hca-api-methods {HCABrowser}R Documentation

HCA API methods

Description

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

Check the status of a checkout request

Usage

getBundlesCheckout(hca, ...)
deleteBundle(hca, ...)
getBundle(hca, ...)
putBundle(hca, ...)
postBundlesCheckout(hca, ...)
putCollection(hca, ...)
deleteCollection(hca, ...)
getCollection(hca, ...)
patchCollection(hca, ...)
getFile(hca, ...)
headFile(hca, ...)
putFile(hca, ...)
postSearch(hca, ...)
getSubscriptions(hca, ...)
putSubscription(hca, ...)
deleteSubscription(hca, ...)
getSubscription(hca, ...)

## S4 method for signature 'HCABrowser'
getBundlesCheckout(hca, checkout_job_id,
  replica = c("aws", "gcp", "azure"))

## S4 method for signature 'HCABrowser'
deleteBundle(hca, uuid, replica = c("aws", "gcp",
  "azure"), version = NULL, reason = NULL)

## S4 method for signature 'HCABrowser'
getBundle(hca, uuid, replica = c("aws", "gcp",
  "azure"), version = NULL, directurls = NULL, presignedurls = FALSE,
  token = NULL)

## S4 method for signature 'HCABrowser'
putBundle(hca, uuid, replica = c("aws", "gcp",
  "azure"), version = NULL, creator_uid, files)

## S4 method for signature 'HCABrowser'
postBundlesCheckout(hca, uuid, replica = c("aws",
  "gcp", "azure"), destination = NULL, email = NULL)

## S4 method for signature 'HCABrowser'
putCollection(hca, uuid, replica = c("aws", "gcp",
  "azure"), version, contents, description, details, name)

## S4 method for signature 'HCABrowser'
deleteCollection(hca, uuid, replica = c("aws",
  "gcp", "azure"))

## S4 method for signature 'HCABrowser'
getCollection(hca, uuid, replica = c("aws", "gcp",
  "azure"), version = NULL)

## S4 method for signature 'HCABrowser'
patchCollection(hca, uuid, replica = c("aws",
  "gcp", "azure"), version, add_contents, description, details, name,
  remove_contents)

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

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

## S4 method for signature 'HCABrowser'
putFile(hca, uuid, creator_uid, source_url,
  version = NULL)

## S4 method for signature 'HCABrowser'
postSearch(hca, replica = c("aws", "gcp",
  "azure"), output_format = c("summary", "raw"), es_query = NULL,
  per_page = 100, search_after = NULL, json = NULL)

## S4 method for signature 'HCABrowser'
getSubscriptions(hca, replica = c("aws", "gcp",
  "azure"))

## S4 method for signature 'HCABrowser'
putSubscription(hca, replica = c("aws", "gcp",
  "azure"), attachments, callback_url, encoding, es_query, form_fields,
  hmac_key_id, hmac_secret_key, method, payload_form_field)

## S4 method for signature 'HCABrowser'
deleteSubscription(hca, uuid, replica = c("aws",
  "gcp", "azure"))

## S4 method for signature 'HCABrowser'
getSubscription(hca, uuid, replica = c("aws",
  "gcp", "azure"))

Arguments

hca

An HCABrowser object that is the subject of the request.

checkout_job_id

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

replica

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

uuid

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

version

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

reason

character(1). User-friendly reason for the bundle or timestamp- specific bundle deletion.

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.

token

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

creator_uid

character(1). User ID who is creating this bundle.

files

list. (ADD DESCRIPTION ON STRUCTURE OF THIS ARGUMENT)

destination

character(1). User-owned destination storage bucket.

email

character(1). An email address to send status updates to.

contents

list. A list of objects describing links to files, bundles, other collections, and metadata fragments that are part of the collection.

description

character(1). A long description of the collection, formatted in Markdown.

details

list. Supplementary JSON metadata for the collection. (ADD DESCRIPTION OF STRUCTURE)

name

character(1). A short name identifying the collection.

add_contents

list. List of items to remove from the collection. Items must match exactly to be removed. Items not found in the collection are ignored. (ADD DESCRIPTION OF LIST OBJECT)

remove_contents

list. List of items to remove from the collection. Items must match exactly to be removed. Items not found in the collection are ignored.

source_url

character(1). Cloud URL for source data.

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.

es_query

list. Elasticsearch query. (ADD DESCRIPTION OF STRUCTURE)

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.

json

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

attachments

list. The set of bundle metadata items to be included in the payload of a notification request to a subscriptionendpoint. Each property in this object represents an attachment to the notification payload. Each attachment will be a child property of the "attachments" property of the payload. The name of such a child property can be chosen freely provided it does not start with an underscore. For example, if the subscription is “' "attachments": "taxon": "type": "jmespath", "expression": "files.biomaterial_j son.biomaterials[].content.biomaterial_core.ncbi_taxon_id[]" “' the corresponding notification payload will contain the following entry “' "attachments": "taxon": [9606, 9606] “' If a general error occurs during the processing of attachments, the notification will be sent with 'attachments' containing only the reserved '_errors' attachment containing a string describing the error. If an error occurs during the processing of a specific attachment, the notification will be sent with all successfully processed attachments and additionally the '_errors' attachment containing an object with one property for each failed attachment. For example, “' "attachments": "taxon": [9606, 9606] "_errors" "biomaterial": "Some error occurred" “' The value of the 'attachments' property must be less than or equal to 128 KiB in size when serialized to JSON and encoded as UTF-8. If it is not, the notification will be sent with "attachments": "_errors": "Attachments too large (131073 bytes)"

callback_url

character(1). The subscriber's URL. An HTTP request is made to the specified URL for every attempt to deliver a notification to the subscriber. If the HTTP response code is 2XX, the delivery attempt is considered successful and no more attemtpts will be made. Otherwise, more attempts will be made with an exponentially increasing delay between attempts, until an attempt is successful or the a maximum number of attempts is reached.

encoding

character(1). The MIME type describing the encoding of the request body. Either "application/json" or "multipart/form-data".

form_fields

list. A collection of static form fields to be supplied in the request body, alongside the actual notification payload.

hmac_key_id

character(1). An optional key ID to use with "hmac_secret_key".

hmac_secret_key

character(1). The key for signing requests to the subscriber's URL. The signature will be constructed according to https://tools.ietf.org/html/draft-cavage-http-signatures and transmitted in the HTTP 'Authorization' header.

method

The HTTP request method to use when delivering a notification to the subscriber.

payload_form_field

character(1). The name of the form field that will hold the notification payload when the request is made. If the default name of the payload field collides with that of a field in 'form_fields', this porperty can be used to rename the payload and avoid the collision. This property is ignored unless 'encoding' is 'multipart/form-data'.

...

Other arguments

Value

an HCABrowser object

Author(s)

Daniel Van Twisk

Examples

hca <- HCABrowser()
#addmore



[Package HCABrowser version 1.0.0 Index]