version 0.3.0

cran · Jan 20, 2020 · 6ca121e · 6ca121e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,28 +1,28 @@
 Package: theiaR
 Title: Download and Manage Data from Theia
-Version: 0.2.0
+Version: 0.3.0
 Authors@R: person("Xavier", "Laviron", email = "xavier.laviron@gmx.fr",
     role = c("aut", "cre"),
     comment = c(ORCID = "0000-0002-9882-3253"))
 Description: Provides a simple interface to search available data provided by
     Theia (<https://theia.cnes.fr>), download it, and manage it. Data can be downloaded
     based on a search result or from a cart file downloaded from Theia website.
 Depends: R (>= 3.5)
-Imports: httr (>= 1.3), R6 (>= 2.3), raster (>= 2.6), tiff (>= 0.1),
-        tools (>= 3.5), XML (>= 3.86), askpass (>= 1.1)
+Imports: httr (>= 1.3), R6 (>= 2.3), raster (>= 2.6), tools (>= 3.5),
+        XML (>= 3.86), askpass (>= 1.1)
 License: GPL (>= 3.0)
 URL: https://github.com/norival/theiaR
 BugReports: https://github.com/norival/theiaR/issues
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
-Suggests: knitr, rmarkdown, covr
+RoxygenNote: 7.0.2
+Suggests: knitr, rmarkdown, covr, gdalcubes
 Collate: 'TheiaAuth.R' 'TheiaTile.R' 'TheiaCollection.R' 'TheiaQuery.R'
         'theiaR.R' 'utils.R'
 VignetteBuilder: knitr
 NeedsCompilation: no
-Packaged: 2019-03-26 12:21:58 UTC; lavironx
+Packaged: 2020-01-20 15:32:30 UTC; xavier
 Author: Xavier Laviron [aut, cre] (<https://orcid.org/0000-0002-9882-3253>)
 Maintainer: Xavier Laviron <xavier.laviron@gmx.fr>
 Repository: CRAN
-Date/Publication: 2019-03-26 12:30:03 UTC
+Date/Publication: 2020-01-20 16:00:02 UTC
diff --git a/MD5 b/MD5
@@ -1,23 +1,23 @@
-f58e7c76a96db32873f59418cc106ce7 *DESCRIPTION
+32cd00ed1a391ef5127de3d0477e1a25 *DESCRIPTION
 ef23d45adbf8c14d401b111bc2893b63 *NAMESPACE
-dd9e59e8e560094d6977fa7dbeda6f9b *NEWS.md
+c9013bfe7c302967f41403a6d86cbce2 *NEWS.md
 27473226eb1ecd86ec6f0a8a019aa46e *R/TheiaAuth.R
-2cb15ee5c6a3645b9c36807e9d304556 *R/TheiaCollection.R
-0e44c42a08c788eac0fd798b7fb9f5b0 *R/TheiaQuery.R
-202587baa754139d02c4724174025151 *R/TheiaTile.R
+1cb7c8c02008cc47242114d95deae30f *R/TheiaCollection.R
+83cd0e0e4d511dc77c4852cd98a39ef9 *R/TheiaQuery.R
+00f6d83b34c6b3a8a31f62a8f7e5b212 *R/TheiaTile.R
 cfb66bdb35f83ff44b9005b69fe14f44 *R/theiaR.R
 47070be27ab473402afac7fc3c34fc84 *R/utils.R
 e88d39c685096c136bb319fa9bcc21b6 *README.md
-f971297cba03e29eb8c3829b6816fa6d *build/vignette.rds
-f3a24f434452b425530cdd6f44d0752b *inst/WORDLIST
-1d16ec6de26a1ee331948214e8a8ebd3 *inst/doc/quick-start.R
+43a92c24ca54a5e5b031f4d8a21366c3 *build/vignette.rds
+8b5cd7638064badfecf54f7761da6b93 *inst/WORDLIST
+6b1a65b62ab33b56d3d992d8244b4c9f *inst/doc/quick-start.R
 ff542859e7d16cd3c52de8f14881841a *inst/doc/quick-start.Rmd
-a94188ffaa28509efc131f9fc32bc633 *inst/doc/quick-start.html
+f4e170ed77266f4987fac3710c8ecfba *inst/doc/quick-start.html
 31f38b1780aff70c46e3de53c853e72d *inst/extdata/cart.meta4
-7a6688ec0b711859a022cdbfd8b299f9 *inst/extdata/dummy_tile.zip
+acdbbf4d5eb10d242c61a1a843bcd28d *inst/templates/gdalcubes_theia.json
 e60ca1b59ddb91d5b7e0a0deaade3f71 *man/TheiaAuth.Rd
-78713cc3c1b83dcf4196b91bb0a3590c *man/TheiaCollection.Rd
+6e12f6337fa5c7ad82f956a04160c11e *man/TheiaCollection.Rd
 b4bbbe6e27b24fdd802952e04de6cb77 *man/TheiaQuery.Rd
-ca5226f7340fa33a548eb5159db04dfa *man/TheiaTile.Rd
-70b672cdce97f164a78472ec59d6fc5d *man/theiaR.Rd
+4108da0c693b84f88ee7912d1662559d *man/TheiaTile.Rd
+c427909fd2fcce0ae42d0ab0e155f664 *man/theiaR.Rd
 ff542859e7d16cd3c52de8f14881841a *vignettes/quick-start.Rmd
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,27 @@
+# theiaR 0.3.0
+
+## New features
+
+- Adds export to gdalcubes' image collection
+
+## Bug fixes
+
+- Fix error due to bad file path on Windows
+
+## Minor changes
+
+- Adds quiet arguments to control verbose output
+- Adds 'check' argument to 'TheiaTile' and 'TheiaCollection' download methods
+- Do not parse meta.data on tile creation, but do it on the fly
+
+
+# theiaR 0.2.1
+
+## Bug fixes
+
+- Fix printing of TheiaQuery objects
+
+
 # theiaR 0.2.0
 
