Merge pull request #26 from nilanjanchatterjee/sf-changes

Bug Fixes

.env

@@ -1,7 +1,7 @@
 # development settings
 CONFIGURATION_FILE=./app-configuration.json
 PRINT_CONFIGURATION=yes
-SOURCE_FILE=./data/raw/input3.rds
+SOURCE_FILE=./data/raw/input4.rds
 OUTPUT_FILE=./data/output/output.rds
 ERROR_FILE=./data/output/error.log
 APP_ARTIFACTS_DIR=./data/output/

.gitignore

@@ -5,3 +5,4 @@
 .DS_Store
 data/output/**
 !data/output/.keep
+*.keep

app-configuration.json

@@ -0,0 +1 @@
+{}

data/raw/README.txt

@@ -0,0 +1,37 @@
+Set of input data to test apps.
+
+*Content*
+- input1: 1 goat, median fix rate = 30mins, tracking duration 7.5 month, gps, local movement
+- input2: 3 storks, median fix rate = 1sec, tracking duration 2 weeks, gps, local movement
+- input3: 1 stork, median fix rate = 1h | 1day | 1 week, tracking duration 11.5 years, argos, includes migration
+- input4: 3 geese, median fix rate = 1h | 4h, tracking duration 1.5 years, gps, includes migration
+
+*I/O types*
+- all data sets are provided as 'move2_loc'
+- input1 & input2 are also provided as 'telemetry.list'
+
+*Projection*
+- for 'move2_loc', data are provided in "lat/long" (EPSG:4326) and projected to "Mollweide" (ESRI:54009) in order to test your app accordingly for not projected and projected data. If your app does not allow projected data or only can deal with projected data, document and either build a automatic transformation in the app or make it fail with an informative error message. The app "Change projection" can be refered to for the user to change the projection of the data acordingly previous to your app.
+
+- the 'telemetry.list' examples are in a "aeqd" projection with 0,0 in the center of the track, as this is a common projection used within the ctmm library
+
+
+*File names*
+input1_move2loc_LatLon.rds
+input1_move2loc_Mollweide.rds
+
+input2_move2loc_LatLon.rds
+input2_move2loc_Mollweide.rds
+
+input3_move2loc_LatLon.rds
+input3_move2loc_Mollweide.rds
+
+input4_move2loc_LatLon.rds
+input4_move2loc_Mollweide.rds
+
+
+input1_telemetrylist_aeqd.rds
+input2_telemetrylist_aeqd.rds
+
+
+

tests/testthat/helper.R

@@ -1,4 +1,5 @@
 test_data <- function(test_file) {
     test_data_root_dir <- test_path("data")
     readRDS(file = file.path(test_data_root_dir, test_file))
-}
+}
+

tests/testthat/setup.R

@@ -1,6 +1,9 @@
 source(file.path("..", "..", "src", "common", "logger.R"))
+source(file.path("..", "..", "src", "common", "runtime_configuration.R"))
 source(file.path("..", "..", "src", "io", "app_files.R"))
 source(file.path("..", "..", "src", "io", "io_handler.R"))
-Sys.setenv("LOCAL_APP_FILES_DIR" = "../../data/local_app_files")
+Sys.setenv("USER_APP_FILE_HOME_DIR" = "../../data/auxiliary/user-files")
+
+clearRecentOutput()
 # the system under test (sut)
-source(file.path("..", "..", "./RFunction.R"))
+source(file.path("..", "..", "./RFunction.R"))

tests/testthat/test_RFunction.R

@@ -0,0 +1,39 @@
+source(here("tests/testthat/helper.R"))
+
+test_data <- test_data("input3_move2loc_LatLon.rds")
+
+
+test_that("function executes with user-passed threshold", {
+  actual <- rFunction(data = test_data, threshold = 6, window = 756)
+  expected_count <- 3164
+  expect_equal(nrow(actual), expected_count)
+})
+
+
+test_that("function executes with default threshold", {
+  actual <- rFunction(data = test_data, window = 756)
+  expected_count <- 3164
+  expect_equal(nrow(actual), expected_count)
+})
+
+
+test_that("function returns nothing and errors with bad window", {
+  actual <- rFunction(data = test_data)
+  expect_null(actual)
+})
+
+
+test_that("function preserves input track attributes", {
+  actual <- rFunction(data = test_data, window = 756)
+  actual_track_data_attributes <- sort(names(mt_track_data(actual)))
+  expected_track_data_attirbutes <- sort(names(mt_track_data(test_data)))
+  expect_equal(actual_track_data_attributes, expected_track_data_attirbutes)
+})
+
+
+test_that("function preserves input track id column", {
+  actual <- rFunction(data = test_data, window = 756)
+  actual_track_id_column <- attr(actual, "track_id")
+  expected_track_id_column <- attr(test_data, "track_id")
+  expect_equal(actual_track_id_column, expected_track_id_column)
+})

tests/testthat/testthat.R

@@ -1 +1,2 @@
-library(testthat)
+library(testthat)
+library(here)