/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.bin.argparser;

import java.io.File;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.EnumSet;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;
import java.util.Map;

import jalview.bin.Console;
import jalview.bin.Jalview;
import jalview.bin.argparser.Arg.Opt;
import jalview.util.FileUtils;

public class ArgParser
{
  protected static final String DOUBLEDASH = "--";

  protected static final String NEGATESTRING = "no";

  // the default linked id prefix used for no id (not even square braces)
  protected static final String DEFAULTLINKEDIDPREFIX = "JALVIEW:";

  // the counter added to the default linked id prefix
  private int defaultLinkedIdCounter = 0;

  // the linked id prefix used for --opennew files
  protected static final String OPENNEWLINKEDIDPREFIX = "OPENNEW:";

  // the counter added to the default linked id prefix
  private int opennewLinkedIdCounter = 0;

  // the linked id used to increment the idCounter (and use the incremented
  // value)
  private static final String INCREMENTAUTOCOUNTERLINKEDID = "{++n}";

  // the linked id used to use the idCounter
  private static final String AUTOCOUNTERLINKEDID = "{n}";

  private int idCounter = 0;

  // flag to say whether {n} subtitutions in output filenames should be made.
  // Turn on and off with --subs and --nosubs
  private boolean substitutions = false;

  protected static final Map<String, Arg> argMap;

  protected Map<String, ArgValuesMap> linkedArgs = new HashMap<>();

  protected List<String> linkedOrder = null;

  protected List<Arg> argList;

  static
  {
    argMap = new HashMap<>();
    for (Arg a : EnumSet.allOf(Arg.class))
    {
      for (String argName : a.getNames())
      {
        if (argMap.containsKey(argName))
        {
          Console.warn("Trying to add argument name multiple times: '"
                  + argName + "'"); // RESTORE THIS WHEN MERGED
          if (argMap.get(argName) != a)
          {
            Console.error(
                    "Trying to add argument name multiple times for different Args: '"
                            + argMap.get(argName).getName() + ":" + argName
                            + "' and '" + a.getName() + ":" + argName
                            + "'");
          }
          continue;
        }
        argMap.put(argName, a);
      }
    }
  }

  public ArgParser(String[] args)
  {
    // Make a mutable new ArrayList so that shell globbing parser works.
    // (When shell file globbing is used, there are a sequence of non-Arg
    // arguments (which are the expanded globbed filenames) that need to be
    // consumed by the --open/--argfile/etc Arg which is most easily done by
    // removing these filenames from the list one at a time. This can't be done
    // with an ArrayList made with only Arrays.asList(String[] args). )
    this(new ArrayList<>(Arrays.asList(args)));
  }

  public ArgParser(List<String> args)
  {
    parse(args);
  }

  private void parse(List<String> args)
  {
    int argIndex = 0;
    boolean openEachInitialFilenames = true;
    for (int i = 0; i < args.size(); i++)
    {
      String arg = args.get(i);

      Console.debug("##### Looking at arg '" + arg + "'");

      // If the first arguments do not start with "--" or "-" or is "open" and
      // is a filename that exists it is probably a file/list of files to open
      // so we fake an Arg.OPEN argument and when adding files only add the
      // single arg[i] and increment the defaultLinkedIdCounter so that each of
      // these files is opened separately.
      if (openEachInitialFilenames && !arg.startsWith(DOUBLEDASH)
              && !arg.startsWith("-") && new File(arg).exists())
      {
        arg = DOUBLEDASH + Arg.OPENNEW.getName();
      }
      else
      {
        openEachInitialFilenames = false;
      }

      String argName = null;
      String val = null;
      List<String> vals = null; // for Opt.GLOB only
      String linkedId = null;
      if (arg.startsWith(DOUBLEDASH))
      {
        int equalPos = arg.indexOf('=');
        if (equalPos > -1)
        {
          argName = arg.substring(DOUBLEDASH.length(), equalPos);
          val = arg.substring(equalPos + 1);
        }
        else
        {
          argName = arg.substring(DOUBLEDASH.length());
        }
        int idOpen = argName.indexOf('[');
        int idClose = argName.indexOf(']');

        if (idOpen > -1 && idClose == argName.length() - 1)
        {
          linkedId = argName.substring(idOpen + 1, idClose);
          argName = argName.substring(0, idOpen);
        }

