// Copyright(C) 1999-2021 National Technology & Engineering Solutions
// of Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
// NTESS, the U.S. Government retains certain rights in this software.
//
// See packages/seacas/LICENSE for details

#include "EJ_SystemInterface.h"
#include "EJ_Version.h"  // for qainfo
#include "EJ_vector3d.h" // for vector3d
#include <SL_tokenize.h> // for tokenize
#include <algorithm>     // for sort, find, transform
#include <cctype>        // for tolower
#include <copyright.h>
#include <cstddef> // for size_t
#include <cstdlib> // for exit, strtod, strtoul, abs, etc
#include <cstring> // for strchr, strlen
#include <fmt/format.h>
#include <iosfwd>  // for ostream
#include <utility> // for pair, make_pair
#include <vector>  // for vector

namespace {
  bool str_equal(const std::string &s1, const std::string &s2)
  {
    return (s1.size() == s2.size()) &&
           std::equal(s1.begin(), s1.end(), s2.begin(),
                      [](char a, char b) { return std::tolower(a) == std::tolower(b); });
  }

  void parse_variable_names(const char *tokens, StringIdVector *variable_list);
  void parse_variable_names(const char *tokens, StringIdVector *variable_list);
  void parse_offset(const char *tokens, vector3d *offset);
  void parse_integer_list(const char *tokens, std::vector<int> *list);
  void parse_part_list(const char *tokens, std::vector<int> *list);
  void parse_omissions(const char *tokens, Omissions *omissions, const std::string &basename,
                       bool require_ids);
} // namespace

SystemInterface::SystemInterface()
{
  offset_.x = 0.0;
  offset_.y = 0.0;
  offset_.z = 0.0;
  enroll_options();
}

SystemInterface::~SystemInterface() = default;

void SystemInterface::enroll_options()
{
  options_.usage("[options] list_of_files_to_join");

  options_.enroll("help", GetLongOption::NoValue, "Print this summary and exit", nullptr);

  options_.enroll("version", GetLongOption::NoValue, "Print version and exit", nullptr);

  options_.enroll("output", GetLongOption::MandatoryValue, "Name of output file to create",
                  "ejoin-out.e");

  options_.enroll(
      "extract_blocks", GetLongOption::MandatoryValue,
      "Use only the specified part/block pairs. The specification is\n"
      "\t\tp#:block_id1:block_id2,p#:block_id1. For example, to\n"
      "\t\tExtract block ids 1,3,4 from part 1; blocks 2 3 4 from part 2;\n"
      "\t\tand block 8 from part5, specify\n"
      "\t\t\t '-extract_blocks p1:1:3:4,p2:2:3:4,p5:8'\n"
      "\t\tIf an extract is specified, then only that id(s) will be used for that part.",
      nullptr);

  options_.enroll("omit_blocks", GetLongOption::MandatoryValue,
                  "Omit the specified part/block pairs. The specification is\n"
                  "\t\tp#:block_id1:block_id2,p#:block_id1. For example, to\n"
                  "\t\tOmit block id 1,3,4 from part 1; block 2 3 4 from part 2;\n"
                  "\t\tand block 8 from part5, specify\n"
                  "\t\t\t '-omit_blocks p1:1:3:4,p2:2:3:4,p5:8'",
                  nullptr);

  options_.enroll("omit_nodesets", GetLongOption::OptionalValue,
                  "If no value, then don't transfer any nodesets to output file.\n"
                  "\t\tIf just p#,p#,... specified, then omit sets on specified parts\n"
                  "\t\tIf p#:id1:id2,p#:id2,id4... then omit the sets with the specified\n"
                  "\t\tid in the specified parts.",
                  nullptr, "ALL");

  options_.enroll("omit_sidesets", GetLongOption::OptionalValue,
                  "If no value, then don't transfer any sidesets to output file.\n"
                  "\t\tIf just p#,p#,... specified, then omit sets on specified parts\n"
                  "\t\tIf p#:id1:id2,p#:id2,id4... then omit the sets with the specified\n"
                  "\t\tid in the specified parts.",
                  nullptr, "ALL");

  options_.enroll("convert_nodal_to_nodesets", GetLongOption::MandatoryValue,
                  "For each part listed (or ALL),\n"
                  "\t\tcreate a nodeset containing the nodes of that part\n"
                  "\t\tand output the nodal fields as nodeset fields instead of nodal fields.\n"
                  "\t\tFormat is comma-separated list of parts (1-based), or ALL",
                  nullptr);

  options_.enroll("match_node_ids", GetLongOption::NoValue,
                  "Combine nodes if their global ids match.", nullptr);

  options_.enroll("match_node_coordinates", GetLongOption::NoValue,
                  "Combine nodes if they are within tolerance distance of each other.", nullptr);

