[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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| 7 | # |
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| 8 | # donnerait |
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| 9 | # |
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| 10 | # <biblioentry id="behara2004"> |
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| 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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| 25 | # <bibliomisc role="doi">doi</bibliomisc> |
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| 26 | # <bibliomisc role="pseudoref">In press.</bibliomisc> |
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| 27 | # <bibliomisc role="internalref">from |
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| 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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| 32 | # |
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| 33 | # example : |
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| 34 | # $ ./bibopa.sh -i /Users/smasson/Bibopa/biball.txt -t raw |
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| 35 | # $ ./bibopa.sh -i data/mail2007-04-25T08:58:16Z.txt -t mailbody |
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| 36 | # |
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| 37 | # see also mailtousernemo.sh |
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| 38 | # |
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| 39 | # original location : |
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| 40 | # /usr/home/fplod/incas/bibnemo/src/bibnemomaf/bibopa.sh sur cerbere.locean-ipsl.upmc.fr |
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| 41 | # |
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| 42 | # update |
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| 43 | # ++ gestion des comments |
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| 44 | # ++ gestion des id existants (cf à la fin) |
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| 45 | # ++ option debug |
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[15] | 46 | # smasson 2007-06-07T16:43:42Z arete.locean-ipsl.upmc.fr (Darwin) |
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| 47 | # Add journals |
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[2] | 48 | # fplod 2007-05-10T09:17:09Z aedon.locean-ipsl.upmc.fr (Darwin) |
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| 49 | # dernières touches |
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| 50 | # fplod 2007-04-25T10:59:49Z cerbere.locean-ipsl.upmc.fr (Linux) |
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| 51 | # add a filein parameter and an option for mailbody |
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| 52 | # comments (line begininig with #) are now possible |
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| 53 | # Sebastien Masson avril 2007 creation |
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| 54 | # |
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| 55 | |
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| 56 | rmbl () { |
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| 57 | echo "$1" | sed -e "s/^ *//" | sed -e "s/ *$//" |
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| 58 | } |
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| 59 | cleanname () { |
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| 60 | echo "$1" | sed -e "s/^ *//" \ |
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| 61 | -e "s/^ *,//" \ |
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| 62 | -e "s/^ *;//" \ |
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| 63 | -e "s/^ *\.//" \ |
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| 64 | -e "s/ *$//" \ |
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| 65 | -e "s/, *$//" \ |
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| 66 | -e "s/; *$//" \ |
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| 67 | -e "s/\. *$//" |
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| 68 | } |
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| 69 | # |
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| 70 | set -o posix |
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| 71 | command=$(basename ${0} .sh) |
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| 72 | log_date=$(date -u +"%Y-%m-%dT%H:%M:%SZ") |
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| 73 | log=/tmp/${command}.${log_date} |
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| 74 | # |
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| 75 | # test if xsltproc is available |
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| 76 | type xsltproc 1> /dev/null 2>&1 |
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| 77 | status=${?} |
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| 78 | if [ ${status} -ne 0 ] |
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| 79 | then |
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| 80 | echo " eee : xsltproc not found" |
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| 81 | exit 1 |
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| 82 | fi |
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| 83 | # |
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| 84 | usage=" Usage : ${command} -i filein -t type" |
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| 85 | # |
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| 86 | while [ ! -z "${1}" ] # ++ pb bash |
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| 87 | do |
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| 88 | case ${1} in |
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| 89 | -i) # filein |
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| 90 | filein=${2} |
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| 91 | shift |
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| 92 | ;; |
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| 93 | -t) # type |
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| 94 | type=${2} |
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| 95 | shift |
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| 96 | ;; |
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| 97 | *) # other choice |
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| 98 | echo "${usage}" |
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| 99 | exit 1 |
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| 100 | ;; |
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| 101 | esac |
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| 102 | shift # next flag |
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| 103 | done |
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| 104 | # |
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| 105 | set -u |
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| 106 | # |
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| 107 | # check for filein |
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| 108 | if [ ! -f ${filein} ] |
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| 109 | then |
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| 110 | echo "eee : ${filein} not found" |
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| 111 | exit 1 |