        Arg a = argMap.get(argName);
        // check for boolean prepended by "no"
        boolean negated = false;
        if (a == null && argName.startsWith(NEGATESTRING) && argMap
                .containsKey(argName.substring(NEGATESTRING.length())))
        {
          argName = argName.substring(NEGATESTRING.length());
          a = argMap.get(argName);
          negated = true;
        }

        // check for config errors
        if (a == null)
        {
          // arg not found
          Console.error("Argument '" + arg + "' not recognised. Ignoring.");
          continue;
        }
        if (!a.hasOption(Opt.BOOLEAN) && negated)
        {
          // used "no" with a non-boolean option
          Console.error("Argument '--" + NEGATESTRING + argName
                  + "' not a boolean option. Ignoring.");
          continue;
        }
        if (!a.hasOption(Opt.STRING) && equalPos > -1)
        {
          // set --argname=value when arg does not accept values
          Console.error("Argument '--" + argName
                  + "' does not expect a value (given as '" + arg
                  + "').  Ignoring.");
          continue;
        }
        if (!a.hasOption(Opt.LINKED) && linkedId != null)
        {
          // set --argname[linkedId] when arg does not use linkedIds
          Console.error("Argument '--" + argName
                  + "' does not expect a linked id (given as '" + arg
                  + "'). Ignoring.");
          continue;
        }

        if (a.hasOption(Opt.STRING) && equalPos == -1)
        {
          // take next arg as value if required, and '=' was not found
          // if (!argE.hasMoreElements())
          if (i + 1 >= args.size())
          {
            // no value to take for arg, which wants a value
            Console.error("Argument '" + a.getName()
                    + "' requires a value, none given. Ignoring.");
            continue;
          }
          // deal with bash globs here (--arg val* is expanded before reaching
          // the JVM). Note that SubVals cannot be used in this case.
          // If using the --arg=val then the glob is preserved and Java globs
          // will be used later. SubVals can be used.
          if (a.hasOption(Opt.GLOB))
          {
            // if this is the first argument with a file list at the start of
            // the args we add filenames from index i instead of i+1
            vals = getShellGlobbedFilenameValues(a, args,
                    openEachInitialFilenames ? i : i + 1);
          }
          else
          {
            val = args.get(i + 1);
          }
        }

        // make NOACTION adjustments
        // default and auto counter increments
        if (a == Arg.INCREMENT)
        {
          defaultLinkedIdCounter++;
        }
        else if (a == Arg.NPP)
        {
          idCounter++;
        }
        else if (a == Arg.SUBSTITUTIONS)
        {
          substitutions = !negated;
        }

        String autoCounterString = null;
        boolean usingAutoCounterLinkedId = false;
        String defaultLinkedId = new StringBuilder(DEFAULTLINKEDIDPREFIX)
                .append(Integer.toString(defaultLinkedIdCounter))
                .toString();
        boolean usingDefaultLinkedId = false;
        if (a == Arg.OPENNEW)
        {
          linkedId = new StringBuilder(OPENNEWLINKEDIDPREFIX)
                  .append(Integer.toString(opennewLinkedIdCounter))
                  .toString();
          opennewLinkedIdCounter++;
        }
        else if (a.hasOption(Opt.LINKED))
        {
          if (linkedId == null)
          {
            // use default linkedId for linked arguments
            linkedId = defaultLinkedId;
            usingDefaultLinkedId = true;
            Console.debug(
                    "Changing linkedId to '" + linkedId + "' from " + arg);
          }
          else if (linkedId.equals(AUTOCOUNTERLINKEDID))
          {
            // turn {n} to the autoCounter
            autoCounterString = Integer.toString(idCounter);
            linkedId = autoCounterString;
            usingAutoCounterLinkedId = true;
            Console.debug(
                    "Changing linkedId to '" + linkedId + "' from " + arg);
          }
          else if (linkedId.equals(INCREMENTAUTOCOUNTERLINKEDID))
          {
            // turn {++n} to the incremented autoCounter
            autoCounterString = Integer.toString(++idCounter);
            linkedId = autoCounterString;
            usingAutoCounterLinkedId = true;
            Console.debug(
                    "Changing linkedId to '" + linkedId + "' from " + arg);
          }
        }