#if 0
  options_.enroll("match_elem_ids", GetLongOption::NoValue,
                  "Combine elements if their global ids match and they are compatible.\n"
                  "\t\tCompatible = same element type, nodes of the two elements match",
                  nullptr);

  options_.enroll("match_element_coordinates", GetLongOption::NoValue,
                  "Combine elements if their centroids are within tolerance distance\n"
                  "\t\tand they are compatible (same element type, nodes match).",
                  nullptr);
#endif

  options_.enroll("tolerance", GetLongOption::MandatoryValue,
                  "Maximum distance between two nodes to be considered colocated.", nullptr);

  options_.enroll(
      "block_prefix", GetLongOption::MandatoryValue,
      "Prefix used on the input block names of second and subsequent meshes to make them\n"
      "\t\tunique.  Default is 'p'.  Example: block1, p1_block1, p2_block1.",
      "p");

  options_.enroll("offset", GetLongOption::MandatoryValue,
                  "Comma-separated x,y,z offset for coordinates of second and subsequent meshes.\n"
                  "\t\tThe offset will be multiplied by the part number-1 so:\n"
                  "\t\tP1: no offset; P2: 1x, 1y, 1z; P3: 2x, 2y, 2z; P(n+1): nx, ny, nz",
                  nullptr);

  options_.enroll("steps", GetLongOption::MandatoryValue,
                  "Specify subset of timesteps to transfer to output file.\n"
                  "\t\tFormat is beg:end:step. 1:10:2 --> 1,3,5,7,9\n"
                  "\t\tTo only transfer last step, use '-steps LAST'",
                  "1:");

  options_.enroll("gvar", GetLongOption::MandatoryValue,
                  "Comma-separated list of global variables to be joined or ALL or NONE.", nullptr);

  options_.enroll("evar", GetLongOption::MandatoryValue,
                  "Comma-separated list of element variables to be joined or ALL or NONE.\n"
                  "\t\tVariables can be limited to certain blocks by appending a\n"
                  "\t\tcolon followed by the block id.  E.g. -evar sigxx:10:20",
                  nullptr);

  options_.enroll("nvar", GetLongOption::MandatoryValue,
                  "Comma-separated list of nodal variables to be joined or ALL or NONE.", nullptr);

  options_.enroll("nsetvar", GetLongOption::MandatoryValue,
                  "Comma-separated list of nodeset variables to be joined or ALL or NONE.\n"
                  "\t\tVariables can be limited to certain sets by appending a\n"
                  "\t\tcolon followed by the nodeset id.  E.g. -nsetvar sigxx:10:20",
                  nullptr);

  options_.enroll("ssetvar", GetLongOption::MandatoryValue,
                  "Comma-separated list of sideset variables to be joined or ALL or NONE.\n"
                  "\t\tVariables can be limited to certain sidesets by appending a\n"
                  "\t\tcolon followed by the sideset id.  E.g. -ssetvar sigxx:10:20",
                  nullptr);

  options_.enroll(
      "info_records", GetLongOption::OptionalValue,
      "If no value specified or not present,\n"
      "\t\tthen don't transfer any information records to output file.\n"
      "\t\tIf 'p#,p#,...' specified, then only transfer information records on specified parts\n"
      "\t\tIf 'all' specified, then transfer all information records",
      nullptr, "NONE");

  options_.enroll("ignore_element_ids", GetLongOption::NoValue,
                  "Ignore the element id maps on the input database and just use a 1..#elements id "
                  "map on output.\n"
                  "\t\tMuch faster for large models if do not need specific element global ids",
                  nullptr);