 ## New features

diff --git a/R/TheiaCollection.R b/R/TheiaCollection.R
@@ -14,12 +14,14 @@
 #'                             query     = NULL,
 #'                             dir.path  = NULL,
 #'                             check     = TRUE)
+#'                             quiet     = TRUE)
 #'
-#'    c$download(auth, overwrite = FALSE)
+#'    c$download(auth, overwrite = FALSE, check = TRUE, quiet = TRUE)
 #'    c$check()
 #'    c$status
 #'    c$extract(overwrite = FALSE, dest.dir = NULL)
 #'    c$read(bands)
+#'    c$as_gdalcube(out.file = "gdalcube_collection.sqlite")
 #' }
 #'
 #' @section Arguments:
@@ -28,6 +30,7 @@
 #'    \item{c:}{A \code{TheiaCollection} object}
 #'    \item{dir.path:}{The path to the directory containing zip files}
 #'    \item{check:}{Whether or not to check existing files on collection's creation}
+#'    \item{quiet:}{Control verbose output}
 #'    \item{tiles:}{A list of TheiaTile objects}
 #'    \item{cart:}{An XML cart parsed from a 'meta4' file downloaded from Theia}
 #'    website. Used only if Collection is created from a cart
@@ -39,12 +42,13 @@
 #'    Or a \code{\link{TheiaAuth}} object}
 #'    \item{overwrite:}{Overwrite existing tiles (default to `FALSE`)}
 #'    \item{bands:}{A character vector of bands to load from tiles}
+#'    \item{out.file:}{Filename to store gdalcubes' image collection}
 #'  }
 #'
 #' @section Details:
 #'    \code{TheiaCollection$new()} Create a new instance of the class
 #'
-#'    \code{c$download(overwrite = FALSE)} Download the tiles of the collection
+#'    \code{c$download(overwrite = FALSE, check = TRUE)} Download the tiles of the collection
 #'    and check the resulting files
 #'
 #'    \code{$ccheck()} Check the tiles of the collection
@@ -58,6 +62,10 @@
 #'    (as specified in Theia's product information), and return a list of
 #'    RasterStack objects (one stack per tile)
 #'
+#'    \code{c$as_gdalcube(out.file)} Create a `gdalcubes` image collection from
+#'    downloaded tiles. See \url{https://github.com/appelmar/gdalcubes_R} for
+#'    more details.
+#'
 #' @examples
 #'
 #' \donttest{
@@ -114,9 +122,16 @@ TheiaCollection <-
                                        tiles      = NULL,
                                        query      = NULL,
                                        dir.path   = NULL,
-                                       check      = TRUE)
+                                       check      = TRUE,
+                                       quiet      = TRUE)
                  {
-                   .TheiaCollection_initialize(self, cart.path, tiles, query, dir.path, check)
+                   if (quiet == TRUE) {
+                     suppressMessages({
+                       .TheiaCollection_initialize(self, cart.path, tiles, query, dir.path, check)
+                     })
+                   } else {
+                     .TheiaCollection_initialize(self, cart.path, tiles, query, dir.path, check)
+                   }
                  },
 
