[r] Proper prefixing for shape-related methods

apis/r/DESCRIPTION

@@ -6,7 +6,7 @@ Description: Interface for working with 'TileDB'-based Stack of Matrices,
     like those commonly used for single cell data analysis. It is documented at
     <https://github.com/single-cell-data>; a formal specification available is at
     <https://github.com/single-cell-data/SOMA/blob/main/abstract_specification.md>.
-Version: 1.15.99.9
+Version: 1.15.99.10
 Authors@R: c(
     person(given = "Aaron", family = "Wolen",
            role = c("cre", "aut"), email = "[email protected]",

apis/r/NEWS.md

@@ -17,6 +17,7 @@
 * Fix `is_named_list` bug for half-named lists [#3183](https://github.com/single-cell-data/TileDB-SOMA/pull/3183)
 * Expose block/random writer for sparse arrays [#3204](https://github.com/single-cell-data/TileDB-SOMA/pull/3204)
 * Min-sizing for dataframes/arrays with new shape feature [#3208](https://github.com/single-cell-data/TileDB-SOMA/pull/3208)
+* Proper prefixing for shape-related methods [#3237](https://github.com/single-cell-data/TileDB-SOMA/pull/3237)
 
 # tiledbsoma 1.14.1
 

apis/r/R/RcppExports.R

@@ -238,16 +238,16 @@ c_schema <- function(uri, ctxxp) {
     .Call(`_tiledbsoma_c_schema`, uri, ctxxp)
 }
 
-resize <- function(uri, new_shape, ctxxp) {
-    invisible(.Call(`_tiledbsoma_resize`, uri, new_shape, ctxxp))
+resize <- function(uri, new_shape, function_name_for_messages, ctxxp) {
+    invisible(.Call(`_tiledbsoma_resize`, uri, new_shape, function_name_for_messages, ctxxp))
 }
 
-resize_soma_joinid_shape <- function(uri, new_shape, ctxxp) {
-    invisible(.Call(`_tiledbsoma_resize_soma_joinid_shape`, uri, new_shape, ctxxp))
+resize_soma_joinid_shape <- function(uri, new_shape, function_name_for_messages, ctxxp) {
+    invisible(.Call(`_tiledbsoma_resize_soma_joinid_shape`, uri, new_shape, function_name_for_messages, ctxxp))
 }
 
-tiledbsoma_upgrade_shape <- function(uri, new_shape, ctxxp) {
-    invisible(.Call(`_tiledbsoma_tiledbsoma_upgrade_shape`, uri, new_shape, ctxxp))
+tiledbsoma_upgrade_shape <- function(uri, new_shape, function_name_for_messages, ctxxp) {
+    invisible(.Call(`_tiledbsoma_tiledbsoma_upgrade_shape`, uri, new_shape, function_name_for_messages, ctxxp))
 }
 
 c_update_dataframe_schema <- function(uri, ctxxp, column_names_to_drop, add_cols_types, add_cols_enum_value_types, add_cols_enum_ordered) {

apis/r/R/SOMADataFrame.R

@@ -415,13 +415,14 @@ SOMADataFrame <- R6::R6Class(
     #' @param new_shape An integer, greater than or equal to 1 + the
     #' `soma_joinid` domain slot.
     #' @return No return value
-    resize_soma_joinid_shape = function(new_shape) {
-
+    tiledbsoma_resize_soma_joinid_shape = function(new_shape) {
       stopifnot("'new_shape' must be an integer" = rlang::is_integerish(new_shape, n = 1) ||
         (bit64::is.integer64(new_shape) && length(new_shape) == 1)
       )
       # Checking slotwise new shape >= old shape, and <= max_shape, is already done in libtiledbsoma
-      invisible(resize_soma_joinid_shape(self$uri, new_shape, private$.soma_context))
+      invisible(
+        resize_soma_joinid_shape(
+          self$uri, new_shape, .name_of_function(), private$.soma_context))
     }
 
   ),

apis/r/R/SOMANDArrayBase.R

@@ -108,7 +108,7 @@ SOMANDArrayBase <- R6::R6Class(
           (bit64::is.integer64(new_shape) && length(new_shape) == self$ndim())
       )
       # Checking slotwise new shape >= old shape, and <= max_shape, is already done in libtiledbsoma
-      resize(self$uri, new_shape, private$.soma_context)
+      resize(self$uri, new_shape, .name_of_function(), private$.soma_context)
     },
 
