Jbl/1036970 lax check for duplicate subblocks

CMakeLists.txt

@@ -9,7 +9,7 @@ cmake_policy(SET CMP0091 NEW) # enable new "MSVC runtime library selection" (htt
 # Note that the CMake-variables <Projectname>_VERSION_MAJOR, <Projectname>_VERSION_MINOR, ... are defined by this statement,
 #  which are used in the build (so that - if changing the name here, change also the usage of those variables).
 project ("czicompress"
-         VERSION 0.4.1)
+         VERSION 0.5.0)
 
 set(czicompress_VERSION_PATCH_FLAGS "-alpha")
 set(czicompress_VERSION_TWEAK_FLAGS "")
@@ -29,7 +29,7 @@ include(FetchContent)
 FetchContent_Declare(
   libczi
   GIT_REPOSITORY https://github.com/ZEISS/libczi.git
-  GIT_TAG        c9954d58759ef6dd7d7c6a53c163ea8349855392
+  GIT_TAG        05bc1ebdca520ba2c5bfc3b9fcde76c548e98545
 )
 
 if(NOT libCZI_POPULATED)

README.md

@@ -48,7 +48,7 @@ Clicking on these artifacts will download a ZIP file with the executable. The ex
 Start the executable from the command line, providing the required command line arguments.
 
 ```
-Usage: czicompress [OPTIONS]
+Usage: czicompress.exe [OPTIONS]
 
 Options:
   -h,--help         Print this help message and exit
@@ -73,6 +73,13 @@ Options:
                     Specify compression parameters. The default is
                     'zstd1:ExplicitLevel=1;PreProcess=HiLoByteUnpack'.
 
+  -w,--overwrite    If the output file exists, try to overwrite it.
+
+  --ignore_duplicate_subblocks BOOLEAN
+                    If this option is enabled, the operation will ignore if
+                    duplicate subblocks are encountered in the source document.
+                    Otherwise, an error will be reported. The default is 'on'.
+
 
 Copies the content of a CZI-file into another CZI-file changing the compression
 of the image data.

app/CZIcompress.cpp

@@ -95,13 +95,15 @@ int main(int argc, char** argv)
 
     // Create an "output-stream-object"
     const auto output_stream =
-        libCZI::CreateOutputStreamForFile(utils::utf8::WidenUtf8(command_line_options.GetOutputFileName()).c_str(), false);
+        libCZI::CreateOutputStreamForFile(utils::utf8::WidenUtf8(command_line_options.GetOutputFileName()).c_str(), command_line_options.GetOverwriteExistingFile());
 
-    // create the "CZI-writer"-object
-    const auto writer = libCZI::CreateCZIWriter();
+    // create (and configure) the "CZI-writer"-object
+    libCZI::CZIWriterOptions czi_writer_options;
+    czi_writer_options.allow_duplicate_subblocks = command_line_options.GetIgnoreDuplicateSubblocks();
+    const auto writer = libCZI::CreateCZIWriter(&czi_writer_options);
 
     // GUID_NULL here means that a new Guid is created
-    const auto czi_writer_info = std::make_shared<libCZI::CCziWriterInfo>(GUID{0, 0, 0, {0, 0, 0, 0, 0, 0, 0, 0}});
+    const auto czi_writer_info = std::make_shared<libCZI::CCziWriterInfo>(libCZI::GUID{0, 0, 0, {0, 0, 0, 0, 0, 0, 0, 0}});
 
     // TODO(JBL): it might be desirable to make reservations for the
     //            subblock-directory-/attachments-directory-/metadata-segment

capi/capi.cpp

@@ -46,14 +46,17 @@ class FileProcessor final
     open_options.ignore_sizem_for_pyramid_subblocks = true;
     reader->Open(stream, &open_options);
 
-    // create the "CZI-writer"-object
+    // create the stream-object representing the destination file
     const std::string output_string(output_path);
     const auto output_stream = libCZI::CreateOutputStreamForFile(utils::utf8::WidenUtf8(output_string).c_str(), false);
 
-    const auto writer = libCZI::CreateCZIWriter();
+    // create (and configure) the "CZI-writer"-object - it is configured to ignore "duplicate subblocks"
+    libCZI::CZIWriterOptions czi_writer_options;
+    czi_writer_options.allow_duplicate_subblocks = true;
+    const auto writer = libCZI::CreateCZIWriter(&czi_writer_options);
 