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| 112 | fi |
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| 113 | # |
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| 114 | case ${type} in |
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| 115 | raw) # file like data/biball.txt |
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| 116 | fileraw=${filein} |
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| 117 | ;; |
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| 118 | mailbody) # file like data/mail2007-04-25T08:58:16Z.txt |
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| 119 | fileraw=/tmp/$(basename ${filein}).raw |
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| 120 | echo "# from ${filein}" > ${fileraw} |
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| 121 | echo "# ${log_date}" >> ${fileraw} |
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| 122 | echo "# corrections" >> ${fileraw} |
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| 123 | grep "correction_.*=" ${filein} | grep -v "correction_.*=$" | \ |
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| 124 | sed -e "s/correction_.*=//">> ${fileraw} |
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| 125 | echo "# new references" >> ${fileraw} |
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| 126 | awk "/newreferences=/,/comments=/" ${filein} | sed -e "s/newreferences=//" -e "/comments=/d" >> ${fileraw} |
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| 127 | #more ${fileraw} # ++ if debug |
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| 128 | #read a #++ if debug |
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| 129 | ;; |
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| 130 | *) |
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| 131 | echo "eee : type should be raw or mailbody" |
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| 132 | exit 1 |
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| 133 | ;; |
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| 134 | esac |
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| 135 | # |
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| 136 | # check for output |
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| 137 | fileou=$( basename ${filein} .txt).xml |
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| 138 | if [ -f ${fileou} ] |
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| 139 | then |
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| 140 | echo "eee : ${fileou} already exist" |
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| 141 | #exit 1 # ++ if not debug |
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| 142 | fi |
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| 143 | # |
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| 144 | jlist[1]="J. Climate" |
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| 145 | jlist[2]="Journal of Climate" |
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| 146 | jlist[3]="Ocean Modelling" |
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| 147 | jlist[4]="Geophys. Res. Lett." |
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| 148 | jlist[5]="J. Geophys. Res." |
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| 149 | jlist[6]="Tellus A" |
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| 150 | jlist[7]="Tellus B" |
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| 151 | jlist[8]="J. Phys. Oceanogr." |
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| 152 | jlist[9]="Clim. Dyn." |
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| 153 | jlist[10]="Climate Dynamics" |
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| 154 | jlist[11]="Dyn. Atmos. Oceans" |
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| 155 | jlist[12]="Mon. Wea. Rev." |
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| 156 | jlist[13]="Global Biogeochem. Cycles" |
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| 157 | jlist[14]="Nonlinear Processes in Geophysics" |
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| 158 | jlist[15]="Ocean Science" |
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| 159 | jlist[16]="J. Mar. Systems" |
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| 160 | jlist[17]="J. Atmos. Sc." |
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| 161 | jlist[18]="Proc. Royal Soc." |
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| 162 | jlist[19]="Bull. Amer. Meteorol. Soc." |
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| 163 | jlist[20]="Ocean Dyn." |
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| 164 | jlist[21]="Geophysical Monograph Series" |
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| 165 | jlist[22]="Paleoceanography" |
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| 166 | jlist[23]="Annales Geophysicae" |
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| 167 | jlist[24]="Annals of Geophys." |
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| 168 | jlist[25]="Deep Sea Research Part II: Topical Studies in Oceanography" |
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| 169 | jlist[26]="Deep Sea Res. II" |
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| 170 | jlist[27]="Atmospheric Chemistry and Physics" |
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| 171 | jlist[28]="Atmospheric Chemistry and Physics Discussions" |
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| 172 | jlist[29]="Earth Plan. Sc. Lett." |
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| 173 | jlist[30]="J. Mar. Res." |
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| 174 | jlist[31]="PCMDI Report Series" |
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| 175 | jlist[32]="J. Mar. Syst." |
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| 176 | jlist[33]="Note du Pole de Modelisation" |
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| 177 | jlist[34]="Calculateurs Paralleles" |
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| 178 | jlist[35]="Note Scientifique du Pole de Modelisation" |
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| 179 | jlist[36]="Lecture Notes in Computer Science" |
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| 180 | jlist[37]="Prog. Oceanogr." |
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| 181 | jlist[38]="Deep Sea Research Part I: Oceanographic Research Papers" |
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| 182 | jlist[39]="Deep Sea Res. I" |
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| 183 | jlist[40]="IEEE Trans. Geosci. Remote Sensing" |
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| 184 | jlist[41]="ECMWF Tech. Memorandum" |
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| 185 | jlist[42]="J. Environ. Radioactivity" |
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| 186 | jlist[43]="Int. WOCE Newsletter" |
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| 187 | jlist[44]="C. R. Acad. Sci. Paris" |
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| 188 | jlist[45]="C. R. Acad. Sci. Paris, Earth and Planetary Sciences" |
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| 189 | jlist[46]="In The mathematics of models for climatology and environment" |
