icedb::Databases::Database Class Reference

#include <Database.hpp>

Inheritance diagram for icedb::Databases::Database:

Public Types
typedef std::unique_ptr< Database >	Database_ptr

Public Member Functions
virtual	~Database ()
virtual Groups::Group::Group_ptr	openGroup (const std::string &path)=0
virtual Groups::Group::Group_ptr	createGroup (const std::string &path)=0
virtual Groups::Group::Group_ptr	createGroupStructure (const std::string &groupName)=0
virtual Groups::Group::Group_ptr	createGroupStructure (const std::vector< std::string > &groupNames)=0

Static Public Member Functions
static Database_ptr	createSampleDatabase (const std::string &location)
static Database_ptr	createSingleFileDatabase (const std::string &location)
static Database_ptr	openDatabase (const std::string &location, fs::IOopenFlags flags=fs::IOopenFlags::READ_ONLY)
static Database_ptr	openVirtualDatabase (size_t memSizeInBytes)
static void	indexDatabase (const std::string &location)

Protected Member Functions
	Database ()

Detailed Description

Definition at line 16 of file Database.hpp.

Member Typedef Documentation

Database_ptr

typedef std::unique_ptr<Database> icedb::Databases::Database::Database_ptr

Definition at line 20 of file Database.hpp.

Constructor & Destructor Documentation

Database()

icedb::Databases::Database::Database ( )

protected

Definition at line 66 of file databases.cpp.

{}

~Database()

icedb::Databases::Database::~Database ( )

virtual

Definition at line 64 of file databases.cpp.

{}

Member Function Documentation

createGroup()

virtual Groups::Group::Group_ptr icedb::Databases::Database::createGroup ( const std::string &  path )

pure virtual

Implemented in icedb::Databases::Database_impl.

createGroupStructure() [1/2]

virtual Groups::Group::Group_ptr icedb::Databases::Database::createGroupStructure ( const std::string &  groupName )

pure virtual

Implemented in icedb::Databases::Database_impl.

createGroupStructure() [2/2]

virtual Groups::Group::Group_ptr icedb::Databases::Database::createGroupStructure ( const std::vector< std::string > &  groupNames )

pure virtual

Implemented in icedb::Databases::Database_impl.

createSampleDatabase()

Database::Database_ptr icedb::Databases::Database::createSampleDatabase ( const std::string &  location )

static

Definition at line 68 of file databases.cpp.

References icedb::fs::hdf5::getHDF5IOflags(), icedb::Databases::Database_impl::makeDatabaseFileStandard(), openDatabase(), icedb::fs::READ_WRITE, and icedb::fs::TRUNCATE.

Referenced by main().

        {
            const auto flag_truncate = fs::hdf5::getHDF5IOflags(fs::IOopenFlags::TRUNCATE);
            
            sfs::path pBase(location);
            sfs::create_directories(pBase);
            Expects(sfs::exists(pBase));

            sfs::create_directory(pBase / "3d_Structures");
            sfs::create_directory(pBase / "Physical_Particle_Properties");
            sfs::create_directory(pBase / "Extended_Scattering_Variables");
            sfs::create_directory(pBase / "Essential_Scattering_Variables");
            sfs::create_directory(pBase / "Testing");

            Database_impl::makeDatabaseFileStandard((pBase / "3d_Structures" / "3dS-1.hdf5").string());
            Database_impl::makeDatabaseFileStandard((pBase / "3d_Structures" / "3dS-2.hdf5").string());
            Database_impl::makeDatabaseFileStandard((pBase / "3d_Structures" / "3dS-3.hdf5").string());
            Database_impl::makeDatabaseFileStandard((pBase / "Physical_Particle_Properties" / "ppp.hdf5").string());
            Database_impl::makeDatabaseFileStandard((pBase / "Essential_Scattering_Variables" / "esv1.hdf5").string());
            Database_impl::makeDatabaseFileStandard((pBase / "Essential_Scattering_Variables" / "esv2.hdf5").string());
            Database_impl::makeDatabaseFileStandard((pBase / "Testing" / "scratch.hdf5").string());
            Database_impl::makeDatabaseFileStandard((pBase / "metadata.hdf5").string());

            return (openDatabase(location, icedb::fs::IOopenFlags::READ_WRITE));
        }

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createSingleFileDatabase()

Database::Database_ptr icedb::Databases::Database::createSingleFileDatabase ( const std::string &  location )

static

Definition at line 95 of file databases.cpp.

References icedb::fs::hdf5::getHDF5IOflags(), icedb::Databases::Database_impl::makeDatabaseFileStandard(), openDatabase(), icedb::fs::READ_WRITE, and icedb::fs::TRUNCATE.

Referenced by openDatabase().

                                       {
            const auto flag_truncate = fs::hdf5::getHDF5IOflags(fs::IOopenFlags::TRUNCATE);

            //sfs::path pBase(location);
            //sfs::create_directories(pBase);
            //Expects(sfs::exists(pBase));
            Database_impl::makeDatabaseFileStandard(location);

            return (openDatabase(location, icedb::fs::IOopenFlags::READ_WRITE));
        }

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indexDatabase()

void icedb::Databases::Database::indexDatabase ( const std::string &  location )

static

Todo:

createGroupStructure cannot currently handle passing back an H5File (in the no groups case). It is a bug in HDF5. Once fixed, the if-else cases should be collapsed into one.

Definition at line 161 of file databases.cpp.

