samples

Find samples

Lists samples, filtering by data passed as URL parameters.

Errors

StatusDescription
400 Invalid query

Request

get
/samples

Response

{
  "status": "200"
}

Create a sample

Creates a new sample with the given name, labels and subtractions.

Parameters

Name Type Required Description
files array true
group integer false
host string false
isolate string false
labels array false
library_type false
locale string false
name string true
notes string false
subtractions array false

Errors

StatusDescription
400 Invalid input
403 Not permitted

Request

post
/samples

Response

{
  "example": {
    "all_read": false,
    "all_write": false,
    "artifacts": [],
    "created_at": "2022-05-20T23:48:00.901000Z",
    "format": "fastq",
    "group": {
      "id": 4,
      "name": "Sidney"
    },
    "group_read": true,
    "group_write": true,
    "hold": true,
    "host": "Malus domestica",
    "id": "9zn468u9",
    "is_legacy": false,
    "isolate": "",
    "labels": [],
    "library_type": "normal",
    "locale": "",
    "name": "HX8",
    "notes": "",
    "nuvs": false,
    "paired": true,
    "pathoscope": true,
    "quality": {
      "bases": [
        [
          36,
          37,
          37,
          37,
          37,
          37
        ],
        [
          36,
          37,
          37,
          37,
          37,
          37
        ]
      ],
      "composition": [
        [
          29,
          18,
          15,
          36.5
        ],
        [
          25.5,
          19,
          31.5,
          22
        ]
      ],
      "count": 94601674,
      "encoding": "Sanger / Illumina 1.9\n",
      "gc": 43,
      "length": [
        150,
        150
      ],
      "sequences": [
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        18,
        298
      ]
    },
    "reads": [
      {
        "download_url": "/samples/9zn468u9/reads/reads_1.fq.gz",
        "id": 713,
        "name": "reads_1.fq.gz",
        "name_on_disk": "reads_1.fq.gz",
        "sample": "9zn468u9",
        "size": 3540467819,
        "upload": null,
        "uploaded_at": "2022-05-21T00:10:27.418000Z"
      },
      {
        "download_url": "/samples/9zn468u9/reads/reads_2.fq.gz",
        "id": 714,
        "name": "reads_2.fq.gz",
        "name_on_disk": "reads_2.fq.gz",
        "sample": "9zn468u9",
        "size": 3321721014,
        "upload": null,
        "uploaded_at": "2022-05-21T00:11:10.743000Z"
      }
    ],
    "ready": true,
    "subtractions": [
      {
        "id": "0nhpi36p",
        "name": "Malus domestica"
      }
    ],
    "user": {
      "administrator": true,
      "handle": "mrott",
      "id": "ihvze2u9"
    },
    "workflows": {
      "aodp": "incompatible",
      "nuvs": "none",
      "pathoscope": "none"
    }
  },
  "status": "201"
}

Delete a sample

Removes a sample document and all associated analyses.

Request

delete
/samples/{sample_id}

Get a sample

Fetches the details for a sample.