  options_.enroll("netcdf4", GetLongOption::NoValue,
                  "Create output database using the HDF5-based "
                  "netcdf which allows for up to 2.1 GB "
                  "nodes and elements",
                  nullptr);

  options_.enroll("64-bit", GetLongOption::NoValue,
                  "True if forcing the use of 64-bit integers for the output file", nullptr);

  options_.enroll(
      "zlib", GetLongOption::NoValue,
      "Use the Zlib / libz compression method if compression is enabled (default) [exodus only].",
      nullptr);

  options_.enroll("szip", GetLongOption::NoValue,
                  "Use SZip compression. [exodus only, enables netcdf-4]", nullptr);

  options_.enroll(
      "compress", GetLongOption::MandatoryValue,
      "Specify the hdf5 (netcdf4) compression level [0..9] to be used on the output file.",
      nullptr);

  options_.enroll("disable_field_recognition", GetLongOption::NoValue,
                  "Do not try to combine scalar fields into higher-order fields such as\n"
                  "\t\tvectors or tensors based on the field suffix",
                  nullptr);

  options_.enroll("copyright", GetLongOption::NoValue, "Show copyright and license data.", nullptr);
}

bool SystemInterface::parse_options(int argc, char **argv)
{
  int option_index = options_.parse(argc, argv);
  if (option_index < 1) {
    return false;
  }

  if (options_.retrieve("help") != nullptr) {
    options_.usage();
    fmt::print(stderr, "\n\tCan also set options via EJOIN_OPTIONS environment variable.\n"
                       "\n\t->->-> Send email to gdsjaar@sandia.gov for ejoin support.<-<-<-\n");
    exit(EXIT_SUCCESS);
  }

  if (options_.retrieve("version") != nullptr) {
    // Version is printed up front, just exit...
    exit(0);
  }

  if (options_.retrieve("copyright") != nullptr) {
    fmt::print("{}", copyright("2010-2021"));
    exit(EXIT_SUCCESS);
  }

  // Parse remaining options as directory paths.
  // Note that inputFiles_.size() is the number of parts which can be used in
  // parsing of other options...

  if (option_index < argc) {
    while (option_index < argc) {
      inputFiles_.emplace_back(argv[option_index++]);
    }
  }
  else {
    fmt::print(stderr, "\nERROR: no files specified\n\n");
    return false;
  }

  size_t part_count = inputFiles_.size();
  blockOmissions_.resize(part_count);
  blockInclusions_.resize(part_count);
  nsetOmissions_.resize(part_count);
  ssetOmissions_.resize(part_count);

  // Get options from environment variable also...
  char *options = getenv("EJOIN_OPTIONS");
  if (options != nullptr) {
    fmt::print(
        stderr,
        "\nThe following options were specified via the EJOIN_OPTIONS environment variable:\n"
        "\t{}\n\n",
        options);
    options_.parse(options, options_.basename(*argv));
  }

  outputName_  = options_.get_option_value("output", outputName_);
  blockPrefix_ = options_.get_option_value("block_prefix", blockPrefix_);

  {
    const char *temp = options_.retrieve("offset");
    if (temp != nullptr) {
      parse_offset(temp, &offset_);
    }
  }

  tolerance_ = options_.get_option_value("tolerance", tolerance_);

  {
    const char *temp = options_.retrieve("steps");
    if (temp != nullptr) {
      parse_step_option(temp);
    }
  }

  {
    const char *temp = options_.retrieve("convert_nodal_to_nodesets");
    if (temp != nullptr) {
      parse_integer_list(temp, &nodesetConvertParts_);
      std::sort(nodesetConvertParts_.begin(), nodesetConvertParts_.end());
    }
  }

  {
    const char *temp = options_.retrieve("info_records");
    if (temp != nullptr) {
      parse_part_list(temp, &infoRecordParts_);
      std::sort(infoRecordParts_.begin(), infoRecordParts_.end());
    }
  }

  {
    const char *temp = options_.retrieve("omit_blocks");
    if (temp != nullptr) {
      parse_omissions(temp, &blockOmissions_, "block", true);
    }
  }

