| [2] | 1 | #!/bin/bash |
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| 2 | # |
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| 3 | # Behera, S. K., J. Luo, S. Masson, S. Rao, S. Gualdi, P. Delecluse, A. |
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| 4 | # Navarra and T. Yamagata, 2004 : Paramount Impact of the Indian Ocean |
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| 5 | # Dipole on the East African Short Rains: A CGCM Study, J. Climate, In |
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| 6 | # press. |
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| [22] | 7 | # |
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| [2] | 8 | # donnerait |
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| [22] | 9 | # |
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| [56] | 10 | # <biblioentry xml:id="behara2004"> |
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| [2] | 11 | # <authorgroup> |
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| 12 | # <author><surname>Behera</surname> <firstname>S. K.</firstname> </author> |
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| 13 | # <author><firstname>J.</firstname> <surname>Luo</surname></author> |
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| 14 | # <author><firstname>S.</firstname> <surname>Masson</surname></author> |
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| 15 | # <author><firstname>S.</firstname> <surname>Rao</surname></author> |
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| 16 | # <author><firstname>S.</firstname> <surname>Gualdi</surname></author> |
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| 17 | # <author><firstname>P.</firstname> <surname>Delecluse</surname></author> |
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| 18 | # <author><firstname>A.</firstname> <surname>Navara</surname></author> |
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| 19 | # <author><firstname>T.</firstname> <surname>Yamagata</surname></author> |
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| 20 | # </authorgroup> |
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| 21 | # <date>2004</date> |
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| 22 | # <title>Paramount Impact of the Indian Ocean Dipole on the East African |
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| 23 | # Short Rains: A CGCM Study</title> |
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| 24 | # <publishername>J. Climate</publishername> |
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| [45] | 25 | # <biblioid class="doi">doi</biblioid> |
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| [2] | 26 | # <bibliomisc role="pseudoref">In press.</bibliomisc> |
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| [22] | 27 | # <bibliomisc role="internalref">from |
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| [2] | 28 | # http://www.lodyc.jussieu.fr/~opatlod/NEMO_v1/6_Menu/2_page/index.html |
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| 29 | # 2007-03-29T16:24:31Z fplod by hand</bibliomisc> |
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| 30 | # </biblioentry> |
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| 31 | # |
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| [45] | 32 | # @book{MetReiCoh2004 , |
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| 33 | # author = {Michael Metcalf and |
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| 34 | # John Reid and Malcolm Cohen}, |
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| 35 | # title = {Fortran 95/2003 explained}, |
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| 36 | # year = {2004}, |
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| 37 | # publisher = {Oxford University Press}, |
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| 38 | # edition = {Third}, |
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| 39 | # ISBN = {0-19-852693-8}, |
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| 40 | # pages = {434} |
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| 41 | # } |
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| 42 | # donnerait |
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| [56] | 43 | # <biblioentry xml:id="MetReiCoh2004"> |
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| [45] | 44 | # <authorgroup> |
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| 45 | # <author><firstname>Michael</firstname> <surname>Metcalf</surname></author> |
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| 46 | # <author><firstname>John</firstname> <surname>Reid</surname></author> |
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| 47 | # <author><firstname>Malcolm</firstname> <surname>Cohen</surname></author> |
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| 48 | # </authorgroup> |
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| 49 | # <date>2004}</date> |
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| 50 | # <title>Fortran 95/2003 explained</title> |
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| 51 | # <publisher><publishername>Oxford University Press</publishername></publisher> |
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| 52 | # <biblioid class="isbn">0-19-852693-8</biblioid> |
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| 53 | # <pagenums>434</pagenums> |
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| 54 | # <edition>Third</edition> |
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| [22] | 55 | # |
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| [2] | 56 | # example : |
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| [47] | 57 | # $ ./bibopa.sh -p birefnemo -i data/biball.txt -t raw |
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| [56] | 58 | # $ ./bibopa.sh -p bibrefnemo -i data/mail2007-05-10T09:01:56Z -t mailbody |
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| [47] | 59 | # $ ./bibopa.sh -p polyfortran -i data/petitpolyfp.bib -t bibtex -l fr |
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| [56] | 60 | # $ ./bibopa.sh -p demo1 -i data/bibdemo1.txt -t raw -l fr |
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| [2] | 61 | # |
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| [31] | 62 | # see also mailtouser.sh |
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| [2] | 63 | # |
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| 64 | # original location : |
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| 65 | # /usr/home/fplod/incas/bibnemo/src/bibnemomaf/bibopa.sh sur cerbere.locean-ipsl.upmc.fr |
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| 66 | # |
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| 67 | # update |
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| [22] | 68 | # ++ gestion des comments |
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| [2] | 69 | # ++ gestion des id existants (cf à la fin) |
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| 70 | # ++ option debug |
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| [33] | 71 | # $Id$ |
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| [56] | 72 | # fplod 2008-04-30T07:11:58Z aedon.locean-ipsl.upmc.fr (Darwin) |
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| 73 | # chgt for dbk5 out |
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| 74 | # xmlto 0.0.18 does'nt like this docbook release. remove |
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| 75 | # usage of xml (xmlstarlet) for validation |
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| 76 | # bug fix |
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| 77 | # add journal names from demo1 |
