/*
 * Copyright 2018 Google LLC.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions
 * are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice,
 *    this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the distribution.
 *
 * 3. Neither the name of the copyright holder nor the names of its
 *    contributors may be used to endorse or promote products derived from this
 *    software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 * POSSIBILITY OF SUCH DAMAGE.
 */

// Implementation of bedgraph_reader.h
#include "third_party/nucleus/io/bedgraph_reader.h"

#include <algorithm>
#include <utility>
#include <vector>

#include "absl/strings/match.h"
#include "absl/strings/numbers.h"
#include "absl/strings/str_split.h"
#include "third_party/nucleus/platform/types.h"
#include "third_party/nucleus/protos/bedgraph.pb.h"
#include "third_party/nucleus/util/utils.h"

namespace nucleus {

constexpr char BED_COMMENT_PREFIX[] = "#";

// -----------------------------------------------------------------------------
//
// Reader for BedGraph format data.
//
// -----------------------------------------------------------------------------

namespace {

::nucleus::Status ConvertToPb(const string& line,
                              nucleus::genomics::v1::BedGraphRecord* record) {
  DCHECK_NE(nullptr, record) << "BedGraph record cannot be null";
  record->Clear();

  std::vector<string> tokens = absl::StrSplit(line, '\t');
  if (tokens.size() != 4) {
    return ::nucleus::Unknown("BedGraph record has invalid number of fields");
  }
  record->set_reference_name(tokens[0]);
  int64 start, end = 0;
  if (!absl::SimpleAtoi(tokens[1], &start) ||
      !absl::SimpleAtoi(tokens[2], &end)) {
    return ::nucleus::Unknown(
        "Unable to parse start and end positions in BedGraph");
  }
  record->set_start(start);
  record->set_end(end);
  double value = 0;
  if (!absl::SimpleAtod(tokens[3].c_str(), &value)) {
    return ::nucleus::Unknown("Unable to parse data value in BedGraph");
  }
  record->set_data_value(value);
  return ::nucleus::Status();
}

}  // namespace

// Iterable class for traversing all BedGraph records in the file.
class BedGraphFullFileIterable : public BedGraphIterable {
 public:
  // Advance to the next record.
  StatusOr<bool> Next(nucleus::genomics::v1::BedGraphRecord* out) override;

  // Constructor is invoked via BedGraphReader::Iterate.
  BedGraphFullFileIterable(const BedGraphReader* reader);
  ~BedGraphFullFileIterable() override;
};

StatusOr<std::unique_ptr<BedGraphReader>> BedGraphReader::FromFile(
    const string& bedgraph_path) {
  StatusOr<std::unique_ptr<TextReader>> status_or =
      TextReader::FromFile(bedgraph_path);
  NUCLEUS_RETURN_IF_ERROR(status_or.status());
  return std::unique_ptr<BedGraphReader>(
      new BedGraphReader(std::move(status_or.ValueOrDie())));
}

BedGraphReader::BedGraphReader(std::unique_ptr<TextReader> text_reader)
    : text_reader_(std::move(text_reader)) {}

BedGraphReader::~BedGraphReader() {
  if (!text_reader_) {
    return;
  }
  ::nucleus::Status status = Close();
  if (!status.ok()) {
    LOG(WARNING) << "Closing BedGraphReader encountered an error";
  }
}

::nucleus::Status BedGraphReader::Close() {
  if (!text_reader_) {
    return ::nucleus::FailedPrecondition("BedGraphReader already closed");
  }
  ::nucleus::Status status = text_reader_->Close();
  text_reader_ = nullptr;
  return status;
}

StatusOr<std::shared_ptr<BedGraphIterable>> BedGraphReader::Iterate() const {
  if (!text_reader_) {
    return ::nucleus::FailedPrecondition(
        "Cannot iterate a closed BedGraphReader");
  }
  return StatusOr<std::shared_ptr<BedGraphIterable>>(
      MakeIterable<BedGraphFullFileIterable>(this));
}

// Iterable class definitions.
StatusOr<bool> BedGraphFullFileIterable::Next(
    nucleus::genomics::v1::BedGraphRecord* out) {
  NUCLEUS_RETURN_IF_ERROR(CheckIsAlive());
  const BedGraphReader* bedgraph_reader =
      static_cast<const BedGraphReader*>(reader_);
  string line;
  do {
    StatusOr<string> line_or = bedgraph_reader->text_reader_->ReadLine();
    if (!line_or.ok()) {
      if (::nucleus::IsOutOfRange(line_or.status())) {
        return false;
      }
      return line_or.status();
    }
    line = line_or.ValueOrDie();
  } while (absl::StartsWith(line, BED_COMMENT_PREFIX));
  NUCLEUS_RETURN_IF_ERROR(ConvertToPb(line, out));
  return true;
}

BedGraphFullFileIterable::~BedGraphFullFileIterable() {}

BedGraphFullFileIterable::BedGraphFullFileIterable(const BedGraphReader* reader)
    : Iterable(reader) {}

}  // namespace nucleus