property.cc

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/*
 * Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org)
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 *
 */
 
// Standard includes
#include <algorithm>
#include <cstring>
#include <fstream>
#include <iomanip>
#include <iostream>
#include <iterator>
#include <stack>
#include <stdexcept>
#include <string>
 
// Third party includes
#include <boost/algorithm/string.hpp>
#include <boost/format.hpp>
#include <expat.h>
#include <unistd.h>
#include <vector>
 
// Local VOTCA includes
#include "votca/tools/colors.h"
#include "votca/tools/property.h"
#include "votca/tools/propertyiomanipulator.h"
#include "votca/tools/tokenizer.h"
 
namespace votca {
namespace tools {
using namespace std;
// ostream modifier defines the output format, level, indentation
const Index Property::IOindex = std::ios_base::xalloc();
 
const Property &Property::get(const string &key) const {
  Tokenizer tok(key, ".");
  Tokenizer::iterator n = tok.begin();
  if (n == tok.end()) {
    return *this;
  }
 
  const Property *p;
  map<string, std::vector<Index>>::const_iterator iter;
  if (*n == "") {
    p = this;
  } else {
    iter = map_.find(*n);
    if (iter == map_.end()) {
      throw std::runtime_error("property not found: " + key);
    }
    p = &properties_[iter->second.back()];
  }
  ++n;
  try {
    for (; n != tok.end(); ++n) {
      p = &p->get(*n);
    }
  } catch (std::runtime_error &) {  // catch here to get full key in
                                    // exception
    throw std::runtime_error("property not found: " + key);
  }
 
  return *p;
}
 
Property &Property::get(const string &key) {
  return const_cast<Property &>(static_cast<const Property &>(*this).get(key));
}
 
Property &Property::set(const std::string &key, const std::string &value) {
  Property &p = get(key);
  p.value() = value;
  return p;
}
 
Property &Property::addTree(const std::string &key, const std::string &value) {
  return addTree(Tokenizer(key, ".").ToVector(), value);
}
 
Property &Property::addTree(const std::vector<std::string> &key,
                            const std::string &value) {
 
  if (key.size() == 1) {
    return add(key[0], value);
  } else {
    std::vector<std::string> subkey(key.begin() + 1, key.end());
    if (this->exists(key[0])) {
      return this->get(key[0]).addTree(subkey, value);
    } else {
      return this->add(key[0], "").addTree(subkey, value);
    }
  }
}
 
Property &Property::add(const std::string &key, const std::string &value) {
  std::string path = path_;
  if (path != "") {
    path = path + ".";
  }
  properties_.push_back(Property(key, value, path + name_));
  map_[key].push_back(Index(properties_.size()) - 1);
  return properties_.back();
}
 
bool Property::hasAttribute(const std::string &attribute) const {
  return attributes_.find(attribute) != attributes_.end();
}
 
bool Property::exists(const std::string &key) const {
  try {
    get(key);
  } catch (std::exception &) {
    return false;
  }
  return true;
}
 
void FixPath(tools::Property &prop, std::string path) {
  prop.path() = path;
  if (path != "") {
    path += ".";
  }
  path += prop.name();
  for (tools::Property &child : prop) {
    FixPath(child, path);
  }
}
 
Property &Property::add(const Property &other) {
 
  properties_.push_back(other);
  map_[other.name()].push_back((properties_.size()) - 1);
 
  std::string path = path_;
  if (path != "") {
    path += ".";
  }
  path += name_;
  FixPath(properties_.back(), path);
  return properties_.back();
}
 
Property &Property::getOradd(const std::string &key) {
  if (exists(key)) {
    return get(key);
  } else {
    return addTree(key, "");
  }
}
 
std::vector<const Property *> Property::Select(const string &filter) const {
  Tokenizer tok(filter, ".");
  std::vector<const Property *> selection;
  if (tok.begin() == tok.end()) {
    return selection;
  }
  selection.push_back(this);
  for (const auto &n : tok) {
    std::vector<const Property *> selected;
    for (const Property *p : selection) {
      for (const Property &child : *p) {
        if (wildcmp(n, child.name())) {
          selected.push_back(&child);
        }
      }
    }
    selection = selected;
  }
  return selection;
}
 
std::vector<Property *> Property::Select(const string &filter) {
  Tokenizer tok(filter, ".");
  std::vector<Property *> selection;
  if (tok.begin() == tok.end()) {
    return selection;
  }
  selection.push_back(this);
  for (const auto &n : tok) {
    std::vector<Property *> selected;
    for (Property *p : selection) {
      for (Property &child : *p) {
        if (wildcmp(n, child.name())) {
          selected.push_back(&child);
        }
      }
    }
    selection = selected;
  }
  return selection;
}
 
void Property::deleteAttribute(const std::string &attribute) {
  attributes_.erase(attribute);
}
 
static void start_hndl(void *data, const char *el, const char **attr) {
  stack<Property *> *property_stack =
      (stack<Property *> *)XML_GetUserData((XML_Parser *)data);
 