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| [47] | 78 | # fplod 2008-03-12T16:11:07Z aedon.locean-ipsl.upmc.fr (Darwin) |
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| 79 | # add -p option (to overide bibrefnemo in file name and id) |
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| 80 | # add -l option by default en |
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| [44] | 81 | # fplod 2008-03-11T11:25:27Z aedon.locean-ipsl.upmc.fr (Darwin) |
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| 82 | # add bibtex entry (not finished)++ |
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| [21] | 83 | # fplod 2007-06-20T17:18:02Z aedon.locean-ipsl.upmc.fr (Darwin) |
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| 84 | # <bibliomisc role="id"> replace by <biblioid class="doi"> |
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| [15] | 85 | # smasson 2007-06-07T16:43:42Z arete.locean-ipsl.upmc.fr (Darwin) |
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| 86 | # Add journals |
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| [2] | 87 | # fplod 2007-05-10T09:17:09Z aedon.locean-ipsl.upmc.fr (Darwin) |
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| 88 | # dernières touches |
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| 89 | # fplod 2007-04-25T10:59:49Z cerbere.locean-ipsl.upmc.fr (Linux) |
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| 90 | # add a filein parameter and an option for mailbody |
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| 91 | # comments (line begininig with #) are now possible |
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| 92 | # Sebastien Masson avril 2007 creation |
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| [22] | 93 | # |
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| [2] | 94 | |
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| 95 | rmbl () { |
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| [22] | 96 | echo "${1}" | sed -e "s/^ *//" | sed -e "s/ *$//" |
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| [2] | 97 | } |
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| 98 | cleanname () { |
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| [22] | 99 | echo "${1}" | sed -e "s/^ *//" \ |
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| [2] | 100 | -e "s/^ *,//" \ |
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| 101 | -e "s/^ *;//" \ |
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| 102 | -e "s/^ *\.//" \ |
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| 103 | -e "s/ *$//" \ |
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| 104 | -e "s/, *$//" \ |
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| 105 | -e "s/; *$//" \ |
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| 106 | -e "s/\. *$//" |
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| 107 | } |
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| 108 | # |
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| 109 | set -o posix |
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| [56] | 110 | command=$(basename ${0}) |
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| [2] | 111 | log_date=$(date -u +"%Y-%m-%dT%H:%M:%SZ") |
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| 112 | log=/tmp/${command}.${log_date} |
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| 113 | # |
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| 114 | # test if xsltproc is available |
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| 115 | type xsltproc 1> /dev/null 2>&1 |
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| 116 | status=${?} |
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| 117 | if [ ${status} -ne 0 ] |
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| 118 | then |
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| 119 | echo " eee : xsltproc not found" |
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| 120 | exit 1 |
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| 121 | fi |
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| [64] | 122 | unset status |
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| [2] | 123 | # |
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| [56] | 124 | # test if xml is available |
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| 125 | type xml 1> /dev/null 2>&1 |
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| 126 | status=${?} |
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| 127 | if [ ${status} -ne 0 ] |
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| 128 | then |
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| 129 | echo " eee : xml not found" |
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| 130 | exit 1 |
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| 131 | fi |
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| [64] | 132 | unset status |
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| [56] | 133 | # |
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| [47] | 134 | usage=" Usage : ${command} -i filein -t type -p project -l lang" |
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| [2] | 135 | # |
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| [47] | 136 | # default |
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| 137 | lang=en |
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| 138 | # |
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| 139 | minargcount=6 |
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| [56] | 140 | #echo " narg ${#}" |
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| [22] | 141 | if [ ${#} -lt ${minargcount} ] |
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| 142 | then |
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| [47] | 143 | echo "eee : not enought arguments" |
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| 144 | echo "${usage}" |
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| 145 | exit 1 |
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| [22] | 146 | fi |
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| [64] | 147 | unset minargcount |
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| [22] | 148 | # |
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| 149 | while [ ! -z "${1}" ] |
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| [2] | 150 | do |
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| 151 | case ${1} in |
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| [22] | 152 | -i) # filein |
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| [2] | 153 | filein=${2} |
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| 154 | shift |
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| 155 | ;; |
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| [22] | 156 | -t) # type |
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| [2] | 157 | type=${2} |
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| 158 | shift |
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| 159 | ;; |
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| [47] | 160 | -p) |
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| 161 | project=${2} |
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| 162 | shift |
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| 163 | ;; |
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| 164 | -l) |
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| 165 | lang=${2} |
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| 166 | shift |
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| 167 | ;; |
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| [22] | 168 | -h) |
