accessValueSets: Access Value Sets

In earnaud/cedarr: Bio Ontology R API Access

Access Value Sets

Description

Get access to all or part of the value sets by VS collection.

Usage

accessValueSets(
  api.key,
  vs.collection,
  id = NA_character_,
  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 the VS collection at URL format. Not providing it (setting it to NA) will list all value sets in the vs.collection.
sub	character. A sub-item to fetch from the value: can be NA, "tree", or "values". Not evaluated if id is set to NA.
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-collection/{vs_collection}/value-sets

• /vs-collection/{vs_collection}/value-sets/{id}

• /vs-collection/{vs_collection}/value-sets/{id}/tree

• /vs-collection/{vs_collection}/value-sets/{id}/values

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

Value

• If only a VS collection ID is provided: a list of the value sets in this VS collection.

• If a VS collection ID and a value set ID are provided: an entry for the corresponding value set. With sub = "tree", retrieve the root values. If sub = "values", retrieve the value set's values.

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.

Examples

## Not run: 
my.api.key <- readline()

result <- cedarr::accessValueSets(
  my.api.key,
  vs.collection = "CEDARVS",
  id = "http://www.semanticweb.org/jgraybeal/ontologies/2015/7/cedarvaluesets#Study_File_Type"
)

View(result)

## End(Not run)

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