Merge branch 'measurements_archive' into development

DESCRIPTION

@@ -9,6 +9,7 @@ Imports:
     httr,
     digest,
     readr,
+    purrr,
     magrittr
 Suggests:
     maps,

NAMESPACE

@@ -5,6 +5,8 @@ S3method("[",sensebox)
 S3method(osem_measurements,bbox)
 S3method(osem_measurements,default)
 S3method(osem_measurements,sensebox)
+S3method(osem_measurements_archive,default)
+S3method(osem_measurements_archive,sensebox)
 S3method(osem_phenomena,sensebox)
 S3method(plot,osem_measurements)
 S3method(plot,sensebox)
@@ -19,6 +21,7 @@ export(osem_clear_cache)
 export(osem_counts)
 export(osem_endpoint)
 export(osem_measurements)
+export(osem_measurements_archive)
 export(osem_phenomena)
 importFrom(graphics,legend)
 importFrom(graphics,par)

R/api.R

@@ -34,12 +34,10 @@ get_box_ = function (boxId, endpoint, ...) {
     parse_senseboxdata()
 }
 
-get_measurements_ = function (..., endpoint) {
-  result = osem_get_resource(endpoint, c('boxes', 'data'), ..., type = 'text')
-
+parse_measurement_csv = function (resText) {
   # parse the CSV response manually & mute readr
   suppressWarnings({
-    result = readr::read_csv(result, col_types = readr::cols(
+    result = readr::read_csv(resText, col_types = readr::cols(
       # factor as default would raise issues with concatenation of multiple requests
       .default  = readr::col_character(),
       createdAt = readr::col_datetime(),
@@ -53,6 +51,11 @@ get_measurements_ = function (..., endpoint) {
   osem_as_measurements(result)
 }
 
+get_measurements_ = function (..., endpoint) {
+  osem_get_resource(endpoint, c('boxes', 'data'), ..., type = 'text') %>%
+    parse_measurement_csv
+}
+
 get_stats_ = function (endpoint, cache) {
   result = osem_get_resource(endpoint, path = c('stats'), progress = FALSE, cache = cache)
   names(result) = c('boxes', 'measurements', 'measurements_per_minute')

