fixes in to_string + h5 attributes

src/include/base/to_string.cc.h

@@ -33,11 +33,16 @@ namespace CNORXZ
     {
 	std::stringstream ss;
 	ss << "[";
+	if(a.size() == 0){
+	    ss << "]";
+	}
+	else {
 	    auto it = a.begin();
 	    for(; it != a.end()-1; ++it){
 		ss << toString(*it) << ",";
 	    }
 	    ss << toString(*it) << "]";
+	}
 	return ss.str();
     }
 
@@ -46,11 +51,16 @@ namespace CNORXZ
     {
 	std::stringstream ss;
 	ss << "(";
+	if constexpr(N == 0){
+	    ss << ")";
+	}
+	else {
 	    auto it = a.begin();
 	    for(; it != a.end()-1; ++it){
 		ss << toString(*it) << ",";
 	    }
 	    ss << toString(*it) << ")";
+	}
 	return ss.str();
     }
 
@@ -73,6 +83,26 @@ namespace CNORXZ
 	return String("(") + toString(p.first) + "," + toString(p.second) + ")";
     }
 
+    template <typename T, typename S>
+    String ToString<std::map<T,S>>::func(const std::map<T,S>& p)
+    {
+	std::stringstream ss;
+	ss << "{";
+	if(p.size() == 0){
+	    ss << "}";
+	}
+	else {
+	    auto it = p.begin();
+	    auto e = p.end();
+	    e--;
+	    for(; it != e; ++it){
+		ss << toString(it->first) << ":" << toString(it->second) << ",";
+	    }
+	    ss << toString(it->first) << ":" << toString(it->second) << "}";
+	}
+	return ss.str();
+    }
+
     template <typename T>
     String toString(const T& a)
     {

src/include/base/to_string.h

@@ -97,6 +97,20 @@ namespace CNORXZ
 	static String func(const std::pair<T,S>& t);
     };
 
+    /** ***
+	Specialization of ToString for maps
+	@tparam T key type
+	@tparam S value type
+     */
+    template <typename T, typename S>
+    struct ToString<std::map<T,S>>
+    {
+	/** cast to string
+	    @param a map to be casted
+	 */
+	static String func(const std::map<T,S>& t);
+    };
+
     /** ***
 	Specialization of ToString for DType
      */

src/opt/hdf5/include/h5_content_base.cc.h

@@ -78,9 +78,9 @@ namespace CNORXZ
 
 
 	    template <typename T>
-	    inline herr_t writeAttr(hid_t id, const String& name, const T& v, hid_t space_id)
+	    inline herr_t writeAttr(hid_t id, const String& name, const T& v)
 	    {
-		return CreateAttribute<T>::write(id, name, v, space_id);
+		return CreateAttribute<T>::write(id, name, v);
 	    }
 	}
 	

src/opt/hdf5/include/h5_content_base.h

@@ -45,8 +45,8 @@ namespace CNORXZ
 	    ContentBase& addAttribute(const String& name, const T& value);
 	    DType getAttribute(const String& name) const;
 	    bool attributeExists(const String& name) const;
-	    Vector<DType> getAttributes() const;
+	    std::map<String,DType> getAttributes() const;
-	    Vector<DType> getRecursiveAttributes() const; // + all parent's attributes
+	    std::map<String,DType> getRecursiveAttributes() const; // + all parent's attributes
 	    
 	protected:
 	    String mName;

src/opt/hdf5/include/h5_group.cc.h

@@ -71,6 +71,23 @@ namespace CNORXZ
 		recursion(c, std::forward<F>(f));
 	    });
 	}
+
+	template <class F>
+	decltype(auto) Group::iter(F&& f)
+	{
+	    RangePtr gr = *mCont.range()->sub().begin();
+	    auto gi = std::make_shared<UIndex<String>>(gr);
+	    return gi->ifor( operation(std::forward<F>(f), mCont(gi)), NoF{} );
+	}
+
+	template <class F>
+	decltype(auto) Group::iterRecursive(F&& f)
+	{
+	    return iter( [&](const auto& c) {
+		f(c);
+		recursion(c, std::forward<F>(f));
+	    });
+	}
     }
 }
 

src/opt/hdf5/include/h5_group.h

@@ -48,6 +48,12 @@ namespace CNORXZ
 	    template <class F>
 	    decltype(auto) iterRecursive(F&& f) const;
 
