tests/testthat/test-query-condition.R

apis/r/R/QueryCondition.R

@@ -55,9 +55,12 @@ parse_query_condition_new <- function(
   somactx
   ) {
 
-  stopifnot("The schema argument must be an Arrow Schema" =
-    is(schema, "ArrowObject") &&
-    is(schema, "Schema"))
+  stopifnot(
+      "The schema argument must be an Arrow Schema" =
+          is(schema, "ArrowObject") &&
+          is(schema, "Schema"),
+    "The argument must be a somactx object" =
+        is(somactx, "externalptr"))
 
     # ----------------------------------------------------------------
     # Helpers for walking the parse tree
@@ -201,12 +204,12 @@ setClass(
 # ================================================================
 #' Creates a 'tiledbsoma_query_condition' object
 #'
-#' @param ctx (optional) A TileDB Ctx object; if not supplied the default
+#' @param somactx (optional) A TileDB Ctx object; if not supplied the default
 #' context object is retrieved
 #' @return A 'tiledbsoma_query_condition' object
 #' @export
 tiledbsoma_empty_query_condition <- function(somactx) {
-    stopifnot("The argument must be a ctx object" = is(ctx, "externalptr"))
+    stopifnot("The argument must be a somactx object" = is(somactx, "externalptr"))
     ptr <- libtiledbsoma_empty_query_condition(somactx)
     query_condition <- new("tiledbsoma_query_condition", ptr = ptr, init = FALSE)
     invisible(query_condition)

