45 +1,45 @@
{
"description": "An assay contains information relevant to how a sample (in vitro) was converted into digital information (in silico).",
"title": "assay",
"description": "An assay contains information relevant to how a sample (in vitro) was converted into digital information (in silico).",
"title": "assay",
"required": [
"core",
"core",
"assay_id"
],
"additionalProperties": false,
"definitions": {},
"$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/4.4.0/json_schema/core.json"
},
"description": "Type and schema for this object.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/core.json"
},
"name": {
"type": "string",
"type": "string",
"description": "A short, descriptive name for the assay that need not be unique."
},
},
"seq": {
"description": "Information about how a cDNA sample was sequenced.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/seq.json"
},
"description": "Information about how a cDNA sample was sequenced.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/seq.json"
},
"rna": {
"description": "Information about how RNA was converted to cDNA.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/rna.json"
},
"description": "Information about how RNA was converted to cDNA.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/rna.json"
},
"single_cell": {
"description": "Information on single-cell aspects of an assay.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/single_cell.json"
},
"description": "Information on single-cell aspects of an assay.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/single_cell.json"
},
"imaging": {
"description": "Information on image based RNA quantification assays",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/imaging.json"
},
"description": "Information on image based RNA quantification assays",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/imaging.json"
},
"assay_id": {
"type": "string",
"type": "string",
"description": "A unique ID for this assay."
},
},
"description": {
"type": "string",
"type": "string",
"description": "A general description of the assay."
}
}
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57 changes: 34 additions & 23 deletions json_schema/assay_bundle.json
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Expand Up @@ -2,38 +2,49 @@
"definitions": {
"assay_ingest": {
"required": [
"hca_ingest",
"content",
"hca_ingest",
"content",
"core"
],
"type": "object",
],
"type": "object",
"properties": {
"content": {
"type": "object",
"description": "Assay content",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/assay.json"
},
"type": "object",
"description": "Assay content",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/assay.json"
},
"derivation_protocols": {
"items": {
"description": "An array of protocols used in derivation of this sample.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/protocol.json"
},
"description": "An array of protocols used in derivation of this sample.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/protocol.json"
},
"type": "array"
},
},
"hca_ingest": {
"type": "object",
"description": "core fields added by HCA ingest service",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/ingest.json"
},
"type": "object",
"description": "core fields added by HCA ingest service",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/ingest.json"
},
"has_input": {
"type": "string",
"description": "The sample that this assay was performed on."
},
"has_output": {
"items": {
"type": "string"
},
"type": "array",
"description": "The files that were generated from this assay."
},
"core": {
"description": "Type and schema for this object.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/core.json"
"description": "Type and schema for this object.",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/core.json"
}
}
}
},
"$schema": "http://json-schema.org/draft-04/schema#",
"type": "object",
"description": "A schema for an assay bundle",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.4.0/json_schema/assay_bundle.json#/definitions/assay_ingest"
},
"$schema": "http://json-schema.org/draft-04/schema#",
"type": "object",
"description": "A schema for an assay bundle",
"$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.5.0/json_schema/assay_bundle.json#/definitions/assay_ingest"
}
44 changes: 22 additions & 22 deletions json_schema/barcode.json
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@@ -1,38 +1,38 @@
{
"description": "This object describes where a particular type of barcode is in a read.",
"title": "barcode",
"description": "This object describes where a particular type of barcode is in a read.",
"title": "barcode",
"required": [
"offset",
"size",
"offset",
"size",
"read"
],
"additionalProperties": false,
"$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.",
"minimum": 0,
"type": "integer",
"description": "Offset in read of barcode. 0 for beginning of read.",
"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.",
"minimum": 0,
"type": "integer",
"description": "Size of barcode in nucleotides.",
"maximum": 50
}
}
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