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| 169 | echo "${usage}" |
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| 170 | exit 0 |
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| 171 | ;; |
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| [2] | 172 | *) # other choice |
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| 173 | echo "${usage}" |
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| 174 | exit 1 |
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| 175 | ;; |
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| 176 | esac |
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| 177 | shift # next flag |
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| 178 | done |
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| [64] | 179 | unset usage |
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| [22] | 180 | # |
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| [2] | 181 | set -u |
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| 182 | # |
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| [22] | 183 | # check for filein |
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| [2] | 184 | if [ ! -f ${filein} ] |
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| 185 | then |
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| [47] | 186 | echo "eee : ${filein} not found" |
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| 187 | exit 1 |
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| [2] | 188 | fi |
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| 189 | # |
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| 190 | case ${type} in |
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| 191 | raw) # file like data/biball.txt |
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| 192 | fileraw=${filein} |
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| 193 | ;; |
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| 194 | mailbody) # file like data/mail2007-04-25T08:58:16Z.txt |
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| 195 | fileraw=/tmp/$(basename ${filein}).raw |
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| 196 | echo "# from ${filein}" > ${fileraw} |
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| 197 | echo "# ${log_date}" >> ${fileraw} |
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| 198 | echo "# corrections" >> ${fileraw} |
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| 199 | grep "correction_.*=" ${filein} | grep -v "correction_.*=$" | \ |
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| 200 | sed -e "s/correction_.*=//">> ${fileraw} |
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| 201 | echo "# new references" >> ${fileraw} |
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| 202 | awk "/newreferences=/,/comments=/" ${filein} | sed -e "s/newreferences=//" -e "/comments=/d" >> ${fileraw} |
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| 203 | #more ${fileraw} # ++ if debug |
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| 204 | #read a #++ if debug |
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| 205 | ;; |
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| [44] | 206 | bibtex) # file like data/petitpoly.bib |
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| 207 | fileraw=/tmp/$(basename ${filein}).raw |
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| [45] | 208 | awk -f join_endcomma.awk ${filein} >> ${fileraw} |
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| 209 | #more ${fileraw} # ++ if debug |
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| 210 | #read a #++ if debug |
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| [44] | 211 | ;; |
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| [22] | 212 | *) |
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| [44] | 213 | echo "eee : type should be raw, mailbody or bibtex" |
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| [2] | 214 | exit 1 |
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| 215 | ;; |
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| 216 | esac |
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| 217 | # |
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| 218 | # check for output |
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| 219 | fileou=$( basename ${filein} .txt).xml |
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| 220 | if [ -f ${fileou} ] |
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| 221 | then |
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| 222 | echo "eee : ${fileou} already exist" |
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| [56] | 223 | exit 1 |
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| [2] | 224 | fi |
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| 225 | # |
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| [64] | 226 | ij=1 |
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| 227 | jlist[${ij}]="J. Climate" |
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| 228 | ij=$(( ${ij} + 1)) |
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| 229 | jlist[${ij}]="Journal of Climate" |
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| 230 | ij=$(( ${ij} + 1)) |
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| 231 | jlist[${ij}]="Ocean Modelling" |
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| 232 | ij=$(( ${ij} + 1)) |
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| 233 | jlist[${ij}]="Geophys. Res. Lett." |
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| 234 | ij=$(( ${ij} + 1)) |
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| 235 | jlist[${ij}]="J. Geophys. Res." |
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| 236 | ij=$(( ${ij} + 1)) |
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| 237 | jlist[${ij}]="Tellus A" |
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| 238 | ij=$(( ${ij} + 1)) |
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| 239 | jlist[${ij}]="Tellus B" |
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| 240 | ij=$(( ${ij} + 1)) |
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| 241 | jlist[${ij}]="J. Phys. Oceanogr." |
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| 242 | ij=$(( ${ij} + 1)) |
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| 243 | jlist[${ij}]="Clim. Dyn." |
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| 244 | ij=$(( ${ij} + 1)) |
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| 245 | jlist[${ij}]="Climate Dynamics" |
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| 246 | ij=$(( ${ij} + 1)) |
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| 247 | jlist[${ij}]="Dyn. Atmos. Oceans" |
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| 248 | ij=$(( ${ij} + 1)) |
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| 249 | jlist[${ij}]="Mon. Wea. Rev." |
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| 250 | ij=$(( ${ij} + 1)) |
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| 251 | jlist[${ij}]="Global Biogeochem. Cycles" |
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| 252 | ij=$(( ${ij} + 1)) |
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| 253 | jlist[${ij}]="Nonlinear Processes in Geophysics" |
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| 254 | ij=$(( ${ij} + 1)) |
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| 255 | jlist[${ij}]="Ocean Science" |
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| 256 | ij=$(( ${ij} + 1)) |
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| 257 | jlist[${ij}]="J. Mar. Systems" |
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| 258 | ij=$(( ${ij} + 1)) |
