Merge pull request #64 from opencor/issue61

Support for buffer contents
sbmlteam · Jun 4, 2024 · a8a4bba · a8a4bba
2 parents e185a98 + b5bfa68
commit a8a4bba
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Showing 3 changed files with 148 additions and 13 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -346,8 +346,10 @@ endif()
 set(USE_ZLIB ON)
 add_definitions( -DUSE_ZLIB )
 
-if (ZLIB_LIBRARY)
-  set(LIBCOMBINE_LIBS ${LIBCOMBINE_LIBS} ZLIB::ZLIB)
+if (ZLIB_LIBRARY_NAME)
+  set(LIBCOMBINE_LIBS ${LIBCOMBINE_LIBS} ${ZLIB_LIBRARY_NAME})
+elseif (ZLIB_LIBRARY)
+  set(LIBCOMBINE_LIBS ${LIBCOMBINE_LIBS} ${ZLIB_LIBRARY})
 endif()
 
 if (LIBSBML_LIBRARY_NAME)
@@ -356,8 +358,16 @@ elseif (LIBSBML_LIBRARY)
   set(LIBCOMBINE_LIBS ${LIBCOMBINE_LIBS} ${LIBSBML_LIBRARY})
 endif()
 
-if (ZIPPER_LIBRARY)
-  set(LIBCOMBINE_LIBS ${LIBCOMBINE_LIBS} ZIPPER::ZIPPER)
+if (ZIPPER_LIBRARY_NAME)
+  set(LIBCOMBINE_LIBS ${LIBCOMBINE_LIBS} ${ZIPPER_LIBRARY_NAME})
+elseif (ZIPPER_LIBRARY)
+  set(LIBCOMBINE_LIBS ${LIBCOMBINE_LIBS} ${ZIPPER_LIBRARY})
+endif()
+
+if (XML_LIBRARY_NAME)
+  set(LIBCOMBINE_LIBS ${LIBCOMBINE_LIBS} ${XML_LIBRARY_NAME})
+elseif (XML_LIBRARY)
+  set(LIBCOMBINE_LIBS ${LIBCOMBINE_LIBS} ${XML_LIBRARY})
 endif()
 
 set(USING_INTEL FALSE)
@@ -480,6 +490,9 @@ include_directories(${EXTRA_INCLUDE_DIRS})
 endif()
 
 include_directories(${LIBSBML_INCLUDE_DIR})
+include_directories(${XML_INCLUDE_DIR})
+include_directories(${ZLIB_INCLUDE_DIR})
+include_directories(${ZIPPER_INCLUDE_DIR})
 include_directories(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src/)
 include_directories(BEFORE ${CMAKE_CURRENT_BINARY_DIR}/src/)
 
@@ -621,6 +634,10 @@ libCombine version ${LIBCOMBINE_VERSION}
      SBML include dir                = ${LIBSBML_INCLUDE_DIR}
      libSBML compression support     = ${LIBSBML_HAS_MINIZIP}
 
+   XML library configuration:
+     XML library                     = ${XML_LIBRARY}
+     XML include dir                 = ${XML_INCLUDE_DIR}
+
    Zlib library configuration:
      Zlib library                    = ${ZLIB_LIBRARY}
      Zlib include dir                = ${ZLIB_INCLUDE_DIR}

diff --git a/src/combine/combinearchive.cpp b/src/combine/combinearchive.cpp
@@ -12,6 +12,7 @@
 #include <zipper/unzipper.h>
 
 #include <fstream>
+#include <iterator>
 #include <sstream>
 #include <cstdio>
 
@@ -51,7 +52,7 @@ CombineArchive::initializeFromDirectory(const std::string &directory)
 }
 
 bool 
-CombineArchive::initializeFromArchive(
+CombineArchive::initializeFromUnzipper(
   zipper::Unzipper* pUnzipper,
   bool skipOmex/*=false*/)
 {
@@ -153,12 +154,35 @@ CombineArchive::initializeFromArchive(
   }
   catch (const std::exception&)
   {
-    // invalid COMBINE archive, it should always have a manifest
+    // something went wrong
     cleanUp();
     return false;
   }
 
-  return initializeFromArchive(mpUnzipper, skipOmex);
+  return initializeFromUnzipper(mpUnzipper, skipOmex);
+}
+
+bool
+CombineArchive::initializeFromBuffer(
+    const std::vector<unsigned char>& pBuffer,
+    bool skipOmex /*= false*/)
+{
+  cleanUp();
+
+  try
+  {
+    auto buffer = const_cast<std::vector<unsigned char> &>(pBuffer);
+
+    mpUnzipper = new Unzipper(buffer);
+  }
+  catch (const std::exception&)
+  {
+    // something went wrong
+    cleanUp();
+    return false;
+  }
+
+  return initializeFromUnzipper(mpUnzipper, skipOmex);
 }
 
 bool CombineArchive::cleanUp()
@@ -287,9 +311,8 @@ bool CombineArchive::writeToFile(const std::string &fileName)
   return true;
 }
 
