inst/templates/upload_distribution.R

In ScottishCovidResponse/SCRCdata: Processing Scripts for the SCRC Data Pipeline

#' parameter-name
#'
#' Add a distribution to the data registry
#'

library(SCRCdataAPI)



# Go to data.scrc.uk, click on Links, then Generate API Token, and save your
# token in your working directory as token.txt. If the following returns an
# error, then save a carriage return after the token.
key <- readLines("token.txt")
namespace <- "SCRC"

# The product_name is used to identify the data product and will be used to
# generate various file locations:
# (1) data product is saved locally (after processing) to data-raw/[product_name]
# (2) data product is stored on the Boydorr server at
# ../../srv/ftp/scrc/[product_name]
product_name <- "human/infection/SARS-CoV-2/parameter-name"
# The component_name is taken as the last part of the product_name
component_name <- gsub("^.*/([^/]*)$", "\\1", product_name)
# The distribution and its parameters
distribution <- "Gaussian"
parameters <- list(mean = -16.08, SD = 30)
# The version number of the data product
productVersion <- "0.1.0"


# ******************************************************
# Now run the code below and push your toml file to the
# ScottishCovidResponse/DataRepository GitHub repository
# ******************************************************





# default data that should be in database ---------------------------------

# Assuming the toml will be stored in the ScottishCovidResponse/DataRepository
# GitHub repository
productStorageRoot <- "DataRepository"

storage_rootId <- new_storage_root(
  name = productStorageRoot,
  root = "https://raw.githubusercontent.com/ScottishCovidResponse/DataRepository/",
  key = key)

namespaceId <- new_namespace(name = namespace,
                             key = key)


# generate toml -----------------------------------------------------------

path <- paste("master", namespace, product_name, sep = "/")
filename <- paste0(productVersion, ".toml")

create_distribution(filename = filename,
                    path = file.path("data-raw", path),
                    name = component_name,
                    distribution = distribution,
                    parameters = parameters)


# upload data product metadata to database --------------------------------

upload_data_product(storage_root_id = storage_rootId,
                    name = product_name,
                    component_name = component_name,
                    processed_path = file.path("data-raw", path, filename),
                    product_path = file.path(path, filename),
                    version = productVersion,
                    namespace_id = namespaceId,
                    key = key)