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| 190 | jlist[47]="Oceanol. Acta" |
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| 191 | jlist[48]="The global atmosphere and ocean system" |
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| 192 | jlist[49]="NATO Advanced Study Institute" |
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| 193 | jlist[50]="WCRP" |
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| 194 | jlist[51]="The Courier" |
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| 195 | jlist[52]="Elsevier Oceanographic Series" |
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| 196 | jlist[53]="In Conference Proceedings of the 1988 International Conference on Supercomputing" |
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| 197 | jlist[54]="In Science and engineering on Cray Supercomputers" |
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| 198 | jlist[55]="In Modeling the Earth's Climate and its Variability" |
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| 199 | jlist[56]="Fish. Oceanogr." |
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| 200 | jlist[57]="Q. J. R. Meteor. Soc." |
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| 201 | jlist[58]="In High performance computing in the geosciences" |
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| 202 | jlist[59]="Int. J. Numer. Meth. in Fluids" |
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| 203 | jlist[60]="Lecture notes in Physics" |
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| 204 | jlist[61]="J. Meterol. Soc. Japan" |
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| 205 | jlist[62]="Journal of Marine Systems" |
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| 206 | jlist[63]="Canadian Journal of Fisheries and Aquatic Sciences" |
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| 207 | jlist[64]="J. Atmos. Ocean. Tech." |
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| 208 | jlist[65]="EOS" |
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| 209 | jlist[66]="Nature" |
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| 210 | jlist[67]="Physics and Chemistry of the Earth, Part B: Hydrology, Oceans and Atmosphere" |
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| 211 | jlist[68]="Journal of Atmospheric and Oceanic Technology" |
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| 212 | jlist[69]="Lecture Notes in Computational Science Engineering" |
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| 213 | jlist[70]="In Greenhouse Gas Control Technologies" |
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| 214 | jlist[71]="Chemical Geology" |
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| 215 | jlist[72]="Marine Geology" |
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| 216 | jlist[73]="Developments in Paleoenvironmental Research" |
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| 217 | jlist[74]="Science" |
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| 218 | jlist[75]="In Mediterranean Climate Variability" |
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[15] | 219 | jlist[76]="Global and Planetary Change" |
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| 220 | jlist[77]="Physical Review Letters" |
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[2] | 221 | #jlist[]="" |
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| 222 | # |
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| 223 | # |
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| 224 | cat <<EOF > ${fileou} |
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| 225 | <?xml version='1.0' encoding='ISO-8859-1'?> |
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| 226 | <!DOCTYPE bibliography PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN" |
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| 227 | "http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd"> |
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| 228 | <bibliography id="bibrefnemo" lang="en"> |
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| 229 | <bibliographyinfo> |
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| 230 | <date>$( date -u +"%Y-%m-%dT%H:%M:%SZ" )</date> |
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| 231 | </bibliographyinfo> |
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| 232 | EOF |
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| 233 | # |
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| 234 | # strip comments |
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| 235 | fileraw_strict=/tmp/$(basename ${fileraw})_strict |
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| 236 | grep -v "^#" ${fileraw} > ${fileraw_strict} |
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| 237 | totlines=$( wc -l ${fileraw_strict} | awk '{print $1}' ) |
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| 238 | l=1 |
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| 239 | while [ $l -le $totlines ] |
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| 240 | do |
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| 241 | # extract one line |
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| 242 | |
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| 243 | line=$( sed -n ${l}p ${fileraw_strict} ) |
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| 244 | orgline=$( echo $line | sed -e "s/--/- -/g" ) |
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| 245 | line=$( echo $line | sed -e "s/</\</g" -e "s/>/\>/g" ) |
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| 246 | # before the first : |
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| 247 | tmp=${line%%:*} |
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| 248 | # before the last , |
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| 249 | auths=${tmp%,*}, |
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| 250 | # supress and |
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| 251 | auths=$( echo "$auths" | sed -e "s/ and //g" ) |
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| 252 | # after the last , |
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| 253 | year=${tmp##*,} |
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| 254 | year=$( rmbl "$year" ) |
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| 255 | ## first author before the first ., |
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| 256 | first=${auths%%.,*}. |
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| 257 | # its firstname after the last , |
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| 258 | firstfn=${first##*,} |
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| 259 | firstfn=$( rmbl "$firstfn" ) |
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| 260 | # its surname ; before the first , |
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| 261 | firstsn=${first%%,*} |
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| 262 | firstsn=$( rmbl "$firstsn" ) |
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| 263 | ## ref id |
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| 264 | refid=$( echo $firstsn | tr "[:upper:]" "[:lower:]" | tr -s " " "_" | tr -s "'" "_" | recode -d -f ISO-8859-1..flat )$year |
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| 265 | num=$( grep -c "<biblioentry id=\"${refid}_[0-9][0-9]\">" $fileou ) |
