Fix file export

.gitignore

@@ -10,4 +10,5 @@ data/
 check/
 vignettes/data/
 *.Rproj
-.RData
+.RData
+my_vitessce_files/

R/export.R

@@ -17,17 +17,27 @@
 #' vc$export(to = "files", out_dir = "./data")
 export_to_files <- function(config, with_config, base_url, out_dir) {
   routes <- config$get_routes()
+
 
   for(route in routes) {
     # Get the intended web server route, removing the initial "/"
     route_path <- substr(route$path, 2, stringr::str_length(route$path))
     out_path <- file.path(out_dir, route_path)
 
-    dir.create(out_path, showWarnings = FALSE, recursive = TRUE)
-    # Copy the converted files from their original directory to the `out_dir`.
-    static_dir <- route$directory
-    files_to_copy = list.files(static_dir, full.names = TRUE)
-    file.copy(files_to_copy, out_path, recursive = TRUE)
+    if(class(route)[1] == "VitessceConfigServerStaticRoute") {
+      # This is a directory.
+      dir.create(out_path, showWarnings = FALSE, recursive = TRUE)
+      # Copy the converted files from their original directory to the `out_dir`.
+      static_dir <- route$directory
+      files_to_copy <- list.files(static_dir, full.names = TRUE)
+      file.copy(files_to_copy, out_path, recursive = TRUE)
+    } else {
+      # This is a single file.
+      dir.create(dirname(out_path), showWarnings = FALSE, recursive = TRUE)
+      # Copy the converted files from their original directory to the `out_dir`.
+      file_to_copy <- route$file_path
+      file.copy(file_to_copy, out_path, recursive = TRUE)
+    }
   }
 
   if(with_config) {

vignettes/export_files.Rmd

@@ -15,27 +15,32 @@ First, install the dependencies:
 ```r
 install.packages("devtools")
 devtools::install_github("satijalab/seurat-data")
+devtools::install_github("vitessce/vitessceAnalysisR")
 ```
 
 Create the Vitessce configuration:
 
 ```r
 library(vitessceR)
+library(vitessceAnalysisR)
 library(SeuratData)
 
 SeuratData::InstallData("pbmc3k")
 data("pbmc3k.final")
 force(pbmc3k.final)
 
-vc <- VitessceConfig$new("My config")
+adata_path <- file.path("data", "seurat", "pbmc3k.final.h5ad.zarr")
+
+vitessceAnalysisR::seurat_to_anndata_zarr(pbmc3k.final, adata_path)
+
+vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
 dataset <- vc$add_dataset("My dataset")
 dataset <- dataset$add_object(
-  SeuratWrapper$new(
-    pbmc3k.final,
-    cell_embeddings = c("pca", "umap"),
-    cell_embedding_names = c("PCA", "UMAP"),
-    cell_set_meta_names = c("seurat_annotations", "seurat_clusters"),
-    out_dir = file.path("data", "seuratdata")
+  AnnDataWrapper$new(
+    adata_path=adata_path,
+    obs_embedding_paths = c("obsm/X_pca", "obsm/X_umap"),
+    obs_embedding_names = c("PCA", "UMAP"),
+    obs_set_paths = c("obs/seurat_annotations", "obs/seurat_clusters")
   )
 )
 scatterplot <- vc$add_view(dataset, Component$SCATTERPLOT, mapping = "PCA")