apis/r/tests/testthat/test-query-condition.R

@@ -0,0 +1,128 @@
+test_that("DataFrame Factory", {
+    skip_if(!extended_tests())
+    uri <- tempfile()
+    if (dir.exists(uri)) unlink(uri, recursive=TRUE)
+
+    ctx <- soma_context()
+
+    sch <- arrow::schema(
+      arrow::field("soma_joinid", arrow::int64()),
+      arrow::field("int8",   arrow::int8()),
+      arrow::field("int16",  arrow::int16()),
+      arrow::field("int32",  arrow::int32()),
+      arrow::field("int64",  arrow::int64()),
+      arrow::field("uint8",  arrow::uint8()),
+      arrow::field("uint16", arrow::uint16()),
+      arrow::field("uint32", arrow::uint32()),
+      arrow::field("uint64", arrow::uint64()),
+      arrow::field("string", arrow::string()),
+      arrow::field("large_utf8", arrow::large_utf8()),
+      arrow::field("enum",
+          arrow::dictionary(
+              index_type = arrow::int8(),
+              value_type = arrow::utf8(),
+              ordered = TRUE)),
+      arrow::field("float32", arrow::float32()),
+      arrow::field("float64", arrow::float64())
+      # arrow::field("float_column", arrow::float64(), nullable = bl),
+      # arrow::field("string_column", arrow::large_utf8(), nullable = bl)
+      # XXX MORE TO DO
+    )
+
+    sdf <- SOMADataFrameCreate(uri, sch, index_column_names = "soma_joinid")
+    expect_true(sdf$exists())
+    expect_true(dir.exists(uri))
+
+    tbl <- arrow::arrow_table(
+        soma_joinid = 1L:10L,
+        int32 = 101L:110L,
+        string = c("apple", "ball", "cat", "dog", "egg", "fig", "goose", "hay", "ice", "jam"),
+        large_utf8 = c("APPLE", "BALL", "CAT", "DOG", "EGG", "FIG", "GOOSE", "HAY", "ICE", "JAM"),
+        enum = factor(
+            c("red", "yellow", "green", "red", "red", "red", "yellow", "green", "red", "green"),
+            levels = c("red", "yellow", "green")),
+        float32 = 1.5:10.5,
+        float64 = 11.5:20.5,
+        schema = sch)
+    sdf$write(tbl)
+    sdf$close()
+
+    sdf$reopen("READ")
+
+    cases <- list(
+      'soma_joinid > 5' = function(df) {
+          expect_true(all(df$soma_joinid == 6:10))
+          expect_true(all(df$int32 == 106:110))
+      },
+      'soma_joinid == 10' = function(df) {
+          expect_true(all(df$soma_joinid == 10))
+          expect_true(all(df$int32 == 110))
+          expect_true(all(df$enum == "green"))
+      },
+      'soma_joinid > 4 && soma_joinid < 8' = function(df) {
+          expect_true(all(df$soma_joinid == 5:7))
+          expect_true(all(df$string == c("egg", "fig", "goose")))
+          expect_true(all(df$large_utr8 == c("EGG", "FIG", "GOOSE")))
+      },
+      'soma_joinid < 4 || soma_joinid > 8' = function(df) {
+          expect_true(all(df$soma_joinid == c(1:3, 9:10)))
+      },
+
+      'string == "dog"' = function(df) {
+          expect_true(df$soma_joinid == c(4))
+      },
+      'string %in% c("fig", "dog")' = function(df) {
+          expect_true(all(df$soma_joinid == c(4, 6)))
+      },
+      'string %nin% c("fig", "dog")' = function(df) {
+          expect_true(all(df$soma_joinid == c(1, 2, 3, 5, 7, 8, 9, 10)))
+      },
+
+      'enum == "red"' = function(df) {
+          expect_true(all(df$soma_joinid == c(1, 4, 5, 6, 9)))
+      },
+      'enum != "red"' = function(df) {
+          expect_true(all(df$soma_joinid == c(2, 3, 7, 8, 10)))
+      },
+      'enum == "orange"' = function(df) {
+          expect_true(all(df$soma_joinid == c(4, 6)))
+      },
+      'enum != "orange"' = function(df) {
+          expect_true(all(df$soma_joinid == 1:10))
+      },
+      'enum %in% c("red", "green")' = function(df) {
+          expect_true(all(df$soma_joinid == c(1, 3, 4, 5, 6, 8, 9, 10)))
+      }, 
+      'enum %nin% c("red", "green")' = function(df) {
+          expect_true(all(df$soma_joinid == c(2, 7)))
+      },
+      'enum %in% c("orange", "green")' = function(df) {
+          expect_true(all(df$soma_joinid == c(3, 8, 10)))
+      },
+      'enum %nin% c("orange", "green")' = function(df) {
+          expect_true(all(df$soma_joinid == c(1, 2, 4, 5, 6, 7, 9)))
+      },
+      'enum %in% c("orange", "yellow")' = function(df) {
+          expect_true(all(df$soma_joinid == c()))
+      },
+      'enum %nin% c("orange", "purple")' = function(df) {
+          expect_true(all(df$soma_joinid == 1:10))
+      }
+    )
+
+    for (query_string in names(cases)) {
+        parsed <- do.call(
+            what = tiledbsoma:::parse_query_condition_new,
+            args = list(expr=str2lang(query_string), schema=sch, somactx=ctx))
+        clib_value_filter <- parsed@ptr
+
+        sr <- sr_setup(uri = sdf$uri, ctx, qc=clib_value_filter)
+        iter <- TableReadIter$new(sr)
+        tbl <- iter$read_next()
+        expect_true(iter$read_complete())
+        df <- as.data.frame(tbl)
+        cases[[query_string]](df)
+    }
+
+    sdf$close()
+})

libtiledbsoma/test/common.cc

@@ -119,17 +119,12 @@ create_arrow_schema_and_index_columns(
 // Create index-column info only, no schema involving the attrs
 ArrowTable create_column_index_info(const std::vector<DimInfo>& dim_infos) {
     for (auto info : dim_infos) {
-        LOG_DEBUG(fmt::format("create_column_index_info name={}", info.name));
-
-        LOG_DEBUG(fmt::format(
-            "create_column_index_info type={}",
-            tiledb::impl::to_str(info.tiledb_datatype)));
-
-        LOG_DEBUG(
-            fmt::format("create_column_index_info dim_max={}", info.dim_max));
-
         LOG_DEBUG(fmt::format(
-            "create_column_index_info ucd={}", info.use_current_domain));
+            "create_column_index_info name={} type={} dim_max={} ucd={}",
+            info.name,
+            tiledb::impl::to_str(info.tiledb_datatype),
+            info.dim_max,
+            info.use_current_domain));
     }
 
     auto index_cols_info_schema = _create_index_cols_info_schema(dim_infos);