hca-api-methods: HCA API methods

Description Usage Arguments Value Author(s) Examples

Description

Methods to access the Human Cell Atlas's Data Coordination Platform (HCA DCP) by means of the platform's REST API.

Usage

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listBundles(x, ...)
getBundleCheckout(x, ...)
getBundle(x, ...)
checkoutBundle(x, ...)
getFile(x, ...)
headFile(x, ...)
searchBundles(x, ...)

## S4 method for signature 'HCABrowser'
listBundles(x, replica = c("aws", "gcp"), token, per_page = 100, search_after)

## S4 method for signature 'HCABrowser'
getBundleCheckout(x, replica = c("aws", "gcp"), checkout_job_id)

## S4 method for signature 'HCABrowser'
getBundle(
  x,
  uuid,
  version,
  replica = c("aws", "gcp"),
  directurls,
  presignedurls,
  token,
  per_page = 500
)

## S4 method for signature 'HCABrowser'
checkoutBundle(x, uuid, version, replica = c("aws", "gcp"), json_request_body)

## S4 method for signature 'HCABrowser'
getFile(x, uuid, replica = c("aws", "gcp"), version, token)

## S4 method for signature 'HCABrowser'
headFile(x, uuid, replica = c("aws", "gcp"), version)

## S4 method for signature 'HCABrowser'
searchBundles(
  x,
  json_request_body = getEsQuery(x),
  output_format = c("summary", "raw"),
  replica = c("aws", "gcp"),
  per_page = 100,
  search_after
)

Arguments

x

An HCABrowser object that is the subject of the request.

replica

character(1). A replica to fetch form. Can either be set to "aws", "gcp", or "azure". DEFAULT is "aws".

token

Token. Token to manage retries. End users constructing queries should not set this parameter. Use get_token() to generate.

per_page

numeric(1). Max number of results to return per page.

search_after

character(1). **Search-After-Context**. An internal state pointer parameter for use with pagination. The API client should not need to set this parameter directly; it should instead directly fetch the URL given in the "Link" header.

checkout_job_id

character(1). A RFC4122-complliant ID for the checkout job request.

uuid

character(1). A RFC4122-compliant ID for the bundle.

version

character(1). Timestamp of bundle creation in RFC3339.

directurls

logical(1). Include direct-access URLs in the response. This is mutually exclusive with the presignedurls parameter. DEFAULT is NULL.

presignedurls

logical(1). Include presigned URLs in the response. This is mutually exclusive with the directurls parameter.

json_request_body

character(1) of a json query to be executed.

output_format

character(1). Specifies the output format. Either "summary" or "raw". The default format, "summary", is a list of UUIDs for bundles that match the query. Set this parameter to "raw" to get the verbatim JSON metadata for bundles that match the query.

...

Additional arguments.

Value

an HCABrowser object

Author(s)

Daniel Van Twisk

Examples

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hca <- HCABrowser()
#addmore

HCABrowser documentation built on Nov. 8, 2020, 7:24 p.m.