+	    template <class F>
+	    decltype(auto) iter(F&& f);
+
+	    template <class F>
+	    decltype(auto) iterRecursive(F&& f);
+
 	protected:
 
 	    template <typename C, class F>

src/opt/hdf5/include/h5_table.h

@@ -51,9 +51,12 @@ namespace CNORXZ
 	    STable& appendRecord(const Tuple<Ts...>& t);
 	    STable& appendRecord(const MArray<Tuple<Ts...>>& t);
 
+	    MArray<Tuple<Ts...>> read();
+	    
 	    template <class F>
 	    decltype(auto) iterRecords(F&& f) const;
 	};
+
     }
 }
 

src/opt/hdf5/lib/h5_content_base.cc

@@ -56,11 +56,37 @@ namespace CNORXZ
 	    }
 	    case H5T_STRING: {
 		const SizeT asize = H5Tget_size(atype_id);
-		Vector<char> v(asize);
+		Vector<char> v(asize+1);
 		H5Aread(attr, atype_id, v.data());
 		o = DType( String( v.data() ) );
 		break;
 	    }
+	    case H5T_ARRAY: {
+		const int ndims = H5Tget_array_ndims(atype_id);
+		CXZ_ASSERT(ndims, "array of dimension " << ndims << " not supported");
+		hsize_t dims;
+		H5Tget_array_dims(atype_id, &dims);
+		const hid_t att_id = H5Tget_super(atype_id);
+		const H5T_class_t atc = H5Tget_class(att_id);
+		switch(atc){
+		case H5T_INTEGER: {
+		    Vector<Int> v(dims);
+		    H5Aread(attr, atype_id, v.data());
+		    o = DType(v);
+		    break;
+		}
+		case H5T_FLOAT: {
+		    Vector<Double> v(dims);
+		    H5Aread(attr, atype_id, v.data());
+		    o = DType(v);
+		    break;
+		}
+		default:
+		    CXZ_ERROR("attribute type id " << atype_id << " not supported");
+		}
+		H5Tclose(att_id);
+		break;
+	    }
 	    default:
 		CXZ_ERROR("attribute type id " << atype_id << " not supported");
 	    }
@@ -78,12 +104,12 @@ namespace CNORXZ
 	    return ret;
 	}
 	
-	Vector<DType> ContentBase::getAttributes() const
+	std::map<String,DType> ContentBase::getAttributes() const
 	{
 	    CXZ_ASSERT(isOpen(), "tried to get attribute of closed object");
 	    struct ItData
 	    {
-		Vector<DType> d;
+		std::map<String,DType> d;
 		const ContentBase* _this;
 	    } itdata;
 	    itdata._this = this;
@@ -91,7 +117,8 @@ namespace CNORXZ
 			   const H5A_info_t* ainfo, void *op_data)
 	    {
 		ItData* x = reinterpret_cast<ItData*>(op_data);
-		x->d.push_back( x->_this->getAttribute( String(attr_name) ) );
+		const String n = attr_name;
+		x->d[n] = x->_this->getAttribute( String(attr_name) );
 		return static_cast<herr_t>(0);
 	    };
 	    H5Aiterate(id(), H5_INDEX_NAME, H5_ITER_NATIVE, nullptr,
@@ -99,12 +126,12 @@ namespace CNORXZ
 	    return itdata.d;
 	}
 	
-	Vector<DType> ContentBase::getRecursiveAttributes() const
+	std::map<String,DType> ContentBase::getRecursiveAttributes() const
 	{
-	    Vector<DType> out = getAttributes();
+	    std::map<String,DType> out = getAttributes();
 	    if(mParent){
-		Vector<DType> par = mParent->getRecursiveAttributes();
+		std::map<String,DType> par = mParent->getRecursiveAttributes();
-		out.insert(out.begin(), par.begin(), par.end());
+		out.insert(par.begin(), par.end());
 	    }
 	    return out;
 	}

src/opt/hdf5/lib/h5_file.cc

@@ -28,6 +28,9 @@ namespace CNORXZ
 	
 	File& File::open()
 	{
+	    if(isOpen()){
+		return *this;
+	    }
 	    Int ex = this->exists();
 	    const String fn = this->filename();
 	    CXZ_ASSERT( ex != 2, "tried to open non-h5 file '" << fn << "'" );

