accessValues: Explore values in CEDAR

In earnaud/cedarr: Bio Ontology R API Access

Explore values in CEDAR

Description

Find value by id.

Usage

accessValues(
  api.key,
  vs.collection,
  id,
  sub = NA_character_,
  output.mode = "content",
  page.index = 1,
  page.size = 50
)

Arguments

api.key	character. An API Key is required to access any API call. It is used within cedarr as a header for http requests. An API key is linked to a CEDAR account (https://cedar.metadatacenter.org/profile)
vs.collection	character. A VS collection id.
id	character. A value ID in a value sets from the VS collection.
sub	character. A sub-item to fetch from the value. Not evaluated if id is set to NA. Else, can be NA, "value-set", "tree" or "all-values". "value-set" allows to get the value-set the value belongs to.
output.mode	character. "full" will return the whole response object (from httr) or "content" will fetch the interest values from the response object. Getting the whole object might be interesting to have a look at system metadata, or in case of error to debug the connection. (defaults to "content")
page.index	integer. Index of the page to be returned (defaults to 1st page).
page.size	integer. Number of results per page, capped at 50. (defaults to 50).

Details

This function matches the following queries from the Swagger UI (https://terminology.metadatacenter.org/api/#/):

• /vs-collections/{vs_collection}/values/{id}

• /vs-collections/{vs_collection}/values/{id}/tree

• /vs-collections/{vs_collection}/values/{id}/all-values

• /vs-collections/{vs_collection}/values/{id}/value-set

These differents requests are differenciated by the id and sub arguments.

Value

• If a single value ID is provided: an entry for the corresponding value.

• If a value ID is provided and sub = "tree": get value tree (only for regular values).

• If a value ID is provided and sub = "all-values": find all values in the value set that the given value belongs to.

• If a value ID is provided and sub = "value-set": an entry for the value set the target values belong to.

If output.mode = "full", the whole http response object (see httr::response). It is structured as a list with response metadata wrapping the content item which contains the wanted result.

If output.mode = "content", the content item is directly returned, containing database metadata and the interesting information in the collection subitem.

earnaud/cedarr documentation built on Oct. 25, 2022, 6:27 a.m.