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| 266 | num=$(( $num + 1 )) |
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| 267 | [ $num -le 9 ] && num=0$num |
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| 268 | refid=${refid}_$num |
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| 269 | |
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| 270 | cat <<EOF >> $fileou |
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| 271 | <biblioentry id="${refid}"> |
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| 272 | <!-- date |
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| 273 | $( date -u +"%Y-%m-%dT%H:%M:%SZ" ) |
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| 274 | --> |
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| 275 | <!-- original text |
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| 276 | $orgline |
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| 277 | --> |
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| 278 | <authorgroup> |
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| 279 | <author> <personname> <surname>${firstsn}</surname> <firstname>${firstfn}</firstname> </personname> </author> |
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| 280 | EOF |
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| 281 | |
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| 282 | ## other authors.. |
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| 283 | previous=${first}, |
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| 284 | # next authors... |
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| 285 | next=${auths##*${previous}} |
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| 286 | # while the next author is not empty |
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| 287 | while [ "$next" != "" ] |
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| 288 | do |
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| 289 | # get the first next author; before the first , |
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| 290 | next=${next%%,*} |
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| 291 | # its surname ; after the last . |
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| 292 | nextsn=${next##*.} |
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| 293 | nextsn=$( rmbl "$nextsn" ) |
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| 294 | # its firstname ; before the last . |
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| 295 | nextfn=${next%.*}. |
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| 296 | nextfn=$( rmbl "$nextfn" ) |
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| 297 | # |
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| 298 | echo " <author> <personname> <surname>${nextsn}</surname> <firstname>${nextfn}</firstname> </personname> </author>" >> ${fileou} |
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| 299 | previous=${next}, |
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| 300 | next=${auths##*${previous}} |
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| 301 | |
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| 302 | done |
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| 303 | echo " </authorgroup>" >> $fileou |
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| 304 | |
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| 305 | # end of the line ; after the first : |
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| 306 | endline=${line#*:} |
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| 307 | |
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| 308 | ## find the journal |
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| 309 | j=1 |
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| 310 | jfound="" |
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| 311 | jlistsize=${#jlist[@]} |
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| 312 | while [[ $j -le $jlistsize && "${jfound}" == "" ]] |
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| 313 | do |
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| 314 | ok=$( echo $endline | grep -ci "${jlist[j]} *," ) |
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| 315 | [ $ok -eq 1 ] && jfound="${jlist[j]}" |
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| 316 | j=$(( $j + 1 )) |
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| 317 | done |
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| 318 | if [ "$jfound" == "" ] |
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| 319 | then |
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| 320 | echo ERROR Journal not found |
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| 321 | echo $endline |
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| 322 | exit |
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| 323 | fi |
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| 324 | ## title |
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| 325 | # before the first : |
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| 326 | title=${endline%%${jfound}*} |
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| 327 | title=$( cleanname "$title" ) |
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| 328 | echo " <title>${title}</title>" >> $fileou |
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| 329 | ## end |
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| 330 | ## end of the line ; after the first ${jfound} |
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| 331 | endline=${endline#*${jfound}} |
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| 332 | endline=$( cleanname "$endline" ) |
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| 333 | ## doi |
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| 334 | endline=$( echo $endline | sed -e "s/[dD][oO][iI] *\t* *: *\t* */doi:/" ) |
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| 335 | ok=$( echo $endline | grep -ic "doi:" ) |
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| 336 | if [ $ok -eq 1 ] |
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| 337 | then |
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| 338 | doi=${endline##*doi:} |
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| 339 | echo " <bibliomisc role=\"doi\">${doi}</bibliomisc>" >> $fileou |
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| 340 | endline=${endline%doi:*} |
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| 341 | endline=$( cleanname "$endline" ) |
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| 342 | else |
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| 343 | echo non doi: $line |
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| 344 | fi |
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| 345 | num=$( echo $endline | tr -dc "," | wc -c ) |
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| 346 | case $num in |
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| 347 | 1) |
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| 348 | ### echo $num: ${endline} |
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| 349 | vol=${endline%,*} |
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| 350 | vol=$( cleanname "$vol" ) |
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| 351 | pag=${endline##*,} |
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| 352 | pag=$( cleanname "$pag" ) |
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| 353 | cat <<EOF >> $fileou |
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| 354 | <biblioset relation="journal"> |
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| 355 | <title>${jfound}</title> |
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| 356 | <volumenum>${vol}</volumenum><pagenums>${pag}</pagenums> |
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| 357 | <pubdate>${year}</pubdate> |
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| 358 | </biblioset> |
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| 359 | EOF |
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| 360 | ;; |
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| 361 | 2) |
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| 362 | vol=${endline%,*} |
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| 363 | vol=$( cleanname "$vol" ) |
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| 364 | iss=${vol##*,} |
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| 365 | iss=$( cleanname "$iss" ) |
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| 366 | vol=${vol%,*} |
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| 367 | vol=$( cleanname "$vol" ) |
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| 368 | pag=${endline##*,} |
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| 369 | pag=$( cleanname "$pag" ) |
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| 370 | cat <<EOF >> $fileou |
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| 371 | <biblioset role="journal"> |
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| 372 | <title>${jfound}</title> |
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| 373 | <volumenum>${vol}</volumenum><issuenum>${iss}</issuenum><pagenums>${pag}</pagenums> |
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| 374 | <pubdate>${year}</pubdate> |
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| 375 | </biblioset> |
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| 376 | EOF |
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| 377 | ;; |
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| 378 | *) |
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| 379 | echo $num: ${endline} |
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| 380 | cat <<EOF >> $fileou |
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| 381 | <biblioset role="journal"> |
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| 382 | <title>${jfound}</title> |
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| 383 | <pubdate>${year}</pubdate> |
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| 384 | <bibliomisc>${endline}</bibliomisc> |
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| 385 | </biblioset> |
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| 386 | EOF |
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| 387 | ;; |
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| 388 | esac |
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| 389 | |
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| 390 | cat <<EOF >> $fileou |
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| 391 | </biblioentry> |
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| 392 | |
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| 393 | EOF |
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| 394 | |
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| 395 | |
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| 396 | |
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| 397 | |
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| 398 | |
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| 399 | l=$(( $l + 1 )) |
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| 400 | |
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| 401 | done |
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| 402 | echo "</bibliography>" >> $fileou |
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| 403 | |
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| 404 | xsltproc \ |
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| 405 | --output $( basename ${filein} .txt).html \ |
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| 406 | http://docbook.sourceforge.net/release/xsl/current/xhtml/docbook.xsl \ |
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| 407 | ${fileou} |
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| 408 | |
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| 409 | xmlto pdf ${fileou} 2> xml.err |
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| 410 | # |
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| 411 | # clean |
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| 412 | echo "iii : xml.err contains stderr from the following command " |
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| 413 | echo "iii : which was done just to check consistence of ${fileou}" |
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| 414 | echo "iii : xmlto pdf ${fileou}" |
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| 415 | rm -i xml.err |
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| 416 | case ${type} in |
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| 417 | raw) |
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| 418 | echo "iii : ${fileraw_strict} contains a copy of input file without comments" |
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| 419 | rm -i ${fileraw_strict} |
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| 420 | ;; |
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| 421 | mailbody) |
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| 422 | echo "iii : ${fileraw} contains a copy of input file" |
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| 423 | rm -i ${fileraw} |
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| 424 | echo "iii : ${fileraw_strict} contains a copy of input file without comments" |
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| 425 | rm -i ${fileraw_strict} |
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| 426 | ;; |
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| 427 | esac |
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| 428 | # |
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| 429 | echo " iii : you have a some new or modified bibliographic references in ${fileou} (biblioentry)" |
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| 430 | echo " iii : you can add them in bibrefnemo.xml" #++ filename path |
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| 431 | echo " iii : modify date in bibrefnemo.xml" #++ filename path |
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| 432 | echo " iii : but please take care of id last part (after underscore) that may" |
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| 433 | echo " iii : be in conflict with existing ones" #++ pour s'affranchir de ce souci il faudrait donner en entrée complémentaire le fichier à compléter. |
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| 434 | # |
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| 435 | exit 0 |
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