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+#!/bin/bash
+
+## Copyright Ian Jauslin 2015-2017
+## 
+## 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.
+
+# directory containing the engine files
+enginedir=/usr/share/BBlog/engines
+enginedir=/home/ian/Programs/BBlog2/engines
+
+# version
+version=2.1
+
+function print_config {
+  echo "engine: $engine"
+  echo "db: $db"
+  echo "conf: $conf"
+  echo "aux: $aux"
+  echo "format: $format"
+  echo "outbib: $outbib"
+  echo "order: $order" 
+  echo "aux_cmd: $aux_cmd"
+  echo "ref_map: $ref_map"
+}
+
+# defaults
+function set_defaults {
+  engine="sqlite"
+  db=""
+  conf=""
+  aux='*.aux'
+  format='\bibitem[%citeref%]{%token%}%n%%author% - {\it %title%}, %journal%, %year%.%n%'
+  outbib=''
+  order="alphabetical"
+  aux_cmd='\\citation{'
+  ref_map=''
+}
+
+# read cli args
+function read_cli {
+
+  flag=""
+  for arg in "$@"; do
+    case "$arg" in
+      "-e" )
+	flag="engine" ;;
+      "-d" )
+	flag="db" ;;
+      "-c" )
+	flag="conf" ;;
+      "-a" )
+	flag="aux" ;;
+      "-f" )
+	flag="format" ;;
+      "-b" )
+	flag="outbib" ;;
+      "-o" )
+	flag="order" ;;
+      "-A" )
+	flag="aux_cmd" ;;
+      "-F" )
+	flag="filter" ;;
+      "-r" )
+	flag="ref_map" ;;
+      # version
+      "-v" )
+	echo "$version"; exit ;;
+      * )
+	if [ -n "$flag" ]; then
+	  # treat filters differently
+	  if [ "$flag" != 'filter' ]; then
+	    eval "$flag='$arg'"
+	    # flag the variable as set
+	    eval "set_$flag=1"
+	  else
+	    field="${arg%%:*}"
+	    value="${arg#*:}"
+	    eval "filter_$field='$value'"
+	    eval "set_filter_$field=1"
+	  fi
+	  flag=""
+	fi
+    esac
+  done
+}
+
+# read config file
+function read_config {
+  extra_entries_index=0
+
+  if [ -n "$conf" ]; then
+    [ -f "$conf" ] || { echo "error: $conf: no such file" 1>&2 ; exit -1 ; }
+    while read -r confline; do
+      flag=""
+      field="${confline%%:*}"
+      value="${confline#*:}"
+      # remove spaces
+      field=$(echo "$field" | sed -r 's/ *$//')
+      value=$(echo "$value" | sed -r 's/^ *//')
+      case "$field" in
+	"engine" )
+	  flag="engine" ;;
+	"database" )
+	  flag="db" ;;
+	"aux" )
+	  flag="aux" ;;
+	"format" )
+	  flag="format" ;;
+	"out_file" )
+	  flag="outbib" ;;
+	"order" )
+	  flag="order" ;;
+	"aux_cmd" )
+	  flag="aux_cmd" ;;
+	"ref_map" )
+	  flag="ref_map" ;;
+	"filter" )
+	  # set flag to the specific filter
+	  flag="filter_${value%%:*}"
+	  # reset value
+	  value="${value#*:}" ;;
+	"extra" )
+	  extra[$extra_entries_index]="$value"
+	  extra_entries_index=$((extra_entries_index+1)) ;;
+      esac
+
+      if [ -n "$flag" ]; then
+	# check it was not set on the command line
+	eval "[ -n \"\$set_$flag\" -a \"\$set_$flag\" = 1 ] || $flag='$value'"
+      fi
+    done <"$conf"
+
+    # sort extra entries
+    if [ "$extra_entries_index" -gt 0 -a "$order" = "alphabetical" ]; then
+      IFS=$'\n' extra=($(echo "${extra[*]}" | sort -k 1,1 -t :))
+    fi
+  fi
+}
+
+# check the configuration
+function check_config {
+  # check whether the engine exists
+  [ -e "$enginedir/$engine.sh" ] || { echo "error: engine $engine not found in $enginedir" 1>&2; exit -1 ; }
+
+  # check the database and aux file
+  for file in "$db" "$aux"; do
+    [[ "$file" =~ '*' || -e "$file" ]] || { echo "error: $file: no such file" 1>&2 ; exit -1 ; }
+  done
+
+  # check the $order variable
