source: branches/bibliolocean/src/genbib.sh @ 354

#! /bin/sh -x
#+
#
# =========
# genbib.sh
# =========
#
# SYNOPSIS
# ========
#
# .. code-block:: bash
#
#    ./genbib.sh
#
# DESCRIPTION
# ===========
#
# TODO
# ====
#
# plainnat pourvoir les doi dans le pdf mais des effets de bord
# sur les champs url et un doi ne passe pas peut-être à cause de "-"
#
# pb avec l'apostrophe dans les noms d'auteurs avec bibtool
#
# pb biber pour manger toutes les références : TeX capacity exceeded, sorry
#
# find missing hal/tel reference with bibtool
#
# produce HTML files by year
#
# good looking of \delta on jabref outputs
#
# ++ doublons
#
# ask for installation of biber on cratos
#
# jabref.preferences.xml : cleaning
#
# jabref doesn't handle multiple url
#
# could not encode : still some trouble with degre sign
#
# add a test on unescaped ampersand
#
# a solution for symbols :
# bibtex2html --no-abstract --no-keywords --title "Bibliographie du LOCEAN" --footer "$(date)" --style "alpha" --use-keys --raw-url  ~/locean/hal/gtbiblio/biblioref.bib
#
# Pour récupérer tous les bibtexkey dans le html produit :
#
# .. code-block:: bash
#
#    grep ">bib<" biblioref.html | sed -e "s/.*#//" -e "s/\">.*$//"  > list1
#
# Pour récupérer tous les bibtexkey dans le fichier original:
#
# .. code-block:: bash
#
#    grep "@.*{" ../data/biblioref.bib | sed -e "/PREAM/d" -e "s/.*{//" -e "s/,$//" > list2
#
# Faire la différence:
#
# .. code-block:: bash
#
#    sdiff list1 list2
#
# vérifier que les mois sont dans la liste
#
# .. code-block:: bash
#
#    locale -k abmon | tr [:upper:] [:lower:]
#
# changer le titre des pages HTML
#
# contrÎler le vocabulaire des champs pour avoir la liste des mots utilisés
# nb : c'est mieux de faire ça aprÚs avoir resauver sous jabref pour
# uniformiser les séparateurs et les blancs devant
# chaque option:
#
# .. code-block:: bash
#
#    grep " = {" biblioref.bib | awk -F = '{print $1}' | sed -e "s/ //g" | sort -u
#
# pour voir nom/prénom dans la version bibtex (seulemen pour l'oeil ++):
#
# .. code-block:: bash
#
#    grep "author" biblioref.bib | sed -e "s/author = {//" -e "s/},$//" |  awk -F " and" '{print $NF}' | sort -u | more
#
# Pour corriger la version docbook : remplacer lastname par surname,
# ajouter la balise debut <bibliography>,
# remplacer authorgroup dans la doctype par bibliography
#
# Pour voir les nom_prenom à patir de la version docbook :
#
# .. code-block:: bash
#
#    xml sel -t -m "//author" -v "concat(surname,' ',firstname)" -n /usr/work/incas/fplod/public_html/gtbiblio/all.docbook.jabref.xml | sort -u |more
#
# ou sur mac lion:
#
# .. code-block:: bash
#
#    xmlstarlet sel -t -m "//author" -v "concat(surname,' ',firstname)" -n /tmp/fplod/public_html/gtbiblio/all.docbook.jabref.xml | sort -u |more
#
# pour voir la liste des journaux:
#
# .. code-block:: bash
#
#    grep "journal *= *{" biblioref.bib |  sed -e "s/journal *= {//" -e "s/},$//g" | sort -u | more
#
# EVOLUTIONS
# ==========
#
# $Id$
#
# $URL$
#
# - fplod 20130411T144927Z cratos.locean-ipsl.upmc.fr (Linux)
#
#   * suppress test on comma in author field
# - fplod 20130325T145636Z halios.locean-ipsl.upmc.fr (Darwin)
#
#   * add usage of biber (only on halios now)
#
# - fplod 20121108T094612Z cratos.locean-ipsl.upmc.fr (Linux)
#
#   * externalisation de hal dans genprehal.sh
#
# - fplod 20121015T100652Z cratos.locean-ipsl.upmc.fr (Linux)
#
#   * usage of define_author.sh
#
# - fplod 20120703T135330Z cratos (Linux)
#
#   * usage of PROJECT env. variables
#
# - fplod 20120703T105755Z cratos (Linux)
#
#   * change snapo to caraus/snapo-co2
#
# - fplod 20120419T121614Z cratos (Linux)
#
#   * add copy of sorttable.js in dirwww
#   * add copy of sorttable.css in dirwww
#
# - fplod 20120322
#
#   * add authors mainly from Bondy
#
# - fplod 20120223
#
#   * apply locean_tablerefsabsbibsort format for author (was locean_listrefs)
#
# - fplod 20120217
#
#   * ajout des auteurs de l'équipe surf
#
# - fplod 20120131
#
#   * les non publiés sont maintenant tout simplement des @unpublished
#     (plus de ruse avec year={xxxx, *})
#
# - fplod 20111010T073116Z aedon.locean-ipsl.upmc.fr (Darwin)
#
#   * création page thesesud
#
# - fplod 20110610T100740Z aedon.locean-ipsl.upmc.fr (Darwin)
#
#   * suppression upmc et labex
#   * ajout création page these
#
# - fplod 20110511T155810Z cratos.locean-ipsl.upmc.fr (Linux)
#
#   * replace /tmp by /usr/work/incas/
#
# - fplod 20110427T110808Z cratos.locean-ipsl.upmc.fr (Linux)
#
#   * la production pdflatex+bibtex ne fonctionne plus sur aedon.