     #' @description Allows the array to have a resizeable shape as described in the
@@ -125,7 +125,7 @@ SOMANDArrayBase <- R6::R6Class(
           (bit64::is.integer64(shape) && length(shape) == self$ndim())
       )
       # Checking slotwise new shape >= old shape, and <= max_shape, is already done in libtiledbsoma
-      tiledbsoma_upgrade_shape(self$uri, shape, private$.soma_context)
+      tiledbsoma_upgrade_shape(self$uri, shape, .name_of_function(), private$.soma_context)
     }
 
   ),

apis/r/R/utils.R

@@ -303,3 +303,22 @@ SOMA_ENCODING_VERSION <- "1.1.0"
 ##' @importFrom spdl setup
 ##' @useDynLib tiledbsoma, .registration=TRUE
 NULL
+
+# This is for internal logging purposes. Context:
+# * We have R (and Python) code with function names the user invokes.
+# * These call C++ functions which can throw their own error messages.
+# * It's crucial that the C++ code "knows" the name of the function
+#   as typed by the user, not whatever (possibly out-of-date) guess
+#   the C++ code may have.
+.name_of_function <- function() {
+  # Tricky bits:
+  # * This might be `obj$foo`
+  # * The sys.call can return a parse-tree component (typeof = language)
+  #   with the '$', 'obj', and 'foo' -- hence the as.character
+  # * Even then there can be a second component returned like 'c(1)'
+  #   -- hence the [[1]]
+  # * Then remove the 'obj$' from 'obj$foo'
+  name <- as.character(sys.call(sys.parent(n=1)))[[1]]
+  name <- sub('.*\\$', replacement = '', x = name)
+  return(name)
+}

apis/r/R/write_soma.R

@@ -259,7 +259,7 @@ write_soma.data.frame <- function(
     }
   }
   if (ingest_mode %in% c('resume') && sdf$tiledbsoma_has_upgraded_domain()) {
-    sdf$resize_soma_joinid_shape(nrow(x))
+    sdf$tiledbsoma_resize_soma_joinid_shape(nrow(x))
   }
   if (!is.null(tbl)) {
     sdf$write(tbl)