Errors

StatusDescription
403
404

Request

get
/samples/{sample_id}

Response

{
  "example": {
    "all_read": false,
    "all_write": false,
    "artifacts": [],
    "created_at": "2022-05-20T23:48:00.901000Z",
    "format": "fastq",
    "group": {
      "id": 4,
      "name": "Sidney"
    },
    "group_read": true,
    "group_write": true,
    "hold": true,
    "host": "Malus domestica",
    "id": "9zn468u9",
    "is_legacy": false,
    "isolate": "",
    "labels": [],
    "library_type": "normal",
    "locale": "",
    "name": "HX8",
    "notes": "",
    "nuvs": false,
    "paired": true,
    "pathoscope": true,
    "quality": {
      "bases": [
        [
          36,
          37,
          37,
          37,
          37,
          37
        ],
        [
          36,
          37,
          37,
          37,
          37,
          37
        ]
      ],
      "composition": [
        [
          29,
          18,
          15,
          36.5
        ],
        [
          25.5,
          19,
          31.5,
          22
        ]
      ],
      "count": 94601674,
      "encoding": "Sanger / Illumina 1.9\n",
      "gc": 43,
      "length": [
        150,
        150
      ],
      "sequences": [
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        18,
        298
      ]
    },
    "reads": [
      {
        "download_url": "/samples/9zn468u9/reads/reads_1.fq.gz",
        "id": 713,
        "name": "reads_1.fq.gz",
        "name_on_disk": "reads_1.fq.gz",
        "sample": "9zn468u9",
        "size": 3540467819,
        "upload": null,
        "uploaded_at": "2022-05-21T00:10:27.418000Z"
      },
      {
        "download_url": "/samples/9zn468u9/reads/reads_2.fq.gz",
        "id": 714,
        "name": "reads_2.fq.gz",
        "name_on_disk": "reads_2.fq.gz",
        "sample": "9zn468u9",
        "size": 3321721014,
        "upload": null,
        "uploaded_at": "2022-05-21T00:11:10.743000Z"
      }
    ],
    "ready": true,
    "subtractions": [
      {
        "id": "0nhpi36p",
        "name": "Malus domestica"
      }
    ],
    "user": {
      "administrator": true,
      "handle": "mrott",
      "id": "ihvze2u9"
    },
    "workflows": {
      "aodp": "incompatible",
      "nuvs": "none",
      "pathoscope": "none"
    }
  },
  "status": "200"
}

Update a sample

Updates a sample using its 'sample id'.

Parameters

Name Type Required Description
host string false
isolate string false
labels array false
locale string false
name string false
notes string false
subtractions array false

Errors

StatusDescription
400 Sample name is already in use
403 Insufficient rights
404 Not found

Request

patch
/samples/{sample_id}
{
  "host": "Tobacco",
  "labels": [
    1,
    5,
    6
  ],
  "name": "Tobacco mosaic viru"
}

Response

{
  "example": {
    "all_read": false,
    "all_write": false,
    "artifacts": [],
    "created_at": "2022-05-20T23:48:00.901000Z",
    "format": "fastq",
    "group": {
      "id": 4,
      "name": "Sidney"
    },
    "group_read": true,
    "group_write": true,
    "hold": true,
    "host": "Tobacco",
    "id": "9zn468u9",
    "is_legacy": false,
    "isolate": "",
    "labels": [
      1,
      5,
      6
    ],
    "library_type": "normal",
    "locale": "",
    "name": "Tobacco mosaic viru",
    "notes": "",
    "nuvs": false,
    "paired": true,
    "pathoscope": true,
    "quality": {
      "bases": [
        [
          36,
          37,
          37,
          37,
          37,
          37
        ],
        [
          36,
          37,
          37,
          37,
          37,
          37
        ]
      ],
      "composition": [
        [
          29,
          18,
          15,
          36.5
        ],
        [
          25.5,
          19,
          31.5,
          22
        ]
      ],
      "count": 94601674,
      "encoding": "Sanger / Illumina 1.9\n",
      "gc": 43,
      "length": [
        150,
        150
      ],
      "sequences": [
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        18,
        298
      ]
    },
    "reads": [
      {
        "download_url": "/samples/9zn468u9/reads/reads_1.fq.gz",
        "id": 713,
        "name": "reads_1.fq.gz",
        "name_on_disk": "reads_1.fq.gz",
        "sample": "9zn468u9",
        "size": 3540467819,
        "upload": null,
        "uploaded_at": "2022-05-21T00:10:27.418000Z"
      },
      {
        "download_url": "/samples/9zn468u9/reads/reads_2.fq.gz",
        "id": 714,
        "name": "reads_2.fq.gz",
        "name_on_disk": "reads_2.fq.gz",
        "sample": "9zn468u9",
        "size": 3321721014,
        "upload": null,
        "uploaded_at": "2022-05-21T00:11:10.743000Z"
      }
    ],
    "ready": true,
    "subtractions": [
      {
        "id": "0nhpi36p",
        "name": "Malus domestica"
      }
    ],
    "user": {
      "administrator": true,
      "handle": "mrott",
      "id": "ihvze2u9"
    },
    "workflows": {
      "aodp": "incompatible",
      "nuvs": "none",
      "pathoscope": "none"
    }
  },
  "status": "200"
}

Get analyses

Lists the analyses associated with the given sample_id.