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| 259 | jlist[${ij}]="J. Atmos. Sc." |
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| 260 | ij=$(( ${ij} + 1)) |
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| 261 | jlist[${ij}]="Proc. Royal Soc." |
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| 262 | ij=$(( ${ij} + 1)) |
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| 263 | jlist[${ij}]="Bull. Amer. Meteorol. Soc." |
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| 264 | ij=$(( ${ij} + 1)) |
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| 265 | jlist[${ij}]="Ocean Dyn." |
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| 266 | ij=$(( ${ij} + 1)) |
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| [65] | 267 | jlist[${ij}]="Geophysical Monograph Series, Earth's Climate: The Ocean-Atmosphere Interaction" |
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| [64] | 268 | ij=$(( ${ij} + 1)) |
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| 269 | jlist[${ij}]="Paleoceanography" |
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| 270 | ij=$(( ${ij} + 1)) |
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| 271 | jlist[${ij}]="Annales Geophysicae" |
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| 272 | ij=$(( ${ij} + 1)) |
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| 273 | jlist[${ij}]="Annals of Geophys." |
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| 274 | ij=$(( ${ij} + 1)) |
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| 275 | jlist[${ij}]="Deep Sea Research Part II: Topical Studies in Oceanography" |
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| 276 | ij=$(( ${ij} + 1)) |
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| 277 | jlist[${ij}]="Deep Sea Res. II" |
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| 278 | ij=$(( ${ij} + 1)) |
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| 279 | jlist[${ij}]="Atmospheric Chemistry and Physics" |
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| 280 | ij=$(( ${ij} + 1)) |
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| 281 | jlist[${ij}]="Atmospheric Chemistry and Physics Discussions" |
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| 282 | ij=$(( ${ij} + 1)) |
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| 283 | jlist[${ij}]="Earth Plan. Sc. Lett." |
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| 284 | ij=$(( ${ij} + 1)) |
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| 285 | jlist[${ij}]="J. Mar. Res." |
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| 286 | ij=$(( ${ij} + 1)) |
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| 287 | jlist[${ij}]="PCMDI Report Series" |
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| 288 | ij=$(( ${ij} + 1)) |
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| 289 | jlist[${ij}]="J. Mar. Syst." |
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| 290 | ij=$(( ${ij} + 1)) |
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| 291 | jlist[${ij}]="Note du Pole de Modelisation" |
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| 292 | ij=$(( ${ij} + 1)) |
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| 293 | jlist[${ij}]="Calculateurs Paralleles" |
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| 294 | ij=$(( ${ij} + 1)) |
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| 295 | jlist[${ij}]="Note Scientifique du Pole de Modelisation" |
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| 296 | ij=$(( ${ij} + 1)) |
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| 297 | jlist[${ij}]="Lecture Notes in Computer Science" |
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| 298 | ij=$(( ${ij} + 1)) |
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| 299 | jlist[${ij}]="Prog. Oceanogr." |
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| 300 | ij=$(( ${ij} + 1)) |
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| 301 | jlist[${ij}]="Deep Sea Research Part I: Oceanographic Research Papers" |
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| 302 | ij=$(( ${ij} + 1)) |
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| 303 | jlist[${ij}]="Deep Sea Res. I" |
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| 304 | ij=$(( ${ij} + 1)) |
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| 305 | jlist[${ij}]="IEEE Trans. Geosci. Remote Sensing" |
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| 306 | ij=$(( ${ij} + 1)) |
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| 307 | jlist[${ij}]="ECMWF Tech. Memorandum" |
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| 308 | ij=$(( ${ij} + 1)) |
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| 309 | jlist[${ij}]="J. Environ. Radioactivity" |
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| 310 | ij=$(( ${ij} + 1)) |
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| 311 | jlist[${ij}]="Int. WOCE Newsletter" |
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| 312 | ij=$(( ${ij} + 1)) |
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| 313 | jlist[${ij}]="C. R. Acad. Sci. Paris" |
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| 314 | ij=$(( ${ij} + 1)) |
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| 315 | jlist[${ij}]="C. R. Acad. Sci. Paris, Earth and Planetary Sciences" |
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| 316 | ij=$(( ${ij} + 1)) |
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| 317 | jlist[${ij}]="In The mathematics of models for climatology and environment" |
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| 318 | ij=$(( ${ij} + 1)) |
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| 319 | jlist[${ij}]="Oceanol. Acta" |
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| 320 | ij=$(( ${ij} + 1)) |
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| 321 | jlist[${ij}]="The global atmosphere and ocean system" |
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| 322 | ij=$(( ${ij} + 1)) |
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| 323 | jlist[${ij}]="NATO Advanced Study Institute" |
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| 324 | ij=$(( ${ij} + 1)) |
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| 325 | jlist[${ij}]="WCRP" |
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| 326 | ij=$(( ${ij} + 1)) |
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| 327 | jlist[${ij}]="The Courier" |
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| 328 | ij=$(( ${ij} + 1)) |
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| 329 | jlist[${ij}]="Elsevier Oceanographic Series" |
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| 330 | ij=$(( ${ij} + 1)) |
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| 331 | jlist[${ij}]="In Conference Proceedings of the 1988 International Conference on Supercomputing" |
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| 332 | ij=$(( ${ij} + 1)) |
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| 333 | jlist[${ij}]="In Science and engineering on Cray Supercomputers" |
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| 334 | ij=$(( ${ij} + 1)) |
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| 335 | jlist[${ij}]="In Modeling the Earth's Climate and its Variability" |
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| 336 | ij=$(( ${ij} + 1)) |
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| 337 | jlist[${ij}]="Fish. Oceanogr." |
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| 338 | ij=$(( ${ij} + 1)) |
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| 339 | jlist[${ij}]="Q. J. R. Meteor. Soc." |
