analyses

Find analyses

Lists analyses based on a search term.

The response will only list analyses on which the user agent has read rights.

Request

get
/analyses

Response

{
  "example": {
    "documents": [
      {
        "created_at": "2022-08-15T17:42:35.979000Z",
        "id": "ofv7rp4v",
        "index": {
          "id": "u3lm1rk8",
          "version": 14
        },
        "job": {
          "id": "us3toy8j"
        },
        "ready": true,
        "reference": {
          "id": "d19exr83",
          "name": "New Plant Viruses"
        },
        "sample": {
          "id": "7tu8c5m5"
        },
        "subtractions": [
          {
            "id": "1sk885at",
            "name": "Vitis vinifera"
          }
        ],
        "updated_at": "2022-08-15T17:42:35.979000Z",
        "user": {
          "administrator": true,
          "handle": "mrott",
          "id": "ihvze2u9"
        },
        "workflow": "pathoscope_bowtie"
      }
    ],
    "found_count": 2621,
    "page": 1,
    "page_count": 105,
    "per_page": 25,
    "total_count": 2621
  },
  "status": "200"
}

Download an analysis

Downloads analysis data in CSV or XSLX format. The returned format depends on the extension included in the request path.

Errors

StatusDescription
404 Not found

Request

get
/analyses/documents/{analysis_id}.{extension}

Response

{
  "status": "200"
}

Delete an analysis

Permanently deletes an analysis.

Request

delete
/analyses/{analysis_id}

Get an analysis

Fetches the details of an analysis.

Errors

StatusDescription
400 Parent sample does not exist
403 Insufficient rights
404 Not found

Request

get
/analyses/{analysis_id}

Response

{
  "example": {
    "created_at": "2022-08-15T17:42:35.979000Z",
    "files": [
      {
        "analysis": "ofv7rp4v",
        "description": null,
        "format": "tsv",
        "id": 3145,
        "name": "report.tsv",
        "name_on_disk": "3145-report.tsv",
        "size": 4120,
        "uploaded_at": "2022-08-15T17:48:02.467000Z"
      }
    ],
    "id": "ofv7rp4v",
    "index": {
      "id": "u3lm1rk8",
      "version": 14
    },
    "job": {
      "id": "us3toy8j"
    },
    "ready": true,
    "reference": {
      "id": "d19exr83",
      "name": "New Plant Viruses"
    },
    "results": {
      "hits": [
        {
          "abbreviation": "GLRaV3",
          "id": "6tli5mz3",
          "isolates": [
            {
              "default": false,
              "id": "qauxg1g9",
              "sequences": [],
              "source_name": "WA-MR",
              "source_type": "isolate"
            }
          ],
          "length": 18671,
          "name": "Grapevine leafroll-associated virus 3",
          "version": 30
        }
      ],
      "read_count": 584,
      "subtracted_count": 0
    },
    "sample": {
      "id": "7tu8c5m5"
    },
    "subtractions": [
      {
        "id": "1sk885at",
        "name": "Vitis vinifera"
      }
    ],
    "updated_at": "2022-08-15T17:42:35.979000Z",
    "user": {
      "administrator": true,
      "handle": "mrott",
      "id": "ihvze2u9"
    },
    "workflow": "pathoscope_bowtie"
  },
  "status": "200"
}

Download an analysis file

Downloads a file associated with an analysis. Some workflows retain key files after the complete.

Errors

StatusDescription
404 Not found

Request

get
/analyses/{analysis_id}/files/{upload_id}

Response

{
  "status": "200"
}

BLAST a NuVs contig

BLASTs a sequence that is part of a NuVs result record. The resulting BLAST data will be attached to that sequence.

Errors

StatusDescription
400 Parent sample does not exist
403 Insufficient rights
404 Sequence not found
409 Analysis is still running

Request

put
/analyses/{analysis_id}/{sequence_index}/blast

Response

{
  "status": "200"
}