References icedb::fs::impl::collectActualHDF5files(), icedb::fs::hdf5::createGroupStructure(), icedb::fs::hdf5::explodeHDF5groupPath(), icedb::Databases::Database_impl::makeDatabaseFileStandard(), and icedb::fs::impl::resolveSymlinkPathandForceExists().

Referenced by main().

        {
            sfs::path pBaseS = fs::impl::resolveSymlinkPathandForceExists(location);
            fs::impl::CollectedFilesRet_Type mountFiles = fs::impl::collectActualHDF5files(pBaseS);
            Expects(mountFiles.size() > 0);
            if (mountFiles.size() == 1) return;

            std::unique_ptr<Database_impl> res = std::make_unique<Database_impl>();
            res->hFile = Database_impl::makeDatabaseFileStandard(location + "/index.hdf5");

            // Check for the existence of the appropriate groups in the relative path tree
            // Create any missing groups in the relative path tree, and then make the link.
            for (const auto &toMount : mountFiles) {
                std::string mountStr = toMount.second;
                if (mountStr == "index.hdf5") continue;
                auto explodedPath = fs::hdf5::explodeHDF5groupPath(mountStr);
                std::string linkName = *(explodedPath.rbegin());
                explodedPath.pop_back();

                if (explodedPath.size()) {
                    auto grp = fs::hdf5::createGroupStructure(explodedPath, *(res->hFile.get()));
                    H5Lcreate_external(toMount.second.c_str(), "/", grp.getLocId(), linkName.c_str(), H5P_DEFAULT, H5P_DEFAULT);
                } else {
                    H5Lcreate_external(toMount.second.c_str(), "/", res->hFile->getLocId(), linkName.c_str(), H5P_DEFAULT, H5P_DEFAULT);
                }
            }

        }

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openDatabase()

Database::Database_ptr icedb::Databases::Database::openDatabase ( const std::string &  location, fs::IOopenFlags  flags = fs::IOopenFlags::READ_ONLY  )

static

Note

HDF5 C++ bug in constness on 1.8.5, CentOS 6. I cannot directly pass H5P_DEFAULT to the trivial constructor for H5::PropList as an rvalue

Definition at line 118 of file databases.cpp.

References icedb::fs::impl::collectActualHDF5files(), icedb::fs::CREATE, icedb::fs::hdf5::createGroupStructure(), createSingleFileDatabase(), icedb::fs::hdf5::getHDF5IOflags(), icedb::fs::impl::resolveSymLinks(), and icedb::fs::TRUNCATE.

Referenced by createSampleDatabase(), createSingleFileDatabase(), and main().

        {
            sfs::path pBaseS = fs::impl::resolveSymLinks(location);
            if (!sfs::exists(pBaseS)) {
                if (flags == fs::IOopenFlags::TRUNCATE || flags == fs::IOopenFlags::CREATE) {
                    return createSingleFileDatabase(location);
                } else throw(std::invalid_argument("Attempting to open a database root that does not exist. Did you mean to first create this database?"));
            }
            fs::impl::CollectedFilesRet_Type mountFiles = fs::impl::collectActualHDF5files(pBaseS);
            unsigned int Hflags = fs::hdf5::getHDF5IOflags(flags);
            auto res = std::make_unique<Database_impl>();
            //std::unique_ptr<Database_impl, mem::icedb_delete<Database_impl> > res(new Database_impl);
                //= std::make_unique(<Database_impl, mem::icedb_delete<Database_impl> >();

            Expects(mountFiles.size() > 0);
            if (mountFiles.size() == 1) {
                res->hFile = std::make_shared<H5::H5File>(
                    mountFiles.begin()->first.string().c_str(), Hflags, H5P_DEFAULT);
            }
            else {
                res->hFile = res->hFileImage.getHFile();

                // Check for the existence of the appropriate groups in the relative path tree
                // Create any missing groups in the relative path tree
                for (const auto &toMount : mountFiles) {
                    std::string mountStr = toMount.second;
                    if (mountStr == "index.hdf5") continue;
                    H5::Group grp = icedb::fs::hdf5::createGroupStructure(mountStr, *(res->hFile.get()));
                    // Open files and mount in the relative path tree
                    std::shared_ptr<H5::H5File> newHfile = std::make_shared<H5::H5File>(toMount.first.string(), Hflags);
                    //res._impl->mappedFiles[toMount.second] = newHfile;

                    H5::PropList pl(H5P_DEFAULT);
                    res->hFile->mount(toMount.second, *(newHfile.get()), pl);
                }
            }

            return std::move(res);
        }

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openGroup()

virtual Groups::Group::Group_ptr icedb::Databases::Database::openGroup ( const std::string &  path )

pure virtual

Implemented in icedb::Databases::Database_impl.

openVirtualDatabase()

Database::Database_ptr icedb::Databases::Database::openVirtualDatabase ( size_t  memSizeInBytes )

static

Definition at line 107 of file databases.cpp.

        {
            auto res = std::make_unique<Database_impl>();
            //std::unique_ptr<Database_impl, mem::icedb_delete<Database_impl> > res(new Database_impl);
            //= std::make_unique(<Database_impl, mem::icedb_delete<Database_impl> >();
            res->hFile = res->hFileImage.getHFile();

            return std::move(res);
        }

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The documentation for this class was generated from the following files:

• lib/icedb/Database.hpp
• lib/src/databases.cpp