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| 340 | ij=$(( ${ij} + 1)) |
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| 341 | jlist[${ij}]="In High performance computing in the geosciences" |
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| 342 | ij=$(( ${ij} + 1)) |
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| 343 | jlist[${ij}]="Int. J. Numer. Meth. in Fluids" |
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| 344 | ij=$(( ${ij} + 1)) |
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| 345 | jlist[${ij}]="Lecture notes in Physics" |
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| 346 | ij=$(( ${ij} + 1)) |
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| 347 | jlist[${ij}]="J. Meterol. Soc. Japan" |
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| 348 | ij=$(( ${ij} + 1)) |
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| 349 | jlist[${ij}]="Journal of Marine Systems" |
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| 350 | ij=$(( ${ij} + 1)) |
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| 351 | jlist[${ij}]="Canadian Journal of Fisheries and Aquatic Sciences" |
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| 352 | ij=$(( ${ij} + 1)) |
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| 353 | jlist[${ij}]="J. Atmos. Ocean. Tech." |
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| 354 | ij=$(( ${ij} + 1)) |
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| 355 | jlist[${ij}]="EOS" |
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| 356 | ij=$(( ${ij} + 1)) |
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| 357 | jlist[${ij}]="Nature" |
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| 358 | ij=$(( ${ij} + 1)) |
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| 359 | jlist[${ij}]="Physics and Chemistry of the Earth, Part B: Hydrology, Oceans and Atmosphere" |
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| 360 | ij=$(( ${ij} + 1)) |
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| 361 | jlist[${ij}]="Journal of Atmospheric and Oceanic Technology" |
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| 362 | ij=$(( ${ij} + 1)) |
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| 363 | jlist[${ij}]="Lecture Notes in Computational Science Engineering" |
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| 364 | ij=$(( ${ij} + 1)) |
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| 365 | jlist[${ij}]="In Greenhouse Gas Control Technologies" |
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| 366 | ij=$(( ${ij} + 1)) |
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| 367 | jlist[${ij}]="Chemical Geology" |
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| 368 | ij=$(( ${ij} + 1)) |
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| 369 | jlist[${ij}]="Marine Geology" |
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| 370 | ij=$(( ${ij} + 1)) |
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| 371 | jlist[${ij}]="Developments in Paleoenvironmental Research" |
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| 372 | ij=$(( ${ij} + 1)) |
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| 373 | jlist[${ij}]="Science" |
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| 374 | ij=$(( ${ij} + 1)) |
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| 375 | jlist[${ij}]="In Mediterranean Climate Variability" |
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| 376 | ij=$(( ${ij} + 1)) |
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| 377 | jlist[${ij}]="Global and Planetary Change" |
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| 378 | ij=$(( ${ij} + 1)) |
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| 379 | jlist[${ij}]="Physical Review Letters" |
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| [56] | 380 | # |
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| 381 | # following Journal name are fake ones for demo1 : references extracted from |
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| 382 | # Cantratrix Sopronica L. written by Georges Perec |
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| 383 | #find in http://www-rocq.inria.fr/who/Marc.Thiriet/PsFil/Biblio/cantatrix.ps |
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| 384 | ij=$(( ${ij} + 1)) |
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| [64] | 385 | jlist[$ij]="Res. Proc. neurophysiol. Fanatic Soc." |
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| [56] | 386 | ij=$(( ${ij} + 1)) |
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| 387 | jlist[$ij]="New Records Ass. J." |
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| 388 | ij=$(( ${ij} + 1)) |
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| 389 | jlist[$ij]="Am. J. Allegrol." |
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| 390 | ij=$(( ${ij} + 1)) |
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| 391 | jlist[$ij]="J. Neurochem. Neurocytol. Enzymol." |
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| 392 | ij=$(( ${ij} + 1)) |
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| 393 | jlist[$ij]="Hammersmith J." |
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| 394 | ij=$(( ${ij} + 1)) |
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| 395 | jlist[$ij]="Nasa Rept." |
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| 396 | ij=$(( ${ij} + 1)) |
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| 397 | jlist[$ij]="C.r. Assoc. Conc. Lam." |
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| 398 | ij=$(( ${ij} + 1)) |
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| 399 | jlist[$ij]="Gaz. med. franco-rus." |
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| 400 | ij=$(( ${ij} + 1)) |
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| 401 | jlist[$ij]="Amer. J. music. Deciency" |
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| [2] | 402 | # |
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| 403 | cat <<EOF > ${fileou} |
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| 404 | <?xml version='1.0' encoding='ISO-8859-1'?> |
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| [56] | 405 | <bibliography |
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| 406 | version="5.0" |
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| 407 | xmlns="http://docbook.org/ns/docbook" |
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| 408 | xml:id="bib${project}ref" |
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| 409 | xml:lang="${lang}"> |
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| 410 | |
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| 411 | <info> |
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| [2] | 412 | <date>$( date -u +"%Y-%m-%dT%H:%M:%SZ" )</date> |
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| [56] | 413 | </info> |
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| [2] | 414 | EOF |
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| [64] | 415 | unset lang |
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| [2] | 416 | # |
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| 417 | # strip comments |
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| 418 | fileraw_strict=/tmp/$(basename ${fileraw})_strict |
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| 419 | grep -v "^#" ${fileraw} > ${fileraw_strict} |
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| 420 | totlines=$( wc -l ${fileraw_strict} | awk '{print $1}' ) |
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| 421 | l=1 |
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| [21] | 422 | while [ ${l} -le ${totlines} ] |