apis/r/src/RcppExports.cpp

@@ -553,38 +553,41 @@ BEGIN_RCPP
 END_RCPP
 }
 // resize
-void resize(const std::string& uri, Rcpp::NumericVector new_shape, Rcpp::XPtr<somactx_wrap_t> ctxxp);
-RcppExport SEXP _tiledbsoma_resize(SEXP uriSEXP, SEXP new_shapeSEXP, SEXP ctxxpSEXP) {
+void resize(const std::string& uri, Rcpp::NumericVector new_shape, std::string function_name_for_messages, Rcpp::XPtr<somactx_wrap_t> ctxxp);
+RcppExport SEXP _tiledbsoma_resize(SEXP uriSEXP, SEXP new_shapeSEXP, SEXP function_name_for_messagesSEXP, SEXP ctxxpSEXP) {
 BEGIN_RCPP
     Rcpp::RNGScope rcpp_rngScope_gen;
     Rcpp::traits::input_parameter< const std::string& >::type uri(uriSEXP);
     Rcpp::traits::input_parameter< Rcpp::NumericVector >::type new_shape(new_shapeSEXP);
+    Rcpp::traits::input_parameter< std::string >::type function_name_for_messages(function_name_for_messagesSEXP);
     Rcpp::traits::input_parameter< Rcpp::XPtr<somactx_wrap_t> >::type ctxxp(ctxxpSEXP);
-    resize(uri, new_shape, ctxxp);
+    resize(uri, new_shape, function_name_for_messages, ctxxp);
     return R_NilValue;
 END_RCPP
 }
 // resize_soma_joinid_shape
-void resize_soma_joinid_shape(const std::string& uri, Rcpp::NumericVector new_shape, Rcpp::XPtr<somactx_wrap_t> ctxxp);
-RcppExport SEXP _tiledbsoma_resize_soma_joinid_shape(SEXP uriSEXP, SEXP new_shapeSEXP, SEXP ctxxpSEXP) {
+void resize_soma_joinid_shape(const std::string& uri, Rcpp::NumericVector new_shape, std::string function_name_for_messages, Rcpp::XPtr<somactx_wrap_t> ctxxp);
+RcppExport SEXP _tiledbsoma_resize_soma_joinid_shape(SEXP uriSEXP, SEXP new_shapeSEXP, SEXP function_name_for_messagesSEXP, SEXP ctxxpSEXP) {
 BEGIN_RCPP
     Rcpp::RNGScope rcpp_rngScope_gen;
     Rcpp::traits::input_parameter< const std::string& >::type uri(uriSEXP);
     Rcpp::traits::input_parameter< Rcpp::NumericVector >::type new_shape(new_shapeSEXP);
+    Rcpp::traits::input_parameter< std::string >::type function_name_for_messages(function_name_for_messagesSEXP);
     Rcpp::traits::input_parameter< Rcpp::XPtr<somactx_wrap_t> >::type ctxxp(ctxxpSEXP);
-    resize_soma_joinid_shape(uri, new_shape, ctxxp);
+    resize_soma_joinid_shape(uri, new_shape, function_name_for_messages, ctxxp);
     return R_NilValue;
 END_RCPP
 }
 // tiledbsoma_upgrade_shape
-void tiledbsoma_upgrade_shape(const std::string& uri, Rcpp::NumericVector new_shape, Rcpp::XPtr<somactx_wrap_t> ctxxp);
-RcppExport SEXP _tiledbsoma_tiledbsoma_upgrade_shape(SEXP uriSEXP, SEXP new_shapeSEXP, SEXP ctxxpSEXP) {
+void tiledbsoma_upgrade_shape(const std::string& uri, Rcpp::NumericVector new_shape, std::string function_name_for_messages, Rcpp::XPtr<somactx_wrap_t> ctxxp);
+RcppExport SEXP _tiledbsoma_tiledbsoma_upgrade_shape(SEXP uriSEXP, SEXP new_shapeSEXP, SEXP function_name_for_messagesSEXP, SEXP ctxxpSEXP) {
 BEGIN_RCPP
     Rcpp::RNGScope rcpp_rngScope_gen;
     Rcpp::traits::input_parameter< const std::string& >::type uri(uriSEXP);
     Rcpp::traits::input_parameter< Rcpp::NumericVector >::type new_shape(new_shapeSEXP);
+    Rcpp::traits::input_parameter< std::string >::type function_name_for_messages(function_name_for_messagesSEXP);
     Rcpp::traits::input_parameter< Rcpp::XPtr<somactx_wrap_t> >::type ctxxp(ctxxpSEXP);
-    tiledbsoma_upgrade_shape(uri, new_shape, ctxxp);
+    tiledbsoma_upgrade_shape(uri, new_shape, function_name_for_messages, ctxxp);
     return R_NilValue;
 END_RCPP
 }
@@ -816,9 +819,9 @@ static const R_CallMethodDef CallEntries[] = {
     {"_tiledbsoma_c_dimnames", (DL_FUNC) &_tiledbsoma_c_dimnames, 2},
     {"_tiledbsoma_c_attrnames", (DL_FUNC) &_tiledbsoma_c_attrnames, 2},
     {"_tiledbsoma_c_schema", (DL_FUNC) &_tiledbsoma_c_schema, 2},
-    {"_tiledbsoma_resize", (DL_FUNC) &_tiledbsoma_resize, 3},
-    {"_tiledbsoma_resize_soma_joinid_shape", (DL_FUNC) &_tiledbsoma_resize_soma_joinid_shape, 3},
-    {"_tiledbsoma_tiledbsoma_upgrade_shape", (DL_FUNC) &_tiledbsoma_tiledbsoma_upgrade_shape, 3},
+    {"_tiledbsoma_resize", (DL_FUNC) &_tiledbsoma_resize, 4},
+    {"_tiledbsoma_resize_soma_joinid_shape", (DL_FUNC) &_tiledbsoma_resize_soma_joinid_shape, 4},
+    {"_tiledbsoma_tiledbsoma_upgrade_shape", (DL_FUNC) &_tiledbsoma_tiledbsoma_upgrade_shape, 4},
     {"_tiledbsoma_c_update_dataframe_schema", (DL_FUNC) &_tiledbsoma_c_update_dataframe_schema, 6},
     {"_tiledbsoma_sr_setup", (DL_FUNC) &_tiledbsoma_sr_setup, 10},
     {"_tiledbsoma_sr_complete", (DL_FUNC) &_tiledbsoma_sr_complete, 1},

apis/r/src/rinterface.cpp

@@ -421,41 +421,44 @@ SEXP c_schema(const std::string& uri, Rcpp::XPtr<somactx_wrap_t> ctxxp) {
 void resize(
     const std::string& uri,
     Rcpp::NumericVector new_shape,
+    std::string function_name_for_messages,
     Rcpp::XPtr<somactx_wrap_t> ctxxp) {
     // This function is solely for SparseNDArray and DenseNDArray for which the
     // dims are required by the SOMA spec to be of type int64. Domain-resize for
     // variant-indexed dataframes will be separate work as tracked on
     // https://github.com/single-cell-data/TileDB-SOMA/issues/2407.
     auto sr = tdbs::SOMAArray::open(OpenMode::write, uri, ctxxp->ctxptr);
     std::vector<int64_t> new_shape_i64 = i64_from_rcpp_numeric(new_shape);
-    sr->resize(new_shape_i64, "resize");
+    sr->resize(new_shape_i64, function_name_for_messages);
     sr->close();
 }
 
