Skip to content

Latest commit

 

History

History
executable file
·
111 lines (100 loc) · 3.49 KB

README.md

File metadata and controls

executable file
·
111 lines (100 loc) · 3.49 KB

Example of htsget-elsa process

The following shows how to demonstrate htsget-elsa returning queries based on Elsa manifests.

The url path components for the htsget query determine which release key is used to fetch the manifest, and the file id to query (which is defined in the manifest). For example, consider a htsget query such as:

GET https://htsget-elsa.dev.umccr.org/reads/R001/8AE43A8E4C8111EE84492BBD28BC6E2F?referenceName=20&start=50888919&end=50931436

Here the release key is R001 and the file id - which is obtained from the manifest - is 8AE43A8E4C8111EE84492BBD28BC6E2F. In general, qeuries using htsget-elsa take the following form:

GET https://<htsget_domain>/reads/<release_key>/<file_id>?<query_params>

The release keys and ids for querying can be obtained from Elsa. When defining region restrictions, the allowed regions are enabled in Elsa, and are obtained from https://panelapp.agha.umccr.org.

The following shows some example queries:

Sharing with htsget enabled in Elsa

  1. Enable the htsget sharing on a release with some restrictions.
  2. Grab the JWT token from the data portal: 
    export JWT_TOKEN=<JWT_TOKEN>
  3. Query htsget for an allowed region: 
    curl -H "Authorization: ${JWT_TOKEN}" "https://htsget-elsa.dev.umccr.org/reads/R001/8AE43A8E4C8111EE84492BBD28BC6E2F?referenceName=20&start=50888919&end=50931436"
    Response: 
    {
  "htsget": {
    "format": "BAM",
    "urls": [
      {
        "url": "https://<bucket>.s3.ap-southeast-2.amazonaws.com/<presigned-bam-file>",
        "headers": {
          "Range": "bytes=0-1562"
        },
        "class": "header"
      },

  ...

      {
        "url": "data:;base64,H4sIBAAAAAAA/wYAQkMCABsAAwAAAAAAAAAAAA==",
        "class": "body"
      }
    ]
  }
}
  4. Query htsget for a disallowed region: 
    curl -H "Authorization: ${JWT_TOKEN}" "https://htsget-elsa.dev.umccr.org/reads/R001/8AE43A8E4C8111EE84492BBD28BC6E2F?referenceName=20&start=50931440&end=50931460"
    Response: 
    {
  "htsget": {
    "error": "NotFound",
    "message": "failed to match query with storage"
  }
}
  5. Query for a disallowed chromosome: 
    curl -H "Authorization: ${JWT_TOKEN}" "https://htsget-elsa.dev.umccr.org/reads/R001/8AE43A8E4C8111EE84492BBD28BC6E2F?referenceName=19"
    Response: 
    {
  "htsget": {
    "error": "NotFound",
    "message": "failed to match query with storage"
  }
}
  6. Even if some of the start and end regions are allowed, all regions must be allowed for a response to be returned (e.g. start is allowed, but end is not): 
    curl -H "Authorization: ${JWT_TOKEN}" "https://htsget-elsa.dev.umccr.org/reads/R001/8AE43A8E4C8111EE84492BBD28BC6E2F?referenceName=20&start=50888919&end=51000000"
    Response: 
    {
  "htsget": {
    "error": "NotFound",
    "message": "failed to match query with storage"
  }
}

Sharing with htsget not enabled in Elsa

  1. Grab the JWT token from the data portal: 
    export JWT_TOKEN=<JWT_TOKEN>
  2. Try query htsget: 
    curl -H "Authorization: ${JWT_TOKEN}" "https://htsget-elsa.dev.umccr.org/reads/R001/8AE43A8E4C8111EE84492BBD28BC6E2F?referenceName=20&start=50888919&end=50931436"
    Response: 
    {
  "htsget": {
    "error": "NotFound",
    "message": "failed to match query with storage"
  }
}