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Commit c58eca8e authored by van den Berg's avatar van den Berg
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{
"files": [
{
"filename": "sample1_R1.fastq.gz",
"md5": "c3875788d22baa678c87c8f903cb2350",
"tags": {
"readtype": "forward"
},
"sample_name": "sample5"
},
{
"filename": "sample1_R2.fastq.gz",
"md5": "74cedbb88402dd16a6b4f96e5440fdfd",
"tags": {
"readtype": "umi"
},
"sample_name": "sample5"
},
{
"filename": "sample1_R3.fastq.gz",
"md5": "617e686e88c06ad1d7319f606ebcbfc5",
"tags": {
"readtype": "reverse"
},
"sample_name": "sample5"
}
],
"run_name": "runname5",
"sample_group": {
"samples": [
{
"sample_name": "sample5",
"tags": {
"gender": "V",
"gs_batch": "006",
"gs_sample": "005",
"experimentnr": "1234",
"gs_projectcode": "104785-006",
"sequencer": "Nextseq 500",
"capture_kit": "V7",
"verrichting_id": "9049809068123",
"fractienr": "AD8957"
}
}
],
"group_name": "samplegroup5"
},
"title": "Test for file tags in runs endpoint"
}
{
"files": [
{
"md5": "c3875788d22baa678c87c8f903cb2350",
"filename": "sample1_R1.fastq.gz",
"sample_name": "sample4",
"tags": {
"readtype": "forward"
}
},
{
"md5": "74cedbb88402dd16a6b4f96e5440fdfd",
"filename": "sample1_R2.fastq.gz",
"sample_name": "sample4",
"tags": {
"readtype": "umi"
}
},
{
"md5": "617e686e88c06ad1d7319f606ebcbfc5",
"filename": "sample1_R3.fastq.gz",
"sample_name": "sample4",
"tags": {
"readtype": "reverse"
}
}
],
"sample_group": {
"samples": [
{
"sample_name": "sample4"
}
],
"group_name": "samplegroup4"
},
"run_name": "runname4",
"title": "Test for file tags in runs endpoint"
}
{
"files": [
{
"md5": "c3875788d22baa678c87c8f903cb2350",
"filename": "sample1_R1.fastq.gz",
"sample_name": "sample5",
"tags": {
"readtype": "forward"
}
},
{
"md5": "74cedbb88402dd16a6b4f96e5440fdfd",
"filename": "sample1_R2.fastq.gz",
"sample_name": "sample5",
"tags": {
"readtype": "umi"
}
},
{
"md5": "617e686e88c06ad1d7319f606ebcbfc5",
"filename": "sample1_R3.fastq.gz",
"sample_name": "sample5",
"tags": {
"readtype": "reverse"
}
}
],
"sample_group": {
"samples": [
{
"sample_name": "sample5",
"tags": {
"capture_kit": "Cre v2",
"experimentnr": "1234",
"fractienr": "AD8957",
"gender": "V",
"gs_batch": "006",
"gs_projectcode": "104785-006",
"gs_sample": "005",
"sequencer": "Nextseq 500",
"verrichting_id": "9049809068123"
}
}
],
"group_name": "samplegroup5"
},
"run_name": "runname5",
"title": "Test for file tags in runs endpoint"
}
{
"definitions": {
"Name": {
"description": "Valid name that is unlikely to break parsing, spaces are not allowed",
"type": "string",
"pattern": "^([A-Za-z0-9]+[A-Za-z0-9-_.]*[A-Za-z0-9]+)$|^([A-Za-z0-9])$"
},
"Description": {
"description": "Valid description for objects, no restrictions",
"type": "string"
},
"FileTag": {
"description": "FileTag object, required for Files",
"type": "object",
"required": [
"readtype"
],
"properties": {
"readtype": {
"type": "string",
"enum": [
"forward",
"reverse",
"umi"
]
}
}
},
"File": {
"description": "Minimum required properties for a file",
"type": "object",
"required": [
"md5",
"filename",
"sample_name",
"tags"
],
"additionalProperties": false,
"properties": {
"md5": {
"description": "MD5 checksum of the content of the file",
"type": "string",
"pattern": "^[a-f0-9]{32}$"
},
"filename": {
"description": "Name of the file",
"$ref": "#/definitions/Name"
},
"sample_name": {
"description": "The associated sample of this file",
"$ref": "#/definitions/Name"
},
"tags": {
"description": "The tags that belong to this file",
"$ref": "#/definitions/FileTag"
}
}
},
"SampleGroup": {
"description": "Minimum required properties for a sample group",
"type": "object",
"required": [
"group_name",
"samples"
],
"properties": {
"group_name": {
"description": "Name of the sample group",
"$ref": "#definitions/Name"
},
"samples": {
"description": "An array of one or more Samples",
"type": "array",
"minItems": 1,
"uniqueItems": true,
"items": {
"$ref": "#/definitions/Sample"
}
}
}
},
"Sample": {
"description": "Minimum required properties for a sample",
"type": "object",
"required": [
"sample_name"
],
"additionalProperties": false,
"properties": {
"sample_name": {
"description": "Name of the sample",
"type": "string",
"$ref": "#/definitions/Name"
}
}
},
"EMC_Sample": {
"description": "Minimum required properties for an EMC sample",
"type": "object",
"required": [
"sample_name",
"tags"
],
"additionalProperties": false,
"properties": {
"sample_name": {
"description": "Name of the sample",
"type": "string",
"$ref": "#/definitions/Name"
},
"tags": {
"$ref": "#/definitions/EMC_Tags"
}
}
},
"EMC_Tag": {
"description": "Minimum required properties for EMC Sample tags",
"type": "object",
"required": [
"gender",
"gs_batch",
"gs_sample",