  {
    const char *temp = options_.retrieve("extract_blocks");
    if (temp != nullptr) {
      parse_omissions(temp, &blockInclusions_, "block", true);
    }
  }

  {
    const char *temp = options_.retrieve("omit_nodesets");
    if (temp != nullptr) {
      if (str_equal("ALL", temp)) {
        omitNodesets_ = true;
      }
      else {
        parse_omissions(temp, &nsetOmissions_, "nodelist", false);
      }
    }
    else {
      omitNodesets_ = false;
    }
  }

  {
    const char *temp = options_.retrieve("omit_sidesets");
    if (temp != nullptr) {
      if (str_equal("ALL", temp)) {
        omitSidesets_ = true;
      }
      else {
        parse_omissions(temp, &ssetOmissions_, "surface", false);
      }
    }
    else {
      omitSidesets_ = false;
    }
  }

  {
    const char *temp = options_.retrieve("gvar");
    if (temp != nullptr) {
      parse_variable_names(temp, &globalVarNames_);
    }
  }

  {
    const char *temp = options_.retrieve("nvar");
    if (temp != nullptr) {
      parse_variable_names(temp, &nodeVarNames_);
    }
  }

  {
    const char *temp = options_.retrieve("evar");
    if (temp != nullptr) {
      parse_variable_names(temp, &elemVarNames_);
    }
  }

  {
    const char *temp = options_.retrieve("nsetvar");
    if (temp != nullptr) {
      parse_variable_names(temp, &nsetVarNames_);
    }
  }

  {
    const char *temp = options_.retrieve("ssetvar");
    if (temp != nullptr) {
      parse_variable_names(temp, &ssetVarNames_);
    }
  }

  disableFieldRecognition_ = options_.retrieve("disable_field_recognition") != nullptr;
  useNetcdf4_              = options_.retrieve("netcdf4") != nullptr;
  ignoreElementIds_        = options_.retrieve("ignore_element_ids") != nullptr;

  if (options_.retrieve("64-bit") != nullptr) {
    ints64bit_ = true;
  }

  if (options_.retrieve("szip") != nullptr) {
    szip_ = true;
    zlib_ = false;
  }
  zlib_ = (options_.retrieve("zlib") != nullptr);

  if (szip_ && zlib_) {
    fmt::print(stderr, "ERROR: Only one of 'szip' or 'zlib' can be specified.\n");
  }

  compressionLevel_ = options_.get_option_value("compress", compressionLevel_);

  if (options_.retrieve("match_node_ids") != nullptr) {
    matchNodeIds_ = true;
    matchNodeXYZ_ = false;
  }
  else {
    matchNodeIds_ = false;
  }

  if (options_.retrieve("match_node_coordinates") != nullptr) {
    matchNodeXYZ_ = true;
    matchNodeIds_ = false;
  }
  else {
    matchNodeXYZ_ = false;
  }

#if 0
  if (options_.retrieve("match_elem_ids")) {
    matchElemIds_ = true;
    matchElemXYZ_ = false;
  } else {
    matchElemIds_ = false;
  }

  if (options_.retrieve("match_elem_coordinates")) {
    matchElemXYZ_ = true;
    matchElemIds_ = false;
  } else {
    matchElemXYZ_ = false;
  }
#endif

  return true;
}

bool SystemInterface::convert_nodes_to_nodesets(int part_number) const
{
  if (nodesetConvertParts_.empty()) {
    return false;
  }
  if (nodesetConvertParts_[0] == 0) {
    return true;
  }
  else {
    return std::find(nodesetConvertParts_.cbegin(), nodesetConvertParts_.cend(), part_number) !=
           nodesetConvertParts_.cend();
  }
}

void SystemInterface::parse_step_option(const char *tokens)
{
  //: The defined formats for the count attribute are:<br>
  //:  <ul>
  //:    <li><missing> -- default -- 1 <= count <= oo  (all steps)</li>
  //:    <li>"X"                  -- X <= count <= X  (just step X). If X == LAST, last step
  // only</li>
  //:    <li>"X:Y"                -- X to Y by 1</li>
  //:    <li>"X:"                 -- X to oo by 1</li>
  //:    <li>":Y"                 -- 1 to Y by 1</li>
  //:    <li>"::Z"                -- 1 to oo by Z</li>
  //:    <li>"LAST"               -- last step only</li>
  //:  </ul>
  //: The count and step must always be >= 0

  // Break into tokens separated by ":"

  // Default is given in constructor above...

  if (tokens != nullptr) {
    if (strchr(tokens, ':') != nullptr) {
      // The string contains a separator

      int vals[3];
      vals[0] = stepMin_;
      vals[1] = stepMax_;
      vals[2] = stepInterval_;

      int j = 0;
      for (auto &val : vals) {
        // Parse 'i'th field
        char tmp_str[128];
        ;
        int k = 0;

        while (tokens[j] != '\0' && tokens[j] != ':') {
          tmp_str[k++] = tokens[j++];
        }

        tmp_str[k] = '\0';
        if (strlen(tmp_str) > 0) {
          val = strtoul(tmp_str, nullptr, 0);
        }

        if (tokens[j++] == '\0') {
          break; // Reached end of string
        }
      }
      stepMin_      = abs(vals[0]);
      stepMax_      = abs(vals[1]);
      stepInterval_ = abs(vals[2]);
    }
    else if (str_equal("LAST", tokens)) {
      stepMin_ = stepMax_ = -1;
    }
    else {
      // Does not contain a separator, min == max
      stepMin_ = stepMax_ = strtol(tokens, nullptr, 0);
    }
  }
}

void SystemInterface::show_version()
{
  fmt::print("EJoin\n"
             "\t(A code for merging Exodus databases; with or without results data.)\n"
             "\t(Version: {}) Modified: {}\n",
             qainfo[2], qainfo[1]);
}

namespace {
  std::string LowerCase(const std::string &name)
  {
    std::string s = name;
    std::transform(s.begin(), s.end(), // source
                   s.begin(),          // destination
                   ::tolower);         // operation
    return s;
  }

  using StringVector = std::vector<std::string>;
  void parse_variable_names(const char *tokens, StringIdVector *variable_list)
  {
    // Break into tokens separated by ","
    if (tokens != nullptr) {
      std::string  token_string(tokens);
      StringVector var_list = SLIB::tokenize(token_string, ",");

      // At this point, var_list is either a single string, or a string
      // separated from 1 or more block ids with ":" delimiter.
      // For example, sigxx:1:10:100 would indicate that the variable
      // "sigxx" should be written only for blocks with id 1, 10, and
      // 100.  "sigxx" would indicate that the variable should be
      // written for all blocks.
      auto I = var_list.begin();
      while (I != var_list.end()) {
        StringVector name_id  = SLIB::tokenize(*I, ":");
        std::string  var_name = LowerCase(name_id[0]);
        if (name_id.size() == 1) {
          (*variable_list).emplace_back(var_name, 0);
        }
        else {
          for (size_t i = 1; i < name_id.size(); i++) {
            // Convert string to integer...
            int id = std::stoi(name_id[i]);
            (*variable_list).emplace_back(var_name, id);
          }
        }
        ++I;
      }
      // Sort the list...
      std::sort(
          variable_list->begin(), variable_list->end(),
          [](const std::pair<std::string, size_t> &t1, const std::pair<std::string, size_t> &t2) {
            return t1.first < t2.first || (!(t2.first < t1.first) && t1.second < t2.second);
          });
    }
  }

  void parse_offset(const char *tokens, vector3d *offset)
  {
    // Break into tokens separated by ","
    if (tokens != nullptr) {
      std::string  token_string(tokens);
      StringVector var_list = SLIB::tokenize(token_string, ",");

      // At this point, var_list should contain 1,2,or 3 strings
      // corresponding to the x, y, and z coordinate offsets.
      if (var_list.size() != 3) {
        fmt::print(stderr,
                   "ERROR: Incorrect number of offset components specified--3 required.\n\n");
        offset->x = offset->y = offset->z = 0.0;
        return;
      }

      std::string offx = var_list[0];
      std::string offy = var_list[1];
      std::string offz = var_list[2];
      double      x    = std::stod(offx);
      double      y    = std::stod(offy);
      double      z    = std::stod(offz);

      offset->x = x;
      offset->y = y;
      offset->z = z;
    }
  }

  void parse_integer_list(const char *tokens, std::vector<int> *list)
  {
    // Break into tokens separated by ","
    if (tokens != nullptr) {
      if (LowerCase(tokens) == "all") {
        (*list).push_back(0);
        return;
      }

      std::string  token_string(tokens);
      StringVector part_list = SLIB::tokenize(token_string, ",");

      auto I = part_list.begin();
      while (I != part_list.end()) {
        int id = std::stoi(*I);
        (*list).push_back(id);
        ++I;
      }
    }
  }

  void parse_part_list(const char *tokens, std::vector<int> *list)
  {
    // Break into tokens separated by ","
    // Tokens will be of the form "p$" or "all"
    if (tokens != nullptr) {
      if (LowerCase(tokens) == "all") {
        (*list).push_back(0);
        return;
      }

      std::string  token_string(tokens);
      StringVector part_list = SLIB::tokenize(token_string, ",");

      auto I = part_list.begin();
      while (I != part_list.end()) {
        std::string part = *I;
        if (part[0] == 'p' || part[0] == 'P') {
          std::string part_id(part, 1);
          int         part_num = std::stoi(part_id);
          list->push_back(part_num);
        }
        else {
          fmt::print(stderr,
                     "ERROR: Bad syntax ({}) specifying part number. Use 'p'+ part_number\n"
                     "       For example -info_records p1,p2,p7\n",
                     part);
          exit(EXIT_FAILURE);
        }
        ++I;
      }
    }
  }

  void parse_omissions(const char *tokens, Omissions *omissions, const std::string &basename,
                       bool require_ids)
  {
    //  to Omit block id 1,3,4 from part 1; block 2 3 4 from part 2;
    //  and block 8 from part5, specify
    // '-omit_blocks p1:1:3:4,p2:2:3:4,p5:8'

    // Break into tokens separated by "," Each token will then be a
    // ":" separated list of blocks to be omitted for the specified
    // part.

    // If "require_ids" is true, then there must be at least one id
    // following the part specification.  If false, then it is OK to
    // just specify a part number and all entities (typically nset or
    // sset) will be omitted on that part.

    if (tokens == nullptr) {
      return;
    }

    std::string  token_string(tokens);
    StringVector part_block_list = SLIB::tokenize(token_string, ",");

    // Now, for each token in 'part_block_list', split by ":"
    // The result should be a string starting with 'p' followed by an
    // integer indicating the part followed by 1 or more strings which
    // are the block ids of the blocks to be omitted for that part.
    //
    // Parts are 1-based.  Store the results in the 'omissions' set as
    // the pair (part#, block_id).
    auto I = part_block_list.begin();
    while (I != part_block_list.end()) {
      StringVector part_block = SLIB::tokenize(*I, ":");
      if (part_block.empty() || (part_block[0][0] != 'p' && part_block[0][0] != 'P')) {
        fmt::print(stderr, "ERROR: Bad syntax specifying the part number.  Use 'p' + part number\n"
                           "       For example -omit_blocks p1:1:2:3,p2:2:3:4\n");
        exit(EXIT_FAILURE);
      }
      if (require_ids && part_block.size() == 1) {
        fmt::print(stderr,
                   "ERROR: No block ids were found following the part specification.\n"
                   "       for part {}\n",
                   part_block[0]);
        exit(EXIT_FAILURE);
      }

      // Extract the part number...
      std::string part(part_block[0], 1);
      int         part_num = std::stoi(part) - 1;

      // If no blocks specified for a part, then omit all entities for
      // this part.  Since don't know how many entities there are,
      // store the id as '0' to signify all.
      if (part_block.size() == 1) {
        (*omissions)[part_num].emplace_back("ALL");
      }
      else {
        // Get the list of blocks to omit for this part...
        auto J = part_block.begin();
        ++J; // Skip p#
        while (J != part_block.end()) {
          std::string block = *J;
          std::string name  = basename + '_' + block;
          (*omissions)[part_num].push_back(name);
          ++J;
        }
      }
      ++I;
    }
  }
} // namespace