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| [2] | 423 | do |
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| 424 | # extract one line |
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| 425 | line=$( sed -n ${l}p ${fileraw_strict} ) |
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| [21] | 426 | orgline=$( echo ${line} | sed -e "s/--/- -/g" ) |
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| 427 | line=$( echo ${line} | sed -e "s/</\</g" -e "s/>/\>/g" ) |
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| [46] | 428 | # detect if bibtex or not bibtex (starting with @) |
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| 429 | if [ ${line:0:1} != "@" ] |
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| 430 | then |
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| 431 | # parsing non bibtex line |
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| 432 | bibtex=0 |
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| 433 | # before the first : |
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| 434 | tmp=${line%%:*} |
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| 435 | # before the last , |
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| 436 | auths=${tmp%,*}, |
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| [56] | 437 | # replace "and" by "," |
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| 438 | auths=$( echo "${auths}" | sed -e "s/ and /,/g" ) |
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| [46] | 439 | # after the last , |
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| 440 | year=${tmp##*,} |
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| 441 | year=$( rmbl "${year}" ) |
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| 442 | ## first author before the first ., |
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| 443 | first=${auths%%.,*}. |
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| 444 | # its firstname after the last , |
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| 445 | firstfn=${first##*,} |
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| 446 | firstfn=$( rmbl "${firstfn}" ) |
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| 447 | # its surname ; before the first , |
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| 448 | firstsn=${first%%,*} |
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| 449 | firstsn=$( rmbl "${firstsn}" ) |
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| 450 | ## ref id |
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| 451 | refid=$( echo ${firstsn} | tr "[:upper:]" "[:lower:]" | tr -s " " "_" | tr -s "'" "_" | recode -d -f ISO-8859-1..flat )${year} |
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| [56] | 452 | num=$( grep -c "<biblioentry xml:id=\"${refid}_[0-9][0-9]\">" ${fileou} ) |
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| [46] | 453 | num=$(( ${num} + 1 )) |
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| 454 | [ ${num} -le 9 ] && num=0${num} |
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| 455 | refid=${refid}_${num} |
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| [56] | 456 | hasauthor=1 |
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| [46] | 457 | else |
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| 458 | # parsing bibtex line |
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| 459 | bibtex=1 |
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| 460 | # before the first , |
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| 461 | tmp=${line%%,*} |
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| 462 | endline=${line#*,} |
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| 463 | # refid is after { and before the first comma |
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| 464 | refid=${tmp#*{} |
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| 465 | # ++ test if refid already exist |
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| [47] | 466 | # check if author field is there |
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| 467 | echo ${endline} | grep -q "author" |
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| 468 | hasauthor=${?} |
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| [56] | 469 | if [ ${hasauthor} -eq 0 ] |
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| 470 | then |
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| [47] | 471 | auths=$( echo ${endline} | awk -F "," '{print $1}' | sed -e "s/\(author * = *{\)\(.*\)\(}\)/\2/") |
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| [56] | 472 | #echo "auths $auths" # genre Michael Metcalf and John Reid and Malcolm Cohen |
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| [47] | 473 | else |
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| 474 | echo "pas d'auteurs" # ++ |
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| 475 | fi |
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| [46] | 476 | endline=${endline#*,} |
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| 477 | title=$( echo ${endline} | awk -F "," '{print $1}' | sed -e "s/\(title * = *{\)\(.*\)\(}\)/\2/") |
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| [65] | 478 | #echo "title : ${title}" |
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| [46] | 479 | endline=${endline#*,} |
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| [56] | 480 | #echo ${endline} | awk -F "," '{print $1}' #++debug |
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| [46] | 481 | year=$( echo ${endline} | awk -F "," '{print $1}' | sed -e "s/\(year * = *{\)\(.*\)\(}\)/\2/") |
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| 482 | endline=${endline#*,} |
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| 483 | publisher=$( echo ${endline} | awk -F "," '{print $1}' | sed -e "s/\(publisher * = *{\)\(.*\)\(}\)/\2/") |
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| [47] | 484 | endline=${endline#*,} |
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| 485 | edition=$( echo ${endline} | awk -F "," '{print $1}' | sed -e "s/\(edition * = *{\)\(.*\)\(}\)/\2/") |
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| 486 | endline=${endline#*,} |
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| 487 | isbn=$( echo ${endline} | awk -F "," '{print $1}' | sed -e "s/\(isbn * = *{\)\(.*\)\(}\)/\2/") |
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| 488 | endline=${endline#*,} |
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| 489 | pag=$( echo ${endline} | awk -F "," '{print $1}' | sed -e "s/\(page * = *{\)\(.*\)\(}\)/\2/") |
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| [22] | 490 | |
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| [56] | 491 | if [ ${hasauthor} -eq 1 ] |
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| 492 | then |
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| [47] | 493 | ## first author before the first and |
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| 494 | first=${auths%%and*} |
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| 495 | # its surname after the last " " ++ pas vrai double nom et pb blanc dans la syntaxe |
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| 496 | # firstsn=${first##* } . ok en interactif . pas ok en script |
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| 497 | firstsn=$( echo ${first} | awk '{print $2}') |
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| [56] | 498 | #echo "firstsn $firstsn" |
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| [47] | 499 | # its firstname before the first " " |
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| 500 | firstfn=${first%% *} |
