tests/testthat/test-query-condition.R

single-cell-data · Oct 10, 2024 · e1788fb · e1788fb
1 parent f95efe5
commit e1788fb
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diff --git a/apis/r/R/QueryCondition.R b/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)

diff --git a/apis/r/tests/testthat/test-query-condition.R b/apis/r/tests/testthat/test-query-condition.R
@@ -0,0 +1,91 @@
+# 15:  arrow::field("soma_joinid", arrow::int64(), nullable = FALSE),
+# 16:  arrow::field("i32", arrow::int32(), nullable = FALSE),
+# 17:  arrow::field("f64", arrow::float64(), nullable = FALSE),
+# 18:  arrow::field("utf8", arrow::large_utf8(), nullable = FALSE)
+# 5:   arrow::field("foo", arrow::int32(), nullable = FALSE),
+# 6:   arrow::field("soma_joinid", arrow::int64(), nullable = FALSE),
+# 7:   arrow::field("bar", arrow::float64(), nullable = FALSE),
+# 8:   arrow::field("baz", arrow::large_utf8(), nullable = FALSE)
+# 6:schema <- arrow::schema(arrow::field("soma_joinid", arrow::int64(), nullable = FALSE),
+# 7:   arrow::field("int", arrow::int32(), nullable = FALSE),
+# 8:   arrow::field("A", arrow::dictionary(index_type = arrow::int8(), value_type = arrow::utf8(), ordered = FALSE), nullable=FALSE)
+# 10:  arrow::field("soma_joinid", arrow::int64(), nullable = FALSE),
+# 11:  arrow::field("int", arrow::int32(), nullable = FALSE),
+# 12:  arrow::field("string", arrow::string(), nullable = FALSE),
+# 13:  arrow::field(
+# 8:   arrow::field("foo", arrow::int32(), nullable = FALSE),
+# 9:   arrow::field("soma_joinid", arrow::int64(), nullable = FALSE),
+# 10:  arrow::field("bar", arrow::float64(), nullable = FALSE),
+# 11:  arrow::field("baz", arrow::large_utf8(), nullable = FALSE)
+# 7:   arrow::field("foo", arrow::int32(), nullable = FALSE),
+# 8:   arrow::field("soma_joinid", arrow::int64(), nullable = FALSE),
+# 9:   arrow::field("bar", arrow::float64(), nullable = FALSE),
+# 10:  arrow::field("baz", arrow::large_utf8(), nullable = FALSE)
+# 15:  arrow::field("soma_joinid", arrow::int64(), nullable = FALSE),
+# 16:  arrow::field("string_not_enum", arrow::string(), nullable = FALSE),
+
+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("int32", arrow::int32())
+      # 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$exists())
+    expect_true(dir.exists(uri))
+
+    tbl <- arrow::arrow_table(
+        soma_joinid = 1L:10L,
+        int32 = 101L:110L,
+        schema = sch)
+    sdf$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))
+      },
+      'soma_joinid > 4 && soma_joinid < 8' <- function(df) {
+          expect_true(all(df$soma_joinid == 4:7))
+      },
+      'soma_joinid < 4 || soma_joinid > 8' <- function(df) {
+          expect_true(all(df$soma_joinid == c(1:3, 9:10)))
+      }
+      # louvain == "T cell"
+      # louvain %in% c("T cell", "B cell")
+      # louvain %nin% c("T cell", "B cell")
+      # XXX MORE TO DO
+    )
+
+    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()
+})
diff --git a/libtiledbsoma/test/common.cc b/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);