From 3d069c845b78d4d83c45d388ff9c0dfa4a335edd Mon Sep 17 00:00:00 2001
From: MGousseff <matthieu.gousseff@gmail.com>
Date: Mon, 3 Jun 2024 12:34:53 +0200
Subject: [PATCH] fix fgb import failure when fgb doesn't show layer name in
 metadata (slower, but no way to deduce the table name yet from fgb)

---
 DESCRIPTION                        |  2 +-
 R/importLCZvect.R                  | 36 +++++++++++++++++++++---------
 inst/tinytest/test_importLCZvect.R | 12 +++++++++-
 submissionJourneesR.rmd            | 22 ------------------
 4 files changed, 38 insertions(+), 34 deletions(-)
 delete mode 100644 submissionJourneesR.rmd

diff --git a/DESCRIPTION b/DESCRIPTION
index 0b70242..1904965 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -9,7 +9,7 @@ Description: This lczexplore package automatize the comparison of sets of local
 License: LGPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Imports: RColorBrewer,
           cowplot,
           dplyr,
diff --git a/R/importLCZvect.R b/R/importLCZvect.R
index 97b2f66..d5a4a51 100644
--- a/R/importLCZvect.R
+++ b/R/importLCZvect.R
@@ -44,17 +44,33 @@ importLCZvect<-function(dirPath, file="rsu_lcz.geojson", output="sfFile", column
   colonnes<-colonnes[sapply(colonnes,nchar)!=0]
 
   # Check if all the desired columns are present in the source file and only loads the file if the columns exist
+  ### DOESN'T WORK WITH flatgeobuffer
   nom<-gsub(pattern="(.+?)(\\.[^.]*$|$)",x=file,replacement="\\1")
-  query<-paste0("select * from ",nom," limit 0")
-  sourceCol<-st_read(dsn=fileName, query=query, quiet=!verbose) %>% names
-  inCol<-colonnes%in%sourceCol
-  badCol<-colonnes[!inCol]
-  colErr<-c("It seems that some of the columns you try to import do not exist in the source file,
-            are you sure you meant ",
-                 paste(badCol)," ?")
-  if (prod(inCol)==0){ stop(colErr) } else { 
-    if (drop== TRUE) {sfFile<-sf::st_read(dsn=fileName,quiet=!verbose)[,colonnes] } else {
-      sfFile<-sf::st_read(dsn=fileName,quiet=!verbose)[,]}
+  extension<-gsub(pattern="(.+?)(\\.[^.]*$|$)",x=file,replacement="\\2")
+  if (extension != ".fgb"){ # Some metadata for fgb files do not specify table/layer names
+    query<-paste0("select * from ",nom," limit 0") # So this query wouldn't work with such fgb files
+    sourceCol<-st_read(dsn=fileName, query=query, quiet=!verbose) %>% names
+    inCol<-colonnes%in%sourceCol
+    badCol<-colonnes[!inCol]
+    colErr<-c("It seems that some of the columns you try to import do not exist in the source file,
+              are you sure you meant ",
+                   paste(badCol),"?")
+    if (prod(inCol)==0){ stop(colErr) } else { 
+      if (drop== TRUE) {sfFile<-sf::st_read(dsn=fileName,quiet=!verbose)[,colonnes] } else {
+        sfFile<-sf::st_read(dsn=fileName,quiet=!verbose)[,]}
+    }
+  } else {if (extension == ".fgb") {
+    sfFile<-sf::st_read(dsn=fileName,quiet=!verbose)[,]
+    sourceCol<-names(sfFile)
+    inCol<-colonnes%in%sourceCol
+    badCol<-colonnes[!inCol]
+    colErr<-c("It seems that some of the columns you try to import do not exist in the source file,
+              are you sure you meant ",
+              paste(badCol),"?")
+    if (prod(inCol)==0){ stop(colErr) }
+       
+  }
+  
   }
 
   # if typeLevels is empty
diff --git a/inst/tinytest/test_importLCZvect.R b/inst/tinytest/test_importLCZvect.R
index 7598ac9..48b09dc 100644
--- a/inst/tinytest/test_importLCZvect.R
+++ b/inst/tinytest/test_importLCZvect.R
@@ -105,4 +105,14 @@ expect_warning(importLCZvect(dirPath=paste0(system.file("extdata", package = "lc
 test<-importLCZvect(dirPath=paste0(
   system.file("extdata", package = "lczexplore"),"/bdtopo_2_2/Redon"),file="rsu_lcz.geojson",
               column="LCZ_PRIMARY", geomID="ID_RSU", confid="LCZ_UNIQUENESS_VALUE", drop=FALSE)
-expect_equal("LCZ_SECONDARY"%in%names(test),TRUE)
\ No newline at end of file
+expect_equal("LCZ_SECONDARY"%in%names(test),TRUE)
+
+# Special test with a flatgeobuffer file. 
+test<-importLCZvect(dirPath=paste0(system.file("extdata", package = "lczexplore"),"/bdtopo_2_2/Redon"),
+                            column="LCZ_PRIMARY",geomID="ID_RSU",confid="LCZ_UNIQUENESS_VALUE",verbose=T)
+if (file.exists("test.fgb")) file.remove("test.fgb")
+write_sf(test, "test.fgb")
+expect_silent(test<-importLCZvect(dirPath=getwd(),file="test.fgb",
+                    column="LCZ_PRIMARY",geomID="ID_RSU",confid="LCZ_UNIQUENESS_VALUE",verbose=T))
+rm(test)
+if (file.exists("test.fgb")) file.remove("test.fgb")
diff --git a/submissionJourneesR.rmd b/submissionJourneesR.rmd
deleted file mode 100644
index dd6665d..0000000
--- a/submissionJourneesR.rmd
+++ /dev/null
@@ -1,22 +0,0 @@
---
-title: "R Notebook"
-output: html_notebook
----
-
-The [R plugin](https://www.jetbrains.com/help/pycharm/r-plugin-support.html) for IntelliJ-based IDEs provides
-handy capabilities to work with the [R Markdown](https://www.jetbrains.com/help/pycharm/r-markdown.html) files.
-To [add](https://www.jetbrains.com/help/pycharm/r-markdown.html#add-code-chunk) a new R chunk,
-position the caret at any line or the code chunk, then click "+".
-
-The code chunk appears:
-```{r}
-```
-
-Type any R code in the chunk, for example:
-```{r}
-mycars <- within(mtcars, { cyl <- ordered(cyl) })
-mycars
-```
-
-Now, click the **Run** button on the chunk toolbar to [execute](https://www.jetbrains.com/help/pycharm/r-markdown.html#run-r-code) the chunk code. The result should be placed under the chunk.
-Click the **Knit and Open Document** to build and preview an output.