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| 501 | fi |
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| [46] | 502 | fi |
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| 503 | |
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| [21] | 504 | cat <<EOF >> ${fileou} |
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| [56] | 505 | <biblioentry xml:id="${refid}"> |
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| [2] | 506 | <!-- date |
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| 507 | $( date -u +"%Y-%m-%dT%H:%M:%SZ" ) |
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| 508 | --> |
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| 509 | <!-- original text |
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| [22] | 510 | ${orgline} |
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| [2] | 511 | --> |
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| [47] | 512 | EOF |
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| [56] | 513 | if [ ${hasauthor} -eq 1 ] |
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| 514 | then |
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| [47] | 515 | cat <<EOF >> ${fileou} |
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| [2] | 516 | <authorgroup> |
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| 517 | <author> <personname> <surname>${firstsn}</surname> <firstname>${firstfn}</firstname> </personname> </author> |
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| 518 | EOF |
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| [22] | 519 | |
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| [2] | 520 | ## other authors.. |
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| [46] | 521 | if [ ${bibtex} -eq 0 ] |
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| 522 | then |
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| 523 | previous=${first}, |
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| 524 | # next authors... |
|---|
| 525 | next=${auths##*${previous}} |
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| 526 | fi |
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| 527 | if [ ${bibtex} -eq 1 ] |
|---|
| 528 | then |
|---|
| 529 | previous=${first}"and " |
|---|
| 530 | # next authors... |
|---|
| [56] | 531 | #echo "auths ${auths}" |
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| [46] | 532 | next=${auths##*${previous}} |
|---|
| 533 | if [ "${next}and " = "${previous}" ] |
|---|
| 534 | then |
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| 535 | next="" |
|---|
| 536 | fi |
|---|
| 537 | fi |
|---|
| [56] | 538 | #echo "previous ${previous}" |
|---|
| 539 | #echo "next ${next}" |
|---|
| [2] | 540 | # while the next author is not empty |
|---|
| [21] | 541 | while [ "${next}" != "" ] |
|---|
| [2] | 542 | do |
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| [46] | 543 | if [ ${bibtex} -eq 0 ] |
|---|
| 544 | then |
|---|
| 545 | # get the first next author; before the first , |
|---|
| 546 | next=${next%%,*} |
|---|
| 547 | # its surname ; after the last . |
|---|
| 548 | nextsn=${next##*.} |
|---|
| 549 | nextsn=$( rmbl "${nextsn}" ) |
|---|
| 550 | # its firstname ; before the last . |
|---|
| 551 | nextfn=${next%.*}. |
|---|
| 552 | nextfn=$( rmbl "${nextfn}" ) |
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| 553 | fi |
|---|
| 554 | if [ ${bibtex} -eq 1 ] |
|---|
| 555 | then |
|---|
| 556 | # get the first next author; before the first "and" |
|---|
| 557 | next=${next%%and *} |
|---|
| 558 | # its surname after the last " " ++ pas vrai double nom et pb blanc dans la syntaxe |
|---|
| 559 | # nextsn=${next##* } . ok en interactif . pas ok en script |
|---|
| 560 | nextsn=$( echo ${next} | awk '{print $2}') |
|---|
| [56] | 561 | #echo "nextsn $nextsn" |
|---|
| [46] | 562 | # its nextname before the first " " |
|---|
| 563 | nextfn=${next%% *} |
|---|
| 564 | fi |
|---|
| [2] | 565 | # |
|---|
| 566 | echo " <author> <personname> <surname>${nextsn}</surname> <firstname>${nextfn}</firstname> </personname> </author>" >> ${fileou} |
|---|
| [56] | 567 | #echo " <author> <personname> <surname>${nextsn}</surname> <firstname>${nextfn}</firstname> </personname> </author>" #++debug |
|---|
| [46] | 568 | if [ ${bibtex} -eq 0 ] |
|---|
| 569 | then |
|---|
| 570 | previous=${next}, |
|---|
| 571 | next=${auths##*${previous}} |
|---|
| 572 | fi |
|---|
| 573 | if [ ${bibtex} -eq 1 ] |
|---|
| 574 | then |
|---|
| 575 | previous=${next}"and " |
|---|
| 576 | next=${auths##*${previous}} |
|---|
| 577 | fi |
|---|
| [2] | 578 | done |
|---|
| [21] | 579 | echo " </authorgroup>" >> ${fileou} |
|---|
| [47] | 580 | fi |
|---|
| [22] | 581 | |
|---|
| [2] | 582 | # end of the line ; after the first : |
|---|
| 583 | endline=${line#*:} |
|---|
| 584 | ## find the journal |
|---|
| 585 | j=1 |
|---|
| 586 | jfound="" |
|---|
| 587 | jlistsize=${#jlist[@]} |
|---|
| [22] | 588 | while [[ ${j} -le ${jlistsize} && "${jfound}" == "" ]] |
|---|
| [2] | 589 | do |
|---|
| [22] | 590 | ok=$( echo ${endline} | grep -ci "${jlist[j]} *," ) |
|---|
| [64] | 591 | [ ${ok} -eq 1 ] && jfound="${jlist[j]}" |
|---|
| [22] | 592 | j=$(( ${j} + 1 )) |
|---|
| [2] | 593 | done |
|---|
| [64] | 594 | unset ok |
|---|
| [22] | 595 | if [ "${jfound}" == "" ] |
|---|
| [2] | 596 | then |
|---|
| [22] | 597 | echo "eee: Journal not found " |
|---|
| [21] | 598 | echo "${endline}" |
|---|
| [64] | 599 | #++set |
|---|
| [56] | 600 | #++exit 1 |
|---|
| [47] | 601 | #+++ following lines are not yet validate |
|---|
| 602 | # it might be a book, a manual, a conference, etc. ++ |
|---|
| 603 | echo " <title>${title}</title>" >> ${fileou} |
|---|
| 604 | cat <<EOF >> ${fileou} |
|---|
| 605 | <biblioset relation="nojournal"> |
|---|
| 606 | <title>${title}</title> |
|---|
| 607 | <pagenums>${pag}</pagenums> |
|---|
| 608 | <pubdate>${year}</pubdate> |
|---|
| 609 | </biblioset> |
|---|
| 610 | EOF |
|---|
| 611 | cat <<EOF >> ${fileou} |
|---|
| 612 | </biblioentry> |
|---|
| 613 | |
|---|
| 614 | EOF |
|---|
| 615 | fi # end of if jfound empty (ie not an article) |
|---|
| 616 | if [ "${jfound}" != "" ] |
|---|
| 617 | then |
|---|
| [22] | 618 | ## title |
|---|
| [2] | 619 | # before the first : |
|---|
| 620 | title=${endline%%${jfound}*} |
|---|
| [21] | 621 | title=$( cleanname "${title}" ) |
|---|
| 622 | echo " <title>${title}</title>" >> ${fileou} |
|---|
| [22] | 623 | ## end |
|---|
| [2] | 624 | ## end of the line ; after the first ${jfound} |
|---|
| 625 | endline=${endline#*${jfound}} |
|---|
| [21] | 626 | endline=$( cleanname "${endline}" ) |
|---|
| [2] | 627 | ## doi |
|---|
| [21] | 628 | endline=$( echo ${endline} | sed -e "s/[dD][oO][iI] *\t* *: *\t* */doi:/" ) |
|---|
| 629 | ok=$( echo ${endline} | grep -ic "doi:" ) |
|---|
| [22] | 630 | if [ ${ok} -eq 1 ] |
|---|
| [2] | 631 | then |
|---|
| 632 | doi=${endline##*doi:} |
|---|
| [21] | 633 | echo " <biblioid class=\"doi\">${doi}</biblioid>" >> ${fileou} |
|---|
| [64] | 634 | unset doi |
|---|
| [2] | 635 | endline=${endline%doi:*} |
|---|
| [21] | 636 | endline=$( cleanname "${endline}" ) |
|---|
| [2] | 637 | else |
|---|
| [21] | 638 | echo "non doi: ${line}" |
|---|
| [65] | 639 | echo "" |
|---|
| [2] | 640 | fi |
|---|
| [21] | 641 | num=$( echo ${endline} | tr -dc "," | wc -c ) |
|---|
| 642 | case ${num} in |
|---|
| [65] | 643 | 0) |
|---|
| 644 | ### echo ${num}: ${endline} |
|---|
| 645 | cat <<EOF >> ${fileou} |
|---|
| 646 | <biblioset relation="journal"> |
|---|
| 647 | <title>${jfound}</title> |
|---|
| 648 | <pubdate>${year}</pubdate> |
|---|
| 649 | <bibliomisc>${endline}</bibliomisc> |
|---|
| 650 | </biblioset> |
|---|
| 651 | EOF |
|---|
| 652 | unset jfound |
|---|
| 653 | unset year |