#     malgré le changement d'installation (port vs fink) rien à faire !
#     donc - et ça va plutÎt dans le bon sens - machine de référence = cratos.
#
# - fplod 20110301T091253Z aedon.locean-ipsl.upmc.fr (Darwin)
#
#   * trying to make it run with bibtool 2.51 on zeus
#
# - fplod 20110228T162021Z cratos.locean-ipsl.upmc.fr (Linux)
#
#   * trying to make it run with bibtool 2.51 on cratos (vs 2.48 sur aedon)
#
# - fplod 20101109T144613Z aedon.locean-ipsl.upmc.fr (Darwin)
#
#   * add for upmc 2009-2010
#     ++ suppression in revision, submitted and so on
#     ++ correction $...$ et Monaco C. L. en Lo Monaco C.
#     ++ je ne sais pas pourquoi rien n'apparait en ouvrant le RTF produit
#     avec TextEdit alors que l'on voit qqe chose en l'ouvrant directement avec
#     OpenOffice.
#
# - fplod 20101108T103903Z aedon.locean-ipsl.upmc.fr (Darwin)
#
#   * correction of years selection for 2007-2010
#     because match year 2000.'select={year "20[01][0789].*"}'
#
#   * add for labex a selection of articles published in 2009.
#     ++ suppression in revision, submitted and so on
#     ++ auteurs labo (ipsl) en gras dans document word
#     ++ correction $...$ et Monaco C. L. en Lo Monaco C.
#
# - fplod 20101013T090448Z aedon.locean-ipsl.upmc.fr (Darwin)
#
#   * add specific RTF output for 2007-2010 articles (labex2007_2010.rtf)
#
# - fplod 20100430T131122Z aedon.locean-ipsl.upmc.fr (Darwin)
#
#   * jabref 2.5 -> 2.6
#
# - fplod 20100127T084405Z aedon.locean-ipsl.upmc.fr (Darwin)
#
#   * add generation of HTML files pages by (affectation,year) using bibtool
#
# - fplod 20091120T140131Z aedon.locean-ipsl.upmc.fr (Darwin)
#
#   * fix latex pb : PDF production is now possible
#   * detection of [delta]
#     nb: remplacement de [delta] par \delta ok pour la production de PDF avec
#     pdflatex mais pas ok pour la production d'HTML avec jabref
#
# - fplod 20091117T093404Z aedon.locean-ipsl.upmc.fr (Darwin)
#
#   * add test if bibtool available
#
# - fplod 20091023T125342Z aedon.locean-ipsl.upmc.fr (Darwin)
#
#   * add test if existing {\ : available feature in latex but confusing
#     for author search using bibtool select
#   * add test if , in author field
#
# - fplod 20091021T153653Z aedon.locean-ipsl.upmc.fr (Darwin)
#
#   * outputs HTML, PDF and RTF in dirwww
#
# - fplod 20091020T134644Z aedon.locean-ipsl.upmc.fr (Darwin)
#
#   * usage of bibtool to find years list
#   * usage of bibtool to produce bibtex files by year
#   * usage of bibtool to produce bibtex files by team (instead of
#     biblio_split.sh + grep)
#
# - fplod 20091020T092945Z aedon.locean-ipsl.upmc.fr (Darwin)
#
#   * avoid diacritical and punctuation in filename (list_team_title s
#     list_team_grep)
#
# - fplod 20091016T145245Z aedon.locean-ipsl.upmc.fr (Darwin)
#
#   * use locean_listrefs format for every team
#
# - fplod 2009-08-21T08:20:29Z aedon.locean-ipsl.upmc.fr (Darwin)
#
#   * add locean_listrefs format
#
# - fplod 2009-08-19T15:48:01Z aedon.locean-ipsl.upmc.fr (Darwin)
#
#   * add simplehtml format
#
# - fplod 2009-08-17T07:56:02Z aedon.locean-ipsl.upmc.fr (Darwin)
#
#   * add alpha style
#
# - fplod 2009-08-14T15:39:44Z aedon.locean-ipsl.upmc.fr (Darwin)
#
#   * use -p option to add customized exports format
#   * add loop one latex biblio style
#
# - fplod 2009-08-10T17:08:07Z aedon.locean-ipsl.upmc.fr (Darwin)
#
#   * test with jabref 2.5
#   * add docbook production
#
# - fplod 2009-07-07T10:17:37Z aedon.locean-ipsl.upmc.fr (Darwin)
#
#   * loop on html formats
#
# - fplod 2009-07-03T08:01:21Z aedon.locean-ipsl.upmc.fr (Darwin)
#
#   * add latex+bibtex processing
#
#-
set -u
command=$(basename ${0})
#
system=$(uname)
case "${system}" in
    AIX|IRIX64)
        echo "${command} : www : no specific posix checking"
    ;;
    *)
        set -o posix
    ;;
esac
#
log_date=$(date -u +"%Y%m%dT%H%M%SZ")
log=/tmp/$(basename ${command} .sh).log.${log_date}
#
usage=" Usage : ${command}"
#
# test if bibtool available
tool=bibtool
type ${tool} 1> /dev/null 2>&1
status=${?}
if [ ${status} -ne 0 ]
then
    echo "${command} : eee : ${tool} unavailable" >&2
    exit 1
fi
unset tool
unset status
#
# default
# n.a.
#
hostname=$(hostname)
tmpdir=${PROJECT_LOG}/gtbiblio
dirwww=${PROJECT_OD}/public_html/gtbiblio/
rm -rf ${tmpdir} 2> /dev/null
mkdir -p ${tmpdir}
rm -rf ${dirwww} 2> /dev/null
mkdir -p ${dirwww}
#
. jabref_header.sh
#
# copy javascript and css for sort table in output directory
cp sorttable.js ${dirwww}/
cp sorttable.css ${dirwww}/

