#!/bin/sh

# ===========================================================================
#
#                            PUBLIC DOMAIN NOTICE
#            National Center for Biotechnology Information (NCBI)
#
#  This software/database is a "United States Government Work" under the
#  terms of the United States Copyright Act.  It was written as part of
#  the author's official duties as a United States Government employee and
#  thus cannot be copyrighted.  This software/database is freely available
#  to the public for use. The National Library of Medicine and the U.S.
#  Government do not place any restriction on its use or reproduction.
#  We would, however, appreciate having the NCBI and the author cited in
#  any work or product based on this material.
#
#  Although all reasonable efforts have been taken to ensure the accuracy
#  and reliability of the software and data, the NLM and the U.S.
#  Government do not and cannot warrant the performance or results that
#  may be obtained by using this software or data. The NLM and the U.S.
#  Government disclaim all warranties, express or implied, including
#  warranties of performance, merchantability or fitness for any particular
#  purpose.
#
# ===========================================================================
#
# File Name:  elink
#
# Author:  Jonathan Kans, Aaron Ucko
#
# Version Creation Date:   06/03/2020
#
# ==========================================================================

pth=$( dirname "$0" )

case "$pth" in
  /* )
    ;; # already absolute
  *  )
    pth=$(cd "$pth" && pwd)
    ;;
esac

case ":$PATH:" in
  *:"$pth":* )
    ;;
  * )
    PATH="$PATH:$pth"
    export PATH
    ;;
esac

# handle common flags - dot command is equivalent of "source"

if [ ! -f "$pth"/ecommon.sh ]
then
  echo "${INVT} ERROR: ${LOUD} Unable to find '$pth/ecommon.sh' file${INIT}" >&2
  exit 1
fi

. "$pth"/ecommon.sh

# initialize specific flags

internal=false

target=""

name=""
cmmd=""
mode=""

idtype=""
related=false

cited=false
cites=false

# read command-line arguments

while [ $# -gt 0 ]
do
  case "$1" in
    -internal )
      internal=true
      shift
      ;;
    -newmode | -oldmode )
      shift
      ;;
    -db )
      shift
      if [ $# -gt 0 ]
      then
        db="$1"
        shift
      else
        echo "${INVT} ERROR: ${LOUD} Missing -db argument${INIT}" >&2
        exit 1
      fi
      ;;
    -id )
      shift
      if [ $# -gt 0 ]
      then
        ids="$1"
        shift
      else
        echo "${INVT} ERROR: ${LOUD} Missing -id argument${INIT}" >&2
        exit 1
      fi
      while [ $# -gt 0 ]
      do
        case "$1" in
          -* )
            break
            ;;
          * )
            # concatenate run of UIDs with commas
            ids="$ids,$1"
            shift
            ;;
        esac
      done
      ;;
    -format )
      shift
      if [ $# -gt 0 ]
      then
        shift
        if [ "$1" = "acc" ] || [ "$1" = "accn" ]
        then
          idtype=acc
        fi
      else
        echo "${INVT} ERROR: ${LOUD} Missing -format argument${INIT}" >&2
        exit 1
      fi
      ;;
    -target )
      shift
      if [ $# -gt 0 ]
      then
        target="$1"
        shift
      else
        echo "${INVT} ERROR: ${LOUD} Missing -target argument${INIT}" >&2
        exit 1
      fi
      ;;
    -name | -linkname )
      shift
      if [ $# -gt 0 ]
      then
        name="$1"
        shift
      else
        echo "${INVT} ERROR: ${LOUD} Missing -name argument${INIT}" >&2
        exit 1
      fi
      ;;
    -cmd )
      shift
      if [ $# -gt 0 ]
      then
        cmmd="$1"
        shift
      else
        echo "${INVT} ERROR: ${LOUD} Missing -cmd argument${INIT}" >&2
        exit 1
      fi
      ;;
    -mode )
      shift
      if [ $# -gt 0 ]
      then
        mode="$1"
        shift
      else
        echo "${INVT} ERROR: ${LOUD} Missing -mode argument${INIT}" >&2
        exit 1
      fi
      ;;
    -related )
      related=true
      shift
      ;;
    -neighbor )
      related=true
      shift
      ;;
    -cited )
      cited=true
      shift
      ;;
    -cites )
      cites=true
      shift
      ;;
    -batch )
      # accept -batch flag from old scripts - now standard behavior
      shift
      ;;
    -h | -help | --help | help )
      echo "elink $version"
      echo ""
      cat "$pth/help/elink-help.txt"
      echo ""
      exit 0
      ;;
    -* )
      ParseCommonArgs "$@"
      if [ "$argsConsumed" -gt 0 ]
      then
        shift "$argsConsumed"
      else
        echo "${INVT} ERROR: ${LOUD} Unrecognized option $1${INIT}" >&2
        exit 1
      fi
      ;;
    * )
      # allows while loop to check for multiple flags
      break
      ;;
  esac
done

FinishSetup

# check for ENTREZ_DIRECT message or piped UIDs unless database and UIDs provided in command line

if [ -z "$db" ]
then
  ParseStdin
elif [ -z "$ids" ] && [ -z "$input" ]
then
  ParseStdin
fi

