[Bash] extractBib: extract bib items from a source bibtex database for a given tex file

#!/bin/bash # extract bib items from a source bibtex database for a given tex file # usage: #          extractBib tex-file bibtex-database output-bibtex-file # e.g., #          extractBib mypaper.tex mybibtexdatabase.bib mypaper.bib # http://scriptdemo.blogspot.com function getkeys() {    texfile=$1    mykeys=`grep "cite.*{.*}" ${texfile} | sed -e 's/\ //g' | awk '{for (i=1; i<=NF;i++) {if ($i ~ /cite/) {print $i}}}' | sed -e 's/\}/\n/g' | awk -F\{ '{print $2}' | sed -e 's/\,/\n/g' | sed '/^[\ ]*[\ ]*$/d' | sort | uniq | sed '/^\\\\/d' | sed '/:/d'`     echo ${mykeys} } if [ $# -eq 3 ]; then    texfile=$1; bibfile=$2; outfile=$3 elif [ $# -eq 2 ]; then    texfile=$1; bibfile=$2; outfile="extractbib_"$1 else    echo "usage:"    echo "          extractBib tex-file bibtex-database output-bibtex-file"    exit fi # make sure no overwrite [ -e ${outfile} ] && echo "${outfile} exists alreay! exit" && exit allkeys=`getkeys ${texfile}` if [ ${#allkeys[*]} -ne 0 ]; then    touch ${outfile}    for eachkey in ${allkeys[*]}    do        #echo ${eachkey}        sed -ne "/${eachkey}/,/^[\ ]*\}$/p" ${bibfile} >> ${outfile}    done fi

[Bash] ris2bib: convert RIS citation file to bibtex format

#!/bin/bash # convert ris format to bibtex format # usage: #          ris2bib.sh ris-file(s) #          www.scriptdemp.blogspot.ca getCTag() {    for cTag in $*    do       nl=`grep "^${cTag}" ${ris} | wc -l`       [ ${nl} -ne 0 ] && echo "${cTag}" && exit    done    echo "" } [ $# -eq 0 ] && sed -n '2,5p' `which ris2bib.sh` && exit for ris in $* do     if [ -e ${ris} ]; then        dos2unix ${ris}        auTag=`getCTag AU A1 A2`        tlTag=`getCTag T1 TI`        joTag=`getCTag JO JA`        yrTag=`getCTag PY Y1`        doTag=`getCTag M3 DO`        voTag="VL"; spTag="SP"; epTag="EP"; urTag="UR"; isTag="IS"        publisher=`grep "^PB\ " ${ris} | awk -F\- '{print $2}' | sed -e 's/^\ //g'`        authorList0=`grep "^${auTag}\ " ${ris} | awk -F\- '{print $2"@"}'`        authorList=`echo ${authorList0} | sed -e 's/^\ //g' -e 's/\.\ /\./g' -e "s/\@$//" | sed -e 's/@/\ and\ /g'`        titleStr=`grep "^${tlTag}\ " ${ris} | cut -c7-`        jourStr=`grep "^${joTag}\ " ${ris} | awk -F\- '{print $2}' | sed -e 's/^\ //g'`        volStr=`grep "^${voTag}\ " ${ris} | awk -F\- '{print $2}' | sed -e 's/\ //g'`        SPStr=`grep "^${spTag}\ " ${ris} | awk -F\- '{print $2}' | sed -e 's/\ //g'`        EPStr=`grep "^${epTag}\ " ${ris} | awk -F\- '{print $2}' | sed -e 's/\ //g'`        if [ ${#EPStr} -ne 0 ]; then           pageStr="${SPStr}--${EPStr}"        else           pageStr=${SPStr}        fi        if [ ${#isTag} -ne 0 ]; then           isnStr=`grep "^${isTag}\ " ${ris} | cut -c7-`        fi        yearStr=`grep "^${yrTag}\ " ${ris} | awk -F\- '{print $2}' | sed -e 's/\ //g' | cut -c-4`        if [ ${#doTag} -ne 0 ]; then           doiStr=`grep "^${doTag}\ " ${ris} | awk -F\- '{print $2}' | rev | awk -F\: '{print $1}' | rev | sed -e 's/^\ //g'`        fi        if [ ${#urTag} -ne 0 ]; then           urlStr=`grep "^${urTag}\ " ${ris} | awk -F\- '{print $2}' | sed -e 's/^\ //g'`        fi        #generate the key        mykey=`echo ${authorList} | awk -F\, '{print $1}'`        mykey="${mykey}${yearStr}"        titleKey=`echo ${titleStr} | awk '{print $1""$2}'`        mykey=`echo "${mykey}${titleKey}" | awk '{print tolower($0)}' | sed -e 's/\-//g'`        echo ""        echo @article{"${mykey},"        echo " author={${authorList}},"        echo " title = {{${titleStr}}},"        echo " journal = {${jourStr}},"        echo " year = {${yearStr}},"        echo " volume = {${volStr}},"        [ ${#isnStr} -ne 0 ] && echo " number = {"${isnStr}"},"        [ ${#doiStr} -ne 0 ] && echo " doi = {"${doiStr}"},"        [ ${#urlStr} -ne 0 ] && echo " url = {${urlStr}},"        if [ ${#publisher} -eq 0 ]; then           echo " pages = {${pageStr}}"        else           echo " pages = {${pageStr}},"           echo " publisher = {${publisher}}"        fi        echo " }"        unset auTag tlTag joTag voTag spTag epTag isTag    else       echo ""       echo "${ris} is not found!"       echo ""    fi done

