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solve issue #15 
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‎DESCRIPTION

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LazyData: true
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RoxygenNote: 7.3.1
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Language: en-US
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Config/testthat/start-first: mf_login, mf_list_collections, mf_list_variables, mf_get_url, mf_download_data, mf_import_data

‎NAMESPACE

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export(mf_list_collections)
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export(mf_list_variables)
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export(mf_login)
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export(modisfast)
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import(cli)
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import(dplyr)
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import(httr)
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import(parallel)
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import(purrr)
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import(sf)
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importFrom(cli,cli_alert_success)
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importFrom(curl,has_internet)
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importFrom(lubridate,floor_date)
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importFrom(lubridate,hour)

‎README.Rmd

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@@ -275,4 +275,4 @@ We thank NASA and its partners for making all their Earth science data freely av
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We also thank the contributors that have tested the package, reviewed the documentation and brought valuable feedbacks to improve the package : [Florian de Boissieu](https://github.com/floriandeboissieu), Julien Taconet.
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This work has been developed over the course of several research projects (REACT 1, REACT 2, ANORHYTHM and DIV-YOO) funded by Expertise France and the French National Research Agency (ANR).
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This work has been developed over the course of several research projects (REACT 1, REACT 2, ANORHYTHM and DIV-YOO) funded by Expertise France, the French National Research Agency (ANR), and the French National Research Institute for Sustainable Development (IRD).

‎README.md

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This work has been developed over the course of several research
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projects (REACT 1, REACT 2, ANORHYTHM and DIV-YOO) funded by Expertise
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France and the French National Research Agency (ANR).
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France, the French National Research Agency (ANR), and the French
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National Research Institute for Sustainable Development (IRD).

‎tests/testthat.R

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### Instructions to run the tests in order to verify the functionality of modisfast :
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# - open the file test/testthat/test-modisfast.R
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# - uncomment the 2 first two lines of the script (earthdata_un = "my_username" and earthdata_pw = "my_password")
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# - open the file : test/testthat/helper-modisfast.R
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# - uncomment the lines : earthdata_un = "my_username" and earthdata_pw = "my_password"
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# - replace "my_username" and "my_password" with your own Earthdata username and password
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# - run devtools::test() (or run the script test/testthat/test-modisfast.R manually)
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# - run devtools::test()
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message("tests are not executed automatically")
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‎tests/testthat/helper-modisfast.R

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# here are "global" variable which can be used for all tests, as explained in https://github.com/r-lib/testthat/issues/422
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earthdata_un = "my_username"
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earthdata_pw = "my_password"
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library(sf)
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library(terra)
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roi <- st_as_sf(data.frame(id = "madagascar", geom = "POLYGON((41.95 -11.37,51.26 -11.37,51.26 -26.17,41.95 -26.17,41.95 -11.37))"), wkt = "geom", crs = 4326)
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time_range <- as.Date(c("2023-01-01", "2023-03-31"))

‎tests/testthat/test-mf_download_data.R

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test_that("function mf_download_data() works to download a MODIS datacube", {
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skip_on_cran()
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skip_on_ci()
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urls_modis <- mf_get_url(collection = "MOD13A3.061",
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variables = c("_1_km_monthly_NDVI"),
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roi = roi,
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time_range = time_range
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)
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res_dl_modis <- mf_download_data(df_to_dl = urls_modis)
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expect_is(res_dl_modis,'data.frame') # output is a data.frame
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expect_named(res_dl_modis, c("id_roi","time_start","collection","name","url","destfile", "fileDl", "fileSize", "dlStatus")) # column names are ok
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expect_equal(ncol(res_dl_modis), 9) # there are 9 columns
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expect_equal(nrow(res_dl_modis), 5)# there are 5 rows (corresponding to 5 tiles)
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expect_equal(unique(res_dl_modis$fileDl), TRUE) # all files were properly downloaded (fileDl == TRUE for all files)
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expect_gt(sum(res_dl_modis$fileSize),5500000) # file size for this very specific example should be around 6000000 bites
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expect_lt(sum(res_dl_modis$fileSize),6500000)
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})
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test_that("function mf_download_data() works to download a GPM datacube", {
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skip_on_cran()
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skip_on_ci()
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urls_gpm <- mf_get_url(collection = "GPM_3IMERGDF.07",
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variables = c("precipitation"),
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roi = roi,
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time_range = time_range
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)
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res_dl_gpm <- mf_download_data(df_to_dl = urls_gpm, parallel = TRUE) # download data, with parallelization
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expect_is(res_dl_gpm,'data.frame') # output is a data.frame
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expect_named(res_dl_gpm, c("id_roi","time_start","collection","name","url","destfile", "fileDl", "fileSize", "dlStatus")) # column names are ok
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expect_equal(ncol(res_dl_gpm), 9) # there are 9 columns
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expect_equal(nrow(res_dl_gpm), 90 ) # there are 90 rows (corresponding to 90 dates)
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expect_equal(unique(res_dl_gpm$fileDl), TRUE) # all files were properly downloaded (fileDl == TRUE for all files)
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expect_gt(sum(res_dl_gpm$fileSize),5000000) # file size for this very specific example should be 5500000 bites
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expect_lt(sum(res_dl_gpm$fileSize),6000000)
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})

‎tests/testthat/test-mf_get_url.R

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test_that("function mf_get_url() sends back the expected output for a MODIS query", {
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skip_on_cran()
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skip_on_ci()
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urls_modis <- mf_get_url(collection = "MOD13A3.061",
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variables = c("_1_km_monthly_NDVI"),
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roi = roi,
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time_range = time_range
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)
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expect_is(urls_modis, "data.frame") # output is a data.frame
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expect_named(urls_modis, c("id_roi","time_start","collection","name","url")) # column names are ok
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expect_equal(ncol(urls_modis), 5) # there are 5 columns
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expect_equal(nrow(urls_modis), 5)# there are 5 rows (corresponding to 5 tiles)
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expect_match(urls_modis$url[1], "https://opendap.cr.usgs.gov") # urls starts with the right OPENDAP url
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expect_equal(urls_modis, data.frame(id_roi = rep("madagascar",5),
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time_start = rep(as.Date("2023-01-01"), 5),
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collection = rep("MOD13A3.061", 5),
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name = c("MOD13A3.061.2023001_2023060.h21v10.nc4", "MOD13A3.061.2023001_2023060.h21v11.nc4", "MOD13A3.061.2023001_2023060.h22v10.nc4", "MOD13A3.061.2023001_2023060.h22v11.nc4", "MOD13A3.061.2023001_2023060.h23v10.nc4"),
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url = c( "https://opendap.cr.usgs.gov/opendap/hyrax/MOD13A3.061/h21v10.ncml.nc4?MOD_Grid_monthly_1km_VI_eos_cf_projection,_1_km_monthly_NDVI%5B275:277%5D%5B922:1199%5D%5B1132:1199%5D,time%5B275:277%5D,YDim%5B922:1199%5D,XDim%5B1132:1199%5D",
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"https://opendap.cr.usgs.gov/opendap/hyrax/MOD13A3.061/h21v11.ncml.nc4?MOD_Grid_monthly_1km_VI_eos_cf_projection,_1_km_monthly_NDVI%5B275:277%5D%5B0:749%5D%5B919:1199%5D,time%5B275:277%5D,YDim%5B0:749%5D,XDim%5B919:1199%5D",
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"https://opendap.cr.usgs.gov/opendap/hyrax/MOD13A3.061/h22v10.ncml.nc4?MOD_Grid_monthly_1km_VI_eos_cf_projection,_1_km_monthly_NDVI%5B275:277%5D%5B165:1199%5D%5B0:1199%5D,time%5B275:277%5D,YDim%5B165:1199%5D,XDim%5B0:1199%5D",
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"https://opendap.cr.usgs.gov/opendap/hyrax/MOD13A3.061/h22v11.ncml.nc4?MOD_Grid_monthly_1km_VI_eos_cf_projection,_1_km_monthly_NDVI%5B275:277%5D%5B0:749%5D%5B0:982%5D,time%5B275:277%5D,YDim%5B0:749%5D,XDim%5B0:982%5D",
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"https://opendap.cr.usgs.gov/opendap/hyrax/MOD13A3.061/h23v10.ncml.nc4?MOD_Grid_monthly_1km_VI_eos_cf_projection,_1_km_monthly_NDVI%5B275:277%5D%5B165:351%5D%5B0:40%5D,time%5B275:277%5D,YDim%5B165:351%5D,XDim%5B0:40%5D")
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)
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)
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})
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test_that("function mf_get_url() sends back the expected output for a GPM query", {
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skip_on_cran()
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skip_on_ci()
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urls_gpm <- mf_get_url(collection = "GPM_3IMERGDF.07",
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variables = c("precipitation"),
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roi = roi,
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time_range = time_range
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)
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expect_is(urls_gpm, "data.frame") # output is a data.frame
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expect_named(urls_gpm, c("id_roi","time_start","collection","name","url")) # column names are ok
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expect_equal(ncol(urls_gpm), 5) # there are 5 columns
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expect_equal(nrow(urls_gpm), 90) # there are 90 rows (corresponding to 90 dates)
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expect_match(urls_gpm$url[1], "https://gpm1.gesdisc.eosdis.nasa.gov") # urls starts with the right OPENDAP url
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expect_equal(urls_gpm[1,], data.frame(id_roi = "madagascar",
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time_start = as.Date("2023-01-01"),
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collection = "GPM_3IMERGDF.07",
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name = "3B-DAY.MS.MRG.3IMERG.20230101-S000000-E235959.V07B.nc4",
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url ="https://gpm1.gesdisc.eosdis.nasa.gov/opendap/GPM_L3/GPM_3IMERGDF.07/2023/01/3B-DAY.MS.MRG.3IMERG.20230101-S000000-E235959.V07B.nc4.nc4?precipitation%5B0:0%5D%5B2220:2313%5D%5B639:787%5D,time%5B0:0%5D,lon%5B2220:2313%5D,lat%5B639:787%5D"
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)
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)
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})
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test_that("function mf_get_url() sends back the expected errors when necessary", {
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skip_on_cran()
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skip_on_ci()
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# wrong type for roi
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expect_error(mf_get_url(collection = "MOD13A3.061",
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roi = "not_a_sf_object",
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time_range = as.Date(c("2017-01-01","2017-02-01"))),
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"Argument roi must be an object of class sf or sfc with POLYGON-type feature geometry and at least two columns : 'id' and a geometry column that must not be NULL or NA",
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fixed = TRUE)
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# wrong type for time range
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expect_error(mf_get_url(collection = "MOD13A3.061",
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roi = roi,
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time_range = c("2017-01-01","2017-02-01")),
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"Argument time_range is not of class Date or POSIXlt or is not of length 1 or 2 \n",
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fixed = TRUE)
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# wrong dates
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expect_error(mf_get_url(collection = "MOD13A3.061",
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roi = roi,
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time_range = as.Date(c("2000-01-01","2017-02-01"))),
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"First time frame in time_range argument is before the beginning of the mission\n",
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fixed = TRUE)
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expect_error(mf_get_url(collection = "MOD13A3.061",
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roi = roi,
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time_range = as.Date(c("2000-01-01","1999-02-01"))),
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"Time end is superior to time start in time_range argument \n",
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fixed = TRUE)
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# wrong length for time range
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expect_error(mf_get_url(collection = "MOD13A3.061",
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roi = roi,
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time_range = as.Date(c("2017-01-01","2017-02-01","2017-02-03"))),
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"Argument time_range is not of class Date or POSIXlt or is not of length 1 or 2 \n",
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fixed = TRUE)
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# wrong type for singleNetcdf
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expect_error(mf_get_url(collection = "MOD13A3.061",
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roi = roi,
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time_range = as.Date(c("2017-01-01","2017-02-01")),
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single_netcdf = "TRUE"),
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"single_netcdf argument must be boolean\n",
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fixed = TRUE)
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# Collection does not exist
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expect_error(mf_get_url(collection = "MOD13A3v006",
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roi = roi,
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time_range = as.Date(c("2017-01-01","2017-02-01"))),
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"The collection that you specified does not exist. Check mf_list_collections() to see which collections are implemented\n",
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fixed = TRUE)
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# output format is not specified
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expect_error(mf_get_url(collection = "MOD13A3.061",
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roi = roi,
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time_range = as.Date(c("2017-01-01","2017-02-01")),
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output_format = NA),
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"Specified output format is not valid. Please specify a valid output format \n",
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fixed = TRUE)
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# wrong variables specified
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expect_error(mf_get_url(collection = "MOD13A3.061",
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roi = roi,
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time_range = as.Date(c("2017-01-01","2017-02-01")),
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variables = c("LST_Day_1km","not_a_good_var")),
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"Specified variables do not exist or are not extractable for the specified collection. Use the function mf_list_variables to check which variables are available and extractable for the collection\n",
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fixed = TRUE)
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expect_error(mf_get_url(collection = "MOD13A3.061",
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roi = roi,
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time_range = as.Date(c("2017-01-01","2017-02-01")),
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variables = c("LST_Day_1km","time")),
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"Specified variables do not exist or are not extractable for the specified collection. Use the function mf_list_variables to check which variables are available and extractable for the collection\n",
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fixed = TRUE)
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})