# define team for :
# - search in bibtex file (in loceanteam field)
# - give a element of HTML filename (no diacritical and no punctuation)
iteam=1
list_team_bibtool[${iteam}]="phybiocar"
list_team_title[${iteam}]="phybiocar"
iteam=$(( ${iteam} + 1))
list_team_bibtool[${iteam}]="surf"
list_team_title[${iteam}]="surf"
iteam=$(( ${iteam} + 1))
list_team_bibtool[${iteam}]="varclim"
list_team_title[${iteam}]="varclim"
iteam=$(( ${iteam} + 1))
list_team_bibtool[${iteam}]="austral-boréal"
list_team_title[${iteam}]="austral-boreal"
iteam=$(( ${iteam} + 1))
list_team_bibtool[${iteam}]="bio&pal"
list_team_title[${iteam}]="bio_et_pal"
iteam=$(( ${iteam} + 1))
list_team_bibtool[${iteam}]="paléotropique"
list_team_title[${iteam}]="paleotropique"
iteam=$(( ${iteam} + 1))
list_team_bibtool[${iteam}]="caraus/snapo-co2"
list_team_title[${iteam}]="caraus_snapo-co2"
iteam=$(( ${iteam} + 1))
list_team_bibtool[${iteam}]="dycos"
list_team_title[${iteam}]="dycos"
iteam=$(( ${iteam} + 1))
list_team_bibtool[${iteam}]="prodyam"
list_team_title[${iteam}]="prodyam"
iteam=$(( ${iteam} + 1))
list_team_bibtool[${iteam}]="incas"
list_team_title[${iteam}]="incas"
iteam=$(( ${iteam} + 1))
list_team_bibtool[${iteam}]="mmsa"
list_team_title[${iteam}]="mmsa"
iteam=$(( ${iteam} + 1))
list_team_bibtool[${iteam}]="ditm"
list_team_title[${iteam}]="ditm"
iteam=$(( ${iteam} + 1))
list_team_bibtool[${iteam}]="nemo"
list_team_title[${iteam}]="nemo"
iteam=$(( ${iteam} + 1))
list_team_bibtool[${iteam}]="paleoproxus"
list_team_title[${iteam}]="paleoproxus"
iteam=$(( ${iteam} + 1))
list_team_bibtool[${iteam}]="vartrop"
list_team_title[${iteam}]="vartrop"
#
# define affectation for :
#
# - search in bibtex file (in loceanaffectation field)
# - give a element of HTML filename (no diacritical and no punctuation)
#
iaffectation=1
list_affectation_bibtool[${iaffectation}]="mnhn"
list_affectation_title[${iaffectation}]="mnhn"
iaffectation=$(( ${iaffectation} + 1))
list_affectation_bibtool[${iaffectation}]="cnrs"
list_affectation_title[${iaffectation}]="cnrs"
iaffectation=$(( ${iaffectation} + 1))
list_affectation_bibtool[${iaffectation}]="ird"
list_affectation_title[${iaffectation}]="ird"
iaffectation=$(( ${iaffectation} + 1))
list_affectation_bibtool[${iaffectation}]="upmc"
list_affectation_title[${iaffectation}]="upmc"
iaffectation=$(( ${iaffectation} + 1))
list_affectation_bibtool[${iaffectation}]="uvsq"
list_affectation_title[${iaffectation}]="uvsq"
#
# define bibliography reference file
# ++ pour test biblioref_orig=../../../trunk/data/petitpoly.bib
biblioref_orig=${PROJECT_ID}/biblioref.bib #++ parameter
biblioref=${tmpdir}/all.bib
cp ${biblioref_orig} ${biblioref}
#
# test if "[delta]"
# if so, exit with error
list_bad_delta=""
list_bad_delta=$(grep -n "\[delta\]" ${biblioref})
if [ "${list_bad_delta}" != "" ]
then
    echo "${command} : eee : replace [delta] by \\delta (and check formula) in ${list_bad_delta}"
    exit 1
fi
#
# test if "{\" like {\'e}
# if so, exit with error
list_backslash_after=""
#++ pb regexp list_backslash_after=$(grep -n "\{\\" ${biblioref})
#++grep -n '{\\' ${biblioref}
if [ "${list_backslash_after}" != "" ]
then
    echo "${command} : eee : suppress \"{\\\" in ${list_backslash_after}"
    exit 1
fi
unset list_backslash_after