  Property *cur = property_stack->top();
  Property &np = cur->add(el, "");
 
  for (Index i = 0; attr[i]; i += 2) {
    np.setAttribute(attr[i], attr[i + 1]);
  }
 
  property_stack->push(&np);
}
 
static void end_hndl(void *data, const char *) {
  stack<Property *> *property_stack =
      (stack<Property *> *)XML_GetUserData((XML_Parser *)data);
  property_stack->pop();
}
 
void char_hndl(void *data, const char *txt, int txtlen) {
  stack<Property *> *property_stack =
      (stack<Property *> *)XML_GetUserData((XML_Parser *)data);
 
  Property *cur = property_stack->top();
  cur->value().append(txt, txtlen);
}
 
void Property::LoadFromXML(string filename) {
  ifstream fl;
  fl.open(filename);
  if (!fl.is_open()) {
    throw std::ios_base::failure("Error on open xml file: " + filename);
  }
 
  XML_Parser parser = XML_ParserCreate(nullptr);
  if (!parser) {
    throw std::runtime_error("Couldn't allocate memory for xml parser");
  }
 
  XML_UseParserAsHandlerArg(parser);
  XML_SetElementHandler(parser, start_hndl, end_hndl);
  XML_SetCharacterDataHandler(parser, char_hndl);
 
  stack<Property *> pstack;
  pstack.push(this);
 
  XML_SetUserData(parser, (void *)&pstack);
  while (!fl.eof()) {
    string line;
    tools::getline(fl, line);
    line = line + "\n";
    if (line.length() > (size_t)std::numeric_limits<int>::max()) {
      throw std::runtime_error("Property::LoadFromXML: line is too long");
    }
    if (!XML_Parse(parser, line.c_str(), (int)line.length(), fl.eof())) {
      // expat 2.9 deprecates XML_GetCurrentLineNumber for the 64-bit variant
#if XML_MAJOR_VERSION > 2 || (XML_MAJOR_VERSION == 2 && XML_MINOR_VERSION >= 9)
      const auto line_number = XML_GetCurrentLineNumber64(parser);
#else
      const auto line_number = XML_GetCurrentLineNumber(parser);
#endif
      throw std::ios_base::failure(filename + ": Parse error at line " +
                                   boost::lexical_cast<string>(line_number) +
                                   "\n" +
                                   XML_ErrorString(XML_GetErrorCode(parser)));
    }
  }
  fl.close();
  XML_ParserFree(parser);
}
 
void PrintNodeTXT(std::ostream &out, const Property &p, const Index start_level,
                  Index level = 0, string prefix = "", string offset = "") {
  if ((p.value() != "") || p.HasChildren()) {
    if (level >= start_level) {
      if ((p.value()).find_first_not_of("\t\n ") != std::string::npos) {
        out << offset << prefix << " = " << p.value() << endl;
      }
    } else {
      prefix = "";
    }
  }
 
  for (const Property &prop : p) {
    level++;
    if (prefix == "") {
      PrintNodeTXT(out, prop, start_level, level, prefix + prop.name(), offset);
    } else {
      PrintNodeTXT(out, prop, start_level, level, prefix + "." + prop.name(),
                   offset);
    }
    level--;
  }
}
 
void PrintNodeXML(std::ostream &out, const Property &p,
                  PropertyIOManipulator *piom, Index level = 0,
                  string offset = "") {
  Property::const_AttributeIterator ia;
  bool linebreak = true;
  bool has_value = false;
 
  const ColorSchemeBase *color = &DEFAULT_COLORS;
 
  string indent("");
  Index start_level(0);
 
  if (piom) {
    start_level = piom->getLevel();
    indent = piom->getIndentation();
    color = piom->getColorScheme();
  }
 
  string cKey = color->Magenta();
  string cAttribute = color->Blue();
  string cAttributeValue = color->Green();
  string cReset = color->Reset();
 
  // print starting only from the start_level (the first node (level 0) can be
  // <> </>)
  if (level >= start_level) {
    // print the node name
    out << indent << offset << "<" << cKey << p.name() << cReset;
    // print the node attributes
    for (ia = p.firstAttribute(); ia != p.lastAttribute(); ++ia) {
      out << " " << cAttribute << ia->first << cReset << "=\""
          << cAttributeValue << ia->second << cReset << "\"";
    }
    // print node value if it is not empty
    has_value = ((p.value()).find_first_not_of("\t\n ") != std::string::npos);
    if (has_value || p.HasChildren()) {
      out << ">";
    } else {
      out << "/>" << std::endl;
    }
    if (has_value) {
      out << cAttributeValue << p.value() << cReset;
      linebreak = false;
    }
 