        if (!linkedArgs.containsKey(linkedId))
          linkedArgs.put(linkedId, new ArgValuesMap());

        // do not continue for NOACTION args
        if (a.hasOption(Opt.NOACTION))
          continue;

        ArgValuesMap avm = linkedArgs.get(linkedId);

        // not dealing with both NODUPLICATEVALUES and GLOB
        if (a.hasOption(Opt.NODUPLICATEVALUES) && avm.hasValue(a, val))
        {
          Console.error("Argument '--" + argName
                  + "' cannot contain a duplicate value ('" + val
                  + "'). Ignoring this and subsequent occurrences.");
          continue;
        }

        // check for unique id
        SubVals sv = ArgParser.getSubVals(val);
        String id = sv.get(ArgValues.ID);
        if (id != null && avm.hasId(a, id))
        {
          Console.error("Argument '--" + argName + "' has a duplicate id ('"
                  + id + "'). Ignoring.");
          continue;
        }

        boolean argIndexIncremented = false;
        ArgValues avs = avm.getOrCreateArgValues(a);

        // store appropriate value
        if (a.hasOption(Opt.STRING))
        {
          if (a.hasOption(Opt.GLOB) && vals != null && vals.size() > 0)
          {
            for (String v : vals)
            {
              avs.addValue(makeSubstitutions(v), argIndex++);
              argIndexIncremented = true;
            }
          }
          else
          {
            avs.addValue(makeSubstitutions(val), argIndex);
          }
        }
        else if (a.hasOption(Opt.BOOLEAN))
        {
          avs.setBoolean(!negated, argIndex);
          avs.setNegated(negated);
        }
        else if (a.hasOption(Opt.UNARY))
        {
          avs.setBoolean(true, argIndex);
        }
        avs.incrementCount();
        if (!argIndexIncremented)
          argIndex++;

        // store in appropriate place
        if (a.hasOption(Opt.LINKED))
        {
          // store the order of linkedIds
          if (linkedOrder == null)
            linkedOrder = new ArrayList<>();
          if (!linkedOrder.contains(linkedId))
            linkedOrder.add(linkedId);
        }

        // store arg in the list of args used
        if (argList == null)
          argList = new ArrayList<>();
        if (!argList.contains(a))
          argList.add(a);
      }
    }
  }

  private String makeSubstitutions(String val)
  {
    if (!this.substitutions)
      return val;

    String subvals;
    String rest;
    if (val.indexOf('[') == 0 && val.indexOf(']') > 1)
    {
      int closeBracket = val.indexOf(']');
      if (val.length() == closeBracket)
        return val;
      subvals = val.substring(0, closeBracket + 1);
      rest = val.substring(closeBracket + 1);
    }
    else
    {
      subvals = "";
      rest = val;
    }
    rest.replace(AUTOCOUNTERLINKEDID, String.valueOf(idCounter));
    rest.replace(INCREMENTAUTOCOUNTERLINKEDID, String.valueOf(++idCounter));
    rest.replace("{}", String.valueOf(defaultLinkedIdCounter));