# test if " }"
# if so, exit with error
list_blank_before=""
list_blank_before=$(grep -n " \}" ${biblioref})
if [ "${list_blank_before}" != "" ]
then
    echo "${command} : eee : suppress \" }\" in ${list_blank_before}"
    exit 1
fi
unset list_blank_before

# test if "{ "
# if so, exit with error
list_blank_after=""
list_blank_after=$(grep -n "\{ " ${biblioref})
if [ "${list_blank_after}" != "" ]
then
    echo "${command} : eee : suppress \"{ \" in ${list_blank_after}"
    exit 1
fi
unset list_blank_after

# test if doi in url field (because of HAL bibtex output)
# if so, exit with error
list_doi_in_url=""
list_doi_in_url=$(grep -n "url = {dx" ${biblioref})
if [ "${list_doi_in_url}" != "" ]
then
    echo "${command} : eee : suppress doi from url fied in ${list_doi_in_url}"
    exit 1
fi
unset list_doi_in_url
#
# test if { or } in doi field (because of HAL bibtex output)
# if so, exit with error
list_bad_doi=""
list_bad_doi=$(grep -n "doi = {.*{.*}.*}" ${biblioref})
if [ "${list_bad_doi}" != "" ]
then
    echo "${command} : eee : suppress \{ or \} from doi fied in ${list_bad_doi}"
    exit 1
fi
unset list_bad_doi

