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API Reference

List files (primary method)

get https://cavatica-api.sbgenomics.com/v2

/files

For general information on the API, including formatting, parameters, and pagination, please see the API Overview.

This call returns a list of files and subdirectories in a specified project or directory within a project, with specified properties that you can access. The project or directory whose contents you want to list is specified as a query parameter in the call. Further properties to filter by can also be specified as query parameters.

Note that this call lists both files and subdirectories in the specified project or directory within a project, but not the contents of the subdirectories. To list the contents of a subdirectory, make a new call and specify the subdirectory ID as the parent parameter.

Don't forget that projects on the Platform are specified by their short name.

Further file properties to filter by can also be specified as query parameters.

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File IDs

The file IDs returned by this call are useful for issuing further queries to get more information about a particular file.

https://cavatica-api.sbgenomics.com/v2/files

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Alias call

There is a second method for listing files in a project: GET projects/{project_owner}/{project_name}/files. The call listed here is the primary and preferred method for performing this operation.

Request

Example requests

Since file filtering is a powerful feature, we have included some example usages.

Example 1: List all files in the project 'my-project':

GET /v2/files?project=my-project HTTP/1.1
Host: cavatica-api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74

curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://cavatica-api.sbgenomics.com/v2/files?project=RFranklin/my-project"

Example 2: List all files in 'my-project' with a specific sample ID

GET /v2/files?project=my-project&metadata.sample_id=SAMPLE1 HTTP/1.1
Host: cavatica-api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74

curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://cavatica-api.sbgenomics.com/v2/files?project=RFranklin/my-project&metadata.sample_id=SAMPLE1"

Example 3: List all files in 'my-project' that were produced by a specific task with a specific library and sample ID:

GET /v2/files?project=my-project&metadata.sample_id=ERR315335&origin.task=48f79ccf-12b3-45b6-789c-b1e8d88dabcd HTTP/1.1
Host: cavatica-api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74

curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://cavatica-api.sbgenomics.com/v2/files?project=my-project&metadata.sample_id=ERR315335&origin.task=1262d968-1fda-4f06-a755-917a53a03e7e"

Header Fields

NameDescription
X-SBG-Auth-Token
required		Your CAVATICA authentication token.

Query Parameters

NameData typeDescription
project
required if "parent" is not used		stringSpecified in the following format: {project_owner}/{project}. project_owner is the owner of the project you are listing files from, while project is the project's short name.

Should not be used together with parent. If parent is used, the call will list the content of the specified folder, within the project to which the folder belongs. If project is used, the call will list the content at the root of the project's files.
parent
required if "project" is not used		stringID of the folder whose content you want to list.

Should not be used together with project. If parent is used, the call will list the content of the specified folder, within the project to which the folder belongs. If project is used, the call will list the content at the root of the project's files.
name
stringList file with this name.
metadata.{field}
stringList only files with that have the specified value in metadata field.
origin.task
stringList only files produced by task specified by ID in this field

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Limit your results

Don't forget that you can use filtering with the limit parameter to restrict the number of files returned by this call.

Response

See a list of CAVATICA-specific response codes that may be contained in the body of the response.

Example response body

{
  "href": "https://cavatica-api.sbgenomics.com/v2/files?offset=0&limit=25&project=RFranklin/my-project",
  "items": [
    {
      "href": "https://cavatica-api.sbgenomics.com/v2/files/567890abc9b0307bc0414164",
      "id": "567890abc9b0307bc0414164",
      "name": "1000G_phase1.indels.b37.vc",
      "project": "RFranklin/my-project"
    },
    {
      "href": "https://cavatica-api.sbgenomics.com/v2/files/567890abc1e5339df0414123",
      "id": "567890abc1e5339df0414123",
      "name": "1000G_omni2.5.b37.vcf",
      "project": "RFranklin/my-project"
    },
    {
      "href": "https://cavatica-api.sbgenomics.com/v2/files/567890abc4f3066bc3750174",
      "id": "567890abc4f3066bc3750174",
      "name": "1000G_phase1.snps.high_confidence.b37.vcf",
      "project": "RFranklin/my-project"
    }
  ],
  "links": []
}

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Tips for filtering

When filtering on any resource, including the same field several times with different filtering criteria results in an implicit OR operation for that field and the different criteria.

When filtering by different specified fields, an implicit AND is performed between those criteria. Thus, the call in Example 3 above would return files matching the specified project AND sample ID AND library.

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