R/archive.R

@@ -0,0 +1,135 @@
+# client for archive.opensensemap.org
+# in this archive, CSV files for measurements of each sensor per day is provided.
+
+#' Returns the default endpoint for the archive *download*
+#' While the front end domain is archive.opensensemap.org, file downloads
+#' are provided via sciebo.
+osem_archive_endpoint = function () {
+  'https://uni-muenster.sciebo.de/index.php/s/HyTbguBP4EkqBcp/download?path=/data'
+}
+
+#' Fetch day-wise measurements for a single box from the openSenseMap archive.
+#' 
+#' This function is significantly faster than \code{\link{osem_measurements}} for large
+#' time-frames, as daily CSV dumps for each sensor from
+#' \href{http://archive.opensensemap.org}{archive.opensensemap.org} are used.
+#' Note that the latest data available is from the previous day.
+#' 
+#' By default, data for all sensors of a box is fetched, but you can select a
+#' subset with a \code{\link[dplyr]{dplyr}}-style NSE filter expression.
+#' 
+#' The function will warn when no data is available in the selected period,
+#' but continue the remaining download.
+#' 
+#' @param x A `sensebox data.frame` of a single box, as retrieved via \code{\link{osem_box}},
+#'   to download measurements for.
+#' @param fromDate Start date for measurement download.
+#' @param toDate End date for measurement download (inclusive).
+#' @param sensorFilter A NSE formula matching to \code{x$sensors}, selecting a subset of sensors.
+#' @param progress Whether to print download progress information, defaults to \code{TRUE}.
+#' @return A \code{tbl_df} Containing observations of all selected sensors for each time stamp.
+#' 
+#' @seealso \href{https://archive.opensensemap.org}{openSenseMap archive}
+#' @seealso \code{\link{osem_measurements}}
+#' @seealso \code{\link{osem_box}}
+#' 
+#' @export
+osem_measurements_archive = function (x, ...) UseMethod('osem_measurements_archive')
+
+#' @export
+osem_measurements_archive.default = function (x, ...) {
+  # NOTE: to implement for a different class:
+  # in order to call `archive_fetch_measurements()`, `box` must be a dataframe
+  # with a single row and the columns `X_id` and `name`
+  stop(paste('not implemented for class', toString(class(x))))
+}
+
+#' @describeIn osem_measurements_archive Get daywise measurements for one or
+#' more sensors of a single box
+#' @export
+#' @examples 
+#' # fetch measurements for a single day
+#' box = osem_box('593bcd656ccf3b0011791f5a')
+#' m = osem_measurements_archive(box, as.POSIXlt('2018-09-13'))
+#'   
+#' \donttest{
+#'   # fetch measurements for a date range and selected sensors
+#'   sensors = ~ phenomenon %in% c('Temperatur', 'Beleuchtungsstärke')
+#'   m = osem_measurements_archive(box, as.POSIXlt('2018-09-01'), as.POSIXlt('2018-09-30'), sensorFilter = sensors)
+#' }
+osem_measurements_archive.sensebox = function (x, fromDate, toDate = fromDate, sensorFilter = ~ T, progress = T) {
+  if (nrow(x) != 1)
+    stop('this function only works for exactly one senseBox!')
+  
+  # filter sensors using NSE, for example: `~ phenomenon == 'Temperatur'`
+  sensors = x$sensors[[1]] %>%
+    dplyr::filter(lazyeval::f_eval(sensorFilter, .))
+  
+  # fetch each sensor separately
+  dfs = by(sensors, 1:nrow(sensors), function (sensor) {
+    df = archive_fetch_measurements(x, sensor$id, fromDate, toDate, progress) %>%
+      dplyr::select(createdAt, value) %>%
+      #dplyr::mutate(unit = sensor$unit, sensor = sensor$sensor) %>% # inject sensor metadata
+      dplyr::rename_at(., 'value', function(v) sensor$phenomenon)
+  })
+  
+  # merge all data.frames by timestamp
+  dfs %>% purrr::reduce(dplyr::full_join, 'createdAt')
+}
+
+#' fetch measurements from archive from a single box, and a single sensor
+archive_fetch_measurements = function (box, sensor, fromDate, toDate, progress) {
+  dates = list()
+  from = fromDate
+  while (from <= toDate) {
+    dates = append(dates, list(from))
+    from = from + as.difftime(1, units = 'days')
+  }
+  
+  http_handle = httr::handle(osem_archive_endpoint()) # reuse the http connection for speed! 
+  progress = if (progress && !is_non_interactive()) httr::progress() else NULL
+  
+  measurements = lapply(dates, function(date) {
+    url =  build_archive_url(date, box, sensor)
+    res = httr::GET(url, progress, handle = http_handle)
+  
+    if (httr::http_error(res)) {
+      warning(paste(
+        httr::status_code(res),
+        'on day', format.Date(date, '%F'),
+        'for sensor', sensor
+      ))
+      
+      if (httr::status_code(res) == 404)
+        return(data.frame(createdAt = character(), value = character()))
+    }
+ 
+    measurements = httr::content(res, type = 'text', encoding = 'UTF-8') %>%
+      parse_measurement_csv
+  })
+
+  measurements %>% dplyr::bind_rows()
+}
+
+#' returns URL to fetch measurements from a sensor for a specific date,
+#' based on `osem_archive_endpoint()`
+build_archive_url = function (date, box, sensor) {
+  sensorId = sensor
+  d =  format.Date(date, '%F')
+  format = 'csv'
+  
+  paste(
+    osem_archive_endpoint(),
+    d,
+    osem_box_to_archivename(box),
+    paste(paste(sensorId, d, sep = '-'), format, sep = '.'),
+    sep = '/'
+  )
+}
+
+#' replace chars in box name according to archive script:
+#' https://github.com/sensebox/osem-archiver/blob/612e14b/helpers.sh#L66
+osem_box_to_archivename = function (box) {
+  name = gsub('[^A-Za-z0-9._-]', '_', box$name)
+  paste(box$X_id, name, sep='-')
+}