# test if doi does'nt start with 10
# ++ je ne sais pas rédiger cette contrainte en grep
# if so, exit with error
list_bad_doi=""
list_bad_doi=$(grep "doi = {.*}" ${biblioref} | grep -v "doi = {10")
if [ "${list_bad_doi}" != "" ]
then
    echo "${command} : eee : find and modify ${list_bad_doi} suppress in ${biblioref}"
    exit 1
fi
unset list_bad_doi

# test if { or } in pages field (because of HAL bibtex output)
# if so, exit with error
list_bad_pages=""
list_bad_pages=$(grep -n "pages={.*{.*}.*}" ${biblioref})
if [ "${list_bad_pages}" != "" ]
then
    echo "${command} : eee : suppress \{ or \} from pages field in ${list_bad_pages}"
    #++exit 1
fi
unset list_bad_pages

# test if semi-cadratin++ translation in pages field (because of HAL bibtex output)
# if so, exit with error
#++echo "${command} : eee : ++ suppress ++ semi-cadratin from pages fied in ${list_bad_pages}"
#++exit 1

# artificial header of jabref file to enforce encoding
jabref_header ${tmpdir}/header_jabref
#
#list_style="amsalpha plain alpha"
list_style="plain" #+++
for style in ${list_style}
do
    rm ${dirwww}/$(basename ${biblioref}.${style}.log .log).* 2> /dev/null
    # generation of latex file
    cat << EOF > ${biblioref}.${style}.tex
\documentclass[a4paper]{article}
%++\usepackage[frenchb]{babel}
\usepackage[latin1]{inputenc}
\begin{document}
% force to include all entry of the bibliography
\nocite{*}

% bibliography
\bibliographystyle{${style}}

\bibliography{${biblioref}}
\end{document}
EOF
    #
    # processing bibliography with pdflatex (${dirwww}/${biblioref}.${style}.pdf)
    rm ${dirwww}/$(basename ${biblioref}.${style}.log .log).* 2> /dev/null
    pdflatex -output-directory ${dirwww} ${biblioref}.${style}.tex
    bibtex ${dirwww}/$(basename ${biblioref}.${style})
    #++ warnings
    pdflatex -output-directory ${dirwww} ${biblioref}.${style}.tex
    pdflatex -output-directory ${dirwww} ${biblioref}.${style}.tex
    #
    # remove temporary latex files
    #ls ${dirwww}/$(basename ${biblioref}.${style})*
    rm ${dirwww}/$(basename ${biblioref}.${style}.bbl) ${dirwww}/$(basename ${biblioref}.${style}.blg) ${dirwww}/$(basename ${biblioref}.${style}.log) ${dirwww}/$(basename ${biblioref}.${style}.aux) 2> /dev/null
    #
    rm ${biblioref}.${style}.tex 2> /dev/null
done

echo "fin 1re passe latex+bibtex"
read a
#
# test if biber available
tool=biber
type ${tool} 1> /dev/null 2>&1
status=${?}
if [ ${status} -ne 0 ]
then
    echo "${command} : eee : ${tool} unavailable" >&2
else
    style=biber
    #++option_pdflatex=-interaction=nonstopmode
    option_pdflatex=""
    # processing bibliography with pdflatex (${dirwww}/${biblioref}.${style}.pdf)
    rm ${dirwww}/$(basename ${biblioref}.${style}.log .log).* 2> /dev/null
    sed -e "s@ginette@${biblioref}@" biblio_biber_biblatex.tex > ${biblioref}.${style}.tex
    #
    pdflatex ${option_pdflatex} -output-directory ${dirwww} ${biblioref}.${style}.tex
    biber ${dirwww}/$(basename ${biblioref}.${style}).bcf
    #++ warnings
    pdflatex ${option_pdflatex} -output-directory ${dirwww} ${biblioref}.${style}.tex
    pdflatex ${option_pdflatex} -output-directory ${dirwww} ${biblioref}.${style}.tex
    #
    # remove temporary latex files
    rm ${dirwww}/$(basename ${biblioref}.${style}.bbl) ${dirwww}/$(basename ${biblioref}.${style}.blg) ${dirwww}/$(basename ${biblioref}.${style}.log) ${dirwww}/$(basename ${biblioref}.${style}.aux) ${dirwww}/$(basename ${biblioref}.${style}.bcf) ${dirwww}/$(basename ${biblioref}.${style}.run.xml) 2> /dev/null
    #
    rm ${biblioref}.${style}.tex 2> /dev/null
fi
unset tool
unset status
echo "fin 1re passe latex+biber"
read a
#
# pour vérifier que j'ai bien tout mes styles d'exportation
# pour mémoire
#java -jar ${JABREF_DIR}/JabRef-${JABREF_VERSION}.jar -n true \
#-p ${PROJECT}/../branches/bibliolocean/src/jabref.preferences.xml -h

