Add Google Tests for Arrow and Parquet writers

ci-utils/envs/conda_cpp.txt

@@ -1,5 +1,5 @@
 z5py 
-libtiff 
+libtiff <=4.5.0
 boost >=1.63
 nlohmann_json 
 blosc 

src/nyx/globals.h

@@ -67,6 +67,7 @@ namespace Nyxus
 
 	std::vector<std::tuple<std::vector<std::string>, int, std::vector<double>>> get_feature_values();	
 	std::vector<std::string> get_header(const std::vector<std::tuple<std::string, AvailableFeatures>>& F );
+	std::string get_arrow_filename(const std::string& output_path, const std::string& default_filename, const SaveOption& arrow_file_type);
 
 	void init_feature_buffers();
 	void clear_feature_buffers();	

src/nyx/output_writers.cpp

@@ -26,7 +26,7 @@ arrow::Status ParquetWriter::setup(const std::vector<std::string> &header) {
 
     fields.push_back(arrow::field(header[0], arrow::utf8()));
     fields.push_back(arrow::field(header[1], arrow::utf8()));
-    fields.push_back(arrow::field(header[2], arrow::int64()));
+    fields.push_back(arrow::field(header[2], arrow::int32()));
 
     for (int i = 3; i < header.size(); ++i)
     {
@@ -120,7 +120,7 @@ arrow::Status ParquetWriter::write (const std::vector<std::tuple<std::vector<std
 
     arrays.push_back(segmentation_array);
 
-    arrow::Int64Builder int_builder;
+    arrow::Int32Builder int_builder;
     std::shared_ptr<arrow::Array> labels_array;
     // construct label column
     for (int i = 0; i < num_rows; ++i) {
@@ -168,26 +168,26 @@ arrow::Status ParquetWriter::write (const std::vector<std::tuple<std::vector<std
     ARROW_ASSIGN_OR_RAISE(auto table,
                 arrow::Table::FromRecordBatches(schema_, {batch}));
 
-
-    std::cout << table->ToString() << std::endl;
-
     ARROW_RETURN_NOT_OK(writer_->WriteTable(*table.get(), batch->num_rows()));
 
-
-
     return arrow::Status::OK();
 }
 
 arrow::Status ParquetWriter::close () {
-    arrow::Status status = writer_->Close();
+    auto status = writer_->Close();
 
-        if (!status.ok()) {
-            // Handle read error
-            return status; 
-        }
-        return arrow::Status::OK();
-
+    if (!status.ok()) {
+        // Handle read error
+        return status; 
+    }
 
+    status = output_stream_->Close();
+
+    if (!status.ok()) {
+        // Handle read error
+        return status; 
+    }
+
     return arrow::Status::OK();
 }
 
@@ -198,7 +198,7 @@ arrow::Status ArrowIPCWriter::setup(const std::vector<std::string> &header) {
 
     fields.push_back(arrow::field("intensity_image", arrow::utf8()));
     fields.push_back(arrow::field("segmentation_image", arrow::utf8()));
-    fields.push_back(arrow::field("ROI_label", arrow::int64()));
+    fields.push_back(arrow::field("ROI_label", arrow::int32()));
 
     for (int i = 3; i < header.size(); ++i)
     {
@@ -342,6 +342,14 @@ arrow::Status ArrowIPCWriter::close () {
         // Handle read error
         return status;
     }
+
+    status = output_stream_->Close();
+
+    if (!status.ok()) {
+        // Handle read error
+        return status; 
+    }
+
     return arrow::Status::OK();
 
 }

tests/CMakeLists.txt

@@ -35,4 +35,4 @@ endif()
 
 target_include_directories (runAllTests PUBLIC ${GTEST_INCLUDE_DIRS})
 target_link_directories (runAllTests PUBLIC ${GTEST_LIBRARY_PATH})
-target_link_libraries (runAllTests PUBLIC gtest ${Nyxus_LIBRARIES})
+target_link_libraries (runAllTests PUBLIC gtest ${Nyxus_LIBRARIES})

tests/test_all.cc

@@ -19,6 +19,20 @@
 #include "test_glszm.h"
 #include "test_ngtdm.h"
 #include "test_roi_blacklist.h"
+#include "test_arrow.h"
+#include "test_arrow_file_name.h"
+
+TEST(TEST_NYXUS, TEST_ARROW_FILE_NAME) {
+	test_file_naming();
+}
+
+TEST(TEST_NYXUS, TEST_ARROW) {
+	test_arrow();
+}
+
+TEST(TEST_NYXUS, TEST_PARQUET) {
+	test_parquet();
+}
 
 TEST(TEST_NYXUS, TEST_GABOR){
     test_gabor();