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Merge pull request #38 from qbicsoftware/release/1.3
Prepare release 1.3
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| # IMGAG dropbox | ||
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| ## Expected data structure | ||
| The data structure needs to be a root folder, containing a file `metadata` following the [upload metadata schema](upload-metadata.schema.json). In addition, the folder shall contain files of type `fastq/fastq.gz` and/or `vcf/vcf.gz` and/or `GSvar/GSvar.gz`. | ||
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| Incoming structure overview: | ||
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| ``` | ||
| |-QTEST001AE (top level folder name) | ||
| | | ||
| |- file1.fastq.gz | ||
| |- file2.fastq.gz | ||
| |- metadata | ||
| |- ... | ||
| ``` | ||
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| openBIS structure overview: | ||
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| TODO: ER model. | ||
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| ## Expected metadata | ||
| Metadata is expected to be noted in JSON and following the [upload metadata schema](upload-metadata.schema.json). An example JSON entry can look like this: | ||
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| ``` | ||
| { | ||
| "files": [ | ||
| "reads.1.fastq.gz", | ||
| "reads.2.fastq.gz" | ||
| ], | ||
| "type": "dna_seq", | ||
| "sample1": { | ||
| "genome": "GRCh37", | ||
| "id_genetics": "GS000000_01", | ||
| "id_qbic": "QTEST002AE", | ||
| "processing_system": "Test system", | ||
| "tumor": "no" | ||
| } | ||
| } | ||
| ``` | ||
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| The sample code for `id_qbic` can be of type `Q_TEST_SAMPLE` or `Q_BIOLOGICAL_SAMPLE`. In the latter case, a new sample of type `Q_TEST_SAMPLE` is created and attached as child to the biological sample. The data-set will be registered under this test sample then. |
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drop-boxes/register-imgag-dropbox/upload-metadata.schema.json
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| { | ||
| "$schema": "http://json-schema.org/draft-07/schema", | ||
| "$id": "http://qbic.life/v1/upload-metadata.schema.json", | ||
| "title": "Upload metadata for data registration at QBiC", | ||
| "description": "A full description of mandatory and optional metadata properties that need to/can be included for data registration via QBiC dropboxes.", | ||
| "type": "object", | ||
| "definitions": { | ||
| "qc": { | ||
| "type": "object", | ||
| "properties": { | ||
| "qcml_id": { | ||
| "type": "string", | ||
| "description": "A qcml id following the qzml specification", | ||
| "pattern": "^QC:[0-9]{7}$" | ||
| }, | ||
| "name": { | ||
| "type": "string", | ||
| "description": "Name of the quality control", | ||
| "examples": ["read count", "target region read depth", "Q20 read percentage"] | ||
| }, | ||
| "value": { | ||
| "type": "string", | ||
| "description": "The actual qc value" | ||
| } | ||
| } | ||
| }, | ||
| "sample": { | ||
| "type": "object", | ||
| "properties": { | ||
| "genome": { | ||
| "type": "string", | ||
| "examples": ["GRCh37"] | ||
| }, | ||
| "id_genetics": { | ||
| "type": "string", | ||
| "description": "A sample URI provided by the human genetics department", | ||
| "examples": ["GS000000_01"] | ||
| }, | ||
| "id_qbic": { | ||
| "type": "string", | ||
| "pattern": "Q\\w{4}\\d{3}[A-X][A-X0-9]", | ||
| "description": "QBIC sample code of the analysed biological specimen", | ||
| "examples": ["QTEST001AE"] | ||
| }, | ||
| "processing_system": { | ||
| "type": "string", | ||
| "examples": ["SureSelectXT Human All Exon v5"] | ||
| }, | ||
| "qc": { | ||
| "type": "array", | ||
| "items": { | ||
| "allOf": [ | ||
| { | ||
| "$ref": "#/definitions/qc" | ||
| } | ||
| ] | ||
| } | ||
| }, | ||
| "tumor": { | ||
| "type": "string", | ||
| "enum": ["yes", "no"] | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "properties": { | ||
| "files": { | ||
| "type": "array", | ||
| "items": { "type": "string" }, | ||
| "minItems": 1 | ||
| }, | ||
| "type": { | ||
| "type": "string", | ||
| "enum": ["dna_seq", "rna_seq", "dna_seq_somatic"] | ||
| }, | ||
| "sample1": { "$ref": "#/definitions/sample" }, | ||
| "sample2": { "$ref": "#/definitions/sample" } | ||
| }, | ||
| "required": [ | ||
| "files", | ||
| "type", | ||
| "sample1" | ||
| ] | ||
| } |
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