# processing on the whole bibliography reference file
output_title=all
# generation one RTF file style harvard
rm ${biblioref}.harvard.jabref.rtf 2> /dev/null
java -jar ${JABREF_DIR}/JabRef-${JABREF_VERSION}.jar -n true \
-p ${PROJECT}/../branches/bibliolocean/src/jabref.preferences.xml \
--output ${dirwww}/${output_title}.harvard.jabref.rtf,harvard \
${biblioref}
echo "fin rtf all"
#
# theses
bibtool -- 'select{@phdthesis}'  ${biblioref} -o ${tmpdir}/tmp1.bib
bibtool -- 'select={type ".*doctorat.*"}' -- 'sort.format={%d(year)%N(author)}' ${tmpdir}/tmp1.bib -o ${tmpdir}/tmp2.bib
rm ${tmpdir}/tmp1.bib
java -jar ${JABREF_DIR}/JabRef-${JABREF_VERSION}.jar -n true \
-p ${PROJECT}/../branches/bibliolocean/src/jabref.preferences.xml \
--output ${dirwww}/these.html,locean_tablerefsabsbibsort \
${tmpdir}/tmp2.bib
rm ${tmpdir}/tmp2.bib
echo "fin these"
#
# page thesesud
bibtool -- 'select{@phdthesis}'  ${biblioref} -o ${tmpdir}/tmp1.bib
bibtool -- 'select={type ".*doctorat.*"}' -- 'sort.format={%d(year)%N(author)}' ${tmpdir}/tmp1.bib -o ${tmpdir}/tmp2.bib
bibtool -- 'select={ird_thesesud "oui"}' ${tmpdir}/tmp2.bib \
-o ${tmpdir}/tmp3.bib
rm ${tmpdir}/tmp1.bib ${tmpdir}/tmp2.bib
java -jar ${JABREF_DIR}/JabRef-${JABREF_VERSION}.jar -n true \
-p ${PROJECT}/../branches/bibliolocean/src/jabref.preferences.xml \
--output ${dirwww}/thesesud.html,locean_tablerefsabsbibsort \
${tmpdir}/tmp3.bib
#++rm ${tmpdir}/tmp3.bib
echo "fin thesesud"

# find the years list
# . select all the references with no "," in year field
bibtool -- 'select.non={year ","}' ${biblioref} -o ${tmpdir}/tmp.bib
# . extract year field
list_year=$(grep "^  year               =" ${tmpdir}/tmp.bib | sort -u | sed -e "s/^  year              = {//" -e "s/},//" -e "s/}//")
rm ${tmpdir}/tmp.bib
#
# write a bibtex file for each year of the list
for iyear in ${list_year}
do
    # select year
    bibtool_command="bibtool -- 'select={year \"${iyear}\"}' ${biblioref} -o ${tmpdir}/tmp1.bib"
    eval ${bibtool_command}
    # remove unpublished reference
    bibtool -- 'select.non={@unpublished}' ${tmpdir}/tmp1.bib -o ${tmpdir}/tmp2.bib
    cat ${tmpdir}/header_jabref ${tmpdir}/tmp2.bib > ${tmpdir}/tmp_${iyear}.bib
    rm ${tmpdir}/tmp1.bib
    rm ${tmpdir}/tmp2.bib
done
#++ on ne fait rien de ${tmpdir}/tmp_${iyear}.bib
#
# write a bibtex file for unpublished work
bibtool -- 'select={@unpublished}' ${biblioref} -o ${tmpdir}/tmp2.bib
cat ${tmpdir}/header_jabref ${tmpdir}/tmp2.bib > ${tmpdir}/tmp_unpublished.bib
rm ${tmpdir}/tmp2.bib
#++ on ne fait rien de ${tmpdir}/tmp_unpublished.bib
#
list_format="html simplehtml tablerefs locean_tablerefs locean_tablerefsabsbibsort locean_listrefs"
#+++list_format="" #+++
for format in ${list_format}
do
    echo "format export jabref ${format}"
    # generation one HTML file style ${format}
    rm ${biblioref}.${format}.jabref.html 2> /dev/null
    java -jar ${JABREF_DIR}/JabRef-${JABREF_VERSION}.jar -n true \
    -p ${PROJECT}/../branches/bibliolocean/src/jabref.preferences.xml \
    --output ${dirwww}/${output_title}.${format}.jabref.html,${format} \
    ${biblioref}
    jabref_status=${?}
    if [ ${jabref_status} -ne 0 ]
    then
        echo "${command} : eee : pb with jabref export ${format}"
        exit 1
    fi
done

