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CGC

Overwrite a file's metadata

put https://cgc-api.sbgenomics.com/v2

/files/{file_id}/metadata

This call changes the metadata values for the specified file.

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Metadata

Learn more about metadata fields and their values for your uploaded, private files on the CGC.

Files are specified by their IDs, which you can obtain by making the API call to list files in a project .

https://cgc-api.sbgenomics.com/v2/files/{file_id}/metadata

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PUT and PATCH

The CGC API has two method to modify file metadata. This method uses the HTTP verb PUT, and the other uses the HTTP verb PATCH.

The difference between the two concerns the way that they update the information stored about the user. PATCH allows you to update just one metadata field. On the other hand, a PUT request will fully overwrite the values for all metadata fields. This means that when issuing a PUT request you must enter values for every key required to specify the metadata, even if the values for some keys are unchanged. If you don't specify a value for a given metadata field when making the PUT request, then any existing value for that field will be reset.

Custom metadata fields

Apart from the standard set of metadata fields that can be seen through the visual interface, you are also able to add custom metadata for your files. Custom metadata fields are user-defined key-value pairs that allow you to provide additional metadata associated to files on the CGC. Custom metadata can be added via the command line uploader or via the API, but not through the visual interface.

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Custom metadata fields will not be visible on the visual interface, but their values can be retrieved by getting file details via the API.

When adding custom metadata fields, you need to pay attention to the following set of rules:

  • Keys and values are case sensitive unless explicitly treated differently by a tool or a part of the CGC.
  • Maximum number of key-value pairs per file is 1000.
  • Keys and values are UTF-8 encoded strings.
  • Maximum length of a key is 100 bytes (UTF-8 encoding).
  • Maximum length of a value is 300 bytes (UTF-8 encoding).
  • Null values and keys are ignored and not counted towards the 1000 key-value pair limit.

Request

Example request

Since you need to specify values for all metadata fields, it can be easier to send the data as a file, using the option --data-binary in cURL.

PUT /v2/files/568e69abe9b0307bc0414164/metadata HTTP/1.1
Host: cgc-api.sbgenomics.com
X-SBG-Auth-Token: 3210a98c1db9318fa9d9273156740f74

curl --data-binary "@metadata.json" -s -H "X-SBG-Auth-Token: 3210a98c1db9318fa9d9273156740f74" -H "content-type: application/json" -X PUT "https://cgc-api.sbgenomics.com/v2/files/568e69abe9b0307bc0414164/metadata"

Header Fields

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

Path parameters

NameDescription
file_idThe ID of the file whose details you want to overwrite.

Query parameters

NameData typeDescription
fieldsstringSelector specifying a subset of fields to include in the response.

Request body

In the body of the request, you should enter key-value pairs corresponding to metadata fields and their values.

KeyDatatype of valueDescription of value
Freeform -- enter any stringstringThe value for the corresponding key

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TCGA metadata

You cannot edit the metadata for TCGA files; just for files that you create or upload.

Example request body

{
    "foo": "bar",
    "my_key_1": "my_value_1",
    "my_key_2": "my_value_2",
    "platform": "my_platform",
    "library_ID": "12345"
}

Response

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

Example response body

{
  "library_id": "12345",
  "platform": "my_platform",
  "foo": "bar",
  "my_key_1": "my_value_1",
  "my_key_2": "my_value_2"
}
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