 // [[Rcpp::export]]
 void resize_soma_joinid_shape(
     const std::string& uri,
     Rcpp::NumericVector new_shape,
+    std::string function_name_for_messages,
     Rcpp::XPtr<somactx_wrap_t> ctxxp) {
     // This function is solely for SOMADataFrame.
     auto sr = tdbs::SOMADataFrame::open(uri, OpenMode::write, ctxxp->ctxptr);
     std::vector<int64_t> new_shape_i64 = i64_from_rcpp_numeric(new_shape);
-    sr->resize_soma_joinid_shape(new_shape_i64[0], "resize_soma_joinid_shape");
+    sr->resize_soma_joinid_shape(new_shape_i64[0], function_name_for_messages);
     sr->close();
 }
 
 // [[Rcpp::export]]
 void tiledbsoma_upgrade_shape(
     const std::string& uri,
     Rcpp::NumericVector new_shape,
+    std::string function_name_for_messages,
     Rcpp::XPtr<somactx_wrap_t> ctxxp) {
     // This function is solely for SparseNDArray and DenseNDArray for which the
     // dims are required by the SOMA spec to be of type int64. Domain-resize for
     // variant-indexed dataframes will be separate work as tracked on
     // https://github.com/single-cell-data/TileDB-SOMA/issues/2407.
     auto sr = tdbs::SOMAArray::open(OpenMode::write, uri, ctxxp->ctxptr);
     std::vector<int64_t> new_shape_i64 = i64_from_rcpp_numeric(new_shape);
-    sr->upgrade_shape(new_shape_i64, "tiledbsoma_upgrade_shape");
+    sr->upgrade_shape(new_shape_i64, function_name_for_messages);
     sr->close();
 }
 

apis/r/tests/testthat/test-shape.R

@@ -199,11 +199,11 @@ test_that("SOMADataFrame shape", {
       sdf <- SOMADataFrameOpen(uri, "WRITE")
       if (has_soma_joinid_dim) {
         # It's an error to downsize
-        expect_error(sdf$resize_soma_joinid_shape(new_shape))
+        expect_error(sdf$tiledbsoma_resize_soma_joinid_shape(new_shape))
       } else {
         # There is no problem when soma_joinid is not a dim --
-        # sdf$resize_soma_joinid_shape is a no-op in that case
-        expect_no_condition(sdf$resize_soma_joinid_shape(new_shape))
+        # sdf$tiledbsoma_resize_soma_joinid_shape is a no-op in that case
+        expect_no_condition(sdf$tiledbsoma_resize_soma_joinid_shape(new_shape))
       }
       sdf$close()
 
@@ -238,7 +238,7 @@ test_that("SOMADataFrame shape", {
 
       # Test resize
       sdf <- SOMADataFrameOpen(uri, "WRITE")
-      sdf$resize_soma_joinid_shape(new_shape)
+      sdf$tiledbsoma_resize_soma_joinid_shape(new_shape)
       sdf$close();
 
       # Test writes out of old bounds, within new bounds, after resize

apis/r/tests/testthat/test-write-soma-resume.R

@@ -166,7 +166,7 @@ test_that("Resume-mode data frames", {
 
   if (.new_shape_feature_flag_is_enabled()) {
     sdfp$reopen("WRITE")
-    sdfp$resize_soma_joinid_shape(nrow(co2))
+    sdfp$tiledbsoma_resize_soma_joinid_shape(nrow(co2))
   }
 
   expect_s3_class(

libtiledbsoma/src/soma/soma_array.cc

@@ -1665,14 +1665,14 @@ void SOMAArray::_set_shape_helper(
         // Upgrading an array to install a current domain
         if (!_get_current_domain().is_empty()) {
             throw TileDBSOMAError(fmt::format(
-                "{}: array must not already have a shape",
+                "{}: array must not already have a shape: please upgrade it",
                 function_name_for_messages));
         }
     } else {
         // Expanding an array's current domain
         if (_get_current_domain().is_empty()) {
             throw TileDBSOMAError(fmt::format(
-                "{} array must already have a shape",
+                "{} array must already have a shape: please upgrade it",
                 function_name_for_messages));
         }
     }