# generation of DocBook
format=docbook
rm ${biblioref}.${format}.jabref.html 2> /dev/null
java -jar ${JABREF_DIR}/JabRef-${JABREF_VERSION}.jar -n true \
-p ${PROJECT}/../branches/bibliolocean/src/jabref.preferences.xml \
--output ${dirwww}/${output_title}.${format}.jabref.xml,${format} \
${biblioref}
jabref_status=${?}
if [ ${jabref_status} -ne 0 ]
then
    echo "${command} : eee : pb with jabref export ${format}"
    exit 1
fi

# loop on teams to build bibliography reference file
iteam=1
nbteam=${#list_team_bibtool[@]}
#+++nbteam=0
while [ ${iteam} -le ${nbteam} ]
do
    echo "team title = ${list_team_title[iteam]}"
    echo "team grep = ${list_team_bibtool[iteam]}"
    biblioref_team=${tmpdir}/${list_team_title[iteam]}.bib
    bibtool_command="bibtool -- 'select={loceanteam \"${list_team_bibtool[iteam]}\"}' ${biblioref} -o ${tmpdir}/tmp1.bib"
    eval ${bibtool_command}
    # test if no file found ++
    cat ${tmpdir}/header_jabref ${tmpdir}/tmp1.bib > ${biblioref_team}
    format=locean_listrefs
    # generation one HTML file style ${format}
    rm ${biblioref}.${format}.jabref.html 2> /dev/null
    java -jar ${JABREF_DIR}/JabRef-${JABREF_VERSION}.jar -n true \
    -p ${PROJECT}/../branches/bibliolocean/src/jabref.preferences.xml \
    --output ${dirwww}/${list_team_title[iteam]}.${format}.jabref.html,${format} \
    ${biblioref_team}
    jabref_status=${?}
    if [ ${jabref_status} -ne 0 ]
    then
        echo "${command} : eee : pb with jabref export ${format}"
        exit 1
    fi
    #++ else
    #++ echo "${command} : iii : no reference for team ${team}"
    #++ fi
    iteam=$(( ${iteam} + 1 ))
done

