add progress bar to db() update

mtmorgan · Sep 10, 2024 · 1526e3b · 1526e3b
1 parent 525c4aa
commit 1526e3b
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Showing 4 changed files with 30 additions and 11 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: cellxgenedp
 Title: Discover and Access Single Cell Data Sets in the CELLxGENE Data Portal
-Version: 1.9.0
+Version: 1.9.1
 Authors@R: 
     c(person(
         given = "Martin",
@@ -21,7 +21,7 @@ Encoding: UTF-8
 Collate: db.R collections.R datasets.R files.R facets.R keys.R
     cellxgene.R utilities.R publisher_metadata.R cxg.R
 Depends: dplyr
-Imports: httr, curl, utils, tools, shiny, DT, rjsoncons
+Imports: httr, curl, utils, tools, cli, shiny, DT, rjsoncons
 Suggests:
     zellkonverter,
     SingleCellExperiment,
@@ -36,6 +36,6 @@ biocViews: SingleCell, DataImport, ThirdPartyClient
 URL: https://mtmorgan.github.io/cellxgenedp/, https://github.com/mtmorgan/cellxgenedp
 BugReports: https://github.com/mtmorgan/cellxgenedp/issues
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 VignetteBuilder: knitr
 Config/testthat/edition: 3
diff --git a/NAMESPACE b/NAMESPACE
@@ -17,6 +17,9 @@ export(publisher_metadata)
 importFrom(DT,datatable)
 importFrom(DT,formatStyle)
 importFrom(DT,renderDataTable)
+importFrom(cli,cli_progress_bar)
+importFrom(cli,cli_progress_done)
+importFrom(cli,cli_progress_update)
 importFrom(curl,nslookup)
 importFrom(dplyr,.data)
 importFrom(dplyr,across)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# cellxgenedp 1.10
+
+SIGNIFICANT USER-VISIBLE CHANGES
+
+* (v.1.9.1) Add progress bar when updated `db()`
+
 # cellxgenedp 1.8
 
 SIGNIFICANT USER-VISIBLE CHANGES

diff --git a/R/db.R b/R/db.R
@@ -12,15 +12,25 @@
         bind_rows()
 }
 
+#' @importFrom cli cli_progress_bar cli_progress_update
+#'     cli_progress_done
 .db_detail <-
-    function(id, overwrite)
+    function(collection_id, overwrite)
 {
-    ## be sure to return a result & check for errors
-    tryCatch({
-        uri <- paste0(.COLLECTIONS, id)
-        path <- .cellxgene_cache_get(uri, overwrite = overwrite)
-        readLines(path)
-    }, error = identity)
+    n_collections <- length(collection_id)
+    result <- vector("list", n_collections)
+    cli_progress_bar("Collections", total = n_collections)
+    for (i in seq_len(n_collections)) {
+        ## be sure to return a result & check for errors
+        result[[i]] <- tryCatch({
+            uri <- paste0(.COLLECTIONS, collection_id[[i]])
+            path <- .cellxgene_cache_get(uri, overwrite = overwrite)
+            readLines(path)
+        }, error = identity)
+        cli_progress_update()
+    }
+    cli_progress_done()
+    result
 }
 
 .db_first <- local({
@@ -81,7 +91,7 @@ db <-
     if (overwrite)
         message("updating database and collections...")
     db <- .db(overwrite)
-    details <- lapply(db$collection_id, .db_detail, overwrite = overwrite)
+    details <- .db_detail(db$collection_id, overwrite)
     errors <- vapply(details, inherits, logical(1), "error")
     if (any(errors)) {
         stop(