    // check if we need the end of the line or not
    if (!has_value && p.HasChildren()) {
      out << std::endl;
    }
    if (!has_value && !p.HasChildren()) {
      linebreak = false;
    }
  }
 
  // continue iteratively through the rest of the nodes
  for (const Property &prop : p) {
    level++;
    if (level > start_level) {
      offset += "\t";
    }
    PrintNodeXML(out, prop, piom, level, offset);
    if (level > start_level) {
      offset.resize(offset.size() - 1);
    }
    level--;
  }
 
  if (level >= start_level) {
    if (linebreak) {
      out << indent << offset << "</" << cKey << p.name() << cReset << ">"
          << std::endl;
    } else if (has_value) {
      out << "</" << cKey << p.name() << cReset << ">" << std::endl;
    }
  }
}
 
void PrintNodeHLP(std::ostream &out, const Property &p,
                  const Index start_level = 0, Index level = 0,
                  const string &prefix = "", const string &offset = "") {
 
  Color<csRGB> RGB;  // Using RGB palette
  string fmt = "t|%1%%|15t|" + string(RGB.Blue()) + "%2%" +
               string(RGB.Green()) + "%|40t|%3%%|55t|" + string(RGB.Reset()) +
               "%4%\n";
 
  Index leveloffset = level;
  string help("");
  // if this is the head node, print the header
  if (level == start_level) {
    string head_name = string(RGB.Magenta()) + p.name();
    if (p.hasAttribute("help")) {
      if (p.hasAttribute("help")) {
        help = string(RGB.Red()) + p.getAttribute<string>("help");
      }
      out << boost::format(" %1%: %|18t| %2%" + string(RGB.Reset()) + "\n") %
                 head_name % help;
    }
    leveloffset = 0;
    out << boost::format("%|3" + fmt) % "OPTION" % "DEFAULT" % "UNIT" %
               "DESCRIPTION";
  }
 
  if (level > start_level) {
    string ofmt = "%|" + boost::lexical_cast<string>(leveloffset) + fmt;
    string unit("");
    if (p.hasAttribute("unit")) {
      unit = p.getAttribute<string>("unit");
    }
    string defaults("");
    if (p.hasAttribute("default")) {
      defaults = p.getAttribute<string>("default");
    }
    if (p.hasAttribute("help")) {
      help = p.getAttribute<string>("help");
    }
    if (!unit.empty()) {
      unit = "[" + unit + "]";
    }
    if (!defaults.empty()) {
      defaults = "(" + defaults + ")";
    }
 
    string name = p.name();
 
    out << boost::format(ofmt) % name % defaults % unit % help;
  }
 
  for (const Property &pp : p) {
    level++;
    if (prefix == "") {
      PrintNodeHLP(out, pp, start_level, level, pp.name(), offset);
    } else {
      PrintNodeHLP(out, pp, start_level, level, prefix + "." + pp.name(),
                   offset);
    }
    level--;
  }
}
 
std::ostream &operator<<(std::ostream &out, const Property &p) {
  if (!out.good()) {
    return out;
  }
 
  std::ostream::sentry sentry(out);
 
  if (sentry) {
    // get the property format object attached to the stream
    PropertyIOManipulator *pm =
        (PropertyIOManipulator *)out.pword(int(Property::getIOindex()));
 
    string indentation("");
    Index level = 0;
 
    PropertyIOManipulator::Type type = PropertyIOManipulator::XML;
    if (pm) {
      indentation = pm->getIndentation();
      level = pm->getLevel();
      type = pm->getType();
      // check if we > or >> to a file and remove color codes
      // if ( out.tellp() != -1 )  - not suitable for pipes
      if (!isatty(STDOUT_FILENO) || !isatty(STDERR_FILENO)) {
        pm->setColorScheme<csDefault>();
      }
    }
 
    switch (type) {
      default:
        PrintNodeTXT(out, p, level);
        break;
      case PropertyIOManipulator::XML:
        PrintNodeXML(out, p, pm);
        break;
      case PropertyIOManipulator::TXT:
        PrintNodeTXT(out, p, level, 0, "", indentation);
        break;
      case PropertyIOManipulator::HLP:
        PrintNodeHLP(out, p, level, 0, "", indentation);
        break;
    }
  }
 
  return out;
}
}  // namespace tools
}  // namespace votca