"gs_projectcode",
"sequencer",
"capture_kit",
"verrichting_id",
"fractienr"
],
"additionalProperties": false,
"properties": {
"gender": {
"$ref": "#/definitions/Name"
},
"gs_batch": {
"$ref": "#/definitions/Name"
},
"gs_sample": {
"$ref": "#/definitions/Name"
},
"experimentnr": {
"$ref": "#/definitions/Name"
},
"gs_projectcode": {
"$ref": "#/definitions/Name"
},
"sequencer": {
"$ref": "#/definitions/Description"
},
"capture_kit": {
"$ref": "#/definitions/Description"
},
"verrichtingen_id": {
"$ref": "#/definitions/Name"
},
"fractienr": {
"$ref": "#/definitions/Name"
}
}
}
},
"title": "Minimal transfer metadata",
"description": "Transfer schema for Illumina data. With or without UMI",
"type": "object",
"required": [
"title",
"sample_group",
"run_name",
"files"
],
"additionalProperties": false,
"properties": {
"files": {
"description": "An array of one or more Files",
"type": "array",
"minItems": 1,
"uniqueItems": true,
"items": {
"$ref": "#/definitions/File"
}
},
"sample_group": {
"description": "Sample group information for this transfer",
"$ref": "#/definitions/SampleGroup"
},
"run_name": {
"description": "Run name for this transfer",
"$ref": "#/definitions/Name"
},
"title": {
"description": "Title of this transfer, this will be used in the notification email",
"$ref": "#/definitions/Description"
}
}
}
{
"definitions": {
"Name": {
"description": "Valid name that is unlikely to break parsing, spaces are not allowed",
"type": "string",
"pattern": "^([A-Za-z0-9]+[A-Za-z0-9-_.]*[A-Za-z0-9]+)$|^([A-Za-z0-9])$"
},
"Description": {
"description": "Valid description for objects, no restrictions",
"type": "string"
},
"FileTag": {
"description": "FileTag object, required for Files",
"type": "object",
"required": [
"readtype"
],
"properties": {
"readtype": {
"type": "string",
"enum": [
"forward",
"reverse",
"umi"
]
}
}
},
"File": {
"description": "Minimum required properties for a file",
"type": "object",
"required": [
"md5",
"filename",
"sample_name",
"tags"
],
"additionalProperties": false,
"properties": {
"md5": {
"description": "MD5 checksum of the content of the file",
"type": "string",
"pattern": "^[a-f0-9]{32}$"
},
"filename": {
"description": "Name of the file",
"$ref": "#/definitions/Name"
},
"sample_name": {
"description": "The associated sample of this file",
"$ref": "#/definitions/Name"
},
"tags": {
"description": "The tags that belong to this file",
"$ref": "#/definitions/FileTag"
}
}
},
"SampleGroup": {
"description": "Minimum required properties for a sample group",
"type": "object",
"required": [
"group_name",
"samples"
],
"properties": {
"group_name": {
"description": "Name of the sample group",
"$ref": "#definitions/Name"
},
"samples": {
"description": "An array of one or more Samples",
"type": "array",
"minItems": 1,
"uniqueItems": true,
"items": {
"$ref": "#/definitions/Sample"
}
}
}
},
"Sample": {
"description": "Minimum required properties for an EMC sample",
"type": "object",
"required": [
"sample_name",
"tags"
],
"additionalProperties": false,
"properties": {
"sample_name": {
"description": "Name of the sample",
"type": "string",
"$ref": "#/definitions/Name"
},
"tags": {
"$ref": "#/definitions/SampleTag"
}
}
},
"SampleTag": {
"description": "Minimum required properties for EMC Sample tags",
"type": "object",
"required": [
"gender",
"gs_batch",
"gs_sample",
"gs_projectcode",
"sequencer",
"capture_kit",
"verrichting_id",
"fractienr"
],
"additionalProperties": false,
"properties": {
"gender": {
"enum": [
"V",
"M",
"O"
]
},
"gs_batch": {
"$ref": "#/definitions/Name"
},
"gs_sample": {
"$ref": "#/definitions/Name"
},
"experimentnr": {
"$ref": "#/definitions/Name"
},
"gs_projectcode": {
"$ref": "#/definitions/Name"
},
"sequencer": {
"$ref": "#/definitions/Description"
},
"capture_kit": {
"enum": [
"Cardio",
"Cre v2",
"V7_CNV",
"Human all exon V7"
]
},
"verrichting_id": {
"$ref": "#/definitions/Name"
},
"fractienr": {
"$ref": "#/definitions/Name"
}
}
}
},
"title": "Minimal transfer metadata",
"description": "Transfer schema for Illumina data. With or without UMI",
"type": "object",
"required": [
"title",
"sample_group",
"run_name",
"files"
],
"additionalProperties": false,
"properties": {
"files": {
"description": "An array of one or more Files",
"type": "array",
"minItems": 1,
"uniqueItems": true,
"items": {
"$ref": "#/definitions/File"
}
},
"sample_group": {
"description": "Sample group information for this transfer",
"$ref": "#/definitions/SampleGroup"
},
"run_name": {
"description": "Run name for this transfer",
"$ref": "#/definitions/Name"
},
"title": {
"description": "Title of this transfer, this will be used in the notification email",
"$ref": "#/definitions/Description"
}
}
}
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