src/opt/hdf5/lib/h5_group.cc

@@ -30,6 +30,7 @@ namespace CNORXZ
 	
 	Group& Group::open()
 	{
+	    if(not isOpen()){
 		if(this->exists()){
 		    mId = H5Gopen( mParent->id(), mName.c_str(), H5P_DEFAULT );
 		}
@@ -38,6 +39,7 @@ namespace CNORXZ
 				     H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
 		}
 		this->mkCont();
+	    }
 	    return *this;
 	}
 	

src/opt/hdf5/tests/h5_basic_unit_test.cc

@@ -80,16 +80,27 @@ namespace
 	File h5f(mFileName, false);
 	EXPECT_FALSE(h5f.ro());
 	h5f.open();
+	h5f.addAttribute("fprop", static_cast<Double>(3.141));
 	h5f.addGroup("gr1");
+	h5f.getGroup("gr1")->addAttribute("att1", String("text"));
 	h5f.addGroup("gr2");
 	h5f.addGroup("foo");
-	h5f.addGroup("moregroups");
 	h5f.addGroup("bar");
-	h5f.getGroup("moregroups")->open().addGroup("evenmore");
+	h5f.addGroup("moregroups");
-	h5f.getGroup("moregroups")->getGroup("evenmore")->open().addGroup("we");
+	auto moregroups = h5f.getGroup("moregroups");
-	h5f.getGroup("moregroups")->getGroup("evenmore")->addGroup("need");
+	moregroups->open().addGroup("evenmore");
-	h5f.getGroup("moregroups")->getGroup("evenmore")->addGroup("more");
+	auto evenmore = moregroups->getGroup("evenmore");
-	h5f.getGroup("moregroups")->getGroup("evenmore")->addGroup("groups");
+	evenmore->open();
+	evenmore->addAttribute("moreatt", static_cast<Int>(12));
+	evenmore->addGroup("we");
+	evenmore->getGroup("we")->addAttribute("wex", static_cast<Int>(9));
+	evenmore->getGroup("we")->addAttribute("xy", String("xys"));
+	evenmore->addGroup("need");
+	evenmore->getGroup("need")->addAttribute("wex", static_cast<Int>(7));
+	evenmore->addGroup("more");
+	evenmore->getGroup("more")->addAttribute("wex", static_cast<Int>(4));
+	evenmore->addGroup("groups");
+	evenmore->getGroup("groups")->addAttribute("wex", static_cast<Int>(2));
 	EXPECT_EQ(h5f.get().size(), 5u);
 	h5f.close();
     }
@@ -100,6 +111,7 @@ namespace
 	h5f.open();
 	h5f.getGroup("gr1")->open().addTable("tab1", mTabA, mFs);
 	h5f.getGroup("gr2")->open().addTable("tab1", mTabA, mFs);
+	h5f.getGroup("moregroups")->open().getGroup("evenmore")->open().getGroup("need")->open().addTable("tab1", mTabA, mFs);
 	h5f.close();
     }
     
@@ -114,13 +126,30 @@ namespace
 	auto gr1 = h5f.getGroup("gr1");
 	gr1->open();
 	auto tab = gr1->getTable("tab1");
+	DType att = gr1->getAttribute("att1");
+	EXPECT_EQ(att.str(), "text");
 	VCHECK(tab->path());
 	EXPECT_EQ(tab->fields()->size(), 3u);
 	EXPECT_EQ(tab->records()->size(), 5u);
 	h5f.iter( [](const auto& c) { VCHECK(c->path()); } )();
 	h5f.iterRecursive( [](const auto& c) { VCHECK(c->path()); } )();
+	h5f.iterRecursive( [](const auto& c) { c->open(); VCHECK(toString(c->getRecursiveAttributes())); } )();
+	h5f.iterRecursive( [](const auto& c) {
+	    if(c->type() == ContentType::TABLE) { c->open(); VCHECK(toString(c->getRecursiveAttributes())); }
+	} )();
 	h5f.close();
     }
+
+    TEST_F(Group_Test, ReadTable)
+    {
+	File h5f(mFileName, true);
+	h5f.open();
+	auto tab = h5f.getGroup("gr1")->open().getTable("tab1");
+	EXPECT_EQ(tab->fields()->size(), 3u);
+	EXPECT_EQ(tab->records()->size(), 5u);
+
+	
+    }
 }
 
 // check write to new file