# needHistory allows reuse of GenerateUidList

if [ -z "$ids$rest$input" ]
then
  needHistory=true
fi

# take database from dbase value or -db argument

if [ -z "$dbase" ]
then
  dbase="$db"
fi

# check for missing required arguments

if [ -z "$dbase" ]
then
  echo "${INVT} ERROR: ${LOUD} Missing -db argument${INIT}" >&2
  exit 1
fi

# check for PubMed preview server

case "${ELINK_PREVIEW}" in
  "" | [FfNn]* | 0 | [Oo][Ff][Ff] )
    ;;
  * )
    if [ "$dbase" = "pubmed" ]
    then
      base="https://eutilspreview.ncbi.nlm.nih.gov/entrez/eutils/"
    fi
    ;;
esac

# convert spaces between UIDs to commas

ids=$( echo "$ids" | sed -e "s/ /,/g; s/,,*/,/g" )

# cmd aliases

case "$cmmd" in
  history )
    cmmd="neighbor_history"
    ;;
  score )
    cmmd="neighbor_score"
    if [ -z "$target" ]
    then
      target="$dbase"
    fi
    ;;
  llibs )
    cmmd="llinkslib"
    ;;
esac

# special cases for target, cmd, and linkname

case "$cmmd" in
  acheck )
    ;;
  ncheck | lcheck | llinks | llinkslib | prlinks )
    target=""
    ;;
  * )
    if [ -z "$target" ] && [ "$related" = false ] && [ "$cited" = false ] && [ "$cites" = false ]
    then
      echo "${INVT} ERROR: ${LOUD} Must supply -target or -related on command line${INIT}" >&2
      exit 1
    fi
    if [ -z "$target" ]
    then
      target="$dbase"
    fi

    if [ -z "$name" ]
    then
      # set default name
      name="${dbase}_${target}"
      # special case for pubmed_pmc - commented out now that the link has returned
      # if [ $name = "pubmed_pmc" ]
      # then
        # name="pubmed_pmc_local"
      # fi
    fi
    ;;
esac

if [ -z "$cmmd" ]
then
  cmmd="neighbor_history"
fi

if [ "$dbase" = "nlmcatalog" ]
then
  echo "${INVT} ERROR: ${LOUD} Entrez Direct does not support links for the nlmcatalog database${INIT}" >&2
  exit 1
fi

# input reality checks

if [ "$needHistory" = true ]
then
  if [ -t 0 ]
  then
    echo "${INVT} ERROR: ${LOUD} ENTREZ_DIRECT message not piped from stdin${INIT}" >&2
    exit 1
  fi
  if [ -z "$web_env" ]
  then
    echo "${INVT} ERROR: ${LOUD} WebEnv value not found in elink input${INIT}" >&2
    exit 1
  fi
  if [ -z "$qry_key" ]
  then
    echo "${INVT} ERROR: ${LOUD} QueryKey value not found in elink input${INIT}" >&2
    exit 1
  fi
  if [ "$num" -lt 1 ]
  then
    # print message with count of 0 if no results to process
    WriteEDirect "$target" "$web_env" "$qry_key" "0" "$stp" "$err"
    exit 0
  fi
fi

if [ "$cited" = true ] || [ "$cites" = true ]
then
  if [ "$dbase" != "pubmed" ]
  then
    echo "${INVT} ERROR: ${LOUD} -cited or -cites can only be used with -db pubmed${INIT}" >&2
    exit 1
  fi
fi

# lookup accessions in -id argument or piped from stdin

LookupSpecialAccessions

# -cited or -cites access the NIH Open Citation Collection dataset (see PMID 31600197)

PostInIcite() {

  if [ -n "$web_env" ]
  then
    epost -db pubmed -web "$web_env" -log "$log"
  else
    epost -db pubmed -log "$log"
  fi
}

LinkInIcite() {

  iciteElement="$1"
  GenerateUidList "$dbase" |
  join-into-groups-of 100 |
  while read uids
  do
    nquire -get https://icite.od.nih.gov/api/pubs -pmids "$uids" |
    transmute -j2x |
    xtract -pattern opt -sep "\n" -element "$iciteElement"
  done |
  accn-at-a-time |
  sort -n | uniq |
  PostInIcite
}

QueryIcite() {

  cits=$( LinkInIcite "$1" )

  if [ -n "$cits" ]
  then
    ParseMessage "$cits" ENTREZ_DIRECT \
                  dbase Db web_env WebEnv qry_key QueryKey \
                  num Count stp Step
  fi

