fixed state data d/l & added tests+travis

.Rbuildignore

@@ -6,4 +6,4 @@
 ^crunch/.*
 ^README_files/
 ^README_files/.*
-^README-.*
+^README-.*

.travis.yml

@@ -1,23 +1,5 @@
-language: c
+# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
 
-before_install:
+language: R
-  - curl -OL http://raw.github.com/craigcitro/r-travis/master/scripts/travis-tool.sh
+sudo: false
-  - chmod 755 ./travis-tool.sh
+cache: packages
-  - ./travis-tool.sh bootstrap
-
-install:
-  - ./travis-tool.sh install_github plyr
-  - ./travis-tool.sh install_deps
-
-script: ./travis-tool.sh run_tests
-
-on_failure:
-  - ./travis-tool.sh dump_logs
-
-branches:
-  except:
-  - /-expt$/
-  notifications:
-    email:
-      on_success: change
-      on_failure: change

DESCRIPTION

@@ -5,6 +5,7 @@ Version: 0.5.1
 Date: 2016-12-05
 Author: Bob Rudis (bob@rud.is)
 Maintainer: Bob Rudis <bob@rud.is>
+Encoding: UTF-8
 Description: The U.S. Centers for Disease Control (CDC) maintains a portal
     <http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html> for
     accessing state, regional and national influenza statistics as well as
@@ -23,7 +24,8 @@ Imports:
     dplyr,
     utils,
     purrr,
-    readr
+    readr,
+    V8
 Depends:
     R (>= 3.2.0)
 RoxygenNote: 5.0.1

NAMESPACE

@@ -4,6 +4,7 @@ export(get_flu_data)
 export(get_mortality_surveillance_data)
 export(get_state_data)
 export(get_weekly_flu_report)
+import(V8)
 import(dplyr)
 import(httr)
 import(utils)

NEWS.md

@@ -1,6 +1,7 @@
 # cscfluview 0.5.1
 
 * Replaced `http` URLs with `https` as `http` ones no longer work (fixes #6)
+* Fixed State data download (CDC changed the hidden API)
 
 # cdcfluview 0.5.0
 

R/aaa.r

@@ -0,0 +1 @@
+utils::globalVariables(".")

R/cdcfluview-package.R

@@ -13,4 +13,5 @@
 #' @import httr xml2 dplyr utils
 #' @importFrom purrr map map_df map_chr map_lgl discard keep
 #' @importFrom readr read_csv
+#' @import V8
 NULL

R/get_state_data.r

@@ -10,7 +10,7 @@
 #'
 #' @param years a vector of years to retrieve data for (i.e. \code{2014} for CDC
 #'        flu season 2014-2015). Default value is the current year and all
-#'        \code{years} values should be > \code{1997}
+#'        \code{years} values should be >= \code{2008}
 #' @return A \code{data.frame} of state-level data for the specified seasons
 #'         (also classed as \code{cdcstatedata})
 #' @export
@@ -26,34 +26,22 @@
 #' }
 get_state_data <- function(years=as.numeric(format(Sys.Date(), "%Y"))) {
 
-  if (any(years < 1997))
+  if (any(years < 2008))
-    stop("Error: years should be > 1997")
+    stop("Error: years should be >= 2008")
 
-  years <- years - 1960
+  years <- c((years - 1960), 1)
+  years <- paste0(years, collapse=",")
 
-  out_file <- tempfile(fileext=".zip")
+  tmp <- httr::GET(sprintf("https://gis.cdc.gov/grasp/fluView1/Phase1DownloadDataP/%s", years))
-
-  params <- list(EndMMWRID=0,
-                 StartMMWRID=0,
-                 QueryType=1,
-                 DataMode="STATE",
-                 SeasonsList=paste0(years, collapse=","))
-
-  tmp <- httr::POST("https://gis.cdc.gov/grasp/fluview/FluViewPhase1CustomDownload.ashx",
-              body=params,
-              write_disk(out_file))
 
   stop_for_status(tmp)
 
-  if (!(file.exists(out_file)))
+  res <- httr::content(tmp, as="parsed")
-    stop("Error: cannot process downloaded data")
-
-  out_dir <- tempdir()
-
-  files <- unzip(out_file, exdir=out_dir, overwrite=TRUE)
 
-    out <- read.csv(files, header=TRUE, stringsAsFactors=FALSE)
+  ctx <- v8()
-  # out <- readr::read_csv(files, col_types="cccccic")
+  ctx$eval(JS(sprintf("var dat=%s;", res)))
+  res <- ctx$get("dat", flatten=FALSE)
+  out <- suppressMessages(readr::type_convert(res$datadownload))
 
   class(out) <- c("cdcstatedata", class(out))
 

R/mortalty.r

@@ -76,3 +76,4 @@ get_mortality_surveillance_data <- function() {
   )
 
 }
+

man/get_state_data.Rd

@@ -9,7 +9,7 @@ get_state_data(years = as.numeric(format(Sys.Date(), "\%Y")))
 \arguments{
 \item{years}{a vector of years to retrieve data for (i.e. \code{2014} for CDC
 flu season 2014-2015). Default value is the current year and all
-\code{years} values should be > \code{1997}}
+\code{years} values should be >= \code{2008}}
 }
 \value{
 A \code{data.frame} of state-level data for the specified seasons

tests/testthat/test-cdcfluview.R

@@ -1,6 +1,8 @@
 context("basic functionality")
 test_that("we can do something", {
 
-  #expect_that(some_function(), is_a("data.frame"))
+  expect_that(dim(get_flu_data("hhs", years=2015)), equals(c(520L, 15L)))
+
+  expect_that(dim(get_state_data(2008)), equals(c(2494L, 8L)))
 
 })