Errors

StatusDescription
403 Insufficient rights
404 Not found

Request

get
/samples/{sample_id}/analyses

Response

{
  "status": "200"
}

Start analysis job

Starts an analysis job for a given sample.

Parameters

Name Type Required Description
ml integer false
ref_id string true
subtractions array false
workflow true

Errors

StatusDescription
400 Invalid input
403 Insufficient rights
404 Not found

Request

post
/samples/{sample_id}/analyses

Response

{
  "example": {
    "created_at": "2022-05-21T01:28:55.441000Z",
    "id": "m9ktiz0i",
    "index": {
      "id": "9c5u6wsq",
      "version": 13
    },
    "job": {
      "id": "bt8nwg9z"
    },
    "ready": true,
    "reference": {
      "id": "d19exr83",
      "name": "New Plant Viruses"
    },
    "sample": {
      "id": "9zn468u9"
    },
    "subtractions": [
      {
        "id": "0nhpi36p",
        "name": "Malus domestica"
      }
    ],
    "updated_at": "2022-05-21T01:28:55.441000Z",
    "user": {
      "administrator": true,
      "handle": "mrott",
      "id": "ihvze2u9"
    },
    "workflow": "pathoscope_bowtie"
  },
  "status": "201"
}

Update rights settings

Updates the rights settings for the specified sample document.

Parameters

Name Type Required Description
all_read boolean false
all_write boolean false
group false
group_read boolean false
group_write boolean false

Errors

StatusDescription
400 Group does not exist
403 Must be administrator or sample owner
404 Not found

Request

patch
/samples/{sample_id}/rights
{
  "group": "administrator",
  "group_read": true,
  "group_write": true
}

Response

{
  "example": {
    "all_read": false,
    "all_write": false,
    "artifacts": [],
    "created_at": "2022-05-20T23:48:00.901000Z",
    "format": "fastq",
    "group": "administrator",
    "group_read": true,
    "group_write": true,
    "hold": true,
    "host": "virus",
    "id": "9zn468u9",
    "is_legacy": false,
    "isolate": "",
    "labels": [
      1,
      5,
      6
    ],
    "library_type": "normal",
    "locale": "",
    "name": "foo",
    "notes": "",
    "nuvs": false,
    "paired": true,
    "pathoscope": true,
    "quality": {
      "bases": [
        [
          36,
          37,
          37,
          37,
          37,
          37
        ],
        [
          36,
          37,
          37,
          37,
          37,
          37
        ]
      ],
      "composition": [
        [
          29,
          18,
          15,
          36.5
        ],
        [
          25.5,
          19,
          31.5,
          22
        ]
      ],
      "count": 94601674,
      "encoding": "Sanger / Illumina 1.9\n",
      "gc": 43,
      "length": [
        150,
        150
      ],
      "sequences": [
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        0,
        18,
        298
      ]
    },
    "reads": [
      {
        "download_url": "/samples/9zn468u9/reads/reads_1.fq.gz",
        "id": 713,
        "name": "reads_1.fq.gz",
        "name_on_disk": "reads_1.fq.gz",
        "sample": "9zn468u9",
        "size": 3540467819,
        "upload": null,
        "uploaded_at": "2022-05-21T00:10:27.418000Z"
      },
      {
        "download_url": "/samples/9zn468u9/reads/reads_2.fq.gz",
        "id": 714,
        "name": "reads_2.fq.gz",
        "name_on_disk": "reads_2.fq.gz",
        "sample": "9zn468u9",
        "size": 3321721014,
        "upload": null,
        "uploaded_at": "2022-05-21T00:11:10.743000Z"
      }
    ],
    "ready": true,
    "subtractions": [
      {
        "id": "0nhpi36p",
        "name": "Malus domestica"
      }
    ],
    "user": {
      "administrator": true,
      "handle": "mrott",
      "id": "ihvze2u9"
    },
    "workflows": {
      "aodp": "incompatible",
      "nuvs": "none",
      "pathoscope": "none"
    }
  },
  "status": "200"
}