     // GUID_NULL here means that a new Guid is created
-    const auto czi_writer_info = std::make_shared<libCZI::CCziWriterInfo>(GUID{0, 0, 0, {0, 0, 0, 0, 0, 0, 0, 0}});
+    const auto czi_writer_info = std::make_shared<libCZI::CCziWriterInfo>(libCZI::GUID{0, 0, 0, {0, 0, 0, 0, 0, 0, 0, 0}});
 
     // TODO(JBL): it might be desirable to make reservations for the
     // subblock-directory-/attachments-directory-/metadata-segment

lib/include/commandlineoptions.h

@@ -29,7 +29,8 @@ class CommandLineOptions
   std::string output_filename_;
   CompressionStrategy compression_strategy_{CompressionStrategy::kInvalid};
   libCZI::Utils::CompressionOption compression_option_;
-
+  bool overwrite_existing_file_{false};
+  bool ignore_duplicate_subblocks_{true};
 public:
   /// Values that represent the result of the "Parse"-operation.
   enum class ParseResult
@@ -91,6 +92,16 @@ class CommandLineOptions
   /// \returns    The compression option.
   const libCZI::Utils::CompressionOption& GetCompressionOption() const { return this->compression_option_; }
 
+  /// Gets a boolean indicating whether when creating the output file, it is to be overwritten if it already exists.
+  ///
+  /// \returns  True if an existing file is to be overwritten (if it exists); false otherwise.
+  bool GetOverwriteExistingFile() const { return this->overwrite_existing_file_; }
+
+  /// Gets a boolean indicating whether the CZIWriter object should be configured to ignore duplicate subblocks.
+  ///
+  /// \returns  True if duplicate subblocks are to be ignored (with the CZIWriter object); false otherwise.
+  bool GetIgnoreDuplicateSubblocks() const { return this->ignore_duplicate_subblocks_; }
+
 private:
   static std::string GetFooterText();
 };

lib/src/commandlineoptions.cpp

@@ -42,8 +42,9 @@ class CustomFormatter : public CLI::Formatter
     usage << result_from_stock_implementation << endl
           << "  version: " << CZICOMPRESS_VERSION_MAJOR << "." << CZICOMPRESS_VERSION_MINOR << "." << CZICOMPRESS_VERSION_PATCH;
     std::string tweak(CZICOMPRESS_VERSION_TWEAK);
-    if (!tweak.empty()) {
-       usage << "." << tweak;
+    if (!tweak.empty())
+    {
+      usage << "." << tweak;
     }
     usage << endl;
     return usage.str();
@@ -144,6 +145,18 @@ CommandLineOptions::ParseResult CommandLineOptions::Parse(int argc, const char*
   string source_filename;           // NOLINT(misc-const-correctness)
   string destination_filename;      // NOLINT(misc-const-correctness)
   string compression_options_text;  // NOLINT(misc-const-correctness)
+  bool overwrite_existing_file{false};
+  bool ignore_duplicate_subblocks{false};
+
+  // specify the string-to-enum-mapping for a boolean option
+  std::map<std::string, bool> map_string_to_boolean{
+      {"0", false},
+      {"false", false},
+      {"no", false},
+      {"1", true},
+      {"true", true},
+      {"yes", true},
+  };
 
   // specify the string-to-enum-mapping for "command"
   const std::map<std::string, Command> map_string_to_command{{"compress", Command::kCompress}, {"decompress", Command::kDecompress}};
@@ -188,6 +201,14 @@ CommandLineOptions::ParseResult CommandLineOptions::Parse(int argc, const char*
       ->option_text("COMPRESSION_OPTIONS")
       ->default_val(CommandLineOptions::kDefaultCompressionOptions);
 
+  app.add_flag("-w,--overwrite", overwrite_existing_file, "If the output file exists, try to overwrite it.");
+  app.add_option("--ignore_duplicate_subblocks", ignore_duplicate_subblocks,
+                 "If this option is enabled, the operation will ignore if duplicate subblocks are encountered in the source document. "
+                 "Otherwise, an error will be reported. The default is 'on'.")
+      ->option_text("BOOLEAN")
+      ->default_val(true)