‎tests/testthat/test-mf_import_data.R

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test_that("function mf_import_data() works to import a MODIS datacube", {
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skip_on_cran()
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skip_on_ci()
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modis_directory <- dirname(list.files(path = tempdir(), pattern = "MOD13A3.061.2023001_2023060.h21v10.nc4", recursive = TRUE, full.names = TRUE))
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r_to_test_modis <- mf_import_data(
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path = modis_directory,
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collection = "MOD13A3.061"
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)
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# the resulting raster should be equal to :
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# > r_to_test_modis
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# class : SpatRaster
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# dimensions : 1785, 1522, 3 (nrow, ncol, nlyr)
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# resolution : 926.6254, 926.6254 (x, y)
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# extent : 4186957, 5597281, -2918407, -1264380 (xmin, xmax, ymin, ymax)
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# coord. ref. : +proj=sinu +lon_0=0 +x_0=0 +y_0=0 +R=6371007.181 +units=m +no_defs
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# source(s) : memory
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# varname : _1_km_monthly_NDVI (1 km monthly NDVI)
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# names : _1_km_monthly_NDVI_1, _1_km_monthly_NDVI_2, _1_km_monthly_NDVI_3
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# min values : -0.2000, -0.2, -0.1993
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# max values : 0.9868, 1.0, 1.0000
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# time (days) : 2023-01-01 to 2023-03-01
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expect_is(r_to_test_modis,'SpatRaster') # output is a SpatRaster
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expect_equal(dim(r_to_test_modis),c(1785, 1522, 3)) # dimension
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expect_equal(round(res(r_to_test_modis)),c(927, 927)) # resolution
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expect_equal(ext(r_to_test_modis),ext(4186957.01926165, 5597280.9283724, -2918406.80140823, -1264380.40340488)) # extent
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expect_equal(time(r_to_test_modis),as.Date(c("2023-01-01", "2023-02-01", "2023-03-01"))) # dates
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expect_equal(names(r_to_test_modis), c("_1_km_monthly_NDVI_1", "_1_km_monthly_NDVI_2", "_1_km_monthly_NDVI_3"))
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expect_equal(varnames(r_to_test_modis), "_1_km_monthly_NDVI")
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})
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test_that("function mf_import_data() works to import a GPM datacube", {
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skip_on_cran()
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skip_on_ci()
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gpm_directory <- dirname(list.files(path = tempdir(), pattern = "3B-DAY.MS.MRG.3IMERG.20230101-S000000-E235959.V07B.nc4", recursive = TRUE, full.names = TRUE))
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r_to_test_gpm <- mf_import_data(
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path = gpm_directory,
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collection = "GPM_3IMERGDF.07"
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)
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# the resulting raster should be equal to :
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# > r_to_test_gpm
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# class : SpatRaster
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# dimensions : 149, 94, 90 (nrow, ncol, nlyr)
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# resolution : 0.09999999, 0.1 (x, y)
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# extent : 42, 51.4, -26.1, -11.2 (xmin, xmax, ymin, ymax)
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# coord. ref. : lon/lat WGS 84 (EPSG:4326)
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# source(s) : memory
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# varname : precipitation (Daily mean precipitation rate (combined microwave-IR) estimate. Formerly precipitationCal.)
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# names : preci~ation, preci~ation, preci~ation, preci~ation, preci~ation, preci~ation, ...
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# min values : 0.000, 0.000, 0.00, 0.00, 0.00, 0.00, ...
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# max values : 169.725, 175.575, 106.55, 138.54, 172.57, 167.06, ...
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# time (days) : 2023-01-01 to 2023-03-31
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expect_is(r_to_test_gpm,'SpatRaster') # output is a SpatRaster
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expect_equal(dim(r_to_test_gpm),c(149, 94, 90)) # dimension
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expect_equal(round(res(r_to_test_gpm),1),c(0.1,0.1)) # resolution
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expect_equal(ext(r_to_test_gpm),ext(41.9999992411624, 51.3999984700193, -26.1, -11.2)) # extent
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expect_equal(time(r_to_test_gpm),seq(as.Date("2023-01-01"),as.Date("2023-03-31"), 1)) # dates
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expect_equal(varnames(r_to_test_gpm), "precipitation") # variable names
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})