R/box.R

@@ -155,8 +155,18 @@ parse_senseboxdata = function (boxdata) {
   if (!is.null(thebox$updatedAt))
     thebox$updatedAt = as.POSIXct(strptime(thebox$updatedAt, format = '%FT%T', tz = 'GMT'))
 
+  # create a dataframe of sensors
+  thebox$sensors = sensors %>%
+    lapply(as.data.frame, stringsAsFactors = F) %>%
+    dplyr::bind_rows(.) %>%
+    dplyr::select(phenomenon = title, id = X_id, unit, sensor = sensorType) %>%
+    list
+
   # extract metadata from sensors
-  thebox$phenomena = lapply(sensors, function(s) s$title) %>% unlist %>% list
+  thebox$phenomena = sensors %>%
+    setNames(lapply(., function (s) s$`_id`)) %>%
+    lapply(function(s) s$title) %>%
+    unlist %>% list # convert to vector
 
   # FIXME: if one sensor has NA, max() returns bullshit
   get_last_measurement = function(s) {

R/opensensmapr.R

@@ -37,16 +37,27 @@
 #' }
 #'
 #' @section Retrieving measurements:
-#' Measurements can be retrieved through \code{\link{osem_measurements}} for a
-#' given phenomenon only. A subset of measurements may be selected by
-#'
+#' There are two ways to retrieve measurements:
 #' \itemize{
-#'   \item a list of senseBoxes, previously retrieved through
-#'     \code{\link{osem_box}} or \code{\link{osem_boxes}}.
-#'   \item a geographic bounding box, which can be generated with the
-#'     \code{\link[sf]{sf}} package.
-#'   \item a time frame
-#'   \item a exposure type of the given box
+#'   \item \code{\link{osem_measurements_archive}}:
+#'     Downloads measurements for a \emph{single box} from the openSenseMap archive.
+#'     This function does not provide realtime data, but is suitable for long time frames.
+#'     
+#'   \item \code{\link{osem_measurements}}:
+#'     This function retrieves (realtime) measurements from the API. It works for a
+#'     \emph{single phenomenon} only, but provides various filters to select sensors by
+#'     
+#'     \itemize{
+#'       \item a list of senseBoxes, previously retrieved through
+#'         \code{\link{osem_box}} or \code{\link{osem_boxes}}.
+#'       \item a geographic bounding box, which can be generated with the
+#'         \code{\link[sf]{sf}} package.
+#'       \item a time frame
+#'       \item a exposure type of the given box
+#'     }
+#'     
+#'     Use this function with caution for long time frames, as the API becomes
+#'     quite slow is limited to 10.000 measurements per 30 day interval.
 #' }
 #'
 #' Data is returned as \code{tibble} with the class \code{osem_measurements}.

man/build_archive_url.Rd

@@ -0,0 +1,13 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/archive.R
+\name{build_archive_url}
+\alias{build_archive_url}
+\title{returns URL to fetch measurements from a sensor for a specific date,
+based on `osem_archive_endpoint()`}
+\usage{
+build_archive_url(date, box, sensor)
+}
+\description{
+returns URL to fetch measurements from a sensor for a specific date,
+based on `osem_archive_endpoint()`
+}

man/osem_archive_endpoint.Rd

@@ -0,0 +1,15 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/archive.R
+\name{osem_archive_endpoint}
+\alias{osem_archive_endpoint}
+\title{Default endpoint for the archive download
+front end domain is archive.opensensemap.org, but file download
+is provided via sciebo}
+\usage{
+osem_archive_endpoint()
+}
+\description{
+Default endpoint for the archive download
+front end domain is archive.opensensemap.org, but file download
+is provided via sciebo
+}

