accessProvisional: Access Provisional Classes

In earnaud/cedarr: Bio Ontology R API Access

Access Provisional Classes

Description

Get all provisional classes in a particular ontology (including provisional value sets and provisional values).

Usage

accessProvisional(
  api.key,
  ontology = 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)
ontology	character. Ontology name to display. In this context, ontology can be set to NA: this will list all provisional classes from CEDAR.
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 query from the Swagger UI (https://terminology.metadatacenter.org/api/#/):

• ontology/{ontology}/classes/provisional

Value

Since this function targets classes provisionnaly available, it is expected to get an empty result.

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::accessProvisional(
  my.api.key,
  "ENVO"
)

View(result)

## End(Not run)

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