R/nppes.R

In ajdamico/lodown: locally download and prepare publicly-available microdata

get_catalog_nppes <-
	function( data_name = "nppes" , output_dir , ... ){
		
	# read in the whole NPI files page
	npi.datapage <- suppressWarnings( readLines( "http://download.cms.gov/nppes/NPI_Files.html" ) )

	# find the first line containing the data dissemination link
	npi.dataline <- npi.datapage[ grep( "NPPES_Data_Dissemination_" , npi.datapage ) ][1]

	# pull out the zipped file's name from that line
	fn <- paste0( "http://download.cms.gov/nppes/" , gsub( "(.*)(NPPES_Data_Dissemination_.*\\.zip)(.*)$" , "\\2" , npi.dataline ) )
	
	catalog <-
		data.frame(
			full_url = fn ,
			output_folder = output_dir ,
			stringsAsFactors = FALSE
		)

	catalog

}


lodown_nppes <-
	function( data_name = "nppes" , catalog , path_to_7za = '7za' , ... ){

		on.exit( print( catalog ) )
	
		if( nrow( catalog ) != 1 ) stop( "nppes catalog must be exactly one record" )
		
		dir.create( catalog[ , 'output_folder' ] , showWarnings = FALSE )
		
		if( ( .Platform$OS.type != 'windows' ) && ( system( paste0('"', path_to_7za , '" -h' ) ) != 0 ) ) stop( "you need to install 7-zip.  if you already have it, include a path_to_7za='/directory/7za' parameter" )
 		
		tf <- tempfile()
		
		download.file( catalog$full_url , tf , mode = 'wb' )
		
		# extract the file, platform-specific
		if ( .Platform$OS.type == 'windows' ){

			unzipped_files <- unzip_warn_fail( tf , exdir = catalog[ , 'output_folder' ] )

		} else {

			# build the string to send to the terminal on non-windows systems
			dos.command <- paste0( '"' , path_to_7za , '" x ' , tf , ' -o"' , catalog[ , 'output_folder' ] , '"' )
			system( dos.command )
			unzipped_files <- list.files( catalog[ , 'output_folder' ] , full.names = TRUE , recursive = TRUE )

		}

		csv.file <- unzipped_files[ grepl( '^npidata_pfile_(.*)\\.csv$' , basename( unzipped_files ) , ignore.case = TRUE ) & !grepl( 'FileHeader' , basename( unzipped_files ) , ignore.case = TRUE ) ]

		catalog$case_count <- R.utils::countLines( csv.file ) - 1

		file.remove( tf )
		
		on.exit()
		
		catalog

	}