  WriteEDirect "$dbase" "$web_env" "$qry_key" "$num" "$stp" "$err"
}

if [ "$cited" = true ]
then
  # equivalent of -name pubmed_pubmed_citedin (for pubmed records also in pmc)
  QueryIcite "cited_by"

  exit 0
fi

if [ "$cites" = true ]
then
  # equivalent of -name pubmed_pubmed_refs (for pubmed records also in pmc)
  QueryIcite "references"

  exit 0
fi

# helper function adds link-specific arguments (if set)

RunWithLinkArgs() {

  if [ "$log" = true ]
  then
    printf "." >&2
  fi

  AddIfNotEmpty -dbfrom "$dbase" \
  AddIfNotEmpty -db "$target" \
  AddIfNotEmpty -cmd "$cmmd" \
  AddIfNotEmpty -linkname "$name" \
  AddIfNotEmpty -retmode "$mode" \
  AddIfNotEmpty -idtype "$idtype" \
  RunWithCommonArgs "$@"
}

# non-history link requests generate XML results

if [ "$cmmd" != "neighbor_history" ]
then
  GenerateUidList "$dbase" |
  join-into-groups-of 500 |
  while read uids
  do
    uids=$( echo "$uids" | tr ',' ' ' )
    set nquire -url "$base" elink.fcgi
    # $uids is unquoted so the shell will perform word splitting on it
    for uid in $uids
    do
      # individual -id arguments get a separate set of link results for each uid
      set "$@" -id "$uid"
    done
    RunWithLinkArgs "$@" |
    transmute -format indent -doctype ""
  done

  exit 0
fi

# helper function adds web environment argument for history (if set)

RunWithLinkHistoryArgs() {

  AddIfNotEmpty -WebEnv "$web_env" \
  RunWithLinkArgs "$@"
}

# -cmd neighbor_history

wb="$web_env"

LinkInGroups() {

  if [ "$log" = true ]
  then
    printf "ELink\n" >&2
  fi

  GenerateUidList "$dbase" |
  join-into-groups-of 500 |
  while read uids
  do
    err=""
    res=$( RunWithLinkHistoryArgs nquire -url "$base" elink.fcgi -id "$uids" )

    if [ -n "$res" ]
    then
      dt=""
      ParseMessage "$res" eLinkResult dt DbTo web_env WebEnv qry_key QueryKey

      if [ -n "$err" ]
      then
        echo "${INVT} ERROR: ${LOUD} elink failed - $err${INIT}" >&2
        exit 1
      fi
      if [ -z "$web_env" ]
      then
        echo "WebEnv value not found in elink output - WebEnv1 $wb"
        exit 1
      fi
      if [ -n "$wb" ] && [ "$web_env" != "$wb" ]
      then
        echo "WebEnv mismatch in elink output - WebEnv1 $wb, WebEnv2 $web_env"
        exit 1
      fi

      WriteEDirectStep "$dt" "$web_env" "$qry_key" "$err"
    fi
  done

  if [ "$log" = true ]
  then
    printf "\n" >&2
  fi
}

lnks=$( LinkInGroups )

if [ -n "$lnks" ]
then
  # extract first database and webenv values, and all key numbers
  comps=$( echo "$lnks" | xtract -wrp Set,Rec -pattern ENTREZ_DIRECT \
           -wrp Web -element WebEnv -wrp Key -element QueryKey )

  wbnv=$( echo "$comps" | xtract -pattern Set -first Web )
  qrry=$( echo "$comps" | xtract -pattern Set -block Rec -pfx "(#" -sfx ")" -tab " OR " -element Key )

  err=""
  num=""
  if [ -z "$qrry" ]
  then
    # no neighbors or links can be a normal response,
    # e.g., elink -db gene -id 496376 -target medgen
    WriteEDirect "$target" "$web_env" "$qry_key" "0" "$stp" "$err"
    exit 0
  fi

  # send search command, e.g, "(#1) OR (#2)", along with database and web environment
  srch=$( RunWithCommonArgs nquire -get "$base" esearch.fcgi -db "$target" \
          -WebEnv "$wbnv" -term "$qrry" -retmax 0 -usehistory y )

  if [ -n "$srch" ]
  then
    res=$( echo "$srch" | sed -e 's|<TranslationStack>.*</TranslationStack>||' )
    ParseMessage "$srch" eSearchResult web_env WebEnv qry_key QueryKey num Count
  fi

  if [ -n "$num" ] && [ "$num" -lt 1 ]
  then
    uids=$( GenerateUidList "$dbase" | head -n 500 | join-into-groups-of 500 )
    res=$( RunWithCommonArgs nquire -url "$base" elink.fcgi \
           -dbfrom "$dbase" -id "$uids" -cmd "acheck" )

    if [ -n "$res" ]
    then
      ParseMessage "$res" eLinkResult ignore DbFrom

      if [ -z "$err" ]
      then
        tst=$( echo "$res" | xtract -pattern LinkInfo -if LinkName -equals "$name" -element LinkName )
        if [ -n "$tst" ]
        then
          echo "${INVT} ERROR: ${LOUD} UNEXPECTED EMPTY LINK RESULT FOR ${name}${INIT}" >&2
        fi
      else
        echo "${INVT} ERROR: ${LOUD} -cmd acheck TEST FAILED - ${err}${INIT}" >&2
      fi
    fi
  fi

  WriteEDirect "$target" "$web_env" "$qry_key" "$num" "$stp" "$err"

  exit 0
fi

# warn on error

echo "${INVT} ERROR: ${LOUD} ELink failure${INIT}" >&2
exit 1