From 60d05345a0413c18215a2892c031367ed28fe05a Mon Sep 17 00:00:00 2001
From: Ivo Kwee <ivo.kwee@gmail.com>
Date: Wed, 8 Nov 2023 16:51:30 +0100
Subject: [PATCH] fix: bug related to updateDatasetFolder() and dimension error
 (CRITICAL)

---
 R/pgx-files.R     | 16 ++++++++++++----
 R/pgx-signature.R |  4 ++++
 2 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/R/pgx-files.R b/R/pgx-files.R
index ba44b3de..876a0057 100644
--- a/R/pgx-files.R
+++ b/R/pgx-files.R
@@ -821,18 +821,21 @@ pgxinfo.updateDatasetFolder <- function(pgx.dir,
       fc.add <- any(!colnames(allFC) %in% cn)
       fc.del <- any(!cn %in% colnames(allFC))
       if (fc.add) {
-        dbg("[pgxinfo.updateDatasetFolder] adding sigDB (full create)")
         pgx.createSignatureDatabaseH5.fromMatrix(sigdb.file, X = allFC)
-      }
+        cn <- rhdf5::h5read(sigdb.file, "data/colnames")  ## new size
+      }      
+      
       if (fc.del) {
         del <- which(!cn %in% colnames(allFC))
         ##        cn[del] <- paste("[DELETED]", sub(".*\\] ", "", cn[del]))
         cn[del] <- paste("[DELETED]", cn[del])
         rhdf5::h5delete(sigdb.file, "data/colnames")
         rhdf5::h5write(cn, sigdb.file, "data/colnames")
+        Sys.sleep(0.1)  ## time to write...
         if (delete.old) {
           dbg("[pgxinfo.updateDatasetFolder] deleting sigDB entry")
           sigdb.removeDataset(sigdb.file, "DELETED")
+          Sys.sleep(0.1)  ## allow write time
         } else {
           dbg("[pgxinfo.updateDatasetFolder] deletions tagged but not removed")
         }
@@ -846,12 +849,17 @@ pgxinfo.updateDatasetFolder <- function(pgx.dir,
     if (!file.exists(tsne.file) || pgxfc.changed) {
       cn <- rhdf5::h5read(sigdb.file, "data/colnames")
       tsne <- rhdf5::h5read(sigdb.file, "clustering/tsne2d")
+      length(cn)
+      dim(tsne)
+      if(length(cn) != nrow(tsne)) {
+        dbg("[pgxinfo.updateDatasetFolder] ***ERROR**** length mismatch!")
+      }
       rownames(tsne) <- cn
-      colnames(tsne) <- paste0("tsne.", 1:2)
+      colnames(tsne) <- paste0("tsne.", 1:ncol(tsne))
       utils::write.csv(tsne, file = tsne.file)
     }
   }
-
+  dbg("[pgxinfo.updateDatasetFolder] done!")
   return()
 }
 
diff --git a/R/pgx-signature.R b/R/pgx-signature.R
index 2db1a41c..a59b60af 100644
--- a/R/pgx-signature.R
+++ b/R/pgx-signature.R
@@ -372,6 +372,9 @@ pgx.createSignatureDatabaseH5.fromMatrix <- function(h5.file, X, update.only = F
     rhdf5::h5write(pos[["pca2d"]], h5.file, "clustering/pca2d") ## can write list??
     rhdf5::h5write(pos[["tsne2d"]], h5.file, "clustering/tsne2d") ## can write list??
     rhdf5::h5write(pos[["umap2d"]], h5.file, "clustering/umap2d") ## can write list??
+
+    dbg("[pgx.createSignatureDatabaseH5.fromMatrix] dim.tsne2d = ", dim(pos[["tsne2d"]]))
+    dbg("[pgx.createSignatureDatabaseH5.fromMatrix] clustering done")
   }
 
   ## --------------------------------------------------
@@ -380,6 +383,7 @@ pgx.createSignatureDatabaseH5.fromMatrix <- function(h5.file, X, update.only = F
   pgx.addEnrichmentSignaturesH5(h5.file, X = X, mc.cores = 0, methods = "rankcor")
 
   ## done!
+  dbg("[pgx.createSignatureDatabaseH5.fromMatrix] done!")
   rhdf5::h5closeAll()
 }