+  [ "$order" != "alphabetical" -a "$order" != "appearance" ] && { echo "error: order should be one of 'alphabetical' or 'appearance' (read $order)" 1>&2 ; exit -1 ; }
+
+  # check for ref_map
+  [ -n "$ref_map" ] && [ ! -e "$ref_map" ] && { echo "error: $ref_map: no such file" 1>&2 ; exit -1 ; }
+}
+
+function replace_format {
+  out="$1"
+
+  # replace newlines
+  out="${out//\%n\%/\\n}"
+
+  # if the ref of the entry has been mapped, fetch the old citeref
+  if [ -n "$ref_map" ]; then
+    citeref=$(inverse_map_citeref "$citeref")
+  fi
+
+  # first search for conditionals
+  # while '|' is still in $out
+  while : ; do
+    # find next '|'
+    tmp=${out#*|}
+    # save text before '|'
+    pre=${out%%|*}
+    # check whether it was found
+    [ "$tmp" = "$out" ] && break
+    # find next '|'
+    command=${tmp%%|*}
+    # save text after '|'
+    post=${tmp#*|}
+    # check whether it was found
+    [ "$command" = "$tmp" ] && { echo "error: '|'s do not match in '$1'" 1>&2 ; exit -1 ; }
+
+    # extract field
+    field="${command%%\?*}"
+    repl="${command##*\?}"
+
+    # check whether field is empty
+    val=$(eval "echo \$$field")
+    if [ -n "$val" ]; then
+      out="$pre$repl$post"
+    else
+      out="$pre$post"
+    fi
+  done
+
+  # replace '%'
+  # while '%' is still in $out
+  while : ; do
+    # find next '%'
+    tmp=${out#*%}
+    # check whether it was found
+    [ "$tmp" = "$out" ] && break
+    # find next '%'
+    command=${tmp%%%*}
+    # check whether it was found
+    [ "$command" = "$tmp" ] && { echo "error: '%'s do not match in '$1'" 1>&2 ; exit -1 ; }
+
+    # the field entry may be followed by a filter
+    field="${command%:*}"
+    # filter
+    filter="${command##*:}"
+
+    # apply filter
+    if [ -n "$filter" ]; then
+      sed_cmd=$(eval "echo \$filter_$filter")
+      replacement=$(eval "echo \$$field" | sed -r "$sed_cmd" )
+    else
+      replacement=$(eval "echo \$$field")
+    fi
+
+    out="${out//\%$command\%/$replacement}"
+  done
+
+  # finish replacing newlines
+  out="${out//\\n/%}"
+  out=$(echo "$out" | tr "%" "\n")
+  echo "$out"
+}
+
+function escape_string {
+  str="$1"
+  str="${str//\\/\\\\}"
+  str="${str//\`/\\\`}"
+  str="${str//\"/\\\"}"
+  str="${str//\$/\\\$}"
+  echo "$str"
+}
+
+# replace a citeref according to a ref_map
+function map_citeref {
+  # check whether a ref_map was specified
+  [ -z "$ref_map" ] && { echo "$1" ; return 0 ; }
+
+  oldref="$1"
+  newref=$(echo "$oldref" | sed -r -f "$ref_map")
+  echo "$newref"
+}
+
+# find the pre-image of a citeref through the ref_map
+function inverse_map_citeref {
+  # check whether a ref_map was specified
+  [ -z "$ref_map" ] && { echo "$1" ; return 0 ; }
+
+  newref="$1"
+
+  foundref=0
+  # sift through aux file
+  grep -h "$aux_cmd" $aux | while read -r ref; do
+    eval "ref=\${ref#$aux_cmd}"
+    ref="${ref%\}}"
+    # replace the ref via the ref_map
+    possibleref=$(map_citeref "$ref")
+    # check whether the ref is the right one
+    if [ "$possibleref" = "$newref" ]; then
+      echo "$ref"
+      foundref=1
+      return 1
+    fi
+  done && echo "$foundref$newref"
+}
+
+# format entries
+function format_BBlog_entries {
+  # keep track of tokens to avoid repetitions
+  token_list=""
+
+  has_there_been_a_nonempty_line_so_far=0
+
+  while read -r line; do
+    # if line has 0 size, then new entry
+    if [ -z "$line" ]; then
+      # skip if it is the first line
+      if [ $has_there_been_a_nonempty_line_so_far = 1 ]; then