‎tests/testthat/test-mf_list_collections.R

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test_that("function mf_list_collections() sends back the expected output", {
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skip_on_cran()
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skip_on_ci()
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coll <- mf_list_collections()
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expect_is(coll,'data.frame') # output is a data.frame
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expect_equal(ncol(coll), 26) # there are 26 columns
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expect_named(coll, c("collection" ,"source","long_name" ,"nature","provider" ,
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"url_metadata", "doi", "version", "spatial_resolution_m" , "temporal_resolution",
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"temporal_resolution_unit", "spatial_coverage", "start_date", "end_date","indicative_latency_days" ,
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"url_manual_access" ,"status","login", "url_opendapserver" , "url_programmatic_access" ,
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"url_opendapexample","dim_lon","dim_lat","dim_time" ,"dim_proj", "crs" )) # column names are ok
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# number of rows is not tested since it can evolve with integration of additional opendap data sources
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})

‎tests/testthat/test-mf_list_variables.R

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test_that("function mf_list_variables() sends back the expected output", {
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skip_on_cran()
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skip_on_ci()
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# here we test with the collections "MOD13A3.061" and "GPM_3IMERGDF.07"
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vars_mod13a3 <- mf_list_variables(collection = "MOD13A3.061")
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expect_is(vars_mod13a3,'data.frame') # output is a data.frame
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expect_named(vars_mod13a3, c("name","long_name","units","indices","all_info","extractable_with_modisfast")) # column names are ok
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expect_equal(nrow(vars_mod13a3), 17) # there are 17 rows (corresponding to 17 variables/bands for this collection)
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vars_gpm <- mf_list_variables(collection = "GPM_3IMERGDF.07")
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expect_is(vars_gpm,'data.frame') # output is a data.frame
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expect_named(vars_gpm, c("name","long_name","units","indices","all_info","extractable_with_modisfast")) # column names are ok
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expect_equal(nrow(vars_gpm), 14) # there are 14 rows (corresponding to 14 variables/bands for this collection)
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})
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‎tests/testthat/test-mf_login.R

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test_that("function mf_login() sends back the expected outputs and errors when necessary", {
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skip_on_cran()
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skip_on_ci()
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expect_error(mf_login(credentials = c(earthdata_un,earthdata_pw,"hello")),"credentials must be a vector character string of length 2 (username and password)\n", fixed = TRUE)
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expect_error(mf_login(credentials = c(earthdata_un)),"credentials must be a vector character string of length 2 (username and password)\n", fixed = TRUE)
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expect_error(mf_login(credentials = c(earthdata_un,"wrong password"))) # error if wrong password is provided
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expect_error(mf_login(credentials = c("wrong username",earthdata_pw))) # error if wrong username is provided
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expect_no_error(mf_login(credentials = c(earthdata_un,earthdata_pw))) # no error if right password or username are provided
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})

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