More logging

R/AnnotationDataframe.R

@@ -34,6 +34,8 @@ AnnotationDataframe <- R6::R6Class(
         "'index_col' must be a scalar character" = is_scalar_character(index_col)
       )
 
+      spdl::debug("Populating {} at '{}' with data.frame data", self$class(), self$uri)
+
       # convert rownames to a column
       x[[index_col]] <- rownames(x)
       if (!self$exists()) {
@@ -58,6 +60,7 @@ AnnotationDataframe <- R6::R6Class(
     #' @return A [`data.frame`] with row names containing values from the index
     #'    dimension
     to_dataframe = function(attrs = NULL) {
+      spdl::debug("Returning {} at '{}' to data.frame", self$class(), self$uri)
       spdl::info(sprintf("Reading %s into memory from '%s'", self$class(), self$uri))
 
       # Check for legacy validity mode metadata tag

R/AnnotationGroup.R

@@ -43,6 +43,7 @@ AnnotationGroup <- R6::R6Class(
 
       # Assuming all members are TileDBArrays
       for (member in names(self$members)) {
+        spdl::debug("Setting the query for '{}'", member)
         self$members[[member]]$set_query(dims, attr_filter)
       }
     },
@@ -53,6 +54,7 @@ AnnotationGroup <- R6::R6Class(
     #' @return NULL
     reset_query = function(dims = TRUE, attr_filter = TRUE) {
       for (member in names(self$members)) {
+        spdl::debug("Resetting the query for '{}'", member)
         self$members[[member]]$reset_query(dims, attr_filter)
       }
     }

R/AnnotationMatrix.R

@@ -27,6 +27,7 @@ AnnotationMatrix <- R6::R6Class(
         "'index_col' must be a scalar character" = is_scalar_character(index_col)
       )
       private$validate_matrix(x)
+      spdl::debug("Populating {} at '{}' with matrix data", self$class(), self$uri)
 
       # convert to a data frame containing the index column
       x <- as.data.frame(x)
@@ -46,6 +47,8 @@ AnnotationMatrix <- R6::R6Class(
     #' @return A [`matrix`]
     to_matrix = function(attrs = NULL, batch_mode = FALSE) {
 
+      spdl::debug("Returning {} at '{}' as a matrix", self$class(), self$uri)
+
       df <- private$read_data(
         attrs = attrs,
         batch_mode = batch_mode,

R/AnnotationMatrixGroup.R

@@ -26,6 +26,7 @@ AnnotationMatrixGroup <- R6::R6Class(
       # TODO: Verify that the matrix is aligned to the group's dimension
 
       # create the new array
+      spdl::debug("Adding matrix as '{}' to group at '{}'", name, self$uri)
       array_uri <- file_path(self$uri, name)
       array <- AnnotationMatrix$new(
         uri = array_uri,

R/AnnotationPairwiseMatrix.R

@@ -26,6 +26,7 @@ AnnotationPairwiseMatrix <- R6::R6Class(
         "'value_col' must be a scalar character" = is_scalar_character(value_col)
       )
       private$validate_matrix(x)
+      spdl::debug("Populating {} at '{}' with matrix data", self$class(), self$uri)
 
       x <- matrix_to_coo(
         x = x,
@@ -65,6 +66,11 @@ AnnotationPairwiseMatrix <- R6::R6Class(
     #' @description Read annotation data from TileDB into a sparse matrix
     #' @return A [`Matrix::dgTMatrix-class`].
     to_sparse_matrix = function() {
+      spdl::info(sprintf(
+        "Reading %s into sparse dgT matrix from '%s'",
+        self$class(),
+        self$uri
+      ))
       dataframe_to_dgtmatrix(
         self$to_dataframe(),
         index_cols = self$dimnames()
@@ -75,6 +81,11 @@ AnnotationPairwiseMatrix <- R6::R6Class(
     #' @return A [`SeuratObject::Graph-class`]
     #' @importFrom SeuratObject DefaultAssay
     to_seurat_graph = function() {
+      spdl::info(sprintf(
+        "Reading %s into SeuratObject::Graph from '%s'",
+        self$class(),
+        self$uri
+      ))
       assay <- self$get_metadata(key = "assay_used")
       object <- SeuratObject::as.Graph(self$to_sparse_matrix())
       SeuratObject::DefaultAssay(object) <- assay

R/AnnotationPairwiseMatrixGroup.R

@@ -26,6 +26,7 @@ AnnotationPairwiseMatrixGroup <- R6::R6Class(
 
       # TODO: Verify that the matrix is aligned to the group's dimension
       # create the new array
+      spdl::debug("Adding {} as '{}' to group at '{}'", self$class(), name, self$uri)
       array_uri <- file_path(self$uri, name)
       array <- AnnotationPairwiseMatrix$new(
         uri = array_uri,
@@ -65,6 +66,7 @@ AnnotationPairwiseMatrixGroup <- R6::R6Class(
       assay <- SeuratObject::DefaultAssay(object)
       array_name <- paste0(prefix, technique)
 
+      spdl::debug("Adding SeuratObject::Graph as '{}' to group at '{}'", array_name, self$uri)
       self$add_matrix(
         data = as(object, "TsparseMatrix"),
         name = array_name,

R/AssayMatrix.R

@@ -34,6 +34,8 @@ AssayMatrix <- R6::R6Class(
       )
       private$validate_matrix(x)
 
+      spdl::debug("Populating {} at '{}' with matrix data", self$class(), self$uri)
+
       self$from_dataframe(
         matrix_to_coo(x, index_cols = index_cols, value_cols = value_col),
         index_cols = index_cols
@@ -52,6 +54,7 @@ AssayMatrix <- R6::R6Class(
         length(index_cols) == 2,
         all(index_cols %in% colnames(x))
       )
+      spdl::debug("Populating {} at '{}' with triplet data", self$class(), self$uri)
       if (!self$exists()) {
         private$create_empty_array(x, index_cols)
       } else {
@@ -66,6 +69,7 @@ AssayMatrix <- R6::R6Class(
     #' @return A [`Matrix::dgTMatrix-class`].
     #' @importFrom vctrs vec_rbind
     to_dataframe = function(attrs = NULL, batch_mode = FALSE) {
+      spdl::debug("Returning {} at '{}' as triplets", self$class(), self$uri)
       private$read_data(
         attrs = attrs,
         batch_mode = batch_mode,
@@ -83,6 +87,8 @@ AssayMatrix <- R6::R6Class(
       }
       stopifnot(is_scalar_character(attr))
 
+      spdl::debug("Returning {} at '{}' as a dgT matrix", self$class(), self$uri)
+
       assay_data <- private$read_data(
         attrs = attr,
         batch_mode = batch_mode,

R/AssayMatrixGroup.R

@@ -26,6 +26,8 @@ AssayMatrixGroup <- R6::R6Class(
         stop("Must provide a `matrix` to ingest into the new AnnotationMatrix")
       }
 
+      spdl::debug("Populating {} at '{}' with matrix data", self$class(), self$uri)
+
       # create the new array
       array_uri <- file_path(self$uri, name)
       array <- AssayMatrix$new(

R/CommandsArray.R

@@ -23,6 +23,8 @@ CommandsArray <- R6::R6Class(
         )
       }
 
+      spdl::debug("Populating {} at '{}' with SeuratCommand data", self$class(), self$uri)
+
       # Convert from list of objects to list of dataframes.
       command_dataframes <- lapply(x, as.data.frame.SeuratCommand)