+	# check whether an extra entry precedes it
+	# alphabetical order
+	if [ "$order" = "alphabetical" ]; then
+	  old_token="$token"
+	  old_citeref="$citeref"
+	  while [[ ${#extra} -gt 0 && "${extra[0]%%:*}" < "$prauth$year" ]]; do
+	    reftokval="${extra[0]#*:}"
+	    citeref="${reftokval%%:*}"
+	    tokval="${reftokval#*:}"
+	    token="${tokval%%:*}"
+	    value="${tokval#*:}"
+	    # check whether token is unique
+	    token=$(replace_repeated_token "$token" "$token_list")
+	    # add token to list
+	    token_list="$token_list;$token"
+
+	    replace_format "$value"
+
+	    IFS=$'\n' extra=($(echo "${extra[*]:1}"))
+	  done
+	  token="$old_token"
+	  citeref="$old_citeref"
+
+	  # check whether token is unique
+	  token=$(replace_repeated_token "$token" "$token_list")
+	  # add token to list
+	  token_list="$token_list;$token"
+
+	  replace_format "$format"
+	  
+	# appearance order
+	else
+	  foundit=0
+	  if [ ${#extra} -gt 0 ]; then
+	    for entry in "${extra[@]}"; do
+	      ref="${entry#*:}"
+	      ref="${ref%%:*}"
+	      if [ "$ref" = "$citeref" ]; then
+		old_token="$token"
+		old_citeref="$citeref"
+
+		citeref="$ref"
+		token="${entry#*:*:}"
+		value="${token#*:}"
+		token="${token%%:*}"
+		# check whether token is unique
+		token=$(replace_repeated_token "$token" "$token_list")
+		# add token to list
+		token_list="$token_list;$token"
+
+		replace_format "$value"
+
+		token="$old_token"
+		citeref="$old_citeref"
+		foundit=1
+		break
+	      fi
+	    done
+	  fi
+
+	  if [ $foundit = 0 ]; then
+	    # check whether token is unique
+	    token=$(replace_repeated_token "$token" "$token_list")
+	    # add token to list
+	    token_list="$token_list;$token"
+
+	    replace_format "$format"
+	  fi
+	fi
+      fi
+      has_there_been_a_nonempty_line_so_far=0
+    else
+      eval "$line"
+      has_there_been_a_nonempty_line_so_far=1
+    fi
+  done
+
+  # add remaining extra entries (only for alphabetical order)
+  if [ "$order" = "alphabetical" ]; then
+    while [ ${#extra} -gt 0 ]; do
+      reftokval="${extra[0]#*:}"
+      citeref="${reftokval%%:*}"
+      tokval="${reftokval#*:}"
+      token="${tokval%%:*}"
+      value="${tokval#*:}"
+      # check whether token is unique
+      token=$(replace_repeated_token "$token" "$token_list")
+      # add token to list
+      token_list="$token_list;$token"
+
+      replace_format "$value"
+      IFS=$'\n' extra=($(echo "${extra[*]:1}"))
+    done
+  fi
+}
+
+# replace a token that already exists
+function replace_repeated_token {
+  token="$1"
+  list="$2"
+
+  out="$token"
+  i=0
+  while $(echo "$token_list;" | grep -q ";$out;"); do
+    i=$((i+1))
+    out="$token"$(alpha_number $i)
+  done
+
+  echo "$out"
+}
+
+# convert an integer to base 26
+function alpha_number {
+  num="$1"
+  rem="$num"
+  out=""
+  letters=(a b c d e f g h i j k l m n o p q r s t u v w x y z)
+  while [ "$rem" -gt 0 ]; do
+    digit=$((rem-26*(rem/26)))
+    out="${letters[$digit]}$out"
+    rem=$(((rem-digit)/26))
+  done
+
+  echo "$out"
+}
+
+
+set_defaults
+read_cli "$@"
+read_config
+check_config
+source "$enginedir/$engine.sh"
+
+# check whether to order by alphabetical order or appearance
+[ "$order" = "alphabetical" ] && fetch_cmd=fetch_BBlog_entries_alpha || fetch_cmd=fetch_BBlog_entries_appearance
+
+# fetch entries
+if [ -n "$outbib" ]; then
+  "$fetch_cmd" | format_BBlog_entries > "$outbib"
+else
+  "$fetch_cmd" | format_BBlog_entries
+fi
+