[Bash] convert agu citation to bibtex format

#!/bin/bash # convert citation string from agu website to a bibtex format # usage: #           agu2bib.sh 'citeString' #   note:  #          1: need single quotations #          2: the whole command should be in one line #         www.scriptdemo.blogspot.ca getLastChar() {   echo -n $* | tail -c1 } fixVolNum() {   # get number from volume-string   volstr=$1   if [ `getLastChar ${volstr}` == ")" ]; then      numStr=`echo ${volstr} | awk -F\( '{print $2}' | rev | cut -c2- | rev`      volstr=`echo ${numStr} | sed -e "s/\(${numStr}\)//"`      echo "${volstr} ${numStr}" && exit   else      nf=`echo $volstr | awk -F\: '{print NF}'`      if [ ${nf} -eq 2 ]; then         echo ${volstr} | awk -F\: '{print $1" "$2}' && exit      else         echo "${volstr}" && exit      fi   fi } fixPageNum() {    echo $1 | sed -e 's/–/--/g' | sed -e 's/----/--/' } revName() {    nf=`echo $* | awk '{print NF}'`    if [ $nf -ge 2 ]; then       lastName=`echo $* | rev | awk '{print $1}' | rev`       restName=`echo $* | sed -e "s/${lastName}//" | sed -e 's/\.\ /\./g' | sed -e 's/\ $//'`       echo "${lastName}, ${restName}"    else       echo $*    fi } getAuthor() {     nf=`echo $* | awk --field-separator=" and " '{print NF}'`     if [ ${nf} -eq 1 ]; then        # one author        # Myers, P. G. ==> Myers, P.G.        echo $* | sed -e 's/\.\ /\./g'        exit     else        # more than one author        lastOne=`echo $* | awk --field-separator=" and " '{print $2}'`        lastOne=`revName ${lastOne}`        # how to get first one        str0=`echo $* | awk --field-separator=" and " '{print $1}' | sed -e 's/\,$//'`        nf=`echo ${str0} | awk -F\, '{print NF}'`        if [ ${nf} -eq 1 ]; then           echo "${str0} and ${lastOne}"           exit        fi        fl2=`echo ${str0} | awk -F\, '{print $2}'`        indNext=2        if [ `getLastChar ${fl2}` == "." ]; then           # take first two fields as the first author           fl1=`echo ${str0} | awk -F\, '{print $1}'`           fl2=`echo ${fl2} | sed -e 's/\.\ /\./g' | sed -e 's/\ $//'`           firstOne="${fl1}, ${fl2}"           indNext=3        fi        outStr=${firstOne}        for (( n=${indNext}; n<=${nf}; n++))        do            cfl=`echo ${str0} | cut -d\, -f ${n}`            cnameStr=`revName ${cfl}`            outStr="${outStr} and ${cnameStr}"        done        echo "${outStr} and ${lastOne}" && exit     fi } [ $# -eq 0 ] && sed -n '2,7p' `which agu2bib.sh` && exit isDebug=0 nLen=4 inStr=$* nTLen=${#inStr} nLoop=`expr ${nTLen} - ${nLen} - 1` isFound=0 jTag="" for (( nL=1; nL<=${nLoop}; nL++ )) do     subStr=${inStr:${nL}:${nLen}} # index starts from ZERO     if [[ ${subStr} =~ "[1-2][0-9][0-9][0-9]" ]]; then        [ ${isDebug} -eq 1 ] && set -x        nL0=${nL}        tmpChar=`echo ${inStr} | cut -c${nL0}`        while [ "${tmpChar}" != ' ' ]        do              nL0=`expr ${nL0} - 1`              tmpChar=`echo ${inStr} | cut -c${nL0}`        done        myStr0=`echo ${inStr} | cut -c-${nL0} | sed -e 's/\ $//g' -e 's/\,$//g'`        nL1=`expr ${nL} + ${nLen} + 1`        tmpChar=`echo ${inStr} | cut -c${nL1}`        [ "${tmpChar}" == ":" ] && jTag="ams"        while [ "${tmpChar}" != ' ' ]        do              [ "${tmpChar}" == ":" ] && jTag="ams"              nL1=`expr ${nL1} + 1`              tmpChar=`echo ${inStr} | cut -c${nL1}`        done        myStr1=`echo ${inStr} | cut -c${nL1}-`        yearStr=${subStr}        isFound=1        break     fi done [ ${isDebug} -eq 1 ] && set +x [ ${isFound} -eq 0 ] && echo "can find the publicsh time!" && exit [ ${isDebug} -eq 1 ] && echo "second half: ${myStr1}" # get doi doi=`echo ${myStr1} | rev | awk -F, '{print $1}' | rev | sed -e 's/\ //g'` if [[ ${doi} =~ "doi*" ]] || [[ ${doi} =~ "DOI*" ]]; then    isDOI=1    doi=`echo ${doi} | sed -e 's/\.$//'`    pages=`echo ${myStr1} | rev | awk -F, '{print $2}' | rev | sed -e 's/\ //g'`    vol=`echo ${myStr1} | rev | awk -F, '{print $3}' | rev | sed -e 's/\ //g'`    if [ "${#jTag}" -eq 0 ]; then       jour=`echo ${myStr1} | rev | awk -F, '{print $4}' | rev`    fi else    isDOI=0    pages=${doi} && unset doi    pages=`echo ${pages} | sed -e 's/\.$//'`    vol=`echo ${myStr1} | rev | awk -F, '{print $2}' | rev | sed -e 's/\ //g'`    if [ "${#jTag}" -eq 0 ]; then       jour=`echo ${myStr1} | rev | awk -F, '{print $3}' | rev`    fi fi if [ ${#jTag} -eq 0 ]; then    indOfJour=`awk -v a="${myStr1}" -v b="${jour}" 'BEGIN{print index(a,b)}'`    indOfJour=`expr ${indOfJour} - 3`    title=`echo ${myStr1} | cut -c-${indOfJour}` else    title=`echo ${myStr1} | awk -F\. '{print $1}'`    nL1=`expr ${#title} + 2`    myStr1=`echo ${myStr1} | cut -c${nL1}-`    jour=`echo ${myStr1} | awk -F\, '{print $1}'`    nf=`echo ${myStr0} | awk -F\, '{print NF}'`    if [ ${nf} -gt 2 ]; then       myStr0=`echo ${myStr0} | rev | sed -e 's/\,/\ dna\ /' | rev`    fi fi # get author string [ ${isDebug} -eq 1 ] && echo "first half: ${myStr0}" author=`getAuthor "${myStr0}"` pages=`fixPageNum ${pages}` volStr=`fixVolNum ${vol}` vol=`echo ${volStr} | awk '{print $1}'` num=`echo ${volStr} | awk '{print $2}'` #generate the key mykey=`echo ${author} | awk -F\, '{print $1}'` mykey="${mykey}${yearStr}" titleKey=`echo ${title} | awk '{print $1""$2}'` mykey=`echo "${mykey}${titleKey}" | awk '{print tolower($0)}' | sed -e 's/\-//g'` #output echo "@article{${mykey}," echo " author={${author}}," echo " title = {{${title}}}," echo " journal = {${jour}}," echo " year = {${yearStr}}," echo " volume = {${vol}}," [ ${#num} -ne 0 ] && echo " number = { ${num}}," if [ ${isDOI} -eq 1 ]; then    echo " pages = {${pages}},"    echo " doi = {${doi}}" else    echo " pages = {${pages}}" fi echo "}"

Example:

Output: