// File Description
/// \file DataSetXsd.cpp
/// \brief Implements the XSD- and namespace-related classes for DataSetXML.
//
// Author: Derek Barnett

#include "PbbamInternalConfig.h"

#include "pbbam/DataSetXsd.h"

#include <unordered_map>

namespace PacBio {
namespace BAM {
namespace internal {

// clang-format off
static std::map<XsdType, NamespaceInfo> DefaultRegistry()
{
    const auto result = std::map<XsdType, NamespaceInfo>
    {
        { XsdType::NONE,                   NamespaceInfo{ "", "" } },
        { XsdType::AUTOMATION_CONSTRAINTS, NamespaceInfo{ "",       "http://pacificbiosciences.com/PacBioAutomationConstraints.xsd" } },
        { XsdType::BASE_DATA_MODEL,        NamespaceInfo{ "pbbase", "http://pacificbiosciences.com/PacBioBaseDataModel.xsd" } },
        { XsdType::COLLECTION_METADATA,    NamespaceInfo{ "pbmeta", "http://pacificbiosciences.com/PacBioCollectionMetadata.xsd" } },
        { XsdType::COMMON_MESSAGES,        NamespaceInfo{ "",       "http://pacificbiosciences.com/PacBioCommonMessages.xsd" } },
        { XsdType::DATA_MODEL,             NamespaceInfo{ "pbdm",   "http://pacificbiosciences.com/PacBioDataModel.xsd" } },
        { XsdType::DATA_STORE,             NamespaceInfo{ "",       "http://pacificbiosciences.com/PacBioDataStore.xsd" } },
        { XsdType::DATASETS,               NamespaceInfo{ "pbds",   "http://pacificbiosciences.com/PacBioDatasets.xsd" } },
        { XsdType::DECL_DATA,              NamespaceInfo{ "",       "http://pacificbiosciences.com/PacBioDeclData.xsd" } },
        { XsdType::PART_NUMBERS,           NamespaceInfo{ "pbpn",   "http://pacificbiosciences.com/PacBioPartNumbers.xsd" } },
        { XsdType::PRIMARY_METRICS,        NamespaceInfo{ "",       "http://pacificbiosciences.com/PacBioPrimaryMetrics.xsd" } },
        { XsdType::REAGENT_KIT,            NamespaceInfo{ "pbrk",   "http://pacificbiosciences.com/PacBioReagentKit.xsd" } },
        { XsdType::RIGHTS_AND_ROLES,       NamespaceInfo{ "",       "http://pacificbiosciences.com/PacBioRightsAndRoles.xsd" } },
        { XsdType::SAMPLE_INFO,            NamespaceInfo{ "pbsample", "http://pacificbiosciences.com/PacBioSampleInfo.xsd" } },
        { XsdType::SEEDING_DATA,           NamespaceInfo{ "",       "http://pacificbiosciences.com/PacBioSeedingData.xsd" } }
    };
    return result;
}

static const auto elementRegistry = std::unordered_map<std::string, XsdType>
{
    // 'pbbase' elements
    //
    { "AutomationParameter" ,  XsdType::BASE_DATA_MODEL },
    { "AutomationParameters" , XsdType::BASE_DATA_MODEL },
    { "BinCount" ,             XsdType::BASE_DATA_MODEL },
    { "BinCounts" ,            XsdType::BASE_DATA_MODEL },
    { "BinLabel" ,             XsdType::BASE_DATA_MODEL },
    { "BinLabels" ,            XsdType::BASE_DATA_MODEL },
    { "BinWidth" ,             XsdType::BASE_DATA_MODEL },
    { "ExternalResource" ,     XsdType::BASE_DATA_MODEL },
    { "ExternalResources" ,    XsdType::BASE_DATA_MODEL },
    { "FileIndex" ,            XsdType::BASE_DATA_MODEL },
    { "FileIndices" ,          XsdType::BASE_DATA_MODEL },
    { "MaxBinValue" ,          XsdType::BASE_DATA_MODEL },
    { "MaxOutlierValue" ,      XsdType::BASE_DATA_MODEL },
    { "MetricDescription" ,    XsdType::BASE_DATA_MODEL },
    { "NumBins" ,              XsdType::BASE_DATA_MODEL },
    { "Properties" ,           XsdType::BASE_DATA_MODEL },
    { "Property" ,             XsdType::BASE_DATA_MODEL },
    { "Sample95thPct" ,        XsdType::BASE_DATA_MODEL },
    { "SampleMean" ,           XsdType::BASE_DATA_MODEL },
    { "SampleMed" ,            XsdType::BASE_DATA_MODEL },
    { "SampleSize" ,           XsdType::BASE_DATA_MODEL },
    { "SampleStd" ,            XsdType::BASE_DATA_MODEL },

    // 'pbds' elements
    //
    { "AdapterDimerFraction",  XsdType::DATASETS },
    { "AlignmentSet",          XsdType::DATASETS },
    { "BarcodeConstruction",   XsdType::DATASETS },
    { "BarcodeSet",            XsdType::DATASETS },
    { "ConsensusAlignmentSet", XsdType::DATASETS },
    { "ConsensusReadSet",      XsdType::DATASETS },
    { "Contig",                XsdType::DATASETS },
    { "Contigs",               XsdType::DATASETS },
    { "ContigSet",             XsdType::DATASETS },
    { "ControlReadLenDist",    XsdType::DATASETS },
    { "ControlReadQualDist",   XsdType::DATASETS },
    { "DataSetMetdata",        XsdType::DATASETS },
    { "DataSet",               XsdType::DATASETS },
    { "DataSets",              XsdType::DATASETS },
    { "Filter",                XsdType::DATASETS },
    { "Filters",               XsdType::DATASETS },
    { "HdfSubreadSet",         XsdType::DATASETS },
    { "InsertReadLenDist",     XsdType::DATASETS },
    { "InsertReadQualDist" ,   XsdType::DATASETS },
    { "MedianInsertDist",      XsdType::DATASETS },
    { "NumRecords",            XsdType::DATASETS },
    { "NumSequencingZmws",     XsdType::DATASETS },
    { "Organism",              XsdType::DATASETS },
    { "ParentTool",            XsdType::DATASETS },
    { "Ploidy",                XsdType::DATASETS },
    { "ProdDist",              XsdType::DATASETS },
    { "Provenance",            XsdType::DATASETS },
    { "ReadLenDist",           XsdType::DATASETS },
    { "ReadQualDist",          XsdType::DATASETS },
    { "ReadTypeDist",          XsdType::DATASETS },
    { "ReferenceSet",          XsdType::DATASETS },
    { "ShortInsertFraction",   XsdType::DATASETS },
    { "SubreadSet",            XsdType::DATASETS },
    { "SummaryStats",          XsdType::DATASETS },
    { "TotalLength",           XsdType::DATASETS },
    { "TranscriptSet",         XsdType::DATASETS },
    { "TranscriptAlignmentSet",XsdType::DATASETS },

    // 'pbmeta' elements
    //
    { "Automation",           XsdType::COLLECTION_METADATA },
    { "AutomationName",       XsdType::COLLECTION_METADATA },
    { "CellIndex",            XsdType::COLLECTION_METADATA },
    { "CellPac",              XsdType::COLLECTION_METADATA },
    { "CollectionFileCopy",   XsdType::COLLECTION_METADATA },
    { "CollectionMetadata",   XsdType::COLLECTION_METADATA },
    { "CollectionNumber",     XsdType::COLLECTION_METADATA },
    { "CollectionPathUri",    XsdType::COLLECTION_METADATA },
    { "Collections",          XsdType::COLLECTION_METADATA },
    { "Concentration",        XsdType::COLLECTION_METADATA },
    { "ConfigFileName",       XsdType::COLLECTION_METADATA },
    { "CopyFiles",            XsdType::COLLECTION_METADATA },
    { "InstCtrlVer",          XsdType::COLLECTION_METADATA },
    { "MetricsVerbosity",     XsdType::COLLECTION_METADATA },
    { "Name",                 XsdType::COLLECTION_METADATA },
    { "OutputOptions",        XsdType::COLLECTION_METADATA },
    { "PlateId",              XsdType::COLLECTION_METADATA },
    { "Primary",              XsdType::COLLECTION_METADATA },
    { "Readout",              XsdType::COLLECTION_METADATA },
    { "ResultsFolder",        XsdType::COLLECTION_METADATA },
    { "RunDetails",           XsdType::COLLECTION_METADATA },
    { "RunId",                XsdType::COLLECTION_METADATA },
    { "SampleReuseEnabled",   XsdType::COLLECTION_METADATA },
    { "SequencingCondition",  XsdType::COLLECTION_METADATA },
    { "SigProcVer",           XsdType::COLLECTION_METADATA },
    { "SizeSelectionEnabled", XsdType::COLLECTION_METADATA },
    { "StageHotstartEnabled", XsdType::COLLECTION_METADATA },
    { "UseCount",             XsdType::COLLECTION_METADATA },
    { "WellName",             XsdType::COLLECTION_METADATA },
    { "WellSample",           XsdType::COLLECTION_METADATA },

    // 'pbsample' elements
    //
    { "BioSample",         XsdType::SAMPLE_INFO },
    { "BioSamplePointer",  XsdType::SAMPLE_INFO },
    { "BioSamplePointers", XsdType::SAMPLE_INFO },
    { "BioSamples",        XsdType::SAMPLE_INFO }
};
// clang-format on

}  // namespace internal

// ---------------
// NamespaceInfo
// ---------------

NamespaceInfo::NamespaceInfo(std::string name, std::string uri)
    : name_(std::move(name)), uri_(std::move(uri))
{
}

// -------------------
// NamespaceRegistry
// -------------------

NamespaceRegistry::NamespaceRegistry() : data_(internal::DefaultRegistry()) {}

const NamespaceInfo& NamespaceRegistry::DefaultNamespace() const { return Namespace(DefaultXsd()); }

XsdType NamespaceRegistry::DefaultXsd() const { return defaultXsdType_; }

const NamespaceInfo& NamespaceRegistry::Namespace(const XsdType& xsd) const
{
    return data_.at(xsd);
}

void NamespaceRegistry::Register(const XsdType& xsd, const NamespaceInfo& namespaceInfo)
{
    data_[xsd] = namespaceInfo;
}

void NamespaceRegistry::SetDefaultXsd(const XsdType& xsd) { defaultXsdType_ = xsd; }

XsdType NamespaceRegistry::XsdForElement(const std::string& elementLabel) const
{
    const auto iter = internal::elementRegistry.find(elementLabel);
    return (iter == internal::elementRegistry.cend() ? XsdType::NONE : iter->second);
}

XsdType NamespaceRegistry::XsdForUri(const std::string& uri) const
{
    for (const auto& entry : data_) {
        const auto& info = entry.second;
        if (info.Uri() == uri) return entry.first;
    }
    return XsdType::NONE;
}

}  // namespace BAM
}  // namespace PacBio