+      ->transform(CLI::CheckedTransformer(map_string_to_boolean, CLI::ignore_case));
+
   const auto formatter = make_shared<CustomFormatter>();
   app.formatter(formatter);
   app.footer(CommandLineOptions::GetFooterText());
@@ -217,6 +238,9 @@ CommandLineOptions::ParseResult CommandLineOptions::Parse(int argc, const char*
     this->compression_option_ = libCZI::Utils::ParseCompressionOptions(compression_options_text);
   }
 
+  this->overwrite_existing_file_ = overwrite_existing_file;
+  this->ignore_duplicate_subblocks_ = ignore_duplicate_subblocks;
+
   return CommandLineOptions::ParseResult::kOk;
 }
 

tests/test_copyoperation.cpp

@@ -40,7 +40,7 @@ static tuple<shared_ptr<void>, size_t> CreateCziWithFourSubblockInMosaicArrangem
   auto writer = libCZI::CreateCZIWriter();
   auto outStream = make_shared<CMemOutputStream>(0);
 
-  auto spWriterInfo = make_shared<libCZI::CCziWriterInfo>(GUID{0x1234567, 0x89ab, 0xcdef, {1, 2, 3, 4, 5, 6, 7, 8}},  // NOLINT
+  auto spWriterInfo = make_shared<libCZI::CCziWriterInfo>(libCZI::GUID{0x1234567, 0x89ab, 0xcdef, {1, 2, 3, 4, 5, 6, 7, 8}},  // NOLINT
                                                           libCZI::CDimBounds{{libCZI::DimensionIndex::C, 0, 1}},      // set a bounds for C
                                                           0, 3);  // set a bounds M : 0<=m<=0
   writer->Create(outStream, spWriterInfo);
@@ -162,7 +162,7 @@ TEST_CASE("copyczi.1: run compression on simple synthetic document", "[copyczi]"
   // create a CZI-writer object on a new memory stream
   auto writer = libCZI::CreateCZIWriter();
   const auto memory_backed_stream_destination_document = make_shared<CMemInputOutputStream>(0);
-  const auto writer_info = make_shared<libCZI::CCziWriterInfo>(GUID{0x0, 0x0, 0x0, {0, 0, 0, 0, 0, 0, 0, 0}});
+  const auto writer_info = make_shared<libCZI::CCziWriterInfo>(libCZI::GUID{0x0, 0x0, 0x0, {0, 0, 0, 0, 0, 0, 0, 0}});
   writer->Create(memory_backed_stream_destination_document, writer_info);
 
   // act
@@ -218,7 +218,7 @@ TEST_CASE("copyczi.2: run compression on simple synthetic document changes compr
   // create a CZI-writer object on a new memory stream
   auto writer = libCZI::CreateCZIWriter();
   const auto memory_backed_stream_destination_document = make_shared<CMemInputOutputStream>(0);
-  const auto writer_info = make_shared<libCZI::CCziWriterInfo>(GUID{0x0, 0x0, 0x0, {0, 0, 0, 0, 0, 0, 0, 0}});
+  const auto writer_info = make_shared<libCZI::CCziWriterInfo>(libCZI::GUID{0x0, 0x0, 0x0, {0, 0, 0, 0, 0, 0, 0, 0}});
   writer->Create(memory_backed_stream_destination_document, writer_info);
 
   // act
@@ -280,7 +280,7 @@ TEST_CASE("copyczi.3: run decompression on simple synthetically compressed docum
   // create a CZI-writer object on a new memory stream
   auto writer = libCZI::CreateCZIWriter();
   const auto memory_backed_stream_destination_document = make_shared<CMemInputOutputStream>(0);
-  const auto writer_info = make_shared<libCZI::CCziWriterInfo>(GUID{0x0, 0x0, 0x0, {0, 0, 0, 0, 0, 0, 0, 0}});
+  const auto writer_info = make_shared<libCZI::CCziWriterInfo>(libCZI::GUID{0x0, 0x0, 0x0, {0, 0, 0, 0, 0, 0, 0, 0}});
   writer->Create(memory_backed_stream_destination_document, writer_info);
 
   // act
@@ -309,7 +309,7 @@ TEST_CASE("copyczi.3: run decompression on simple synthetically compressed docum
   // create a CZI-writer object on a new memory stream
   auto writer_2 = libCZI::CreateCZIWriter();
   const auto memory_backed_stream_destination_document_2 = make_shared<CMemInputOutputStream>(0);
-  const auto writer_info_2 = make_shared<libCZI::CCziWriterInfo>(GUID{0x0, 0x0, 0x0, {0, 0, 0, 0, 0, 0, 0, 0}});
+  const auto writer_info_2 = make_shared<libCZI::CCziWriterInfo>(libCZI::GUID{0x0, 0x0, 0x0, {0, 0, 0, 0, 0, 0, 0, 0}});
   writer_2->Create(memory_backed_stream_destination_document_2, writer_info_2);
 
   // act