-bool
-CombineArchive::getStream(const std::string &name,
-                          std::ifstream &stream)
+std::map<std::string, std::string>::iterator
+CombineArchive::mapIterator(const std::string &name)
 {
   std::map<std::string, std::string>::iterator it = mMap.find(name);
   if (it == mMap.end()) 
@@ -301,9 +324,19 @@ CombineArchive::getStream(const std::string &name,
       if (name.find("/") == 0)
         it = mMap.find(name.substr(1));
       if (it == mMap.end())
-        return false;
+        return mMap.end();
     }
   }
+  return it;
+}
+
+bool
+CombineArchive::getStream(const std::string &name,
+                          std::ifstream &stream)
+{
+  auto it = mapIterator(name);
+  if (it == mMap.end())
+    return false;
 
   std::string filename = (*it).second;
   if (filename.find("unzipper://") == 0)
@@ -504,6 +537,23 @@ CombineArchive::addFile(std::istream &stream,
   return addFile(tempFilename, targetName, format, isMaster);
 }
 
+bool
+CombineArchive::addFileFromBuffer(const std::vector<unsigned char> &buffer,
+                                  const std::string &targetName,
+                                  const std::string &format,
+                                  bool isMaster)
+{
+  std::string tempFilename = Util::getTempFilename();
+  mTempFiles.push_back(tempFilename);
+
+  std::ofstream out(tempFilename.c_str(), std::ios::out | std::ios::binary);
+
+  std::copy(buffer.begin(), buffer.end(),
+            std::ostream_iterator<unsigned char>(out));
+
+  return addFile(tempFilename, targetName, format, isMaster);
+}
+
 int
 CombineArchive::addMetadata(const std::string &targetName,
                             const OmexDescription &description)
@@ -553,3 +603,23 @@ CombineArchive::extractEntryToString(const std::string& name)
   extractEntryToStream(name, stream);
   return stream.str();
 }
+
+std::vector<unsigned char>
+CombineArchive::extractEntryToBuffer(const std::string& name)
+{
+  auto it = mapIterator(name);
+  if (it == mMap.end())
+    return {};
+
+  std::string filename = (*it).second;
+  if (filename.find("unzipper://") == 0)
+    filename = filename.substr(std::string("unzipper://").length());
+
+  if (mpUnzipper == NULL)
+    return {};
+
+  std::vector<unsigned char> res;
+  mpUnzipper->extractEntryToMemory(filename, res);
+
+  return res;
+}
diff --git a/src/combine/combinearchive.h b/src/combine/combinearchive.h
@@ -118,6 +118,23 @@ class LIBCOMBINE_EXTERN CombineArchive
                const std::string& targetName,
                const std::string& format,
                bool isMaster = false);
+
+  /**
+   * Adds the given buffer to the archive.
+   *
+   * @param buffer the buffer of the file to be added to the archive.
+   * @param targetName the target name of the file in the archive
+   * @param format the format that this file has
+   * @param isMaster boolean indicating whether the file should be
+   *        opened first if there are multiple ones.
+   *
+   * @return boolean indicating success or failure
+   */
+  bool addFileFromBuffer(const std::vector<unsigned char>& buffer,
+               const std::string& targetName,
+               const std::string& format,
+               bool isMaster = false);
+
   /**
    * Adds the given metadata to the list.
    *
@@ -165,6 +182,15 @@ class LIBCOMBINE_EXTERN CombineArchive
    */
   std::string extractEntryToString(const std::string& name);
 
+  /**
+   * extracts the given entry and returns the contents as a buffer.
+   *
+   * @param name the entry to be extracted
+   *
+   * @return the content of the entry, or empty if not found.
+   */
+  std::vector<unsigned char> extractEntryToBuffer(const std::string& name);
+
   /**
    * extracts all entries in this archive into the given directory.
    *
@@ -210,10 +236,23 @@ class LIBCOMBINE_EXTERN CombineArchive
    *
    * @return boolean indicating success or failure
    */
-  bool initializeFromArchive(zipper::Unzipper* pUnzipper,
-                             bool skipOmex=false);
+  bool initializeFromUnzipper(zipper::Unzipper* pUnzipper,
+                              bool skipOmex=false);
 
 
+  /**
+   * initializes this instance from a buffer
+   *
+   * @param buffer the buffer
+   * @param skipOmex optional flag indicating whether meta data processing
+   *        should be skipped or not (default). The metadata processing, removes
+   *        annotations in the restricted 2014 subset of the OMEX Metadata and
+   *        adds them to the convenience classes.
+   *
+   * @return boolean indicating success or failure
+   */
+  bool initializeFromBuffer(const std::vector<unsigned char>& pBuffer,
+                            bool skipOmex=false);
 
   /**
    * @return the manifest
@@ -389,6 +428,15 @@ class LIBCOMBINE_EXTERN CombineArchive
    *
    */
   int addMetadataToArchive(OmexDescription& desc, zipper::Zipper* zipper);
+
+  /**
+   * returns the map iterator for the given file.
+   *
+   * @param name the name that should be in the current map of files
+   *
+   * @return the map iterator
+  */
+  std::map<std::string, std::string>::iterator mapIterator(const std::string &name);
 };
 
 LIBCOMBINE_CPP_NAMESPACE_END