begin hdf5

src/opt/hdf5/include/h5_content_base.h

@@ -0,0 +1,51 @@
+
+#ifndef __cxz_h5_content_base_h__
+#define __cxz_h5_content_base_h__
+
+#include "cnorxz.h"
+
+namespace CNORXZ
+{
+    namespace hdf5
+    {
+	enum class ContentType {
+	    ATTR = 1,
+	    FILE = 2,
+	    GROUP = 3,
+	    DSET = 4,
+	    TABLE = 5,
+	    VALUE = 6,
+	};
+	    
+	class ContentBase
+	{
+	public:
+	    DEFAULT_MEMBERS(ContentBase);
+	    ContentBase(const String& _name, const ContentBase* _parent = nullptr);
+	    virtual ~ContentBase() = default;
+
+	    virtual ContentType type() const = 0;
+	    virtual bool ro() const = 0;
+	    virtual ContentBase& load() = 0;
+	    virtual ContentBase& write() = 0;
+	    virtual ContentBase& close() = 0;
+	    virtual MArray<ContentBase>* get() = 0;
+	    virtual const MArray<ContentBase>* get() const = 0;
+	    virtual String path() const = 0;
+	    virtual String file() const = 0;
+
+	    const String& name() const;
+	    const ContentBase* parent() const;
+	    RangePtr range() const;
+	    
+	protected:
+	    String mName;
+	    const ContentBase* mParent = nullptr;
+	    RangePtr mRange;
+	};
+    }
+
+    typedef Sptr<ContentType> ContentPtr;
+}
+
+#endif

src/opt/hdf5/include/h5_file.h

@@ -0,0 +1,41 @@
+
+#ifndef __cxz_h5_file_h__
+#define __cxz_h5_file_h__
+
+#include "h5_content_base.h"
+#include <hdf5.h>
+
+namespace CNORXZ
+{
+    namespace hdf5
+    {
+	// maybe introduce abstraction layer between as base for File and Group
+	class File : public ContentBase
+	{
+	public:
+	    DEFAULT_MEMBERS(File);
+	    File(const String& fname, bool _ro = true);
+	    ~File();
+
+	    virtual ContentType type() const override final;
+	    virtual bool ro() const override final;
+	    virtual File& load() override final;
+	    virtual File& write() override final;
+	    virtual File& close() override final;
+	    virtual MArray<ContentBase>* get() override final;
+	    virtual const MArray<ContentBase>* get() const override final;
+	    virtual String path() const override final;
+	    virtual String filename() const override final;
+
+	    Int exists() const;
+	    File& append(const ContentPtr& c);
+	    
+	private:
+	    bool mRo = true;
+	    hid_t mId = 0;
+	    MArray<ContentPtr> mCont;
+	};
+    }
+}
+
+#endif

src/opt/hdf5/lib/h5_content_base.cc

@@ -0,0 +1,27 @@
+
+#include "h5_content_base.h"
+
+namespace CNORXZ
+{
+    namespace hdf5
+    {
+	ContentBase::ContentBase(const String& _name, const ContentBase* _parent) :
+	    mName(_name), mParent(parent)
+	{}
+
+	const String& ContentBase::name() const
+	{
+	    return mName;
+	}
+
+	const ContentBase* ContentBase::parent() const
+	{
+	    return mParent;
+	}
+
+	RangePtr ContentBase::range() const
+	{
+	    return mRange;
+	}
+    }
+}

src/opt/hdf5/lib/h5_file.cc

@@ -0,0 +1,110 @@
+
+#include "h5_file.h"
+
+namespace CNORXZ
+{
+    namespace hdf5
+    {
+	File::File(const String& fname, bool _ro) :
+	    ContentBase(fname),
+	    mRo(_ro)
+	{
+	    Int ex = this->exists();
+	    const String fn = this->filename();
+	    CXZ_ASSERT( ex != 2, "tried to open non-h5 file '" << fn << "'" );
+	    if(this->ro()){
+		CXZ_ASSERT( ex == 1, "could not open file as read-only: '"
+			    << fn << "' does not exist'");
+		mId = H5Fopen( fn.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT );
+	    }
+	    else {
+		if(ex == 1){
+		    mId = H5Fopen( fn.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
+		}
+		else {
+		    mId = H5Fcreate( fn.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT );
+		}
+	    }
+	    CXZ_ASSERT( mId > 0, "error while opening file '" << fn << "'" );
+	}
+
+	File::~File()
+	{
+	    this->close();
+	}
+
+	ContentType File::type() const
+	{
+	    return ContentType::FILE;
+	}
+	
+	bool File::ro() const
+	{
+	    return mRo;
+	}
+	
+	File& File::load()
+	{
+	    // !!!
+	    
+	    return *this;
+	}
+	
+	File& File::write()
+	{
+	    CXZ_ASSERT( not mRo, "could not write to file: opened as read-only" );
+	    for(auto& x: mCont){
+		x.write();
+	    }
+	    return *this;
+	}
+	
+	File& File::close()
+	{
+	    for(auto& x: mCont){
+		x.close();
+	    }
+	    if(mId != 0){
+		H5Fclose(mId);
+	    }
+	    return *this;
+	}
+	
+	MArray<ContentBase>* File::get()
+	{
+	    return &mCont;
+	}
+	
+	const MArray<ContentBase>* File::get() const
+	{
+	    return &mCont;
+	}
+	    
+	String File::path() const
+	{
+	    return String("/");
+	}
+	
+	String File::filename() const
+	{
+	    return name();
+	}
+
+	Int File::exists() const
+	{
+	    Int ex = 0;
+	    std::ifstream fs(this->filename().c_str(), std::ios_base::binary);
+	    if(fs.good()){
+		ex = 1; // file exists
+	    }
+	    fs.close();
+	    if(ex != 0){
+		if(H5Fis_hdf5(this->filename().c_str()) <= 0){
+		    ex = 2; // file not in h5 format
+		}
+	    }
+	    return ex;
+	}
+	
+    }
+}