man/osem_box_to_archivename.Rd

@@ -0,0 +1,13 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/archive.R
+\name{osem_box_to_archivename}
+\alias{osem_box_to_archivename}
+\title{replace chars in box name according to archive script:
+https://github.com/sensebox/osem-archiver/blob/612e14b/helpers.sh#L66}
+\usage{
+osem_box_to_archivename(box)
+}
+\description{
+replace chars in box name according to archive script:
+https://github.com/sensebox/osem-archiver/blob/612e14b/helpers.sh#L66
+}

man/osem_measurements_archive.Rd

@@ -0,0 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/archive.R
+\name{osem_measurements_archive}
+\alias{osem_measurements_archive}
+\alias{osem_measurements_archive.sensebox}
+\title{Get day-wise measurements for a single box from the openSenseMap archive.}
+\usage{
+osem_measurements_archive(x, ...)
+
+\method{osem_measurements_archive}{sensebox}(x, fromDate,
+  toDate = fromDate, sensorFilter = ~T, progress = T)
+}
+\description{
+This function is significantly faster than `osem_measurements()` for large
+time-frames, as dayly CSV dumps for each sensor from
+<archive.opensensemap.org> are used.
+Note that the latest data available is from the previous day.
+By default, data for all sensors of a box is fetched, but you can select a
+subset with a `dplyr`-style NSE filter expression.
+}
+\section{Methods (by class)}{
+\itemize{
+\item \code{sensebox}: Get daywise measurements for one or
+more sensors of a single box
+}}
+
+\examples{
+
+\donttest{
+  # fetch measurements for a single day
+  box = osem_box('593bcd656ccf3b0011791f5a')
+  m = osem_measurements_archive(box, as.POSIXlt('2018-09-13'))
+  
+  # fetch measurements for a date range and selected sensors
+  sensors = ~ phenomenon \%in\% c('Temperatur', 'Beleuchtungsstärke')
+  m = osem_measurements_archive(box, as.POSIXlt('2018-09-01'), as.POSIXlt('2018-09-30'), sensorFilter = sensors)
+}
+}

tests/testthat/test_archive.R

@@ -0,0 +1,53 @@
+source('testhelpers.R')
+
+context('osem_box_to_archivename()')
+
+try({
+  boxes = osem_boxes(grouptag = 'ifgi')
+  box = filter(boxes, row_number() == 1) 
+})
+
+test_that('osem_box_to_archive_name does the correct character replacements', {
+  b = data.frame(
+    name = 'aA1._- äß!"?$%&/',
+    X_id = 'UUID'
+  )
+  
+  archivename = opensensmapr:::osem_box_to_archivename(b)
+  expect_equal(archivename, 'UUID-aA1._-__________')
+})
+
+test_that('osem_box_to_archive_name works for one box', {
+  if (is.null(box)) skip('no box data could be fetched')
+
+  archivename = opensensmapr:::osem_box_to_archivename(box)
+  expect_length(archivename, 1)
+  expect_type(archivename, 'character')
+})
+
+test_that('osem_box_to_archive_name works for multiple boxes', {
+  if (is.null(boxes)) skip('no box data available')
+
+  archivename = opensensmapr:::osem_box_to_archivename(boxes)
+  expect_length(archivename, nrow(boxes))
+  expect_type(archivename, 'character')
+})
+
+context('osem_measurements_archive()')
+
+test_that('osem_measurements_archive works for one box', {
+  if (is.null(box)) skip('no box data could be fetched')
+
+  m = osem_measurements_archive(box, as.POSIXlt('2018-08-08'))
+  expect_length(m, nrow(box$sensors[[1]]) + 1) # one column for each sensor + createdAt
+  expect_s3_class(m, c('osem_measurements', 'tbl_df'))
+})
+
+test_that('osem_measurements_archive fails for multiple boxes', {
+  if (is.null(boxes)) skip('no box data available')
+
+  expect_error(
+    osem_measurements_archive(boxes, as.POSIXlt('2018-08-08')),
+    'this function only works for exactly one senseBox!'
+  )
+})