|---|
| 654 | ;; |
|---|
| 655 | |
|---|
| [22] | 656 | 1) |
|---|
| [21] | 657 | ### echo ${num}: ${endline} |
|---|
| [2] | 658 | vol=${endline%,*} |
|---|
| [21] | 659 | vol=$( cleanname "${vol}" ) |
|---|
| [22] | 660 | pag=${endline##*,} |
|---|
| [21] | 661 | pag=$( cleanname "${pag}" ) |
|---|
| 662 | cat <<EOF >> ${fileou} |
|---|
| [2] | 663 | <biblioset relation="journal"> |
|---|
| 664 | <title>${jfound}</title> |
|---|
| 665 | <volumenum>${vol}</volumenum><pagenums>${pag}</pagenums> |
|---|
| 666 | <pubdate>${year}</pubdate> |
|---|
| 667 | </biblioset> |
|---|
| 668 | EOF |
|---|
| [65] | 669 | unset vol |
|---|
| 670 | unset pag |
|---|
| 671 | unset jfound |
|---|
| 672 | unset year |
|---|
| [2] | 673 | ;; |
|---|
| [22] | 674 | 2) |
|---|
| [2] | 675 | vol=${endline%,*} |
|---|
| [21] | 676 | vol=$( cleanname "${vol}" ) |
|---|
| [22] | 677 | iss=${vol##*,} |
|---|
| [21] | 678 | iss=$( cleanname "${iss}" ) |
|---|
| [2] | 679 | vol=${vol%,*} |
|---|
| [21] | 680 | vol=$( cleanname "${vol}" ) |
|---|
| [22] | 681 | pag=${endline##*,} |
|---|
| [21] | 682 | pag=$( cleanname "${pag}" ) |
|---|
| 683 | cat <<EOF >> ${fileou} |
|---|
| [64] | 684 | <biblioset relation="journal"> |
|---|
| [2] | 685 | <title>${jfound}</title> |
|---|
| 686 | <volumenum>${vol}</volumenum><issuenum>${iss}</issuenum><pagenums>${pag}</pagenums> |
|---|
| 687 | <pubdate>${year}</pubdate> |
|---|
| 688 | </biblioset> |
|---|
| 689 | EOF |
|---|
| [65] | 690 | unset vol |
|---|
| 691 | unset pag |
|---|
| 692 | unset jfound |
|---|
| 693 | unset year |
|---|
| 694 | unset iss |
|---|
| [2] | 695 | ;; |
|---|
| [65] | 696 | 6) |
|---|
| 697 | conftitle=${endline%%,*} |
|---|
| 698 | endline=${endline#*,} |
|---|
| 699 | confdates=${endline%%,*} # day(s) month |
|---|
| 700 | endline=${endline#*,} |
|---|
| 701 | confdates="${confdates}, ${endline%%,*}" # day(s) month and year |
|---|
| 702 | confdates=$( cleanname "${confdates}" ) |
|---|
| 703 | endline=${endline#*,} |
|---|
| 704 | confaddress=${endline%%,*} # Town |
|---|
| 705 | endline=${endline#*,} |
|---|
| 706 | confaddress="${confaddress}, ${endline%%,*}" # Town and country |
|---|
| 707 | confaddress=$( cleanname "${confaddress}" ) |
|---|
| 708 | endline=${endline#*,} |
|---|
| 709 | publishername=${endline%%,*} |
|---|
| 710 | publishername=$( cleanname "${publishername}" ) |
|---|
| 711 | endline=${endline#*,} |
|---|
| 712 | pag=${endline##*,} |
|---|
| 713 | pag=$( cleanname "${pag}" ) |
|---|
| 714 | #set |
|---|
| 715 | #read a |
|---|
| 716 | cat <<EOF >> ${fileou} |
|---|
| 717 | <biblioset relation="conference"> |
|---|
| 718 | <title>${jfound}</title> |
|---|
| 719 | <pubdate>${year}</pubdate> |
|---|
| 720 | <publisher><publishername>${publishername}</publishername></publisher> |
|---|
| 721 | <pagenums>${pag}</pagenums> |
|---|
| 722 | <confgroup> |
|---|
| 723 | <conftitle>${conftitle}</conftitle> |
|---|
| 724 | <confdates>${confdates}</confdates> |
|---|
| 725 | <address>${confaddress}</address> |
|---|
| 726 | </confgroup> |
|---|
| 727 | </biblioset> |
|---|
| 728 | EOF |
|---|
| 729 | unset confaddress |
|---|
| 730 | unset conftitle |
|---|
| 731 | unset confdates |
|---|
| 732 | unset pag |
|---|
| 733 | unset publishername |
|---|
| 734 | unset year |
|---|
| 735 | unset jfound |
|---|
| 736 | ;; |
|---|
| 737 | 10) |
|---|
| 738 | publishername=${endline%%Editors,*} |
|---|
| 739 | publishername="${publishername} Editors" |
|---|
| 740 | publishername=$( cleanname "${publishername}" ) |
|---|
| 741 | endline=${endline#*Editors,} |
|---|
| 742 | vol=${endline%%,*} |
|---|
| 743 | vol=$( cleanname "${vol}" ) |
|---|
| 744 | endline=${endline#*,} |
|---|
| 745 | pag=${endline%%,*} |
|---|
| 746 | pag=$( cleanname "${pag}" ) |
|---|
| 747 | endline=${endline#*,} |
|---|
| 748 | isbn=${endline%%,*} |
|---|
| 749 | isbn=$(echo ${isbn} | sed -e "s/ISBN ://") |
|---|
| 750 | isbn=$( cleanname "${isbn}" ) |
|---|
| 751 | endline=${endline#*,} |
|---|
| 752 | agu=${endline%%,*} |
|---|
| 753 | agu=$(echo ${agu} | sed -e "s/AGU ://") |
|---|
| 754 | agu=$( cleanname "${agu}" ) |
|---|
| 755 | |
|---|
| 756 | endline=${endline#*${agu}} |
|---|
| 757 | endline=$( cleanname "${endline}" ) |
|---|
| 758 | endline=$( cleanname "${endline}" ) |
|---|
| 759 | |
|---|
| 760 | cat <<EOF >> ${fileou} |
|---|
| 761 | <biblioid class="isbn">${isbn}</biblioid> |
|---|
| 762 | <biblioid class="other" otherclass="AGU">${agu}</biblioid> |
|---|
| 763 | <biblioset relation="journal"> |
|---|
| 764 | <title>${jfound}</title> |
|---|
| 765 | <pubdate>${year}</pubdate> |
|---|
| 766 | <publisher><publishername>${publishername}</publishername></publisher> |
|---|
| 767 | <volumenum>${vol}</volumenum> |
|---|
| 768 | <pagenums>${pag}</pagenums> |
|---|
| 769 | <bibliomisc>${endline}</bibliomisc> |
|---|
| 770 | </biblioset> |
|---|
| 771 | EOF |
|---|
| 772 | unset isbn |
|---|
| 773 | unset agu |
|---|
| 774 | unset pag |
|---|
| 775 | unset publishername |
|---|
| 776 | unset year |
|---|
| 777 | unset jfound |
|---|
| 778 | unset vol |
|---|
| 779 | |
|---|
| 780 | ;; |
|---|
| [2] | 781 | *) |
|---|
| [65] | 782 | echo ${num}: ${endline} # ++debug |
|---|
| 783 | #set |
|---|
| 784 | #exit 1 #++ debug |
|---|
| [21] | 785 | cat <<EOF >> ${fileou} |
|---|
| [64] | 786 | <biblioset relation="journal"> |
|---|
| [2] | 787 | <title>${jfound}</title> |
|---|
| 788 | <pubdate>${year}</pubdate> |
|---|
| 789 | <bibliomisc>${endline}</bibliomisc> |
|---|
| 790 | </biblioset> |
|---|
| 791 | EOF |
|---|
| 792 | ;; |
|---|
| 793 | esac |
|---|
| [22] | 794 | |
|---|
| [21] | 795 | cat <<EOF >> ${fileou} |
|---|
| [2] | 796 | </biblioentry> |
|---|
| [22] | 797 | |
|---|
| [2] | 798 | EOF |
|---|
| [47] | 799 | fi # end of if jfound not empty |
|---|
| [65] | 800 | unset title |
|---|
| 801 | unset vol |
|---|
| 802 | unset year |
|---|
| 803 | unset pag |
|---|
| [22] | 804 | l=$(( ${l} + 1 )) |
|---|
| 805 | |
|---|
| [2] | 806 | done |
|---|
| [64] | 807 | unset totlines |
|---|
| 808 | unset l |
|---|
| [21] | 809 | echo "</bibliography>" >> ${fileou} |
|---|
| [2] | 810 | |
|---|
| [56] | 811 | xml val --err \ |
|---|
| 812 | --xsd http://www.docbook.org/xml/5.0/xsd/docbook.xsd \ |
|---|
| 813 | ${fileou} 1> xmlstarlet.log 2>&1 |
|---|
| [2] | 814 | |
|---|
| 815 | # clean |
|---|
| [56] | 816 | echo "iii : xslstarlet.log contains sdtout and stderr from xml command on ${fileou}" |
|---|
| [22] | 817 | echo "iii : which was done just to check consistence of ${fileou}" |
|---|
| [56] | 818 | more xmlstarlet.log |
|---|
| 819 | rm -i xmlstarlet.log |
|---|
| 820 | # |
|---|
| [2] | 821 | case ${type} in |
|---|
| [22] | 822 | raw) |
|---|
| [2] | 823 | echo "iii : ${fileraw_strict} contains a copy of input file without comments" |
|---|
| 824 | rm -i ${fileraw_strict} |
|---|
| 825 | ;; |
|---|
| 826 | mailbody) |
|---|
| 827 | echo "iii : ${fileraw} contains a copy of input file" |
|---|
| 828 | rm -i ${fileraw} |
|---|
| 829 | echo "iii : ${fileraw_strict} contains a copy of input file without comments" |
|---|
| 830 | rm -i ${fileraw_strict} |
|---|
| 831 | ;; |
|---|
| 832 | esac |
|---|
| 833 | # |
|---|
| 834 | echo " iii : you have a some new or modified bibliographic references in ${fileou} (biblioentry)" |
|---|
| [47] | 835 | echo " iii : you can add them in ${fileou}" #++ filename path |
|---|
| 836 | echo " iii : modify date in ${fileou}" #++ filename path |
|---|
| [2] | 837 | echo " iii : but please take care of id last part (after underscore) that may" |
|---|
| 838 | echo " iii : be in conflict with existing ones" #++ pour s'affranchir de ce souci il faudrait donner en entrée complémentaire le fichier à compléter. |
|---|
| 839 | # |
|---|
| 840 | exit 0 |
|---|