                  print = function(...)
@@ -129,9 +144,9 @@ TheiaCollection <-
                    .TheiaCollection_check(self)
                  },
 
-                 download = function(auth, overwrite = FALSE)
+                 download = function(auth, overwrite = FALSE, check = TRUE, quiet = TRUE)
                  {
-                   .TheiaCollection_download(self, auth, overwrite)
+                   .TheiaCollection_download(self, auth, overwrite, check, quiet)
                  },
 
                  extract = function(overwrite = FALSE, dest.dir = NULL)
@@ -142,6 +157,11 @@ TheiaCollection <-
                  read = function(bands)
                  {
                    .TheiaCollection_read(self, private, bands)
+                 },
+
+                 as_gdalcube = function(out.file)
+                 {
+                   .TheiaCollection_as_gdalcube(self, private, out.file)
                  }),
 
             # active -----------------------------------------------------------
@@ -246,7 +266,7 @@ TheiaCollection <-
 }
 
 
-.TheiaCollection_download <- function(self, auth, overwrite)
+.TheiaCollection_download <- function(self, auth, overwrite, check, quiet)
 {
   if (is.character(auth)) {
     # create authentification system if not supplied
@@ -255,10 +275,10 @@ TheiaCollection <-
 
   # download needed tiles
   lapply(self$tiles,
-         function(x, auth, overwrite) {
-           x$download(auth, overwrite = overwrite)
+         function(x, auth, overwrite, check, quiet) {
+           x$download(auth, overwrite = overwrite, check = check, quiet)
          },
-         auth = auth, overwrite = overwrite)
+         auth = auth, overwrite = overwrite, check = check, quiet = quiet)
 
   return(invisible(self))
 }
@@ -303,3 +323,33 @@ TheiaCollection <-
 
   return(tiles.list)
 }
+
+
+.TheiaCollection_as_gdalcube <- function(self, private, out.file = "gdalcube_collection.sqlite")
+{
+  # export collection as a gdalcube image collection
+  if (!(requireNamespace("gdalcubes", quietly = TRUE))) {
+    # check if package 'gdalcubes' is installed
+    stop("Package 'gdalcubes' needed for this function. Please install it.",
+         call. = FALSE)
+  }
+
+  if (!(all(as.logical(self$status$exists)))) {
+    # check if all files are downloaded
+    stop("Some files in the collection are not downloaded. Please check `mycollection$status()`",
+         call. = FALSE)
+  }
+
+  # extract file paths to collection
+  files <- unname(sapply(self$tiles, function(x) x$file.path))
+
+  # create gdalcubes image collection
+  gdalcubes.col <-
+    gdalcubes::create_image_collection(files    = files,
+                                       format   = system.file("templates",
+                                                              "gdalcubes_theia.json",
+                                                              package = "theiaR"),
+                                       out_file = out.file)
+
+  return(gdalcubes.col)
+}
diff --git a/R/TheiaQuery.R b/R/TheiaQuery.R
@@ -129,11 +129,15 @@ TheiaQuery <-
 
   cat("Search terms:\n")
 
+  # get maximum length of search terms to format printing
+  max.chars <- max(nchar(names(self$query))) + 1
+
+  # print search terms
   lapply(1:length(self$query),
          function(x) {
            l <- nchar(names(self$query))[[x]]
 
-           cat("   ", names(self$query)[[x]], rep(" ", 11 - l), ": ",
+           cat("   ", names(self$query)[[x]], rep(" ", max.chars - l), ": ",
                self$query[[x]], "\n",
                sep = "")