# loop on affectations to build bibliography reference file
format=locean_listrefs
iaffectation=1
nbaffectation=${#list_affectation_bibtool[@]}
while [ ${iaffectation} -le ${nbaffectation} ]
do
    echo "affectation title = ${list_affectation_title[iaffectation]}"
    echo "affectation grep = ${list_affectation_bibtool[iaffectation]}"
    bibtool_command="bibtool -- 'select={loceanaffectation \"${list_affectation_bibtool[iaffectation]}\"}' ${biblioref} -o ${tmpdir}/tmp1.bib"
    eval ${bibtool_command}
    # test if no file found ++
    # select all the references of unpublished work
    bibtool -- 'select={@unpublished}' ${tmpdir}/tmp1.bib -o ${tmpdir}/tmp2.bib
    biblioref_affectation_unpublished=${tmpdir}/${list_affectation_title[iaffectation]}_${iyear}.bib
    cat ${tmpdir}/header_jabref ${tmpdir}/tmp2.bib > ${biblioref_affectation_unpublished}
    # generation one HTML file style ${format}
    rm ${biblioref}.${format}.jabref.html 2> /dev/null
    java -jar ${JABREF_DIR}/JabRef-${JABREF_VERSION}.jar -n true \
    -p ${PROJECT}/../branches/bibliolocean/src/jabref.preferences.xml \
    --output ${dirwww}/${list_affectation_title[iaffectation]}_unpublished.${format}.jabref.html,${format} \
    ${biblioref_affectation_unpublished}
    jabref_status=${?}
    if [ ${jabref_status} -ne 0 ]
    then
        echo "${command} : eee : pb with jabref export ${format}"
        exit 1
    fi
    # find the years list
    # . select all the references of published work
    bibtool -- 'select.non={@unpublished}' ${tmpdir}/tmp1.bib -o ${tmpdir}/tmp2.bib
    # . extract year field
    list_year=$(grep "^  year           =" ${tmpdir}/tmp2.bib | sed -e "s/^  year               = {//" -e "s/},//" -e "s/}$//" | sort -u)
    echo "list_years for ${list_affectation_title[iaffectation]} : ${list_year}"
    # write a bibtex file for each year of the list
    for iyear in ${list_year}
    do
        # select year
        bibtool_command="bibtool -- 'select={year \"${iyear}\"}' ${tmpdir}/tmp1.bib -o ${tmpdir}/tmp3.bib"
        eval ${bibtool_command}
        biblioref_affectation_year=${tmpdir}/${list_affectation_title[iaffectation]}_${iyear}.bib
        cat ${tmpdir}/header_jabref ${tmpdir}/tmp3.bib > ${biblioref_affectation_year}
        # generation one HTML file style ${format}
        rm ${biblioref}.${format}.jabref.html 2> /dev/null
        java -jar ${JABREF_DIR}/JabRef-${JABREF_VERSION}.jar -n true \
        -p ${PROJECT}/../branches/bibliolocean/src/jabref.preferences.xml \
        --output ${dirwww}/${list_affectation_title[iaffectation]}_${iyear}.${format}.jabref.html,${format} \
        ${biblioref_affectation_year}
        jabref_status=${?}
        if [ ${jabref_status} -ne 0 ]
        then
            echo "${command} : eee : pb with jabref export ${format}"
            exit 1
        fi
        #++ else
        #++ echo "${command} : iii : no reference for affectation ${affectation}"
        #++ fi
    # end of loop on years
    done
    iaffectation=$(( ${iaffectation} + 1 ))
done

. define_authors.sh
#
# loop on authors to build bibliography reference file
iauthor=1
nbauthor=${#list_author_bibtool[@]}
#++nbauthor=0 #+++
while [ ${iauthor} -le ${nbauthor} ]
do
    rm ${tmpdir}/tmp1.bib 2> /dev/null
    echo "author title = ${list_author_title[iauthor]}"
    echo "author grep = ${list_author_bibtool[iauthor]}"
    biblioref_author=${tmpdir}/${list_author_file[iauthor]}.bib
    bibtool_command="bibtool -- 'select={author \"${list_author_bibtool[iauthor]}\"}' ${biblioref} -o ${tmpdir}/tmp1.bib"
    eval ${bibtool_command}
    # test if no file found ++
    cat ${tmpdir}/header_jabref ${tmpdir}/tmp1.bib > ${biblioref_author}
    format=locean_tablerefsabsbibsort
    # generation one HTML file style ${format}
    rm ${dirwww}/${list_author_file[iauthor]}.${format}.jabref.html 2> /dev/null
    java -jar ${JABREF_DIR}/JabRef-${JABREF_VERSION}.jar -n true \
    -p ${PROJECT}/../branches/bibliolocean/src/jabref.preferences.xml \
    --output ${dirwww}/${list_author_file[iauthor]}.${format}.jabref.html,${format} \
    ${biblioref_author}
    jabref_status=${?}
    if [ ${jabref_status} -ne 0 ]
    then
        echo "${command} : eee : pb with jabref export ${format}"
        exit 1
    fi
    #++ else
    #++ echo "${command} : iii : no reference for author ${team}"
    #++ fi
    iauthor=$(( ${iauthor} + 1 ))
done
echo "fin auteurs"

#++rm ${biblioref} 2> /dev/null
#++rm ${biblioref}_hal 2> /dev/null
#++rm ${tmpdir}/header_jabref 2> /dev/null

exit 0