    return new StringBuilder(subvals).append(rest).toString();
  }

  /*
   * A helper method to take a list of String args where we're expecting
   * {"--previousargs", "--arg", "file1", "file2", "file3", "--otheroptionsornot"}
   * and the index of the globbed arg, here 1.  It returns a
   * List<String> {"file1", "file2", "file3"}
   * *and remove these from the original list object* so that processing
   * can continue from where it has left off, e.g. args has become
   * {"--previousargs", "--arg", "--otheroptionsornot"}
   * so the next increment carries on from the next --arg if available.
   */
  protected static List<String> getShellGlobbedFilenameValues(Arg a,
          List<String> args, int i)
  {
    List<String> vals = new ArrayList<>();
    while (i < args.size() && !args.get(i).startsWith(DOUBLEDASH))
    {
      vals.add(args.remove(i));
      if (!a.hasOption(Opt.GLOB))
        break;
    }
    return vals;
  }

  public boolean isSet(Arg a)
  {
    return a.hasOption(Opt.LINKED) ? isSet("", a) : isSet(null, a);
  }

  public boolean isSet(String linkedId, Arg a)
  {
    ArgValuesMap avm = linkedArgs.get(linkedId);
    return avm == null ? false : avm.containsArg(a);
  }

  public boolean getBool(Arg a)
  {
    if (!a.hasOption(Opt.BOOLEAN) && !a.hasOption(Opt.UNARY))
    {
      Console.warn("Getting boolean from non boolean Arg '" + a.getName()
              + "'.");
    }
    return a.hasOption(Opt.LINKED) ? getBool("", a) : getBool(null, a);
  }

  public boolean getBool(String linkedId, Arg a)
  {
    ArgValuesMap avm = linkedArgs.get(linkedId);
    if (avm == null)
      return a.getDefaultBoolValue();
    ArgValues avs = avm.getArgValues(a);
    return avs == null ? a.getDefaultBoolValue() : avs.getBoolean();
  }

  public List<String> linkedIds()
  {
    return linkedOrder;
  }

  public ArgValuesMap linkedArgs(String id)
  {
    return linkedArgs.get(id);
  }

  @Override
  public String toString()
  {
    StringBuilder sb = new StringBuilder();
    sb.append("UNLINKED\n");
    sb.append(argValuesMapToString(linkedArgs.get(null)));
    if (linkedIds() != null)
    {
      sb.append("LINKED\n");
      for (String id : linkedIds())
      {
        // already listed these as UNLINKED args
        if (id == null)
          continue;

        ArgValuesMap avm = linkedArgs(id);
        sb.append("ID: '").append(id).append("'\n");
        sb.append(argValuesMapToString(avm));
      }
    }
    return sb.toString();
  }

  private static String argValuesMapToString(ArgValuesMap avm)
  {
    if (avm == null)
      return null;
    StringBuilder sb = new StringBuilder();
    for (Arg a : avm.getArgKeys())
    {
      ArgValues v = avm.getArgValues(a);
      sb.append(v.toString());
      sb.append("\n");
    }
    return sb.toString();
  }

  public static SubVals getSubVals(String item)
  {
    return new SubVals(item);
  }

  public static ArgParser parseArgFiles(List<String> argFilenameGlobs)
  {
    List<File> argFiles = new ArrayList<>();

    for (String pattern : argFilenameGlobs)
    {
      // I don't think we want to dedup files, making life easier
      argFiles.addAll(FileUtils.getFilesFromGlob(pattern));
    }

    return parseArgFileList(argFiles);
  }

  public static ArgParser parseArgFileList(List<File> argFiles)
  {
    List<String> argsList = new ArrayList<>();
    for (File argFile : argFiles)
    {
      if (!argFile.exists())
      {
        String message = DOUBLEDASH
                + Arg.ARGFILE.name().toLowerCase(Locale.ROOT) + "=\""
                + argFile.getPath() + "\": File does not exist.";
        Jalview.exit(message, 2);
      }
      try
      {
        argsList.addAll(Files.readAllLines(Paths.get(argFile.getPath())));
      } catch (IOException e)
      {
        String message = DOUBLEDASH
                + Arg.ARGFILE.name().toLowerCase(Locale.ROOT) + "=\""
                + argFile.getPath() + "\": File could not be read.";
        Jalview.exit(message, 3);
      }
    }
    return new ArgParser(argsList);
  }

}